FMO DATABASE

FMODB ID: VQ281

Calculation Name: 3BNV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BNV

Chain ID: A

ChEMBL ID:

UniProt ID: Q0R4E3

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1264926.715236
FMO2-HF: Nuclear repulsion	1209875.058603
FMO2-HF: Total energy	-55051.656633
FMO2-MP2: Total energy	-55212.801333

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:13:LEU)

Summations of interaction energy for fragment #1(A:13:LEU)

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.
-4.187	1.812	1.038	-1.879	-5.157	0

Interaction energy analysis for fragmet #1(A:13:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / 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].
3	A	15	GLU	-1	-1.044	-1.002	2.995	-1.781	1.129	0.061	-1.210	-1.761
4	A	16	TYR	0	-0.028	-0.018	3.271	0.588	1.264	0.017	-0.107	-0.586
5	A	17	ALA	0	0.009	0.000	7.452	0.568	0.568	0.000	0.000	0.000
6	A	18	SER	0	-0.052	-0.014	8.212	-0.139	-0.139	0.000	0.000	0.000
7	A	19	ALA	0	0.046	-0.006	9.697	-0.051	-0.051	0.000	0.000	0.000
8	A	20	GLU	-1	-0.928	-0.964	10.543	-0.345	-0.345	0.000	0.000	0.000
9	A	21	ASP	-1	-0.794	-0.881	11.984	-0.876	-0.876	0.000	0.000	0.000
10	A	22	ILE	0	0.026	0.011	7.546	0.069	0.069	0.000	0.000	0.000
11	A	23	SER	0	-0.069	-0.054	11.629	0.128	0.128	0.000	0.000	0.000
12	A	24	ARG	1	0.844	0.931	14.112	0.428	0.428	0.000	0.000	0.000
13	A	25	VAL	0	0.069	0.050	13.355	0.056	0.056	0.000	0.000	0.000
14	A	26	ARG	1	0.910	0.966	10.133	0.398	0.398	0.000	0.000	0.000
15	A	27	ALA	0	-0.062	-0.029	16.036	0.048	0.048	0.000	0.000	0.000
16	A	28	GLU	-1	-0.926	-0.970	18.916	-0.336	-0.336	0.000	0.000	0.000
17	A	29	LEU	0	-0.083	-0.029	16.988	0.011	0.011	0.000	0.000	0.000
18	A	30	LEU	0	-0.003	-0.008	19.757	0.033	0.033	0.000	0.000	0.000
19	A	31	THR	0	-0.018	0.007	19.820	0.021	0.021	0.000	0.000	0.000
20	A	32	CYS	0	-0.073	-0.047	19.126	-0.021	-0.021	0.000	0.000	0.000
21	A	33	PRO	0	0.050	0.026	18.696	-0.023	-0.023	0.000	0.000	0.000
22	A	34	GLU	-1	-0.926	-0.966	18.525	-0.068	-0.068	0.000	0.000	0.000
23	A	35	LEU	0	-0.076	-0.028	16.019	0.033	0.033	0.000	0.000	0.000
24	A	36	ASN	0	0.073	0.034	13.182	-0.064	-0.064	0.000	0.000	0.000
25	A	37	THR	0	0.056	0.017	9.636	0.062	0.062	0.000	0.000	0.000
26	A	38	SER	0	-0.043	-0.019	9.027	-0.157	-0.157	0.000	0.000	0.000
27	A	39	LEU	0	-0.071	-0.034	9.845	0.002	0.002	0.000	0.000	0.000
28	A	40	ALA	0	-0.027	-0.017	12.504	-0.021	-0.021	0.000	0.000	0.000
29	A	41	GLY	0	0.043	0.027	9.324	-0.047	-0.047	0.000	0.000	0.000
30	A	42	THR	0	-0.007	-0.013	7.255	0.420	0.420	0.000	0.000	0.000
31	A	43	ILE	0	-0.042	-0.021	10.055	-0.143	-0.143	0.000	0.000	0.000
32	A	44	ILE	0	-0.033	-0.023	9.282	-0.005	-0.005	0.000	0.000	0.000
33	A	45	GLU	-1	-0.886	-0.956	11.986	-0.654	-0.654	0.000	0.000	0.000
34	A	46	ILE	0	-0.031	-0.021	15.687	0.003	0.003	0.000	0.000	0.000
35	A	47	ASP	-1	-0.796	-0.893	19.037	-0.340	-0.340	0.000	0.000	0.000
36	A	48	LYS	1	0.838	0.927	22.677	0.236	0.236	0.000	0.000	0.000
37	A	49	ASN	0	-0.063	-0.024	25.687	0.005	0.005	0.000	0.000	0.000
38	A	50	TYR	0	0.050	0.019	18.482	-0.012	-0.012	0.000	0.000	0.000
39	A	51	ALA	0	0.027	0.019	17.726	0.007	0.007	0.000	0.000	0.000
40	A	52	LYS	1	0.966	1.002	13.736	0.947	0.947	0.000	0.000	0.000
41	A	53	SER	0	0.000	-0.013	12.072	-0.032	-0.032	0.000	0.000	0.000
42	A	54	ILE	0	0.040	0.027	4.965	0.051	0.051	0.000	0.000	0.000
43	A	55	LEU	0	0.012	0.004	8.145	0.027	0.027	0.000	0.000	0.000
44	A	56	ILE	0	0.010	0.011	2.421	-1.748	0.042	0.875	-0.464	-2.201
45	A	57	THR	0	-0.030	-0.023	5.283	0.465	0.541	-0.001	-0.002	-0.073
46	A	58	THR	0	0.098	0.021	5.635	0.162	0.162	0.000	0.000	0.000
47	A	59	SER	0	0.010	-0.021	7.669	-0.038	-0.038	0.000	0.000	0.000
48	A	60	GLU	-1	-0.984	-0.985	10.504	0.233	0.233	0.000	0.000	0.000
49	A	61	MET	0	-0.053	0.013	10.308	-0.073	-0.073	0.000	0.000	0.000
50	A	62	VAL	0	-0.030	-0.009	12.429	-0.045	-0.045	0.000	0.000	0.000
51	A	63	ALA	0	-0.054	-0.030	14.653	0.005	0.005	0.000	0.000	0.000
52	A	64	ASP	-1	-0.847	-0.938	17.392	0.001	0.001	0.000	0.000	0.000
53	A	65	ASP	-1	-0.929	-0.939	17.066	0.097	0.097	0.000	0.000	0.000
54	A	66	GLN	0	-0.098	-0.080	17.366	0.014	0.014	0.000	0.000	0.000
55	A	67	GLY	0	-0.033	-0.007	13.350	-0.006	-0.006	0.000	0.000	0.000
56	A	68	LEU	0	0.018	0.023	12.863	-0.056	-0.056	0.000	0.000	0.000
57	A	69	ILE	0	0.003	0.003	10.169	0.026	0.026	0.000	0.000	0.000
58	A	70	PHE	0	-0.011	-0.001	13.971	-0.019	-0.019	0.000	0.000	0.000
59	A	71	ASP	-1	-0.820	-0.930	15.946	-0.258	-0.258	0.000	0.000	0.000
60	A	72	ALA	0	-0.043	-0.020	17.491	-0.040	-0.040	0.000	0.000	0.000
61	A	73	PHE	0	0.035	0.023	13.423	-0.008	-0.008	0.000	0.000	0.000
62	A	74	ILE	0	0.028	0.029	13.715	-0.073	-0.073	0.000	0.000	0.000
63	A	75	PHE	0	-0.039	-0.024	15.163	-0.033	-0.033	0.000	0.000	0.000
64	A	76	ALA	0	-0.018	-0.015	15.817	-0.009	-0.009	0.000	0.000	0.000
65	A	77	ALA	0	0.076	0.041	12.865	-0.003	-0.003	0.000	0.000	0.000
66	A	78	ALA	0	-0.016	-0.015	14.697	-0.016	-0.016	0.000	0.000	0.000
67	A	79	ASN	0	-0.058	-0.040	17.607	0.019	0.019	0.000	0.000	0.000
68	A	80	TYR	0	0.002	0.003	13.208	0.019	0.019	0.000	0.000	0.000
69	A	81	VAL	0	0.060	0.022	15.520	0.028	0.028	0.000	0.000	0.000
70	A	82	ALA	0	-0.003	-0.006	17.482	0.031	0.031	0.000	0.000	0.000
71	A	83	GLN	0	0.014	0.029	20.991	0.044	0.044	0.000	0.000	0.000
72	A	84	ALA	0	0.034	0.016	18.093	0.026	0.026	0.000	0.000	0.000
73	A	85	SER	0	-0.078	-0.048	20.064	0.021	0.021	0.000	0.000	0.000
74	A	86	ILE	0	-0.089	-0.051	22.236	0.034	0.034	0.000	0.000	0.000
75	A	87	ASN	0	0.018	0.004	22.320	0.020	0.020	0.000	0.000	0.000
76	A	88	LYS	1	0.923	0.962	23.797	0.204	0.204	0.000	0.000	0.000
77	A	89	GLU	-1	-0.903	-0.945	25.579	-0.143	-0.143	0.000	0.000	0.000
78	A	90	PHE	0	-0.018	-0.004	26.595	0.004	0.004	0.000	0.000	0.000
79	A	91	SER	0	-0.005	-0.022	25.638	0.000	0.000	0.000	0.000	0.000
80	A	92	VAL	0	-0.011	0.013	26.801	0.002	0.002	0.000	0.000	0.000
81	A	93	ILE	0	0.006	0.001	23.596	-0.005	-0.005	0.000	0.000	0.000
82	A	94	ILE	0	-0.045	-0.025	27.322	0.014	0.014	0.000	0.000	0.000
83	A	95	GLY	0	0.016	0.008	28.979	0.014	0.014	0.000	0.000	0.000
84	A	96	SER	0	-0.032	-0.011	25.380	-0.018	-0.018	0.000	0.000	0.000
85	A	97	LYS	1	0.933	0.972	26.885	0.194	0.194	0.000	0.000	0.000
86	A	98	CYS	0	-0.021	-0.004	22.433	-0.021	-0.021	0.000	0.000	0.000
87	A	99	PHE	0	-0.054	-0.023	23.297	0.034	0.034	0.000	0.000	0.000
88	A	100	PHE	0	0.063	0.020	18.597	-0.027	-0.027	0.000	0.000	0.000
89	A	101	TYR	0	-0.100	-0.072	19.943	0.038	0.038	0.000	0.000	0.000
90	A	102	ALA	0	0.016	-0.006	17.535	0.026	0.026	0.000	0.000	0.000
91	A	103	PRO	0	-0.001	0.030	16.472	-0.036	-0.036	0.000	0.000	0.000
92	A	104	LEU	0	0.034	0.000	9.696	-0.017	-0.017	0.000	0.000	0.000
93	A	105	LYS	1	0.943	0.978	11.033	0.204	0.204	0.000	0.000	0.000
94	A	106	LEU	0	-0.018	-0.016	7.750	-0.073	-0.073	0.000	0.000	0.000
95	A	107	GLY	0	-0.053	-0.026	5.144	0.125	0.125	0.000	0.000	0.000
96	A	108	ASP	-1	-0.886	-0.936	4.733	-0.786	-0.702	-0.001	-0.002	-0.080
97	A	109	VAL	0	-0.022	-0.018	3.012	-0.514	-0.051	0.087	-0.094	-0.456
98	A	110	LEU	0	-0.041	-0.011	5.946	0.198	0.198	0.000	0.000	0.000
99	A	111	GLU	-1	-0.898	-0.963	9.077	-1.729	-1.729	0.000	0.000	0.000
100	A	112	LEU	0	-0.070	-0.039	11.068	0.223	0.223	0.000	0.000	0.000
101	A	113	GLU	-1	-0.910	-0.950	14.275	-0.714	-0.714	0.000	0.000	0.000
102	A	114	ALA	0	-0.026	-0.019	17.357	0.058	0.058	0.000	0.000	0.000
103	A	115	HIS	0	0.030	0.014	20.332	0.027	0.027	0.000	0.000	0.000
104	A	116	ALA	0	-0.042	-0.010	23.869	0.020	0.020	0.000	0.000	0.000
105	A	117	LEU	0	-0.013	-0.011	26.689	0.007	0.007	0.000	0.000	0.000
106	A	118	PHE	0	-0.026	-0.018	30.138	0.005	0.005	0.000	0.000	0.000
107	A	119	ASP	-1	-0.785	-0.928	32.395	-0.151	-0.151	0.000	0.000	0.000
108	A	120	GLU	-1	-0.955	-0.966	33.685	-0.180	-0.180	0.000	0.000	0.000
109	A	121	THR	0	-0.087	-0.021	35.437	0.010	0.010	0.000	0.000	0.000
110	A	122	SER	0	-0.025	0.001	35.955	0.007	0.007	0.000	0.000	0.000
111	A	123	LYS	1	0.890	0.943	33.862	0.119	0.119	0.000	0.000	0.000
112	A	124	LYS	1	0.906	0.960	32.625	0.139	0.139	0.000	0.000	0.000
113	A	125	ARG	1	0.876	0.924	29.081	0.224	0.224	0.000	0.000	0.000
114	A	126	ASP	-1	-0.865	-0.932	29.142	-0.194	-0.194	0.000	0.000	0.000
115	A	127	VAL	0	-0.009	0.002	22.902	-0.004	-0.004	0.000	0.000	0.000
116	A	128	LYS	1	0.891	0.950	24.098	0.303	0.303	0.000	0.000	0.000
117	A	129	VAL	0	0.031	0.014	18.271	-0.022	-0.022	0.000	0.000	0.000
118	A	130	VAL	0	-0.032	-0.019	17.707	0.053	0.053	0.000	0.000	0.000
119	A	131	GLY	0	0.028	0.008	15.055	-0.060	-0.060	0.000	0.000	0.000
120	A	132	HIS	0	0.006	-0.004	13.435	0.156	0.156	0.000	0.000	0.000
121	A	133	VAL	0	0.049	0.037	9.066	-0.142	-0.142	0.000	0.000	0.000
122	A	134	LYS	1	0.969	0.977	8.439	0.822	0.822	0.000	0.000	0.000
123	A	135	GLU	-1	-0.899	-0.950	11.275	-0.516	-0.516	0.000	0.000	0.000
124	A	136	ILE	0	-0.013	0.006	14.362	0.071	0.071	0.000	0.000	0.000
125	A	137	LYS	1	0.882	0.945	15.223	0.304	0.304	0.000	0.000	0.000
126	A	138	MET	0	-0.002	0.003	13.513	0.058	0.058	0.000	0.000	0.000
127	A	139	PHE	0	-0.005	-0.013	16.820	0.050	0.050	0.000	0.000	0.000
128	A	140	GLU	-1	-0.820	-0.882	18.605	-0.350	-0.350	0.000	0.000	0.000
129	A	141	GLY	0	-0.017	-0.008	21.638	0.033	0.033	0.000	0.000	0.000
130	A	142	THR	0	-0.057	-0.016	23.626	-0.019	-0.019	0.000	0.000	0.000
131	A	143	ILE	0	0.007	-0.005	21.654	0.022	0.022	0.000	0.000	0.000
132	A	144	GLN	0	-0.047	-0.022	25.782	0.005	0.005	0.000	0.000	0.000
133	A	145	VAL	0	0.039	0.026	25.231	0.007	0.007	0.000	0.000	0.000
134	A	146	VAL	0	-0.009	-0.009	28.186	0.009	0.009	0.000	0.000	0.000
135	A	147	SER	0	-0.022	-0.012	29.616	-0.004	-0.004	0.000	0.000	0.000
136	A	148	THR	0	-0.064	-0.066	31.305	0.007	0.007	0.000	0.000	0.000
137	A	149	ASP	-1	-0.876	-0.945	32.638	-0.121	-0.121	0.000	0.000	0.000
138	A	150	GLU	-1	-0.852	-0.920	34.190	-0.074	-0.074	0.000	0.000	0.000
139	A	151	HIS	0	0.045	0.052	28.576	0.000	0.000	0.000	0.000	0.000
140	A	152	ILE	0	0.037	0.014	31.289	0.008	0.008	0.000	0.000	0.000
141	A	153	PHE	0	-0.048	-0.024	30.379	0.004	0.004	0.000	0.000	0.000
142	A	154	LYS	1	0.824	0.919	34.974	0.079	0.079	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:13:LEU)