FMO DATABASE

FMODB ID: 5G2KZ

Calculation Name: 7XCT-F-Other547

Preferred Name:

Target Type:

Ligand Name: s-adenosylmethionine | norleucine

Ligand 3-letter code: SAM | NLE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7XCT

Chain ID: F

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-526359.387719
FMO2-HF: Nuclear repulsion	491975.15911
FMO2-HF: Total energy	-34384.228609
FMO2-MP2: Total energy	-34486.679974

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:15:ALA)

Summations of interaction energy for fragment #1(A:15:ALA)

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.
166.559	167.952	-0.006	-0.604	-0.783	-0.001

Interaction energy analysis for fragmet #1(A:15:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.924 / q_NPA : 0.959

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

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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	17	ARG	1	1.010	0.993	3.881	40.221	41.614	-0.006	-0.604	-0.783	-0.001
4	A	18	HIS	0	0.066	0.043	5.937	-0.275	-0.275	0.000	0.000	0.000	0.000
5	A	19	ARG	1	0.996	1.002	7.823	22.730	22.730	0.000	0.000	0.000	0.000
6	A	20	LYS	1	0.952	0.981	9.528	24.403	24.403	0.000	0.000	0.000	0.000
7	A	21	VAL	0	-0.010	-0.008	11.733	1.163	1.163	0.000	0.000	0.000	0.000
8	A	22	LEU	0	0.010	0.011	15.118	0.017	0.017	0.000	0.000	0.000	0.000
9	A	23	ARG	1	0.961	0.968	15.003	18.624	18.624	0.000	0.000	0.000	0.000
10	A	24	ASP	-1	-0.832	-0.902	20.746	-12.928	-12.928	0.000	0.000	0.000	0.000
11	A	25	ASN	0	-0.022	-0.017	21.175	0.371	0.371	0.000	0.000	0.000	0.000
12	A	26	ILE	0	0.024	0.011	25.335	0.269	0.269	0.000	0.000	0.000	0.000
13	A	27	GLN	0	0.039	0.008	27.979	0.428	0.428	0.000	0.000	0.000	0.000
14	A	28	GLY	0	-0.008	0.004	28.236	0.246	0.246	0.000	0.000	0.000	0.000
15	A	29	ILE	0	-0.014	0.010	29.149	0.302	0.302	0.000	0.000	0.000	0.000
16	A	30	THR	0	0.084	0.037	32.421	0.301	0.301	0.000	0.000	0.000	0.000
17	A	31	LYS	1	1.017	1.016	33.976	8.053	8.053	0.000	0.000	0.000	0.000
18	A	32	PRO	0	-0.056	-0.058	36.304	0.252	0.252	0.000	0.000	0.000	0.000
19	A	33	ALA	0	-0.068	-0.039	35.498	0.117	0.117	0.000	0.000	0.000	0.000
20	A	34	ILE	0	0.066	0.066	36.021	0.098	0.098	0.000	0.000	0.000	0.000
21	A	35	ARG	1	0.940	0.962	39.297	7.392	7.392	0.000	0.000	0.000	0.000
22	A	36	ARG	1	0.937	0.977	37.356	7.876	7.876	0.000	0.000	0.000	0.000
23	A	37	LEU	0	0.031	0.018	37.719	0.142	0.142	0.000	0.000	0.000	0.000
24	A	38	ALA	0	0.035	0.007	42.156	0.169	0.169	0.000	0.000	0.000	0.000
25	A	39	ARG	1	0.791	0.883	44.973	6.692	6.692	0.000	0.000	0.000	0.000
26	A	40	ARG	1	0.994	0.998	42.714	7.315	7.315	0.000	0.000	0.000	0.000
27	A	41	GLY	0	0.020	0.026	46.850	0.080	0.080	0.000	0.000	0.000	0.000
28	A	42	GLY	0	0.036	0.029	48.494	0.102	0.102	0.000	0.000	0.000	0.000
29	A	43	VAL	0	0.000	0.012	47.797	0.110	0.110	0.000	0.000	0.000	0.000
30	A	44	LYS	1	1.027	1.013	50.010	5.498	5.498	0.000	0.000	0.000	0.000
31	A	45	ARG	1	0.934	0.961	50.421	5.991	5.991	0.000	0.000	0.000	0.000
32	A	46	ILE	0	0.032	0.012	44.225	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	47	SER	0	0.032	0.021	46.940	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	48	GLY	0	0.013	-0.009	43.441	-0.129	-0.129	0.000	0.000	0.000	0.000
35	A	49	LEU	0	0.089	0.039	41.823	-0.198	-0.198	0.000	0.000	0.000	0.000
36	A	50	ILE	0	0.023	0.016	41.629	-0.120	-0.120	0.000	0.000	0.000	0.000
37	A	51	TYR	0	-0.053	-0.036	38.039	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	52	GLU	-1	-0.751	-0.849	34.982	-9.444	-9.444	0.000	0.000	0.000	0.000
39	A	53	GLU	-1	-0.877	-0.926	37.385	-7.877	-7.877	0.000	0.000	0.000	0.000
40	A	54	THR	0	-0.119	-0.093	38.601	0.000	0.000	0.000	0.000	0.000	0.000
41	A	55	ARG	1	0.776	0.872	32.364	9.165	9.165	0.000	0.000	0.000	0.000
42	A	56	GLY	0	0.059	0.053	33.973	-0.301	-0.301	0.000	0.000	0.000	0.000
43	A	57	VAL	0	0.039	-0.002	36.055	-0.103	-0.103	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.078	-0.048	33.671	-0.122	-0.122	0.000	0.000	0.000	0.000
45	A	59	LYS	1	0.823	0.923	27.996	10.735	10.735	0.000	0.000	0.000	0.000
46	A	60	VAL	0	0.073	0.031	32.738	-0.142	-0.142	0.000	0.000	0.000	0.000
47	A	61	PHE	0	-0.010	-0.010	35.312	0.075	0.075	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.010	0.005	29.653	-0.213	-0.213	0.000	0.000	0.000	0.000
49	A	63	GLU	-1	-0.825	-0.913	28.761	-11.187	-11.187	0.000	0.000	0.000	0.000
50	A	64	ASN	0	-0.008	-0.008	31.417	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	65	VAL	0	-0.020	0.026	33.356	0.173	0.173	0.000	0.000	0.000	0.000
52	A	66	ILE	0	-0.004	-0.015	26.940	-0.110	-0.110	0.000	0.000	0.000	0.000
53	A	67	ARG	1	0.862	0.932	29.295	9.931	9.931	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.741	-0.873	30.718	-8.464	-8.464	0.000	0.000	0.000	0.000
55	A	69	ALA	0	-0.019	0.017	31.006	0.156	0.156	0.000	0.000	0.000	0.000
56	A	70	VAL	0	-0.010	-0.028	26.171	-0.070	-0.070	0.000	0.000	0.000	0.000
57	A	71	THR	0	0.054	0.027	29.259	0.171	0.171	0.000	0.000	0.000	0.000
58	A	72	TYR	0	-0.024	-0.010	31.440	0.226	0.226	0.000	0.000	0.000	0.000
59	A	73	THR	0	-0.057	-0.062	26.895	-0.099	-0.099	0.000	0.000	0.000	0.000
60	A	74	GLU	-1	-0.997	-0.983	27.488	-11.337	-11.337	0.000	0.000	0.000	0.000
61	A	75	HIS	0	0.027	0.021	29.005	-0.208	-0.208	0.000	0.000	0.000	0.000
62	A	76	ALA	0	-0.018	-0.012	31.478	0.098	0.098	0.000	0.000	0.000	0.000
63	A	77	LYS	1	0.923	0.959	28.187	10.142	10.142	0.000	0.000	0.000	0.000
64	A	78	ARG	1	0.868	0.909	27.187	9.810	9.810	0.000	0.000	0.000	0.000
65	A	79	LYS	1	0.928	0.981	18.247	15.077	15.077	0.000	0.000	0.000	0.000
66	A	80	THR	0	-0.042	-0.028	23.230	-0.673	-0.673	0.000	0.000	0.000	0.000
67	A	81	VAL	0	0.027	0.025	25.229	0.420	0.420	0.000	0.000	0.000	0.000
68	A	82	THR	0	-0.045	-0.045	27.940	-0.168	-0.168	0.000	0.000	0.000	0.000
69	A	83	ALA	0	0.046	0.016	30.850	0.013	0.013	0.000	0.000	0.000	0.000
70	A	84	MET	0	0.044	0.040	33.970	0.162	0.162	0.000	0.000	0.000	0.000
71	A	85	ASP	-1	-0.742	-0.825	31.606	-10.062	-10.062	0.000	0.000	0.000	0.000
72	A	86	VAL	0	0.001	-0.007	31.744	0.014	0.014	0.000	0.000	0.000	0.000
73	A	87	VAL	0	-0.029	-0.016	34.405	0.208	0.208	0.000	0.000	0.000	0.000
74	A	88	TYR	0	0.030	0.007	36.853	-0.118	-0.118	0.000	0.000	0.000	0.000
75	A	89	ALA	0	0.037	0.044	34.937	0.081	0.081	0.000	0.000	0.000	0.000
76	A	90	LEU	0	0.005	-0.016	37.053	0.223	0.223	0.000	0.000	0.000	0.000
77	A	91	LYS	1	0.910	0.948	39.419	6.771	6.771	0.000	0.000	0.000	0.000
78	A	92	ARG	1	0.916	0.968	38.632	8.254	8.254	0.000	0.000	0.000	0.000
79	A	93	GLN	0	-0.099	-0.062	36.627	0.203	0.203	0.000	0.000	0.000	0.000
80	A	94	GLY	0	0.017	0.009	42.108	0.051	0.051	0.000	0.000	0.000	0.000
81	A	95	ARG	1	0.926	0.970	41.366	7.550	7.550	0.000	0.000	0.000	0.000
82	A	96	THR	0	0.029	0.010	42.756	-0.176	-0.176	0.000	0.000	0.000	0.000
83	A	97	LEU	0	-0.020	0.002	38.800	0.056	0.056	0.000	0.000	0.000	0.000
84	A	98	TYR	0	0.032	0.006	42.924	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	99	GLY	0	0.027	0.004	42.711	-0.074	-0.074	0.000	0.000	0.000	0.000
86	A	100	PHE	0	-0.044	-0.021	36.017	-0.131	-0.131	0.000	0.000	0.000	0.000
87	A	101	GLY	0	-0.033	-0.032	38.093	-0.196	-0.196	0.000	0.000	0.000	0.000
88	A	102	GLY	-1	-0.908	-0.926	41.036	-7.048	-7.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ALA)