FMO DATABASE

FMODB ID: 1VYGZ

Calculation Name: 6KMX-A-Other547

Preferred Name:

Target Type:

Ligand 3-letter code: F6C | CLA | CL0 | BCR | LMG | LHG | LMT | PQN | SF4 | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6KMX

Chain ID: A

ChEMBL ID:

UniProt ID: A0A1Z3

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-477798.752882
FMO2-HF: Nuclear repulsion	444911.389925
FMO2-HF: Total energy	-32887.362957
FMO2-MP2: Total energy	-32974.034491

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-119.59	-116.027	19.155	-11.26	-11.456	-0.113

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.880

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	4	SER	0	0.018	0.000	3.605	0.479	1.796	0.007	-0.575	-0.749	-0.001
44	A	45	THR	0	-0.013	-0.022	3.817	1.138	1.316	0.001	-0.040	-0.139	0.000
45	A	46	GLU	-1	-0.961	-1.001	1.998	-58.353	-56.626	5.347	-3.942	-3.131	-0.018
46	A	47	ASP	-1	-0.783	-0.874	2.804	-32.016	-32.688	-0.007	1.255	-0.576	-0.004
47	A	48	CYS	0	-0.116	-0.044	4.094	5.780	5.890	-0.001	-0.015	-0.094	0.000
48	A	49	VAL	0	0.052	0.022	4.655	-6.549	-6.404	-0.001	-0.008	-0.137	0.000
69	A	70	GLY	0	0.017	0.002	4.466	3.727	3.818	-0.001	-0.020	-0.070	0.000
70	A	71	ALA	0	-0.015	-0.001	2.857	4.089	4.871	0.082	-0.263	-0.601	0.000
71	A	72	GLU	-1	-0.775	-0.872	1.733	-91.022	-93.042	12.485	-6.549	-3.915	-0.086
72	A	73	THR	0	-0.039	-0.024	2.368	0.704	2.005	1.161	-0.838	-1.624	-0.002
73	A	74	THR	0	0.060	0.022	5.213	1.036	1.063	-0.001	-0.002	-0.023	0.000
75	A	76	SER	0	-0.012	-0.031	2.865	-1.253	-0.667	0.084	-0.258	-0.412	-0.002
76	A	77	MET	0	0.000	-0.012	4.943	3.785	3.776	-0.001	-0.005	0.015	0.000
4	A	5	VAL	0	-0.011	0.005	6.210	4.578	4.578	0.000	0.000	0.000	0.000
5	A	6	LYS	1	0.876	0.944	8.527	31.086	31.086	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.011	0.001	12.172	0.327	0.327	0.000	0.000	0.000	0.000
7	A	8	TYR	0	0.008	0.010	15.502	-0.701	-0.701	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.888	-0.947	18.798	-13.515	-13.515	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.025	-0.003	22.075	0.449	0.449	0.000	0.000	0.000	0.000
10	A	11	CYS	0	-0.044	0.001	20.313	0.331	0.331	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.042	0.016	22.374	0.325	0.325	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.054	0.015	22.617	0.351	0.351	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.056	-0.004	22.784	-0.129	-0.129	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.004	-0.008	20.567	0.243	0.243	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.023	-0.005	20.246	-0.449	-0.449	0.000	0.000	0.000	0.000
16	A	17	CYS	0	0.010	0.009	15.850	-0.168	-0.168	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.038	0.010	15.701	-0.822	-0.822	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.907	0.942	16.770	12.214	12.214	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.000	0.017	17.263	0.266	0.266	0.000	0.000	0.000	0.000
20	A	21	CYS	0	-0.057	-0.009	11.605	-1.131	-1.131	0.000	0.000	0.000	0.000
21	A	22	PRO	0	-0.051	-0.034	13.086	0.398	0.398	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.011	-0.009	9.246	0.302	0.302	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.847	-0.901	10.769	-20.144	-20.144	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.027	-0.002	7.326	-0.397	-0.397	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.054	-0.036	9.691	-0.692	-0.692	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.804	-0.889	12.654	-17.539	-17.539	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.063	-0.002	16.012	-0.540	-0.540	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.037	0.028	17.935	0.296	0.296	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.011	0.006	20.686	0.148	0.148	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.051	-0.026	22.529	-0.475	-0.475	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.914	-0.957	24.372	-10.572	-10.572	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.022	0.028	26.041	0.291	0.291	0.000	0.000	0.000	0.000
33	A	34	CYS	0	-0.068	-0.031	25.050	0.197	0.197	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.951	0.967	28.261	9.276	9.276	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.006	-0.001	26.420	0.270	0.270	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.037	0.026	27.612	-0.082	-0.082	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.047	-0.040	22.501	-0.276	-0.276	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.009	0.003	18.819	0.156	0.156	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.010	-0.009	16.187	-0.114	-0.114	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.015	-0.016	14.511	-0.438	-0.438	0.000	0.000	0.000	0.000
41	A	42	SER	0	0.023	-0.020	9.164	0.550	0.550	0.000	0.000	0.000	0.000
42	A	43	PRO	0	-0.006	0.012	9.160	-2.803	-2.803	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.818	0.906	7.746	19.899	19.899	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.008	0.004	7.322	0.646	0.646	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.048	-0.025	8.392	2.296	2.296	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.875	0.936	11.680	25.830	25.830	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.994	1.006	13.619	18.508	18.508	0.000	0.000	0.000	0.000
53	A	54	CYS	0	-0.013	-0.002	11.864	0.675	0.675	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.767	-0.895	13.792	-21.341	-21.341	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.059	-0.034	16.564	0.911	0.911	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.008	-0.003	18.639	0.779	0.779	0.000	0.000	0.000	0.000
57	A	58	CYS	-1	-0.859	-0.848	18.933	-14.421	-14.421	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.009	-0.015	20.816	0.225	0.225	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.037	-0.047	22.559	0.659	0.659	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.920	-0.939	23.703	-12.260	-12.260	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.021	-0.025	19.457	0.164	0.164	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.013	-0.012	18.426	-0.225	-0.225	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.009	-0.023	19.450	-0.355	-0.355	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.049	-0.020	12.478	-0.642	-0.642	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.881	0.955	13.834	19.661	19.661	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.010	-0.013	8.060	-1.651	-1.651	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.034	-0.025	9.304	1.788	1.788	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.003	-0.004	6.880	-5.152	-5.152	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.865	0.936	5.140	36.078	36.078	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.021	-0.005	8.088	3.088	3.088	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.067	-0.022	10.162	2.183	2.183	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.033	-0.024	12.267	-0.417	-0.417	0.000	0.000	0.000	0.000
80	A	81	TYR	-1	-0.939	-0.962	14.211	-19.128	-19.128	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)