FMO DATABASE

FMODB ID: 89J4Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1446774.085186
FMO2-HF: Nuclear repulsion	1385387.251952
FMO2-HF: Total energy	-61386.833234
FMO2-MP2: Total energy	-61564.109596

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.
4.077	6.077	-0.002	-0.864	-1.133	0.003

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 : -0.028 / q_NPA : -0.026

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	-0.021	-0.018	3.844	1.094	2.567	-0.001	-0.599	-0.873	0.002
4	A	4	PHE	0	0.002	-0.006	6.131	-0.148	-0.148	0.000	0.000	0.000	0.000
5	A	5	ASN	0	-0.005	-0.002	7.851	0.471	0.471	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.747	-0.858	10.174	0.345	0.345	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.057	-0.006	13.254	0.044	0.044	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.049	0.011	16.272	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.793	-0.877	18.761	0.336	0.336	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.012	0.028	17.022	-0.044	-0.044	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.799	0.874	19.054	-0.295	-0.295	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.870	0.935	21.291	-0.149	-0.149	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.009	0.016	22.158	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.016	-0.017	25.159	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.851	-0.913	28.621	0.072	0.072	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.886	0.917	27.811	-0.051	-0.051	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.022	0.001	25.509	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.887	0.945	25.805	-0.023	-0.023	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.041	0.027	21.563	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.040	0.014	25.393	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.001	0.004	23.956	0.000	0.000	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.035	0.022	26.505	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.847	0.892	26.751	0.078	0.078	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.816	-0.897	28.246	-0.079	-0.079	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.020	0.016	30.329	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.891	-0.938	31.891	-0.026	-0.026	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.035	-0.002	30.909	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.050	-0.036	25.606	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.056	-0.032	29.859	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.896	-0.944	28.852	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.083	-0.024	27.281	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.030	0.011	20.689	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.041	-0.015	22.642	0.015	0.015	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.016	0.018	19.905	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	HIS	0	0.011	-0.012	22.598	0.012	0.012	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.891	0.914	21.772	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.056	-0.029	14.569	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.003	-0.014	16.125	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.047	-0.002	13.669	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.023	0.027	14.975	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.012	-0.005	8.077	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.010	0.002	12.544	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.060	0.011	11.241	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.878	0.952	12.189	0.413	0.413	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.887	-0.942	6.000	-1.967	-1.967	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.898	0.901	9.749	0.284	0.284	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.909	0.969	6.822	1.731	1.731	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.012	-0.021	4.325	-0.241	-0.110	-0.001	-0.015	-0.115	0.000
49	A	49	ALA	0	-0.026	0.011	8.022	0.186	0.186	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.774	-0.863	10.880	0.176	0.176	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.052	-0.026	13.917	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.023	-0.001	14.387	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.003	-0.017	14.892	0.036	0.036	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.818	-0.905	16.100	-0.274	-0.274	0.000	0.000	0.000	0.000
55	A	55	HIS	0	0.053	0.066	17.785	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.035	0.002	18.110	-0.021	-0.021	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.050	-0.020	18.367	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.011	0.016	15.681	0.023	0.023	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.035	0.008	12.030	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.810	0.890	6.132	1.692	1.692	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.024	0.003	3.904	0.590	0.986	0.000	-0.250	-0.145	0.001
62	A	62	HIS	0	0.001	0.010	9.306	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.046	0.017	12.956	0.045	0.045	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.007	0.013	12.619	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.018	-0.004	14.575	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.003	-0.032	15.019	0.086	0.086	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.042	-0.043	17.813	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.842	0.906	19.478	-0.243	-0.243	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.842	-0.893	22.024	0.177	0.177	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.010	-0.006	25.021	0.020	0.020	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.865	-0.948	27.542	0.131	0.131	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.913	0.956	31.281	-0.096	-0.096	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.902	-0.939	33.904	0.086	0.086	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.757	0.866	37.514	-0.083	-0.083	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.049	0.011	39.858	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.816	-0.890	43.094	0.071	0.071	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.030	0.023	42.482	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.075	-0.027	41.539	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	MET	0	0.020	0.021	35.075	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.010	-0.013	35.234	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.851	0.911	28.079	-0.161	-0.161	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.065	-0.045	29.306	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.001	0.001	23.727	0.011	0.011	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.805	0.900	25.213	-0.149	-0.149	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.020	0.018	22.579	0.027	0.027	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.014	-0.043	20.634	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.004	0.016	18.567	0.018	0.018	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.025	-0.006	15.053	0.035	0.035	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.743	-0.827	15.395	0.023	0.023	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.039	-0.022	9.486	0.055	0.055	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.027	0.015	11.603	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.097	-0.057	13.999	-0.062	-0.062	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.011	-0.016	15.016	0.009	0.009	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.075	-0.057	17.483	0.032	0.032	0.000	0.000	0.000	0.000
95	A	95	LYS	1	1.002	1.024	18.554	0.014	0.014	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.033	-0.011	17.861	-0.026	-0.026	0.000	0.000	0.000	0.000
97	A	97	TYR	0	-0.030	-0.015	20.533	0.018	0.018	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.033	0.015	23.389	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.028	-0.042	26.151	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.827	-0.907	28.590	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	101	SER	0	0.006	0.019	28.106	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.081	-0.035	23.902	0.004	0.004	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.027	-0.011	19.581	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.862	-0.920	21.392	0.105	0.105	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.006	-0.002	16.162	0.015	0.015	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.032	-0.035	12.190	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.860	0.918	16.253	-0.135	-0.135	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.007	-0.002	15.267	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	109	TYR	0	0.022	0.008	20.528	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.796	-0.857	23.195	0.139	0.139	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.016	-0.004	22.389	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.002	-0.011	26.183	0.005	0.005	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.883	-0.946	29.488	0.047	0.047	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.830	0.888	31.114	-0.042	-0.042	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.780	-0.848	27.585	0.062	0.062	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.028	-0.029	27.944	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.022	-0.010	21.490	0.006	0.006	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.828	0.896	23.297	0.014	0.014	0.000	0.000	0.000	0.000
119	A	119	PHE	0	-0.003	0.000	18.086	0.005	0.005	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.003	-0.020	20.178	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.016	-0.025	20.852	0.023	0.023	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.039	-0.022	21.224	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.035	-0.017	23.202	0.006	0.006	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.913	0.951	22.020	0.113	0.113	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.867	-0.910	24.651	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.026	-0.032	20.026	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.049	0.040	25.541	0.006	0.006	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.030	0.010	24.914	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.014	0.006	27.657	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	HIS	1	0.869	0.922	29.300	-0.064	-0.064	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.879	-0.909	31.576	0.042	0.042	0.000	0.000	0.000	0.000
132	A	132	ASN	0	-0.025	-0.017	34.657	0.004	0.004	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.013	-0.002	37.568	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.075	0.034	39.413	0.000	0.000	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.904	-0.952	39.958	0.051	0.051	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.042	-0.023	36.535	0.002	0.002	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.824	-0.915	40.091	0.042	0.042	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.011	0.000	43.224	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	139	HIS	0	-0.023	-0.014	39.478	0.004	0.004	0.000	0.000	0.000	0.000
140	A	140	HIS	0	-0.002	-0.006	38.563	0.003	0.003	0.000	0.000	0.000	0.000
141	A	141	HIS	0	0.020	0.019	43.674	0.000	0.000	0.000	0.000	0.000	0.000
142	A	142	HIS	0	0.006	0.002	46.263	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	HIS	0	-0.030	0.010	41.637	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	144	HIS	0	-0.073	-0.010	46.520	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	HIS	0	-0.120	-0.087	48.362	-0.004	-0.004	0.000	0.000	0.000	0.000

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