FMO DATABASE

FMODB ID: NN3JQ

Calculation Name: 3VPY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VPY

Chain ID: A

ChEMBL ID:

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	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1447171.699839
FMO2-HF: Nuclear repulsion	1385784.623246
FMO2-HF: Total energy	-61387.076593
FMO2-MP2: Total energy	-61564.290268

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.
1.741	3.3	-0.016	-0.607	-0.936	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 : -0.018 / 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	-0.019	-0.016	3.866	0.637	1.822	-0.014	-0.452	-0.719	0.001
4	A	4	PHE	0	0.005	-0.012	6.463	-0.064	-0.064	0.000	0.000	0.000	0.000
5	A	5	ASN	0	-0.005	-0.006	7.470	0.412	0.412	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.724	-0.830	9.930	0.273	0.273	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.039	0.005	13.054	0.013	0.013	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.044	0.007	16.032	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.791	-0.871	18.775	0.213	0.213	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.005	0.022	16.599	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.782	0.859	18.629	-0.201	-0.201	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.873	0.942	20.616	-0.161	-0.161	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.026	0.011	21.522	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.016	-0.018	24.707	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.826	-0.898	28.048	0.087	0.087	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.871	0.916	27.444	-0.076	-0.076	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.020	-0.008	25.370	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.865	0.933	25.900	-0.079	-0.079	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.036	0.025	21.666	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.054	0.014	25.564	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.010	0.009	23.671	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.045	0.020	26.361	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.825	0.874	26.530	-0.030	-0.030	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.833	-0.888	28.262	0.026	0.026	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.041	0.030	30.524	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.893	-0.937	32.292	0.036	0.036	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.040	-0.011	30.851	0.004	0.004	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.049	-0.038	25.565	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.069	-0.049	29.807	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.886	-0.928	28.944	0.074	0.074	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.068	-0.015	27.356	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.025	0.011	20.638	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.012	0.003	22.948	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.019	0.032	20.085	0.016	0.016	0.000	0.000	0.000	0.000
35	A	35	HIS	0	0.034	0.001	22.708	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.898	0.912	21.543	-0.138	-0.138	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.071	-0.036	14.651	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.013	-0.029	15.478	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.053	-0.005	13.523	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.020	0.011	14.917	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.009	0.000	7.995	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.008	0.004	12.589	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.056	0.010	11.402	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.880	0.950	12.464	0.110	0.110	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.839	-0.905	6.055	-0.352	-0.352	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.898	0.902	9.674	0.012	0.012	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.912	0.971	6.911	-0.515	-0.515	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.016	-0.021	4.553	0.021	0.136	-0.001	-0.010	-0.103	0.000
49	A	49	ALA	0	-0.034	0.007	8.424	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.781	-0.870	11.138	0.444	0.444	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.032	-0.015	14.101	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.028	-0.006	14.653	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.003	-0.012	15.149	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.804	-0.896	16.585	0.066	0.066	0.000	0.000	0.000	0.000
55	A	55	HIS	0	0.077	0.078	18.094	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.019	-0.005	18.183	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.050	-0.025	18.236	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.026	0.015	15.871	0.001	0.001	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.028	-0.007	12.056	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.772	0.869	6.198	0.712	0.712	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.032	0.010	3.811	0.576	0.835	-0.001	-0.145	-0.114	0.000
62	A	62	HIS	0	0.011	0.013	9.380	-0.073	-0.073	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.034	0.010	12.996	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	VAL	0	0.011	0.010	12.473	0.023	0.023	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.018	-0.006	14.517	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.003	-0.032	14.761	0.069	0.069	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.029	-0.036	17.377	-0.035	-0.035	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.797	0.877	19.259	-0.171	-0.171	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.835	-0.891	21.645	0.123	0.123	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.004	0.006	24.578	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.853	-0.940	27.390	0.083	0.083	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.888	0.947	31.101	-0.076	-0.076	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.897	-0.938	33.707	0.058	0.058	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.753	0.869	37.292	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.039	0.007	39.776	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.799	-0.883	42.925	0.052	0.052	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.020	0.013	42.578	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.072	-0.025	41.514	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	MET	0	0.016	0.027	35.041	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.022	-0.005	35.189	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.839	0.908	27.373	-0.115	-0.115	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.059	-0.050	28.885	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.003	0.001	23.398	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.811	0.908	24.906	-0.112	-0.112	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.033	0.022	22.147	0.018	0.018	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.023	-0.057	20.424	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.015	0.003	18.606	0.025	0.025	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.008	0.006	14.857	0.010	0.010	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.728	-0.818	15.575	0.048	0.048	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.047	-0.025	9.630	0.027	0.027	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.028	0.014	11.635	-0.042	-0.042	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.099	-0.064	14.240	-0.042	-0.042	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.006	-0.016	15.538	0.008	0.008	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.066	-0.037	18.143	0.011	0.011	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.984	1.011	19.059	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.038	-0.012	18.047	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	TYR	0	-0.047	-0.025	20.714	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.017	0.002	23.481	0.007	0.007	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.005	-0.031	26.412	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.816	-0.898	28.355	0.035	0.035	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.001	0.025	27.984	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.058	-0.028	24.406	0.005	0.005	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.022	-0.008	19.897	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.847	-0.903	21.420	0.053	0.053	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.018	-0.011	15.875	0.013	0.013	0.000	0.000	0.000	0.000
106	A	106	GLN	0	-0.021	-0.026	11.792	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.828	0.899	15.929	-0.077	-0.077	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.011	-0.002	15.041	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	109	TYR	0	0.028	0.013	20.383	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.794	-0.857	22.979	0.117	0.117	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.018	-0.002	22.581	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.006	-0.011	26.323	0.003	0.003	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.870	-0.939	29.323	0.073	0.073	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.833	0.891	31.527	-0.066	-0.066	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.775	-0.852	27.625	0.078	0.078	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.022	-0.015	28.228	0.004	0.004	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.026	-0.011	21.875	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.818	0.890	23.446	-0.039	-0.039	0.000	0.000	0.000	0.000
119	A	119	PHE	0	-0.002	-0.003	18.078	0.003	0.003	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.004	-0.015	19.914	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.015	-0.021	20.625	0.009	0.009	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.037	-0.019	21.368	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.004	-0.015	23.406	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.841	0.920	21.466	-0.068	-0.068	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.875	-0.917	24.346	0.041	0.041	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.021	-0.026	19.906	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.039	0.027	25.356	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.027	0.004	25.093	0.005	0.005	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.006	-0.001	27.743	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	HIS	1	0.857	0.916	29.261	-0.077	-0.077	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.854	-0.898	31.467	0.075	0.075	0.000	0.000	0.000	0.000
132	A	132	ASN	0	-0.036	-0.029	34.587	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.021	0.003	37.541	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.060	0.025	39.417	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.891	-0.941	39.918	0.052	0.052	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.039	-0.018	35.994	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.821	-0.909	39.716	0.052	0.052	0.000	0.000	0.000	0.000
138	A	138	HIS	0	-0.015	0.003	42.782	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	139	HIS	0	-0.014	-0.013	38.878	0.001	0.001	0.000	0.000	0.000	0.000
140	A	140	HIS	0	-0.013	-0.006	38.117	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	HIS	0	0.026	0.019	43.230	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	HIS	0	-0.004	-0.003	45.680	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	HIS	0	-0.038	-0.026	40.948	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	144	HIS	0	-0.073	-0.014	45.896	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	HIS	0	-0.112	-0.058	48.046	-0.005	-0.005	0.000	0.000	0.000	0.000

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