Data from Palsson Lab									Data from Hatzimanikatis Lab															
SimPheny ID	abbreviation   	new since iJR904	officialName   	formula        	charge         	casNumber   	KEGG cmpd ID	notes	formula	charge	Gibbs free energy of formation	uncertainty in Gibbs energy								FORMULA	CHARGE	ENERGY	ERROR	
286	10fthf	No	10-Formyltetrahydrofolate	C20H21N7O7	-2	692-29-5	C00234	"KEGG - C00234
Neutral MF = C20H23N7O7
SMP
CHS
checked N groups - NCD
Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR
Pipeline Pilot indicates this N is not charged JLR"	C20H21N7O7	-2	-150.15	14.7349									-2	-150.15	14.7349	
26140	12dgr120	Yes	"1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)"	C27H52O5	0		C00641	"KEGG - C00641
AMF"	C27H52O5	0	-168.961	15.4791									0	-168.961	15.4791	
26106	12dgr140	Yes	"1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)"	C31H60O5	0		C00641	"KEGG - C00641
AMF"	C31H60O5	0	-165.311	18.0854									0	-165.311	18.0854	
26115	12dgr141	Yes	"1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-C14:1)"	C31H56O5	0		C00641	"KEGG - C00641
AMF"	C31H56O5	0	-127.221	15.9338									0	-127.221	15.9338	
26113	12dgr160	Yes	"1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)"	C35H68O5	0		C00641	"KEGG - C00641
AMF"	C35H68O5	0	-161.662	20.7158									0	-161.662	20.7158	
26116	12dgr161	Yes	"1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1)"	C35H64O5	0		C00641	"KEGG - C00641
AMF"	C35H64O5	0	-123.571	18.4761									0	-123.571	18.4761	
26114	12dgr180	Yes	"1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)"	C39H76O5	0		C00641	"KEGG - C00641
AMF"	C39H76O5	0	-158.012	23.362									0	-158.012	23.362	
26117	12dgr181	Yes	"1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1)"	C39H72O5	0		C00641	"KEGG - C00641
AMF"	C39H72O5	0	-119.922	21.0577									0	-119.922	21.0577	
2181	12ppd-R	Yes	"(R)-Propane-1,2-diol"	C3H8O2	0	4254-14-2	C02912	"KEGG - C02912
SMP
CHS"	C3H8O2	0	-79.6245	2.28875									0	-79.6245	2.28875	
1889	12ppd-S	No	"(S)-Propane-1,2-diol"	C3H8O2	0	4254-14-2	C02917	"KEGG - C02917
SMP
CHS"	C3H8O2	0	-79.6245	2.28875									0	-79.6245	2.28875	
288	13dpg	No	3-Phospho-D-glyceroyl phosphate	C3H4O10P2	-4	None	C00236	"KEGG - C00236
Neutral MF = C3H8O10P2
SMP
CHS"	C3H6O10P2	-2	-585.702	2.78262									-2	-585.702	2.78262	
22230	14glucan	Yes	"1,4-alpha-D-glucan"	C36H62O31	0			"AMF
made up formula to match malthx, the highest carbon maltodextrin that is transported in the model"	C36H62O31	0	-1009.72	52.1332									0	-1009.72	52.1332	
1359	15dap	No	"1,5-Diaminopentane"	C5H16N2	2	462-94-2	C01672	"KEGG - C01672
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C5H16N2	2	-7.2493	4.38561									2	-7.2493	4.38561	
26390	1agpe120	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0)	C17H36NO7P1	0		C04438	"KEGG - C04438
AMF"	C17H36NO7P	0	-341.851	10.1403									0	-341.851	10.1403	
26391	1agpe140	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0)	C19H40NO7P1	0		C04438	"KEGG - C04438
AMF"	C19H40NO7P	0	-340.026	11.4089									0	-340.026	11.4089
26392	1agpe141	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1)	C19H38NO7P1	0		C04438	"KEGG - C04438
AMF"	C19H38NO7P	0	-322.575	10.9534									0	-322.575	10.9534
26393	1agpe160	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0)	C21H44NO7P1	0		C04438	"KEGG - C04438
AMF"	C21H44NO7P	0	-338.201	12.6943									0	-338.201	12.6943
26394	1agpe161	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1)	C21H42NO7P1	0		C04438	"KEGG - C04438
AMF"	C21H42NO7P	0	-319.156	11.5643									0	-319.156	11.5643
26395	1agpe180	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0)	C23H48NO7P1	0		C04438	"KEGG - C04438
AMF"	C23H48NO7P	0	-336.377	13.9919									0	-336.377	13.9919
26396	1agpe181	Yes	1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1)	C23H46NO7P1	0		C04438	"KEGG - C04438
AMF"	C23H46NO7P	0	-317.331	12.8342									0	-317.331	12.8342
26383	1agpg120	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0)	C18H36O9P1	-1			AMF	C18H36O9P	-1	-413.29	10.5055									-1	-413.29	10.5055
26384	1agpg140	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0)	C20H40O9P1	-1			AMF	C20H40O9P	-1	-411.465	11.7347									-1	-411.465	11.7347
26385	1agpg141	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1)	C20H38O9P1	-1			AMF	C20H38O9P	-1	-394.014	11.2924									-1	-394.014	11.2924
26386	1agpg160	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0)	C22H44O9P1	-1			AMF	C22H44O9P	-1	-409.64	12.9879									-1	-409.64	12.9879
26387	1agpg161	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1)	C22H42O9P1	-1			AMF	C22H42O9P	-1	-390.595	11.8859									-1	-390.595	11.8859
26388	1agpg180	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0)	C24H48O9P1	-1			AMF	C24H48O9P	-1	-407.815	14.2588									-1	-407.815	14.2588
26389	1agpg181	Yes	1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1)	C24H46O9P1	-1			AMF	C24H46O9P	-1	-388.77	13.1247									-1	-388.77	13.1247
26132	1ddecg3p	Yes	1-dodecanoyl-sn-glycerol 3-phosphate	C15H29O7P1	-2		C00681	"KEGG - C00681
AMF"	C15H30O7P	-1	-355.958	8.63623									-1	-355.958	8.63623
26054	1hdec9eg3p	Yes	1-hexadec-9-enoyl-sn-glycerol 3-phosphate	C19H35O7P1	-2			AMF	C19H36O7P	-1	-333.264	10.092									-1	-333.264	10.092
26051	1hdecg3p	Yes	1-hexadecanoyl-sn-glycerol 3-phosphate	C19H37O7P1	-2		C00681	AMF	C19H38O7P	-1	-352.309	11.2078									-1	-352.309	11.2078
26055	1odec11eg3p	Yes	1-octadec-11-enoyl-sn-glycerol 3-phosphate	C21H39O7P1	-2			AMF	C21H40O7P	-1	-331.439	11.366									-1	-331.439	11.366
26052	1odecg3p	Yes	1-octadecanoyl-sn-glycerol 3-phosphate	C21H41O7P1	-2		C00681	AMF	C21H42O7P	-1	-350.484	12.5139									-1	-350.484	12.5139
2994	1pyr5c	No	1-Pyrroline-5-carboxylate	C5H6NO2	-1		C03912	"KEGG - C03912
Neutral MF = C5H7NO2
SMP
CHS
Checked N-groups JLR,NCD"	C5H6NO2	-1	-56.9657	4.34411									-1	-56.9657	4.34411
26053	1tdec7eg3p	Yes	1-tetradec-7-enoyl-sn-glycerol 3-phosphate	C17H31O7P1	-2		C00681	AMF	C17H32O7P	-1	-335.088	8.84056									-1	-335.088	8.84056
26050	1tdecg3p	Yes	1-tetradecanoyl-sn-glycerol 3-phosphate	C17H33O7P1	-2		C00681	AMF	C17H34O7P	-1	-354.134	9.91349									-1	-354.134	9.91349
1697	23camp	Yes	"2',3'-Cyclic AMP"	C10H11N5O6P	-1	9014-63-5	C02353	"KEGG - C02353
AMF"	C10H11N5O6P	-1	-194.188	13.6141									-1	-194.188	13.6141
1698	23ccmp	Yes	"2',3'-Cyclic CMP"	C9H11N3O7P	-1		C02354	"KEGG - C02354
AMF"	C9H11N3O7P	-1	-272.925	10.4651									-1	-272.925	10.4651
4602	23cgmp	Yes	"2',3'-Cyclic GMP"	C10H11N5O7P	-1		C06194	"KEGG - C06194
AMF"	C10H11N5O7P	-1	-243.383	12.819									-1	-243.383	12.819
1699	23cump	Yes	"2',3'-Cyclic UMP"	C9H10N2O8P	-1	9014-63-5	C02355	"KEGG - C02355
AMF"	C9H10N2O8P	-1	-326.613	10.9317									-1	-326.613	10.9317
18003	23dappa	Yes	"2,3-diaminopropionate"	C3H9N2O2	1		C06393	"MKA
L- and D- forms not distinguished here

"	C3H9N2O2	1	-87.8184	3.2513									1	-87.8184	3.2513
10362	23ddhb	No	"2,3-Dihydro-2,3-dihydroxybenzoate"	C7H7O4	-1		C04171	"KEGG - C04171
Neutral MF = C7H8O4
SMP
CHS"	C7H7O4	-1	-128.077	6.00355									-1	-128.077	6.00355
258	23dhb	No	"2,3-Dihydroxybenzoate"	C7H5O4	-1	303-38-8	C00196	"KEGG - C00196
Neutral MF = C7H6O4
SMP
CHS"	C7H5O4	-1	-128.297	12.6645									-1	-128.297	12.6645
15091	23dhba	No	"(2,3-Dihydroxybenzoyl)adenylate"	C17H17N5O10P	-1		C04030	"KEGG - C04030
Neutral MF = C17H18N5O10P
SMP
CHS
Check groups AMF, JLR, SAB"	C17H17N5O10P	-1	-334.695	18.0346									-1	-334.695	18.0346
21297	23dhbzs	Yes	"2,3-dihydroxybenzoylserine"	C10H10NO6	-1			AMF	C10H10NO6	-1	-190.668	13.0918									-1	-190.668	13.0918
2398	23dhdp	No	"2,3-Dihydrodipicolinate"	C7H5NO4	-2		C03340	"KEGG - C03340
Neutral MF = C7H7NO4
SMP
CHS
(close compound-dipicolinic acid has a pKa of 2.16 and 4.76)
Checked N-groups JLR "	C7H5NO4	-2	-125.816	4.92319									-2	-125.816	4.92319
3067	23dhmb	No	"(R)-2,3-Dihydroxy-3-methylbutanoate"	C5H9O4	-1		C04272	"KEGG - C04272 (C04039 Deleted)
Neutral MF = C5H10O4
SMP
CHS"	C5H9O4	-1	-159.599	3.80982									-1	-159.599	3.80982
3129	23dhmp	No	"(R)-2,3-Dihydroxy-3-methylpentanoate"	C6H11O4	-1		C06007	"KEGG - C06007 (C04104 Deleted)
Neutral MF = C6H12O4
SMP
CHS"	C6H11O4	-1	-158.687	3.86916									-1	-158.687	3.86916
4195	23doguln	No	"2,3-Dioxo-L-gulonate"	C6H7O7	-1	583-08-4	C05409	"KEGG - C05409
Neutral-C6H8O7
JLR"	C6H7O7	-1	-251.245	4.43912									-1	-251.245	4.43912
3554	25aics	No	(S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate	C13H15N4O12P	-4		C04823	"KEGG - C04823
Neutral MF = C13H19N4O12P
SMP
CHS
Checked N-groups JLR"	C13H16N4O12P	-3	-478.983	10.064									-3	-478.983	10.064
9067	25dkglcn	No	"2,5-diketo-D-gluconate"	C6H7O7	-1		C02780	"KEGG C02780
Neutal - C6H8O7
JLR"	C6H7O7	-1	-251.245	4.43912									-1	-251.245	4.43912
8249	25drapp	No	"2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate"	C9H14N5O8P	-2			"Neidhardt, pg 658
JLR- similar to 25dhpp except ketone group in the nitrogen ring rather than the OH group
Checked N-groups, agrees with ACD software, JLR"	C9H15N5O8P	-1	-322.712	12.5974									-1	-322.712	12.5974
11429	26dap-LL	No	"LL-2,6-Diaminoheptanedioate"	C7H14N2O4	0	583-93-7	C00666	"KEGG - C00666
Neutral MF = C7H14N2O4
SMP
CHS
Changed according to Genomatica JLR"	C7H14N2O4	0	-162.913	4.58622									0	-162.913	4.58622
449	26dap-M	No	"meso-2,6-Diaminoheptanedioate"	C7H14N2O4	0	None	C00680	"KEGG - C00680
Neutral MF = C7H14N2O4
SMP
CHS
Changed according to Genomatica JLR"	C7H14N2O4	0	-162.913	4.58622									0	-162.913	4.58622
26342	2agpe120	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0)	C17H36NO7P1	0		C05973	"KEGG - C05973
AMF"	C17H36NO7P	0	-341.851	10.1403									0	-341.851	10.1403
26345	2agpe140	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0)	C19H40NO7P1	0		C05973	"KEGG - C05973
AMF"	C19H40NO7P	0	-340.026	11.4089									0	-340.026	11.4089
26346	2agpe141	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1)	C19H38NO7P1	0		C05973	"KEGG - C05973
AMF"	C19H38NO7P	0	-320.981	10.3148									0	-320.981	10.3148
26344	2agpe160	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0)	C21H44NO7P1	0		C05973	"KEGG - C05973
AMF"	C21H44NO7P	0	-338.201	12.6943									0	-338.201	12.6943
26347	2agpe161	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1)	C21H42NO7P1	0		C05973	"KEGG - C05973
AMF"	C21H42NO7P	0	-319.156	11.5643									0	-319.156	11.5643
26343	2agpe180	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0)	C23H48NO7P1	0		C05973	"KEGG - C05973
AMF"	C23H48NO7P	0	-336.377	13.9919									0	-336.377	13.9919
26348	2agpe181	Yes	2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1)	C23H46NO7P1	0		C05973	"KEGG - C05973
AMF"	C23H46NO7P	0	-317.331	12.8342									0	-317.331	12.8342
26349	2agpg120	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0)	C18H36O9P1	-1			AMF	C18H36O9P	-1	-413.29	10.5055									-1	-413.29	10.5055
26351	2agpg140	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0)	C20H40O9P1	-1			AMF	C20H40O9P	-1	-411.465	11.7347									-1	-411.465	11.7347
26354	2agpg141	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1)	C20H38O9P1	-1			AMF	C20H38O9P	-1	-392.42	10.6741									-1	-392.42	10.6741
26352	2agpg160	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0)	C22H44O9P1	-1			AMF	C22H44O9P	-1	-409.64	12.9879									-1	-409.64	12.9879
26355	2agpg161	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1)	C22H42O9P1	-1			AMF	C22H42O9P	-1	-390.595	11.8859									-1	-390.595	11.8859
26353	2agpg180	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0)	C24H48O9P1	-1			AMF	C24H48O9P	-1	-407.815	14.2588									-1	-407.815	14.2588
26356	2agpg181	Yes	2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1)	C24H46O9P1	-1			AMF	C24H46O9P	-1	-388.77	13.1247									-1	-388.77	13.1247
437	2ahbut	No	(S)-2-Aceto-2-hydroxybutanoate	C6H9O4	-1		C06006	"KEGG - C06006 (C00659 Deleted)
Neutral MF = C6H10O4
SMP
CHS"	C6H9O4	-1	-149.504	3.69439									-1	-149.504	3.69439
21347	2amsa	Yes	2-Aminomalonate semialdehyde	C3H5NO3	0		C11822	0	C3H5NO3	0	-112.724	2.32186									0	-112.724	2.32186
2707	2aobut	No	L-2-Amino-3-oxobutanoate	C4H7NO3	0		C03508	"KEGG - C03508 (C03214 Deleted)
Neutral MF = C4H7NO3
SMP
CHS
Checked N-groups JLR"	C4H7NO3	0	-113.757	2.58954									0	-113.757	2.58954
7152	2cpr5p	No	1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate	C12H13NO9P	-3		C01302	"KEGG - C01302
Neutral MF = C12H16NO9P
SMP
Checked N-groups JLR"	C12H14NO9P	-2	-392.397	9.60051									-2	-392.397	9.60051
3353	2dda7p	No	2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate	C7H10O10P	-3		C04691	"KEGG - C04691
Neutral MF = C7H13O10P
SMP
CHS"	C7H11O10P	-2	-472.026	5.62984									-2	-472.026	5.62984
26357	2ddecg3p	Yes	2-dodecanoyl-sn-glycerol 3-phosphate	C15H29O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C15H30O7P	-1	-355.958	8.63623									-1	-355.958	8.63623
3930	2ddg6p	No	2-Dehydro-3-deoxy-D-gluconate 6-phosphate	C6H8O9P	-3		C04442	"KEGG - C04442
Neutral MF = C6H11O9P
SMP
CHS"	C6H9O9P	-2	-435.104	4.18418									-2	-435.104	4.18418
264	2ddglcn	No	2-Dehydro-3-deoxy-D-gluconate	C6H9O6	-1	None	C00204	"KEGG - C00204
Neutral MF = C6H10O6
SMP
CHS"	C6H9O6	-1	-222.594	4.06518									-1	-222.594	4.06518
946	2dh3dgal	No	2-Dehydro-3-deoxy-D-galactonate	C6H9O6	-1		C01216	"KEGG - C01216
Neutral-C6H10O6
JLR"	C6H9O6	-1	-222.594	4.06518									-1	-222.594	4.06518
997	2dh3dgal6p	No	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	C6H8O9P	-3		C01286	"KEGG - C01286
Neutral-C6H11O9P
JLR"	C6H9O9P	-2	-435.104	4.18418									-2	-435.104	4.18418
1118	2dhglcn	No	2-Dehydro-D-gluconate	C6H9O7	-1		C00629	"KEGG - C00629
Neutral-C6H10O7
JLR"	C6H9O7	-1	-260.427	5.41724									-1	-260.427	5.41724
9068	2dhguln	No	2-Dehydro-L-gulonate	C6H9O7	-1			"No Kegg entry
Neutral- C6H10O7
JLR"	C6H9O7	-1	-260.427	5.41724									-1	-260.427	5.41724
800	2dhp	No	2-Dehydropantoate	C6H9O4	-1		C00966	"KEGG - C00966
Neutral MF = C6H10O4
SMP 
CHS"	C6H9O4	-1	-147.706	3.37314									-1	-147.706	3.37314
4305	2dmmq8	No	2-Demethylmenaquinone 8	C50H70O2	0		C05818	"KEGG - C05818
General Formula = C15H14O2(C5H8)n; n = 7 for 2dmmq8
SMP"	C50H70O2	0	173.374	22.2036									0	173.374	22.2036
6326	2dmmql8	No	2-Demethylmenaquinol 8	C50H72O2	0			JLR	C50H72O2	0	152.029	25.5453									0	152.029	25.5453
446	2dr1p	No	2-Deoxy-D-ribose 1-phosphate	C5H9O7P	-2		C00672	"KEGG - C00672
Neutral MF = C5H11O7P
SMP
CHS"	C5H10O7P	-1	-352.577	5.99168									-1	-352.577	5.99168
447	2dr5p	No	2-Deoxy-D-ribose 5-phosphate	C5H9O7P	-2	102916-66-5	C00673	"KEGG - C00673
Neutral MF = C5H11O7P
SMP
CHS"	C5H10O7P	-1	-353.766	6.22523									-1	-353.766	6.22523
906	2h3oppan	No	2-Hydroxy-3-oxopropanoate	C3H3O4	-1		C01146	"KEGG - C01146
Neutral-C3H4O4
JLR"	C3H3O4	-1	-149.234	2.201									-1	-149.234	2.201
26362	2hdec9eg3p	Yes	2-hexadec-9-enoyl-sn-glycerol 3-phosphate	C19H35O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C19H36O7P	-1	-333.264	10.092									-1	-333.264	10.092
26359	2hdecg3p	Yes	2-hexadecanoyl-sn-glycerol 3-phosphate	C19H37O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C19H38O7P	-1	-352.309	11.2078									-1	-352.309	11.2078
1886	2ippm	No	2-Isopropylmaleate	C7H8O4	-2		C02631	"KEGG - C02631
Neutral MF = C7H10O4
SMP "	C7H8O4	-2	-140.355	3.51618									-2	-140.355	3.51618
5757	2kmb	No	2-keto-4-methylthiobutyrate	C5H7O3S	-1			"No KEGG Entry
JEM has it as KMB
Neutral MF = C5H8O3S
SMP"	C5H7O3S	-1	-98.773	3.42997									-1	-98.773	3.42997
3501	2mahmp	No	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate	C6H8N3O7P2	-3	745-65-3	C04752	"KEGG - C04752
Neutral MF = C6H11N3O7P2
SMP
Checked N-groups JLR"	C6H9N3O7P2	-2	-405.828	8.22137									-2	-405.828	8.22137
3219	2mcacn	No	cis-2-Methylaconitate	C7H5O6	-3	99-98-9	C04225	"KEGG - C04225
Neutral-C7H8O6
JLR"	C7H5O6	-3	-219.664	4.51101									-3	-219.664	4.51101
1591	2mcit	No	2-Methylcitrate	C7H7O7	-3	96-17-3	C02225	"KEGG - C02225
NCD
JLR"	C7H7O7	-3	-277.906	4.18062									-3	-277.906	4.18062
6321	2me4p	No	2-C-methyl-D-erythritol 4-phosphate	C5H11O7P	-2		C11434	"KEGG C11434
Neutral MF = C5H13O7P
SMP"	C5H12O7P	-1	-365.525	3.94665									-1	-365.525	3.94665
6331	2mecdp	No	"2-C-methyl-D-erythritol 2,4-cyclodiphosphate"	C5H10O9P2	-2		C11453	"KEGG ID- C11453
Neutral MF = C5H12O9P2
SMP"	C5H10O9P2	-2	-485.6	6.69771									-2	-485.6	6.69771
1071	2obut	No	2-Oxobutanoate	C4H5O3	-1	600-18-0	C00109	"KEGG - C00109
Neutral MF = C4H6O3
SMP
CHS
NCD"	C4H5O3	-1	-112.432	1.94348									-1	-112.432	1.94348
26363	2odec11eg3p	Yes	2-octadec-11-enoyl-sn-glycerol 3-phosphate	C21H39O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C21H40O7P	-1	-331.439	11.366									-1	-331.439	11.366
26360	2odecg3p	Yes	2-octadecanoyl-sn-glycerol 3-phosphate	C21H41O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C21H42O7P	-1	-350.484	12.5139									-1	-350.484	12.5139
10904	2ohph	No	2-Octaprenyl-6-hydroxyphenol	C46H70O2	0		C05811	"KEGG - C05811
SMP
CHS"	C46H70O2	0	141.975	24.0298									0	141.975	24.0298
8204	2ombzl	No	"2-Octaprenyl-6-methoxy-1,4-benzoquinol"	C47H72O3	0			"Neidhardt page 651
JLR"	C47H72O3	0	114.688	25.5238									0	114.688	25.5238
8212	2omhmbl	No	"2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol"	C48H74O4	0			"Neidhardt page 651
JLR"	C48H74O4	0	73.1552	30.2796									0	73.1552	30.2796
8207	2ommbl	No	"2-Octaprenyl-3-methyl-6-methoxy- 1,4-benzoquinol"	C48H74O3	0			"Neidhardt page 651
JLR"	C48H74O3	0	112.304	27.3181									0	112.304	27.3181
4483	2omph	No	2-Octaprenyl-6-methoxyphenol	C47H72O2	0		C05812	"KEGG - C05812
SMP
CHS"	C47H72O2	0	153.837	23.5597									0	153.837	23.5597
4482	2oph	No	2-Octaprenylphenol	C46H70O	0		C05810	"KEGG - C05810
SMP
CHS"	C46H70O	0	181.124	22.4371									0	181.124	22.4371
11026	2p4c2me	No	2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	C14H22N3O17P3	-4			"No KEGG Entry
Neutral MF = C14H26N3O17P3
SMP
Checked N-groups JLR"	C14H23N3O17P3	-3	-849.324	10.8059									-3	-849.324	10.8059
1120	2pg	No	D-Glycerate 2-phosphate	C3H4O7P	-3		C00631	"KEGG - C00631
Neutral MF = C3H7O7P
SMP
CHS"	C3H5O7P	-2	-370.167	2.46719									-2	-370.167	2.46719
813	2pglyc	No	2-Phosphoglycolate	C2H2O6P	-3		C00988	"KEGG - C00988
Neutral MF = C2H5O6P
SMP
CHS"	C2H3O6P	-2	-334.435	1.80959									-2	-334.435	1.80959
4304	2shchc	No	"2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate"	C11H10O6	-2		C05817	"KEGG - C05817
Neutral MF = C11H12O6
SMP
CHS"	C11H10O6	-2	-193.99	6.13886									-2	-193.99	6.13886
26361	2tdec7eg3p	Yes	2-tetradec-7-enoyl-sn-glycerol 3-phosphate	C17H31O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C17H32O7P	-1	-335.088	8.84056									-1	-335.088	8.84056
26358	2tdecg3p	Yes	2-tetradecanoyl-sn-glycerol 3-phosphate	C17H33O7P1	-2	52-52-8	C03974	"KEGG - C03974
AMF"	C17H34O7P	-1	-354.134	9.91349									-1	-354.134	9.91349
21298	2tpr3dpcoa	Yes	2'-(5''-triphosphoribosyl)-3'-dephospho-CoA	C26H40N7O26P5S	-6			AMF	C26H41N7O26P5S	-5	-1291.28	20.3048									-5	-1291.28	20.3048
3087	34dhpac	Yes	"3,4-Dihydroxyphenylacetaldehyde"	C8H8O3	0	145-14-2	C04043	"KEGG - C04043
SAB"	C8H8O3	0	-74.8703	12.6947									0	-74.8703	12.6947
772	34hpp	No	3-(4-Hydroxyphenyl)pyruvate	C9H7O4	-1		C01179	"KEGG - C01179
Neutral MF = C9H8O4
SMP
CHS"	C9H7O4	-1	-115.975	9.39955									-1	-115.975	9.39955
18604	3amp	Yes	3'-AMP	C10H12N5O7P	-2	84-21-9	C01367	"MKA
AMF"	C10H13N5O7P	-1	-258.844	12.6557									-1	-258.844	12.6557
2681	3c2hmp	No	3-Carboxy-2-hydroxy-4-methylpentanoate	C7H10O5	-2		C04411	"KEGG - C04411
Neutral MF = C7H12O5
SMP
CHS"	C7H10O5	-2	-197.145	4.63129									-2	-197.145	4.63129
1803	3c3hmp	No	3-Carboxy-3-hydroxy-4-methylpentanoate	C7H10O5	-2		C02504	"KEGG - C02504
Neutral MF = C7H12O5
SMP
CHS"	C7H10O5	-2	-197.145	4.63129									-2	-197.145	4.63129
3228	3c4mop	No	3-Carboxy-4-methyl-2-oxopentanoate	C7H8O5	-2		C04236	"KEGG - C04236
Neutral MF = C7H10O5
SMP"	C7H8O5	-2	-187.963	3.79907									-2	-187.963	3.79907
18607	3cmp	Yes	3'-cmp	C9H12N3O8P	-2		C05822	"MKA
AMF"	C9H13N3O8P	-1	-337.581	9.18376									-1	-337.581	9.18376
1111	3dhguln	No	3-Dehydro-L-gulonate	C6H9O7	-1		C00618	"KEGG - C00618
Neutral-C6H10O7
JLR
NCD
MKA"	C6H9O7	-1	-260.427	5.41724									-1	-260.427	5.41724
9125	3dhgulnp	Yes	3-keto-L-gulonate-6-phosphate	C6H8O10P	-3			"No Kegg entry
Neutral-C6H11O10P
JLR"	C6H9O10P	-2	-472.938	5.5071									-2	-472.938	5.5071
498	3dhq	No	3-Dehydroquinate	C7H9O6	-1		C00944	"KEGG - C00944
Neutral MF = C7H10O6
SMP
CHS"	C7H9O6	-1	-214.27	5.89833									-1	-214.27	5.89833
1199	3dhsk	No	3-Dehydroshikimate	C7H7O5	-1	10457-99-5	C02637	"KEGG - C02637
Neutral MF = C7H8O5
SMP
CHS"	C7H7O5	-1	-166.352	5.08774									-1	-166.352	5.08774
4601	3gmp	Yes	3'-GMP	C10H12N5O8P	-2	497-76-7	C06193	"KEGG - C06193
AMF"	C10H13N5O8P	-1	-308.038	11.7962									-1	-308.038	11.7962
988	3haACP	Yes	(3R)-3-Hydroxyacyl-[acyl-carrier protein]	C15H27N2O9PRS	-1		C01271	"KEGG - C01271

added formula, renamed from 3R3haprot - NCD
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C15H27N2O9PRS	-1	-391.649	9.85769									-1	-391.649	9.85769
905	3hbcoa	Yes	(S)-3-Hydroxybutanoyl-CoA	C25H38N7O18P3S	-4		C01144	"KEGG - C01144
Neutral MF = C25H42N7O18P3S
SMP"	C25H39N7O18P3S	-3	-817.923	16.3988									-3	-817.923	16.3988
26042	3hcddec5eACP	Yes	(R)-3-hydroxy-cis-dodec-5-enoyl-[acyl-carrier protein]	C23H41N2O9PRS	-1			AMF	C23H41N2O9PRS	-1	-365.305	12.2455									-1	-365.305	12.2455
9394	3hcinnm	No	3-hydroxycinnamic acid	C9H7O3	-1			"No Kegg entry see PMID: 9603882
Neutral-C9H8O3
JLR"	C9H7O3	-1	-68.2779	9.48426									-1	-68.2779	9.48426
26040	3hcmrs7eACP	Yes	(R)-3-hydroxy-cis-myristol-7-eoyl-[acyl-carrier protein]	C25H45N2O9PRS	-1			AMF	C25H45N2O9PRS	-1	-363.48	13.1775									-1	-363.48	13.1775
26043	3hcpalm9eACP	Yes	(R)-3-hydroxy-cis-palm-9-eoyl-[acyl-carrier protein]	C27H49N2O9PRS	-1			AMF	C27H49N2O9PRS	-1	-361.656	14.1769									-1	-361.656	14.1769
26044	3hcvac11eACP	Yes	(R)-3-hydroxy-cis-vacc-11-enoyl-[acyl-carrier protein]	C29H53N2O9PRS	-1			AMF	C29H53N2O9PRS	-1	-359.831	15.2304									-1	-359.831	15.2304
3793	3hdcoa	Yes	(S)-3-Hydroxydecanoyl-CoA	C31H50N7O18P3S	-4		C05264	"KEGG - C05264
Neutral MF = C31H54N7O18P3S
SMP"	C31H51N7O18P3S	-3	-812.449	17.9888									-3	-812.449	17.9888
3791	3hddcoa	Yes	(S)-3-Hydroxydodecanoyl-CoA	C33H54N7O18P3S	-4		C05262	"KEGG - C05262
Neutral MF = C33H58N7O18P3S
SMP"	C33H55N7O18P3S	-3	-810.624	18.6845									-3	-810.624	18.6845
4250	3hddecACP	Yes	(R)-3-Hydroxydodecanoyl-[acyl-carrier protein]	C23H43N2O9PRS	-1	8/6/83	C05757	"KEGG - C05757
AMF"	C23H43N2O9PRS	-1	-384.35	13.0413									-1	-384.35	13.0413
3303	3hdecACP	Yes	(R)-3-Hydroxydecanoyl-[acyl-carrier protein]	C21H39N2O9PRS	-1	320-77-4	C04619	"KEGG - C04619
AMF"	C21H39N2O9PRS	-1	-386.175	12.0988									-1	-386.175	12.0988
3797	3hhcoa	Yes	(S)-3-Hydroxyhexanoyl-CoA	C27H42N7O18P3S	-4		C05268	"KEGG - C05268
Neutral MF = C27H46N7O18P3S
SMP"	C27H43N7O18P3S	-3	-816.098	16.8375									-3	-816.098	16.8375
9558	3hhdcoa	Yes	(S)-3-Hydroxyhexadecanoyl-CoA	C37H62N7O18P3S	-4		C05258	"KEGG - C05258
Neutral MF = C37H66N7O18P3S
SMP"	C37H63N7O18P3S	-3	-806.974	20.2751									-3	-806.974	20.2751
11011	3hhexACP	Yes	(R)-3-Hydroxyhexanoyl-[acyl-carrier protein]	C17H31N2O9PRS	-1	8/6/83	C05747	"KEGG - C05747
AMF"	C17H31N2O9PRS	-1	-389.825	10.4848									-1	-389.825	10.4848
8352	3hmrsACP	No	(R)-3-Hydroxytetradecanoyl-[acyl-carrier protein]	C25H47N2O9PRS	-1		C04688	"Based on NH page 1040 and 615
JLR
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C25H47N2O9PRS	-1	-382.525	14.0504									-1	-382.525	14.0504
3795	3hocoa	Yes	(S)-3-Hydroxyoctanoyl-CoA	C29H46N7O18P3S	-4		C05266	"KEGG - C05266
Neutral MF = C29H50N7O18P3S
SMP"	C29H47N7O18P3S	-3	-814.274	17.3703									-3	-814.274	17.3703
10665	3hoctaACP	Yes	(R)-3-Hydroxyoctadecanoyl-[acyl-carrier protein]	C29H55N2O9PRS	-1			"tv (3/25/03)
AMF"	C29H55N2O9PRS	-1	-378.876	16.218									-1	-378.876	16.218
25943	3hoctACP	Yes	(R)-3-Hydroxyoctanoyl-[acyl-carrier protein]	C19H35N2O9PRS	-1		C04620	AMF	C19H35N2O9PRS	-1	-388	11.2399									-1	-388	11.2399
8403	3hodcoa	Yes	(S)-3-Hydroxyoctadecanoyl-CoA	C39H66N7O18P3S	-4			NCD	C39H67N7O18P3S	-3	-805.15	21.1549									-3	-805.15	21.1549
11870	3hpalmACP	Yes	R-3-hydroxypalmitoyl-[acyl-carrier protein]	C27H51N2O9PRS	-1		C04633	"tv (3/26/03)
AMF"	C27H51N2O9PRS	-1	-380.701	15.1128									-1	-380.701	15.1128
9393	3hpppn	No	3-(3-hydroxy-phenyl)propionate	C9H9O3	-1			"No Kegg entry see PMID: 9603882
Neutral
JLR"	C9H9O3	-1	-87.323	9.39163									-1	-87.323	9.39163
3789	3htdcoa	Yes	(S)-3-Hydroxytetradecanoyl-CoA	C35H58N7O18P3S	-4		C05260	"KEGG - C05260
Neutral MF = C35H62N7O18P3S
SMP"	C35H59N7O18P3S	-3	-808.799	19.4492									-3	-808.799	19.4492
11266	3ig3p	No	C'-(3-Indolyl)-glycerol 3-phosphate	C11H12NO6P	-2		C03506	"KEGG - C03506
Neutral MF = C11H14NO6P
SMP
Checked N-groups JLR"	C11H13NO6P	-1	-270.863	9.31536									-1	-270.863	9.31536
225	3mob	No	3-Methyl-2-oxobutanoate	C5H7O3	-1		C00141	"KEGG - C00141
Neutral MF = C5H8O3
SMP
CHS"	C5H7O3	-1	-111.043	2.75963									-1	-111.043	2.75963
445	3mop	No	(S)-3-Methyl-2-oxopentanoate	C6H9O3	-1		C00671	"KEGG - C00671
Neutral MF = C6H10O3
C003465 and C03911 are deleted
SMP
CHS
"	C6H9O3	-1	-110.131	2.84098									-1	-110.131	2.84098
26038	3ocddec5eACP	Yes	3-oxo-cis-dodec-5-enoyl-[acyl-carrier protein]	C23H39N2O9PRS	-1			AMF	C23H39N2O9PRS	-1	-356.123	12.3309									-1	-356.123	12.3309
26039	3ocmrs7eACP	Yes	3-oxo-cis-myristol-7-eoyl-[acyl-carrier protein]	C25H43N2O9PRS	-1			AMF	C25H43N2O9PRS	-1	-354.298	13.2568									-1	-354.298	13.2568
26045	3ocpalm9eACP	Yes	3-oxo-cis-palm-9-eoyl-[acyl-carrier protein]	C27H47N2O9PRS	-1			AMF	C27H47N2O9PRS	-1	-354.067	14.6512									-1	-354.067	14.6512
26046	3ocvac11eACP	Yes	3-oxo-cis-vacc-11-enoyl-[acyl-carrier protein]	C29H51N2O9PRS	-1			AMF	C29H51N2O9PRS	-1	-350.649	15.2991									-1	-350.649	15.2991
3794	3odcoa	Yes	3-Oxodecanoyl-CoA	C31H48N7O18P3S	-4		C05265	"KEGG - C05265
Neutral MF = C31H52N7O18P3S
SMP"	C31H49N7O18P3S	-3	-803.267	17.9685									-3	-803.267	17.9685
3792	3oddcoa	Yes	3-Oxododecanoyl-CoA	C33H52N7O18P3S	-4		C05263	"KEGG - C05263
Neutral MF = C33H56N7O18P3S
SMP"	C33H53N7O18P3S	-3	-801.442	18.665									-3	-801.442	18.665
4249	3oddecACP	Yes	3-Oxododecanoyl-[acyl-carrier protein]	C23H41N2O9PRS	-1	8/6/83	C05756	"KEGG - C05756
AMF"	C23H41N2O9PRS	-1	-375.168	13.1214									-1	-375.168	13.1214
4247	3odecACP	Yes	3-Oxodecanoyl-[acyl-carrier protein]	C21H37N2O9PRS	-1	8/6/83	C05753	"KEGG - C05753
AMF"	C21H37N2O9PRS	-1	-376.993	12.1852									-1	-376.993	12.1852
3798	3ohcoa	Yes	3-Oxohexanoyl-CoA	C27H40N7O18P3S	-4	5096-70-8	C05269	"KEGG - C05269
Neutral MF = C27H44N7O18P3S
SMP"	C27H41N7O18P3S	-3	-806.916	16.8158									-3	-806.916	16.8158
3788	3ohdcoa	Yes	3-Oxohexadecanoyl-CoA	C37H60N7O18P3S	-4		C05259	"KEGG - C05259
Neutral MF = C37H64N7O18P3S
SMP"	C37H61N7O18P3S	-3	-797.792	20.257									-3	-797.792	20.257
4242	3ohexACP	Yes	3-Oxohexanoyl-[acyl-carrier protein]	C17H29N2O9PRS	-1	8/6/83	C05746	"KEGG - C05746
AMF"	C17H29N2O9PRS	-1	-380.642	10.5844									-1	-380.642	10.5844
10993	3omrsACP	Yes	3-Oxotetradecanoyl-[acyl-carrier protein]	C25H45N2O9PRS	-1	8/6/83	C05759	"KEGG - C05759
AMF"	C25H45N2O9PRS	-1	-373.343	14.1248									-1	-373.343	14.1248
3796	3oocoa	Yes	3-Oxooctanoyl-CoA	C29H44N7O18P3S	-4		C05267	"KEGG - C05267
Neutral MF = C29H48N7O18P3S
SMP"	C29H45N7O18P3S	-3	-805.091	17.3492									-3	-805.091	17.3492
4245	3ooctACP	Yes	3-Oxooctanoyl-[acyl-carrier protein]	C19H33N2O9PRS	-1	8/6/83	C05750	"KEGG - C05750
AMF"	C19H33N2O9PRS	-1	-378.818	11.3328									-1	-378.818	11.3328
26130	3ooctdACP	Yes	3-Oxooctadecanoyl-[acyl-carrier protein]	C29H53N2O9PRS	-1			AMF	C29H53N2O9PRS	-1	-369.694	16.2825									-1	-369.694	16.2825
13976	3oodcoa	Yes	3-Oxooctadecanoyl-CoA	C39H64N7O18P3S	-4			SMP (2/7/03)	C39H65N7O18P3S	-3	-795.968	21.1376									-3	-795.968	21.1376
4254	3opalmACP	Yes	3-Oxohexadecanoyl-[acyl-carrier protein]	C27H49N2O9PRS	-1	8/6/83	C05762	"KEGG - C05762
AMF"	C27H49N2O9PRS	-1	-371.519	15.182									-1	-371.519	15.182
4481	3ophb	No	3-Octaprenyl-4-hydroxybenzoate	C47H69O3	-1		C05809	"KEGG - C05809
Neutral MF = C47H70O3
SMP
CHS"	C47H69O3	-1	99.5189	23.1129									-1	99.5189	23.1129
3790	3otdcoa	Yes	3-Oxotetradecanoyl-CoA	C35H56N7O18P3S	-4		C05261	"KEGG - C05261
Neutral MF = C35H60N7O18P3S
SMP"	C35H57N7O18P3S	-3	-799.617	19.4304									-3	-799.617	19.4304
259	3pg	No	3-Phospho-D-glycerate	C3H4O7P	-3		C00197	"KEGG - C00197
Neutral MF = C3H7O7P
Deleted C00597
SMP
CHS"	C3H5O7P	-2	-371.356	2.47228									-2	-371.356	2.47228
9544	3php	No	3-Phosphohydroxypyruvate	C3H2O7P	-3		C03232	"KEGG - C03232
Neutral MF = C3H5O7P
SMP
CHS"	C3H3O7P	-2	-362.174	2.18867									-2	-362.174	2.18867
7139	3psme	No	5-O-(1-Carboxyvinyl)-3-phosphoshikimate	C10H9O10P	-4		C01269	"KEGG - C01269
Neutral MF = C10H13O10P
SMP"	C10H10O10P	-3	-429.133	6.72232									-3	-429.133	6.72232
1105	3sala	Yes	3-Sulfino-L-alanine	C3H5NO4S	-2	1115-65-7	C00606	"KEGG - C00606
Neutral MF = C3H7NO4S
SMP
CHS"	C3H6NO4S	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
526	3ump	Yes	3'-UMP	C9H11N2O9P	-2	35170-03-7	C01368	"KEGG - C01368
AMF"	C9H12N2O9P	-1	-391.268	9.71211									-1	-391.268	9.71211
176	4abut	No	4-Aminobutanoate	C4H9NO2	0	56-12-2	C00334	"KEGG - C00334
Neutral MF = C4H9NO2
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO2	0	-85.5818	2.62876									0	-85.5818	2.62876
376	4abutn	No	4-Aminobutanal	C4H10NO	1		C00555	"KEGG - C00555
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C4H10NO	1	-33.0677	2.68687									1	-33.0677	2.68687
385	4abz	No	4-Aminobenzoate	C7H6NO2	-1	150-13-0	C00568	"KEGG - C00568
Neutral MF = C7H7NO2
SMP
CHS
Checked N-groups JLR"	C7H6NO2	-1	-50.5724	8.6449									-1	-50.5724	8.6449
6422	4adcho	No	4-amino-4-deoxychorismate	C10H10NO5	-1		C11355	"KEGG - C11355 MM
Neutral MF = C10H11NO5
SMP
Note: NH pg 667 has metab drawn incorrectly should be carboxylic not methyl group
 (pka of N group around 9,using ACD software)
Checked N-groups JLR"	C10H10NO5	-1	-136.804	6.7265									-1	-136.804	6.7265
992	4ahmmp	No	4-Amino-5-hydroxymethyl-2-methylpyrimidine	C6H9N3O	0	73-67-6	C01279	"KEGG - C01279
Neutral
SMP
CHS
Checked N-groups JLR"	C6H9N3O	0	14.5361	8.07239									0	14.5361	8.07239
3999	4ampm	No	4-Amino-2-methyl-5-phosphomethylpyrimidine	C6H8N3O4P	-2		C04556	"KEGG - C04556
Neutral MF = C6H10N3O4P
SMP
CHS
Checked N-groups JLR"	C6H9N3O4P	-1	-197.974	8.13297									-1	-197.974	8.13297
6328	4c2me	No	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol	C14H23N3O14P2	-2		C11435	"KEGG C11435
Neutral MF = C14H25N3O14P2
SMP
Checked N-groups JLR"	C14H23N3O14P2	-2	-641.026	10.5977									-2	-641.026	10.5977
2758	4h2opntn	No	4-Hydroxy-2-oxopentanoate	C5H7O4	-1	111844-33-8	C03589	"KEGG - C03589
Neutral-C5H8O4
JLR"	C5H7O4	-1	-149.354	2.5719									-1	-149.354	2.5719
5872	4hba	No	4-Hydroxy-benzyl alcohol	C7H8O2	0			tv	C7H8O2	0	-46.2452	9.32605									0	-46.2452	9.32605
234	4hbz	No	4-Hydroxybenzoate	C7H5O3	-1	99-96-7	C00156	"KEGG - C00156
Neutral MF = C7H6O3
SMP
CHS"	C7H5O3	-1	-89.1478	9.2941									-1	-89.1478	9.2941
2887	4hoxpacd	Yes	4-Hydroxyphenylacetaldehyde	C8H8O2	0	60-11-7	C03765	"KEGG - C03765
SAB"	C8H8O2	0	-35.7212	9.33514									0	-35.7212	9.33514
8737	4hthr	No	4-Hydroxy-L-threonine	C4H9NO4	0		C06056	"KEGG C06056
JLR
Checked N JLR"	C4H9NO4	0	-159.257	3.37071									0	-159.257	3.37071
3272	4mhetz	No	4-Methyl-5-(2-hydroxyethyl)-thiazole	C6H9NOS	0	137-00-8	C04294	"KEGG - C04294
Neutral
SMP
CHS
Checked N-groups JLR"	C6H9NOS	0	-5.60459	5.5207									0	-5.60459	5.5207
285	4mop	No	4-Methyl-2-oxopentanoate	C6H9O3	-1		C00233	"KEGG - C00233
Neutral MF = C6H10O3
SMP
CHS"	C6H9O3	-1	-110.131	2.84098									-1	-110.131	2.84098
2627	4mpetz	No	4-Methyl-5-(2-phosphoethyl)-thiazole	C6H8NO4PS	-2		C04327	"KEGG - C04327
Neutral MF = C6H10NO4PS
SMP
CHS
Checked N-groups JLR"	C6H9NO4PS	-1	-218.115	5.60891									-1	-218.115	5.60891
2319	4pasp	No	4-Phospho-L-aspartate	C4H6NO7P	-2		C03082	"KEGG - C03082
Neutral MF = C4H8NO7P
SMP 
CHS
Changed according to Genomatica JLR"	C4H7NO7P	-1	-378.672	2.67742									-1	-378.672	2.67742
1954	4per	No	4-Phospho-D-erythronate	C4H6O8P	-3		C03393	"KEGG - C03393
Neutral MF = C4H9O8P
SMP
CHS"	C4H7O8P	-2	-408.277	3.82424									-2	-408.277	3.82424
2022	4ppan	No	D-4'-Phosphopantothenate	C9H15NO8P	-3		C03492	"KEGG - C03492
Neutral MF = C9H18NO8P
SMP
CHS
Checked N-groups JLR"	C9H16NO8P	-2	-395.928	5.04625									-2	-395.928	5.04625
2645	4ppcys	No	N-((R)-4-Phosphopantothenoyl)-L-cysteine	C12H20N2O9PS	-3		C04352	"KEGG - C04352
Neutral MF = C12H23N2O9PS
SMP
CHS
Checked N-groups JLR"	C12H21N2O9PS	-2	-419.008	7.82756									-2	-419.008	7.82756
3484	4r5au	No	4-(1-D-Ribitylamino)-5-aminouracil	C9H16N4O6	0		C04732	"KEGG - C04732
SMP
Checked N-groups, agrees with ACD software, JLR"	C9H16N4O6	0	-186.904	9.83832									0	-186.904	9.83832
10916	5aizc	No	5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate	C9H11N3O9P	-3		C04751	"KEGG - C04751
Neutral MF = C9H14N3O9P
SMP
CHS
Checked N-groups JLR"	C9H13N3O9P	-1	-378.148	9.47909									-1	-378.148	9.47909
424	5aop	No	5-Amino-4-oxopentanoate	C5H9NO3	0	106-60-5	C00430	"KEGG - C00430
Neutral MF = C5H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C5H9NO3	0	-113.321	2.90276									0	-113.321	2.90276
3938	5aprbu	No	5-Amino-6-(5'-phosphoribitylamino)uracil	C9H15N4O9P	-2		C04454	"KEGG - C04454
Neutral MF = C9H17N4O9P
SMP
Checked N-groups NCD, JLR"	C9H16N4O9P	-1	-399.414	9.88809									-1	-399.414	9.88809
986	5apru	No	5-Amino-6-(5'-phosphoribosylamino)uracil	C9H13N4O9P	-2		C01268	"KEGG - C01268
Neutral MF = C9H15N4O9P
SMP
Checked N-groups JLR, NCD"	C9H14N4O9P	-1	-389.054	10.9779									-1	-389.054	10.9779
6593	5caiz	No	5-phosphoribosyl-5-carboxyaminoimidazole	C9H11N3O9P	-3			"JLR - could not find the metabolite in KEGG.  Metabolite is in Neidhardt,"" Escherichia coli and Salmonella cellular and molecular biology"" 2nd edition, page 563.  Used in E. coli purine biosynthesis
Checked N-groups JLR"	C9H13N3O9P	-1	-378.148	9.47909									-1	-378.148	9.47909
695	5dglcn	No	5-Dehydro-D-gluconate	C6H9O7	-1		C01062	"KEGG - C01062
Neutral-C6H10O7
JLR"	C6H9O7	-1	-260.427	5.41724									-1	-260.427	5.41724
448	5dh4dglc	No	5-Dehydro-4-deoxy-D-glucarate	C6H6O7	-2		C00679	"KEGG - C00679
Neutral-C6H8O7
JLR"	C6H6O7	-2	-265.496	4.08869									-2	-265.496	4.08869
3193	5mdr1p	No	5-Methylthio-5-deoxy-D-ribose 1-phosphate	C6H11O7PS	-2		C04188	"KEGG - C04188
Neutral MF = C6H13O7PS
SMP
CHS"	C6H12O7PS	-1	-342.761	7.74907									-1	-342.761	7.74907
3277	5mdru1p	No	5-Methylthio-5-deoxy-D-ribulose 1-phosphate	C6H11O7PS	-2		C04582	"KEGG - C04582
Neutral MF = C6H13O7PS
SMP
CHS"	C6H12O7PS	-1	-343.136	4.923									-1	-343.136	4.923
243	5mta	No	5-Methylthioadenosine	C11H15N5O3S	0	2457-80-9	C00170	"KEGG - C00170
Neutral MF = C11H15N5O3S
SMP
CHS
Checked N-groups JLR"	C11H15N5O3S	0	2.45611	12.9856									0	2.45611	12.9856
431	5mthf	No	5-Methyltetrahydrofolate	C20H24N7O6	-1		C00440	"KEGG - C00440
Neutral MF = C20H25N7O6
SMP
CHS
Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR
Note that Kegg structure is incorrect, in one of the rings there should be a N rather than a C (see thf)
Agrees with pipeline pilot"	C20H23N7O6	-2	-106.381	13.658									-2	-106.381	13.658
2324	5mtr	No	5-Methylthio-D-ribose	C6H12O4S	0		C03089	"KEGG - C03089
Neutral Compound
SMP
CHS"	C6H12O4S	0	-131.439	8.0466									0	-131.439	8.0466
3520	5prdmbz	No	"N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole"	C14H17N2O7P	-2		C04778	"KEGG - C04778
Neutral MF = C14H19N2O7P
SMP
JLR
Checked N-groups JLR"	C14H18N2O7P	-1	-288.608	11.895									-1	-288.608	11.895
8267	6hmhpt	No	6-hydroxymethyl dihydropterin	C7H9N5O2	0			"JLR- Neidhardt pg 667; different from 2ahhmp because Ketone vs. OH group on nitrogen ring
Checked N-groups, ACD software indicates N should be protonated JLR
Pipeline Pilot indicates this N is not charged JLR
checked - AMF"	C7H9N5O2	0	-8.12795	10.0186									0	-8.12795	10.0186
8269	6hmhptpp	No	6-hydroxymethyl-dihydropterin pyrophosphate	C7H8N5O8P2	-3			"JLR - Neidhardt pg 667, different from 2ahhmd because Ketone vs. OH group on nitrogen ring
Checked N-groups, ACD software indicates N should be protonated JLR
Pipeline Pilot indicates this N is not charged JLR"	C7H9N5O8P2	-2	-428.492	10.1391									-2	-428.492	10.1391
182	6pgc	No	6-Phospho-D-gluconate	C6H10O10P	-3		C00345	"KEGG - C00345
Neutral MF = C6H13O10P
SMP
CHS"	C6H11O10P	-2	-482.12	6.97677									-2	-482.12	6.97677
963	6pgl	No	"6-phospho-D-glucono-1,5-lactone"	C6H9O9P	-2	None	C01236	"KEGG - C01236
Neutral MF = C6H11O9P
SMP
CHS"	C6H10O9P	-1	-428.267	7.59162									-1	-428.267	7.59162
873	8aonn	No	8-Amino-7-oxononanoate	C9H17NO3	0		C01092	"KEGG - C01092
Neutral MF = C9H17NO3
SMP
CHS
Changed according to Genomatica JLR"	C9H17NO3	0	-109.195	4.25399									0	-109.195	4.25399
4943	aacald	No	Aminoacetaldehyde	C2H6NO	1	452-86-8	C06735	"KEGG - C06735
Checked N JLR"	C2H6NO	1	-34.8924	1.89056									1	-34.8924	1.89056
174	aacoa	No	Acetoacetyl-CoA	C25H36N7O18P3S	-4	1420-36-6	C00332	"KEGG - C00332
Neutral MF = C25H40N7O18P3S
SMP
CHS"	C25H37N7O18P3S	-3	-808.741	16.3765									-3	-808.741	16.3765
1533	aact	Yes	Aminoacetone	C3H8NO	1	298-08-8	C01888	"KEGG - C01888
Neutral Compound
SMP
Checked N-groups JLR"	C3H8NO	1	-35.9248	2.21108									1	-35.9248	2.21108
319	ac	No	Acetate	C2H3O2	-1	64-19-7	C00033	"KEGG - C00033
Neutral MF = C2H4O2
SMP
CHS"	C2H3O2	-1	-85.6057	1.34381									-1	-85.6057	1.34381
9016	acac	No	Acetoacetate	C4H5O3	-1	541-50-4	C00164	"KEGG - C00164
NCD"	C4H5O3	-1	-112.432	1.94348									-1	-112.432	1.94348
5509	acACP	No	Acetyl-ACP	C13H23N2O8PRS	-1			"tv
Neidhardt
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C13H23N2O8PRS	-1	-355.64	9.14601									-1	-355.64	9.14601
1052	acald	No	Acetaldehyde	C2H4O	0	75-07-0	C00084	"KEGG - C00084
Neutral Compound
SMP
CHS"	C2H4O	0	-33.0915	1.45421									0	-33.0915	1.45421
4054	acanth	Yes	N-Acetylanthranilate	C9H8NO3	-1	89-52-1	C06332	"KEGG - C06332
AMF"	C9H8NO3	-1	-80.7366	8.98794									-1	-80.7366	8.98794
11537	accoa	No	Acetyl-CoA	C23H34N7O17P3S	-4	72-89-9	C00024	"KEGG - C00024
Neutral MF = C23H38N7O17P3S
SMP
CHS"	C23H35N7O17P3S	-3	-781.914	15.8637									-3	-781.914	15.8637
3775	acetol	Yes	Acetol	C3H6O2	0	116-09-6	C05235	"KEGG - C05235
NCD"	C3H6O2	0	-70.4423	1.97901									0	-70.4423	1.97901
2957	acg5p	No	N-Acetyl-L-glutamyl 5-phosphate	C7H9NO8P	-3		C04133	"KEGG - C04133
Neutral MF = C7H12NO8P
SMP
CHS
Checked N-groups JLR"	C7H10NO8P	-2	-403.401	3.95848									-2	-403.401	3.95848
975	acg5sa	No	N-Acetyl-L-glutamate 5-semialdehyde	C7H10NO4	-1	None	C01250	"KEGG - C01250
Neutral MF = C7H11NO4
SMP
CHS
Checked N-groups JLR"	C7H10NO4	-1	-136.54	3.78783									-1	-136.54	3.78783
899	acgal	Yes	N-Acetyl-D-galactosamine	C8H15NO6	0	14215-68-0; 1811-31-0	C01132	"KEGG - C01132
Neutral Compound
SMP
NCD"	C8H15NO6	0	-207.358	9.33655									0	-207.358	9.33655
19195	acgal1p	Yes	N-Acetyl-D-galactosamine 1-phosphate	C8H14NO9P	-2			"not in KEGG
NCD"	C8H15NO9P	-1	-418.68	9.08139									-1	-418.68	9.08139
224	acgam	Yes	N-Acetyl-D-glucosamine	C8H15NO6	0	7512-17-6	C00140	"KEGG - C00140
Neutral Compound
SMP
Checked N-groups JLR"	C8H15NO6	0	-207.358	9.33655									0	-207.358	9.33655
3247	acgam1p	No	N-Acetyl-D-glucosamine 1-phosphate	C8H14NO9P	-2	None	C04256	"KEGG - C04256
Neutral MF = C8H16NO9P
SMP
CHS
Checked N-groups JLR"	C8H15NO9P	-1	-418.68	9.08139									-1	-418.68	9.08139
192	acgam6p	No	N-Acetyl-D-glucosamine 6-phosphate	C8H14NO9P	-2	102029-88-9	C00357	"KEGG - C00357
Neutral MF = C8H16NO9P
SMP
CHS
Checked N-groups JLR"	C8H15NO9P	-1	-419.868	9.38898									-1	-419.868	9.38898
1208	acglc-D	Yes	6-Acetyl-D-glucose	C8H14O7	0	107-85-7	C02655	"KEGG - C02655
AMF"	C8H14O7	0	-254.855	9.54739									0	-254.855	9.54739
1115	acglu	No	N-Acetyl-L-glutamate	C7H9NO5	-2	1188-37-0	C00624	"KEGG - C00624
Neutral MF = C7H11NO5
SMP
CHS
Checked N-groups JLR"	C7H9NO5	-2	-189.055	3.96695									-2	-189.055	3.96695
1728	acmalt	Yes	Acetyl-maltose	C14H24O12	0		C02130	"KEGG - C02130
Neutral Compound
SMP"	C14H24O12	0	-411.162	17.4483									0	-411.162	17.4483
1129	acmana	No	N-Acetyl-D-mannosamine	C8H15NO6	0	3615-17-6	C00645	"KEGG - C00645
Neutral Compound
SMP
Checked N-groups JLR"	C8H15NO6	0	-207.358	9.33655									0	-207.358	9.33655
11865	acmanap	No	N-Acetyl-D-mannosamine 6-phosphate	C8H14NO9P	-2	157296-99-6	C04257	"KEGG - C04257
Neutral-C8H16NO9P
JLR
Checked N JLR"	C8H15NO9P	-1	-419.868	9.38898									-1	-419.868	9.38898
2040	acmum	Yes	N-Acetylmuramate	C11H18NO8	-1	61633-75-8	C02713	"KEGG - C02713
JLR Checked N-Groups"	C11H18NO8	-1	-269.957	9.42171									-1	-269.957	9.42171
12407	acmum6p	Yes	N-acetylmuramate 6-phosphate	C11H17NO11P	-3			"Not in KEGG see PMID 15060041
JLR
AMF"	C11H18NO11P	-2	-482.468	9.47366									-2	-482.468	9.47366
134	acnam	No	N-Acetylneuraminate	C11H18NO9	-1	131-48-6	C00270	"KEGG - C00270
Neutral MF = C11H19NO9
SMP
CHS
Checked N-groups JLR"	C11H18NO9	-1	-320.998	8.27191									-1	-320.998	8.27191
22094	acolipa	Yes	4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A	C181H314N3O103P4	-9			AMF	C181H314N3O103P4	-9	No Energy	No Energy									-9	1.00E+07	1.00E+07
417	acon-C	Yes	cis-Aconitate	C6H3O6	-3	585-84-2	C00417	"KEGG - C00417
Neutral MF = C6H6O6
SMP
CHS"	C6H3O6	-3	-220.965	3.43702									-3	-220.965	3.43702
9959	aconm	No	E-3-carboxy-2-pentenedioate 6-methyl ester	C7H6O6	-2			"Not in Kegg (see PMID 11329290, figure 1)
Neutral-C7H8O6
JLR"	C7H6O6	-2	-215.603	3.42556									-2	-215.603	3.42556
1194	acon-T	No	trans-Aconitate	C6H3O6	-3	4023-65-8	C02341	"KEGG - C02341
Neutral MF = C6H6O6
SMP
CHS"	C6H3O6	-3	-220.965	3.43702									-3	-220.965	3.43702
428	acorn	No	N2-Acetyl-L-ornithine	C7H14N2O3	0	None	C00437	"KEGG - C00437
Neutral MF = C7H14N2O3
SMP
CHS
Changed according to Genomatica JLR"	C7H14N2O3	0	-111.634	4.17476									0	-111.634	4.17476
69	ACP	No	acyl carrier protein	C11H21N2O7PRS	-1		C00229	"tv
formula deducted by substraction the elemental compositon from (MalACP + CoA) - MalCoA
checked with Neidhardt
JLR needed to add an H, pka of thiol (-SH) is 9 to 12.
JLR changed to include 4-phosphopantetheinyl moiety (see PMID 11867633)"	C11H21N2O7PRS	-1	-322.987	7.92709									-1	-322.987	7.92709
808	acser	No	O-Acetyl-L-serine	C5H9NO4	0	66638-22-0	C00979	"KEGG - C00979
Neutral MF = C5H9NO4
SMP
CHS
Changed according to Genomatica JLR"	C5H9NO4	0	-158.965	2.97574									0	-158.965	2.97574
10494	actACP	No	Acetoacetyl-ACP	C15H25N2O9PRS	-1		C05744	"tv
Neidhardt
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C15H25N2O9PRS	-1	-382.467	9.96349									-1	-382.467	9.96349
281	actp	No	Acetyl phosphate	C2H3O5P	-2	19926-71-7	C00227	"KEGG - C00227
Neutral MF = C2H5O5P
SMP
CHS"	C2H4O5P	-1	-299.952	1.85382									-1	-299.952	1.85382
228	ade	No	Adenine	C5H5N5	0	73-24-5	C00147	"KEGG - C00147
Neutral Compound
SMP
CHS"	C5H5N5	0	75.0314	10.4859									0	75.0314	10.4859
270	adn	No	Adenosine	C10H13N5O4	0	58-61-7	C00212	"KEGG - C00212
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H13N5O4	0	-47.5218	12.7294									0	-47.5218	12.7294
5428	adocbi	No	Adenosyl cobinamide	C58H84CoN16O11	1	7625-23-2	C06508	"KEGG - C06508
(removed 3 H's from the ring)
JLR
before charge was +3 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

8/2004 Redone old values were C58H85CoN16O11 with +6 charge (by JLR)"	C58H84CoN16O11	1	No Energy	No Energy									1	1.00E+07	1.00E+07
4772	adocbip	No	Adenosyl cobinamide phosphate	C58H83CoN16O14P	-1	7625-23-2	C06509	"KEGG - C06509
Kegg shows C58H88CoN16O14P 
(removed 3 H's from the ring and 2 from the phosphate group)
JLR
before charge was +1 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

8/2004 REDONE old values were C58H84CoN16O14P charge +4 (by JLR)"	C58H83CoN16O14P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
10925	adocbl	No	Adenosylcobalamin	C72H100CoN18O17P	0	13870-90-1	C00194	"KEGG - C00194
Kegg shows C72H105CoN18O17P
(removed 3 H from ring, 1H from phosphate group, 1H from ribazole group)
JLR
before charge was +3 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

8/2004 REDONE old values were C72H101CoN18O17P charge +7 (by JLR)"	C72H100CoN18O17P	0	No Energy	No Energy									0	1.00E+07	1.00E+07
471	adp	No	ADP	C10H12N5O10P2	-3	20398-34-9	C00008	"KEGG - C00008
Neutral MF = C10H15N5O10P2
SMP
CHS"	C10H13N5O10P2	-2	-467.886	12.8244									-2	-467.886	12.8244
112	adpglc	No	ADPglucose	C16H23N5O15P2	-2		C00498	"KEGG - C00498
Neutral MF = C16H25N5O15P2
SMP
CHS"	C16H23N5O15P2	-2	-625.509	19.2013									-2	-625.509	19.2013
4773	"adphep-D,D"	No	ADP-D-glycero-D-manno-heptose	C17H25N5O16P2	-2	119-61-9	C06397	"KEGG - C06397
Neutral-C17H27N5016P2
JLR
Checked N JLR"	C17H25N5O16P2	-2	-662.43	19.6384									-2	-662.43	19.6384
9429	"adphep-L,D"	No	ADP-L-glycero-D-manno-heptose	C17H25N5O16P2	-2		C06398	"Kegg- C06398
Neutral-C17H27N5O16P2
JLR
Checked N JLR"	C17H25N5O16P2	-2	-662.43	19.6384									-2	-662.43	19.6384
151	adprib	Yes	ADPribose	C15H21N5O14P2	-2		C00301	"KEGG - C00301
Neutral MF = C15H23N5O14P2
SMP
CHS
checked N groups - NCD"	C15H21N5O14P2	-2	-588.699	17.8421									-2	-588.699	17.8421
4921	ag	Yes	silver	Ag	1	7440-22-4	C06710	KEGG - C06710	Ag	1	No Energy	No Energy									1	1.00E+07	1.00E+07
11002	agdpcbi	No	Adenosine-GDP-cobinamide	C68H95CoN21O21P2	-1	7625-23-2	C06510	"KEGG - C06510
Kegg shows C68H100CoN21O21P2
(removed 3 H's from ring and 2 from phosphate groups)
JLR
before charge was +1 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

8/2004 REDONE old values were C68H96CoN21O21P2 charge +4 (by JLR)"	C68H95CoN21O21P2	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
247	agm	No	Agmatine	C5H16N4	2	306-60-5	C00179	"KEGG - C00179
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C5H16N4	2	7.37101	5.34286									2	7.37101	5.34286
310	ahcys	No	S-Adenosyl-L-homocysteine	C14H20N6O5S	0	979-92-0	C00021	"KEGG - C00021
Neutral MF = C14H20N6O5S
SMP
CHS
Changed according to Genomatica JLR"	C14H20N6O5S	0	-75.352	13.2495									0	-75.352	13.2495
3611	ahdt	No	"2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate"	C9H12N5O13P3	-4		C04895	"KEGG - C04895
Neutral MF = C9H16N5O13P3
SMP
Checked N-groups, ACD software indicates a N is protonated, JLR
Pipeline Pilot indicates that this N is not protonated. JLR"	C9H13N5O13P3	-3	-710.188	10.8852									-3	-710.188	10.8852
3340	aicar	No	5-Amino-1-(5-Phospho-D-ribosyl)imidazole-4-carboxamide	C9H13N4O8P	-2	3031-94-5	C04677	"KEGG - C04677
Neutral MF = C9H15N4O8P
SMP
CHS
Checked N-groups JLR"	C9H14N4O8P	-1	-331.429	10.0207									-1	-331.429	10.0207
1941	air	No	5-amino-1-(5-phospho-D-ribosyl)imidazole	C8H12N3O7P	-2	25635-88-5	C03373	"KEGG - C03373
Neutral MF = C8H14N3O7P
SMP
CHS
Checked N-groups JLR"	C8H13N3O7P	-1	-298.083	9.0337									-1	-298.083	9.0337
314	akg	No	2-Oxoglutarate	C5H4O5	-2	328-50-7	C00026	"KEGG - C00026
Neutral MF = C5H6O5
SMP
CHS"	C5H4O5	-2	-190.741	2.59501									-2	-190.741	2.59501
817	alaala	No	D-Alanyl-D-alanine	C6H12N2O3	0	923-16-0	C00993	"KEGG - C00993
Neutral MF = C6H12N2O3
SMP
CHS
Changed according to Genomatica JLR
"	C6H12N2O3	0	-112.07	4.52427									0	-112.07	4.52427
1063	ala-B	No	beta-Alanine	C3H7NO2	0	107-95-9	C00099	"KEGG - C00099
Neutral MF = C3H7NO2
SMP
CHS
Changed according to Genomatica JLR"	C3H7NO2	0	-86.4942	2.15226									0	-86.4942	2.15226
73	alac-S	No	(S)-2-Acetolactate	C5H7O4	-1		C06010	"KEGG - C06010 (C00900 Deleted)
Neutral MF = C5H8O4
SMP
CHS"	C5H7O4	-1	-150.417	3.6322									-1	-150.417	3.6322
1093	ala-D	No	D-Alanine	C3H7NO2	0	338-69-2	C00133	"KEGG - C00133
Neutral MF = C3H7NO2
SMP
CHS
Changed according to Genomatica JLR"	C3H7NO2	0	-86.0175	2.27816									0	-86.0175	2.27816
11412	ala-L	No	L-Alanine	C3H7NO2	0	56-41-7	C00041	"KEGG - C00041
Neutral MF = C3H7NO2
SMP
CHS
Changed according to Genomatica JLR"	C3H7NO2	0	-86.0175	2.27816									0	-86.0175	2.27816
7096	alatrna	Yes	L-Alanyl-tRNA(Ala)	C3H6NOR	1		C00886	"KEGG - C00886
SMP
adjusted for Genomatica's change to aa - NCD
"	C13H18N6O4R	1	-42.1473	12.8202									1	-42.1473	12.8202
2224	all6p	Yes	D-Allose 6-phosphate	C6H11O9P	-2	147-94-4	C02962	KEGG - C02962	C6H12O9P	-1	-430.737	9.43168									-1	-430.737	9.43168
612	all-D	Yes	D-Allose	C6H12O6	0	2595-97-3	C01487	"KEGG - C01487
JLR"	C6H12O6	0	-218.227	9.37949									0	-218.227	9.37949
1262	alltn	No	Allantoin	C4H6N4O3	0	97-59-6	C01551	"KEGG - C01551
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C4H6N4O3	0	-102.662	9.54272									0	-102.662	9.54272
113	alltt	No	Allantoate	C4H7N4O4	-1	99-16-1	C00499	"KEGG - C00499
Neutral MF = C4H8N4O4
SMP
CHS
Checked N-groups JLR"	C4H7N4O4	-1	-156.59	8.97759									-1	-156.59	8.97759
15385	allul6p	Yes	Allulose 6-phosphate	C6H11O9P	-2			"No KEGG entry
see allulose and PMID 9401019
JLR"	C6H12O9P	-1	-430.035	5.6422									-1	-430.035	5.6422
1283	alpp	Yes	applipoprotein	X	0	6244-92-4	C01834	"KEGG - C01834
AMF
generic lipoprotein for acyl transfering"	C3H6NOR2S	1	-14.4915	3.46066									1	-14.4915	3.46066
660	altrn	No	D-Altronate	C6H11O7	-1		C00817	"KEGG - C00817
Neutral MF = C6H12O7
No L-altronate found in Chemfinder
SMP
CHS"	C6H11O7	-1	-269.61	6.90606									-1	-269.61	6.90606
1086	amet	No	S-Adenosyl-L-methionine	C15H23N6O5S	1	29908-03-0	C00019	"KEGG - C00019
Neutral MF = C15H23N6O5S; neutral form has charge +1 - NCD
SMP
CHS
Changed according to Genomatica JLR
"	C15H23N6O5S	1	No Energy	No Energy									1	1.00E+07	1.00E+07
903	ametam	No	S-Adenosylmethioninamine	C14H24N6O3S	2		C01137	"KEGG - C01137
SMP
Changed according to Genomatica JLR"	C14H24N6O3S	2	No Energy	No Energy									2	1.00E+07	1.00E+07
2693	amob	No	S-Adenosyl-4-methylthio-2-oxobutanoate	C15H19N5O6S	0		C04425	"KEGG - C04425
Neutral MF = C15H20N5O6S
SMP
CHS
Checked N-groups JLR
"	C15H19N5O6S	0	No Energy	No Energy									0	1.00E+07	1.00E+07
309	amp	No	AMP	C10H12N5O7P	-2	61-19-8	C00020	"KEGG - C00020
Neutral MF = C10H14N5O7P
SMP
CHS"	C10H13N5O7P	-1	-260.032	12.7679									-1	-260.032	12.7679
21427	anhgm	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid	C19H29N2O12	-1			AMF	C19H29N2O12	-1	-369.269	15.8267									-1	-369.269	15.8267
21428	anhgm3p	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide	C34H52N6O19	-2			AMF	C34H52N6O19	-2	-601.719	22.1698									-2	-601.719	22.1698
21429	anhgm4p	Yes	N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide	C37H57N7O20	-2			AMF	C37H57N7O20	-2	-627.771	24.6025									-2	-627.771	24.6025
21513	anhm	Yes	"1,6-anhydrous-N-Acetylmuramate"	C11H16NO7	-1			AMF	C11H16NO7	-1	-221.839	7.3947									-1	-221.839	7.3947
21511	anhm3p	Yes	"1,6-anhydrous-N-Acetylmuramyl-tripeptide"	C26H39N5O14	-2			AMF	C26H39N5O14	-2	-454.288	15.5048									-2	-454.288	15.5048
21512	anhm4p	Yes	"1,6-anhydrous-N-Acetylmuramyl-tetrapeptide"	C29H44N6O15	-2			AMF	C29H44N6O15	-2	-480.341	18.3302									-2	-480.341	18.3302
1070	anth	No	Anthranilate	C7H6NO2	-1	118-92-3	C00108	"KEGG - C00108
Neutral MF = C7H7NO2
SMP
CHS
Checked N-groups JLR"	C7H6NO2	-1	-50.5724	8.6449									-1	-50.5724	8.6449
8976	ap4a	No	"P1,P4-Bis(5'-adenosyl) tetraphosphate"	C20H24N10O19P4	-4		C01260	"Kegg- C01260
Neutral-C20H28N10O19P4
JLR"	C20H24N10O19P4	-4	-872.503	25.7248									-4	-872.503	25.7248
3098	ap5a	No	"P1,P5-Bis(5'-adenosyl) pentaphosphate"	C20H24N10O22P5	-5	4637-56-3	C04058	"KEGG - C04058
Neutral-C20H29N10O22P5
JLR"	C20H24N10O22P5	-5	-1080.36	25.9208									-5	-1080.36	25.9208
26365	apg120	Yes	acyl phosphatidylglycerol (n-C12:0)	C42H80O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C42H80O11P	-1	-466.308	23.9973									-1	-466.308	23.9973
26366	apg140	Yes	acyl phosphatidylglycerol (n-C14:0)	C48H92O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C48H92O11P	-1	-460.833	27.8957									-1	-460.833	27.8957
26369	apg141	Yes	acyl phosphatidylglycerol (n-C14:1)	C48H86O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C48H86O11P	-1	-403.698	24.6578									-1	-403.698	24.6578
26367	apg160	Yes	acyl phosphatidylglycerol (n-C16:0)	C54H104O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C54H104O11P	-1	-455.359	31.832									-1	-455.359	31.832
26370	apg161	Yes	acyl phosphatidylglycerol (n-C16:1)	C54H98O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C54H98O11P	-1	-398.224	28.4659									-1	-398.224	28.4659
26368	apg180	Yes	acyl phosphatidylglycerol (n-C18:0)	C60H116O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C60H116O11P	-1	-449.885	35.7936									-1	-449.885	35.7936
26371	apg181	Yes	acyl phosphatidylglycerol (n-C18:1)	C60H110O11P	-1			"each acyl chain is the same lenght and sam level of saturation
AMF"	C60H110O11P	-1	-392.749	32.3328									-1	-392.749	32.3328
8800	apoACP	No	apoprotein [acyl carrier protein]	RHO	0			JLR	HOR	0	No Energy	No Energy									0	1.00E+07	1.00E+07
279	aps	No	Adenosine 5'-phosphosulfate	C10H12N5O10PS	-2		C00224	"KEGG - C00224
Neutral MF = C10H14N5O10PS
SMP
CHS
Checked N-groups JLR"	C10H12N5O10PS	-2	-368.225	13.0284									-2	-368.225	13.0284
886	ara5p	No	D-Arabinose 5-phosphate	C5H9O8P	-2		C01112	"KEGG - C01112
neutral MF = C5H11O8P
SMP
CHS
JLR- had incorrect charge should be -2"	C5H10O8P	-1	-392.685	5.39643									-1	-392.685	5.39643
307	arab-L	No	L-Arabinose	C5H10O5	0	147-81-9	C00259	"KEGG - C00259
Neutral Compound
SMP
CHS"	C5H10O5	0	-180.969	8.29386									0	-180.969	8.29386
22128	aragund	Yes	O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate	C71H115N1O17P2	-2			AMF	C71H115NO17P2	-2	-504.315	34.2892									-2	-504.315	34.2892
4596	arbt6p	No	Arbutin 6-phosphate	C12H15O10P	-2		C06187	"KEGG - C06187
Neutral MF = C12H17O10P
SMP"	C12H16O10P	-1	-419.959	12.9659									-1	-419.959	12.9659
19380	arbtn	Yes	aerobactin minus Fe3	C22H33N4O13	-3			0	C22H33N4O13	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
11290	arbtn-fe3	Yes	Aerobactin	C22H33FeN4O13	0	61-33-6	C05554	"KEGG - C05554
AMF

is a siderophore -  Fe-scavenging molecule. requires secretion and re-uptake pathways"	C22H33FeN4O13	0	No Energy	No Energy									0	1.00E+07	1.00E+07
337	arg-L	No	L-Arginine	C6H15N4O2	1	74-79-3	C00062	"KEGG - C00062
Neutral MF = C6H14N4O2
SMP
CHS
Changed according to Genomatica JLR"	C6H15N4O2	1	-70.4609	5.25635									1	-70.4609	5.25635
1962	argsuc	No	N(omega)-(L-Arginino)succinate	C10H17N4O6	-1	None	C03406	"KEGG - C03406
Neutral MF = C10H18N4O6
SMP
CHS
Changed according to Genomatica JLR
pKa = 9.58 nitrogen group"	C10H17N4O6	-1	-218.015	7.09256									-1	-218.015	7.09256
7099	argtrna	Yes	L-Arginyl-tRNA(Arg)	C6H14N4OR	2		C02163	"KEGG - C02163
SMP
adjusted for Genomatica's change to aa - NCD"	C16H26N9O4R	2	-26.5907	13.9865									2	-26.5907	13.9865
11868	ascb6p	Yes	L-ascorbate-6-phosphate	C6H7O9P	-2			"No Kegg Entry
JLR"	C6H7O9P	-2	-396.579	6.37564									-2	-396.579	6.37564
11279	ascb-L	Yes	L-Ascorbate	C6H8O6	0	50-81-7	C00072	"KEGG - C00072
JLR"	C6H7O6	-1	-184.069	6.29819									-1	-184.069	6.29819
232	asn-L	No	L-Asparagine	C4H8N2O3	0	70-47-3	C00152	"KEGG - C00152
Neutral MF = C4H8N2O3
SMP
CHS
Changed according to Genomatica JLR"	C4H8N2O3	0	-121.133	3.47125									0	-121.133	3.47125
7111	asntrna	Yes	L-Asparaginyl-tRNA(Asn)	C4H7N2O2R	1		C03402	"KEGG - C03402
SMP
adjusted for Genomatica's change to aa - NCD"	C14H19N7O5R	1	-77.2629	13.3499									1	-77.2629	13.3499
4908	aso3	Yes	arsenite	AsO3	-3		C06697	"KEGG - C06697
AMF"	AsO3	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
606	aso4	Yes	arsenate	AsO4	-3	7778-39-4	C01478	"KEGG - C01478
AMF"	AsO4	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
330	asp-L	No	L-Aspartate	C4H6NO4	-1	56-84-8	C00049	"KEGG - C00049
Neutral MF = C4H7NO4
SMP
CHS
Changed according to Genomatica JLR"	C4H6NO4	-1	-164.326	2.68993									-1	-164.326	2.68993
432	aspsa	No	L-Aspartate 4-semialdehyde	C4H7NO3	0	None	C00441	"KEGG - C00441
Neutral MF = C4H7NO3
SMP
CHS
Changed according to Genomatica JLR"	C4H7NO3	0	-111.812	2.41799									0	-111.812	2.41799
7106	asptrna	Yes	L-Aspartyl-tRNA(Asp)	C4H5NO3R	0		C02984	"KEGG - C02984
SMP
"	C14H17N6O6R	0	-120.456	12.8692									0	-120.456	12.8692
3421	athr-L	Yes	L-Allo-threonine	C4H9NO3	0	28954-12-3	C05519	"KEGG - C05519
AMF"	C4H9NO3	0	-122.939	3.29766									0	-122.939	3.29766
465	atp	No	ATP	C10H12N5O13P3	-4	56-65-5	C00002	"KEGG - C00002
Neutral MF = C10H16N5O13P3
SMP
CHS"	C10H13N5O13P3	-3	-675.739	12.9924									-3	-675.739	12.9924
733	b2coa	Yes	trans-But-2-enoyl-CoA	C25H36N7O17P3S	-4	102680-35-3	C00877	"KEGG - C00877
Neutral MF = C25H40N7O17P3S
SMP"	C25H37N7O17P3S	-3	-761.044	15.9759									-3	-761.044	15.9759
9449	bbtcoa	No	gamma-butyrobetainyl-CoA	C28H46N8O17P3S	-3			"No Kegg Entry
gamma-butyrobetaine with a CoA attached
+1 charge on butyrobetaine -4 charge on CoA
JLR
Checked N-groups JLR
"	C28H47N8O17P3S	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
392	betald	No	Betaine aldehyde	C5H12NO	1		C00576	"KEGG - C00576
JLR
Checked N-groups JLR"	C5H12NO	1	No Energy	No Energy									1	1.00E+07	1.00E+07
22245	bglycogen	Yes	branching glycogen	C6H10O5	0			"AMF
"	C6H9O5	-1	-149.887	6.95145									-1	-149.887	6.95145
556	btal	Yes	Butanal	C4H8O	0	123-72-8	C01412	"KEGG - C01412
Neutral Compound
SMP"	C4H8O	0	-31.2668	1.98425									0	-31.2668	1.98425
222	btcoa	No	Butanoyl-CoA	C25H38N7O17P3S	-4		C00136	"KEGG - C00136
Neutral MF = C25H42N7O17P3S
SMP"	C25H39N7O17P3S	-3	-780.089	16.2608									-3	-780.089	16.2608
1079	btn	No	Biotin	C10H15N2O3S	-1	58-85-5	C00120	"KEGG - C00120
Neutral MF = C10H16N2O3S
SMP
CHS
Checked N-groups JLR"	C10H15N2O3S	-1	-100.484	8.93751									-1	-100.484	8.93751
9958	btnso	No	d-biotin d-sulfoxide	C10H15N2O4S	-1			"Not in Kegg (see PMID 10747793, figure 1)
Neutral- C10H16N2O4S
JLR
Checked N-groups JLR"	C10H15N2O4S	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
294	but	No	Butyrate (n-C4:0)	C4H7O2	-1	107-92-6	C00246	"KEGG - C00246
Neutral MF = C4H8O2
SMP
changed compound class from peptides - NCD"	C4H7O2	-1	-83.7809	1.90482									-1	-83.7809	1.90482
3236	but2eACP	Yes	But-2-enoyl-[acyl-carrier protein]	C15H25N2O8PRS	-1	128-33-6	C04246	"KEGG - C04246
AMF"	C15H25N2O8PRS	-1	-334.771	9.33919									-1	-334.771	9.33919
4241	butACP	Yes	Butyryl-ACP (n-C4:0ACP)	C15H27N2O8PRS	-1	8/6/83	C05745	"KEGG - C05745
AMF"	C15H27N2O8PRS	-1	-353.816	9.72546									-1	-353.816	9.72546
22149	butso3	Yes	butanesulfonate	C4H9O3S	-1			AMF	C4H9O3S	-1	-126.836	3.03176									-1	-126.836	3.03176
8980	camp	No	cAMP	C10H11N5O6P	-1		C00575	"Kegg C00575
Neutral-C10H12N5O6P
JLR"	C10H11N5O6P	-1	-193.74	13.6927									-1	-193.74	13.6927
429	cbasp	No	N-Carbamoyl-L-aspartate	C5H6N2O5	-2		C00438	"KEGG - C00438
Neutral MF = C5H8N2O5
SMP
CHS
Checked N-groups JLR"	C5H6N2O5	-2	-198.256	4.9856									-2	-198.256	4.9856
4266	cbi	No	Cobinamide	C48H72CoN11O8	0	1867-62-5	C05774	"KEGG - C05774
Kegg shows C48H75CoN11O8
(removed 3H's from ring)
JLR 
before charge was +3 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

Note: (Assumed that Co charge is +1 and no hydrogens are removed RM) this was not taken into account for this molecule H75 charge =0

8/2004 REDONE old values were C48H73CoN11O8 charge +5 (by JLR)"	C48H72CoN11O8	0	No Energy	No Energy									0	1.00E+07	1.00E+07
10988	cbl1	No	Cob(I)alamin	C62H88CoN13O14P	-1	18534-66-2	C00853	"KEGG - C00853
Kegg shows C62H93CoN13O14P
(removed 3 H from ring, 1H from phosphate group, 1H from ribazole group)
JLR
before charge was +3 (no charge on Co was taken into account).  New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR
ADD H and a +1 charge for N in ring JLR

Note: (Updated with Pipeline Pilot Calculations (1 H from the phosphate group removed) RM)-dind't take this into account

8/2004 REDONE old values were C62H89CoN13O14P charge +6 (by JLR)"	C62H88CoN13O14P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
11004	cbp	No	Carbamoyl phosphate	CH2NO5P	-2		C00169	"KEGG - C00169
Neutral MF = CH4NO5P
SMP
CHS
Checked N-groups JLR"	CH2NO5P	-2	-294.45	3.57842									-2	-294.45	3.57842
13909	cd2	Yes	Cadmium	Cd	2		C01413	"KEGG - C01413
SMP (02/16/03)"	Cd	2	No Energy	No Energy									2	1.00E+07	1.00E+07
26034	cddec5eACP	Yes	cis-dodec-5-enoyl-[acyl-carrier protein] (n-C12:1)	C23H41N2O8PRS	-1			AMF	C23H41N2O8PRS	-1	-327.471	12.3625									-1	-327.471	12.3625
26033	cdec3eACP	Yes	cis-dec-3-enoyl-[acyl-carrier protein] (n-C10:1)	C21H37N2O8PRS	-1			AMF	C21H37N2O8PRS	-1	-329.296	11.4438									-1	-329.296	11.4438
1073	cdp	No	CDP	C9H12N3O11P2	-3	63-38-7	C00112	"KEGG - C00112
Neutral MF = C9H15N3O11P2
SMP
CHS"	C9H13N3O11P2	-2	-546.623	9.41491									-2	-546.623	9.41491
26134	cdpdddecg	Yes	"CDP-1,2-didodecanoylglycerol"	C36H63N3O15P2	-2		C00269	"KEGG - C00269
AMF"	C36H63N3O15P2	-2	-656.972	18.7053									-2	-656.972	18.7053
26076	cdpdhdec9eg	Yes	"CDP-1,2-dihexadec-9-enoylglycerol"	C44H75N3O15P2	-2		C00269	AMF	C44H75N3O15P2	-2	-611.582	21.3377									-2	-611.582	21.3377
26073	cdpdhdecg	Yes	"CDP-1,2-dihexadecanoylglycerol"	C44H79N3O15P2	-2		C00269	"KEGG - C00269
AMF"	C44H79N3O15P2	-2	-649.673	23.3821									-2	-649.673	23.3821
26077	cdpdodec11eg	Yes	"CDP-1,2-dioctadec-11-enoylglycerol"	C48H83N3O15P2	-2		C00269	AMF	C48H83N3O15P2	-2	-607.933	23.6855									-2	-607.933	23.6855
26074	cdpdodecg	Yes	"CDP-1,2-dioctadecanoylglycerol"	C48H87N3O15P2	-2		C00269	AMF	C48H87N3O15P2	-2	-646.023	25.8265									-2	-646.023	25.8265
26075	cdpdtdec7eg	Yes	"CDP-1,2-ditetradec-7-enoylglycerol"	C40H67N3O15P2	-2		C00269	AMF	C40H67N3O15P2	-2	-615.232	19.0833									-2	-615.232	19.0833
26072	cdpdtdecg	Yes	"CDP-1,2-ditetradecanoylglycerol"	C40H71N3O15P2	-2		C00269	AMF	C40H71N3O15P2	-2	-653.322	21.0003									-2	-653.322	21.0003
9376	cechddd	No	"cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol"	C9H11O4	-1			"No Kegg entry, see figure 1 PMID: 9603882
Neutral-C9H12O4
JLR"	C9H11O4	-1	-126.253	6.15347									-1	-126.253	6.15347
9374	cenchddd	No	"cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol"	C9H9O4	-1			"No KEGG entry see Figure 1in PMID: 9603882 
Neutral-C9H10O4
JLR"	C9H9O4	-1	-107.208	6.29393									-1	-107.208	6.29393
7908	cgly	Yes	Cys-Gly	C5H10N2O3S	0	19246-18-5	C01419	"KEGG - C01419 
NCD
changed to protonated form - NCD"	C5H10N2O3S	0	-110.486	4.25748									0	-110.486	4.25748
1075	chol	No	Choline	C5H14NO	1	62-49-7	C00114	"KEGG - C00114
SMP
Checked N-groups JLR"	C5H14NO	1	No Energy	No Energy									1	1.00E+07	1.00E+07
299	chor	No	chorismate	C10H8O6	-2	55508-12-8	C00251	"KEGG - C00251
Neutral MF = C10H10O6
SMP
CHS"	C10H8O6	-2	-173.314	6.68574									-2	-173.314	6.68574
419	cinnm	No	trans-Cinnamate	C9H7O2	-1	140-10-3	C00423	"KEGG - C00423
Neutral-C9H8O2
JLR"	C9H7O2	-1	-29.1288	8.2292									-1	-29.1288	8.2292
236	cit	No	Citrate	C6H5O7	-3	77-92-9	C00158	"KEGG - C00158
Neutral MF = C6H8O7
SMP
CHS"	C6H5O7	-3	-279.295	4.0576									-3	-279.295	4.0576
169	citr-L	No	L-Citrulline	C6H13N3O3	0	372-75-8	C00327	"KEGG - C00327
Neutral MF = C6H13N3O3
SMP
CHS
Changed according to Genomatica JLR"	C6H13N3O3	0	-119.923	5.28347									0	-119.923	5.28347
8744	ckdo	No	CMP-3-deoxy-D-manno-octulosonate	C17H24N3O15P	-2			"JLR-
like KEGG C04121 except ring structure (see NH page 1044)
"	C17H24N3O15P	-2	-576.594	12.7991									-2	-576.594	12.7991
5268	cl	Yes	Chloride	Cl	-1		C00115	0	Cl	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
26137	clpn120	Yes	"cardiolipin (tetradodecanoyl, n-C12:0)"	C57H108O17P2	-2		C05980	"KEGG - C05980
AMF"	C57H108O17P2	-2	-761.663	32.6071									-2	-761.663	32.6071
4430	clpn140	Yes	"cardiolipin (tetratetradecanoyl, n-C14:0)"	C65H124O17P2	-2		C05980	"KEGG - C05980
AMF"	C65H124O17P2	-2	-754.363	37.7853									-2	-754.363	37.7853
26092	clpn141	Yes	"cardiolipin (tetratetradec-7-enoyl, n-C14:1)"	C65H116O17P2	-2		C05980	"KEGG - C05980
AMF"	C65H116O17P2	-2	-678.183	33.4718									-2	-678.183	33.4718
26089	clpn160	Yes	"cardiolipin (tetrahexadecanoyl, n-C16:0)"	C73H140O17P2	-2		C05980	"KEGG - C05980
AMF"	C73H140O17P2	-2	-747.064	43.0181									-2	-747.064	43.0181
26091	clpn161	Yes	"cardiolipin (tetrahexadec-9-enoyl, n-C16:1)"	C73H132O17P2	-2		C05980	"KEGG - C05980
AMF"	C73H132O17P2	-2	-670.884	38.5339									-2	-670.884	38.5339
26090	clpn180	Yes	"cardiolipin (tetraoctadecanoyl, n-C18:0)"	C81H156O17P2	-2		C05980	"KEGG - C05980
AMF"	C81H156O17P2	-2	-739.765	48.2877									-2	-739.765	48.2877
26093	clpn181	Yes	"cardiolipin (tetraoctadec-11-enoyl, n-C18:1)"	C81H148O17P2	-2		C05980	"KEGG - C05980
AMF"	C81H148O17P2	-2	-663.585	43.6771									-2	-663.585	43.6771
11376	cmp	No	CMP	C9H12N3O8P	-2	84-52-6	C00055	"KEGG - C00055
Neutral MF = C9H14N3O8P
SMP
CHS"	C9H13N3O8P	-1	-338.769	9.33781									-1	-338.769	9.33781
474	co2	No	CO2	CO2	0	124-38-9	C00011	"KEGG - C00011
Neutral Compound
SMP
CHS"	CO2	0	-92.3	0.5									0	-92.3	0.5
473	coa	No	Coenzyme A	C21H32N7O16P3S	-4	85-61-0	C00010	"KEGG - C00010
Neutral MF = C21H36N7O16P3S
SMP
CHS
Checked N JLR
Note the H is attached to the S on the CoA"	C21H33N7O16P3S	-3	-749.261	15.1936									-3	-749.261	15.1936
244	cobalt2	Yes	Co2+	Co	2	7440-48-4	C00175	KEGG - C00175	Co	2	No Energy	No Energy									2	1.00E+07	1.00E+07
22093	colipa	Yes	core oligosaccharide lipid A	C176H303N2O100P4	-11			AMF	C176H303N2O100P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
26182	cpe160	Yes	"cyclopropane phosphatidylethanolamine (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)"	C39H74N1O8P1	0			"AMF
"	C39H73NO8P	-1	-275.321	21.6591									-1	-275.321	21.6591
26183	cpe180	Yes	"cyclopropane phosphatidylethanolamine (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)"	C43H82N1O8P1	0			AMF	C43H81NO8P	-1	-271.672	24.0514									-1	-271.672	24.0514
26185	cpg160	Yes	"cyclopropane phosphatidylglycerol (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)"	C40H74O10P1	-1			AMF	C40H74O10P	-1	-370.939	21.6602									-1	-370.939	21.6602
26186	cpg180	Yes	"cyclopropane phosphatidylglycerol (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)"	C44H82O10P1	-1			AMF	C44H82O10P	-1	-367.29	24.0524									-1	-367.29	24.0524
16107	cpgn	Yes	coprogen	C35H52N6O13Fe	-1			"AMF
"	C35H52N6O13Fe	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
22446	cpgn-un	Yes	coprogen unloaded (no Fe(III))	C35H52N6O13	-4			AMF	C35H52N6O13	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
2442	cpppg3	No	Coproporphyrinogen III	C36H40N4O8	-4	2624-63-7	C03263	"KEGG - C03263
Deleted C02667 (Coproporphyrinogen)
Neutral MF = C36H44N4O8
SMP
CHS
Checked N-groups JLR"	C36H40N4O8	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
163	crn	No	L-Carnitine	C7H15NO3	0	44985-71-9	C00318	"KEGG - C00318
At neutral pH, this compound is neutral due to positive on nitrogen and negative charge on carboxyl ends.
SMP
Checked N-groups JLR"	C7H15NO3	0	No Energy	No Energy									0	1.00E+07	1.00E+07
9447	crncoa	No	L-Carnitinyl-CoA	C28H46N8O18P3S	-3			"No Kegg Entry
Carnitine with a CoA attached
+1 charge on carnitine -4 charge on CoA
JLR
Checked N-groups JLR"	C28H47N8O18P3S	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
22160	crn-D	Yes	D-Carnitine	C7H15NO3	0		C00487	"KEGG - C00487
AMF
"	C7H15NO3	0	No Energy	No Energy									0	1.00E+07	1.00E+07
22161	crnDcoa	Yes	D-carnitinyl-CoA	C28H46N8O18P3S	-3			AMF	C28H47N8O18P3S	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
212	csn	No	Cytosine	C4H5N3O	0	71-30-7	C00380	"KEGG - C00380
Neutral Compound
SMP
CHS"	C4H5N3O	0	-3.70546	5.84202									0	-3.70546	5.84202
3136	ctbt	No	crotonobetaine	C7H13NO2	0	6666-46-2	C04114	"KEGG - C04114
Compound is neutral at pH 7, +1 on N, -1 on O
JLR
Checked N-groups JLR"	C7H13NO2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
9448	ctbtcoa	No	crotonobetainyl-CoA	C28H44N8O17P3S	-3			"No Kegg Entry
crotonobetaine with a CoA attached
+1 charge on crotonobetaine -4 charge on CoA
JLR
Checked N-groups JLR"	C28H45N8O17P3S	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
338	ctp	No	CTP	C9H12N3O14P3	-4	65-47-4	C00063	"KEGG - C00063
Neutral MF = C9H16N3O14P3
SMP
CHS"	C9H13N3O14P3	-3	-754.476	9.6425									-3	-754.476	9.6425
21279	cu	Yes	Cu+	Cu	1			C00070	Cu	1	No Energy	No Energy									1	1.00E+07	1.00E+07
5271	cu2	Yes	Cu2+	Cu	2			Two entries are made for Cu: Cu3+ and Cu2+	Cu	2	No Energy	No Energy									2	1.00E+07	1.00E+07
245	cyan	No	Hydrogen cyanide	CHN	0	57-12-5	C01326	"KEGG - C01326
JLR
pKa of H attached to C is 9.3
Checked N-groups JLR
"	CHN	0	28.609	5.5756									0	28.609	5.5756
560	cynt	No	Cyanate	CNO	-1	420-05-3	C01417	"KEGG - C01417
Neutral-CHNO
JLR
Checked N-groups JLR"	CNO	-1	-5.04986	5.46619									-1	-5.04986	5.46619
11128	cys-D	Yes	D-Cysteine	C3H7NO2S	0	921-01-7	C00793	"KEGG - C00793
JLR
Changed according to Genomatica JLR"	C3H7NO2S	0	-83.0442	2.9362									0	-83.0442	2.9362
1062	cys-L	No	L-Cysteine	C3H7NO2S	0	52-90-4	C00097	"KEGG - C00097
Neutral MF = C3H7NO2S
SMP
CHS
Changed according to Genomatica JLR"	C3H7NO2S	0	-83.0442	2.9362									0	-83.0442	2.9362
1150	cyst-L	No	L-Cystathionine	C7H14N2O4S	0	56-88-2	C02291	"KEGG - C02291
Neutral MF = C7H14N2O4S
SMP
CHS
Changed according to Genomatica JLR
"	C7H14N2O4S	0	-150.166	5.25871									0	-150.166	5.25871
7109	cystrna	Yes	L-Cysteinyl-tRNA(Cys)	C3H6NOSR	1		C03125	"KEGG - C03125
SMP
adjusted for Genomatica's change to aa - NCD
"	C13H18N6O4RS	1	-39.1739	12.9885									1	-39.1739	12.9885
92	cytd	No	Cytidine	C9H13N3O5	0	65-46-3	C00475	"KEGG - C00475
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C9H13N3O5	0	-126.259	9.2851									0	-126.259	9.2851
380	dad-2	No	Deoxyadenosine	C10H13N5O3	0	958-09-8	C00559	"KEGG - C00559
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H13N5O3	0	-7.36013	12.0199									0	-7.36013	12.0199
3751	dad-5	Yes	5'-Deoxyadenosine	C10H13N5O3	0		C05198	"KEGG - C05198
Neutral Compound
SMP
CHS"	C10H13N5O3	0	-11.2034	12.7103									0	-11.2034	12.7103
265	dadp	No	dADP	C10H12N5O9P2	-3	None	C00206	"KEGG - C00206
Neutral MF = C10H15N5O9P2
SMP
CHS"	C10H13N5O9P2	-2	-427.724	12.1205									-2	-427.724	12.1205
193	damp	No	dAMP	C10H12N5O6P	-2	653-63-4	C00360	"KEGG - C00360
Neutral MF = C10H14N5O6P
SMP
CHS"	C10H13N5O6P	-1	-219.871	12.0607									-1	-219.871	12.0607
676	dann	No	"7,8-Diaminononanoate"	C9H21N2O2	1		C01037	"KEGG - C01037
Neutral MF = C9H20N2O2
SMP
CHS
Changed according to Genomatica JLR"	C9H21N2O2	1	-81.8674	5.17043									1	-81.8674	5.17043
1091	datp	No	dATP	C10H12N5O12P3	-4	1927-31-7	C00131	"KEGG - C00131
Neutral MF = C10H16N5O12P3
SMP
CHS"	C10H13N5O12P3	-3	-635.577	12.2981									-3	-635.577	12.2981
10	db4p	No	"3,4-dihydroxy-2-butanone 4-phosphate"	C4H7O6P	-2			"No KEGG Entry
Neutral MF = C4H9O6P
SMP"	C4H8O6P	-1	-319.874	2.78131									-1	-319.874	2.78131
3804	dc2coa	Yes	trans-Dec-2-enoyl-CoA	C31H48N7O17P3S	-4		C05275	"KEGG - C05275
Neutral MF = C31H52N7O17P3S
SMP"	C31H49N7O17P3S	-3	-755.57	17.4481									-3	-755.57	17.4481
1277	dca	Yes	Decanoate (n-C10:0)	C10H19O2	-1	334-48-5	C01571	"KEGG - C01571
Neutral MF = C10H20O2
SMP
saturated fatty acid, 10 carbons
changed compound class from peptide to fatty acid - NCD"	C10H19O2	-1	-78.3066	5.56472									-1	-78.3066	5.56472
7929	dcaACP	Yes	Decanoyl-ACP (n-C10:0ACP)	C21H39N2O8PRS	-1		C05755	"JLR- saturated fatty acid, 10 carbons attached to ACP
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C21H39N2O8PRS	-1	-348.341	12.2172									-1	-348.341	12.2172
3803	dcacoa	Yes	Decanoyl-CoA (n-C10:0CoA)	C31H50N7O17P3S	-4		C05274	"KEGG - C05274
Neutral MF = C31H54N7O17P3S
SMP"	C31H51N7O17P3S	-3	-774.615	18.0155									-3	-774.615	18.0155
2908	dcamp	No	"N6-(1,2-Dicarboxyethyl)-AMP"	C14H14N5O11P	-4		C03794	"KEGG - C03794
Neutral MF = C14H18N5O11P
SMP
CHS
Checked N-groups JLR"	C14H15N5O11P	-3	-407.587	13.0377									-3	-407.587	13.0377
5272	dcdp	No	dCDP	C9H12N3O10P2	-3	None	C00705	"KEGG - C00705
Neutral MF = C9H15N3O10P2
SMP
CHS"	C9H13N3O10P2	-2	-506.461	8.431									-2	-506.461	8.431
290	dcmp	No	dCMP	C9H12N3O7P	-2	1032-65-1	C00239	"KEGG - C00239
Neutral MF = C9H14N3O7P
SMP
CHS"	C9H13N3O7P	-1	-298.608	8.34481									-1	-298.608	8.34481
78	dctp	No	dCTP	C9H12N3O13P3	-4	2056-98-6	C00458	"KEGG - C00458
Neutral MF = C9H16N3O13P3
SMP
CHS"	C9H13N3O13P3	-3	-714.314	8.68441									-3	-714.314	8.68441
10918	dcyt	No	Deoxycytidine	C9H13N3O4	0	951-77-9	C00881	"KEGG - C00881
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C9H13N3O4	0	-86.097	8.28579									0	-86.097	8.28579
2416	dd2coa	Yes	trans-Dodec-2-enoyl-CoA	C33H52N7O17P3S	-4		C03221	"KEGG - C03221
Neutral MF = C33H56N7O17P3S
SMP"	C33H53N7O17P3S	-3	-753.745	18.1143									-3	-753.745	18.1143
1919	ddca	Yes	Dodecanoate (n-C12:0)	C12H23O2	-1	143-07-7	C02679	"KEGG - C02679
Neutral MF = C12H24O2
SMP
saturated fatty acid, 12 carbons
changed compound class from peptides to fatty acid - NCD"	C12H23O2	-1	-76.4818	6.8825									-1	-76.4818	6.8825
10497	ddcaACP	No	Dodecanoyl-ACP (n-C12:0ACP)	C23H43N2O8PRS	-1		C05223	"KEGG C05223
tv
Neidhardt
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C23H43N2O8PRS	-1	-346.517	13.2203									-1	-346.517	13.2203
1383	ddcacoa	Yes	Dodecanoyl-CoA (n-C12:0CoA)	C33H54N7O17P3S	-4	6244-92-4	C01832	"KEGG - C01832
Neutral MF = C33H58N7O17P3S
SMP"	C33H55N7O17P3S	-3	-772.79	18.7589									-3	-772.79	18.7589
194	dgdp	No	dGDP	C10H12N5O10P2	-3		C00361	"KEGG - C00361
Neutral MF=C10H15N5O10P2
CHS"	C10H13N5O10P2	-2	-476.919	11.2201									-2	-476.919	11.2201
195	dgmp	No	dGMP	C10H12N5O7P	-2	902-04-5	C00362	"KEGG - C00362
Neutral MF = C10H14N5O7P
SMP
CHS"	C10H13N5O7P	-1	-269.065	11.1555									-1	-269.065	11.1555
172	dgsn	No	Deoxyguanosine	C10H13N5O4	0	961-07-9	C00330	"KEGG - C00330
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H13N5O4	0	-56.5548	11.1114									0	-56.5548	11.1114
143	dgtp	No	dGTP	C10H12N5O13P3	-4	2564-35-4	C00286	"KEGG - C00286
Neutral MF = C10H16N5O13P3
SMP
CHS"	C10H13N5O13P3	-3	-684.772	11.4117									-3	-684.772	11.4117
251	dha	No	Dihydroxyacetone	C3H6O3	0	96-26-4	C00184	KEGG - C00184	C3H6O3	0	-106.761	2.70027									0	-106.761	2.70027
1072	dhap	No	Dihydroxyacetone phosphate	C3H5O6P	-2	57-04-5	C00111	"KEGG - C00111
Neutral MF = C3H7O6P
SMP
CHS"	C3H6O6P	-1	-319.271	2.50929									-1	-319.271	2.50929
9379	dhcinnm	No	"2,3-dihydroxicinnamic acid"	C9H7O4	-1			"No Kegg entry see figure 1 PMID: 9603882
Neutral-C9H8O4
JLR"	C9H7O4	-1	-107.427	12.8047									-1	-107.427	12.8047
10505	dhf	No	"7,8-Dihydrofolate"	C19H19N7O6	-2	4033-27-6	C00415	"KEGG - C00415
Neutral MF = C19H21N7O6
SMP
CHS
Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR
Pipeline Pilot indicates this N is not charged JLR"	C19H19N7O6	-2	-110.86	14.2792									-2	-110.86	14.2792
22235	dhmptp	Yes	dihydromonapterin-triphosphate	C9H12N5O13P3	-4			AMF	C9H13N5O13P3	-3	-710.188	10.8852									-3	-710.188	10.8852
2809	dhna	No	"1,4-Dihydroxy-2-naphthoate"	C11H7O4	-1		C03657	"KEGG - C03657
Neutral MF = C11H8O4
SMP
CHS"	C11H7O4	-1	-118.242	15.3466									-1	-118.242	15.3466
3592	dhnpt	No	Dihydroneopterin	C9H13N5O4	0		C04874	"KEGG - C04874
SMP
CHS
Checked N-groups, ACD software indicates N should be protonated JLR
Pipeline Pilot indicates this N is not charged JLR
checked - AMF"	C9H13N5O4	0	-81.9706	10.5699									0	-81.9706	10.5699
177	dhor-S	No	(S)-Dihydroorotate	C5H5N2O4	-1	5988-19-2	C00337	"KEGG - C00337
Neutral MF = C5H6N2O4
SMP
Checked N-groups JLR"	C5H5N2O4	-1	-145.569	6.94503									-1	-145.569	6.94503
8264	dhpmp	No	Dihydroneopterin monophosphate	C9H12N5O7P	-2		C05925	"KEGG - C05925  MM
JLR- Neidhardt pg 667
Checked N-groups, ACD indicates that the N should be protonated JLR
Pipeline Pilot indicates this N is not charged JLR
checked AMF"	C9H13N5O7P	-1	-294.481	10.6163									-1	-294.481	10.6163
3088	dhpppn	No	"3-(2,3-Dihydroxyphenyl)propanoate"	C9H9O4	-1	145-14-2	C04044	"KEGG - C04044
Neutral-C9H10O4
JLR"	C9H9O4	-1	-126.472	12.7363									-1	-126.472	12.7363
663	dhpt	No	Dihydropteroate	C14H13N6O3	-1		C00921	"KEGG - C00921
Neutral MF = C14H14N6O3
SMP
CHS
Checked N-groups, agrees with ACD software JLR"	C14H13N6O3	-1	-7.41093	13.2248									-1	-7.41093	13.2248
9537	dhptd	No	"4,5-dihydroxy-2,3-pentanedione"	C5H8O4	0		C11838	"KEGG C11838
See PMID: 11489131 
JLR"	C5H8O4	0	-135.103	3.3617									0	-135.103	3.3617
1032	didp	Yes	dIDP	C10H11N4O10P2	-3		C01344	"KEGG - C01344
Neutral MF = C10H14N4O10P2
SMP
CHS"	C10H12N4O10P2	-2	-481.411	11.1732									-2	-481.411	11.1732
9639	dimp	Yes	dIMP	C10H11N4O7P	-2		C06196	"KEGG - C06196 (figure in Kegg is inconsistent with other inosine bases) IT
Neutral MF = C10H15N4O7P 
SMP
CHS"	C10H13N4O7P	0	-278.477	10.4815									0	-278.477	10.4815
3417	din	No	Deoxyinosine	C10H12N4O4	0	890-38-0	C05512	"KEGG - C05512
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H12N4O4	0	-61.0475	11.064									0	-61.0475	11.064
1033	ditp	Yes	dITP	C10H11N4O13P3	-4	66701-25-5	C01345	"KEGG - C01345
Neutral MF = C10H15N4O13P3
SMP
CHS"	C10H12N4O13P3	-3	-689.265	11.3656									-3	-689.265	11.3656
8766	dkmpp	No	"2,3-diketo-5-methylthio-1-phosphopentane"	C6H9O6PS	-2			JLR- no kegg entry	C6H10O6PS	-1	-296.12	4.43969									-1	-296.12	4.43969
2342	dmbzid	No	"5,6-Dimethylbenzimidazole"	C9H10N2	0	582-60-5	C03114	"KEGG - C03114
SMP
JLR
Checked N-groups JLR"	C9H10N2	0	46.4559	9.40344									0	46.4559	9.40344
2629	dmlz	No	"6,7-Dimethyl-8-(1-D-ribityl)lumazine"	C13H18N4O6	0		C04332	"KEGG - C04332
Neutral Compound
SMP
CHS
Checked N-groups, agrees with ACD software, JLR, NCD"	C13H18N4O6	0	-136.792	11.6859									0	-136.792	11.6859
38	dmpp	No	Dimethylallyl diphosphate	C5H9O7P2	-3	358-71-4	C00235	"KEGG - C00235
Neutral MF = C5H12O7P2
SMP
CHS"	C5H10O7P2	-2	-440.896	3.37869									-2	-440.896	3.37869
395	dms	No	Dimethyl sulfide	C2H6S	0	75-18-3	C00580	KEGG - C00580	C2H6S	0	6.36243	3.23235									0	6.36243	3.23235
9065	dmso	No	Dimethyl sulfoxide	C2H6OS	0		C11143	"KEGG C11143
JLR"	C2H6OS	0	No Energy	No Energy									0	1.00E+07	1.00E+07
724	dnad	No	Deamino-NAD+	C21H24N6O15P2	-2		C00857	"KEGG - C00857
Neutral MF = C21H27N6O15P2
SMP
Checked N-groups JLR"	C21H24N6O15P2	-2	-579.678	20.3697									-2	-579.678	20.3697
2882	dopa	Yes	Dopamine	C8H12NO2	1	51-61-6	C03758	"KEGG - C03758
SAB"	C8H12NO2	1	-49.9643	12.7798									1	-49.9643	12.7798
737	dpcoa	No	Dephospho-CoA	C21H33N7O13P2S	-2		C00882	"KEGG - C00882
Neutral MF = C21H35N7O13P2S
SMP
CHS
Checked N-groups JLR"	C21H33N7O13P2S	-2	-537.939	15.3475									-2	-537.939	15.3475
26278	dsbaox	Yes	periplasmic protein disulfide isomerase I (oxidized)	X	0			AMF	X	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26277	dsbard	Yes	periplasmic protein disulfide isomerase I (reduced)	XH2	0			"AMF
"	XH2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26282	dsbcox	Yes	protein disulfide isomerase II (oxidized)	X	0			AMF	X	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26279	dsbcrd	Yes	protein disulfide isomerase II (reduced)	XH2	0			AMF	XH2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26283	dsbdox	Yes	fused thiol:disulfide interchange protein (oxidized)	X	0			AMF	X	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26280	dsbdrd	Yes	fused thiol:disulfide interchange protein (reduced)	XH2	0			AMF	XH2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26284	dsbgox	Yes	periplasmic disulfide isomerase/thiol-disulphide oxidase (oxidized)	X	0			AMF	X	0	No Energy	No Energy									0	1.00E+07	1.00E+07
26281	dsbgrd	Yes	periplasmic disulfide isomerase/thiol-disulphide oxidase (reduced)	XH2	0			AMF	XH2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
2542	dscl	Yes	dihydrosirohydrochlorin	C42H41N4O16	-7	65207-12-7	C02463	"KEGG - C02463
Neutral MF = C42H48N4O16
SMP
Checked N-groups, agrees with ACD software, JLR"	C42H41N4O16	-7	No Energy	No Energy									-7	1.00E+07	1.00E+07
10716	dtbt	No	Dethiobiotin	C10H17N2O3	-1		C01909	"KEGG - C01909
Neutral MF = C10H18N2O3
SMP
CHS
Checked N-groups JLR"	C10H17N2O3	-1	-107.678	7.78215									-1	-107.678	7.78215
196	dtdp	No	dTDP	C10H13N2O11P2	-3		C00363	"KEGG - C00363
Neutral MF = C10H16N2O11P2
SMP
CHS"	C10H14N2O11P2	-2	-557.466	8.94575									-2	-557.466	8.94575
9095	dtdp4aaddg	No	"dTDP-4-acetamido-4,6-dideoxy-D-galactose"	C18H27N3O15P2	-2			"No Kegg entry (similar to C04268 excent amino group on sugar is has an acetyl group on it)
Neutral-C18H29N3O15P2
JLR
Checked N-groups JLR"	C18H27N3O15P2	-2	-667.902	16.382									-2	-667.902	16.382
3064	dtdp4addg	No	"dTDP-4-amino-4,6-dideoxy-D-glucose"	C16H26N3O14P2	-1	157296-99-6	C04268	"KEGG - C04268
Neutral-C16H25N3O14P2
JLR
Checked N-groups JLR"	C16H26N3O14P2	-1	-642.261	15.6912									-1	-642.261	15.6912
453	dtdp4d6dg	No	dTDP-4-dehydro-6-deoxy-D-glucose	C16H22N2O15P2	-2		C00687	"KEGG - C00687
Neutral-C16H24N2O15P2
JLR
Checked N-groups JLR"	C16H22N2O15P2	-2	-672.548	14.9999									-2	-672.548	14.9999
11394	dtdp4d6dm	No	dTDP-4-dehydro-6-deoxy-L-mannose	C16H22N2O15P2	-2		C00688	"KEGG - C00688
Neutral-C16H24N2O15P2
JLR
Checked N-groups JLR"	C16H22N2O15P2	-2	-672.548	14.9999									-2	-672.548	14.9999
712	dtdpglu	No	dTDPglucose	C16H24N2O16P2	-2	2009-24-7	C00842	"KEGG - C00842
Neutral-C16H26N2O16P2
JLR
Checked N-groups JLR"	C16H24N2O16P2	-2	-715.089	15.9259									-2	-715.089	15.9259
2288	dtdprmn	No	dTDP-L-rhamnose	C16H24N2O15P2	-2	572-96-3	C03319	"KEGG - C03319
Neutral-C16H26N2O15P2
JLR
Checked N-groups JLR"	C16H24N2O15P2	-2	-678.77	15.9421									-2	-678.77	15.9421
197	dtmp	No	dTMP	C10H13N2O8P	-2	365-07-1	C00364	"KEGG - C00364
Neutral MF = C10H15N2O8P
Thymine is normally found as a deoxyriboside
SMP
CHS"	C10H14N2O8P	-1	-349.612	8.86457									-1	-349.612	8.86457
79	dttp	No	dTTP	C10H13N2O14P3	-4		C00459	"KEGG - C00459
Neutral MF = C10H17N2O14P3
SMP
CHS"	C10H14N2O14P3	-3	-765.319	9.18497									-3	-765.319	9.18497
1034	dudp	No	dUDP	C9H11N2O11P2	-3		C01346	"KEGG - C01346
Neutral MF = C9H14N2O11P2
SMP
CHS"	C9H12N2O11P2	-2	-560.148	9.00363									-2	-560.148	9.00363
198	dump	No	dUMP	C9H11N2O8P	-2	964-26-1	C00365	"KEGG - C00365
Neutral MF = C9H13N2O8P
SMP
CHS"	C9H12N2O8P	-1	-352.295	8.92298									-1	-352.295	8.92298
355	duri	No	Deoxyuridine	C9H12N2O5	0	951-78-0	C00526	"KEGG - C00526
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C9H12N2O5	0	-139.784	8.8678									0	-139.784	8.8678
80	dutp	No	dUTP	C9H11N2O14P3	-4		C00460	"KEGG - C00460
Neutral MF = C9H15N2O14P3
SMP
CHS"	C9H12N2O14P3	-3	-768.002	9.24135									-3	-768.002	9.24135
5780	dxyl	No	1-deoxy-D-xylulose	C5H10O4	0		C06257	"KEGG C06257
tv
Neidhardt pg 683"	C5H10O4	0	-144.897	5.84499									0	-144.897	5.84499
6320	dxyl5p	No	1-deoxy-D-xylulose 5-phosphate	C5H9O7P	-2		C11437	"KEGG C11437
Used by enzymes (EC 4.1.3.37 & 1.1.1.267)
Neutral MF = C5H11O7P
SMP"	C5H10O7P	-1	-356.796	4.03092									-1	-356.796	4.03092
10791	e4p	No	D-Erythrose 4-phosphate	C4H7O7P	-2	585-18-2	C00279	"KEGG - C00279
Neutral MF = C4H9O7P
SMP
CHS"	C4H8O7P	-1	-355.763	3.86441									-1	-355.763	3.86441
22117	eca2und	Yes	(enterobacterial common antigen)x2 undecaprenyl-diphosphate	C103H162N6O37P2	-4			AMF	C103H162N6O37P2	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
22118	eca3und	Yes	(enterobacterial common antigen)x3 undecaprenyl-diphosphate	C127H198N9O52P2	-5			AMF	C127H198N9O52P2	-5	No Energy	No Energy									-5	1.00E+07	1.00E+07
22120	eca4colipa	Yes	(enterobacterial common antigen)x4 core oligosaccharide lipid A	C272H447N14O160P4	-15			AMF	C272H447N14O160P4	-15	No Energy	No Energy									-15	1.00E+07	1.00E+07
22119	eca4und	Yes	(enterobacterial common antigen)x3 undecaprenyl-diphosphate	C151H234N12O67P2	-6			AMF	C151H234N12O67P2	-6	No Energy	No Energy									-6	1.00E+07	1.00E+07
2677	eig3p	No	D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate	C6H9N2O6P	-2		C04666	"KEGG - C04666
Neutral MF = C6H11N2O6P
SMP
CHS
Checked N-groups JLR"	C6H10N2O6P	-1	-287.501	6.26674									-1	-287.501	6.26674
22025	enlipa	Yes	phosphoethanolamine KDO(2)-lipid (A)	C112H202N3O42P3	-6			AMF	C112H204N3O42P3	-4	-1674.26	58.1996									-4	-1674.26	58.1996
11862	enter	No	Enterochelin	C30H27N3O15	0			"Similar to KEGG - C05821
The side chains should be the same, in Kegg one has an alcohol instead of a ketone.
See PMID 9214294 for picture.
JLR"	C30H27N3O15	0	-410.108	40.1527									0	-410.108	40.1527
254	etha	No	Ethanolamine	C2H8NO	1	141-43-5	C00189	"KEGG - C00189
Checked N-groups JLR"	C2H8NO	1	-44.504	2.18439									1	-44.504	2.18439
22148	ethso3	Yes	ethanesulfonate	C2H5O3S	-1			AMF	C2H5O3S	-1	-128.661	2.3551									-1	-128.661	2.3551
87	etoh	No	Ethanol	C2H6O	0	64-17-5	C00469	"KEGG - C00469
Neutral Compound
SMP
CHS"	C2H6O	0	-42.7031	1.54945									0	-42.7031	1.54945
2235	f1p	No	D-Fructose 1-phosphate	C6H11O9P	-2	15978-08-2	C02976	"KEGG - C02976
Merged with KEGG - C01094
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-430.984	6.84677									-1	-430.984	6.84677
1053	f6p	No	D-Fructose 6-phosphate	C6H11O9P	-2	643-13-0	C00085	"KEGG - C00085
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-430.984	6.84677									-1	-430.984	6.84677
478	fad	No	Flavin adenine dinucleotide oxidized	C27H31N9O15P2	-2	146-14-5	C00016	"KEGG - C00016
Neutral MF = C27H33N9O15P2 (FAD)
SMP
Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD"	C27H31N9O15P2	-2	-537.463	23.1773									-2	-537.463	23.1773
42	fadh2	No	Flavin adenine dinucleotide reduced	C27H33N9O15P2	-2		C01352	"KEGG - C01352
Neutral MF = C27H35N9O15P2 (FADH2)
SMP
Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD"	C27H33N9O15P2	-2	-553.539	22.436									-2	-553.539	22.436
340	fald	Yes	Formaldehyde	CH2O	0	50-00-0	C00067	"KEGG - C00067
Neutral Compound
SMP
CHS"	CH2O	0	-36.1	0.5									0	-36.1	0.5
878	fc1p	No	L-Fuculose 1-phosphate	C6H11O8P	-2	None	C01099	"KEGG - C01099
Neutral MF = C6H13O8P
SMP
NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR"	C6H12O8P	-1	-393.23	8.94203									-1	-393.23	8.94203
43	fcl-L	No	L-fuculose	C6H12O5	0		C01721	"KEGG - C01721
Neutral Compound
SMP
CHS
NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR"	C6H12O5	0	-181.908	9.35349									0	-181.908	9.35349
189	fdp	No	"D-Fructose 1,6-bisphosphate"	C6H10O12P2	-4	488-69-7	C00354	"KEGG - C00354
Neutral MF = C6H14O12P2
SMP
CHS"	C6H12O12P2	-2	-643.494	7.19722									-2	-643.494	7.19722
312	fe2	No	Fe2+	Fe	2	None	C00023	"KEGG - C00023
Neutral Compound
SMP
CHS"	Fe	2	No Energy	No Energy									2	1.00E+07	1.00E+07
5267	fe3	Yes	Fe3+	Fe	3	None		"Neutral Compound
SMP
CHS"	Fe	3	No Energy	No Energy									3	1.00E+07	1.00E+07
4627	fe3dcit	Yes	Fe(III)dicitrate	C12H10FeO14	-3	90-02-8	C06229	"KEGG - C06229
AMF- not sure if any h complexed with iron or carboxyls"	C12H10FeO14	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
22289	fe3dhbzs	Yes	"ferric 2,3-dihydroxybenzoylserine"	C10H10NO6Fe	2			AMF	C10H10NO6Fe	2	No Energy	No Energy									2	1.00E+07	1.00E+07
4626	fe3hox	Yes	Fe(III)hydroxamate	C9H18O6N3Fe	0		C06227	"KEGG - C06227

formula corrected, 3/24/05 MKA
contains ""R"" groups - replaced with ethyl groups
"	C9H18O6N3Fe	0	No Energy	No Energy									0	1.00E+07	1.00E+07
19375	fe3hox-un	Yes	"Fe(III)hydoxamate, unloaded"	C9H18O6N3	-3			"not produced by K-12 ecoli
formula not certain - contains ""R"" group (replaced w/ ethyl groups);   Fe(III)hydroxamate chemistry unclear, but must lose Fe within cell to be recycled
MKA"	C9H18O6N3	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
9616	fecrm	Yes	Ferrichrome	C27H42FeN9O12	0	90-02-8	C06228	"KEGG - C06228
AMF
CHEMID (015630645)"	C27H42FeN9O12	0	No Energy	No Energy									0	1.00E+07	1.00E+07
19379	fecrm-un	Yes	Ferrichrome minus Fe(III)	C27H42N9O12	-3			CHEMID (015630645)	C27H42N9O12	-3	No Energy	No Energy									-3	1.00E+07	1.00E+07
4628	feenter	Yes	Fe-enterobactin	C30H27FeN3O15	3	90-02-8	C06230	KEGG - C06230	C30H27FeN3O15	3	No Energy	No Energy									3	1.00E+07	1.00E+07
16013	feoxam	Yes	ferroxamine	C25H46FeN6O8	1			"C07597
AMF"	C25H46FeN6O8	1	No Energy	No Energy									1	1.00E+07	1.00E+07
19381	feoxam-un	Yes	ferroxamine minus Fe(3)	C25H46N6O8	-2			"siderophore
"	C25H46N6O8	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
2663	fgam	No	N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide	C8H13N2O9P	-2		C04376	"KEGG - C04376
Neutral MF = C8H15N2O9P
SMP
CHS
Checked N-groups JLR"	C8H14N2O9P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
2153	fldox	Yes	flavodoxin (oxidized)	X	0	121-69-7	C02869	KEGG - C02869	X	0	No Energy	No Energy									0	1.00E+07	1.00E+07
2062	fldrd	Yes	flavodoxin (reduced)	XH2	0	358-71-4	C02745	KEGG - C02745	XH2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
2465	fmettrna	Yes	N-Formylmethionyl-tRNA	C6H9NO2SR	0		C03294	"KEGG - C03294
SMP"	C16H21N6O5RS	0	No Energy	No Energy									0	1.00E+07	1.00E+07
336	fmn	No	FMN	C17H19N4O9P	-2	146-17-8	C00061	"KEGG - C00061
Neutral MF = C17H21N4O9P
SMP
CHS
Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD"	C17H20N4O9P	-1	-340.699	13.8308									-1	-340.699	13.8308
9453	fmnh2	Yes	Reduced FMN	C17H21N4O9P	-2	67-63-0		"KEGG - C01847
Neutral-C17H23N4O9P
JLR
"	C17H22N4O9P	-1	-356.776	14.836									-1	-356.776	14.836
334	for	No	Formate	CH1O2	-1	64-18-6	C00058	"KEGG - C00058
Neutral MF = CH2O2
SMP
CHS"	CHO2	-1	-84.9	0.5									-1	-84.9	0.5
3319	fpram	No	2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine	C8H15N3O8P	-1		C04640	"KEGG - C04640
Neutral MF = C8H16N3O8P
SMP
CHS
Changed according to Genomatica JLR"	C8H15N3O8P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
3486	fprica	No	5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide	C10H13N4O9P	-2		C04734	"KEGG - C04734
Neutral MF = C10H15N4O9P
SMP
Checked N-groups JLR"	C10H14N4O9P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
10388	frdp	No	Farnesyl diphosphate	C15H25O7P2	-3	13058-04-3	C00448	"KEGG - C00448
Neutral MF = C15H28O7P2
SMP"	C15H26O7P2	-2	-392.906	7.97286									-2	-392.906	7.97286
1061	fru	No	D-Fructose	C6H12O6	0	57-48-7	C00095	"KEGG - C00095
Deleted KEGG -C01496 (fructose)
Neutral Compound
SMP
CHS"	C6H12O6	0	-218.473	6.91905									0	-218.473	6.91905
17892	frulys	Yes	fructoselysine	C12H25N2O7	1			MKA	C12H25N2O7	1	-249.684	9.89374									1	-249.684	9.89374
17998	frulysp	Yes	fructoselysine Phosphate	C12H24N2O10P	-1			"MKA
AMF
"	C12H25N2O10P	0	-462.195	9.94323									0	-462.195	9.94323
750	fruur	No	D-Fructuronate	C6H9O7	-1	669-90-9	C00905	"KEGG - C00905
Neutral MF = C6H10O7
SMP
CHS"	C6H9O7	-1	-261.376	6.66261									-1	-261.376	6.66261
2240	fuc1p-L	No	L-Fucose 1-phosphate	C6H11O8P	-2	526-31-8	C02985	"KEGG - C02985
Neutral-C6H13O8P
JLR"	C6H12O8P	-1	-393.23	8.94203									-1	-393.23	8.94203
833	fuc-L	No	L-Fucose	C6H12O5	0	2438-80-4	C01019	"KEGG - C01019
Neutral Compound
SMP"	C6H12O5	0	-181.908	9.35349									0	-181.908	9.35349
1081	fum	No	Fumarate	C4H2O4	-2	110-17-8	C00122	"KEGG - C00122
Neutral MF = C4H4O4
SMP
CHS"	C4H2O4	-2	-143.957	2.63947									-2	-143.957	2.63947
1066	g1p	No	D-Glucose 1-phosphate	C6H11O9P	-2	59-56-3	C00103	"KEGG - C00103
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-429.548	8.96923									-1	-429.548	8.96923
438	g3p	No	Glyceraldehyde 3-phosphate	C3H5O6P	-2	142-10-9	C00661	"KEGG - C00661
Neutral MF = C3H7O6P
SMP
CHS
JLR (deleted duplicate entry, Dglyad3p.  g3p should be KEGG- C00118)"	C3H6O6P	-1	-318.842	2.53398									-1	-318.842	2.53398
444	g3pc	No	sn-Glycero-3-phosphocholine	C8H20NO6P	0		C00670	"KEGG - C00670
Normally has a + charge (C8H21NO6P)
JLR"	C8H20NO6P	0	No Energy	No Energy									0	1.00E+07	1.00E+07
961	g3pe	No	sn-Glycero-3-phosphoethanolamine	C5H14NO6P	0		C01233	"KEGG - C01233
Neutral-C5H14NO6P
JLR
Checked N JLR"	C5H14NO6P	0	-314.346	4.19922									0	-314.346	4.19922
2449	g3pg	No	Glycerophosphoglycerol	C6H14O8P	-1	11034-93-8	C03274	"KEGG - C03274
Neutral-C6H15O8P
JLR"	C6H14O8P	-1	-385.785	5.2106									-1	-385.785	5.2106
954	g3pi	No	sn-Glycero-3-phospho-1-inositol	C9H18O11P	-1		C01225	"KEGG - C01225
Neutral-C9H19O11P
JLR"	C9H18O11P	-1	-488.707	11.8054									-1	-488.707	11.8054
8967	g3ps	No	Glycerophosphoserine	C6H13NO8P	-1			"No Kegg entry
Neutral-C6H14NO8P
JLR
Checked N JLR"	C6H13NO8P	-1	-392.178	4.42306									-1	-392.178	4.42306
765	g6p	No	D-Glucose 6-phosphate	C6H11O9P	-2	56-73-5	C00092	"KEGG - C00092
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-430.737	9.43168									-1	-430.737	9.43168
22090	gagicolipa	Yes	galactosyl-glucosyl-inner core oligosaccharide lipid A	C157H271N2O84P4	-11			AMF	C157H271N2O84P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
1083	gal	No	D-Galactose	C6H12O6	0	59-23-4	C00124	"KEGG - C00124
Deleted KEGG - C01582 (Galactose)
Neutral Compound
SMP
CHS"	C6H12O6	0	-218.227	9.37949									0	-218.227	9.37949
434	gal1p	No	alpha-D-Galactose 1-phosphate	C6H11O9P	-2	2255-14-3	C00446	"KEGG - C00446
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-429.548	8.96923									-1	-429.548	8.96923
1002	gal-bD	Yes	beta D-Galactose	C6H12O6	0	33419-42-0	C01582	"KEGG - C01582
NCD"	C6H12O6	0	-218.227	9.37949									0	-218.227	9.37949
735	galct-D	No	D-Galactarate	C6H8O8	-2	526-99-8	C00879	"KEGG - C00879
Neutral-C6H10O8
JLR"	C6H8O8	-2	-312.512	6.98546									-2	-312.512	6.98546
736	galctn-D	No	D-Galactonate	C6H11O7	-1		C00880	"KEGG - C00880
Neutral-C6H12O7
JLR"	C6H11O7	-1	-269.61	6.90606									-1	-269.61	6.90606
1377	galt	Yes	Galactitol	C6H14O6	0	608-66-2	C01697	"KEGG - C01697
Neutral Compound
SMP"	C6H14O6	0	-226.707	7.15378									0	-226.707	7.15378
6457	galt1p	No	Galactitol 1-phosphate	C6H13O9P	-2		C06311	"KEGG- C06311
Neutral MF = C6H15O9P
JLR"	C6H14O9P	-1	-439.218	7.0839									-1	-439.218	7.0839
175	galur	No	D-Galacturonate	C6H9O7	-1	685-73-4	C00333	"KEGG - C00333
Neutral MF = C6H10O7
SMP
CHS"	C6H9O7	-1	-261.129	9.34772									-1	-261.129	9.34772
171	gam	Yes	D-Glucosamine	C6H14NO5	1	3416-24-8	C00329	"KEGG - C00329
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C6H14NO5	1	-181.717	8.94635									1	-181.717	8.94635
4572	gam1p	No	D-Glucosamine 1-phosphate	C6H13NO8P	-1		C06156	"KEGG - C06156
Neutral MF = C6H14NO8P
SMP
CHS
Changed according to Genomatica JLR"	C6H14NO8P	0	-393.039	8.67972									0	-393.039	8.67972
187	gam6p	No	D-Glucosamine 6-phosphate	C6H13NO8P	-1	3616-42-0	C00352	"KEGG - C00352
Neutral MF = C6H14NO8P
SMP
CHS
Changed according to Genomatica JLR"	C6H14NO8P	0	-394.228	9.00105									0	-394.228	9.00105
10804	gar	No	N1-(5-Phospho-D-ribosyl)glycinamide	C7H14N2O8P	-1		C03838	"KEGG - C03838
Neutral MF = C7H15N2O8P
SMP
CHS
Changed according to Genomatica JLR"	C7H15N2O8P	0	-384.86	7.97092									0	-384.86	7.97092
22129	garagund	Yes	glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate	C77H125N1O22P2	-2			AMF	C77H125NO22P2	-2	-662.614	39.3948									-2	-662.614	39.3948
9450	gbbtn	No	gamma-butyrobetaine	C7H15NO2	0			"No Kegg entry, it is in EcoCyc
Compound is a zwitterion, + charge on N and - charge on O
JLR
Checked N-groups JLR"	C7H15NO2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
10800	gcald	No	Glycolaldehyde	C2H4O2	0		C00266	"KEGG - C00266
SMP
CHS"	C2H4O2	0	-69.41	1.61302									0	-69.41	1.61302
321	gdp	No	GDP	C10H12N5O11P2	-3	146-91-8	C00035	"KEGG - C00035
Neutral MF = C10H15N5O11P2
SMP
CHS"	C10H13N5O11P2	-2	-517.08	11.977									-2	-517.08	11.977
952	gdpddman	No	GDP-4-dehydro-6-deoxy-D-mannose	C16H21N5O15P2	-2		C01222	"KEGG - C01222
Neutral: C16H23N5O15P2
JLR
Checked N-groups JLR"	C16H21N5O15P2	-2	-632.163	17.4439									-2	-632.163	17.4439
168	gdpfuc	No	GDP-L-fucose	C16H23N5O15P2	-2		C00325	"KEGG - C00325
KEGG glycan: G10615
Neutral: C16H25N5O15P2
JLR"	C16H23N5O15P2	-2	-638.385	18.6085									-2	-638.385	18.6085
9064	gdpmann	No	GDP-D-mannose	C16H23N5O16P2	-2		C00096	"KEGG C00096
Neutral:C16H25N5O16P2
JLR
Checked N-groups JLR"	C16H23N5O16P2	-2	-674.704	18.646									-2	-674.704	18.646
3889	gdpofuc	No	GDP-4-oxo-L-fucose	C16H21N5O15P2	-2	583-08-4	C05389	"KEGG - C05389
Neutral: C16H23N5O15P2
JLR
Checked N-Groups JLR"	C16H21N5O15P2	-2	-632.163	17.4439									-2	-632.163	17.4439
3963	gdptp	Yes	Guanosine 3'-diphosphate 5'-triphosphate	C10H11N5O20P5	-7		C04494	"KEGG - C04494
Neutral MF = C10H18N5O20P5
SMP
CHS"	C10H13N5O20P5	-5	-1143.31	12.5173									-5	-1143.31	12.5173
22130	gfgaragund	Yes	galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate	C83H135N1O27P2	-2			AMF	C83H135NO27P2	-2	-821.025	44.6354									-2	-821.025	44.6354
18600	gg4abut	Yes	gamma-glutamyl-gamma aminobutyric acid	C9H15O5N2	-1			MKA	C9H15N2O5	-1	-189.031	5.12921									-1	-189.031	5.12921
22091	ggagicolipa	Yes	glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A	C163H281N2O89P4	-11			AMF	C163H281N2O89P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
18597	ggbutal	Yes	gamma-glutamyl-gamma-butyraldehyde	C9H16O4N2	0			MKA	C9H16N2O4	0	-136.517	4.99197									0	-136.517	4.99197
22092	gggagicolipa	Yes	glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A	C169H291N2O94P4	-11			AMF	C169H291N2O94P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
18596	ggptrc	Yes	gamma-glutamyl-putrescine	C9H20O3N3	1			"MKA
AMF"	C9H20N3O3	1	-111.611	5.88693									1	-111.611	5.88693
22089	gicolipa	Yes	glucosyl-inner core oligosaccharide lipid A	C151H261N2O79P4	-11			AMF	C151H261N2O79P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
318	glc-D	No	D-Glucose	C6H12O6	0	50-99-7	C00031	"KEGG - C00031
Deleted KEGG - C00267 (alpha-D-Glucose)
Deleted KEGG - C00221 (beta-D-Glucose)
L-glucose is abbreviated as glc-L
SMP
CHS"	C6H12O6	0	-218.227	9.37949									0	-218.227	9.37949
305	glcn	No	D-Gluconate	C6H11O7	-1	526-95-4	C00257	"KEGG - C00257
Neutral MF = C6H12O7
SMP
CHS"	C6H11O7	-1	-269.61	6.90606									-1	-269.61	6.90606
632	glcr	No	D-Glucarate	C6H8O8	-2	87-73-0	C00818	"KEGG - C00818
KEGG - C00767 has Glucarate is deleted from the database
Neutral MF = C6H10O8
SMP
CHS"	C6H8O8	-2	-312.512	6.98546									-2	-312.512	6.98546
256	glcur	No	D-Glucuronate	C6H9O7	-1	12/3/56	C00191	"KEGG - C00191
Neutral MF = C6H10O7
SMP
CHS"	C6H9O7	-1	-261.129	9.34772									-1	-261.129	9.34772
3887	glcur1p	Yes	D-Glucuronate 1-phosphate	C6H8O10P	-3	583-08-4	C05385	"KEGG - C05385
NCD"	C6H9O10P	-2	-472.451	8.936									-2	-472.451	8.936
11299	gln-L	No	L-Glutamine	C5H10N2O3	0	56-85-9	C00064	"KEGG - C00064
Neutral MF = C5H10N2O3
SMP
CHS"	C5H10N2O3	0	-120.221	3.66285									0	-120.221	3.66285
7100	glntrna	Yes	L-Glutaminyl-tRNA(Gln)	C5H9N2O2R	1		C02282	"KEGG - C02282
SMP
adjusted for Genomatica's change to aa - NCD
"	C15H21N7O5R	1	-76.3505	13.435									1	-76.3505	13.435
2004	glu1sa	No	L-Glutamate 1-semialdehyde	C5H9NO3	0	None	C03741	"KEGG - C03741
Neutral MF = C5H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C5H9NO3	0	-110.9	2.68581									0	-110.9	2.68581
2458	glu5p	No	L-Glutamate 5-phosphate	C5H8NO7P	-2		C03287	"KEGG - C03287
Neutral MF = C5H10NO7P
SMP
Changed according to Genomatica JLR"	C5H9NO7P	-1	-377.76	2.92156									-1	-377.76	2.92156
761	glu5sa	No	L-Glutamate 5-semialdehyde	C5H9NO3	0	None	C01165	"KEGG - C01165
Neutral MF = C5H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C5H9NO3	0	-110.9	2.68581									0	-110.9	2.68581
443	glucys	No	gamma-L-Glutamyl-L-cysteine	C8H13N2O5S	-1	686-58-8	C00669	"KEGG - C00669
Neutral MF = C8H14N2O5S
SMP
CHS
Changed according to Genomatica JLR"	C8H13N2O5S	-1	-186.493	5.21744									-1	-186.493	5.21744
273	glu-D	No	D-Glutamate	C5H8NO4	-1	56-86-0	C00217	"KEGG - C00217
Neutral MF = C5H9NO4
SMP
CHS
Changed according to Genomatica JLR"	C5H8NO4	-1	-163.414	2.93302									-1	-163.414	2.93302
313	glu-L	No	L-Glutamate	C5H8NO4	-1	56-86-0	C00025	"KEGG - C00025
Neutral MF = C5H9NO4
SMP
CHS
Changed according to Genomatica JLR"	C5H8NO4	-1	-163.414	2.93302									-1	-163.414	2.93302
2242	glutrna	No	L-Glutamyl-tRNA(Glu)	C5H7NO3R	0	None	C02987	"KEGG - C02987
X = (C5H8O6PR)n
Represent as neutral
SMP; MF changed on May 7, 2002
CHS
Changed according to Genomatica JLR"	C15H19N6O6R	0	-119.544	12.9574									0	-119.544	12.9574
329	glx	No	Glyoxylate	C2H1O3	-1	298-12-4	C00048	"KEGG - C00048
Neutral MF = C2H2O3
SMP
CHS"	C2HO3	-1	-112.313	1.41663									-1	-112.313	1.41663
323	gly	No	Glycine	C2H5NO2	0	56-40-6	C00037	"KEGG - C00037
Nonchiral compound
Neutral MF = C2H5NO2
SMP
CHS
Changed according to Genomatica JLR"	C2H5NO2	0	-87.4066	1.80702									0	-87.4066	1.80702
393	glyald	No	D-Glyceraldehyde	C3H6O3	0	453-17-8	C00577	"KEGG - C00577
KEGG has non-chiral glyceraldehyde (367-47-5)
Neutral Compound
SMP
CHS"	C3H6O3	0	-106.331	2.33225									0	-106.331	2.33225
503	glyb	No	Glycine betaine	C5H11NO2	0	107-43-7	C00719	"KEGG - C00719
SMP
Checked N-groups JLR"	C5H11NO2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
1077	glyc	No	Glycerol	C3H8O3	0	56-81-5	C00116	"KEGG - C00116
Neutral Compound
SMP
CHS"	C3H8O3	0	-115.943	2.93485									0	-115.943	2.93485
2237	glyc2p	Yes	Glycerol 2-phosphate	C3H7O6P	-2	3249-68-1	C02979	"KEGG - C02979
AMF"	C3H8O6P	-1	-327.265	3.09353									-1	-327.265	3.09353
55	glyc3p	No	Glycerol 3-phosphate	C3H7O6P	-2		C00093	"KEGG - C00093
Neutral MF = C3H9O6P
SMP "	C3H8O6P	-1	-328.454	2.76015									-1	-328.454	2.76015
237	glyclt	No	Glycolate	C2H3O3	-1	79-14-1	C00160	"KEGG - C00160
Neutral MF = C2H4O3
SMP
CHS"	C2H3O3	-1	-121.924	1.51424									-1	-121.924	1.51424
5796	glycogen	No	glycogen	C6H10O5	0		C00182	"KEGG- C00182	
MF revised on May-7-2002
Deleted previous entry ""glcgn""
Polymer with unit MF = C6H10O5
SMP"	C6H9O5	-1	-149.887	6.95145									-1	-149.887	6.95145
306	glyc-R	No	(R)-Glycerate	C3H5O4	-1	473-81-4	C00258	"KEGG - C00258
Neutral MF = C3H6O4
SMP
CHS"	C3H5O4	-1	-158.846	2.26506									-1	-158.846	2.26506
7101	glytrna	Yes	Glycyl-tRNA(Gly)	C2H4NOR	1		C02412	"KEGG - C02412
SMP
adjusted for Genomatica's change to aa - NCD
"	C12H16N6O4R	1	-43.5364	12.7806									1	-43.5364	12.7806
9431	gmhep17bp	No	"D-Glycero-D-manno-heptose 1,7-bisphosphate"	C7H12O13P2	-4		C11472	"Kegg C11472
Neutral- C7H16O13P2
JLR"	C7H14O13P2	-2	-678.98	9.63071									-2	-678.98	9.63071
9430	gmhep1p	No	D-Glycero-D-manno-heptose 1-phosphate	C7H13O10P	-2		C07838	"KEGG C07838
Neutral C7H15O10P"	C7H14O10P	-1	-466.47	9.57961									-1	-466.47	9.57961
9434	gmhep7p	No	D-Glycero-D-manno-heptose 7-phosphate	C7H13O10P	-2		C07836	"Kegg C07836
Neutral-C7H15O10P
JLR"	C7H14O10P	-1	-467.659	10.1541									-1	-467.659	10.1541
226	gmp	No	GMP	C10H12N5O8P	-2	85-32-5	C00144	"KEGG - C00144
Neutral = C10H14N5O8P
SMP
CHS"	C10H13N5O8P	-1	-309.227	11.9165									-1	-309.227	11.9165
8979	gp4g	No	"P1,P4-Bis(5'-guanosyl) tetraphosphate"	C20H24N10O21P4	-4		C01261	"Kegg- C01261
Neutral-C20H28N10O21P4
JLR"	C20H24N10O21P4	-4	-970.892	24.0354									-4	-970.892	24.0354
179	grdp	No	Geranyl diphosphate	C10H17O7P2	-3		C00341	"KEGG - C00341
Neutral MF = C10H20O7P2
SMP"	C10H18O7P2	-2	-416.901	5.56731									-2	-416.901	5.56731
22268	grxox	Yes	glutaredoxin (oxidized)	X	0			"AMf
C07293"	C6H7NO2R2S2	0	-45.3635	7.03074									0	-45.3635	7.03074
22267	grxrd	Yes	glutaredoxin (reduced)	XH2	0			"AMF
C07292"	C6H9NO2R2S2	0	-45.5437	5.99427									0	-45.5437	5.99427
5279	gsn	No	Guanosine	C10H13N5O5	0	118-00-3	C00387	"KEGG - C00387
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H13N5O5	0	-96.7165	11.8752									0	-96.7165	11.8752
1087	gthox	No	Oxidized glutathione	C20H30N6O12S2	-2		C00127	"KEGG - C00127
Neutral MF = C20H32N6O12S2
SMP
CHS
Changed according to Genomatica JLR"	C20H30N6O12S2	-2	-420.264	14.5154									-2	-420.264	14.5154
11388	gthrd	No	Reduced glutathione	C10H16N3O6S	-1	70-18-8	C00051	"KEGG - C00051
Neutral MF = C10H17N3O6S
SMP
CHS
Changed according to Genomatica JLR"	C10H16N3O6S	-1	-213.935	7.40438									-1	-213.935	7.40438
327	gtp	No	GTP	C10H12N5O14P3	-4	86-01-1	C00044	"KEGG - C00044
Neutral MF = C10H16N5O14P3
SMP
CHS"	C10H13N5O14P3	-3	-724.934	12.1567									-3	-724.934	12.1567
4235	gtspmd	No	Glutathionylspermidine	C17H36N6O5S	2	8/6/83	C05730	"KEGG - C05730
Neutral-C17H34N6O5S
JLR
Checked N-groups JLR"	C17H36N6O5S	2	-154.092	12.3017									2	-154.092	12.3017
291	gua	No	Guanine	C5H5N5O	0	73-40-5	C00242	"KEGG - C00242
Neutral Compound
SMP
CHS"	C5H5N5O	0	25.8368	9.96302									0	25.8368	9.96302
1049	h	No	H+	H	1	12408-02-5	C00080	KEGG - C00080	H	1	-9.50E+00	-9.50E+00									1	-9.50E+00	-9.50E+00
141	h2	No	H2	H2	0	1333-74-0	C00282	KEGG - C00282	H2	0	0	0.5									0	0	0.5
8188	h2mb4p	No	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate	C5H9O8P2	-3		C11811	"KEGG C11811
JLR
see PMID 12010124"	C5H10O8P2	-2	-477.215	3.30154									-2	-477.215	3.30154
317	h2o	No	H2O	H2O	0	7732-18-5	C00001	KEGG - C00001	H2O	0	-56.6	0.5									0	-56.6	0.5
315	h2o2	No	Hydrogen peroxide	H2O2	0	7722-84-1	C00027	"KEGG - C00027
Neutral Compound
SMP
CHS"	H2O2	0	-32.124	0.5									0	-32.124	0.5
142	h2s	No	Hydrogen sulfide	H2S	0	6/4/83	C00283	"KEGG - C00283
Neutral Compound
SMP
CHS"	H2S	0	-6.65	0.5									0	-6.65	0.5
22097	hacolipa	Yes	hepta-acylated core oligosaccharide lipid A (E. coli)	C192H333N2O101P4	-11			AMF	C192H333N2O101P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
22098	halipa	Yes	hepta-acylated KDO(2)-lipid (A)	C126H226N2O40P2	-6			AMF	C126H228N2O40P2	-4	-1499.72	65.383									-4	-1499.72	65.383
144	hco3	No	Bicarbonate	CHO3	-1	71-52-3	C00288	"KEGG - C00288
SMP
CHS"	CHO3	-1	-140.2	0.5									-1	-140.2	0.5
3844	hcys-L	No	L-Homocysteine	C4H9NO2S	0	6027-13-0	C00155	"KEGG - C00155
Deleted C05330
Neutral MF = C4H9NO2S
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO2S	0	-82.1318	3.16041									0	-82.1318	3.16041
297	hdca	No	Hexadecanoate (n-C16:0)	C16H31O2	-1	57-10-3	C00249	"KEGG - C00249
Neutral MF = C16H32O2
SMP
CHS
changed official name from Fatty acid (Palmitate, n-C16:0) to hexadecanoic acid; abbreviation chagned from fa8 to hdca; changed compound class from reviewed to fatty acid - NCD
C16:0"	C16H31O2	-1	-72.8322	9.54512									-1	-72.8322	9.54512
5725	hdcea	No	Hexadecenoate (n-C16:1)	C16H29O2	-1			"KEGG - C08362
Neutral MF = C16H30O2
SMP
monounsaturated fatty acid, 16 carbons
changed name from Fatty acid (n-C16:1) to hexadecenoic acid; changed abbreviation from fa7 to hdcea; changed compound class from peptides to fatty acid - NCD
updated names, added KEGG entry"	C16H29O2	-1	-53.7871	8.42541									-1	-53.7871	8.42541
8780	hdcoa	Yes	Hexadecenoyl-CoA (n-C16:1CoA)	C37H60N7O17P3S	-4			"NCD
C16:1 - C16H29O2 (charge -1)
CoA - C21H32N7O16P3S (charge -4)
NJ
"	C37H61N7O17P3S	-3	-750.096	19.6583									-3	-750.096	19.6583
3801	hdd2coa	Yes	trans-Hexadec-2-enoyl-CoA	C37H60N7O17P3S	-4		C05272	"KEGG - C05272
Neutral MF = C37H64N7O17P3S
SMP
1 degree of unsaturation"	C37H61N7O17P3S	-3	-750.096	19.6583									-3	-750.096	19.6583
10496	hdeACP	No	cis-hexadec-9-enoyl-[acyl-carrier protein] (n-C16:1)	C27H49N2O8PRS	-1			"tv
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C27H49N2O8PRS	-1	-323.822	14.4051									-1	-323.822	14.4051
5846	hemeO	No	Heme O	C49H56FeN4O5	-2			"No KEGG Entry
Neutral MF = C49H58FeN4O5
SMP 
Note Neidhardt picture (pg 734) is incorrect
Checked N-groups, JLR"	C49H56FeN4O5	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
4244	hexACP	Yes	Hexanoyl-ACP (n-C6:0ACP)	C17H31N2O8PRS	-1	8/6/83	C05749	"KEGG - C05749
AMF"	C17H31N2O8PRS	-1	-351.991	10.4482									-1	-351.991	10.4482
460	hg2	Yes	Hg2+	Hg	2		C00703	KEGG - C00703	Hg	2	No Energy	No Energy									2	1.00E+07	1.00E+07
22065	hhlipa	Yes	heptosyl-heptosyl-kdo2-lipidA	C124H220N2O51P2	-6			AMF	C124H222N2O51P2	-4	-1868.29	69.2656									-4	-1868.29	69.2656
11120	his-L	No	L-Histidine	C6H9N3O2	0	71-00-1	C00135	"KEGG - C00135
Neutral MF = C6H9N3O2
SMP
CHS
Changed according to Genomatica JLR"	C6H9N3O2	0	-43.55	5.49409									0	-43.55	5.49409
879	hisp	No	L-Histidinol phosphate	C6H11N3O4P	-1	25679-93-0	C01100	"KEGG - C01100
Neutral MF = C6H12N3O4P
SMP
CHS
Changed according to Genomatica JLR"	C6H12N3O4P	0	-213.158	5.71602									0	-213.158	5.71602
11864	histd	No	L-Histidinol	C6H12N3O	1	None	C00860	"KEGG - C00860
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C6H13N3O	2	-4.17334	5.80815									2	-4.17334	5.80815
7107	histrna	Yes	L-Histidyl-tRNA(His)	C6H8N3OR	1		C02988	"KEGG - C02988
SMP
adjusted for Genomatica's change to aa - NCD
"	C16H20N8O4R	1	0.320292	16.1111									1	0.320292	16.1111
3953	hkndd	No	"2-Hydroxy-6-oxonona-2,4-diene-1,9-dioate"	C9H8O6	-2	53-42-9	C04479	"KEGG - C04479
Neutral-C9H10O6
JLR
Changed to -2 charge"	C9H8O6	-2	-186.923	4.35966									-2	-186.923	4.35966
9382	hkntd	No	2-hydroxy-6-ketononatrienedioate	C9H6O6	-2			"No Kegg entry, see PMID: 9603882
Neutral- C9H8O6
JLR
Changed to -2 charge"	C9H6O6	-2	-167.878	5.60961									-2	-167.878	5.60961
22064	hlipa	Yes	heptosyl-kdo2-lipidA	C117H208N2O45P2	-6			AMF	C117H210N2O45P2	-4	-1673.07	62.8656									-4	-1673.07	62.8656
838	hmbil	No	Hydroxymethylbilane	C40H38N4O17	-8	73023-76-4	C01024	"KEGG - C01024
Neutral MF = C40H46N4O17
SMP
CHS
Checked N-groups JLR"	C40H38N4O17	-8	-475.446	33.8421									-8	-475.446	33.8421
9538	hmfurn	No	4-hydroxy-5-methyl-3(2H)-furanone	C5H6O3	0			"No Kegg Entry
See PMID: 11489131 
JLR"	C5H5O3	-1	-66.9148	6.02975									-1	-66.9148	6.02975
21355	hmgth	Yes	hydroxymethylglutathione	C11H18N3O7S	-1			AMF	C11H18N3O7S	-1	-239.567	7.91214									-1	-239.567	7.91214
131	hom-L	No	L-Homoserine	C4H9NO3	0	672-15-1	C00263	"KEGG - C00263
Neutral MF = C4H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO3	0	-121.424	2.65406									0	-121.424	2.65406
22075	hphhlipa	Yes	heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA	C131H231N2O60P3	-8			AMF	C131H234N2O60P3	-5	-2273.36	75.9948									-5	-2273.36	75.9948
242	hpyr	No	Hydroxypyruvate	C3H3O4	-1	1113-60-6	C00168	"KEGG - C00168
Neutral MF = C3H4O4
SMP
CHS"	C3H3O4	-1	-149.663	1.95156									-1	-149.663	1.95156
358	hqn	No	Hydroquinone	C6H6O2	0	123-31-9	C00530	"KEGG - C00530
SMP"	C6H6O2	0	-46.692	11.3845									0	-46.692	11.3845
3800	hx2coa	Yes	trans-Hex-2-enoyl-CoA	C27H40N7O17P3S	-4		C05271	"KEGG - C05271
Neutral MF = C27H44N7O17P3S
SMP"	C27H41N7O17P3S	-3	-759.219	16.3703									-3	-759.219	16.3703
1004	hxa	Yes	Hexanoate (n-C6:0)	C6H11O2	-1	142-62-1	C01585	"KEGG - C01585
Neutral MF = C6H12O2
SMP
changed compound class from peptides - NCD"	C6H11O2	-1	-81.9561	3.01594									-1	-81.9561	3.01594
218	hxan	No	Hypoxanthine	C5H4N4O	0	68-94-0	C00262	"KEGG - C00262
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C5H4N4O	0	21.344	9.91017									0	21.344	9.91017
3799	hxcoa	Yes	Hexanoyl-CoA (n-C6:0CoA)	C27H42N7O17P3S	-4		C05270	"KEGG - C05270
Neutral MF = C27H46N7O18P3S
SMP"	C27H43N7O17P3S	-3	-778.265	16.7576									-3	-778.265	16.7576
4323	iasp	No	Iminoaspartate	C4H3NO4	-2		C05840	"KEGG - C05840
Neutral MF = C4H5NO4
SMP
Checked N-groups, agrees with ACD software, JLR
Updated after checking with Pipeline Pilot, RM ==> C4H3NO4    -2"	C4H3NO4	-2	-163.365	3.94911									-2	-163.365	3.94911
740	ichor	No	Isochorismate	C10H8O6	-2		C00885	"KEGG - C00885
Neutral MF = C10H10O6
SMP
CHS"	C10H8O6	-2	-173.314	6.68574									-2	-173.314	6.68574
158	icit	No	Isocitrate	C6H5O7	-3	30810-51-6	C00311	"KEGG - C00311
Neutral MF = C6H8O7
SMP
CHS"	C6H5O7	-3	-277.755	3.89929									-3	-277.755	3.89929
22072	icolipa	Yes	inner core oligosaccharide lipid A (E coli)	C145H251N2O74P4	-11			AMF	C145H251N2O74P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
11158	idon-L	No	L-Idonate	C6H11O7	-1	1114-17-6	C00770	"KEGG - C00770
Neutral-C6H12O7
JLR"	C6H11O7	-1	-269.61	6.90606									-1	-269.61	6.90606
1067	idp	No	IDP	C10H11N4O11P2	-3	86-04-4	C00104	"KEGG - C00104
Neutral MF = C10H14N4O11P2
SMP
CHS
Checked N-groups JLR"	C10H12N4O11P2	-2	-521.573	11.9331									-2	-521.573	11.9331
410	ile-L	No	L-Isoleucine	C6H13NO2	0	73-32-5	C00407	"KEGG - C00407
Neutral MF = C6H13NO2
SMP
CHS
Changed according to Genomatica JLR"	C6H13NO2	0	-82.8037	3.57585									0	-82.8037	3.57585
7110	iletrna	Yes	L-Isoleucyl-tRNA(Ile)	C6H12NOR	1		C03127	"KEGG - C03127
SMP
adjusted for Genomatica's change to aa - NCD

"	C16H24N6O4R	1	-38.9334	13.1478									1	-38.9334	13.1478
7138	imacp	No	3-(Imidazol-4-yl)-2-oxopropyl phosphate	C6H7N2O5P	-2		C01267	"KEGG - C01267
Neutral MF = C6H9N2O5P
SMP
CHS
Checked N-groups JLR"	C6H8N2O5P	-1	-240.485	5.55017									-1	-240.485	5.55017
1090	imp	No	IMP	C10H11N4O8P	-2	131-99-7	C00130	"KEGG - C00130
Neutral MF = C10H13N4O8P
SMP
CHS
Checked N-groups JLR"	C10H12N4O8P	-1	-313.72	11.8724									-1	-313.72	11.8724
82	indole	No	Indole	C8H7N	0	120-72-9	C00463	"KEGG - C00463
Checked N-groups JLR"	C8H7N	0	49.1258	8.66001									0	49.1258	8.66001
223	inost	No	myo-Inositol	C6H12O6	0	87-89-8	C00137	"KEGG - C00137
Neutral Compound
SMP
CHS"	C6H12O6	0	-220.857	11.427									0	-220.857	11.427
147	ins	No	Inosine	C10H12N4O5	0	58-63-9	C00294	"KEGG - C00294
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H12N4O5	0	-101.209	11.8309									0	-101.209	11.8309
1089	ipdp	No	Isopentenyl diphosphate	C5H9O7P2	-3		C00129	"KEGG - C00129
Neutral MF = C5H12O7P2
SMP"	C5H10O7P2	-2	-442.49	3.60863									-2	-442.49	3.60863
3701	isetac	Yes	Isethionic acid	C2H5O4S	-1	107-36-8	C05123	"KEGG - C05123
SAB
charged following taurine's charge"	C2H5O4S	-1	-164.979	2.63531									-1	-164.979	2.63531
1050	itp	No	ITP	C10H11N4O14P3	-4	132-06-9	C00081	"KEGG - C00081
Neutral MF = C10H15N4O14P3
SMP
CHS
Checked N-groups JLR"	C10H12N4O14P3	-3	-729.426	12.1135									-3	-729.426	12.1135
289	k	No	potassium	K	1		C00238	KEGG - C00238	K	1	No Energy	No Energy									1	1.00E+07	1.00E+07
778	kdo	No	3-Deoxy-D-manno-2-octulosonate	C8H13O8	-1		C01187	"KEGG - C01187
Neutral MF = C8H14O8
SMP
CHS"	C8H13O8	-1	-296.436	7.1117									-1	-296.436	7.1117
8360	kdo2lipid4	No	KDO(2)-lipid IV(A)	C84H148N2O37P2	-6		C06025	"KEGG C06025 
Neutral C84H154N2O37P2
JLR - NH page 1043"	C84H150N2O37P2	-4	-1428.65	45.6391									-4	-1428.65	45.6391
8361	kdo2lipid4L	No	KDO(2)-lipid IV(A) with laurate	C96H170N2O38P2	-6		C06251	"C06251
NH page 1043
Neutral-C96H176N2O38P2
JLR"	C96H172N2O38P2	-4	-1454.16	50.6329									-4	-1454.16	50.6329
11297	kdo2lipid4p	No	KDO(2)-lipid IV(A) with palmitoleoyl	C100H176N2O38P2	-6			"see PMID 10092655
Neutral-C100H182N2O38P2
JLR"	C100H178N2O38P2	-4	-1431.47	51.7184									-4	-1431.47	51.7184
3952	kdo8p	No	3-Deoxy-D-manno-octulosonate 8-phosphate	C8H12O11P	-3		C04478	"KEGG - C04478
Neutral MF = C8H15O11P
SMP
CHS"	C8H13O11P	-2	-507.456	7.48604									-2	-507.456	7.48604
8745	kdolipid4	No	KDO-lipid IV(A)	C76H137N2O30P2	-5		C06024	"KEGG- C06024 
Neutral C76H142N2O30P2
JLR-"	C76H139N2O30P2	-3	-1193.44	40.9484									-3	-1193.44	40.9484
22077	kphphhlipa	Yes	kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA	C139H241N2O70P4	-11			AMF	C139H245N2O70P4	-7	-2721.7	78.853									-7	-2721.7	78.853
304	lac-D	No	D-Lactate	C3H5O3	-1	10326-41-7	C00256	"KEGG - C00256
Neutral MF = C3H6O3
SMP
CHS"	C3H5O3	-1	-122.527	2.15485									-1	-122.527	2.15485
10931	lac-L	No	L-Lactate	C3H5O3	-1	79-33-4	C00186	"KEGG - C00186
Neutral MF = C3H6O3
SMP
CHS"	C3H5O3	-1	-122.527	2.15485									-1	-122.527	2.15485
21424	LalaDglu	Yes	L-alanine-D-glutamate	C8H13N2O5	-1			AMF	C8H13N2O5	-1	-189.466	4.68699									-1	-189.466	4.68699
21425	LalaDgluMdap	Yes	"L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate"	C15H25N4O8	-1			AMF	C15H25N4O8	-1	-292.415	9.11915									-1	-292.415	9.11915
21426	LalaDgluMdapDala	Yes	"L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine"	C18H30N5O9	-1			AMF	C18H30N5O9	-1	-318.467	11.8123									-1	-318.467	11.8123
21556	LalaLglu	Yes	L-alanine-L-glutamate	C8H13N2O5	-1			"AMF
dont think its the same as gluala"	C8H13N2O5	-1	-189.466	4.68699									-1	-189.466	4.68699
491	lald-D	Yes	D-Lactaldehyde	C3H6O2	0	None	C00937	"KEGG - C00937
Neutral Compound
SMP
CHS"	C3H6O2	0	-70.0129	2.22537									0	-70.0129	2.22537
420	lald-L	No	L-Lactaldehyde	C3H6O2	0	598-35-6	C00424	"KEGG - C00424
Neutral Compound
SMP
CHS"	C3H6O2	0	-70.0129	2.22537									0	-70.0129	2.22537
292	lcts	No	Lactose	C12H22O11	0	63-42-3	C00243	"KEGG - C00243
Neutral Compound
SMP
CHS"	C12H22O11	0	-376.526	17.7716									0	-376.526	17.7716
1082	leu-L	No	L-Leucine	C6H13NO2	0	61-90-5	C00123	"KEGG - C00123
Neutral MF = C6H13NO2
SMP
CHS
Changed according to Genomatica JLR"	C6H13NO2	0	-82.8037	3.57585									0	-82.8037	3.57585
7098	leutrna	Yes	L-Leucyl-tRNA(Leu)	C6H12NOR	1		C02047	"KEGG -C02047
SMP
adjusted for Genomatica's change to aa - NCD
"	C16H24N6O4R	1	-38.9334	13.1478									1	-38.9334	13.1478
2477	lgt-S	No	(R)-S-Lactoylglutathione	C13H20N3O8S	-1	59-85-8	C03451	"KEGG - C03451
Neutral MF = C13H21N3O8S
SMP
CHS
Changed according to Genomatica JLR"	C13H20N3O8S	-1	-283.509	8.96324									-1	-283.509	8.96324
4466	lipa	No	KDO(2)-lipid (A)	C110H196N2O39P2	-6	598-35-6	C06026	"KEGG - C06026 
NH page 1043
JLR"	C110H198N2O39P2	-4	-1477.85	57.2057									-4	-1477.85	57.2057
9012	lipa_cold	No	cold adapted KDO(2)-lipid (A)	C114H202N2O39P2	-6			"see PMID 10092655
Neutral C114H208N2O39P2
JLR"	C114H204N2O39P2	-4	-1455.16	58.3563									-4	-1455.16	58.3563
3637	lipidA	No	"2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate"	C68H126N2O23P2	-4	None		"Neutral MF = C68H130N2O23P2
SMP
CHS
JLR- similar to C04919 but phosphate is on a different oxygen(see NH pg 1043). 
Changed to -4 charge"	C68H128N2O23P2	-2	-957.426	36.9051									-2	-957.426	36.9051
5873	lipidAds	No	Lipid A Disaccharide	C68H127N2O20P	-2		C04932	"tv
Kegg C04932"	C68H128N2O20P	-1	-744.916	36.8918									-1	-744.916	36.8918
3555	lipidX	No	"2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate"	C34H64NO12P	-2	None	C04824	"KEGG - C04824
Neutral MF = C34H66NO12P
SMP
CHS
Checked N-groups JLR"	C34H65NO12P	-1	-507.087	18.4902									-1	-507.087	18.4902
26364	lpp	Yes	lipoprotein	XC16H30O1	0	6244-92-4	C01834	"KEGG - C01834
AMF
lipoprotein that has been N-acylated"	C19H35NO2R2S	0	-27.3589	11.1446									0	-27.3589	11.1446
328	lys-L	No	L-Lysine	C6H15N2O2	1	56-87-1	C00047	"KEGG - C00047
Neutral MF = C6H14N2O2
SMP
CHS
Changed according to Genomatica JLR"	C6H15N2O2	1	-85.0813	4.17198									1	-85.0813	4.17198
5855	lystrna	Yes	L-Lysine-tRNA (Lys)	C6H14N2OR	2		C01931	"KEGG - C01931
SMP
adjusted for Genomatica's change to aa - NCD"	C16H26N7O4R	2	-41.211	13.4245									2	-41.211	13.4245
1236	lyx-L	Yes	L-Lyxose	C5H10O5	0	1949-78-6	C01508	"KEGG - C01508
JLR"	C5H10O5	0	-180.969	8.29386									0	-180.969	8.29386
50	malACP	No	Malonyl-[acyl-carrier protein]	C14H22N2O10PRS	-2	None	C01209	"KEGG - C01209
Error in KEGG: ACP attached to Malonyl via a S, NOT Oxygen. 
Checked with Neidhardt (tv)
Neutral MF = C3H3O3R
(S)R = [acyl-carrier protein]
SMP
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
"	C14H22N2O10PRS	-2	-433.949	9.20468									-2	-433.949	9.20468
11267	malcoa	No	Malonyl-CoA	C24H33N7O19P3S	-5	524-14-1	C00083	"KEGG - C00083
Neutral MF = C24H38N7O19P3S
SMP
CHS"	C24H34N7O19P3S	-4	-860.223	15.9262									-4	-860.223	15.9262
230	mal-L	No	L-Malate	C4H4O5	-2	97-67-6	C00149	"KEGG - C00149
Neutral MF = C4H6O5
SMP
CHS"	C4H4O5	-2	-200.836	2.58632									-2	-200.836	2.58632
267	malt	No	Maltose	C12H22O11	0	69-79-4	C00208	"KEGG - C00208
Neutral Compound
SMP
CHS"	C12H22O11	0	-376.526	17.7716									0	-376.526	17.7716
2247	malt6p	No	Maltose 6'-phosphate	C12H21O14P	-2	None	C02995	"KEGG - C02995
Neutral MF = C12H23O14P
SMP
CHS"	C12H22O14P	-1	-589.036	17.7436									-1	-589.036	17.7436
9036	malthp	No	Maltoheptaose	C42H72O36	0			"Not in Kegg
JLR"	C42H72O36	0	-1168.02	60.7539									0	-1168.02	60.7539
1564	malthx	No	Maltohexaose	C36H62O31	0	34620-77-4	C01936	"KEGG - C01936
JLR"	C36H62O31	0	-1009.72	52.1332									0	-1009.72	52.1332
9035	maltpt	No	Maltopentaose	C30H52O26	0			"Not in Kegg
JLR"	C30H52O26	0	-851.423	43.5174									0	-851.423	43.5174
1284	malttr	No	Maltotriose	C18H32O16	0	1109-28-0	C01835	"KEGG - C01835
JLR"	C18H32O16	0	-534.825	26.3201									0	-534.825	26.3201
1658	maltttr	No	Maltotetraose	C24H42O21	0	34612-38-9	C02052	"KEGG - C02052
JLR"	C24H42O21	0	-693.124	34.9103									0	-693.124	34.9103
11018	man	Yes	D-Mannose	C6H12O6	0	3458-28-4	C00159	"KEGG - C00159
Neutral Compound
SMP
CHS"	C6H12O6	0	-218.227	9.37949									0	-218.227	9.37949
2920	man1p	No	D-Mannose 1-phosphate	C6H11O9P	-2		C03812	"KEGG - C03812
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-429.548	8.96923									-1	-429.548	8.96923
137	man6p	No	D-Mannose 6-phosphate	C6H11O9P	-2	None	C00275	"KEGG - C00275
Neutral MF = C6H13O9P
SMP
CHS"	C6H12O9P	-1	-430.737	9.43168									-1	-430.737	9.43168
12435	man6pglyc	Yes	2(alpha-D-Mannosyl-6-phosphate)-D-glycerate	C9H14O12P	-3			"JLR- not in Kegg
The same as manglyc but with a phosphate group on the 6th carbon of the mannose moiety"	C9H15O12P	-2	-529.655	9.33865									-2	-529.655	9.33865
128	mana	No	D-Mannonate	C6H11O7	-1		C00514	"KEGG - C00514
Neutral MF = C6H12O7
SMP"	C6H11O7	-1	-269.61	6.90606									-1	-269.61	6.90606
12434	manglyc	Yes	2(alpha-D-Mannosyl)-D-glycerate	C9H15O9	-1		C11544	"KEGG C11544
   "	C9H15O9	-1	-317.145	9.39177									-1	-317.145	9.39177
3898	melib	No	Melibiose	C12H22O11	0	585-99-9	C05402	"KEGG - C05402
Neutral compound
CAS # covers alpha-D-(+)-Melibiose hydrate 
SMP
CHS"	C12H22O11	0	-378.518	18.2002									0	-378.518	18.2002
794	mercppyr	Yes	Mercaptopyruvate	C3H3O3S	-1		C00957	KEGG - C00957	C3H3O3S	-1	-110.372	2.5986									-1	-110.372	2.5986
723	met-D	No	D-Methionine	C5H10NO2S	0	348-67-4	C00855	"KEGG - C00855
Neutral MF = C5H11NO2S
SMP
CHS
Changed according to Genomatica JLR"	C5H11NO2S	0	-71.4456	3.69232									0	-71.4456	3.69232
433	methf	No	"5,10-Methenyltetrahydrofolate"	C20H20N7O6	-1		C00445	"KEGG - C00445
Merged with C04270
Neutral MF = C20H22N7O6
netural form has +1 charge -NCD
SMP
CHS
Checked N-groups, agrees with ACD software, NCD, JLR
Agrees with pipeline pilot"	C20H20N7O6	-1	-102.677	13.9116									-1	-102.677	13.9116
343	met-L	No	L-Methionine	C5H11NO2S	0	63-68-3	C00073	"KEGG - C00073
Neutral MF = C5H11NO2S
SMP
CHS
Changed according to Genomatica JLR"	C5H11NO2S	0	-71.4456	3.69232									0	-71.4456	3.69232
18416	metsox-R-L	Yes	L-methionine-R-sulfoxide	C5H11NO3S	0			"MKA
KEGG - C02989
Neutral MF = C5H11NO3S
SMP
Checked N-groups, JLR

"	C5H11NO3S	0	No Energy	No Energy									0	1.00E+07	1.00E+07
10541	metsox-S-L	Yes	L-Methionine-S-Sulfoxide	C5H11NO3S	0		C02989	"KEGG - C02989
Neutral MF = C5H11NO3S
SMP
Checked N-groups, JLR
Kegg C02989"	C5H11NO3S	0	No Energy	No Energy									0	1.00E+07	1.00E+07
5854	mettrna	Yes	L-Methionyl-tRNA (Met)	C5H10NOSR	1		C02430	"KEGG - C02430
SMP
adjusted for Genomatica's change to aa - NCD"	C15H22N6O4RS	1	-27.5754	13.2145									1	-27.5754	13.2145
12857	mg2	Yes	magnesium	Mg	2		C00305	"KEGG - C00305
SMP"	Mg	2	No Energy	No Energy									2	1.00E+07	1.00E+07
8983	mi1p-D	No	1D-myo-Inositol 1-phosphate	C6H11O9P	-2		C01177	"Kegg C01177
Neutral-C6H13O9P
JLR"	C6H12O9P	-1	-432.179	10.8348									-1	-432.179	10.8348
3284	micit	No	methylisocitrate	C7H7O7	-3	20298-95-7	C04593	"KEGG - C04593
Neutral-C7H10O7
JLR"	C7H7O7	-3	-277.906	4.18062									-3	-277.906	4.18062
938	minohp	Yes	myo-Inositol hexakisphosphate	C6H6O24P6	-12		C01204	"KEGG - C01204
JLR"	C6H12O24P6	-6	-1488.79	12.8457									-6	-1488.79	12.8457
11043	mlthf	No	"5,10-Methylenetetrahydrofolate"	C20H21N7O6	-2		C00143	"KEGG - C00143
Neutral MF = C20H23N7O6
SMP
CHS
Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR
Pipeline Pilot indicates this N is not charged JLR"	C20H21N7O6	-2	-99.4574	14.2017									-2	-99.4574	14.2017
943	mmcoa-R	No	(R)-Methylmalonyl-CoA	C25H35N7O19P3S	-5		C01213	"KEGG - C01213
Neutral MF = C25H40N7O19P3S
SMP
Checked N-groups JLR"	C25H36N7O19P3S	-4	-858.834	16.0243									-4	-858.834	16.0243
451	mmcoa-S	No	(S)-Methylmalonyl-CoA	C25H35N7O19P3S	-5		C00683	"KEGG - C00683
Neutral MF = C25H40N7O19P3S
SMP
CHS
Checked N-groups JLR"	C25H36N7O19P3S	-4	-858.834	16.0243									-4	-858.834	16.0243
2185	mmet	Yes	S-Methyl-L-methionine	C6H14NO2S	1	4289-98-9	C03172	"KEGG - C03172
NCD
changed to protonated form, added charge - NCD"	C6H14NO2S	1	No Energy	No Energy									1	1.00E+07	1.00E+07
320	mn2	Yes	Mn2+	Mn	2	None	C00034	"KEGG - C00034
SMP
CHS"	Mn	2	No Energy	No Energy									2	1.00E+07	1.00E+07
400	mnl	Yes	D-Mannitol	C6H14O6	0	69-65-8	C00392	"KEGG - C00392
SMP"	C6H14O6	0	-226.707	7.15378									0	-226.707	7.15378
1128	mnl1p	No	D-Mannitol 1-phosphate	C6H13O9P	-2		C00644	"KEGG - C00644
Neutral MF = C6H15O9P
SMP"	C6H14O9P	-1	-439.218	7.0839									-1	-439.218	7.0839
4630	mobd	Yes	Molybdate	MoO4	-2		C06232	"KEGG - C06232
Neutral MF = H2MoO4
SMP"	MoO4	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
4306	mql8	No	Menaquinol 8	C51H74O2	0		C05819	"KEGG - C05819
General Formula = C16H18O2(C5H8)n; n = 7 for mql7
SMP"	C51H74O2	0	149.645	26.728									0	149.645	26.728
9	mqn8	No	Menaquinone 8	C51H72O2	0	84-81-1	C00828	"KEGG - C00828
General Formula = C16H16O2(C5H8)n; n = 7 for mqn8; See also mq
SMP
CHS"	C51H72O2	0	176.057	22.8104									0	176.057	22.8104
21348	mso3	Yes	methanesulfonate	CH3O3S	-1			0	CH3O3S	-1	-129.573	2.2563									-1	-129.573	2.2563
370	mthgxl	No	Methylglyoxal	C3H4O2	0	78-98-8	C00546	"KEGG - C00546
Neutral Compound
SMP
CHS"	C3H4O2	0	-60.8307	1.90536									0	-60.8307	1.90536
25720	murein3p3p	Yes	"two linked disacharide tripeptide murein units (uncrosslinked, middle of chain)"	C68H104N12O38	-4			"AMF
PMID: 9751644 has a good figure"	C68H104N12O38	-4	-1191.63	46.061									-4	-1191.63	46.061
25725	murein3px3p	Yes	"two disacharide linked murein units, tripeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)"	C68H102N12O37	-4			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslink is between A2pm->A2pm"	C68H102N12O37	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
25718	murein3px4p	Yes	"two disacharide linked murein units, tripeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)"	C71H107N13O38	-4			"AMF
PMID: 9751644 has a good figure"	C71H107N13O38	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
25793	murein4p3p	Yes	"two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain)"	C71H109N13O39	-4			"AMF
PMID: 9751644 has a good figure"	C71H109N13O39	-4	-1217.68	48.3598									-4	-1217.68	48.3598
25719	murein4p4p	Yes	"two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)"	C74H114N14O40	-4			"AMF
PMID: 9751644 has a good figure"	C74H114N14O40	-4	-1243.73	50.7618									-4	-1243.73	50.7618
25717	murein4px4p	Yes	"two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)"	C74H112N14O39	-4			"AMF
PMID: 9751644 has a good figure"	C74H112N14O39	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
25839	murein4px4p4p	Yes	"three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala), one uncrosslinked tetrapaptide) (middle of chain)"	C111H169N21O59	-6			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslinks are between A2pm->D-ala"	C111H169N21O59	-6	No Energy	No Energy									-6	1.00E+07	1.00E+07
25723	murein4px4px4p	Yes	three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)	C111H167N21O58	-6			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslinks are between A2pm->D-ala"	C111H167N21O58	-6	No Energy	No Energy									-6	1.00E+07	1.00E+07
25794	murein5p3p	Yes	"two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain)"	C74H114N14O40	-4			"AMF
PMID: 9751644 has a good figure"	C74H114N14O40	-4	-1243.73	50.7618									-4	-1243.73	50.7618
25792	murein5p4p	Yes	"two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain)"	C77H119N15O41	-4			"AMF
PMID: 9751644 has a good figure"	C77H119N15O41	-4	-1269.79	53.2531									-4	-1269.79	53.2531
21438	murein5p5p	Yes	"two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)"	C80H124N16O42	-4			"AMF
this is formed when two uaagmda units come together and lose their undecprenyl chains
[GlcNac-MurNac-pentapeptide(beta1->4)GlcNac-MurNac-pentapeptide] unit
only the leading oxygen from the ether bond to the next unit is kept on the MurNac, the one from the previous unit connected to the terminal GlcNac is not considered
PMID: 9751644 has a good figure"	C80H124N16O42	-4	-1295.84	55.8216									-4	-1295.84	55.8216
25721	murein5p5p5p	Yes	"three linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)"	C120H186N24O63	-6			AMF	C120H189N24O63	-3	-1901.08	85.792									-3	-1901.08	85.792
25724	murein5px3p	Yes	"two disacharide linked murein units, pentapeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)"	C74H112N14O39	-4			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslink is between A2pm->A2pm"	C74H112N14O39	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
25716	murein5px4p	Yes	"two disacharide linked murein units, pentapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)"	C77H117N15O40	-4			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslink is between A2pm->D-ala"	C77H117N15O40	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
25722	murein5px4px4p	Yes	three disacharide linked murein units (pentapeptide corsslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)	C114H172N22O59	-6			"AMF
PMID: 9751644 has a good figure
basic 2 unit crosslinked murein chain from the middle of a murein chain
The murein crosslinks are between A2pm->D-ala"	C114H172N22O59	-6	No Energy	No Energy									-6	1.00E+07	1.00E+07
10495	myrsACP	No	Myristoyl-ACP (n-C14:0ACP)	C25H47N2O8PRS	-1		C05761	"KEGG C05761
tv 
myrs component = C14H27O (3/25/03)
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C25H47N2O8PRS	-1	-344.692	14.2806									-1	-344.692	14.2806
1108	N1aspmd	No	N1-Acetylspermidine	C9H23N3O	2	34450-16-3	C00612	"KEGG - C00612
JLR
capitalized N at beginning of abbrev -NCD
Checked N-groups JLR"	C9H23N3O	2	-25.7627	6.16625									2	-25.7627	6.16625
10910	n2o	Yes	Nitrous oxide	N2O	0	10024-97-2	C00887	"KEGG - C00887
SMP
CHS"	N2O	0	No Energy	No Energy									0	1.00E+07	1.00E+07
842	n8aspmd	No	N8-Acetylspermidine	C9H23N3O	2	34450-15-2	C01029	"KEGG - C01029
JLR
Checked N-groups JLR"	C9H23N3O	2	-25.7627	6.16625									2	-25.7627	6.16625
1023	na1	No	Sodium	Na	1	7440-23-5	C01330	"KEGG - C01330
SMP
CHS"	Na	1	No Energy	No Energy									1	1.00E+07	1.00E+07
301	nac	No	Nicotinate	C6H4NO2	-1	59-67-6	C00253	"KEGG - C00253
Neutral MF = C6H5NO2
SMP
CHS
Checked N-groups JLR"	C6H4NO2	-1	-37.6396	6.62298									-1	-37.6396	6.62298
466	nad	No	Nicotinamide adenine dinucleotide	C21H26N7O14P2	-1	53-84-9	C00003	"KEGG - C00003
Neutral MF = C21H28N7O14P2 (Charge +1)
SMP
CHS
Checked N-groups JLR (agrees with ACD software)"	C21H26N7O14P2	-1	-536.485	20.6768									-1	-536.485	20.6768
467	nadh	No	Nicotinamide adenine dinucleotide - reduced	C21H27N7O14P2	-2	53-84-9	C00004	"KEGG - C00004
Neutral MF = C21H29N7O14P2
SMP
CHS
Checked N-groups, agrees with ACD software, NCD, JLR"	C21H27N7O14P2	-2	-531.431	20.5321									-2	-531.431	20.5321
469	nadp	No	Nicotinamide adenine dinucleotide phosphate	C21H25N7O17P3	-3	53-59-8	C00006	"KEGG - C00006
Original KEGG MF = C21H29N7O17P3 (+1)
SMP
CHS
Checked N-groups JLR"	C21H26N7O17P3	-2	-747.807	20.4939									-2	-747.807	20.4939
468	nadph	No	Nicotinamide adenine dinucleotide phosphate - reduced	C21H26N7O17P3	-4	2646-71-1	C00005	"KEGG - C00005
Neutral MF = C21H30N7O17P3
SMP
CHS
Checked N-groups, agrees with ACD software, NCD, JLR"	C21H27N7O17P3	-3	-742.752	20.348									-3	-742.752	20.348
233	ncam	No	Nicotinamide	C6H6N2O	0	98-92-0	C00153	"KEGG - C00153
SMP
CHS
Checked N-groups JLR"	C6H6N2O	0	5.5534	7.09759									0	5.5534	7.09759
476	nh4	No	Ammonium	H4N	1	66701-25-5	C01342	"KEGG - C01342
Charged Compound
Diiferentiate Ammonia from Ammonium
SMP
CHS
Checked N-groups JLR"	H4N	1	-18.1	0.5									1	-18.1	0.5
10781	ni2	Yes	nickel	Ni	2		C00291	KEGG - C00291	Ni	2	No Energy	No Energy									2	1.00E+07	1.00E+07
776	nicrnt	No	Nicotinate D-ribonucleotide	C11H12NO9P	-2		C01185	"KEGG - C01185
Neutral MF = C11H15NO9P
SMP
Checked N-groups JLR"	C11H13NO9P	-1	-382.914	9.8251									-1	-382.914	9.8251
77	nmn	No	NMN	C11H14N2O8P	-1	1094-61-7	C00455	"KEGG - C00455
Correct MF = C11H16N2O8P
KEGG MF = C11H15N2O8P with charge +1
SMP
Checked N-groups JLR"	C11H15N2O8P	0	-339.721	10.1511									0	-339.721	10.1511
2239	Nmtrp	Yes	N-Methyltryptophan	C12H14N2O2	0	526-31-8	C02983	KEGG - C02983	C12H14N2O2	0	-18.896	9.01811									0	-18.896	9.01811
361	no	Yes	Nitric oxide	NO	0	10102-43-9	C00533	"KEGG - C00533
SMP
CHS"	NO	0	No Energy	No Energy									0	1.00E+07	1.00E+07
11261	no2	No	Nitrite	NO2	-1	7697-37-2	C00088	"KEGG - C00088
Neutral MF = HNO2
SMP
CHS
Checked N-groups JLR"	NO2	-1	-7	0.5									-1	-7	0.5
5270	no3	No	Nitrate	NO3	-1		C00244	"KEGG - C00244
Neutral MF = HNO3
SMP
CHS
Checked N-goups JLR"	NO3	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
22132	o16a2und	Yes	(O16 antigen)x2 undecaprenyl diphosphate	C123H200N2O57P2	-2			AMF	C123H200N2O57P2	-2	-1758.38	88.9621									-2	-1758.38	88.9621
22133	o16a3und	Yes	(O16 antigen)x3 undecaprenyl diphosphate	C157H255N3O82P2	-2			AMF	C157H255N3O82P2	-2	-2537.44	128.874									-2	-2537.44	128.874
22135	o16a4colipa	Yes	(O16 antigen)x4 core oligosaccharide lipid A	C312H523N6O200P4	-11			AMF	C312H523N6O200P4	-11	No Energy	No Energy									-11	1.00E+07	1.00E+07
22134	o16a4und	Yes	(O16 antigen)x4 undecaprenyl diphosphate	C191H310N4O107P2	-2			"AMF
"	C191H310N4O107P2	-2	-3316.49	169.492									-2	-3316.49	169.492
22131	o16aund	Yes	O16 antigen undecaprenyl diphosphate	C89H145N1O32P2	-2			AMF - structure from PMID: 7517391	C89H145NO32P2	-2	-979.324	51.4248									-2	-979.324	51.4248
470	o2	No	O2	O2	0	7782-44-7	C00007	"KEGG - C00007
SMP
CHS"	O2	0	0	0.5									0	0	0.5
461	o2-	No	Superoxide anion	O2	-1		C00704	"KEGG - C00704
JLR"	O2	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
322	oaa	No	Oxaloacetate	C4H2O5	-2	328-42-7	C00036	"KEGG - C00036
Neutral MF = C4H4O5
SMP
CHS"	C4H2O5	-2	-191.654	2.31672									-2	-191.654	2.31672
3805	oc2coa	Yes	trans-Oct-2-enoyl-CoA	C29H44N7O17P3S	-4		C05276	"KEGG - C05276
Neutral MF = C29H48N7O18P3S
SMP"	C29H45N7O17P3S	-3	-757.395	16.8638									-3	-757.395	16.8638
7928	ocACP	Yes	Octanoyl-ACP (n-C8:0ACP)	C19H35N2O8PRS	-1		C05752	"JLR- saturated fatty acid with 8 carbons attached to ACP
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C19H35N2O8PRS	-1	-350.166	11.2867									-1	-350.166	11.2867
10688	occoa	Yes	Octanoyl-CoA (n-C8:0CoA)	C29H46N7O17P3S	-4		C01944	"KEGG - C01944
Neutral MF = C29H50N7O17P3S
SMP"	C29H47N7O17P3S	-3	-776.44	17.3455									-3	-776.44	17.3455
1249	ocdca	No	octadecanoate (n-C18:0)	C18H35O2	-1	57-11-4	C01530	"KEGG - C01530
Neutral MF = C18H36O2
SID: 38708
CID: 78387
SMP
saturated fatty acid, 18 carbons
changed compound class from peptides to fatty acids - NCD"	C18H35O2	-1	-71.0075	10.8833									-1	-71.0075	10.8833
5936	ocdcaACP	Yes	Octadecanoyl-ACP (n-C18:0ACP)	C29H55N2O8PRS	-1			"tv
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)"	C29H55N2O8PRS	-1	-341.042	16.5285									-1	-341.042	16.5285
8769	ocdcea	No	octadecenoate (n-C18:1)	C18H33O2	-1			"monounsaturated fatty acid, 18 carbons
KEGG - C00712
NCD
updated by NJ"	C18H33O2	-1	-51.9623	9.73038									-1	-51.9623	9.73038
5354	octa	Yes	octanoate (n-C8:0)	C8H15O2	-1	124-07-2	C06423	"KEGG - C06423
Neutral MF = C8H16O2
SMP
changed compound class from peptides - NCD"	C8H15O2	-1	-80.1314	4.26714									-1	-80.1314	4.26714
2970	octdp	No	all-trans-Octaprenyl diphosphate	C40H65O7P2	-3		C04146	"KEGG - C04146
Neutral MF = C40H68O7P2
SMP"	C40H66O7P2	-2	-272.929	20.5258									-2	-272.929	20.5258
5871	octeACP	No	cis-octadec-11-enoyl-[acyl-carrier protein] (n-C18:1)	C29H53N2O8PRS	-1			"tv
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C29H53N2O8PRS	-1	-323.591	15.9569									-1	-323.591	15.9569
8401	od2coa	Yes	trans-Octadec-2-enoyl-CoA	C39H64N7O17P3S	-4			"NCD
C18:1 - C18H33O2 (charge -1)
C21H32N7O16P3S (charge -4)
NJ"	C39H65N7O17P3S	-3	-748.271	20.5202									-3	-748.271	20.5202
8782	odecoa	Yes	Octadecenoyl-CoA (n-C18:1CoA)	C39H64N7O17P3S	-4			"NCD
KEGG - C00510
C18:1 C18H33O2 (charge -1)
CoA - C21H32N7O16P3S charge (-4)
NJ"	C39H65N7O17P3S	-3	-748.271	20.5202									-3	-748.271	20.5202
8083	ohpb	No	2-Oxo-3-hydroxy-4-phosphobutanoate	C4H4O8P	-3		C06054	"KEGG - C06054
Neutral-C4H7O8P
JLR"	C4H5O8P	-2	-399.095	2.76185									-2	-399.095	2.76185
1097	op4en	No	2-Oxopent-4-enoate	C5H5O3	-1		C00596	"KEGG - C00596
Neutral-C5H6O3
JLR"	C5H5O3	-1	-84.294	3.55823									-1	-84.294	3.55823
1304	orn	No	Ornithine	C5H13N2O2	1	70-26-8	C01602	"KEGG - C01602
Neutral MF = C5H12N2O2
SMP
CHS
Checked N-groups JLR"	C5H13N2O2	1	-85.9936	3.77041									1	-85.9936	3.77041
148	orot	No	Orotate	C5H3N2O4	-1	65-86-1	C00295	"KEGG - C00295
Neutral MF = C5H4N2O4
SMP
CHS
Checked N-groups JLR"	C5H3N2O4	-1	-133.931	7.30002									-1	-133.931	7.30002
881	orot5p	No	Orotidine 5'-phosphate	C10H10N2O11P	-3	2149-82-8	C01103	"KEGG - C01103
Neutral MF = C10H13N2O11P
SMP
Checked N-groups JLR"	C10H11N2O11P	-2	-468.995	9.79957									-2	-468.995	9.79957
580	oxam	Yes	Oxamate	C2H2NO3	-1	471-47-6	C01444	"KEGG - C01444
JLR- Checked protonation state"	C2H2NO3	-1	-121.634	2.86527									-1	-121.634	2.86527
651	oxur	Yes	Oxalureate	C3H3N2O4	-1	585-05-7	C00802	"KEGG - C00802
Checked Protonation state JLR"	C3H3N2O4	-1	-149.988	4.99771									-1	-149.988	4.99771
26133	pa120	Yes	"1,2-didodecanoyl-sn-glycerol 3-phosphate"	C27H51O8P1	-2		C00416	"KEGG - C00416
AMF"	C27H52O8P	-1	-381.471	15.5108									-1	-381.471	15.5108
26056	pa140	Yes	"1,2-ditetradecanoyl-sn-glycerol 3-phosphate"	C31H59O8P1	-2		C00416	AMF	C31H60O8P	-1	-377.822	18.1126									-1	-377.822	18.1126
26059	pa141	Yes	"1,2-ditetradec-7-enoyl-sn-glycerol 3-phosphate"	C31H55O8P1	-2		C00416	AMF	C31H56O8P	-1	-339.731	15.9646									-1	-339.731	15.9646
26057	pa160	Yes	"1,2-dihexadecanoyl-sn-glycerol 3-phosphate"	C35H67O8P1	-2		C00416	AMF	C35H68O8P	-1	-374.172	20.7395									-1	-374.172	20.7395
26060	pa161	Yes	"1,2-dihexadec-9-enoyl-sn-glycerol 3-phosphate"	C35H63O8P1	-2		C00416	AMF	C35H64O8P	-1	-336.082	18.5027									-1	-336.082	18.5027
26058	pa180	Yes	"1,2-dioctadecanoyl-sn-glycerol 3-phosphate"	C39H75O8P1	-2		C00416	AMF	C39H76O8P	-1	-370.523	23.383									-1	-370.523	23.383
26061	pa181	Yes	"1,2-dioctadec-11-enoyl-sn-glycerol 3-phosphate"	C39H71O8P1	-2		C00416	AMF	C39H72O8P	-1	-332.432	21.081									-1	-332.432	21.081
9657	pac	No	Phenylacetic acid	C8H7O2	-1	CAS: 103-82-2	C07086	"Kegg C07086
Neutral-C8H8O2
JLR"	C8H7O2	-1	-49.0863	8.03769									-1	-49.0863	8.03769
1100	pacald	No	Phenylacetaldehyde	C8H8O	0	122-78-1	C00601	"KEGG - C00601
JLR"	C8H8O	0	3.42788	8.05688									0	3.42788	8.05688
5870	palmACP	No	Palmitoyl-ACP (n-C16:0ACP)	C27H51N2O8PRS	-1		C05764	"KEGG- C05764
tv
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C27H51N2O8PRS	-1	-342.867	15.3864									-1	-342.867	15.3864
900	pan4p	No	Pantetheine 4'-phosphate	C11H21N2O7PS	-2		C01134	"KEGG - C01134
Neutral MF = C11H23N2O7PS
SMP
CHS
Checked N-groups JLR"	C11H22N2O7PS	-1	-341.176	7.76221									-1	-341.176	7.76221
351	pant-R	No	(R)-Pantoate	C6H11O4	-1	470-29-1	C00522	"KEGG - C00522
Neutral MF = C6H12O4
SMP
CHS"	C6H11O4	-1	-156.888	3.5637									-1	-156.888	3.5637
333	pap	No	"Adenosine 3',5'-bisphosphate"	C10H11N5O10P2	-4	1053-73-2	C00054	"KEGG - C00054
Neutral MF = C10H15N5O10P2
SMP
CHS"	C10H13N5O10P2	-2	-471.354	12.6944									-2	-471.354	12.6944
332	paps	No	3'-Phosphoadenylyl sulfate	C10H11N5O13P2S	-4	482-67-7	C00053	"KEGG - C00053
Neutral MF = C10H15N5O13P2S
SMP
Checked N-groups JLR"	C10H12N5O13P2S	-3	-579.547	12.9564									-3	-579.547	12.9564
1116	pdx5p	No	Pyridoxine 5'-phosphate	C8H10NO6P	-2	447-05-2	C00627	"KEGG - C00627
Neutral MF = C8H12NO6P
SMP
CHS
Checked N-groups JLR"	C8H11NO6P	-1	-274.741	8.77112									-1	-274.741	8.77112
26139	pe120	Yes	"phosphatidylethanolamine (didodecanoyl, n-C12:0)"	C29H58N1O8P1	0		C00350	"KEGG - C00350
AMF"	C29H58NO8P	0	-367.364	16.9425									0	-367.364	16.9425
26100	pe140	Yes	"phosphatidylethanolamine (ditetradecanoyl, n-C14:0)"	C33H66N1O8P1	0		C00350	"KEGG - C00350
AMF"	C33H66NO8P	0	-363.714	19.5402									0	-363.714	19.5402
26103	pe141	Yes	"phosphatidylethanolamine (ditetradec-7-enoyl, n-C14:1)"	C33H62N1O8P1	0		C00350	"KEGG - C00350
AMF"	C33H62NO8P	0	-325.624	17.3589									0	-325.624	17.3589
26101	pe160	Yes	"phosphatidylethanolamine (dihexadecanoyl, n-C16:0)"	C37H74N1O8P1	0		C00350	"KEGG - C00350
AMF"	C37H74NO8P	0	-360.065	22.1624									0	-360.065	22.1624
26104	pe161	Yes	"phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)"	C37H70N1O8P1	0		C00350	"KEGG - C00350
AMF"	C37H70NO8P	0	-321.974	19.9024									0	-321.974	19.9024
26102	pe180	Yes	"phosphatidylethanolamine (dioctadecanoyl, n-C18:0)"	C41H82N1O8P1	0		C00350	"KEGG - C00350
AMF"	C41H82NO8P	0	-356.415	24.8013									0	-356.415	24.8013
26105	pe181	Yes	"phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1)"	C41H78N1O8P1	0		C00350	"KEGG - C00350
AMF"	C41H78NO8P	0	-318.325	22.4823									0	-318.325	22.4823
9637	peamn	No	Phenethylamine	C8H12N	1	64-04-0	C05332	"KEGG - C05332
JLR
Checked N-groups JLR"	C8H12N	1	28.3339	8.19042									1	28.3339	8.19042
344	pep	No	Phosphoenolpyruvate	C3H2O6P	-3	138-08-9	C00074	"KEGG - C00074
Neutral MF = C3H5O6P
SMP
CHS"	C3H3O6P	-2	-315.683	3.10581									-2	-315.683	3.10581
26136	pg120	Yes	"Phosphatidylglycerol (didodecanoyl, n-C12:0)"	C30H58O10P1	-1		C00344	"KEGG - C00344
AMF"	C30H58O10P	-1	-438.803	17.081									-1	-438.803	17.081
26083	pg140	Yes	"Phosphatidylglycerol (ditetradecanoyl, n-C14:0)"	C34H66O10P1	-1		C00344	"KEGG - C00344
AMF"	C34H66O10P	-1	-435.153	19.6604									-1	-435.153	19.6604
26086	pg141	Yes	"Phosphatidylglycerol (ditetradec-7-enoyl, n-C14:1)"	C34H62O10P1	-1		C00344	"KEGG - C00344
AMF"	C34H62O10P	-1	-397.063	17.4941									-1	-397.063	17.4941
26084	pg160	Yes	"Phosphatidylglycerol (dihexadecanoyl, n-C16:0)"	C38H74O10P1	-1		C00344	"KEGG - C00344
AMF"	C38H74O10P	-1	-431.504	22.2684									-1	-431.504	22.2684
26087	pg161	Yes	"Phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1)"	C38H70O10P1	-1		C00344	"KEGG - C00344
AMF"	C38H70O10P	-1	-393.413	20.0204									-1	-393.413	20.0204
26085	pg180	Yes	"Phosphatidylglycerol (dioctadecanoyl, n-C18:0)"	C42H82O10P1	-1		C00344	"KEGG - C00344
AMF"	C42H82O10P	-1	-427.854	24.8961									-1	-427.854	24.8961
26088	pg181	Yes	"Phosphatidylglycerol (dioctadec-11-enoyl, n-C18:1)"	C42H78O10P1	-1		C00344	"KEGG - C00344
AMF"	C42H78O10P	-1	-389.764	22.5869									-1	-389.764	22.5869
26135	pgp120	Yes	"Phosphatidylglycerophosphate (didodecanoyl, n-C12:0)"	C30H57O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C30H58O13P2	-2	-651.313	17.1097									-2	-651.313	17.1097
2979	pgp140	Yes	"Phosphatidylglycerophosphate (ditetradecanoyl, n-C14:0)"	C34H65O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C34H66O13P2	-2	-647.664	19.6854									-2	-647.664	19.6854
26080	pgp141	Yes	"Phosphatidylglycerophosphate (ditetradec-7-enoyl, n-C14:1)"	C34H61O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C34H62O13P2	-2	-609.574	17.5222									-2	-609.574	17.5222
26078	pgp160	Yes	"Phosphatidylglycerophosphate (dihexadecanoyl, n-C16:0)"	C38H73O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C38H74O13P2	-2	-644.014	22.2905									-2	-644.014	22.2905
26081	pgp161	Yes	"Phosphatidylglycerophosphate (dihexadec-9-enoyl, n-C16:1)"	C38H69O13P2	-3	94-62-2		"KEGG - C03892
AMF"	C38H70O13P2	-2	-605.924	20.0449									-2	-605.924	20.0449
26079	pgp180	Yes	"Phosphatidylglycerophosphate (dioctadecanoyl, n-C18:0)"	C42H81O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C42H82O13P2	-2	-640.365	24.9158									-2	-640.365	24.9158
26082	pgp181	Yes	"Phosphatidylglycerophosphate (dioctadec-11-enoyl, n-C18:1)"	C42H77O13P2	-3	94-62-2	C03892	"KEGG - C03892
AMF"	C42H78O13P2	-2	-602.274	22.6086									-2	-602.274	22.6086
397	phaccoa	No	Phenylacetyl-CoA	C29H38N7O17P3S	-4		C00582	"KEGG - C00582
Neutral-C29H42N7O17P3S
JLR"	C29H39N7O17P3S	-3	-745.395	17.7791									-3	-745.395	17.7791
1048	phe-L	No	L-Phenylalanine	C9H11NO2	0	63-91-2	C00079	"KEGG - C00079
Neutral MF = C9H11NO2
SMP
CHS
Changed according to Genomatica JLR"	C9H11NO2	0	-49.4981	8.24552									0	-49.4981	8.24552
11520	pheme	No	Protoheme	C34H30FeN4O4	-2	14875-96-8	C00032	"KEGG - C00032
Neutral MF = C34H32FeN4O4
Note that chemfinder has the incorrect formula
SMP
CHS
Checked N-groups, JLR"	C34H30FeN4O4	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
7112	phetrna	Yes	L-Phenylalanyl-tRNA(Phe)	C9H10NOR	1		C03511	"KEGG - C03511
SMP
adjusted for Genomatica's change to aa - NCD"	C19H22N6O4R	1	-5.62785	15.1019									1	-5.62785	15.1019
22073	phhlipa	Yes	phospho-heptosyl-heptosyl-kdo2-lipidA	C124H219N2O54P3	-8			AMF	C124H222N2O54P3	-5	-2079.62	69.0753									-5	-2079.62	69.0753
10564	phom	No	O-Phospho-L-homoserine	C4H8NO6P	-2		C01102	"KEGG - C01102
Neutral MF = C4H10NO6P
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO6P	-1	-333.934	2.83297									-1	-333.934	2.83297
22076	phphhlipa	Yes	phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA	C131H230N2O63P4	-10			AMF	C131H234N2O63P4	-6	-2484.68	75.7654									-6	-2484.68	75.7654
240	phpyr	No	Phenylpyruvate	C9H7O3	-1	156-06-9	C00166	"KEGG - C00166
Neutral MF = C9H8O3
SMP
CHS"	C9H7O3	-1	-76.8255	8.13142									-1	-76.8255	8.13142
8887	phthr	No	O-Phospho-4-hydroxy-L-threonine	C4H8NO7P	-2		C06055	"KEGG - C06055
NCD
Checked N-groups JLR"	C4H9NO7P	-1	-371.768	3.51331									-1	-371.768	3.51331
472	pi	No	Phosphate	HO4P	-2	14265-44-2	C00009	"KEGG - C00009
Neutral MF = H3O4P
SMP
CHS
Formula changed to HPO4 (Charge -2) on Feb-26-2002"	HO4P	-2	-261.97	0.5									-2	-261.97	0.5
696	pmcoa	No	Pimeloyl-CoA	C28H41N7O19P3S	-5		C01063	"KEGG - C01063
Neutral MF = C28H46N7O19P3S
SMP
CHS"	C28H42N7O19P3S	-4	-856.573	16.9249									-4	-856.573	16.9249
11029	pmtcoa	Yes	Palmitoyl-CoA (n-C16:0CoA)	C37H62N7O17P3S	-4		C00154	"KEGG - C00154
Neutral MF = C37H66N7O17P3S
SMP
changed compound class from peptides to fatty acids - NCD
C16:0 - C16H31O2 (charge -1)
CoA - C21H32N7O16P3S (charge -4)
NJ"	C37H63N7O17P3S	-3	-769.141	20.433									-3	-769.141	20.433
10928	pnto-R	No	(R)-Pantothenate	C9H16NO5	-1	79-83-4	C00864	"Deleted KEGG - C00864
KEGG - C02349
Neutral MF = C9H17NO5
SMP
CHS
Checked N-groups JLR"	C9H16NO5	-1	-183.418	4.94802									-1	-183.418	4.94802
238	ppa	No	Propionate (n-C3:0)	C3H5O2	-1	79-09-4	C00163	"KEGG - C00163
Neutral MF = C3H6O2
SMP
NCD"	C3H5O2	-1	-84.6933	1.50382									-1	-84.6933	1.50382
96	ppal	Yes	Propanal	C3H6O	0	123-38-6	C00479	"KEGG - C00479
Neutral Compound
SMP"	C3H6O	0	-32.1791	1.60323									0	-32.1791	1.60323
2157	ppap	No	Propanoyl phosphate	C3H5O5P	-2	121-69-7	C02876	"KEGG - C02876
Neutral: C3H7O5P
JLR"	C3H6O5P	-1	-299.039	1.97288									-1	-299.039	1.97288
487	ppbng	No	Porphobilinogen	C10H13N2O4	-1	487-90-1	C00931	"KEGG - C00931
Neutral MF = C10H14N2O4
SMP
Changed according to Genomatica JLR"	C10H13N2O4	-1	-119.068	7.52658									-1	-119.068	7.52658
1064	ppcoa	No	Propanoyl-CoA	C24H36N7O17P3S	-4	317-66-8	C00100	"KEGG - C00100
Neutral MF = C24H40N7O17P3S
SMP
CHS
NCD"	C24H37N7O17P3S	-3	-781.002	16.0493									-3	-781.002	16.0493
957	ppgpp	Yes	"Guanosine 3',5'-bis(diphosphate)"	C10H11N5O17P4	-6		C01228	"KEGG - C01228
Neutral MF = C10H17N5O17P4
SMP"	C10H13N5O17P4	-4	-935.452	12.2251									-4	-935.452	12.2251
302	pphn	No	Prephenate	C10H8O6	-2	126-49-8	C00254	"KEGG - C00254
Neutral MF = C10H10O6
SMP
CHS"	C10H8O6	-2	-198.517	6.62732									-2	-198.517	6.62732
475	ppi	No	Diphosphate	HO7P2	-3	9/3/66	C00013	"KEGG - C00013
Neutral MF = H4O7P2
SMP
CHS
Formula changed to HO7P2 (Charge -3) on Feb-26-2002"	H2O7P2	-2	-480.9	0.5									-2	-480.9	0.5
1772	ppp9	No	Protoporphyrin	C34H32N4O4	-2	553-12-8	C02191	"KEGG - C02191
Neutral MF = C34H34N4O4
SMP
CHS"	C34H32N4O4	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
864	pppg9	No	Protoporphyrinogen IX	C34H38N4O4	-2		C01079	"KEGG - C01079
Neutral MF = C34H40N4O4
SMP
Checked N-groups JLR"	C34H38N4O4	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
2452	pppi	No	Inorganic triphosphate	HO10P3	-4		C03279	"KEGG - C03279
Neutral MF = H5O10P3
SMP"	HO10P3	-4	No Energy	No Energy									-4	1.00E+07	1.00E+07
4152	pppn	No	Phenylpropanoate	C9H9O2	-1	2628-17-3	C05629	"KEGG - C05629
Neutral-C9H10O2
JLR"	C9H9O2	-1	-48.1739	8.12227									-1	-48.1739	8.12227
4912	ppt	Yes	Phosphonate	HO3P	-2	13598-36-2	C06701	"KEGG - C06701
JLR
Pka- 2 and 6.58 (http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf)"	H2O3P	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
2325	pram	No	5-Phospho-beta-D-ribosylamine	C5H11NO7P	-1		C03090	"KEGG - C03090
Neutral MF = C5H12NO7P
SMP
CHS
Changed according to Genomatica JLR"	C5H12NO7P	0	-357.418	7.35056									0	-357.418	7.35056
9634	pran	No	N-(5-Phospho-D-ribosyl)anthranilate	C12H13NO9P	-3	None	C04302	"KEGG - C04302
Neutral MF = C12H16NO9P
SMP
CHS
Checked N-groups JLR"	C12H14NO9P	-2	-391.219	11.2952									-2	-391.219	11.2952
2778	prbamp	No	1-(5-Phosphoribosyl)-AMP	C15H19N5O14P2	-4		C02741	"KEGG - C02741 
Neutral MF = C15H23N5O14P2
SMP
CHS"	C15H22N5O14P2	-1	-605.307	17.2902									-1	-605.307	17.2902
2058	prbatp	No	1-(5-Phosphoribosyl)-ATP	C15H19N5O20P4	-6		C02739	"KEGG - C02739
Neutral MF = C15H25N5O20P4
SMP
CHS"	C15H22N5O20P4	-3	-1021.01	17.4567									-3	-1021.01	17.4567
3612	prfp	No	1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide	C15H21N5O15P2	-4		C04896	"KEGG - C04896
Neutral MF = C15H25N5O15P2
SMP
CHS
Checked N-groups, agrees with ACD software, JLR"	C15H23N5O15P2	-2	-648.429	16.3329									-2	-648.429	16.3329
10680	prlp	No	5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide	C15H21N5O15P2	-4		C04916	"KEGG - C04916
Neutral MF = C15H25N5O15P2
SMP
CHS
Checked N-groups, agrees with ACD software, JLR"	C15H23N5O15P2	-2	-649.607	12.1375									-2	-649.607	12.1375
26302	progly	Yes	L-Prolinylglycine	C7H12N2O3	0			AMF	C7H12N2O3	0	No Energy	No Energy									0	1.00E+07	1.00E+07
229	pro-L	No	L-Proline	C5H9NO2	0	147-85-3	C00148	"KEGG - C00148
Neutral MF = C5H9NO2
SMP
CHS
Changed according to Genomatica JLR"	C5H9NO2	0	No Energy	No Energy									0	1.00E+07	1.00E+07
7104	protrna	Yes	L-Prolyl-tRNA(Pro)	C5H8NOR	1		C02702	"KEGG - C02702
SMP
adjusted for Genomatica's change to aa - NCD"	C15H20N6O4R	1	No Energy	No Energy									1	1.00E+07	1.00E+07
1078	prpp	No	5-Phospho-alpha-D-ribose 1-diphosphate	C5H8O14P3	-5		C00119	"KEGG - C00119
Neutral MF = C5H13O14P3
SMP"	C5H10O14P3	-3	-812.3	7.70882									-3	-812.3	7.70882
26138	ps120	Yes	"phosphatidylserine (didodecanoyl, n-C12:0)"	C30H57N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C30H56NO10P	-2	-444.486	17.1044									-2	-444.486	17.1044
26094	ps140	Yes	"phosphatidylserine (ditetradecanoyl, n-C14:0)"	C34H65N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C34H64NO10P	-2	-440.837	19.6807									-2	-440.837	19.6807
26097	ps141	Yes	"phosphatidylserine (ditetradec-7-enoyl, n-C14:1)"	C34H61N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C34H60NO10P	-2	-402.747	17.5169									-2	-402.747	17.5169
26095	ps160	Yes	"phosphatidylserine (dihexadecanoyl, n-C16:0)"	C38H73N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C38H72NO10P	-2	-437.187	22.2864									-2	-437.187	22.2864
26098	ps161	Yes	"phosphatidylserine (dihexadec-9-enoyl, n-C16:1)"	C38H69N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C38H68NO10P	-2	-399.097	20.0403									-2	-399.097	20.0403
26096	ps180	Yes	"phosphatidylserine (dioctadecanoyl, n-C18:0)"	C42H81N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C42H80NO10P	-2	-433.538	24.9121									-2	-433.538	24.9121
26099	ps181	Yes	"phosphatidylserine (dioctadec-11-enoyl, n-C18:1)"	C42H77N1O10P1	-1		C02737	"KEGG - C02737
AMF"	C42H76NO10P	-2	-395.448	22.6045									-2	-395.448	22.6045
824	pser-L	No	O-Phospho-L-serine	C3H6NO6P	-2	407-41-0	C01005	"KEGG - C01005
Neutral MF = C3H8NO6P
SMP
Changed according to Genomatica JLR
"	C3H7NO6P	-1	-334.847	2.58047									-1	-334.847	2.58047
1094	ptrc	No	Putrescine	C4H14N2	2	110-60-1	C00134	"KEGG - C00134
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C4H14N2	2	-8.16169	3.89011									2	-8.16169	3.89011
1130	pyam5p	No	Pyridoxamine 5'-phosphate	C8H12N2O5P	-1	529-96-4	C00647	"KEGG - C00647
Neutral MF = C8H13N2O5P
SMP
CHS
Checked N-groups JLR, AMF
"	C8H13N2O5P	0	-240.223	8.82638									0	-240.223	8.82638
362	pydam	No	Pyridoxamine	C8H13N2O2	1	85-87-0	C00534	"KEGG - C00534
Neutral Compound
SMP
CHS
Checked N-groups JLR, AMF"	C8H13N2O2	1	-27.7127	8.77059									1	-27.7127	8.77059
298	pydx	No	Pyridoxal	C8H9NO3	0	66-72-8	C00250	"KEGG - C00250
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C8H9NO3	0	-52.6187	8.64602									0	-52.6187	8.64602
479	pydx5p	No	Pyridoxal 5'-phosphate	C8H8NO6P	-2	54-47-7	C00018	"KEGG - C00018
Neutral MF = C8H10NO6P
SMP
CHS
Checked N-groups JLR, AMF
"	C8H9NO6P	-1	-265.129	8.7026									-1	-265.129	8.7026
160	pydxn	No	Pyridoxine	C8H11NO3	0	65-23-6	C00314	"KEGG - C00314
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C8H11NO3	0	-62.2303	8.82766									0	-62.2303	8.82766
311	pyr	No	Pyruvate	C3H3O3	-1	127-17-3	C00022	"KEGG - C00022
Neutral MF = C3H4O3
SMP
CHS"	C3H3O3	-1	-113.345	1.8225									-1	-113.345	1.8225
6324	q8	No	Ubiquinone-8	C49H74O4	0	1339-63-5	C00399	"KEGG C00399
Formula- C14H18O4(C5H8)n , where n=7 for q8
JLR"	C49H74O4	0	112.881	23.7111									0	112.881	23.7111
6325	q8h2	No	Ubiquinol-8	C49H76O4	0		C00390	"KEGG C00390
JLR"	C49H76O4	0	85.0177	29.5969									0	85.0177	29.5969
2854	quln	No	Quinolinate	C7H3NO4	-2	89-00-9	C03722	"KEGG - C03722
Neutral MF = C7H5NO4
SMP
CHS
Checked N-groups JLR"	C7H3NO4	-2	-114.178	6.64859									-2	-114.178	6.64859
909	r15bp	Yes	"D-Ribose 1,5-bisphosphate"	C5H8O11P2	-4	None	C01151	"KEGG - C01151
Neutral MF = C5H12O11P2
SMP
CHS"	C5H10O11P2	-2	-605.249	7.37839									-2	-605.249	7.37839
10390	r1p	No	alpha-D-Ribose 1-phosphate	C5H9O8P	-2	58459-37-3	C00442	"KEGG - C00442
Neutral MF = C5H11O8P
SMP
CHS
"	C5H10O8P	-1	-392.739	7.31156									-1	-392.739	7.31156
1999	r5p	No	alpha-D-Ribose 5-phosphate	C5H9O8P	-2	4300-28-1	C00117	"KEGG - C00117
Delete KEGG - C03736
Neutral MF = C5H11O8P
SMP
CHS
"	C5H10O8P	-1	-393.928	7.69027									-1	-393.928	7.69027
22127	ragund	Yes	rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate	C69H113N1O16P2	-2			AMF	C69H113NO16P2	-2	-469.678	33.9808									-2	-469.678	33.9808
825	rbflvrd	Yes	Reduced riboflavin	C17H22N4O6	0		C01007	KEGG - C01007	C17H22N4O6	0	-137.29	13.2328									0	-137.29	13.2328
122	rbl-L	No	L-Ribulose	C5H10O5	0	488-84-6	C00508	"KEGG - C00508
Neutral Compound
SMP
CHS"	C5H10O5	0	-181.216	5.88651									0	-181.216	5.88651
91	rbt	Yes	Ribitol	C5H12O5	0	488-81-3	C00474	"KEGG - C00474
SMP"	C5H12O5	0	-189.786	5.59587									0	-189.786	5.59587
700	rbt5p	Yes	D-Ribitol 5-phosphate	C5H11O8P	-2		C01068	"KEGG - C01068
Neutral MF = C5H13O8P
SMP"	C5H12O8P	-1	-402.296	5.50625									-1	-402.296	5.50625
4267	rdmbzi	No	"N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole"	C14H18N2O4	0		C05775	"KEGG - C05775
SMP
JLR
Checked N-groups JLR"	C14H18N2O4	0	-76.0974	11.8536									0	-76.0974	11.8536
2726	rhcys	No	S-Ribosyl-L-homocysteine	C9H17NO6S	0	37558-16-0	C03539	"KEGG - C03539
Neutral-C9H17NO6S
JLR
Checked N-groups JLR"	C9H17NO6S	0	-207.255	8.0986									0	-207.255	8.0986
1080	rib-D	No	D-Ribose	C5H10O5	0	50-69-1	C00121	"KEGG - C00121
Neutral Compound
SMP
CHS"	C5H10O5	0	-181.417	7.62618									0	-181.417	7.62618
303	ribflv	No	Riboflavin	C17H20N4O6	0	83-88-5	C00255	"KEGG - C00255
Neutral Compound
SMP
CHS"	C17H20N4O6	0	-128.189	13.7952									0	-128.189	13.7952
726	rml	No	L-Rhamnulose	C6H12O5	0		C00861	"KEGG - C00861
SMP"	C6H12O5	0	-181.206	5.42719									0	-181.206	5.42719
898	rml1p	No	L-Rhamnulose 1-phosphate	C6H11O8P	-2		C01131	"KEGG - C01131
Neutral MF = C6H13O8P
SMP"	C6H12O8P	-1	-393.717	5.51689									-1	-393.717	5.51689
121	rmn	No	L-Rhamnose	C6H12O5	0	3615-41-6	C00507	"KEGG - C00507
SMP"	C6H12O5	0	-181.908	9.35349									0	-181.908	9.35349
261	ru5p-D	No	D-Ribulose 5-phosphate	C5H9O8P	-2	4151-19-3	C00199	"KEGG - C00199
Neutral MF = C5H11O8P
Error in Chemfinder molecular formula
SMP
CHS"	C5H10O8P	-1	-393.114	4.2008									-1	-393.114	4.2008
880	ru5p-L	No	L-Ribulose 5-phosphate	C5H9O8P	-2	4151-19-3	C01101	"KEGG - C01101
Neutral MF = C5H11O8P
SMP"	C5H10O8P	-1	-393.114	4.2008									-1	-393.114	4.2008
140	s7p	No	Sedoheptulose 7-phosphate	C7H13O10P	-2	None	C00281	"KEGG - C00281
Neutral MF = C7H15O10P
SMP
CHS"	C7H14O10P	-1	-466.957	7.19008									-1	-466.957	7.19008
271	sarcs	Yes	Sarcosine	C3H7NO2	0	107-97-1	C00213	"KEGG - C00213
SAB"	C3H7NO2	0	-79.3906	2.62731									0	-79.3906	2.62731
876	sbt6p	No	D-Sorbitol 6-phosphate	C6H13O9P	-2	108392-12-7	C01096	"KEGG - C01096
Neutral MF = C6H15O9P
SMP
CHS"	C6H14O9P	-1	-439.218	7.0839									-1	-439.218	7.0839
645	sbt-D	Yes	D-Sorbitol	C6H14O6	0	50-70-4	C00794	"KEGG - C00794
Neutral Compound
SMP
CHS"	C6H14O6	0	-226.707	7.15378									0	-226.707	7.15378
2375	sbzcoa	No	O-Succinylbenzoyl-CoA	C32H39N7O20P3S	-5		C03160	"KEGG - C03160
Neutral MF = C32H44N7O20P3S
SMP
CHS"	C32H40N7O20P3S	-4	-853.826	18.4913									-4	-853.826	18.4913
4270	scl	Yes	sirohydrochlorin	C42H39N4O16	-7		C05778	"KEGG - C05778
Neutral MF = C42H46N4O16
SMP
Checked N-groups, JLR"	C42H39N4O16	-7	No Energy	No Energy									-7	1.00E+07	1.00E+07
3735	scsertrna	Yes	L-Selenocysteinyl-tRNA(Ser)	C3H6NO2R	1	16561-29-8	C05173	KEGG - C05173	C13H17N6O4RSe	0	-34.6506	13.2619									0	-34.6506	13.2619
1247	seln	No	Selenide	HSe	-1	531-44-2	C01528	"KEGG - C01528
Neutral-H2Se
JLR"	HSe	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
3734	selnp	No	Selenophosphate	H2O3PSe	-1	16561-29-8	C05172	"KEGG - C05172
Neutral H3O3PSe
JLR"	H2O3PSe	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
11861	seramp	No	L-seryl-AMP	C13H19N6O9P	0			"See EcoCyc- L-seryl-AMP
JLR
Checked N-groups JLR"	C13H20N6O9P	1	-342.413	12.1183									1	-342.413	12.1183
512	ser-D	No	D-Serine	C3H7NO3	0	312-84-5	C00740	"KEGG - C00740
Neutral MF = C3H7NO3
SMP
CHS
Changed according to Genomatica JLR
"	C3H7NO3	0	-122.336	2.38267									0	-122.336	2.38267
339	ser-L	No	L-Serine	C3H7NO3	0	56-45-1	C00065	"KEGG - C00065
Neutral MF = C3H7NO3
SMP
CHS
Changed according to Genomatica JLR"	C3H7NO3	0	-122.336	2.38267									0	-122.336	2.38267
7102	sertrna	Yes	L-Seryl-tRNA(Ser)	C3H6NO2R	1		C02553	"KEGG - C02553
SMP
adjusted for Genomatica's change to aa - NCD"	C13H17N6O5R	0	-73.9424	13.1504									0	-73.9424	13.1504
9015	Sfglutth	Yes	S-Formylglutathione	C11H16N3O7S	-1		C01031	"KEGG - C01031
NCD
changed to protonated form, added +1 charge - NCD"	C11H16N3O7S	-1	-229.956	7.65969									-1	-229.956	7.65969
517	sheme	No	Siroheme	C42H36FeN4O16	-8		C00748	"KEGG - C00748
Neutral MF = C42H46FeN4O16
Chemfinder formula is incorrect
SMP
CHS
Checked N-groups, removed H from two N's in ring, JLR"	C42H36FeN4O16	-8	No Energy	No Energy									-8	1.00E+07	1.00E+07
107	skm	No	Shikimate	C7H9O5	-1	138-59-0	C00493	"KEGG - C00493
Neutral MF = C7H10O5
SMP
CHS
"	C7H9O5	-1	-172.575	6.42128									-1	-172.575	6.42128
2188	skm5p	No	Shikimate 5-phosphate	C7H8O8P	-3		C03175	"KEGG - C03175
Neutral MF = C7H11O8P
SMP
CHS
"	C7H9O8P	-2	-383.897	6.04427									-2	-383.897	6.04427
2690	sl26da	No	"N-Succinyl-LL-2,6-diaminoheptanedioate"	C11H16N2O7	-2		C04421	"KEGG - C04421
Neutral MF = C11H18N2O7
SMP
CHS
Changed according to Genomatica JLR"	C11H16N2O7	-2	-265.95	5.9012									-2	-265.95	5.9012
3943	sl2a6o	No	N-Succinyl-2-L-amino-6-oxoheptanedioate	C11H12NO8	-3		C04462	"KEGG - C04462
Neutral MF = C11H15NO8
SMP
CHS
Checked N-groups JLR"	C11H12NO8	-3	-293.278	5.75673									-3	-293.278	5.75673
22358	so2	Yes	sulfur dioxide	O2S	0		C09306	AMF	O2S	0	No Energy	No Energy									0	1.00E+07	1.00E+07
1060	so3	No	Sulfite	O3S	-2	7782-99-2	C00094	"KEGG - C00094
Neutral MF = H2O3S (sulfurous acid)
SMP
CHS"	HO3S	-1	No Energy	No Energy									-1	1.00E+07	1.00E+07
335	so4	No	Sulfate	O4S	-2	7664-93-9	C00059	"KEGG - C00059
Neutral MF = H2O4S (sulfuric acid)
SMP
CHS"	O4S	-2	-177.9	0.5									-2	-177.9	0.5
161	spmd	No	Spermidine	C7H22N3	3	124-20-9	C00315	"KEGG - C00315
Neutral Compound
SMP
CHS
Changed according to Genomatica JLR"	C7H22N3	3	-0.12185	5.9									3	-0.12185	5.9
4303	ssaltpp	No	Succinate semialdehyde-thiamin diphosphate anion	C16H21N4O10P2S	-3		C05816	"KEGG - C05816
Neutral MF  = C16H24N4O10P2S
SMP
JLR
Checked N-groups JLR"	C16H22N4O10P2S	-2	-464.093	12.7614									-2	-464.093	12.7614
8781	stcoa	Yes	Stearoyl-CoA (n-C18:0CoA)	C39H66N7O17P3S	-4	362-66-3	C00412	"KEGG - C00412
NCD
SMP (2/7/03)
C18:0 + CoA"	C39H67N7O17P3S	-3	-767.316	21.349									-3	-767.316	21.349
1860	suc6p	No	Sucrose 6-phosphate	C12H21O14P	-2		C02591	"KEGG - C02591
Neutral MF = C12H23O14P
SMP
CHS"	C12H22O14P	-1	-589.477	15.1505									-1	-589.477	15.1505
2466	sucarg	No	N2-Succinyl-L-arginine	C10H17N4O5	-1	1758-80-1	C03296	"KEGG - C03296
Neutral:C10H18N4O5
JLR
Checked N-groups JLR"	C10H17N4O5	-1	-173.498	7.16169									-1	-173.498	7.16169
2052	sucbz	No	o-Succinylbenzoate	C11H8O5	-2		C02730	"KEGG - C02730
Neutral MF = C11H10O5
SMP
CHS"	C11H8O5	-2	-157.518	8.80757									-2	-157.518	8.80757
325	succ	No	Succinate	C4H4O4	-2	110-15-6	C00042	"KEGG - C00042
Neutral MF = C4H6O4
SMP
CHS"	C4H4O4	-2	-163.002	2.28439									-2	-163.002	2.28439
1058	succoa	No	Succinyl-CoA	C25H35N7O19P3S	-5	604-98-8	C00091	"KEGG - C00091
Neutral MF = C25H40N7O19P3S
SMP
CHS
checked N groups - NCD"	C25H36N7O19P3S	-4	-859.31	16.1394									-4	-859.31	16.1394
4396	sucglu	No	N2-Succinyl-L-glutamate	C9H10NO7	-3	2009-64-5	C05931	"KEGG - C05931
Neutral: C9H13NO7
JLR
Checked N-groups JLR"	C9H10NO7	-3	-266.451	4.94897									-3	-266.451	4.94897
10684	sucgsa	No	N2-Succinyl-L-glutamate 5-semialdehyde	C9H11NO6	-2	2009-64-5	C05932	"KEGG - C05932
Neutral: C9H13NO6
JLR
Checked N-groups JLR"	C9H11NO6	-2	-213.937	4.62658									-2	-213.937	4.62658
890	suchms	No	O-Succinyl-L-homoserine	C8H12NO6	-1	1492-23-5	C01118	"KEGG - C01118
Neutral MF = C8H13NO6
SMP
CHS
Changed according to Genomatica JLR"	C8H12NO6	-1	-235.449	4.15687									-1	-235.449	4.15687
11414	sucorn	No	N2-Succinyl-L-ornithine	C9H15N2O5	-1	80102-04-1	C03415	"KEGG - C03415
Neutral: C9H16N2O5
JLR
Checked N-groups JLR"	C9H15N2O5	-1	-189.031	5.12921									-1	-189.031	5.12921
1056	sucr	Yes	Sucrose	C12H22O11	0	57-50-1	C00089	KEGG - C00089	C12H22O11	0	-376.966	15.2483									0	-376.966	15.2483
284	sucsal	No	Succinic semialdehyde	C4H5O3	-1	692-29-5	C00232	"KEGG - C00232
Neutral MF = C4H6O3
SMP
CHS"	C4H5O3	-1	-110.488	1.95688									-1	-110.488	1.95688
22150	sulfac	Yes	sulfoacetate	C2H2O5S	-2			AMF	C2H2O5S	-2	-207.882	2.33208									-2	-207.882	2.33208
26049	t3c11vaceACP	Yes	trans-3-cis-11-vacceoyl-[acyl-carrier protein]	C29H51N2O8PRS	-1			AMF	C29H51N2O8PRS	-1	-302.952	14.7723									-1	-302.952	14.7723
26047	t3c5ddeceACP	Yes	trans-3-cis-5-dodecenoyl-[acyl-carrier protein]	C23H39N2O8PRS	-1			AMF	C23H39N2O8PRS	-1	-308.426	11.9027									-1	-308.426	11.9027
26041	t3c7mrseACP	Yes	trans-3-cis-7-myristoleoyl-[acyl-carrier protein]	C25H43N2O8PRS	-1			AMF	C25H43N2O8PRS	-1	-306.602	12.7884									-1	-306.602	12.7884
26048	t3c9palmeACP	Yes	trans-3-cis-9-palmitoleoyl-[acyl-carrier protein]	C27H47N2O8PRS	-1			AMF	C27H47N2O8PRS	-1	-304.777	13.7499									-1	-304.777	13.7499
6458	tag6p-D	No	D-Tagatose 6-phosphate	C6H11O9P	-2		C01097	"KEGG - C01097
Neutral MF=C6H13O9P
JLR"	C6H12O9P	-1	-430.984	6.84677									-1	-430.984	6.84677
11517	tagdp-D	No	"D-Tagatose 1,6-biphosphate"	C6H10O12P2	-4		C03785	"KEGG - C03785
Neutral MF = C6H14O12P2
NCD"	C6H12O12P2	-2	-643.494	7.19722									-2	-643.494	7.19722
379	tagur	No	D-Tagaturonate	C6H9O7	-1	None	C00558	"KEGG - C00558
Neutral MF = C6H10O7
SMP
CHS"	C6H9O7	-1	-261.376	6.66261									-1	-261.376	6.66261
746	tartr-L	No	L-tartrate	C4H4O6	-2	87-69-4	C00898	"KEGG - C00898
Neutral-C4H6O6
JLR"	C4H4O6	-2	-238.669	3.84006									-2	-238.669	3.84006
293	taur	No	Taurine	C2H7NO3S	0	107-35-7	C00245	"KEGG - C00245
Neutral MF = C2H7NO3S
SMP
Changed according to Genomatica JLR"	C2H7NO3S	0	-130.462	2.81376									0	-130.462	2.81376
1428	tcynt	No	Thiocyanate	CNS	-1	463-56-9	C01755	"KEGG - C01755
Neutral-CHNS
JLR
Checked N-groups JLR"	CHNS	0	No Energy	No Energy									0	1.00E+07	1.00E+07
3802	td2coa	Yes	trans-Tetradec-2-enoyl-CoA	C35H56N7O17P3S	-4		C05273	"KEGG - C05273
Neutral MF = C35H60N7O17P3S
SMP"	C35H57N7O17P3S	-3	-751.92	18.8538									-3	-751.92	18.8538
1862	tdcoa	Yes	Tetradecanoyl-CoA (n-C14:0CoA)	C35H58N7O17P3S	-4		C02593	"KEGG - C02593
Neutral MF = C35H62N7O17P3S
SMP
changed compound class from peptides to fatty acids - NCD"	C35H59N7O17P3S	-3	-770.965	19.5673									-3	-770.965	19.5673
4251	tddec2eACP	Yes	trans-Dodec-2-enoyl-[acyl-carrier protein]	C23H41N2O8PRS	-1	8/6/83	C05758	"KEGG - C05758
AMF"	C23H41N2O8PRS	-1	-327.471	12.3625									-1	-327.471	12.3625
5939	tdeACP	No	cis-tetradec-7-enoyl-[acyl-carrier protein] (n-C14:1)	C25H45N2O8PRS	-1			"tv
JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)
AMF"	C25H45N2O8PRS	-1	-327.24	13.7482									-1	-327.24	13.7482
4248	tdec2eACP	Yes	trans-Dec-2-enoyl-[acyl-carrier protein]	C21H37N2O8PRS	-1	8/6/83	C05754	"KEGG - C05754
AMF"	C21H37N2O8PRS	-1	-329.296	11.4438									-1	-329.296	11.4438
8779	tdecoa	Yes	Tetradecenoyl-CoA (n-C14:1CoA)	C35H56N7O17P3S	-4			NCD	C35H57N7O17P3S	-3	-751.92	18.8538									-3	-751.92	18.8538
3035	thdp	No	"2,3,4,5-Tetrahydrodipicolinate"	C7H7NO4	-2	52-52-8	C03972	"KEGG - C03972
Neutral MF = C7H9NO4
SMP
CHS
Checked N-groups JLR"	C7H7NO4	-2	-130.152	5.83762									-2	-130.152	5.83762
4243	thex2eACP	Yes	trans-Hex-2-enoyl-[acyl-carrier protein]	C17H29N2O8PRS	-1	8/6/83	C05748	"KEGG - C05748
AMF"	C17H29N2O8PRS	-1	-332.946	9.90735									-1	-332.946	9.90735
1065	thf	No	"5,6,7,8-Tetrahydrofolate"	C19H21N7O6	-2	135-16-0	C00101	"KEGG - C00101
Merged with C03041
Neutral MF = C19H23N7O6
SMP
CHS
Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR
Pipeline Pilot indicates this N is not charged JLR"	C19H21N7O6	-2	-119.638	14.3261									-2	-119.638	14.3261
210	thm	No	Thiamin	C12H17N4OS	1	67-03-8	C00378	"KEGG - C00378
+1 Charged Compound
SMP
CHS
neutral forumula was originally listed - NCD
Changed according to Genomatica JLR"	C12H17N4OS	1	55.5927	12.1187									1	55.5927	12.1187
866	thmmp	No	Thiamin monophosphate	C12H16N4O4PS	-1	532-40-1	C01081	"KEGG - C01081
+1 Charged MF = C12H18N4O4PS
SMP
CHS
Checked N-groups JLR"	C12H17N4O4PS	0	-156.918	12.1591									0	-156.918	12.1591
341	thmpp	No	Thiamine diphosphate	C12H16N4O7P2S	-2	154-87-0	C00068	"KEGG - C00068
Neutral MF = C12H19N4O7P2S
SMP
CHS
Changed charged formula; had wrong number of hydrogens -NCD
Checked N-groups JLR"	C12H17N4O7P2S	-1	-364.771	12.2184									-1	-364.771	12.2184
662	thr-D	Yes	D-Threonine	C4H9NO3	0	632-20-2	C00820	"KEGG - C00820
Neutral MF = C4H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO3	0	-122.939	3.29766									0	-122.939	3.29766
253	thr-L	No	L-Threonine	C4H9NO3	0	72-19-5	C00188	"KEGG - C00188
Neutral MF = C4H9NO3
SMP
CHS
Changed according to Genomatica JLR"	C4H9NO3	0	-122.939	3.29766									0	-122.939	3.29766
16068	thrp	Yes	L-Threonine O-3-phosphate	C4H8NO6P	-2		C12147	"AMF
C12147"	C4H9NO6P	-1	-334.261	3.43964									-1	-334.261	3.43964
7108	thrtrna	Yes	L-Threonyl-tRNA(Thr)	C4H8NO2R	1		C02992	"KEGG - C02992
SMP
adjusted for Genomatica's change to aa - NCD
"	C14H19N6O5R	0	-74.5453	13.4182									0	-74.5453	13.4182
246	thym	No	Thymine	C5H6N2O2	0	65-71-4	C00178	"KEGG - C00178
Neutral Compound
SMP
CHS"	C5H6N2O2	0	-54.7102	7.3074									0	-54.7102	7.3074
5269	thymd	No	Thymidine	C10H14N2O5	0	50-89-5	C00214	"KEGG - C00214
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H14N2O5	0	-137.102	8.80903									0	-137.102	8.80903
383	tma	No	trimethylamine	C3H10N	1	75-50-3	C00565	"KEGG - C00565
pKa=9.8
Checked N-groups JLR"	C3H10N	1	7.94473	3.69537									1	7.94473	3.69537
882	tmao	No	Trimethylamine N-oxide	C3H9NO	0	1184-78-7	C01104	"KEGG - C01104
Zwitter ion, pKa =4.65
Checked N-groups JLR"	C3H10NO	1	No Energy	No Energy									1	1.00E+07	1.00E+07
4252	tmrs2eACP	Yes	trans-Tetradec-2-enoyl-[acyl-carrier protein]	C25H45N2O8PRS	-1	8/6/83	C05760	"KEGG - C05760
AMF"	C25H45N2O8PRS	-1	-325.647	13.3546									-1	-325.647	13.3546
11005	toct2eACP	Yes	trans-Oct-2-enoyl-[acyl-carrier protein]	C19H33N2O8PRS	-1	8/6/83	C05751	"KEGG - C05751
AMF"	C19H33N2O8PRS	-1	-331.121	10.6177									-1	-331.121	10.6177
26131	toctd2eACP	Yes	trans-octadec-2-enoyl-[acyl-carrier protein]	C29H53N2O8PRS	-1			AMF	C29H53N2O8PRS	-1	-321.997	15.502									-1	-321.997	15.502
4255	tpalm2eACP	Yes	trans-Hexadec-2-enoyl-[acyl-carrier protein]	C27H49N2O8PRS	-1	8/6/83	C05763	"KEGG - C05763
AMF"	C27H49N2O8PRS	-1	-323.822	14.4051									-1	-323.822	14.4051
181	trdox	No	Oxidized thioredoxin	X	0		C00343	"KEGG - C00343
SMP"	C6H7NO2R2S2	0	-45.3635	7.03074									0	-45.3635	7.03074
180	trdrd	No	Reduced thioredoxin	XH2	0		C00342	"KEGG - C00342
SMP"	C6H9NO2R2S2	0	-45.5437	5.99427									0	-45.5437	5.99427
867	tre	No	Trehalose	C12H22O11	0	99-20-7	C01083	"KEGG - C01083
Neutral Compound
SMP"	C12H22O11	0	-376.526	17.7716									0	-376.526	17.7716
454	tre6p	No	"alpha,alpha'-Trehalose 6-phosphate"	C12H21O14P	-2	4484-88-2	C00689	"KEGG - C00689
Neutral MF = C12H23O14P
SMP
CHS"	C12H22O14P	-1	-589.036	17.7436									-1	-589.036	17.7436
7097	trnaala	Yes	tRNA(Ala)	R	0		C01635	"KEGG - C01635
SMP
"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1333	trnaarg	Yes	tRNA(Arg)	R	0		C01636	"KEGG - C01636
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
11133	trnaasn	Yes	tRNA(Asn)	R	0		C01637	"KEGG - C01637
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1334	trnaasp	Yes	tRNA(Asp)	R	0		C01638	"KEGG - C01638
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1335	trnacys	Yes	tRNA(Cys)	R	0		C01639	"KEGG - C01639
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1336	trnagln	Yes	tRNA(Gln)	R	0		C01640	"KEGG - C01640
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
46	trnaglu	No	tRNA (Glu)	R	0	None	C01641	"KEGG - C01641
X = (C5H8O6PR)n
Represent as uncharged species
SMP; MF changed on May 7, 2002
CHS"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1337	trnagly	Yes	tRNA(Gly)	R	0		C01642	"KEGG - C01642
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1338	trnahis	Yes	tRNA(His)	R	0		C01643	"KEGG - C01643
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1339	trnaile	Yes	tRNA(Ile)	R	0		C01644	"KEGG - C01644
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1340	trnaleu	Yes	tRNA(Leu)	R	0		C01645	"KEGG - C01645
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
11123	trnalys	Yes	tRNA(Lys)	R	0		C01646	"KEGG - C01646
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1341	trnamet	Yes	tRNA(Met)	R	0		C01647	"KEGG - C01647
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1342	trnaphe	Yes	tRNA(Phe)	R	0		C01648	"KEGG - C01648
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1343	trnapro	Yes	tRNA(Pro)	R	0		C01649	"KEGG - C01649
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
15987	trnasecys	Yes	tRNA(SeCys)	R	0	7625-23-2		0	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1344	trnaser	Yes	tRNA(Ser)	R	0		C01650	"KEGG - C01650
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1345	trnathr	Yes	tRNA(Thr)	R	0		C01651	"KEGG - C01651
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1346	trnatrp	Yes	tRNA(Trp)	R	0		C01652	"KEGG - C01652
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
7092	trnatyr	Yes	tRNA(Tyr)	R	0		C00787	"KEGG - C00787
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1347	trnaval	Yes	tRNA(Val)	R	0		C01653	"KEGG - C01653
SMP"	C10H12N5O3R	0	-7.09865	12.6905									0	-7.09865	12.6905
1047	trp-L	No	L-Tryptophan	C11H12N2O2	0	73-22-3	C00078	"KEGG - C00078
Neutral MF = C11H12N2O2
SMP
CHS
Changed according to Genomatica JLR"	C11H12N2O2	0	-26.912	8.81413									0	-26.912	8.81413
7113	trptrna	Yes	L-Tryptophanyl-tRNA(Trp)	C11H11N2OR	1		C03512	"KEGG - C03512
SMP
adjusted for Genomatica's change to aa - NCD
"	C21H23N7O4R	1	16.9582	16.3768									1	16.9582	16.3768
164	tsul	No	Thiosulfate	O3S2	-2		C00320	"KEGG - C00320
Neutral MF = H2O3S2
SMP"	HO3S2	-1	-127.512	2.84016									-1	-127.512	2.84016
6302	ttdca	No	tetradecanoate (n-C14:0)	C14H27O2	-1	544-63-8	C06424	"KEGG C06424
Neutral MF = C14H28O2
SMP
saturated fatty acid, 14 carbons
changed compound class from peptides to fatty acid - NCD"	C14H27O2	-1	-74.657	8.21076									-1	-74.657	8.21076
8772	ttdcea	No	tetradecenoate (n-C14:1)	C14H25O2	-1			"monounsaturated fatty acid, 14 carbons
NCD"	C14H25O2	-1	-57.2055	7.80231									-1	-57.2055	7.80231
16112	tungs	Yes	tungstate	O4W1	-2			AMF	O4W1	-2	No Energy	No Energy									-2	1.00E+07	1.00E+07
100	tym	Yes	Tyramine	C8H12NO	1	51-67-2	C00483	"KEGG - C00483
AMF"	C8H12NO	1	-10.8152	9.45064									1	-10.8152	9.45064
1051	tyr-L	No	L-Tyrosine	C9H11NO3	0	60-18-4	C00082	"KEGG - C00082
Neutral MF = C9H11NO3
SMP
CHS
Changed according to Genomatica JLR"	C9H11NO3	0	-88.6472	9.49843									0	-88.6472	9.49843
5421	tyrp	Yes	Phosphotyrosine	C9H10NO6P	-2	7625-23-2	C06501	KEGG - C06501	C9H11NO6P	-1	-301.623	8.8033									-1	-301.623	8.8033
7105	tyrtrna	Yes	L-Tyrosyl-tRNA(Tyr)	C9H10NO2R	1		C02839	"KEGG - C02839
SMP
adjusted for Genomatica's change to aa - NCD
"	C19H22N6O5R	1	-44.777	15.8208									1	-44.777	15.8208
3329	u23ga	No	"UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine"	C43H75N3O20P2	-2		C04652	"KEGG - C04652
Neutral MF = C43H77N3O20P2
SMP
CHS
Checked N-groups JLR"	C43H75N3O20P2	-2	-835.471	24.4036									-2	-835.471	24.4036
10924	u3aga	No	UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine	C31H51N3O19P2	-2		C04738	"KEGG - C04738
Neutral MF = C31H53N3O19P2
SMP
CHS
Checked N-groups JLR"	C31H51N3O19P2	-2	-808.586	19.8266									-2	-808.586	19.8266
4462	u3hga	No	UDP-3-O-(3-hydroxytetradecanoyl)-D-glucosamine	C29H50N3O18P2	-1		C06022	"KEGG - C06022
Neutral MF = C29H51N3O18P2
SMP
CHS
Checked N-groups JLR"	C29H50N3O18P2	-1	-782.945	19.3094									-1	-782.945	19.3094
4370	uaagmda	No	"Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala"	C95H152N8O28P2	-4		C05898	"KEGG - C05898
Neutral MF = C95H156N8O28P2
SMP
Changed according to Genomatica JLR"	C95H152N8O28P2	-4	-842.282	43.3636									-4	-842.282	43.3636
3312	uaccg	No	UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine	C20H26N3O19P2	-3		C04631	"KEGG - C04631
Neutral MF = C20H29N3O19P2
SMP
CHS
Checked N-groups JLR"	C20H26N3O19P2	-3	-792.301	17.6555									-3	-792.301	17.6555
326	uacgam	No	UDP-N-acetyl-D-glucosamine	C17H25N3O17P2	-2		C00043	"KEGG - C00043
KEGG glycan: G10610
Neutral MF = C17H27N3O17P2
SMP
CHS
Checked N-groups JLR"	C17H25N3O17P2	-2	-747.064	17.6185									-2	-747.064	17.6185
764	uacmam	No	UDP-N-acetyl-D-mannosamine	C17H25N3O17P2	-2		C01170	"KEGG - C01170
Neutral MF = C17H27N3O17P2
SMP
CHS
Kegg Picture is missing the N on the 2-C of the sugar
Checked N-groups JLR"	C17H25N3O17P2	-2	-747.064	17.6185									-2	-747.064	17.6185
4636	uacmamu	No	UDP-N-acetyl-D-mannosaminouronate	C17H22N3O18P2	-3	90-02-8	C06240	"KEGG - C06240
Neutral-C17H25N3O18P2
JLR
Checked N-groups JLR"	C17H22N3O18P2	-3	-789.967	17.5757									-3	-789.967	17.5757
4369	uagmda	No	"Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine"	C87H139N7O23P2	-4		C05897	"KEGG - C05897
Neutral MF = C87H143N7O23P2
SMP
Changed according to Genomatica JLR"	C87H139N7O23P2	-4	-694.852	38.8144									-4	-694.852	38.8144
942	uama	No	UDP-N-acetylmuramoyl-L-alanine	C23H33N4O20P2	-3		C01212	"KEGG - C01212
Neutral MF = C23H36N4O20P2
SMP
CHS
Checked N-groups JLR"	C23H33N4O20P2	-3	-835.717	18.8108									-3	-835.717	18.8108
456	uamag	No	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate	C28H39N5O23P2	-4		C00692	"KEGG - C00692
Neutral MF = C28H43N5O23P2
SMP
CHS
Checked N-groups JLR"	C28H39N5O23P2	-4	-939.165	20.515									-4	-939.165	20.515
686	uamr	No	UDP-N-acetylmuramate	C20H28N3O19P2	-3		C01050	"KEGG - C01050
Neutral MF = C20H31N3O19P2
SMP
CHS
Checked N-groups JLR"	C20H28N3O19P2	-3	-809.664	17.5836									-3	-809.664	17.5836
2729	udcpdp	No	Undecaprenyl diphosphate	C55H89O7P2	-3		C03543	"KEGG - C03543
Neutral MF = C55H92O7P2
SMP
CHS"	C55H90O7P2	-2	-200.943	28.14									-2	-200.943	28.14
185	udcpp	No	Undecaprenyl phosphate	C55H89O4P	-2		C00348	"KEGG - C00348
Neutral MF = C55H91O4P
SMP
CHS"	C55H90O4P	-1	6.91037	28.1142									-1	6.91037	28.1142
477	udp	No	UDP	C9H11N2O12P2	-3	58-98-0	C00015	"KEGG - C00015
Neutral MF = C9H14N2O12P2
SMP
CHS"	C9H12N2O12P2	-2	-600.31	9.93096									-2	-600.31	9.93096
10912	udpacgal	Yes	UDP-N-acetyl-D-galactosamine	C17H25N3O17P2	-2	None	C00203	"KEGG - C00203
changed to proper charge - NCD"	C17H25N3O17P2	-2	-747.064	17.6185									-2	-747.064	17.6185
316	udpg	No	UDPglucose	C15H22N2O17P2	-2		C00029	"KEGG - C00029
Neutral MF = C15H24N2O17P2
SMP
CHS"	C15H22N2O17P2	-2	-757.933	17.4025									-2	-757.933	17.4025
331	udpgal	No	UDPgalactose	C15H22N2O17P2	-2		C00052	"KEGG - C00052
Neutral MF = C15H24N2O17P2
SMP
CHS"	C15H22N2O17P2	-2	-757.933	17.4025									-2	-757.933	17.4025
1996	udpgalfur	No	"UDP-D-galacto-1,4-furanose"	C15H22N2O17P2	-2	638-23-3	C03733	"KEGG - C03733
Neutral-C15H24N2O17P2
JLR
Checked N-groups JLR"	C15H22N2O17P2	-2	-758.045	16.3294									-2	-758.045	16.3294
241	udpglcur	No	UDP-D-glucuronate	C15H19N2O18P2	-3		C00167	"KEGG - C00167
Neutral-C15H22N2O18P2
JLR
Checked N-groups JLR"	C15H19N2O18P2	-3	-800.836	17.3592									-3	-800.836	17.3592
22054	udpLa4fn	Yes	uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose	C15H21N3O16P2	-2			AMF	C15H22N3O16P2	-1	-711.805	15.0641									-1	-711.805	15.0641
22046	udpLa4n	Yes	uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose	C14H22N3O15P2	-1			AMF	C14H22N3O15P2	-1	-684.166	15.9462									-1	-684.166	15.9462
22045	udpLa4o	Yes	UDP-4-keto-pyranose	C14H18N2O16P2	-2			AMF	C14H18N2O16P2	-2	-714.453	15.2664									-2	-714.453	15.2664
10726	ugmd	No	"UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate"	C35H51N7O26P2	-4		C04877	"KEGG - C04877
Neutral MF = C35H55N7O26P2
SMP
Changed according to Genomatica JLR"	C35H51N7O26P2	-4	-1042.11	23.0877									-4	-1042.11	23.0877
3599	ugmda	No	"UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine"	C41H61N9O28P2	-4		C04882	"KEGG - C04882
Neutral MF = C41H65N9O28P2
SMP
Changed according to Genomatica JLR"	C41H61N9O28P2	-4	-1094.22	27.7068									-4	-1094.22	27.7068
22056	uLa4fn	Yes	undecaprenyl phosphate-4-amino-4-formyl-L-arabinose	C61H99N1O8P1	-1			AMF	C61H100NO8P	0	-104.584	28.9332									0	-104.584	28.9332
22047	uLa4n	Yes	undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose	C60H100N1O7P1	0			AMF	C60H100NO7P	0	-76.9459	29.0994									0	-76.9459	29.0994
21516	um4p	Yes	"UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine"	C38H56N8O27P2	-4			AMF	C38H56N8O27P2	-4	-1068.17	25.295									-4	-1068.17	25.295
1068	ump	No	UMP	C9H11N2O9P	-2	58-97-9	C00105	"KEGG - C00105
Neutral MF = C9H13N2O9P
SMP
CHS"	C9H12N2O9P	-1	-392.457	9.8579									-1	-392.457	9.8579
9105	unaga	No	Undecaprenyl diphospho N-acetyl-glucosamine	C63H103NO12P2	-2			"Not in Kegg
Neutral-C63H105NO12P2
JLR
Checked N-groups"	C63H103NO12P2	-2	-347.697	30.2762									-2	-347.697	30.2762
9106	unagamu	No	Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate	C71H113N2O18P2	-3			"No Kegg entry
Neutral-C71H116N2O18P2
JLR
Checked N-groups JLR"	C71H113N2O18P2	-3	-538.03	34.2061									-3	-538.03	34.2061
9111	unagamuf	No	"Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose"	C79H126N3O22P2	-3			"No Kegg entry
Neutral-C79H129N3O22P2
JLR
Checked N-groups JLR"	C79H126N3O22P2	-3	-620.607	38.3596									-3	-620.607	38.3596
687	uppg3	No	Uroporphyrinogen III	C40H36N4O16	-8	1976-85-8	C01051	"KEGG - C01051
Neutral MF = C40H44N4O16
SMP
CHS
Checked N-groups JLR"	C40H36N4O16	-8	No Energy	No Energy									-8	1.00E+07	1.00E+07
1069	ura	No	Uracil	C4H4N2O2	0	66-22-8	C00106	"KEGG - C00106
Neutral Compound
SMP
CHS"	C4H4N2O2	0	-57.3929	7.37814									0	-57.3929	7.37814
199	urate	Yes	Urate	C5H4N4O3	0	69-93-2	C00366	"KEGG - C00366
Neutral Compound
SMP
CHS"	C5H4N4O3	0	-87.1441	14.0003									0	-87.1441	14.0003
9076	urdglyc	No	(-)-Ureidoglycolate	C3H5N2O4	-1		C00603	"KEGG - C00603
Neutral- C4H6N2O4
JLR
Checked N-groups JLR"	C3H5N2O4	-1	-159.17	4.82366									-1	-159.17	4.82366
1054	urea	No	Urea	CH4N2O	0	57-13-6	C00086	"KEGG - C00086
Neutral Compound
SMP
CHS
Checked N-groups JLR"	CH4N2O	0	-47.04	0.5									0	-47.04	0.5
10727	uri	No	Uridine	C9H12N2O6	0	58-96-8	C00299	"KEGG - C00299
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C9H12N2O6	0	-179.946	9.80798									0	-179.946	9.80798
345	utp	No	UTP	C9H11N2O15P3	-4	63-39-8	C00075	"KEGG - C00075
Neutral MF = C9H15N2O15P3
SMP
CHS"	C9H12N2O15P3	-3	-808.163	10.147									-3	-808.163	10.147
250	val-L	No	L-Valine	C5H11NO2	0	72-18-4	C00183	"KEGG - C00183
Neutral MF = C5H11NO2
SMP
CHS
Changed according to Genomatica JLR"	C5H11NO2	0	-83.7161	3.51156									0	-83.7161	3.51156
7103	valtrna	Yes	L-Valyl-tRNA(Val)	C5H10NOR	1		C02554	"KEGG - C02554
SMP
adjusted for Genomatica's change to aa - NCD
"	C15H22N6O4R	1	-39.8458	13.0957									1	-39.8458	13.0957
216	xan	No	Xanthine	C5H4N4O2	0	69-89-6	C00385	"KEGG - C00385
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C5H4N4O2	0	-27.8506	10.9296									0	-27.8506	10.9296
1028	xdp	Yes	XDP	C10H11N4O12P2	-3	7440-23-5	C01337	"KEGG - C01337
AMF"	C10H12N4O12P2	-2	-570.768	12.3822									-2	-570.768	12.3822
436	xmp	No	Xanthosine 5'-phosphate	C10H11N4O9P	-2	523-98-8	C00655	"KEGG - C00655
Neutral MF = C10H13N4O9P
SMP
CHS
Checked N-groups JLR"	C10H12N4O9P	-1	-362.914	12.3237									-1	-362.914	12.3237
459	xtp	Yes	XTP	C10H11N4O15P3	-4		C00700	"KEGG - C00700
IT"	C10H12N4O15P3	-3	-778.621	12.5561									-3	-778.621	12.5561
10906	xtsn	No	Xanthosine	C10H12N4O6	0	146-80-5	C01762	"KEGG - C01762
Neutral Compound
SMP
CHS
Checked N-groups JLR"	C10H12N4O6	0	-150.404	12.2838									0	-150.404	12.2838
283	xu5p-D	No	D-Xylulose 5-phosphate	C5H9O8P	-2	None	C00231	"KEGG - C00231
Neutral MF = C5H11O8P
SMP
CHS"	C5H10O8P	-1	-393.114	4.2008									-1	-393.114	4.2008
2462	xu5p-L	No	L-Xylulose 5-phosphate	C5H9O8P	-2	None	C03291	"KEGG - C03291
Neutral MF = C5H11O8P
Different from xu5p-D (C00231): Change abbv from xu5p to x5p-L
SMP
CHS"	C5H10O8P	-1	-393.114	4.2008									-1	-393.114	4.2008
248	xyl-D	No	D-Xylose	C5H10O5	0	58-86-6	C00181	"KEGG - C00181
Neutral Compound
SMP
CHS"	C5H10O5	0	-180.969	8.29386									0	-180.969	8.29386
157	xylu-D	No	D-Xylulose	C5H10O5	0	551-84-8	C00310	"KEGG - C00310
Neutral Compound
SMP
CHS"	C5H10O5	0	-181.216	5.88651									0	-181.216	5.88651
159	xylu-L	Yes	L-Xylulose	C5H10O5	0	527-50-4	C00312	"KEGG - C00312
Neutral Compound
SMP
CHS"	C5H10O5	0	-181.216	5.88651									0	-181.216	5.88651
324	zn2	Yes	Zinc	Zn	2	7440-66-6	C00038	KEGG - C00038	Zn	2	No Energy	No Energy									2	1.00E+07	1.00E+07