FMO DATABASE

FMODB ID: LVY59

Calculation Name: 3VQK-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VQK

Chain ID: A

ChEMBL ID:

UniProt ID: Q970D9

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-748935.157135
FMO2-HF: Nuclear repulsion	707467.195352
FMO2-HF: Total energy	-41467.961783
FMO2-MP2: Total energy	-41591.656289

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:17:ARG)

Summations of interaction energy for fragment #1(A:17:ARG)

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.
-150.912	-131.434	35.791	-23.857	-31.411	-0.144

Interaction energy analysis for fragmet #1(A:17:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.787 / q_NPA : 0.894

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	19	PHE	0	0.064	0.018	3.877	-2.885	-1.455	-0.015	-0.755	-0.661	0.002
4	A	20	TYR	0	-0.013	-0.024	3.323	5.245	5.565	0.003	-0.070	-0.252	0.000
5	A	21	GLU	-1	-0.828	-0.938	2.807	-75.900	-71.860	0.496	-2.351	-2.185	-0.023
52	A	68	ILE	0	-0.009	0.004	3.787	1.156	1.488	0.000	-0.109	-0.223	0.000
53	A	69	THR	0	0.018	0.007	2.112	-14.827	-13.068	7.220	-4.485	-4.493	0.003
54	A	70	GLU	-1	-0.838	-0.907	2.218	-79.300	-77.241	9.563	-3.638	-7.984	-0.007
55	A	71	PRO	0	0.001	-0.002	4.401	1.135	1.424	0.005	-0.169	-0.125	0.001
61	A	77	THR	0	-0.027	-0.029	2.923	-6.514	-4.421	0.325	-0.890	-1.527	-0.007
62	A	78	GLN	0	0.042	-0.002	1.977	-39.832	-37.744	7.093	-4.614	-4.567	-0.065
63	A	79	ARG	1	0.990	0.982	2.604	29.685	31.370	2.068	-1.647	-2.107	-0.019
64	A	80	PRO	0	-0.048	-0.008	2.101	-28.859	-27.682	7.968	-4.489	-4.656	-0.044
65	A	81	LYS	1	0.782	0.925	2.881	29.477	31.683	1.065	-0.640	-2.631	0.015
6	A	22	LEU	0	-0.027	0.010	5.633	5.590	5.590	0.000	0.000	0.000	0.000
7	A	23	VAL	0	0.010	-0.006	7.520	2.777	2.777	0.000	0.000	0.000	0.000
8	A	24	TYR	0	0.012	0.038	7.792	2.257	2.257	0.000	0.000	0.000	0.000
9	A	25	PRO	0	0.030	0.007	9.729	0.031	0.031	0.000	0.000	0.000	0.000
10	A	26	PRO	0	-0.006	-0.002	12.280	0.246	0.246	0.000	0.000	0.000	0.000
11	A	27	VAL	0	-0.018	-0.019	15.109	0.178	0.178	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.874	-0.934	18.448	-13.413	-13.413	0.000	0.000	0.000	0.000
13	A	29	MET	0	-0.034	-0.029	21.728	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	30	TYR	0	-0.019	-0.006	25.043	0.198	0.198	0.000	0.000	0.000	0.000
15	A	31	GLU	-1	-0.914	-0.963	28.822	-9.058	-9.058	0.000	0.000	0.000	0.000
16	A	32	GLU	-1	-0.962	-0.975	30.932	-9.789	-9.789	0.000	0.000	0.000	0.000
17	A	33	GLY	0	-0.007	-0.006	33.528	0.178	0.178	0.000	0.000	0.000	0.000
18	A	34	GLY	0	0.008	0.002	36.447	0.181	0.181	0.000	0.000	0.000	0.000
19	A	35	TYR	0	-0.004	-0.016	32.059	-0.080	-0.080	0.000	0.000	0.000	0.000
20	A	36	LEU	0	0.010	0.008	28.988	-0.172	-0.172	0.000	0.000	0.000	0.000
21	A	37	VAL	0	-0.036	-0.008	26.309	-0.231	-0.231	0.000	0.000	0.000	0.000
22	A	38	VAL	0	-0.013	-0.014	21.276	-0.200	-0.200	0.000	0.000	0.000	0.000
23	A	39	VAL	0	-0.005	-0.009	20.530	0.223	0.223	0.000	0.000	0.000	0.000
24	A	40	ALA	0	0.001	0.008	15.982	-0.523	-0.523	0.000	0.000	0.000	0.000
25	A	41	ASP	-1	-0.897	-0.938	14.403	-18.734	-18.734	0.000	0.000	0.000	0.000
26	A	42	LEU	0	-0.056	-0.033	13.036	-1.765	-1.765	0.000	0.000	0.000	0.000
27	A	43	ALA	0	0.065	0.038	12.677	1.155	1.155	0.000	0.000	0.000	0.000
28	A	44	GLY	0	-0.015	-0.011	11.232	-2.161	-2.161	0.000	0.000	0.000	0.000
29	A	45	PHE	0	-0.045	-0.053	10.919	-1.826	-1.826	0.000	0.000	0.000	0.000
30	A	46	ASN	0	0.071	0.057	13.357	-0.204	-0.204	0.000	0.000	0.000	0.000
31	A	47	LYS	1	0.941	0.968	16.387	12.139	12.139	0.000	0.000	0.000	0.000
32	A	48	GLU	-1	-0.902	-0.955	17.711	-13.638	-13.638	0.000	0.000	0.000	0.000
33	A	49	LYS	1	0.925	0.973	11.942	18.369	18.369	0.000	0.000	0.000	0.000
34	A	50	ILE	0	0.010	0.002	15.745	-1.222	-1.222	0.000	0.000	0.000	0.000
35	A	51	LYS	1	0.881	0.957	15.059	18.783	18.783	0.000	0.000	0.000	0.000
36	A	52	ALA	0	0.036	0.032	19.265	-0.542	-0.542	0.000	0.000	0.000	0.000
37	A	53	ARG	1	0.787	0.852	18.117	15.496	15.496	0.000	0.000	0.000	0.000
38	A	54	VAL	0	0.036	0.021	24.117	0.064	0.064	0.000	0.000	0.000	0.000
39	A	55	SER	0	-0.016	-0.024	24.825	0.112	0.112	0.000	0.000	0.000	0.000
40	A	56	GLY	0	0.046	0.017	26.701	0.021	0.021	0.000	0.000	0.000	0.000
41	A	57	GLN	0	-0.032	-0.009	29.457	0.391	0.391	0.000	0.000	0.000	0.000
42	A	58	ASN	0	-0.010	-0.018	28.357	-0.082	-0.082	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.846	-0.902	23.741	-13.122	-13.122	0.000	0.000	0.000	0.000
44	A	60	LEU	0	0.009	0.032	17.720	0.146	0.146	0.000	0.000	0.000	0.000
45	A	61	ILE	0	-0.021	-0.027	19.380	-0.601	-0.601	0.000	0.000	0.000	0.000
46	A	62	ILE	0	0.011	0.014	14.211	0.263	0.263	0.000	0.000	0.000	0.000
47	A	63	GLU	-1	-0.793	-0.897	14.145	-18.133	-18.133	0.000	0.000	0.000	0.000
48	A	64	ALA	0	-0.043	-0.021	13.190	1.476	1.476	0.000	0.000	0.000	0.000
49	A	65	GLU	-1	-0.898	-0.939	7.298	-32.395	-32.395	0.000	0.000	0.000	0.000
50	A	66	ARG	1	0.812	0.908	6.981	34.010	34.010	0.000	0.000	0.000	0.000
51	A	67	GLU	-1	-0.811	-0.922	5.428	-22.794	-22.794	0.000	0.000	0.000	0.000
56	A	72	GLY	0	0.025	0.016	7.950	0.609	0.609	0.000	0.000	0.000	0.000
57	A	73	VAL	0	0.006	-0.003	10.280	-0.378	-0.378	0.000	0.000	0.000	0.000
58	A	74	LYS	1	0.826	0.926	5.692	24.977	24.977	0.000	0.000	0.000	0.000
59	A	75	TYR	0	0.066	0.037	7.939	-0.624	-0.624	0.000	0.000	0.000	0.000
60	A	76	LEU	0	0.061	0.022	5.917	-1.903	-1.903	0.000	0.000	0.000	0.000
66	A	82	TYR	0	0.061	0.015	5.500	5.429	5.429	0.000	0.000	0.000	0.000
67	A	83	VAL	0	-0.006	0.008	6.339	-4.015	-4.015	0.000	0.000	0.000	0.000
68	A	84	ARG	1	0.881	0.941	8.995	20.981	20.981	0.000	0.000	0.000	0.000
69	A	85	LYS	1	0.843	0.913	12.467	23.283	23.283	0.000	0.000	0.000	0.000
70	A	86	VAL	0	-0.019	-0.007	14.941	0.496	0.496	0.000	0.000	0.000	0.000
71	A	87	ILE	0	0.022	-0.003	18.507	-0.092	-0.092	0.000	0.000	0.000	0.000
72	A	88	ARG	1	0.935	0.981	21.453	11.312	11.312	0.000	0.000	0.000	0.000
73	A	89	LEU	0	-0.017	-0.003	25.187	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	90	PRO	0	-0.015	-0.008	27.422	0.212	0.212	0.000	0.000	0.000	0.000
75	A	91	TYR	0	0.088	0.026	30.220	0.123	0.123	0.000	0.000	0.000	0.000
76	A	92	ASN	0	-0.070	-0.017	31.437	0.180	0.180	0.000	0.000	0.000	0.000
77	A	93	VAL	0	0.027	0.003	30.707	-0.080	-0.080	0.000	0.000	0.000	0.000
78	A	94	ALA	0	0.044	0.024	33.799	0.264	0.264	0.000	0.000	0.000	0.000
79	A	95	LYS	1	0.853	0.926	31.509	9.261	9.261	0.000	0.000	0.000	0.000
80	A	96	ASP	-1	-0.920	-0.962	34.168	-8.397	-8.397	0.000	0.000	0.000	0.000
81	A	97	ALA	0	0.015	0.036	35.270	0.099	0.099	0.000	0.000	0.000	0.000
82	A	98	GLU	-1	-0.884	-0.952	32.231	-9.303	-9.303	0.000	0.000	0.000	0.000
83	A	99	ILE	0	-0.012	-0.007	25.992	-0.120	-0.120	0.000	0.000	0.000	0.000
84	A	100	SER	0	0.004	0.014	27.866	-0.263	-0.263	0.000	0.000	0.000	0.000
85	A	101	GLY	0	-0.023	-0.014	25.011	-0.105	-0.105	0.000	0.000	0.000	0.000
86	A	102	LYS	1	0.922	0.958	24.170	11.936	11.936	0.000	0.000	0.000	0.000
87	A	103	TYR	0	-0.028	-0.026	16.345	-0.096	-0.096	0.000	0.000	0.000	0.000
88	A	104	GLU	-1	-0.913	-0.961	22.197	-11.358	-11.358	0.000	0.000	0.000	0.000
89	A	105	ASN	0	-0.001	0.004	20.388	-0.296	-0.296	0.000	0.000	0.000	0.000
90	A	106	GLY	0	-0.011	0.000	17.337	-0.468	-0.468	0.000	0.000	0.000	0.000
91	A	107	VAL	0	0.066	0.028	17.762	-0.783	-0.783	0.000	0.000	0.000	0.000
92	A	108	LEU	0	-0.041	-0.020	16.839	0.695	0.695	0.000	0.000	0.000	0.000
93	A	109	THR	0	0.016	0.016	19.915	0.180	0.180	0.000	0.000	0.000	0.000
94	A	110	ILE	0	-0.051	-0.035	21.477	0.138	0.138	0.000	0.000	0.000	0.000
95	A	111	ARG	1	0.865	0.928	25.625	10.777	10.777	0.000	0.000	0.000	0.000
96	A	112	ILE	0	-0.009	-0.005	26.690	-0.080	-0.080	0.000	0.000	0.000	0.000
97	A	113	PRO	0	0.025	-0.011	30.771	0.104	0.104	0.000	0.000	0.000	0.000
98	A	114	ILE	0	0.043	0.038	33.429	0.142	0.142	0.000	0.000	0.000	0.000
99	A	115	ALA	0	0.014	0.033	35.648	0.212	0.212	0.000	0.000	0.000	0.000
100	A	116	GLY	0	0.049	0.028	38.706	0.016	0.016	0.000	0.000	0.000	0.000
101	A	117	THR	0	-0.051	-0.027	41.723	0.083	0.083	0.000	0.000	0.000	0.000
102	A	118	SER	0	-0.031	-0.023	39.097	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	119	VAL	0	-0.012	-0.005	41.295	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	120	ILE	0	-0.034	-0.025	43.315	0.201	0.201	0.000	0.000	0.000	0.000
105	A	121	LYS	1	0.925	0.951	46.544	6.209	6.209	0.000	0.000	0.000	0.000
106	A	122	ILE	0	-0.025	-0.003	46.187	-0.139	-0.139	0.000	0.000	0.000	0.000
107	A	123	GLU	-2	-1.866	-1.915	49.174	-12.327	-12.327	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:ARG)