FMO DATABASE

FMODB ID: MNJ6Z

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	OptAll
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	-1120081.868504
FMO2-HF: Nuclear repulsion	1067296.138048
FMO2-HF: Total energy	-52785.730456
FMO2-MP2: Total energy	-52938.879082

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.
-4.557	-0.117	3.688	-2.062	-6.067	-0.004

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 : 0.017 / 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	-0.009	-0.013	3.229	-1.111	1.783	0.123	-1.261	-1.757	0.001
4	B	8	LYS	1	0.809	0.886	4.547	0.670	0.738	-0.001	-0.008	-0.059	0.000
5	B	9	SER	0	0.047	0.014	7.739	-0.034	-0.034	0.000	0.000	0.000	0.000
6	B	10	ASN	0	-0.073	-0.045	11.128	0.046	0.046	0.000	0.000	0.000	0.000
7	B	11	HIS	0	0.007	0.002	14.606	-0.045	-0.045	0.000	0.000	0.000	0.000
8	B	12	ASN	0	-0.033	-0.019	16.852	0.022	0.022	0.000	0.000	0.000	0.000
9	B	13	VAL	0	0.003	0.018	12.086	0.002	0.002	0.000	0.000	0.000	0.000
10	B	14	VAL	0	0.045	0.016	8.785	-0.031	-0.031	0.000	0.000	0.000	0.000
11	B	15	TYR	0	-0.041	-0.053	7.632	0.062	0.062	0.000	0.000	0.000	0.000
12	B	16	SER	0	0.058	0.018	2.646	-0.627	-0.323	1.432	-0.519	-1.217	-0.007
13	B	17	CYS	0	-0.070	-0.011	4.883	0.119	0.180	-0.001	-0.003	-0.057	0.000
14	B	18	LYS	1	0.879	0.955	2.453	-1.719	-0.824	0.854	-0.336	-1.413	0.003
15	B	19	TYR	0	0.024	-0.005	6.785	0.019	0.019	0.000	0.000	0.000	0.000
16	B	20	HIS	0	0.035	0.037	10.233	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	21	ILE	0	-0.025	-0.024	12.522	-0.070	-0.070	0.000	0.000	0.000	0.000
18	B	22	VAL	0	0.031	0.018	15.704	0.008	0.008	0.000	0.000	0.000	0.000
19	B	23	TRP	0	-0.031	-0.021	19.054	-0.023	-0.023	0.000	0.000	0.000	0.000
20	B	24	CYS	0	0.014	0.005	22.807	0.010	0.010	0.000	0.000	0.000	0.000
21	B	25	PRO	0	0.003	0.013	26.379	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	26	LYS	1	0.883	0.939	29.472	-0.071	-0.071	0.000	0.000	0.000	0.000
23	B	27	TYR	0	0.024	-0.020	32.377	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	28	ARG	1	0.904	0.963	28.446	-0.154	-0.154	0.000	0.000	0.000	0.000
25	B	29	ARG	1	0.955	0.983	31.917	-0.080	-0.080	0.000	0.000	0.000	0.000
26	B	30	LYS	1	0.894	0.927	31.302	-0.135	-0.135	0.000	0.000	0.000	0.000
27	B	31	VAL	0	-0.019	-0.014	31.337	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	32	LEU	0	-0.033	-0.001	25.488	-0.007	-0.007	0.000	0.000	0.000	0.000
29	B	33	VAL	0	0.017	-0.007	28.620	0.010	0.010	0.000	0.000	0.000	0.000
30	B	34	GLY	0	0.054	0.031	30.093	-0.008	-0.008	0.000	0.000	0.000	0.000
31	B	35	ALA	0	0.047	0.018	29.527	0.004	0.004	0.000	0.000	0.000	0.000
32	B	36	VAL	0	-0.014	0.002	29.289	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	37	GLU	-1	-0.854	-0.911	25.023	0.179	0.179	0.000	0.000	0.000	0.000
34	B	38	MET	0	0.007	0.010	24.870	0.014	0.014	0.000	0.000	0.000	0.000
35	B	39	ARG	1	0.860	0.880	25.280	-0.060	-0.060	0.000	0.000	0.000	0.000
36	B	40	LEU	0	-0.049	-0.021	23.345	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	41	LYS	1	0.864	0.922	20.862	-0.209	-0.209	0.000	0.000	0.000	0.000
38	B	42	GLU	-1	-0.840	-0.909	21.030	0.080	0.080	0.000	0.000	0.000	0.000
39	B	43	ILE	0	-0.008	-0.010	22.604	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	44	ILE	0	-0.024	-0.021	18.163	-0.009	-0.009	0.000	0.000	0.000	0.000
41	B	45	GLN	0	0.051	0.018	15.371	-0.021	-0.021	0.000	0.000	0.000	0.000
42	B	46	GLU	-1	-0.907	-0.925	19.033	0.015	0.015	0.000	0.000	0.000	0.000
43	B	47	VAL	0	-0.008	-0.016	19.732	-0.016	-0.016	0.000	0.000	0.000	0.000
44	B	48	ALA	0	-0.012	-0.004	15.235	-0.015	-0.015	0.000	0.000	0.000	0.000
45	B	49	LYS	1	0.989	0.997	16.547	0.007	0.007	0.000	0.000	0.000	0.000
46	B	50	GLU	-1	-0.875	-0.901	18.067	-0.033	-0.033	0.000	0.000	0.000	0.000
47	B	51	LEU	0	-0.089	-0.063	18.005	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	52	ARG	1	0.928	0.970	15.249	0.138	0.138	0.000	0.000	0.000	0.000
49	B	53	VAL	0	-0.032	0.002	12.211	-0.031	-0.031	0.000	0.000	0.000	0.000
50	B	54	GLU	-1	-0.837	-0.912	6.345	0.070	0.070	0.000	0.000	0.000	0.000
51	B	55	ILE	0	-0.038	-0.034	9.912	0.095	0.095	0.000	0.000	0.000	0.000
52	B	56	ILE	0	-0.025	-0.008	5.519	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	57	GLU	-1	-0.806	-0.895	9.731	0.480	0.480	0.000	0.000	0.000	0.000
54	B	58	MET	0	-0.108	-0.044	12.855	-0.034	-0.034	0.000	0.000	0.000	0.000
55	B	59	GLN	0	0.003	0.014	16.258	-0.069	-0.069	0.000	0.000	0.000	0.000
56	B	60	THR	0	-0.020	-0.042	19.106	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	61	ASP	-1	-0.799	-0.866	22.454	0.210	0.210	0.000	0.000	0.000	0.000
58	B	62	LYS	1	0.989	0.988	25.509	-0.150	-0.150	0.000	0.000	0.000	0.000
59	B	63	ASP	-1	-0.829	-0.900	27.857	0.144	0.144	0.000	0.000	0.000	0.000
60	B	64	HIS	1	0.856	0.895	22.911	-0.202	-0.202	0.000	0.000	0.000	0.000
61	B	65	ILE	0	0.029	0.022	19.904	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	66	HIS	0	-0.033	-0.021	16.735	-0.035	-0.035	0.000	0.000	0.000	0.000
63	B	67	ILE	0	0.023	-0.003	13.468	-0.014	-0.014	0.000	0.000	0.000	0.000
64	B	68	LEU	0	0.017	0.016	7.689	0.006	0.006	0.000	0.000	0.000	0.000
65	B	69	ALA	0	0.028	0.001	9.660	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	70	ASP	-1	-0.756	-0.859	6.129	-0.086	-0.086	0.000	0.000	0.000	0.000
67	B	71	ILE	0	-0.046	-0.032	8.196	-0.081	-0.081	0.000	0.000	0.000	0.000
68	B	72	ASP	-1	-0.705	-0.801	10.734	-0.304	-0.304	0.000	0.000	0.000	0.000
69	B	73	PRO	0	0.006	-0.008	10.703	0.063	0.063	0.000	0.000	0.000	0.000
70	B	74	SER	0	-0.022	-0.027	13.423	0.021	0.021	0.000	0.000	0.000	0.000
71	B	75	PHE	0	-0.055	-0.018	15.777	0.018	0.018	0.000	0.000	0.000	0.000
72	B	76	GLY	0	0.044	0.019	15.572	0.020	0.020	0.000	0.000	0.000	0.000
73	B	77	VAL	0	0.031	0.010	13.778	0.004	0.004	0.000	0.000	0.000	0.000
74	B	78	MET	0	0.039	0.007	15.546	0.015	0.015	0.000	0.000	0.000	0.000
75	B	79	LYS	1	0.882	0.968	18.947	0.011	0.011	0.000	0.000	0.000	0.000
76	B	80	PHE	0	0.066	0.044	15.642	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	81	ILE	0	0.038	0.019	16.857	0.001	0.001	0.000	0.000	0.000	0.000
78	B	82	LYS	1	0.939	0.965	19.803	-0.022	-0.022	0.000	0.000	0.000	0.000
79	B	83	THR	0	-0.008	-0.012	21.779	-0.009	-0.009	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.048	0.040	20.019	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	85	LYS	1	0.836	0.934	22.170	-0.118	-0.118	0.000	0.000	0.000	0.000
82	B	86	GLY	0	0.013	0.004	24.662	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	87	ARG	1	0.781	0.848	25.052	-0.018	-0.018	0.000	0.000	0.000	0.000
84	B	88	SER	0	0.052	0.003	24.884	0.000	0.000	0.000	0.000	0.000	0.000
85	B	89	SER	0	-0.035	-0.026	26.978	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	90	ARG	1	0.903	0.945	29.870	-0.035	-0.035	0.000	0.000	0.000	0.000
87	B	91	ILE	0	0.066	0.041	28.492	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	92	LEU	0	0.059	0.033	27.385	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	93	ARG	1	0.784	0.877	31.680	-0.059	-0.059	0.000	0.000	0.000	0.000
90	B	94	GLN	0	-0.074	-0.044	34.513	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	95	GLU	-1	-0.774	-0.857	31.466	0.057	0.057	0.000	0.000	0.000	0.000
92	B	96	PHE	0	0.025	0.012	31.456	0.001	0.001	0.000	0.000	0.000	0.000
93	B	97	ASN	0	0.070	0.018	36.335	0.001	0.001	0.000	0.000	0.000	0.000
94	B	98	HIS	0	0.038	0.026	34.952	-0.006	-0.006	0.000	0.000	0.000	0.000
95	B	99	LEU	0	0.005	0.000	31.971	0.001	0.001	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.925	0.983	36.011	-0.039	-0.039	0.000	0.000	0.000	0.000
97	B	101	THR	0	-0.024	-0.020	38.311	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	102	LYS	1	0.895	0.948	38.914	-0.056	-0.056	0.000	0.000	0.000	0.000
99	B	103	LEU	0	0.013	0.014	33.805	0.004	0.004	0.000	0.000	0.000	0.000
100	B	104	PRO	0	0.021	0.034	36.815	-0.003	-0.003	0.000	0.000	0.000	0.000
101	B	105	THR	0	-0.015	-0.024	32.675	-0.005	-0.005	0.000	0.000	0.000	0.000
102	B	106	LEU	0	0.050	0.037	28.737	0.002	0.002	0.000	0.000	0.000	0.000
103	B	107	TRP	0	0.020	0.019	25.735	0.011	0.011	0.000	0.000	0.000	0.000
104	B	108	THR	0	0.028	0.012	27.485	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	109	ASN	0	0.008	0.005	28.094	0.003	0.003	0.000	0.000	0.000	0.000
106	B	110	SER	0	0.004	0.013	25.661	-0.002	-0.002	0.000	0.000	0.000	0.000
107	B	111	CYS	0	-0.020	-0.019	20.631	-0.007	-0.007	0.000	0.000	0.000	0.000
108	B	112	PHE	0	0.014	0.024	16.222	-0.018	-0.018	0.000	0.000	0.000	0.000
109	B	113	ILE	0	-0.002	-0.019	14.575	0.008	0.008	0.000	0.000	0.000	0.000
110	B	114	SER	0	0.014	0.021	12.358	-0.037	-0.037	0.000	0.000	0.000	0.000
111	B	115	THR	0	0.018	0.015	9.589	0.019	0.019	0.000	0.000	0.000	0.000
112	B	116	VAL	0	-0.027	-0.024	5.943	0.002	0.002	0.000	0.000	0.000	0.000
113	B	117	GLY	0	0.024	0.006	3.650	-0.392	-0.230	0.005	-0.056	-0.112	0.000
114	B	118	GLY	0	0.004	-0.002	2.588	-0.412	0.353	1.142	-0.681	-1.226	-0.001
115	B	119	ALA	0	0.016	0.019	3.222	0.211	-0.498	0.134	0.802	-0.226	0.000
116	B	120	PRO	0	0.015	0.019	6.928	-0.115	-0.115	0.000	0.000	0.000	0.000
117	B	121	LEU	0	0.053	0.010	9.999	-0.089	-0.089	0.000	0.000	0.000	0.000
118	B	122	ASN	0	0.031	0.007	12.240	-0.016	-0.016	0.000	0.000	0.000	0.000
119	B	123	VAL	0	0.033	0.025	10.770	-0.056	-0.056	0.000	0.000	0.000	0.000
120	B	124	VAL	0	-0.003	0.002	8.813	-0.082	-0.082	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.821	0.895	11.651	-0.187	-0.187	0.000	0.000	0.000	0.000
122	B	126	GLN	0	-0.001	-0.021	15.339	-0.041	-0.041	0.000	0.000	0.000	0.000
123	B	127	TYR	0	-0.020	0.005	11.529	-0.035	-0.035	0.000	0.000	0.000	0.000
124	B	128	ILE	0	-0.013	-0.012	13.420	-0.039	-0.039	0.000	0.000	0.000	0.000
125	B	129	GLU	-1	-0.785	-0.864	16.175	0.070	0.070	0.000	0.000	0.000	0.000
126	B	130	ASN	0	-0.029	-0.026	17.983	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	131	GLN	0	-0.029	0.015	14.978	0.004	0.004	0.000	0.000	0.000	0.000
128	B	132	GLN	0	-0.086	-0.059	19.421	-0.022	-0.022	0.000	0.000	0.000	0.000
129	B	133	ASN	0	-0.008	0.005	21.683	-0.005	-0.005	0.000	0.000	0.000	0.000

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