FMO DATABASE

FMODB ID: YY6K2

Calculation Name: 3VOQ-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VOQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BPZ7

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-997395.961051
FMO2-HF: Nuclear repulsion	948583.002175
FMO2-HF: Total energy	-48812.958876
FMO2-MP2: Total energy	-48954.5582

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:369:GLY )

Summations of interaction energy for fragment #1(A:369:GLY )

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.
-0.419	1.847	0.439	-0.972	-1.731	0.002

Interaction energy analysis for fragmet #1(A:369:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / 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	371	MET	0	0.022	0.004	3.789	-0.043	0.924	0.001	-0.401	-0.566	0.001
4	A	372	ALA	0	0.019	0.018	2.454	-0.464	0.237	0.435	-0.413	-0.724	0.001
5	A	373	THR	0	0.030	0.028	3.258	0.360	0.848	0.003	-0.150	-0.340	0.000
6	A	374	VAL	0	0.015	-0.008	5.237	0.654	0.764	0.000	-0.008	-0.101	0.000
7	A	375	GLN	0	-0.028	-0.015	7.360	0.177	0.177	0.000	0.000	0.000	0.000
8	A	376	ASP	-1	-0.878	-0.951	7.625	-0.799	-0.799	0.000	0.000	0.000	0.000
9	A	377	MET	0	-0.041	-0.019	9.118	0.151	0.151	0.000	0.000	0.000	0.000
10	A	378	LEU	0	-0.025	-0.008	11.417	0.126	0.126	0.000	0.000	0.000	0.000
11	A	379	SER	0	-0.031	0.005	12.402	0.091	0.091	0.000	0.000	0.000	0.000
12	A	380	SER	0	-0.021	-0.022	13.648	0.045	0.045	0.000	0.000	0.000	0.000
13	A	381	HIS	0	0.048	0.063	14.983	0.047	0.047	0.000	0.000	0.000	0.000
14	A	382	HIS	0	0.033	0.036	17.039	0.018	0.018	0.000	0.000	0.000	0.000
15	A	383	TYR	0	0.011	-0.007	18.717	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	384	LYS	1	0.821	0.895	13.622	0.233	0.233	0.000	0.000	0.000	0.000
17	A	385	SER	0	-0.040	-0.005	19.409	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	386	PHE	0	0.044	0.021	15.691	0.004	0.004	0.000	0.000	0.000	0.000
19	A	387	LYS	1	0.845	0.924	21.010	0.078	0.078	0.000	0.000	0.000	0.000
20	A	388	VAL	0	0.060	0.035	21.587	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	389	SER	0	0.020	0.025	24.314	0.013	0.013	0.000	0.000	0.000	0.000
22	A	390	MET	0	-0.002	0.011	26.941	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	391	ILE	0	0.059	0.023	27.747	0.012	0.012	0.000	0.000	0.000	0.000
24	A	392	HIS	1	0.805	0.876	31.247	0.077	0.077	0.000	0.000	0.000	0.000
25	A	393	ARG	1	0.933	0.946	34.943	0.068	0.068	0.000	0.000	0.000	0.000
26	A	394	LEU	0	0.051	0.020	32.719	0.004	0.004	0.000	0.000	0.000	0.000
27	A	395	ARG	1	0.921	0.977	34.818	0.065	0.065	0.000	0.000	0.000	0.000
28	A	396	PHE	0	0.022	0.014	34.960	0.002	0.002	0.000	0.000	0.000	0.000
29	A	397	THR	0	0.040	0.028	29.963	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	398	THR	0	-0.027	0.000	31.906	0.006	0.006	0.000	0.000	0.000	0.000
31	A	399	ASP	-1	-0.873	-0.922	29.333	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	400	VAL	0	-0.075	-0.047	26.860	0.006	0.006	0.000	0.000	0.000	0.000
33	A	401	GLN	0	-0.015	-0.008	25.110	0.003	0.003	0.000	0.000	0.000	0.000
34	A	402	LEU	0	0.010	0.015	22.110	0.005	0.005	0.000	0.000	0.000	0.000
35	A	403	GLY	0	0.013	-0.005	22.780	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	404	ILE	0	0.018	0.014	19.468	0.001	0.001	0.000	0.000	0.000	0.000
37	A	405	SER	0	0.027	0.006	20.699	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	406	GLY	0	0.042	0.003	21.540	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	407	ASP	-1	-0.922	-0.899	22.575	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	408	LYS	1	0.904	0.946	25.260	0.097	0.097	0.000	0.000	0.000	0.000
41	A	409	VAL	0	-0.005	0.008	23.535	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	410	GLU	-1	-0.950	-0.978	26.054	-0.080	-0.080	0.000	0.000	0.000	0.000
43	A	411	ILE	0	-0.004	-0.008	26.919	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	412	ASP	-1	-0.878	-0.940	29.204	-0.065	-0.065	0.000	0.000	0.000	0.000
45	A	413	PRO	0	-0.056	-0.026	30.318	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	414	VAL	0	0.046	0.014	29.329	0.004	0.004	0.000	0.000	0.000	0.000
47	A	415	THR	0	-0.035	-0.023	31.998	0.001	0.001	0.000	0.000	0.000	0.000
48	A	416	ASN	0	-0.050	-0.018	33.938	0.003	0.003	0.000	0.000	0.000	0.000
49	A	417	GLN	0	0.070	0.029	34.788	0.002	0.002	0.000	0.000	0.000	0.000
50	A	418	LYS	1	0.900	0.947	38.716	0.027	0.027	0.000	0.000	0.000	0.000
51	A	419	ALA	0	0.073	0.043	40.393	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	420	SER	0	-0.034	-0.029	42.755	0.003	0.003	0.000	0.000	0.000	0.000
53	A	421	THR	0	0.046	0.011	43.928	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	422	LYS	1	0.990	1.010	46.619	0.025	0.025	0.000	0.000	0.000	0.000
55	A	423	PHE	0	-0.043	-0.027	49.037	0.000	0.000	0.000	0.000	0.000	0.000
56	A	424	TRP	0	0.065	0.045	38.808	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	425	ILE	0	0.016	0.001	40.941	0.000	0.000	0.000	0.000	0.000	0.000
58	A	426	LYS	1	0.989	1.001	40.281	0.043	0.043	0.000	0.000	0.000	0.000
59	A	427	GLN	0	-0.010	-0.004	35.941	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	428	LYS	1	0.834	0.901	37.588	0.059	0.059	0.000	0.000	0.000	0.000
61	A	429	PRO	0	0.061	0.030	33.974	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	430	ILE	0	-0.037	-0.004	31.399	0.003	0.003	0.000	0.000	0.000	0.000
63	A	431	SER	0	-0.003	0.000	30.975	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	432	ILE	0	-0.034	-0.018	28.656	0.005	0.005	0.000	0.000	0.000	0.000
65	A	433	ASP	-1	-0.835	-0.921	28.799	-0.118	-0.118	0.000	0.000	0.000	0.000
66	A	434	SER	0	0.017	-0.028	24.863	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	435	ASP	-1	-0.871	-0.929	26.950	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	436	LEU	0	-0.086	-0.043	29.099	0.004	0.004	0.000	0.000	0.000	0.000
69	A	437	LEU	0	-0.040	-0.013	24.008	0.003	0.003	0.000	0.000	0.000	0.000
70	A	438	CYS	0	-0.089	-0.036	27.660	0.003	0.003	0.000	0.000	0.000	0.000
71	A	439	ALA	0	0.067	0.028	24.479	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	440	CYS	0	-0.016	-0.003	20.395	0.016	0.016	0.000	0.000	0.000	0.000
73	A	441	ASP	-1	-0.879	-0.920	21.127	-0.260	-0.260	0.000	0.000	0.000	0.000
74	A	442	LEU	0	0.022	0.003	18.394	0.018	0.018	0.000	0.000	0.000	0.000
75	A	443	ALA	0	-0.099	-0.069	21.228	0.013	0.013	0.000	0.000	0.000	0.000
76	A	444	GLU	-1	-0.905	-0.967	23.869	-0.121	-0.121	0.000	0.000	0.000	0.000
77	A	445	GLU	-1	-0.889	-0.959	17.192	-0.303	-0.303	0.000	0.000	0.000	0.000
78	A	446	LYS	1	0.920	0.974	22.015	0.111	0.111	0.000	0.000	0.000	0.000
79	A	447	SER	0	-0.053	-0.030	22.389	0.013	0.013	0.000	0.000	0.000	0.000
80	A	448	PRO	0	0.052	0.004	17.786	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	449	SER	0	-0.004	-0.001	19.188	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	450	HIS	0	-0.024	0.003	21.875	0.007	0.007	0.000	0.000	0.000	0.000
83	A	451	ALA	0	0.022	0.025	20.051	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	452	ILE	0	0.041	0.011	22.065	0.009	0.009	0.000	0.000	0.000	0.000
85	A	453	PHE	0	0.046	0.036	21.048	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	454	LYS	1	0.911	0.956	23.195	0.164	0.164	0.000	0.000	0.000	0.000
87	A	455	LEU	0	0.020	0.013	23.710	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	456	THR	0	-0.022	-0.025	26.057	0.015	0.015	0.000	0.000	0.000	0.000
89	A	457	TYR	0	0.014	-0.002	27.981	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	458	LEU	0	0.012	0.009	30.459	0.007	0.007	0.000	0.000	0.000	0.000
91	A	459	SER	0	-0.066	-0.033	33.858	0.002	0.002	0.000	0.000	0.000	0.000
92	A	460	ASN	0	-0.035	-0.032	36.327	0.003	0.003	0.000	0.000	0.000	0.000
93	A	461	HIS	0	0.035	0.025	38.741	0.000	0.000	0.000	0.000	0.000	0.000
94	A	462	ASP	-1	-0.877	-0.912	38.492	-0.074	-0.074	0.000	0.000	0.000	0.000
95	A	463	TYR	0	-0.030	-0.034	33.021	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	464	LYS	1	0.907	0.957	33.611	0.087	0.087	0.000	0.000	0.000	0.000
97	A	465	HIS	0	0.040	0.015	30.624	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	466	LEU	0	-0.052	-0.028	28.618	0.011	0.011	0.000	0.000	0.000	0.000
99	A	467	TYR	0	0.028	0.016	27.420	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	468	PHE	0	-0.011	-0.011	24.203	0.016	0.016	0.000	0.000	0.000	0.000
101	A	469	GLU	-1	-0.927	-0.962	23.810	-0.117	-0.117	0.000	0.000	0.000	0.000
102	A	470	SER	0	-0.005	-0.011	20.160	0.018	0.018	0.000	0.000	0.000	0.000
103	A	471	ASP	-1	-0.774	-0.874	17.022	-0.199	-0.199	0.000	0.000	0.000	0.000
104	A	472	ALA	0	0.044	-0.001	16.708	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	473	ALA	0	-0.049	-0.004	12.982	-0.052	-0.052	0.000	0.000	0.000	0.000
106	A	474	THR	0	-0.027	-0.031	13.707	-0.058	-0.058	0.000	0.000	0.000	0.000
107	A	475	VAL	0	-0.045	-0.006	16.198	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	476	ASN	0	-0.005	-0.019	12.940	0.002	0.002	0.000	0.000	0.000	0.000
109	A	477	GLU	-1	-0.789	-0.853	11.785	-0.388	-0.388	0.000	0.000	0.000	0.000
110	A	478	ILE	0	-0.043	-0.025	13.199	0.002	0.002	0.000	0.000	0.000	0.000
111	A	479	VAL	0	0.018	-0.004	16.543	0.010	0.010	0.000	0.000	0.000	0.000
112	A	480	LEU	0	-0.012	0.004	9.727	0.006	0.006	0.000	0.000	0.000	0.000
113	A	481	LYS	1	0.836	0.916	14.254	0.292	0.292	0.000	0.000	0.000	0.000
114	A	482	VAL	0	-0.011	-0.018	15.360	0.032	0.032	0.000	0.000	0.000	0.000
115	A	483	ASN	0	-0.051	-0.047	16.970	0.048	0.048	0.000	0.000	0.000	0.000
116	A	484	TYR	0	0.027	0.013	9.557	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	485	ILE	0	-0.049	-0.026	16.620	0.033	0.033	0.000	0.000	0.000	0.000
118	A	486	LEU	0	-0.090	-0.044	19.789	0.025	0.025	0.000	0.000	0.000	0.000
119	A	487	GLU	-1	-0.964	-0.990	16.719	-0.433	-0.433	0.000	0.000	0.000	0.000
120	A	488	SER	0	-0.052	-0.039	19.482	0.017	0.017	0.000	0.000	0.000	0.000
121	A	489	ARG	1	0.849	0.939	21.096	0.198	0.198	0.000	0.000	0.000	0.000
122	A	490	ALA	0	0.030	0.016	24.029	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	1	NME	0	-0.056	-0.028	26.171	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:369:GLY )