FMO DATABASE

FMODB ID: V5Z71

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1759148.197628
FMO2-HF: Nuclear repulsion	1694259.881819
FMO2-HF: Total energy	-64888.315809
FMO2-MP2: Total energy	-65080.315082

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.
-4.321	-2.655	9.62	-2.823	-8.464	-0.004

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 : -0.006 / q_NPA : -0.010

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	0.016	3.276	-2.878	-0.440	0.059	-1.331	-1.167	0.000
4	A	323	PHE	0	0.014	0.016	5.606	0.283	0.283	0.000	0.000	0.000	0.000
5	A	324	ASN	0	-0.044	-0.024	2.309	-2.426	-0.268	2.377	-1.476	-3.059	-0.015
6	A	325	ALA	0	-0.010	-0.011	2.017	-0.143	-0.209	5.593	-2.888	-2.640	0.008
7	A	326	THR	0	-0.003	0.005	2.947	3.084	0.170	0.016	3.309	-0.410	-0.002
8	A	327	PHE	0	-0.004	-0.006	6.390	0.103	0.103	0.000	0.000	0.000	0.000
9	A	328	LYS	1	0.881	0.952	2.324	-2.066	-2.016	1.575	-0.437	-1.188	0.005
10	A	329	ILE	0	0.030	0.022	7.390	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	330	SER	0	-0.033	-0.023	9.788	0.095	0.095	0.000	0.000	0.000	0.000
12	A	331	HIS	0	0.008	0.001	11.753	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	332	SER	0	-0.033	0.004	15.317	0.009	0.009	0.000	0.000	0.000	0.000
14	A	333	GLY	0	0.055	0.024	17.742	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	334	PRO	0	-0.015	-0.008	20.589	0.014	0.014	0.000	0.000	0.000	0.000
16	A	335	PHE	0	-0.012	0.012	19.853	0.001	0.001	0.000	0.000	0.000	0.000
17	A	336	ALA	0	0.054	0.045	16.393	0.015	0.015	0.000	0.000	0.000	0.000
18	A	337	THR	0	-0.050	-0.042	13.801	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	338	ILE	0	0.030	0.019	11.466	0.032	0.032	0.000	0.000	0.000	0.000
20	A	339	ASN	0	-0.032	-0.037	8.754	0.022	0.022	0.000	0.000	0.000	0.000
21	A	340	GLY	0	-0.015	-0.006	11.079	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	341	LEU	0	-0.048	-0.009	13.959	0.000	0.000	0.000	0.000	0.000	0.000
23	A	342	ARG	1	0.831	0.866	16.569	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	343	LEU	0	-0.007	0.002	18.434	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	344	GLY	0	0.006	-0.022	20.138	0.010	0.010	0.000	0.000	0.000	0.000
26	A	345	SER	0	-0.036	-0.037	23.585	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	346	ILE	0	0.003	0.007	26.427	0.003	0.003	0.000	0.000	0.000	0.000
28	A	347	PRO	0	0.034	0.007	28.970	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	348	GLU	-1	-0.898	-0.938	29.994	0.039	0.039	0.000	0.000	0.000	0.000
30	A	349	SER	0	-0.035	-0.022	26.023	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	350	VAL	0	0.031	0.015	27.133	0.002	0.002	0.000	0.000	0.000	0.000
32	A	351	VAL	0	-0.047	-0.015	22.789	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	352	PRO	0	-0.007	-0.005	24.917	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	353	TRP	0	0.160	0.050	25.188	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	354	LYS	1	0.942	0.974	24.868	0.031	0.031	0.000	0.000	0.000	0.000
36	A	355	GLU	-1	-0.767	-0.826	20.062	0.001	0.001	0.000	0.000	0.000	0.000
37	A	356	ILE	0	0.035	0.018	20.659	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	357	ASN	0	0.029	0.001	21.650	0.002	0.002	0.000	0.000	0.000	0.000
39	A	358	ALA	0	-0.036	-0.004	19.164	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	359	ALA	0	0.001	0.004	17.049	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	360	LEU	0	0.013	0.001	17.333	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	361	GLY	0	0.012	0.006	19.177	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	362	GLN	0	0.014	0.009	12.926	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	363	LEU	0	0.040	0.033	14.697	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	364	ILE	0	0.003	-0.003	16.176	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	365	LEU	0	0.007	-0.002	14.109	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	366	LEU	0	-0.023	0.019	10.111	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	367	LEU	0	0.013	-0.009	13.696	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	368	ALA	0	0.018	0.008	16.257	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	369	THR	0	-0.069	-0.054	11.666	-0.027	-0.027	0.000	0.000	0.000	0.000
51	A	370	ILE	0	0.025	0.023	12.303	-0.042	-0.042	0.000	0.000	0.000	0.000
52	A	371	ASN	0	0.049	0.009	14.408	0.005	0.005	0.000	0.000	0.000	0.000
53	A	372	LYS	1	0.924	0.973	16.521	0.206	0.206	0.000	0.000	0.000	0.000
54	A	373	ASN	0	-0.068	-0.062	12.972	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	374	LEU	0	-0.014	0.011	13.237	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	375	LYS	1	0.898	0.960	17.106	0.180	0.180	0.000	0.000	0.000	0.000
57	A	376	ILE	0	0.013	0.026	17.993	0.018	0.018	0.000	0.000	0.000	0.000
58	A	377	ASN	0	-0.016	-0.010	21.390	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	378	LEU	0	-0.017	0.003	22.124	0.012	0.012	0.000	0.000	0.000	0.000
60	A	379	VAL	0	0.045	0.022	25.740	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	380	ASP	-1	-0.850	-0.931	29.480	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	381	TYR	0	-0.059	-0.072	25.938	0.002	0.002	0.000	0.000	0.000	0.000
63	A	382	GLU	-1	-0.906	-0.946	25.769	-0.077	-0.077	0.000	0.000	0.000	0.000
64	A	383	LEU	0	-0.016	0.004	19.603	0.005	0.005	0.000	0.000	0.000	0.000
65	A	384	GLN	0	0.016	-0.001	23.484	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	385	PRO	0	0.002	0.002	19.023	0.008	0.008	0.000	0.000	0.000	0.000
67	A	386	MET	0	0.008	-0.001	21.161	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	387	GLY	0	0.045	0.025	20.332	0.008	0.008	0.000	0.000	0.000	0.000
69	A	388	SER	0	-0.007	-0.012	21.393	0.003	0.003	0.000	0.000	0.000	0.000
70	A	389	PHE	0	0.009	0.001	23.494	0.009	0.009	0.000	0.000	0.000	0.000
71	A	390	SER	0	0.043	0.031	21.736	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	391	LYS	1	0.852	0.915	24.101	0.064	0.064	0.000	0.000	0.000	0.000
73	A	392	ILE	0	0.036	0.032	23.995	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.887	0.966	26.824	0.060	0.060	0.000	0.000	0.000	0.000
75	A	394	LYS	1	0.982	0.980	29.192	0.003	0.003	0.000	0.000	0.000	0.000
76	A	395	ARG	1	0.904	0.966	31.206	0.030	0.030	0.000	0.000	0.000	0.000
77	A	396	MET	0	-0.044	-0.013	33.890	0.006	0.006	0.000	0.000	0.000	0.000
78	A	412	ASP	-1	-0.918	-0.966	37.276	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	413	TRP	0	-0.035	-0.022	30.138	0.002	0.002	0.000	0.000	0.000	0.000
80	A	414	LEU	0	-0.009	-0.003	34.040	0.000	0.000	0.000	0.000	0.000	0.000
81	A	415	ILE	0	-0.016	-0.014	30.558	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	416	LEU	0	-0.028	-0.010	29.361	0.004	0.004	0.000	0.000	0.000	0.000
83	A	417	PRO	0	-0.011	-0.003	28.774	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	418	VAL	0	0.023	0.017	22.757	0.006	0.006	0.000	0.000	0.000	0.000
85	A	419	TYR	0	-0.047	-0.023	24.415	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	420	TYR	0	-0.003	-0.006	26.622	0.001	0.001	0.000	0.000	0.000	0.000
87	A	421	ASP	-1	-0.950	-0.967	29.618	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	433	GLU	-1	-0.966	-0.976	35.726	0.006	0.006	0.000	0.000	0.000	0.000
89	A	434	THR	0	0.027	0.027	33.651	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	435	LYS	1	0.962	0.955	33.296	0.018	0.018	0.000	0.000	0.000	0.000
91	A	436	PHE	0	0.022	0.026	26.111	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	437	ASP	-1	-0.708	-0.886	29.252	0.013	0.013	0.000	0.000	0.000	0.000
93	A	438	LYS	1	0.961	0.982	30.124	0.008	0.008	0.000	0.000	0.000	0.000
94	A	439	SER	0	-0.030	-0.011	26.959	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	440	LEU	0	0.023	0.023	24.211	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	441	GLU	-1	-0.881	-0.946	25.520	0.023	0.023	0.000	0.000	0.000	0.000
97	A	442	THR	0	-0.025	-0.043	26.823	0.002	0.002	0.000	0.000	0.000	0.000
98	A	443	THR	0	-0.028	-0.020	21.148	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	444	LEU	0	0.002	0.000	22.453	0.002	0.002	0.000	0.000	0.000	0.000
100	A	445	GLU	-1	-0.886	-0.921	23.779	0.009	0.009	0.000	0.000	0.000	0.000
101	A	446	ILE	0	0.003	0.000	20.961	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	447	ILE	0	-0.006	-0.001	18.355	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	448	SER	0	-0.012	0.000	20.494	0.011	0.011	0.000	0.000	0.000	0.000
104	A	449	GLU	-1	-0.847	-0.925	23.063	0.003	0.003	0.000	0.000	0.000	0.000
105	A	450	ILE	0	-0.021	-0.015	17.315	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	451	THR	0	0.001	-0.018	18.991	0.006	0.006	0.000	0.000	0.000	0.000
107	A	452	ARG	1	0.944	0.979	20.033	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	453	GLN	0	-0.078	-0.056	22.042	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	454	LEU	0	0.012	0.018	14.915	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	455	SER	0	-0.016	-0.023	19.230	0.007	0.007	0.000	0.000	0.000	0.000
111	A	456	THR	0	-0.033	-0.013	20.978	0.003	0.003	0.000	0.000	0.000	0.000
112	A	457	ILE	0	-0.036	-0.030	19.030	0.000	0.000	0.000	0.000	0.000	0.000
113	A	458	ALA	0	-0.044	-0.024	18.440	0.000	0.000	0.000	0.000	0.000	0.000
114	A	459	SER	0	-0.054	-0.014	19.687	0.009	0.009	0.000	0.000	0.000	0.000
115	A	460	SER	0	-0.029	0.006	22.521	0.002	0.002	0.000	0.000	0.000	0.000
116	A	488	LEU	0	-0.054	-0.038	15.805	0.010	0.010	0.000	0.000	0.000	0.000
117	A	489	GLU	-1	-0.922	-0.952	18.215	0.113	0.113	0.000	0.000	0.000	0.000
118	A	490	LEU	0	-0.079	-0.036	16.524	0.028	0.028	0.000	0.000	0.000	0.000
119	A	491	PRO	0	0.010	0.011	16.993	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	492	TYR	0	-0.018	0.000	19.092	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	493	ILE	0	0.073	0.039	22.409	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	494	MET	0	-0.002	0.002	21.642	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	495	ASN	0	-0.008	-0.001	26.083	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	496	LYS	1	0.965	0.983	29.775	-0.028	-0.028	0.000	0.000	0.000	0.000
125	A	497	ASP	-1	-0.809	-0.854	28.886	0.034	0.034	0.000	0.000	0.000	0.000
126	A	498	LYS	1	0.914	0.960	28.864	-0.043	-0.043	0.000	0.000	0.000	0.000
127	A	499	ILE	0	0.014	0.025	21.121	0.001	0.001	0.000	0.000	0.000	0.000
128	A	500	ASN	0	-0.032	-0.029	24.053	0.003	0.003	0.000	0.000	0.000	0.000
129	A	501	GLY	0	-0.015	0.000	26.179	0.001	0.001	0.000	0.000	0.000	0.000
130	A	502	LEU	0	-0.029	-0.012	26.379	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	503	SER	0	-0.025	-0.056	28.163	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	504	VAL	0	-0.017	-0.012	25.015	0.001	0.001	0.000	0.000	0.000	0.000
133	A	505	LYS	1	0.875	0.948	27.660	-0.024	-0.024	0.000	0.000	0.000	0.000
134	A	506	LEU	0	0.004	-0.005	29.083	0.004	0.004	0.000	0.000	0.000	0.000
135	A	507	HIS	0	0.015	-0.003	32.791	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	508	GLY	0	-0.018	-0.005	34.470	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	509	SER	0	-0.035	-0.004	35.268	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	510	SER	0	-0.016	-0.005	32.706	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	511	PRO	0	-0.024	-0.015	27.947	0.002	0.002	0.000	0.000	0.000	0.000
140	A	512	ASN	0	0.101	0.072	29.774	0.003	0.003	0.000	0.000	0.000	0.000
141	A	513	LEU	0	0.086	0.019	26.720	0.002	0.002	0.000	0.000	0.000	0.000
142	A	514	GLU	-1	-0.900	-0.932	27.290	0.056	0.056	0.000	0.000	0.000	0.000
143	A	515	TRP	0	0.043	0.018	24.780	0.007	0.007	0.000	0.000	0.000	0.000
144	A	516	THR	0	0.001	-0.007	23.199	0.000	0.000	0.000	0.000	0.000	0.000
145	A	517	THR	0	-0.056	-0.043	22.862	0.011	0.011	0.000	0.000	0.000	0.000
146	A	518	ALA	0	0.016	0.012	22.914	0.011	0.011	0.000	0.000	0.000	0.000
147	A	519	MET	0	-0.008	-0.007	21.199	0.003	0.003	0.000	0.000	0.000	0.000
148	A	520	LYS	1	0.943	0.973	18.440	-0.121	-0.121	0.000	0.000	0.000	0.000
149	A	521	PHE	0	0.001	-0.001	18.227	0.021	0.021	0.000	0.000	0.000	0.000
150	A	522	LEU	0	0.026	0.013	18.170	0.012	0.012	0.000	0.000	0.000	0.000
151	A	523	LEU	0	0.031	-0.006	14.770	0.001	0.001	0.000	0.000	0.000	0.000
152	A	524	THR	0	-0.030	-0.005	14.152	0.031	0.031	0.000	0.000	0.000	0.000
153	A	525	ASN	0	0.042	-0.010	14.578	0.048	0.048	0.000	0.000	0.000	0.000
154	A	526	VAL	0	0.013	0.010	12.737	0.004	0.004	0.000	0.000	0.000	0.000
155	A	527	LYS	1	0.895	0.947	8.352	-0.481	-0.481	0.000	0.000	0.000	0.000
156	A	528	TRP	0	-0.021	-0.008	10.312	0.063	0.063	0.000	0.000	0.000	0.000
157	A	529	LEU	0	0.033	0.025	12.071	0.009	0.009	0.000	0.000	0.000	0.000
158	A	530	LEU	0	-0.022	-0.021	7.645	-0.037	-0.037	0.000	0.000	0.000	0.000
159	A	531	ALA	0	-0.038	-0.005	7.847	-0.068	-0.068	0.000	0.000	0.000	0.000
160	A	532	PHE	0	0.028	0.004	8.898	-0.014	-0.014	0.000	0.000	0.000	0.000
161	A	533	SER	0	0.019	-0.007	11.296	-0.030	-0.030	0.000	0.000	0.000	0.000
162	A	534	SER	0	-0.021	-0.023	6.914	-0.234	-0.234	0.000	0.000	0.000	0.000
163	A	535	ASN	0	-0.049	-0.029	8.833	0.065	0.065	0.000	0.000	0.000	0.000
164	A	536	LEU	0	-0.017	-0.005	10.522	-0.017	-0.017	0.000	0.000	0.000	0.000
165	A	537	LEU	0	-0.049	-0.018	11.153	-0.021	-0.021	0.000	0.000	0.000	0.000
166	A	538	SER	0	-0.046	0.007	10.619	-0.088	-0.088	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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