FMO DATABASE

FMODB ID: 17VZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1758726.119005
FMO2-HF: Nuclear repulsion	1693836.957809
FMO2-HF: Total energy	-64889.161196
FMO2-MP2: Total energy	-65081.101585

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.
-9.127	-3.29	7.579	-4.528	-8.886	0.002

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 : 0.024 / q_NPA : 0.016

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	0.089	0.020	3.392	-3.728	0.294	0.019	-2.223	-1.817	0.009
4	A	323	PHE	0	0.015	0.015	5.770	0.361	0.361	0.000	0.000	0.000	0.000
5	A	324	ASN	0	-0.016	-0.014	2.435	-2.230	0.067	2.489	-1.546	-3.240	-0.017
6	A	325	ALA	0	0.015	0.017	2.161	-0.499	0.406	3.383	-2.004	-2.284	0.005
7	A	326	THR	0	0.011	0.008	3.125	1.562	0.252	0.011	1.662	-0.362	-0.001
8	A	327	PHE	0	0.004	0.001	6.391	0.063	0.063	0.000	0.000	0.000	0.000
9	A	328	LYS	1	0.833	0.926	2.382	-3.069	-3.146	1.677	-0.417	-1.183	0.006
10	A	329	ILE	0	0.029	0.019	7.162	-0.106	-0.106	0.000	0.000	0.000	0.000
11	A	330	SER	0	-0.023	-0.017	9.664	0.126	0.126	0.000	0.000	0.000	0.000
12	A	331	HIS	0	0.002	0.000	11.638	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	332	SER	0	-0.018	0.011	15.197	0.026	0.026	0.000	0.000	0.000	0.000
14	A	333	GLY	0	0.061	0.030	17.650	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	334	PRO	0	-0.009	0.000	20.442	0.016	0.016	0.000	0.000	0.000	0.000
16	A	335	PHE	0	0.026	0.011	19.719	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	336	ALA	0	0.056	0.045	16.306	0.034	0.034	0.000	0.000	0.000	0.000
18	A	337	THR	0	-0.060	-0.047	13.775	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	338	ILE	0	0.040	0.023	11.273	0.058	0.058	0.000	0.000	0.000	0.000
20	A	339	ASN	0	-0.028	-0.035	8.585	0.074	0.074	0.000	0.000	0.000	0.000
21	A	340	GLY	0	-0.011	-0.003	10.900	-0.037	-0.037	0.000	0.000	0.000	0.000
22	A	341	LEU	0	-0.048	-0.010	13.733	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	342	ARG	1	0.837	0.874	16.356	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	343	LEU	0	-0.015	-0.001	18.219	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	344	GLY	0	0.010	-0.012	19.926	0.005	0.005	0.000	0.000	0.000	0.000
26	A	345	SER	0	-0.038	-0.029	23.356	0.001	0.001	0.000	0.000	0.000	0.000
27	A	346	ILE	0	-0.007	0.002	26.186	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	347	PRO	0	0.039	0.012	28.911	0.001	0.001	0.000	0.000	0.000	0.000
29	A	348	GLU	-1	-0.883	-0.936	29.878	0.108	0.108	0.000	0.000	0.000	0.000
30	A	349	SER	0	-0.056	-0.034	25.925	0.005	0.005	0.000	0.000	0.000	0.000
31	A	350	VAL	0	0.028	0.020	26.995	0.007	0.007	0.000	0.000	0.000	0.000
32	A	351	VAL	0	-0.042	-0.011	22.458	0.003	0.003	0.000	0.000	0.000	0.000
33	A	352	PRO	0	0.001	0.001	24.597	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	353	TRP	0	0.154	0.048	25.013	0.009	0.009	0.000	0.000	0.000	0.000
35	A	354	LYS	1	0.939	0.975	24.867	-0.048	-0.048	0.000	0.000	0.000	0.000
36	A	355	GLU	-1	-0.757	-0.835	19.948	0.162	0.162	0.000	0.000	0.000	0.000
37	A	356	ILE	0	0.033	0.019	20.509	0.006	0.006	0.000	0.000	0.000	0.000
38	A	357	ASN	0	0.021	-0.002	21.511	0.002	0.002	0.000	0.000	0.000	0.000
39	A	358	ALA	0	-0.029	-0.002	19.139	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	359	ALA	0	0.000	0.002	16.924	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	360	LEU	0	0.011	0.001	17.227	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	361	GLY	0	0.012	0.006	19.114	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	362	GLN	0	-0.012	-0.003	12.792	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	363	LEU	0	0.034	0.030	14.674	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	364	ILE	0	0.010	-0.002	16.113	-0.024	-0.024	0.000	0.000	0.000	0.000
46	A	365	LEU	0	0.001	0.000	14.428	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	366	LEU	0	-0.028	0.010	10.236	-0.042	-0.042	0.000	0.000	0.000	0.000
48	A	367	LEU	0	0.014	-0.007	13.725	-0.046	-0.046	0.000	0.000	0.000	0.000
49	A	368	ALA	0	0.017	0.010	16.313	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	369	THR	0	-0.060	-0.044	11.813	-0.039	-0.039	0.000	0.000	0.000	0.000
51	A	370	ILE	0	0.032	0.021	11.920	-0.062	-0.062	0.000	0.000	0.000	0.000
52	A	371	ASN	0	0.048	0.011	14.483	-0.026	-0.026	0.000	0.000	0.000	0.000
53	A	372	LYS	1	0.930	0.976	16.708	0.218	0.218	0.000	0.000	0.000	0.000
54	A	373	ASN	0	-0.072	-0.062	13.250	-0.060	-0.060	0.000	0.000	0.000	0.000
55	A	374	LEU	0	-0.015	0.009	13.257	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	375	LYS	1	0.888	0.956	17.187	0.315	0.315	0.000	0.000	0.000	0.000
57	A	376	ILE	0	0.017	0.024	17.598	0.018	0.018	0.000	0.000	0.000	0.000
58	A	377	ASN	0	-0.016	-0.007	21.462	0.005	0.005	0.000	0.000	0.000	0.000
59	A	378	LEU	0	-0.013	0.006	22.143	0.011	0.011	0.000	0.000	0.000	0.000
60	A	379	VAL	0	0.043	0.020	25.802	0.001	0.001	0.000	0.000	0.000	0.000
61	A	380	ASP	-1	-0.842	-0.912	29.512	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	381	TYR	0	-0.052	-0.072	25.990	0.007	0.007	0.000	0.000	0.000	0.000
63	A	382	GLU	-1	-0.813	-0.886	25.828	-0.075	-0.075	0.000	0.000	0.000	0.000
64	A	383	LEU	0	-0.018	0.007	19.780	0.011	0.011	0.000	0.000	0.000	0.000
65	A	384	GLN	0	0.030	0.009	23.554	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	385	PRO	0	0.006	0.005	19.050	0.013	0.013	0.000	0.000	0.000	0.000
67	A	386	MET	0	0.012	-0.004	21.215	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	387	GLY	0	0.047	0.029	20.336	0.008	0.008	0.000	0.000	0.000	0.000
69	A	388	SER	0	-0.002	-0.005	21.399	0.004	0.004	0.000	0.000	0.000	0.000
70	A	389	PHE	0	-0.010	-0.011	23.451	0.005	0.005	0.000	0.000	0.000	0.000
71	A	390	SER	0	0.047	0.033	21.764	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	391	LYS	1	0.843	0.911	24.099	0.017	0.017	0.000	0.000	0.000	0.000
73	A	392	ILE	0	0.025	0.024	23.888	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	393	LYS	1	0.784	0.891	26.835	0.058	0.058	0.000	0.000	0.000	0.000
75	A	394	LYS	1	0.880	0.910	29.251	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	395	ARG	1	0.894	0.958	31.257	0.047	0.047	0.000	0.000	0.000	0.000
77	A	396	MET	0	-0.034	0.003	33.945	0.007	0.007	0.000	0.000	0.000	0.000
78	A	412	ASP	-1	-0.904	-0.968	37.379	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	413	TRP	0	0.005	0.001	30.149	0.002	0.002	0.000	0.000	0.000	0.000
80	A	414	LEU	0	-0.013	-0.009	34.289	0.003	0.003	0.000	0.000	0.000	0.000
81	A	415	ILE	0	-0.011	-0.016	30.594	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	416	LEU	0	-0.030	-0.007	29.282	0.004	0.004	0.000	0.000	0.000	0.000
83	A	417	PRO	0	-0.001	0.002	28.742	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	418	VAL	0	0.014	0.016	22.827	0.006	0.006	0.000	0.000	0.000	0.000
85	A	419	TYR	0	-0.032	-0.015	24.343	0.001	0.001	0.000	0.000	0.000	0.000
86	A	420	TYR	0	-0.020	-0.017	26.532	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	421	ASP	-1	-0.935	-0.958	29.504	0.045	0.045	0.000	0.000	0.000	0.000
88	A	433	GLU	-1	-0.931	-0.954	35.720	0.029	0.029	0.000	0.000	0.000	0.000
89	A	434	THR	0	-0.023	-0.045	33.576	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	435	LYS	1	0.952	0.945	33.424	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	436	PHE	0	0.031	0.031	26.067	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	437	ASP	-1	-0.714	-0.845	29.145	0.049	0.049	0.000	0.000	0.000	0.000
93	A	438	LYS	1	0.960	0.976	30.127	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	439	SER	0	-0.031	-0.028	26.902	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	440	LEU	0	0.016	0.023	24.203	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	441	GLU	-1	-0.789	-0.896	25.521	0.034	0.034	0.000	0.000	0.000	0.000
97	A	442	THR	0	-0.023	-0.030	26.868	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	443	THR	0	-0.023	-0.024	21.179	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	444	LEU	0	0.005	0.006	22.465	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	445	GLU	-1	-0.812	-0.858	23.780	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	446	ILE	0	0.006	0.001	21.064	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	447	ILE	0	-0.006	0.002	18.376	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	448	SER	0	-0.019	-0.008	20.501	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	449	GLU	-1	-0.752	-0.830	23.069	-0.059	-0.059	0.000	0.000	0.000	0.000
105	A	450	ILE	0	-0.022	-0.012	17.420	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	451	THR	0	0.001	-0.021	18.842	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	452	ARG	1	0.837	0.888	20.048	0.039	0.039	0.000	0.000	0.000	0.000
108	A	453	GLN	0	-0.053	-0.052	22.089	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	454	LEU	0	0.008	0.012	14.835	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	455	SER	0	-0.023	-0.018	19.231	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	456	THR	0	-0.036	-0.019	20.974	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	457	ILE	0	-0.032	-0.026	18.928	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	458	ALA	0	-0.048	-0.023	18.381	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	459	SER	0	-0.053	-0.016	19.669	0.001	0.001	0.000	0.000	0.000	0.000
115	A	460	SER	0	-0.027	0.007	22.538	0.004	0.004	0.000	0.000	0.000	0.000
116	A	488	LEU	0	-0.021	-0.009	16.023	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	489	GLU	-1	-0.954	-0.985	18.182	0.045	0.045	0.000	0.000	0.000	0.000
118	A	490	LEU	0	-0.075	-0.037	16.456	0.021	0.021	0.000	0.000	0.000	0.000
119	A	491	PRO	0	0.018	0.013	16.739	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	492	TYR	0	-0.028	-0.007	18.763	0.004	0.004	0.000	0.000	0.000	0.000
121	A	493	ILE	0	0.072	0.041	22.281	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	494	MET	0	0.014	0.009	21.526	0.011	0.011	0.000	0.000	0.000	0.000
123	A	495	ASN	0	-0.008	-0.007	26.050	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	496	LYS	1	0.960	0.983	29.746	-0.023	-0.023	0.000	0.000	0.000	0.000
125	A	497	ASP	-1	-0.798	-0.862	28.871	0.051	0.051	0.000	0.000	0.000	0.000
126	A	498	LYS	1	0.861	0.927	28.804	-0.062	-0.062	0.000	0.000	0.000	0.000
127	A	499	ILE	0	0.018	0.019	21.144	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	500	ASN	0	-0.034	-0.029	23.930	0.001	0.001	0.000	0.000	0.000	0.000
129	A	501	GLY	0	0.008	0.015	26.077	0.003	0.003	0.000	0.000	0.000	0.000
130	A	502	LEU	0	-0.029	-0.009	26.144	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	503	SER	0	-0.031	-0.034	28.119	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	504	VAL	0	-0.025	-0.015	24.912	0.007	0.007	0.000	0.000	0.000	0.000
133	A	505	LYS	1	0.757	0.879	27.634	-0.041	-0.041	0.000	0.000	0.000	0.000
134	A	506	LEU	0	-0.032	-0.021	29.270	0.005	0.005	0.000	0.000	0.000	0.000
135	A	507	HIS	0	0.015	0.000	32.605	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	508	GLY	0	0.013	0.014	34.345	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	509	SER	0	-0.029	-0.002	35.027	0.001	0.001	0.000	0.000	0.000	0.000
138	A	510	SER	0	0.010	0.008	32.518	0.000	0.000	0.000	0.000	0.000	0.000
139	A	511	PRO	0	-0.051	-0.030	27.747	0.001	0.001	0.000	0.000	0.000	0.000
140	A	512	ASN	0	0.079	0.050	29.623	0.005	0.005	0.000	0.000	0.000	0.000
141	A	513	LEU	0	0.088	0.028	26.507	0.006	0.006	0.000	0.000	0.000	0.000
142	A	514	GLU	-1	-0.829	-0.902	27.171	0.095	0.095	0.000	0.000	0.000	0.000
143	A	515	TRP	0	0.034	0.005	25.076	0.013	0.013	0.000	0.000	0.000	0.000
144	A	516	THR	0	-0.002	-0.009	23.209	0.007	0.007	0.000	0.000	0.000	0.000
145	A	517	THR	0	-0.055	-0.037	22.764	0.022	0.022	0.000	0.000	0.000	0.000
146	A	518	ALA	0	0.015	0.012	22.820	0.012	0.012	0.000	0.000	0.000	0.000
147	A	519	MET	0	-0.003	-0.005	20.978	0.003	0.003	0.000	0.000	0.000	0.000
148	A	520	LYS	1	0.902	0.950	18.230	-0.219	-0.219	0.000	0.000	0.000	0.000
149	A	521	PHE	0	0.000	0.009	18.186	0.026	0.026	0.000	0.000	0.000	0.000
150	A	522	LEU	0	0.012	0.013	18.454	0.003	0.003	0.000	0.000	0.000	0.000
151	A	523	LEU	0	0.041	-0.001	14.371	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	524	THR	0	-0.042	-0.016	14.109	0.047	0.047	0.000	0.000	0.000	0.000
153	A	525	ASN	0	0.037	-0.013	14.515	0.030	0.030	0.000	0.000	0.000	0.000
154	A	526	VAL	0	0.020	0.009	12.831	-0.017	-0.017	0.000	0.000	0.000	0.000
155	A	527	LYS	1	0.885	0.937	8.141	-0.850	-0.850	0.000	0.000	0.000	0.000
156	A	528	TRP	0	-0.010	-0.003	10.272	0.022	0.022	0.000	0.000	0.000	0.000
157	A	529	LEU	0	0.032	0.024	12.091	-0.046	-0.046	0.000	0.000	0.000	0.000
158	A	530	LEU	0	-0.020	-0.014	7.534	-0.071	-0.071	0.000	0.000	0.000	0.000
159	A	531	ALA	0	-0.040	-0.008	7.869	-0.142	-0.142	0.000	0.000	0.000	0.000
160	A	532	PHE	0	0.037	0.010	8.910	-0.146	-0.146	0.000	0.000	0.000	0.000
161	A	533	SER	0	0.017	-0.007	11.348	-0.067	-0.067	0.000	0.000	0.000	0.000
162	A	534	SER	0	-0.061	-0.038	6.924	-0.262	-0.262	0.000	0.000	0.000	0.000
163	A	535	ASN	0	-0.021	-0.018	8.676	-0.195	-0.195	0.000	0.000	0.000	0.000
164	A	536	LEU	0	-0.007	0.004	10.497	-0.027	-0.027	0.000	0.000	0.000	0.000
165	A	537	LEU	0	-0.053	-0.022	11.112	0.000	0.000	0.000	0.000	0.000	0.000
166	A	538	SER	0	-0.063	0.000	10.444	-0.055	-0.055	0.000	0.000	0.000	0.000

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