FMO DATABASE

FMODB ID: LN9M9

Calculation Name: 2VIH-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VIH

Chain ID: B

ChEMBL ID:

UniProt ID: Q933Z0

Base Structure: X-ray

Registration Date: 2023-09-23

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

DOI:

IFIE MAP

IFIE Diagram

Modeling method

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1119627.091812
FMO2-HF: Nuclear repulsion	1066842.448444
FMO2-HF: Total energy	-52784.643368
FMO2-MP2: Total energy	-52937.835355

3D Structure

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(B:5:VAL)

Summations of interaction energy for fragment #1(B:5:VAL)

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.
-4.034	0.096	3.612	-1.812	-5.926	-0.007

Interaction energy analysis for fragmet #1(B:5:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.033

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	B	7	TYR	0	-0.037	-0.027	3.308	-1.083	1.354	0.137	-0.777	-1.798	-0.003
4	B	8	LYS	1	0.877	0.946	4.256	0.127	0.207	0.000	-0.015	-0.064	0.000
5	B	9	SER	0	0.051	0.005	7.693	-0.117	-0.117	0.000	0.000	0.000	0.000
6	B	10	ASN	0	-0.082	-0.015	10.884	0.047	0.047	0.000	0.000	0.000	0.000
7	B	11	HIS	0	-0.005	-0.013	14.258	-0.037	-0.037	0.000	0.000	0.000	0.000
8	B	12	ASN	0	-0.018	-0.015	16.538	0.008	0.008	0.000	0.000	0.000	0.000
9	B	13	VAL	0	-0.002	0.001	11.412	-0.020	-0.020	0.000	0.000	0.000	0.000
10	B	14	VAL	0	0.059	0.042	7.708	0.003	0.003	0.000	0.000	0.000	0.000
11	B	15	TYR	0	-0.023	-0.034	7.540	0.034	0.034	0.000	0.000	0.000	0.000
12	B	16	SER	0	0.091	0.043	2.515	-0.241	-0.114	1.832	-0.596	-1.362	-0.008
13	B	17	CYS	0	-0.090	-0.020	4.707	-0.098	-0.043	-0.001	-0.006	-0.047	0.000
14	B	18	LYS	1	0.949	0.987	2.580	-2.876	-1.887	0.782	-0.418	-1.352	0.005
15	B	19	TYR	0	0.000	-0.011	7.505	-0.100	-0.100	0.000	0.000	0.000	0.000
16	B	20	HIS	0	0.026	0.032	11.014	0.057	0.057	0.000	0.000	0.000	0.000
17	B	21	ILE	0	-0.026	-0.035	13.124	-0.062	-0.062	0.000	0.000	0.000	0.000
18	B	22	VAL	0	0.046	0.026	16.429	0.018	0.018	0.000	0.000	0.000	0.000
19	B	23	TRP	0	-0.038	-0.018	19.339	-0.024	-0.024	0.000	0.000	0.000	0.000
20	B	24	CYS	0	0.028	0.009	23.215	0.009	0.009	0.000	0.000	0.000	0.000
21	B	25	PRO	0	-0.004	-0.005	26.452	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	26	LYS	1	0.950	0.972	29.574	-0.053	-0.053	0.000	0.000	0.000	0.000
23	B	27	TYR	0	-0.008	-0.027	32.695	0.002	0.002	0.000	0.000	0.000	0.000
24	B	28	ARG	1	0.926	0.975	29.409	-0.094	-0.094	0.000	0.000	0.000	0.000
25	B	29	ARG	1	0.939	0.975	31.810	-0.064	-0.064	0.000	0.000	0.000	0.000
26	B	30	LYS	1	0.976	0.981	31.239	-0.089	-0.089	0.000	0.000	0.000	0.000
27	B	31	VAL	0	-0.016	-0.022	30.872	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	32	LEU	0	-0.029	0.004	25.339	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	33	VAL	0	0.036	0.011	28.320	0.007	0.007	0.000	0.000	0.000	0.000
30	B	34	GLY	0	0.041	0.015	30.406	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	35	ALA	0	0.051	0.017	30.153	0.007	0.007	0.000	0.000	0.000	0.000
32	B	36	VAL	0	-0.014	0.008	29.478	0.002	0.002	0.000	0.000	0.000	0.000
33	B	37	GLU	-1	-0.945	-0.967	25.198	0.183	0.183	0.000	0.000	0.000	0.000
34	B	38	MET	0	0.020	-0.003	25.195	0.012	0.012	0.000	0.000	0.000	0.000
35	B	39	ARG	1	0.898	0.938	26.034	-0.102	-0.102	0.000	0.000	0.000	0.000
36	B	40	LEU	0	-0.058	-0.021	23.677	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	41	LYS	1	0.955	0.970	21.428	-0.234	-0.234	0.000	0.000	0.000	0.000
38	B	42	GLU	-1	-0.843	-0.914	21.624	0.146	0.146	0.000	0.000	0.000	0.000
39	B	43	ILE	0	0.002	-0.002	22.968	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	44	ILE	0	-0.039	-0.025	18.363	-0.008	-0.008	0.000	0.000	0.000	0.000
41	B	45	GLN	0	0.028	0.013	16.445	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	46	GLU	-1	-0.970	-0.979	19.330	0.094	0.094	0.000	0.000	0.000	0.000
43	B	47	VAL	0	-0.023	-0.030	19.672	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	48	ALA	0	-0.009	0.000	15.447	-0.015	-0.015	0.000	0.000	0.000	0.000
45	B	49	LYS	1	0.985	1.002	16.684	-0.135	-0.135	0.000	0.000	0.000	0.000
46	B	50	GLU	-1	-0.870	-0.921	17.980	0.040	0.040	0.000	0.000	0.000	0.000
47	B	51	LEU	0	-0.084	-0.050	17.587	-0.021	-0.021	0.000	0.000	0.000	0.000
48	B	52	ARG	1	0.920	0.968	14.944	0.020	0.020	0.000	0.000	0.000	0.000
49	B	53	VAL	0	-0.036	-0.012	12.290	-0.017	-0.017	0.000	0.000	0.000	0.000
50	B	54	GLU	-1	-0.874	-0.931	7.091	0.773	0.773	0.000	0.000	0.000	0.000
51	B	55	ILE	0	-0.045	-0.035	10.547	0.027	0.027	0.000	0.000	0.000	0.000
52	B	56	ILE	0	-0.014	-0.011	6.166	0.030	0.030	0.000	0.000	0.000	0.000
53	B	57	GLU	-1	-0.863	-0.935	10.250	0.595	0.595	0.000	0.000	0.000	0.000
54	B	58	MET	0	-0.071	-0.026	12.888	-0.060	-0.060	0.000	0.000	0.000	0.000
55	B	59	GLN	0	-0.010	0.007	16.348	-0.043	-0.043	0.000	0.000	0.000	0.000
56	B	60	THR	0	0.003	-0.012	18.995	-0.011	-0.011	0.000	0.000	0.000	0.000
57	B	61	ASP	-1	-0.815	-0.887	22.381	0.162	0.162	0.000	0.000	0.000	0.000
58	B	62	LYS	1	0.969	0.960	25.223	-0.122	-0.122	0.000	0.000	0.000	0.000
59	B	63	ASP	-1	-0.906	-0.958	27.557	0.110	0.110	0.000	0.000	0.000	0.000
60	B	64	HIS	1	0.880	0.942	22.637	-0.150	-0.150	0.000	0.000	0.000	0.000
61	B	65	ILE	0	0.025	0.021	20.103	0.004	0.004	0.000	0.000	0.000	0.000
62	B	66	HIS	0	-0.041	-0.026	16.533	-0.032	-0.032	0.000	0.000	0.000	0.000
63	B	67	ILE	0	0.017	-0.009	14.035	0.010	0.010	0.000	0.000	0.000	0.000
64	B	68	LEU	0	0.030	0.033	7.642	-0.044	-0.044	0.000	0.000	0.000	0.000
65	B	69	ALA	0	-0.007	-0.013	10.408	0.045	0.045	0.000	0.000	0.000	0.000
66	B	70	ASP	-1	-0.838	-0.928	5.794	0.251	0.251	0.000	0.000	0.000	0.000
67	B	71	ILE	0	-0.059	-0.040	8.336	-0.053	-0.053	0.000	0.000	0.000	0.000
68	B	72	ASP	-1	-0.763	-0.870	10.665	-0.226	-0.226	0.000	0.000	0.000	0.000
69	B	73	PRO	0	0.018	-0.011	10.408	0.041	0.041	0.000	0.000	0.000	0.000
70	B	74	SER	0	-0.009	-0.004	13.234	0.011	0.011	0.000	0.000	0.000	0.000
71	B	75	PHE	0	-0.053	-0.009	15.511	0.023	0.023	0.000	0.000	0.000	0.000
72	B	76	GLY	0	0.039	0.013	15.498	0.011	0.011	0.000	0.000	0.000	0.000
73	B	77	VAL	0	0.042	0.020	14.079	0.018	0.018	0.000	0.000	0.000	0.000
74	B	78	MET	0	0.040	0.004	15.813	0.020	0.020	0.000	0.000	0.000	0.000
75	B	79	LYS	1	0.925	0.981	19.232	0.006	0.006	0.000	0.000	0.000	0.000
76	B	80	PHE	0	0.081	0.041	16.038	0.003	0.003	0.000	0.000	0.000	0.000
77	B	81	ILE	0	0.044	0.013	17.422	0.008	0.008	0.000	0.000	0.000	0.000
78	B	82	LYS	1	0.923	0.957	20.182	-0.012	-0.012	0.000	0.000	0.000	0.000
79	B	83	THR	0	-0.023	-0.001	21.705	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.045	0.036	20.210	0.001	0.001	0.000	0.000	0.000	0.000
81	B	85	LYS	1	0.874	0.967	22.348	-0.082	-0.082	0.000	0.000	0.000	0.000
82	B	86	GLY	0	0.018	0.000	24.971	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	87	ARG	1	0.865	0.917	24.673	-0.075	-0.075	0.000	0.000	0.000	0.000
84	B	88	SER	0	0.026	-0.001	25.073	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	89	SER	0	-0.039	-0.018	27.165	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	90	ARG	1	0.931	0.953	30.039	-0.050	-0.050	0.000	0.000	0.000	0.000
87	B	91	ILE	0	0.074	0.031	28.280	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	92	LEU	0	0.044	0.030	27.978	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	93	ARG	1	0.804	0.893	31.947	-0.059	-0.059	0.000	0.000	0.000	0.000
90	B	94	GLN	0	-0.086	-0.037	34.648	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	95	GLU	-1	-0.790	-0.879	32.513	0.087	0.087	0.000	0.000	0.000	0.000
92	B	96	PHE	0	0.002	0.003	32.009	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.101	0.041	36.808	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	98	HIS	0	-0.006	-0.013	35.485	-0.006	-0.006	0.000	0.000	0.000	0.000
95	B	99	LEU	0	-0.022	-0.009	32.627	0.000	0.000	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.919	0.957	36.667	-0.047	-0.047	0.000	0.000	0.000	0.000
97	B	101	THR	0	-0.013	-0.008	38.695	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	102	LYS	1	0.943	0.980	39.473	-0.055	-0.055	0.000	0.000	0.000	0.000
99	B	103	LEU	0	-0.010	0.000	34.364	0.001	0.001	0.000	0.000	0.000	0.000
100	B	104	PRO	0	0.044	0.053	37.301	0.000	0.000	0.000	0.000	0.000	0.000
101	B	105	THR	0	-0.036	-0.032	33.322	-0.003	-0.003	0.000	0.000	0.000	0.000
102	B	106	LEU	0	0.044	0.030	29.456	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	107	TRP	0	0.014	0.030	26.414	0.003	0.003	0.000	0.000	0.000	0.000
104	B	108	THR	0	0.027	0.007	28.374	-0.008	-0.008	0.000	0.000	0.000	0.000
105	B	109	ASN	0	0.026	0.007	28.478	0.006	0.006	0.000	0.000	0.000	0.000
106	B	110	SER	0	-0.037	-0.008	26.095	-0.003	-0.003	0.000	0.000	0.000	0.000
107	B	111	CYS	0	-0.026	-0.030	21.153	0.005	0.005	0.000	0.000	0.000	0.000
108	B	112	PHE	0	-0.005	0.019	16.360	-0.016	-0.016	0.000	0.000	0.000	0.000
109	B	113	ILE	0	0.017	-0.012	15.212	0.020	0.020	0.000	0.000	0.000	0.000
110	B	114	SER	0	-0.009	0.005	13.957	-0.030	-0.030	0.000	0.000	0.000	0.000
111	B	115	THR	0	0.049	0.025	10.111	0.064	0.064	0.000	0.000	0.000	0.000
112	B	116	VAL	0	0.002	0.005	6.535	-0.007	-0.007	0.000	0.000	0.000	0.000
113	B	117	GLY	0	0.016	0.003	4.046	-0.113	-0.027	0.000	-0.023	-0.062	0.000
114	B	118	GLY	0	-0.006	-0.007	2.672	-0.427	0.367	0.754	-0.533	-1.015	-0.001
115	B	119	ALA	0	0.003	0.013	3.297	0.251	-0.187	0.108	0.556	-0.226	0.000
116	B	120	PRO	0	0.019	0.014	6.848	0.056	0.056	0.000	0.000	0.000	0.000
117	B	121	LEU	0	0.062	0.010	9.965	-0.078	-0.078	0.000	0.000	0.000	0.000
118	B	122	ASN	0	0.022	0.001	12.271	-0.028	-0.028	0.000	0.000	0.000	0.000
119	B	123	VAL	0	0.019	0.025	10.589	-0.012	-0.012	0.000	0.000	0.000	0.000
120	B	124	VAL	0	0.020	0.008	8.751	-0.043	-0.043	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.942	0.963	11.702	0.120	0.120	0.000	0.000	0.000	0.000
122	B	126	GLN	0	0.022	0.012	15.303	-0.005	-0.005	0.000	0.000	0.000	0.000
123	B	127	TYR	0	-0.017	-0.016	12.462	-0.034	-0.034	0.000	0.000	0.000	0.000
124	B	128	ILE	0	-0.012	-0.005	13.741	-0.008	-0.008	0.000	0.000	0.000	0.000
125	B	129	GLU	-1	-0.963	-0.971	16.238	-0.161	-0.161	0.000	0.000	0.000	0.000
126	B	130	ASN	0	-0.011	-0.002	17.594	0.042	0.042	0.000	0.000	0.000	0.000
127	B	131	GLN	0	-0.038	-0.008	15.661	0.001	0.001	0.000	0.000	0.000	0.000
128	B	132	GLN	0	-0.060	-0.029	19.509	-0.007	-0.007	0.000	0.000	0.000	0.000
129	B	133	ASN	0	-0.015	0.001	22.186	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:5:VAL)