FMO DATABASE

FMODB ID: G5QZ1

Calculation Name: 3VPY-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3VPY

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8W4D8

Base Structure: X-ray

Registration Date: 2023-09-20

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1445460.81477
FMO2-HF: Nuclear repulsion	1384074.89021
FMO2-HF: Total energy	-61385.92456
FMO2-MP2: Total energy	-61563.170129

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:1:THR)

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

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.
-3.644	-1.421	0.006	-1.063	-1.166	-0.001

Interaction energy analysis for fragmet #1(A:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.025

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	3	LEU	0	-0.032	-0.023	3.423	-3.472	-1.797	0.008	-0.793	-0.889	-0.001
4	A	4	PHE	0	0.017	-0.002	5.886	0.650	0.650	0.000	0.000	0.000	0.000
5	A	5	ASN	0	0.001	0.000	7.300	0.259	0.259	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.763	-0.854	9.549	0.194	0.194	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.068	-0.012	12.916	-0.019	-0.019	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.048	0.011	15.725	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.802	-0.898	18.376	-0.126	-0.126	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.011	0.028	16.836	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.858	0.920	18.912	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.891	0.957	21.447	-0.222	-0.222	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.007	0.019	22.276	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.029	-0.027	25.290	0.015	0.015	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.890	-0.939	28.677	0.029	0.029	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.919	0.949	27.847	-0.080	-0.080	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.026	0.004	25.532	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.899	0.952	25.663	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.046	0.031	21.298	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.020	0.002	25.244	0.021	0.021	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.008	0.003	23.894	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.041	0.023	26.395	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.897	0.927	26.197	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.905	-0.955	28.184	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.013	0.008	30.286	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.897	-0.942	31.843	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.034	-0.003	30.824	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.059	-0.043	25.290	0.008	0.008	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.021	-0.016	29.740	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.935	-0.961	28.502	0.123	0.123	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.078	-0.019	27.142	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.030	0.007	20.502	0.018	0.018	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.069	-0.014	23.156	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.044	0.026	19.700	0.018	0.018	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.002	-0.013	22.594	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.903	0.912	21.910	-0.186	-0.186	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.039	-0.022	14.684	0.040	0.040	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.038	-0.049	16.412	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.022	0.016	13.403	-0.082	-0.082	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.018	0.030	14.961	0.100	0.100	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.002	0.000	7.871	-0.142	-0.142	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.010	0.002	12.393	0.113	0.113	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.057	0.009	11.191	-0.154	-0.154	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.878	0.951	12.196	0.315	0.315	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.958	-0.983	5.806	0.204	0.204	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.869	0.876	9.659	-0.121	-0.121	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.914	0.971	6.748	-2.074	-2.074	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.002	-0.014	4.004	0.146	0.287	-0.001	-0.017	-0.123	0.000
49	A	49	ALA	0	-0.038	0.005	7.922	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.772	-0.873	10.730	0.624	0.624	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.057	-0.028	13.731	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.017	0.003	14.288	-0.049	-0.049	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.019	-0.026	14.830	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.785	-0.882	16.082	0.103	0.103	0.000	0.000	0.000	0.000
55	A	55	HIS	0	0.038	0.061	17.764	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.038	0.003	18.142	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.062	-0.025	18.451	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	58	CYS	0	0.005	0.017	15.605	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.032	0.003	12.114	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.889	0.939	7.288	0.565	0.565	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.040	0.010	3.819	0.589	0.996	-0.001	-0.253	-0.154	0.000
62	A	62	HIS	0	0.001	0.009	9.299	-0.159	-0.159	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.050	0.017	12.952	-0.051	-0.051	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.031	0.017	12.589	0.069	0.069	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.031	-0.010	14.575	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.023	-0.030	14.643	0.015	0.015	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.037	-0.042	17.534	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.867	0.920	19.204	0.169	0.169	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.882	-0.931	21.695	0.021	0.021	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.034	-0.016	24.598	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.867	-0.951	27.068	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.918	0.946	30.790	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.911	-0.940	33.483	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.862	0.933	37.039	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.034	0.003	39.508	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.877	-0.945	42.717	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.014	0.018	41.961	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.064	-0.017	41.106	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	79	MET	0	0.030	0.030	34.683	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.045	-0.038	34.961	0.008	0.008	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.847	0.920	28.344	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.049	-0.033	29.035	0.014	0.014	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.003	0.006	23.622	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.809	0.908	24.957	0.076	0.076	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.033	0.020	22.328	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.045	0.016	20.069	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.010	0.017	18.576	0.004	0.004	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.028	-0.009	14.390	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.728	-0.823	15.461	-0.540	-0.540	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.053	-0.027	9.494	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.033	0.018	11.624	-0.170	-0.170	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.109	-0.068	14.009	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.020	-0.017	15.019	0.028	0.028	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.066	-0.051	17.479	0.040	0.040	0.000	0.000	0.000	0.000
95	A	95	LYS	1	1.010	1.025	18.568	0.307	0.307	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.027	-0.003	17.801	0.027	0.027	0.000	0.000	0.000	0.000
97	A	97	TYR	0	-0.034	-0.014	20.538	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.032	0.013	23.472	0.012	0.012	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.026	-0.033	26.151	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.927	-0.967	28.583	-0.099	-0.099	0.000	0.000	0.000	0.000
101	A	101	SER	0	0.005	0.018	28.090	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.082	-0.036	24.033	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.035	-0.018	19.456	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.956	-0.990	21.414	-0.367	-0.367	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.004	0.004	16.300	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.040	-0.042	11.660	-0.100	-0.100	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.962	0.988	15.846	0.332	0.332	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.010	-0.006	15.286	0.011	0.011	0.000	0.000	0.000	0.000
109	A	109	TYR	0	0.013	0.007	19.915	0.010	0.010	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.862	-0.920	22.901	-0.078	-0.078	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.032	-0.013	22.307	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.007	-0.007	26.069	0.013	0.013	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.939	-0.987	29.488	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.907	0.930	30.986	0.012	0.012	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.789	-0.855	27.548	-0.084	-0.084	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.017	-0.022	27.726	0.014	0.014	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.022	-0.007	21.426	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.986	0.999	23.260	0.121	0.121	0.000	0.000	0.000	0.000
119	A	119	PHE	0	0.000	0.001	18.055	-0.024	-0.024	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.002	-0.017	20.189	0.020	0.020	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.017	-0.026	20.886	0.016	0.016	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.040	-0.018	21.175	0.025	0.025	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.030	0.019	23.209	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.906	0.947	22.131	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.927	-0.954	24.613	-0.071	-0.071	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.028	-0.029	20.281	0.016	0.016	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.056	0.046	25.447	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.044	0.002	24.673	0.020	0.020	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.014	0.002	27.524	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	130	HIS	1	0.918	0.964	29.134	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.924	-0.949	31.471	0.059	0.059	0.000	0.000	0.000	0.000
132	A	132	ASN	0	-0.018	-0.018	34.627	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.018	0.003	37.614	0.005	0.005	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.071	0.031	39.463	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.916	-0.953	39.886	0.028	0.028	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.033	-0.025	36.544	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.840	-0.912	40.180	0.006	0.006	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.010	-0.006	43.273	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	139	HIS	0	-0.030	-0.018	39.397	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	140	HIS	0	0.005	-0.007	38.419	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	141	HIS	0	0.018	0.018	43.578	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	142	HIS	0	-0.025	-0.020	46.175	0.000	0.000	0.000	0.000	0.000	0.000
143	A	143	HIS	0	-0.038	-0.028	41.727	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	144	HIS	0	-0.073	-0.011	46.322	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	145	HIS	0	-0.068	-0.019	48.115	-0.002	-0.002	0.000	0.000	0.000	0.000

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