FMO DATABASE

FMODB ID: G6791

Calculation Name: 3VP7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VP7

Chain ID: A

ChEMBL ID:

UniProt ID: Q02948

Base Structure: X-ray

Registration Date: 2023-06-26

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1759801.761059
FMO2-HF: Nuclear repulsion	1694912.278053
FMO2-HF: Total energy	-64889.483006
FMO2-MP2: Total energy	-65081.349652

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(A:320:ILE)

Summations of interaction energy for fragment #1(A:320:ILE)

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.
-8.097	-1.811	5.846	-3.859	-8.273	-0.009

Interaction energy analysis for fragmet #1(A:320:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.021

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	322	ILE	0	0.091	0.025	3.642	-2.644	0.381	0.010	-1.672	-1.363	0.006
4	A	323	PHE	0	0.027	0.024	5.874	0.336	0.336	0.000	0.000	0.000	0.000
5	A	324	ASN	0	0.022	0.002	2.423	-3.320	-0.581	2.151	-1.620	-3.270	-0.018
6	A	325	ALA	0	0.001	0.006	2.292	-1.279	0.038	3.037	-1.949	-2.405	0.001
7	A	326	THR	0	0.003	0.008	3.123	1.704	0.412	0.025	1.643	-0.377	-0.001
8	A	327	PHE	0	0.010	-0.001	5.983	0.121	0.121	0.000	0.000	0.000	0.000
9	A	328	LYS	1	0.843	0.913	2.639	-1.962	-1.465	0.623	-0.261	-0.858	0.003
10	A	329	ILE	0	0.013	0.016	7.202	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	330	SER	0	-0.027	-0.014	9.659	0.125	0.125	0.000	0.000	0.000	0.000
12	A	331	HIS	0	0.004	0.003	11.864	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	332	SER	0	-0.025	-0.003	15.314	0.029	0.029	0.000	0.000	0.000	0.000
14	A	333	GLY	0	0.068	0.035	17.983	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	334	PRO	0	0.015	0.015	20.787	0.011	0.011	0.000	0.000	0.000	0.000
16	A	335	PHE	0	0.013	0.021	19.792	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	336	ALA	0	0.044	0.025	16.433	0.027	0.027	0.000	0.000	0.000	0.000
18	A	337	THR	0	-0.033	-0.028	13.755	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	338	ILE	0	0.017	0.008	11.131	0.027	0.027	0.000	0.000	0.000	0.000
20	A	339	ASN	0	-0.034	-0.028	8.583	0.040	0.040	0.000	0.000	0.000	0.000
21	A	340	GLY	0	0.000	0.011	10.937	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	341	LEU	0	-0.029	-0.005	13.763	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	342	ARG	1	0.845	0.877	16.239	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	343	LEU	0	-0.033	-0.016	17.854	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	344	GLY	0	0.007	-0.015	19.603	0.008	0.008	0.000	0.000	0.000	0.000
26	A	345	SER	0	-0.039	-0.023	22.978	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	346	ILE	0	-0.004	0.002	26.078	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	347	PRO	0	0.037	0.011	29.028	0.000	0.000	0.000	0.000	0.000	0.000
29	A	348	GLU	-1	-0.858	-0.935	30.205	0.071	0.071	0.000	0.000	0.000	0.000
30	A	349	SER	0	-0.070	-0.050	25.959	0.006	0.006	0.000	0.000	0.000	0.000
31	A	350	VAL	0	-0.006	0.021	26.784	0.004	0.004	0.000	0.000	0.000	0.000
32	A	351	VAL	0	-0.020	0.002	22.472	0.001	0.001	0.000	0.000	0.000	0.000
33	A	352	PRO	0	0.002	0.000	24.639	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	353	TRP	0	0.106	0.030	25.146	0.003	0.003	0.000	0.000	0.000	0.000
35	A	354	LYS	1	0.892	0.939	25.028	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	355	GLU	-1	-0.746	-0.824	20.046	0.076	0.076	0.000	0.000	0.000	0.000
37	A	356	ILE	0	0.041	0.027	20.435	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	357	ASN	0	0.005	-0.016	21.211	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	358	ALA	0	-0.004	0.010	19.051	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	359	ALA	0	-0.021	-0.008	16.647	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	360	LEU	0	0.020	0.001	16.954	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	361	GLY	0	0.000	0.000	19.103	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	362	GLN	0	-0.018	-0.008	12.767	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	363	LEU	0	0.033	0.025	14.606	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	364	ILE	0	0.007	-0.004	16.099	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	365	LEU	0	-0.003	-0.002	14.442	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	366	LEU	0	-0.018	0.021	10.517	-0.042	-0.042	0.000	0.000	0.000	0.000
48	A	367	LEU	0	0.022	0.002	13.742	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	368	ALA	0	0.012	0.008	16.451	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	369	THR	0	-0.051	-0.041	12.029	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	370	ILE	0	0.019	0.006	12.019	-0.058	-0.058	0.000	0.000	0.000	0.000
52	A	371	ASN	0	0.041	0.010	14.393	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	372	LYS	1	0.928	0.971	16.921	0.259	0.259	0.000	0.000	0.000	0.000
54	A	373	ASN	0	-0.079	-0.052	13.369	-0.050	-0.050	0.000	0.000	0.000	0.000
55	A	374	LEU	0	-0.008	-0.004	13.254	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	375	LYS	1	0.893	0.956	17.250	0.325	0.325	0.000	0.000	0.000	0.000
57	A	376	ILE	0	0.005	0.026	17.624	0.020	0.020	0.000	0.000	0.000	0.000
58	A	377	ASN	0	-0.003	-0.004	21.494	0.001	0.001	0.000	0.000	0.000	0.000
59	A	378	LEU	0	-0.007	0.001	22.114	0.013	0.013	0.000	0.000	0.000	0.000
60	A	379	VAL	0	0.039	0.024	25.946	0.002	0.002	0.000	0.000	0.000	0.000
61	A	380	ASP	-1	-0.847	-0.901	29.441	-0.054	-0.054	0.000	0.000	0.000	0.000
62	A	381	TYR	0	-0.066	-0.081	26.137	0.006	0.006	0.000	0.000	0.000	0.000
63	A	382	GLU	-1	-0.830	-0.896	25.881	-0.102	-0.102	0.000	0.000	0.000	0.000
64	A	383	LEU	0	-0.010	-0.001	20.041	0.010	0.010	0.000	0.000	0.000	0.000
65	A	384	GLN	0	0.027	0.011	23.496	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	385	PRO	0	0.005	0.002	19.148	0.013	0.013	0.000	0.000	0.000	0.000
67	A	386	MET	0	0.005	0.000	21.286	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	387	GLY	0	0.069	0.039	20.293	0.010	0.010	0.000	0.000	0.000	0.000
69	A	388	SER	0	0.004	0.004	21.376	0.000	0.000	0.000	0.000	0.000	0.000
70	A	389	PHE	0	-0.004	-0.002	23.456	0.007	0.007	0.000	0.000	0.000	0.000
71	A	390	SER	0	0.019	0.003	21.630	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	391	LYS	1	0.838	0.909	23.922	0.055	0.055	0.000	0.000	0.000	0.000
73	A	392	ILE	0	0.032	0.026	23.866	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.779	0.889	26.655	0.084	0.084	0.000	0.000	0.000	0.000
75	A	394	LYS	1	0.891	0.916	28.897	0.022	0.022	0.000	0.000	0.000	0.000
76	A	395	ARG	1	0.817	0.900	31.310	0.064	0.064	0.000	0.000	0.000	0.000
77	A	396	MET	0	-0.065	-0.033	34.294	0.008	0.008	0.000	0.000	0.000	0.000
78	A	412	ASP	-1	-0.795	-0.894	36.879	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	413	TRP	0	-0.009	0.008	30.250	0.001	0.001	0.000	0.000	0.000	0.000
80	A	414	LEU	0	0.004	0.012	34.098	0.003	0.003	0.000	0.000	0.000	0.000
81	A	415	ILE	0	0.002	-0.016	30.677	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	416	LEU	0	-0.030	-0.012	29.097	0.006	0.006	0.000	0.000	0.000	0.000
83	A	417	PRO	0	-0.010	0.006	28.300	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	418	VAL	0	0.013	0.009	22.488	0.006	0.006	0.000	0.000	0.000	0.000
85	A	419	TYR	0	-0.025	-0.010	24.096	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	420	TYR	0	-0.026	-0.023	26.525	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	421	ASP	-1	-0.864	-0.919	29.164	0.008	0.008	0.000	0.000	0.000	0.000
88	A	433	GLU	-1	-0.920	-0.944	35.497	0.007	0.007	0.000	0.000	0.000	0.000
89	A	434	THR	0	-0.032	-0.051	33.617	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	435	LYS	1	0.947	0.947	33.334	0.016	0.016	0.000	0.000	0.000	0.000
91	A	436	PHE	0	0.038	0.032	26.005	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	437	ASP	-1	-0.704	-0.832	29.107	0.015	0.015	0.000	0.000	0.000	0.000
93	A	438	LYS	1	0.971	0.971	30.098	0.018	0.018	0.000	0.000	0.000	0.000
94	A	439	SER	0	-0.032	-0.031	26.932	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	440	LEU	0	0.013	0.027	23.960	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	441	GLU	-1	-0.799	-0.900	25.716	0.007	0.007	0.000	0.000	0.000	0.000
97	A	442	THR	0	-0.028	-0.031	27.051	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	443	THR	0	-0.032	-0.034	21.362	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	444	LEU	0	0.012	0.011	22.563	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	445	GLU	-1	-0.807	-0.842	24.045	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	446	ILE	0	-0.001	0.003	21.172	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	447	ILE	0	0.008	0.003	18.464	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	448	SER	0	-0.010	-0.004	20.405	0.000	0.000	0.000	0.000	0.000	0.000
104	A	449	GLU	-1	-0.760	-0.834	23.044	-0.071	-0.071	0.000	0.000	0.000	0.000
105	A	450	ILE	0	-0.030	-0.015	17.368	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	451	THR	0	-0.003	-0.018	18.983	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	452	ARG	1	0.865	0.912	19.994	0.057	0.057	0.000	0.000	0.000	0.000
108	A	453	GLN	0	-0.039	-0.035	21.835	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	454	LEU	0	0.008	0.000	14.877	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	455	SER	0	-0.024	-0.020	19.005	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	456	THR	0	-0.030	-0.017	21.093	0.005	0.005	0.000	0.000	0.000	0.000
112	A	457	ILE	0	-0.028	-0.019	18.547	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	458	ALA	0	-0.019	-0.019	18.337	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	459	SER	0	-0.060	-0.019	19.609	0.009	0.009	0.000	0.000	0.000	0.000
115	A	460	SER	0	-0.062	-0.015	22.012	0.009	0.009	0.000	0.000	0.000	0.000
116	A	488	LEU	0	-0.015	-0.006	16.011	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	489	GLU	-1	-0.961	-0.987	18.148	0.034	0.034	0.000	0.000	0.000	0.000
118	A	490	LEU	0	-0.054	-0.029	16.240	0.021	0.021	0.000	0.000	0.000	0.000
119	A	491	PRO	0	-0.010	0.004	16.701	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	492	TYR	0	-0.019	-0.004	18.921	0.007	0.007	0.000	0.000	0.000	0.000
121	A	493	ILE	0	0.085	0.047	22.342	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	494	MET	0	0.008	0.002	21.607	0.005	0.005	0.000	0.000	0.000	0.000
123	A	495	ASN	0	-0.003	0.000	26.259	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	496	LYS	1	0.942	0.973	29.939	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	497	ASP	-1	-0.784	-0.858	28.765	0.024	0.024	0.000	0.000	0.000	0.000
126	A	498	LYS	1	0.827	0.930	28.593	-0.040	-0.040	0.000	0.000	0.000	0.000
127	A	499	ILE	0	0.008	0.009	21.256	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	500	ASN	0	-0.020	-0.023	24.224	0.003	0.003	0.000	0.000	0.000	0.000
129	A	501	GLY	0	0.012	0.023	26.348	0.003	0.003	0.000	0.000	0.000	0.000
130	A	502	LEU	0	-0.036	-0.010	26.281	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	503	SER	0	-0.041	-0.061	27.939	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	504	VAL	0	-0.019	-0.018	24.795	0.005	0.005	0.000	0.000	0.000	0.000
133	A	505	LYS	1	0.750	0.872	27.415	-0.016	-0.016	0.000	0.000	0.000	0.000
134	A	506	LEU	0	-0.044	-0.030	29.085	0.005	0.005	0.000	0.000	0.000	0.000
135	A	507	HIS	0	-0.009	-0.017	32.278	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	508	GLY	0	0.019	0.013	34.300	0.000	0.000	0.000	0.000	0.000	0.000
137	A	509	SER	0	-0.001	0.022	35.016	0.000	0.000	0.000	0.000	0.000	0.000
138	A	510	SER	0	0.011	0.009	32.655	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	511	PRO	0	-0.034	-0.022	27.719	0.001	0.001	0.000	0.000	0.000	0.000
140	A	512	ASN	0	0.056	0.034	29.130	0.004	0.004	0.000	0.000	0.000	0.000
141	A	513	LEU	0	0.086	0.036	26.669	0.003	0.003	0.000	0.000	0.000	0.000
142	A	514	GLU	-1	-0.780	-0.870	27.400	0.060	0.060	0.000	0.000	0.000	0.000
143	A	515	TRP	0	0.028	0.006	24.720	0.009	0.009	0.000	0.000	0.000	0.000
144	A	516	THR	0	-0.006	-0.015	23.044	0.002	0.002	0.000	0.000	0.000	0.000
145	A	517	THR	0	-0.043	-0.031	22.773	0.015	0.015	0.000	0.000	0.000	0.000
146	A	518	ALA	0	0.016	0.014	22.909	0.009	0.009	0.000	0.000	0.000	0.000
147	A	519	MET	0	-0.007	-0.001	20.889	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	520	LYS	1	0.893	0.942	18.136	-0.167	-0.167	0.000	0.000	0.000	0.000
149	A	521	PHE	0	0.007	0.017	18.231	0.018	0.018	0.000	0.000	0.000	0.000
150	A	522	LEU	0	0.013	0.021	18.549	0.002	0.002	0.000	0.000	0.000	0.000
151	A	523	LEU	0	0.028	-0.009	13.841	-0.008	-0.008	0.000	0.000	0.000	0.000
152	A	524	THR	0	-0.054	-0.029	14.243	0.030	0.030	0.000	0.000	0.000	0.000
153	A	525	ASN	0	0.024	-0.024	14.646	0.031	0.031	0.000	0.000	0.000	0.000
154	A	526	VAL	0	0.010	0.004	12.837	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	527	LYS	1	0.872	0.919	8.278	-0.610	-0.610	0.000	0.000	0.000	0.000
156	A	528	TRP	0	0.009	0.007	10.223	0.041	0.041	0.000	0.000	0.000	0.000
157	A	529	LEU	0	0.026	0.024	12.461	-0.034	-0.034	0.000	0.000	0.000	0.000
158	A	530	LEU	0	-0.021	-0.003	7.487	-0.070	-0.070	0.000	0.000	0.000	0.000
159	A	531	ALA	0	-0.028	0.000	8.077	-0.133	-0.133	0.000	0.000	0.000	0.000
160	A	532	PHE	0	0.033	0.005	9.125	-0.090	-0.090	0.000	0.000	0.000	0.000
161	A	533	SER	0	0.012	-0.013	11.237	-0.048	-0.048	0.000	0.000	0.000	0.000
162	A	534	SER	0	-0.071	-0.053	6.762	-0.243	-0.243	0.000	0.000	0.000	0.000
163	A	535	ASN	0	-0.008	-0.011	8.343	-0.188	-0.188	0.000	0.000	0.000	0.000
164	A	536	LEU	0	0.007	0.026	10.451	0.005	0.005	0.000	0.000	0.000	0.000
165	A	537	LEU	0	-0.046	-0.020	10.760	-0.005	-0.005	0.000	0.000	0.000	0.000
166	A	538	SER	0	-0.074	-0.014	10.245	-0.064	-0.064	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:320:ILE)