FMO DATABASE

FMODB ID: 98KN2

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	OptHSide
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1120461.110347
FMO2-HF: Nuclear repulsion	1067675.711968
FMO2-HF: Total energy	-52785.39838
FMO2-MP2: Total energy	-52938.597204

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.
-4.92	-0.591	3.291	-1.808	-5.815	-0.002

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 : 0.004 / q_NPA : -0.003

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	-0.029	-0.023	3.451	-0.932	2.036	0.041	-1.137	-1.873	0.004
4	B	8	LYS	1	0.831	0.904	4.411	0.099	0.165	-0.001	-0.012	-0.054	0.000
5	B	9	SER	0	0.059	0.010	7.783	-0.047	-0.047	0.000	0.000	0.000	0.000
6	B	10	ASN	0	-0.078	-0.037	10.978	0.024	0.024	0.000	0.000	0.000	0.000
7	B	11	HIS	0	-0.015	-0.011	14.321	-0.046	-0.046	0.000	0.000	0.000	0.000
8	B	12	ASN	0	-0.015	-0.017	16.630	0.005	0.005	0.000	0.000	0.000	0.000
9	B	13	VAL	0	-0.008	0.008	11.593	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	14	VAL	0	0.059	0.041	7.945	-0.025	-0.025	0.000	0.000	0.000	0.000
11	B	15	TYR	0	-0.041	-0.051	7.576	0.077	0.077	0.000	0.000	0.000	0.000
12	B	16	SER	0	0.074	0.029	2.590	-0.394	-0.026	1.558	-0.608	-1.318	-0.007
13	B	17	CYS	0	-0.086	-0.022	4.822	0.013	0.067	-0.001	-0.005	-0.048	0.000
14	B	18	LYS	1	0.889	0.951	2.542	-2.745	-1.918	0.476	-0.256	-1.048	0.002
15	B	19	TYR	0	0.007	-0.011	7.452	-0.036	-0.036	0.000	0.000	0.000	0.000
16	B	20	HIS	0	0.031	0.039	10.923	-0.012	-0.012	0.000	0.000	0.000	0.000
17	B	21	ILE	0	-0.025	-0.035	13.156	-0.072	-0.072	0.000	0.000	0.000	0.000
18	B	22	VAL	0	0.039	0.025	16.375	0.003	0.003	0.000	0.000	0.000	0.000
19	B	23	TRP	0	-0.020	-0.012	19.210	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	24	CYS	0	-0.001	-0.007	23.217	0.009	0.009	0.000	0.000	0.000	0.000
21	B	25	PRO	0	0.007	0.005	26.474	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	26	LYS	1	0.942	0.966	29.560	-0.095	-0.095	0.000	0.000	0.000	0.000
23	B	27	TYR	0	-0.001	-0.027	32.635	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	28	ARG	1	0.902	0.960	29.140	-0.177	-0.177	0.000	0.000	0.000	0.000
25	B	29	ARG	1	0.949	0.976	31.816	-0.096	-0.096	0.000	0.000	0.000	0.000
26	B	30	LYS	1	0.884	0.922	31.077	-0.150	-0.150	0.000	0.000	0.000	0.000
27	B	31	VAL	0	-0.021	-0.023	31.111	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	32	LEU	0	-0.030	0.007	25.495	-0.008	-0.008	0.000	0.000	0.000	0.000
29	B	33	VAL	0	0.015	-0.005	28.326	0.009	0.009	0.000	0.000	0.000	0.000
30	B	34	GLY	0	0.042	0.016	30.415	-0.007	-0.007	0.000	0.000	0.000	0.000
31	B	35	ALA	0	0.047	0.016	30.176	0.006	0.006	0.000	0.000	0.000	0.000
32	B	36	VAL	0	-0.003	0.008	29.536	0.000	0.000	0.000	0.000	0.000	0.000
33	B	37	GLU	-1	-0.877	-0.910	24.971	0.203	0.203	0.000	0.000	0.000	0.000
34	B	38	MET	0	0.031	0.005	25.271	0.014	0.014	0.000	0.000	0.000	0.000
35	B	39	ARG	1	0.856	0.882	25.923	-0.084	-0.084	0.000	0.000	0.000	0.000
36	B	40	LEU	0	-0.048	-0.021	23.599	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	41	LYS	1	0.902	0.938	21.495	-0.229	-0.229	0.000	0.000	0.000	0.000
38	B	42	GLU	-1	-0.840	-0.896	21.530	0.106	0.106	0.000	0.000	0.000	0.000
39	B	43	ILE	0	-0.004	-0.010	22.916	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	44	ILE	0	-0.020	-0.018	18.333	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	45	GLN	0	0.030	0.016	16.027	-0.013	-0.013	0.000	0.000	0.000	0.000
42	B	46	GLU	-1	-0.916	-0.941	19.325	0.054	0.054	0.000	0.000	0.000	0.000
43	B	47	VAL	0	-0.008	-0.023	19.741	-0.014	-0.014	0.000	0.000	0.000	0.000
44	B	48	ALA	0	-0.004	-0.001	15.356	-0.011	-0.011	0.000	0.000	0.000	0.000
45	B	49	LYS	1	0.994	1.005	16.717	-0.027	-0.027	0.000	0.000	0.000	0.000
46	B	50	GLU	-1	-0.874	-0.900	18.036	0.014	0.014	0.000	0.000	0.000	0.000
47	B	51	LEU	0	-0.091	-0.050	17.830	-0.016	-0.016	0.000	0.000	0.000	0.000
48	B	52	ARG	1	0.920	0.965	15.117	0.080	0.080	0.000	0.000	0.000	0.000
49	B	53	VAL	0	-0.031	-0.008	12.352	-0.005	-0.005	0.000	0.000	0.000	0.000
50	B	54	GLU	-1	-0.856	-0.916	6.763	0.322	0.322	0.000	0.000	0.000	0.000
51	B	55	ILE	0	-0.034	-0.031	10.478	0.095	0.095	0.000	0.000	0.000	0.000
52	B	56	ILE	0	-0.030	-0.019	5.966	0.002	0.002	0.000	0.000	0.000	0.000
53	B	57	GLU	-1	-0.839	-0.917	10.148	0.538	0.538	0.000	0.000	0.000	0.000
54	B	58	MET	0	-0.088	-0.036	12.908	-0.023	-0.023	0.000	0.000	0.000	0.000
55	B	59	GLN	0	-0.006	0.009	16.372	-0.069	-0.069	0.000	0.000	0.000	0.000
56	B	60	THR	0	-0.015	-0.032	18.993	0.000	0.000	0.000	0.000	0.000	0.000
57	B	61	ASP	-1	-0.795	-0.858	22.380	0.234	0.234	0.000	0.000	0.000	0.000
58	B	62	LYS	1	0.983	0.972	25.206	-0.159	-0.159	0.000	0.000	0.000	0.000
59	B	63	ASP	-1	-0.823	-0.897	27.569	0.167	0.167	0.000	0.000	0.000	0.000
60	B	64	HIS	1	0.870	0.915	22.747	-0.233	-0.233	0.000	0.000	0.000	0.000
61	B	65	ILE	0	0.030	0.023	20.083	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	66	HIS	0	-0.042	-0.032	16.552	-0.037	-0.037	0.000	0.000	0.000	0.000
63	B	67	ILE	0	0.014	-0.009	13.928	-0.013	-0.013	0.000	0.000	0.000	0.000
64	B	68	LEU	0	0.028	0.037	7.770	0.001	0.001	0.000	0.000	0.000	0.000
65	B	69	ALA	0	-0.001	-0.009	10.268	-0.010	-0.010	0.000	0.000	0.000	0.000
66	B	70	ASP	-1	-0.731	-0.853	5.803	0.591	0.591	0.000	0.000	0.000	0.000
67	B	71	ILE	0	-0.069	-0.043	8.254	-0.125	-0.125	0.000	0.000	0.000	0.000
68	B	72	ASP	-1	-0.713	-0.822	10.746	-0.143	-0.143	0.000	0.000	0.000	0.000
69	B	73	PRO	0	0.006	-0.008	10.546	0.039	0.039	0.000	0.000	0.000	0.000
70	B	74	SER	0	-0.012	-0.015	13.310	0.004	0.004	0.000	0.000	0.000	0.000
71	B	75	PHE	0	-0.072	-0.019	15.603	0.010	0.010	0.000	0.000	0.000	0.000
72	B	76	GLY	0	0.046	0.017	15.579	0.008	0.008	0.000	0.000	0.000	0.000
73	B	77	VAL	0	0.030	0.012	14.042	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	78	MET	0	0.045	0.008	15.828	0.007	0.007	0.000	0.000	0.000	0.000
75	B	79	LYS	1	0.940	0.989	19.290	-0.041	-0.041	0.000	0.000	0.000	0.000
76	B	80	PHE	0	0.072	0.044	15.823	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	81	ILE	0	0.033	0.012	17.271	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	82	LYS	1	0.924	0.961	20.037	-0.075	-0.075	0.000	0.000	0.000	0.000
79	B	83	THR	0	-0.026	-0.011	21.696	-0.012	-0.012	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.049	0.038	20.081	-0.006	-0.006	0.000	0.000	0.000	0.000
81	B	85	LYS	1	0.849	0.952	22.235	-0.163	-0.163	0.000	0.000	0.000	0.000
82	B	86	GLY	0	0.018	-0.002	24.819	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	87	ARG	1	0.790	0.850	25.014	-0.065	-0.065	0.000	0.000	0.000	0.000
84	B	88	SER	0	0.035	-0.006	24.967	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	89	SER	0	-0.054	-0.026	27.046	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	90	ARG	1	0.911	0.954	29.897	-0.059	-0.059	0.000	0.000	0.000	0.000
87	B	91	ILE	0	0.078	0.029	28.232	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	92	LEU	0	0.047	0.030	27.683	-0.003	-0.003	0.000	0.000	0.000	0.000
89	B	93	ARG	1	0.804	0.895	31.821	-0.082	-0.082	0.000	0.000	0.000	0.000
90	B	94	GLN	0	-0.076	-0.038	34.537	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	95	GLU	-1	-0.781	-0.849	32.076	0.075	0.075	0.000	0.000	0.000	0.000
92	B	96	PHE	0	0.006	0.001	31.808	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.098	0.037	36.669	0.002	0.002	0.000	0.000	0.000	0.000
94	B	98	HIS	0	0.002	-0.004	35.479	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	99	LEU	0	-0.019	-0.009	32.445	0.003	0.003	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.929	0.961	36.486	-0.055	-0.055	0.000	0.000	0.000	0.000
97	B	101	THR	0	-0.023	-0.013	38.529	-0.001	-0.001	0.000	0.000	0.000	0.000
98	B	102	LYS	1	0.945	0.983	39.353	-0.070	-0.070	0.000	0.000	0.000	0.000
99	B	103	LEU	0	0.001	0.005	34.320	0.004	0.004	0.000	0.000	0.000	0.000
100	B	104	PRO	0	0.033	0.044	37.322	-0.002	-0.002	0.000	0.000	0.000	0.000
101	B	105	THR	0	-0.038	-0.028	33.120	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	106	LEU	0	0.045	0.030	29.253	0.000	0.000	0.000	0.000	0.000	0.000
103	B	107	TRP	0	0.007	0.024	26.035	0.011	0.011	0.000	0.000	0.000	0.000
104	B	108	THR	0	0.036	0.015	28.366	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	109	ASN	0	0.028	0.011	28.382	0.004	0.004	0.000	0.000	0.000	0.000
106	B	110	SER	0	-0.005	0.002	26.001	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	111	CYS	0	-0.029	-0.024	21.167	-0.006	-0.006	0.000	0.000	0.000	0.000
108	B	112	PHE	0	0.002	0.019	16.363	-0.020	-0.020	0.000	0.000	0.000	0.000
109	B	113	ILE	0	0.009	-0.016	14.967	0.015	0.015	0.000	0.000	0.000	0.000
110	B	114	SER	0	0.023	0.021	12.914	-0.044	-0.044	0.000	0.000	0.000	0.000
111	B	115	THR	0	0.021	0.019	10.015	0.036	0.036	0.000	0.000	0.000	0.000
112	B	116	VAL	0	-0.027	-0.015	6.333	-0.029	-0.029	0.000	0.000	0.000	0.000
113	B	117	GLY	0	0.032	0.012	4.077	-0.205	-0.116	0.000	-0.025	-0.064	0.000
114	B	118	GLY	0	0.000	-0.004	2.597	-0.319	0.446	1.069	-0.669	-1.165	-0.001
115	B	119	ALA	0	-0.005	0.010	3.128	0.203	-0.605	0.149	0.904	-0.245	0.000
116	B	120	PRO	0	0.017	0.014	6.703	-0.070	-0.070	0.000	0.000	0.000	0.000
117	B	121	LEU	0	0.055	0.009	9.842	-0.089	-0.089	0.000	0.000	0.000	0.000
118	B	122	ASN	0	0.036	0.005	12.192	-0.009	-0.009	0.000	0.000	0.000	0.000
119	B	123	VAL	0	0.024	0.025	10.551	-0.057	-0.057	0.000	0.000	0.000	0.000
120	B	124	VAL	0	0.015	0.007	8.670	-0.088	-0.088	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.827	0.896	11.629	-0.180	-0.180	0.000	0.000	0.000	0.000
122	B	126	GLN	0	0.006	-0.006	15.215	-0.048	-0.048	0.000	0.000	0.000	0.000
123	B	127	TYR	0	-0.010	0.001	12.160	-0.043	-0.043	0.000	0.000	0.000	0.000
124	B	128	ILE	0	-0.002	0.000	13.276	-0.039	-0.039	0.000	0.000	0.000	0.000
125	B	129	GLU	-1	-0.804	-0.871	16.241	0.065	0.065	0.000	0.000	0.000	0.000
126	B	130	ASN	0	-0.070	-0.049	17.751	-0.011	-0.011	0.000	0.000	0.000	0.000
127	B	131	GLN	0	-0.019	0.007	15.218	-0.003	-0.003	0.000	0.000	0.000	0.000
128	B	132	GLN	0	-0.071	-0.042	19.521	-0.014	-0.014	0.000	0.000	0.000	0.000
129	B	133	ASN	0	-0.010	0.007	22.123	-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)