FMO DATABASE

FMODB ID: 3K9LL

Calculation Name: 1VJQ-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VJQ

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-07-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-446977.602911
FMO2-HF: Nuclear repulsion	418327.754399
FMO2-HF: Total energy	-28649.848512
FMO2-MP2: Total energy	-28733.675877

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:1:LYS)

Summations of interaction energy for fragment #1(A:1: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.
-2.227	3.531	1.286	-2.99	-4.053	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.112 / q_NPA : 0.027

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].
4	A	2	THR	0	0.023	0.051	3.763	-0.825	0.534	0.002	-0.873	-0.488	0.004
5	A	3	ILE	0	0.089	-0.074	3.878	-1.900	0.259	-0.016	-1.334	-0.809	0.004
6	A	3	ILE	0	-0.095	0.094	4.451	0.038	0.096	-0.001	-0.006	-0.051	0.000
7	A	4	PHE	0	0.053	-0.087	6.322	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	4	PHE	0	-0.057	0.090	8.075	0.046	0.046	0.000	0.000	0.000	0.000
9	A	5	VAL	0	0.086	-0.089	9.884	0.102	0.102	0.000	0.000	0.000	0.000
10	A	5	VAL	0	-0.121	0.091	11.115	0.013	0.013	0.000	0.000	0.000	0.000
11	A	6	ILE	0	0.153	-0.085	12.861	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	6	ILE	0	-0.068	0.096	12.898	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	7	VAL	0	0.031	-0.117	15.571	0.041	0.041	0.000	0.000	0.000	0.000
14	A	7	VAL	0	-0.120	0.121	18.908	0.002	0.002	0.000	0.000	0.000	0.000
15	A	8	PRO	0	0.025	-0.091	19.247	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	9	THR	0	0.017	0.008	21.797	0.021	0.021	0.000	0.000	0.000	0.000
17	A	9	THR	0	-0.064	0.056	23.769	0.004	0.004	0.000	0.000	0.000	0.000
18	A	10	ASN	0	0.094	-0.067	25.388	0.016	0.016	0.000	0.000	0.000	0.000
19	A	10	ASN	0	-0.082	0.048	26.295	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	11	GLU	0	0.154	-0.084	25.716	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	11	GLU	-1	-0.914	-0.828	27.820	-0.095	-0.095	0.000	0.000	0.000	0.000
22	A	12	GLU	0	-0.001	-0.126	26.204	0.000	0.000	0.000	0.000	0.000	0.000
23	A	12	GLU	-1	-0.914	-0.822	27.524	-0.136	-0.136	0.000	0.000	0.000	0.000
24	A	13	GLN	0	0.040	-0.108	23.064	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	13	GLN	0	-0.047	0.111	22.163	0.002	0.002	0.000	0.000	0.000	0.000
26	A	14	VAL	0	0.077	-0.117	21.653	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	14	VAL	0	-0.051	0.132	22.857	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	15	ALA	0	0.169	-0.075	21.805	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	15	ALA	0	-0.084	0.109	25.642	0.003	0.003	0.000	0.000	0.000	0.000
30	A	16	PHE	0	0.044	-0.087	22.148	0.011	0.011	0.000	0.000	0.000	0.000
31	A	16	PHE	0	-0.061	0.072	19.134	0.002	0.002	0.000	0.000	0.000	0.000
32	A	17	LEU	0	0.043	-0.121	18.061	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	17	LEU	0	-0.038	0.110	16.198	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	18	GLU	0	0.120	-0.099	17.909	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	18	GLU	-1	-0.943	-0.789	21.607	-0.070	-0.070	0.000	0.000	0.000	0.000
36	A	19	ALA	0	0.092	-0.100	20.220	0.026	0.026	0.000	0.000	0.000	0.000
37	A	19	ALA	0	-0.115	0.087	21.783	0.000	0.000	0.000	0.000	0.000	0.000
38	A	20	LEU	0	0.005	-0.122	16.897	0.030	0.030	0.000	0.000	0.000	0.000
39	A	20	LEU	0	-0.075	0.087	15.888	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	21	ALA	0	0.135	-0.075	15.444	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	21	ALA	0	-0.069	0.105	16.215	0.004	0.004	0.000	0.000	0.000	0.000
42	A	22	LYS	0	-0.009	-0.086	16.494	0.043	0.043	0.000	0.000	0.000	0.000
43	A	22	LYS	1	0.703	0.951	20.771	0.072	0.072	0.000	0.000	0.000	0.000
44	A	23	GLN	0	0.016	-0.123	17.320	0.037	0.037	0.000	0.000	0.000	0.000
45	A	23	GLN	0	-0.126	0.055	16.458	0.005	0.005	0.000	0.000	0.000	0.000
46	A	24	ASP	0	0.145	-0.068	15.319	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	24	ASP	-1	-1.040	-0.866	15.209	0.135	0.135	0.000	0.000	0.000	0.000
48	A	25	GLU	0	0.087	-0.137	13.563	0.053	0.053	0.000	0.000	0.000	0.000
49	A	25	GLU	-1	-1.050	-0.853	12.473	-0.495	-0.495	0.000	0.000	0.000	0.000
50	A	26	LEU	0	0.143	-0.094	11.365	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	26	LEU	0	-0.134	0.084	10.941	0.005	0.005	0.000	0.000	0.000	0.000
52	A	27	ASN	0	0.031	-0.070	7.310	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	27	ASN	0	-0.116	0.033	6.227	0.352	0.352	0.000	0.000	0.000	0.000
54	A	28	PHE	0	0.177	-0.054	6.343	-0.280	-0.280	0.000	0.000	0.000	0.000
55	A	28	PHE	0	-0.145	0.076	9.743	-0.116	-0.116	0.000	0.000	0.000	0.000
56	A	29	ASP	0	0.160	-0.076	7.174	-0.032	-0.032	0.000	0.000	0.000	0.000
57	A	29	ASP	-1	-1.020	-0.855	6.969	0.896	0.896	0.000	0.000	0.000	0.000
58	A	30	TRP	0	0.048	-0.114	8.561	-0.048	-0.048	0.000	0.000	0.000	0.000
59	A	30	TRP	0	-0.046	0.105	12.625	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	31	GLN	0	0.125	-0.076	10.661	0.085	0.085	0.000	0.000	0.000	0.000
61	A	31	GLN	0	-0.180	0.036	8.643	0.111	0.111	0.000	0.000	0.000	0.000
62	A	32	ASN	0	0.006	-0.085	11.660	0.058	0.058	0.000	0.000	0.000	0.000
63	A	32	ASN	0	-0.112	0.040	14.742	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	33	PRO	0	0.016	-0.086	15.122	-0.051	-0.051	0.000	0.000	0.000	0.000
65	A	34	PRO	0	0.010	-0.017	17.362	0.000	0.000	0.000	0.000	0.000	0.000
66	A	35	THR	0	-0.021	0.038	19.793	0.020	0.020	0.000	0.000	0.000	0.000
67	A	35	THR	0	-0.070	0.031	21.642	0.002	0.002	0.000	0.000	0.000	0.000
68	A	36	GLU	0	0.139	-0.076	23.274	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	36	GLU	-1	-0.981	-0.859	25.752	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	37	PRO	0	-0.020	-0.107	23.753	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	38	GLY	0	-0.040	-0.024	23.762	0.015	0.015	0.000	0.000	0.000	0.000
72	A	39	GLN	0	0.061	-0.031	21.679	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	39	GLN	0	-0.113	0.113	21.341	0.000	0.000	0.000	0.000	0.000	0.000
74	A	40	PRO	0	-0.017	-0.119	16.499	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	41	VAL	0	0.083	0.015	15.585	0.061	0.061	0.000	0.000	0.000	0.000
76	A	41	VAL	0	-0.093	0.100	14.513	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	42	VAL	0	0.106	-0.083	11.762	-0.115	-0.115	0.000	0.000	0.000	0.000
78	A	42	VAL	0	-0.097	0.086	9.635	0.009	0.009	0.000	0.000	0.000	0.000
79	A	43	ILE	0	0.079	-0.105	9.024	0.193	0.193	0.000	0.000	0.000	0.000
80	A	43	ILE	0	-0.090	0.111	8.087	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	44	LEU	0	0.068	-0.102	4.908	-0.544	-0.538	-0.002	-0.004	0.000	0.000
82	A	44	LEU	0	-0.085	0.096	2.465	-0.396	-0.164	1.057	-0.459	-0.830	0.001
83	A	45	ILE	0	0.008	-0.081	3.961	0.531	0.674	-0.001	-0.030	-0.112	0.000
84	A	45	ILE	0	-0.039	0.103	5.736	0.050	0.050	0.000	0.000	0.000	0.000
85	A	46	PRO	0	0.036	-0.110	3.028	-4.366	-3.434	0.114	-0.515	-0.530	-0.008
86	A	47	SER	0	0.101	0.011	3.180	0.970	0.847	0.047	0.260	-0.185	0.001
87	A	47	SER	0	-0.050	0.051	3.489	-0.991	-1.435	0.001	0.630	-0.186	-0.001
88	A	48	ASP	0	-0.039	-0.109	4.749	0.770	0.881	-0.001	-0.007	-0.103	0.000
89	A	48	ASP	-1	-0.913	-0.838	6.413	-2.432	-2.432	0.000	0.000	0.000	0.000
90	A	49	MET	0	0.016	-0.141	7.301	0.464	0.464	0.000	0.000	0.000	0.000
91	A	49	MET	0	-0.063	0.131	8.189	0.111	0.111	0.000	0.000	0.000	0.000
92	A	50	VAL	0	0.102	-0.089	8.244	0.355	0.355	0.000	0.000	0.000	0.000
93	A	50	VAL	0	-0.099	0.108	6.791	-0.044	-0.044	0.000	0.000	0.000	0.000
94	A	51	GLU	0	0.120	-0.090	9.428	0.176	0.176	0.000	0.000	0.000	0.000
95	A	51	GLU	-1	-1.022	-0.874	12.530	-0.893	-0.893	0.000	0.000	0.000	0.000
96	A	52	TRP	0	0.091	-0.088	12.974	0.103	0.103	0.000	0.000	0.000	0.000
97	A	52	TRP	0	-0.061	0.082	12.135	0.022	0.022	0.000	0.000	0.000	0.000
98	A	53	PHE	0	0.110	-0.092	11.730	0.198	0.198	0.000	0.000	0.000	0.000
99	A	53	PHE	0	-0.058	0.110	11.192	-0.034	-0.034	0.000	0.000	0.000	0.000
100	A	54	LEU	0	0.094	-0.089	13.211	0.125	0.125	0.000	0.000	0.000	0.000
101	A	54	LEU	0	-0.105	0.087	12.831	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	55	GLU	0	0.051	-0.125	14.550	0.097	0.097	0.000	0.000	0.000	0.000
103	A	55	GLU	-1	-0.860	-0.781	17.035	-0.553	-0.553	0.000	0.000	0.000	0.000
104	A	56	MET	0	0.090	-0.086	16.765	0.088	0.088	0.000	0.000	0.000	0.000
105	A	56	MET	0	-0.104	0.095	14.814	0.029	0.029	0.000	0.000	0.000	0.000
106	A	57	LEU	0	0.008	-0.134	16.741	0.083	0.083	0.000	0.000	0.000	0.000
107	A	57	LEU	0	-0.056	0.116	13.862	0.011	0.011	0.000	0.000	0.000	0.000
108	A	58	LYS	0	0.121	-0.095	18.014	0.062	0.062	0.000	0.000	0.000	0.000
109	A	58	LYS	1	0.703	0.975	18.889	0.517	0.517	0.000	0.000	0.000	0.000
110	A	59	ALA	0	0.072	-0.099	20.449	0.046	0.046	0.000	0.000	0.000	0.000
111	A	59	ALA	0	-0.080	0.107	21.611	0.000	0.000	0.000	0.000	0.000	0.000
112	A	60	LYS	0	-0.041	-0.115	21.660	0.035	0.035	0.000	0.000	0.000	0.000
113	A	60	LYS	1	0.805	1.040	21.274	0.276	0.276	0.000	0.000	0.000	0.000
114	A	61	GLY	0	0.025	-0.118	23.116	0.024	0.024	0.000	0.000	0.000	0.000
115	A	62	ILE	0	0.046	-0.010	20.000	0.038	0.038	0.000	0.000	0.000	0.000
116	A	62	ILE	0	-0.097	0.096	19.009	0.001	0.001	0.000	0.000	0.000	0.000
117	A	63	PRO	0	-0.008	-0.107	19.396	-0.045	-0.045	0.000	0.000	0.000	0.000
118	A	64	PHE	0	0.047	0.025	15.539	0.033	0.033	0.000	0.000	0.000	0.000
119	A	64	PHE	0	-0.051	0.086	13.912	-0.029	-0.029	0.000	0.000	0.000	0.000
120	A	65	THR	0	0.028	-0.047	14.625	0.024	0.024	0.000	0.000	0.000	0.000
121	A	65	THR	0	-0.057	0.044	13.828	-0.019	-0.019	0.000	0.000	0.000	0.000
122	A	66	VAL	0	0.089	-0.109	10.600	0.024	0.024	0.000	0.000	0.000	0.000
123	A	66	VAL	0	-0.077	0.102	9.052	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	67	TYR	0	0.035	-0.096	8.934	0.118	0.118	0.000	0.000	0.000	0.000
125	A	67	TYR	0	-0.078	0.094	8.546	0.077	0.077	0.000	0.000	0.000	0.000
126	A	68	VAL	0	0.074	-0.098	5.862	-0.645	-0.645	0.000	0.000	0.000	0.000
127	A	68	VAL	0	-0.041	0.106	6.792	0.000	0.000	0.000	0.000	0.000	0.000
128	A	69	GLU	0	0.180	-0.076	4.365	0.112	0.190	-0.001	-0.008	-0.069	0.000
129	A	69	GLU	-1	-0.957	-0.790	3.383	5.261	6.508	0.087	-0.644	-0.690	-0.004
130	A	70	GLU	0	0.051	-0.136	5.551	0.061	0.061	0.000	0.000	0.000	0.000
131	A	70	GLU	-1	-1.028	-0.855	10.251	-0.062	-0.062	0.000	0.000	0.000	0.000
132	A	71	GLY	0	-0.058	-0.128	8.569	-0.019	-0.019	0.000	0.000	0.000	0.000
133	A	72	GLY	0	0.014	0.002	8.897	0.221	0.221	0.000	0.000	0.000	0.000
134	A	73	SER	0	-0.110	-0.077	10.682	-0.127	-0.127	0.000	0.000	0.000	0.000
135	A	73	SER	0	0.064	0.072	13.075	0.027	0.027	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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