FMO DATABASE

FMODB ID: 3MG2L

Calculation Name: 3C1B-D-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-{[(2r)-2-amino-2-carboxyethyl]sulfanyl}-n,n,n-trimethylethanaminium

Ligand 3-letter code: ML3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C1B

Chain ID: D

ChEMBL ID:

UniProt ID: P06897

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-585979.438051
FMO2-HF: Nuclear repulsion	549196.001387
FMO2-HF: Total energy	-36783.436664
FMO2-MP2: Total energy	-36891.607979

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1228:LYS)

Summations of interaction energy for fragment #1(A:1228:LYS)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
175.297	176.941	0.012	-0.838	-0.818	-0.003

Interaction energy analysis for fragmet #1(A:1228:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.838 / q_NPA : 1.907

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	1230	ARG	1	0.894	0.948	3.360	44.554	46.198	0.012	-0.838	-0.818	-0.003
4	A	1231	LYS	1	0.992	0.994	5.364	68.794	68.794	0.000	0.000	0.000	0.000
5	A	1232	GLU	-1	-0.849	-0.908	7.244	-44.209	-44.209	0.000	0.000	0.000	0.000
6	A	1233	SER	0	-0.026	-0.020	10.821	1.527	1.527	0.000	0.000	0.000	0.000
7	A	1234	TYR	0	0.076	0.033	13.816	0.117	0.117	0.000	0.000	0.000	0.000
8	A	1235	ALA	0	0.039	0.009	15.410	1.593	1.593	0.000	0.000	0.000	0.000
9	A	1236	ILE	0	0.004	-0.007	15.687	1.547	1.547	0.000	0.000	0.000	0.000
10	A	1237	TYR	0	-0.034	-0.018	17.103	0.850	0.850	0.000	0.000	0.000	0.000
11	A	1238	VAL	0	0.047	0.014	20.574	1.202	1.202	0.000	0.000	0.000	0.000
12	A	1239	TYR	0	0.018	0.003	20.779	1.183	1.183	0.000	0.000	0.000	0.000
13	A	1240	LYS	1	0.930	0.971	21.511	27.746	27.746	0.000	0.000	0.000	0.000
14	A	1241	VAL	0	0.043	0.024	24.882	0.754	0.754	0.000	0.000	0.000	0.000
15	A	1242	LEU	0	-0.015	-0.011	24.943	0.692	0.692	0.000	0.000	0.000	0.000
16	A	1243	LYS	1	0.821	0.894	26.021	22.142	22.142	0.000	0.000	0.000	0.000
17	A	1244	GLN	0	-0.033	-0.011	28.562	0.364	0.364	0.000	0.000	0.000	0.000
18	A	1245	VAL	0	-0.043	-0.012	30.128	0.580	0.580	0.000	0.000	0.000	0.000
19	A	1246	HIS	0	0.009	0.005	31.036	0.607	0.607	0.000	0.000	0.000	0.000
20	A	1247	PRO	0	0.038	0.026	30.676	-0.649	-0.649	0.000	0.000	0.000	0.000
21	A	1248	ASP	-1	-0.855	-0.924	30.370	-18.459	-18.459	0.000	0.000	0.000	0.000
22	A	1249	THR	0	-0.043	-0.005	28.605	-0.122	-0.122	0.000	0.000	0.000	0.000
23	A	1250	GLY	0	-0.009	0.002	25.940	-0.651	-0.651	0.000	0.000	0.000	0.000
24	A	1251	ILE	0	0.002	-0.015	21.557	0.392	0.392	0.000	0.000	0.000	0.000
25	A	1252	SER	0	0.039	0.025	21.811	-1.003	-1.003	0.000	0.000	0.000	0.000
26	A	1253	SER	0	0.049	0.011	16.439	0.216	0.216	0.000	0.000	0.000	0.000
27	A	1254	LYS	1	0.991	0.988	17.810	25.242	25.242	0.000	0.000	0.000	0.000
28	A	1255	ALA	0	0.053	0.035	19.861	-0.048	-0.048	0.000	0.000	0.000	0.000
29	A	1256	MET	0	0.021	0.033	17.343	0.202	0.202	0.000	0.000	0.000	0.000
30	A	1257	SER	0	-0.028	-0.011	16.292	-0.787	-0.787	0.000	0.000	0.000	0.000
31	A	1258	ILE	0	0.030	0.026	17.545	-0.196	-0.196	0.000	0.000	0.000	0.000
32	A	1259	MET	0	0.028	0.012	21.027	0.442	0.442	0.000	0.000	0.000	0.000
33	A	1260	ASN	0	0.008	-0.006	14.366	0.375	0.375	0.000	0.000	0.000	0.000
34	A	1261	SER	0	-0.007	-0.007	18.357	-0.612	-0.612	0.000	0.000	0.000	0.000
35	A	1262	PHE	0	0.010	0.007	19.478	0.416	0.416	0.000	0.000	0.000	0.000
36	A	1263	VAL	0	-0.009	-0.004	20.488	0.582	0.582	0.000	0.000	0.000	0.000
37	A	1264	ASN	0	-0.033	-0.022	16.282	-0.095	-0.095	0.000	0.000	0.000	0.000
38	A	1265	ASP	-1	-0.749	-0.825	20.245	-21.735	-21.735	0.000	0.000	0.000	0.000
39	A	1266	VAL	0	-0.016	-0.010	23.261	0.816	0.816	0.000	0.000	0.000	0.000
40	A	1267	PHE	0	-0.021	-0.008	21.076	0.693	0.693	0.000	0.000	0.000	0.000
41	A	1268	GLU	-1	-0.914	-0.965	19.845	-27.007	-27.007	0.000	0.000	0.000	0.000
42	A	1269	ARG	1	0.805	0.865	24.060	21.478	21.478	0.000	0.000	0.000	0.000
43	A	1270	ILE	0	-0.007	-0.004	27.467	0.724	0.724	0.000	0.000	0.000	0.000
44	A	1271	ALA	0	0.014	0.006	25.407	0.617	0.617	0.000	0.000	0.000	0.000
45	A	1272	GLY	0	0.003	0.000	27.395	0.378	0.378	0.000	0.000	0.000	0.000
46	A	1273	GLU	-1	-0.845	-0.907	28.909	-17.314	-17.314	0.000	0.000	0.000	0.000
47	A	1274	ALA	0	-0.002	-0.005	30.490	0.516	0.516	0.000	0.000	0.000	0.000
48	A	1275	SER	0	-0.005	-0.001	29.194	0.598	0.598	0.000	0.000	0.000	0.000
49	A	1276	ARG	1	0.834	0.898	31.098	18.889	18.889	0.000	0.000	0.000	0.000
50	A	1277	LEU	0	0.005	0.015	34.031	0.533	0.533	0.000	0.000	0.000	0.000
51	A	1278	ALA	0	0.024	0.014	33.888	0.544	0.544	0.000	0.000	0.000	0.000
52	A	1279	HIS	0	0.025	0.007	31.414	0.869	0.869	0.000	0.000	0.000	0.000
53	A	1280	TYR	0	-0.031	-0.018	36.457	0.349	0.349	0.000	0.000	0.000	0.000
54	A	1281	ASN	0	-0.081	-0.044	39.264	0.778	0.778	0.000	0.000	0.000	0.000
55	A	1282	LYS	1	0.930	0.968	39.376	14.286	14.286	0.000	0.000	0.000	0.000
56	A	1283	ARG	1	0.888	0.947	37.223	15.287	15.287	0.000	0.000	0.000	0.000
57	A	1284	SER	0	0.037	0.027	34.351	-0.206	-0.206	0.000	0.000	0.000	0.000
58	A	1285	THR	0	-0.024	-0.026	32.697	-0.403	-0.403	0.000	0.000	0.000	0.000
59	A	1286	ILE	0	0.009	0.019	29.125	0.467	0.467	0.000	0.000	0.000	0.000
60	A	1287	THR	0	0.001	-0.024	31.859	-0.288	-0.288	0.000	0.000	0.000	0.000
61	A	1288	SER	0	0.047	0.003	33.361	-0.105	-0.105	0.000	0.000	0.000	0.000
62	A	1289	ARG	1	0.979	1.002	34.296	15.040	15.040	0.000	0.000	0.000	0.000
63	A	1290	GLU	-1	-0.791	-0.873	34.335	-16.549	-16.549	0.000	0.000	0.000	0.000
64	A	1291	ILE	0	0.020	0.016	29.248	-0.058	-0.058	0.000	0.000	0.000	0.000
65	A	1292	GLN	0	0.008	0.010	32.950	0.385	0.385	0.000	0.000	0.000	0.000
66	A	1293	THR	0	-0.051	-0.038	35.948	0.420	0.420	0.000	0.000	0.000	0.000
67	A	1294	ALA	0	0.033	0.014	32.294	0.191	0.191	0.000	0.000	0.000	0.000
68	A	1295	VAL	0	-0.016	-0.011	32.137	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	1296	ARG	1	0.876	0.920	34.361	15.117	15.117	0.000	0.000	0.000	0.000
70	A	1297	LEU	0	-0.032	-0.001	36.186	0.324	0.324	0.000	0.000	0.000	0.000
71	A	1298	LEU	0	-0.015	0.010	29.810	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	1299	LEU	0	-0.029	-0.014	31.447	-0.148	-0.148	0.000	0.000	0.000	0.000
73	A	1300	PRO	0	0.035	0.011	35.343	0.464	0.464	0.000	0.000	0.000	0.000
74	A	1301	GLY	0	0.015	-0.003	38.416	-0.078	-0.078	0.000	0.000	0.000	0.000
75	A	1302	GLU	-1	-0.853	-0.940	40.473	-14.188	-14.188	0.000	0.000	0.000	0.000
76	A	1303	LEU	0	0.023	0.017	33.938	-0.170	-0.170	0.000	0.000	0.000	0.000
77	A	1304	ALA	0	0.025	0.021	36.241	-0.299	-0.299	0.000	0.000	0.000	0.000
78	A	1305	LYS	1	0.944	0.983	37.773	13.968	13.968	0.000	0.000	0.000	0.000
79	A	1306	HIS	0	-0.001	0.011	36.877	0.023	0.023	0.000	0.000	0.000	0.000
80	A	1307	ALA	0	0.021	0.014	33.260	-0.223	-0.223	0.000	0.000	0.000	0.000
81	A	1308	VAL	0	-0.023	-0.013	34.788	-0.260	-0.260	0.000	0.000	0.000	0.000
82	A	1309	SER	0	-0.022	-0.003	37.259	0.123	0.123	0.000	0.000	0.000	0.000
83	A	1310	GLU	-1	-0.812	-0.896	33.676	-16.979	-16.979	0.000	0.000	0.000	0.000
84	A	1311	GLY	0	0.003	0.005	33.061	-0.316	-0.316	0.000	0.000	0.000	0.000
85	A	1312	THR	0	-0.020	-0.035	34.015	-0.103	-0.103	0.000	0.000	0.000	0.000
86	A	1313	LYS	1	0.860	0.929	35.930	16.810	16.810	0.000	0.000	0.000	0.000
87	A	1314	ALA	0	-0.019	-0.005	31.928	0.008	0.008	0.000	0.000	0.000	0.000
88	A	1315	VAL	0	0.002	-0.004	33.435	-0.143	-0.143	0.000	0.000	0.000	0.000
89	A	1316	THR	0	-0.013	-0.005	35.056	0.210	0.210	0.000	0.000	0.000	0.000
90	A	1317	LYS	1	0.959	0.977	34.452	17.410	17.410	0.000	0.000	0.000	0.000
91	A	1318	TYR	0	-0.043	-0.011	30.425	0.067	0.067	0.000	0.000	0.000	0.000
92	A	1319	THR	0	-0.009	-0.025	34.544	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	1320	SER	0	-0.099	-0.050	37.629	0.346	0.346	0.000	0.000	0.000	0.000
94	A	1321	ALA	0	-0.053	-0.018	35.111	0.225	0.225	0.000	0.000	0.000	0.000
95	A	1322	LYS	0	0.043	0.029	34.655	-2.332	-2.332	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1228:LYS)