FMO DATABASE

FMODB ID: 1NJ2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1265613.842612
FMO2-HF: Nuclear repulsion	1210561.219054
FMO2-HF: Total energy	-55052.623558
FMO2-MP2: Total energy	-55213.718795

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.
-3.776	1.405	2.859	-2.108	-5.931	0.003

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 : 0.008 / q_NPA : 0.001

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	15	GLU	-1	-0.985	-0.959	3.266	-1.985	0.860	0.014	-1.136	-1.723	0.002
4	A	16	TYR	0	-0.074	-0.059	2.679	0.187	1.095	0.142	-0.173	-0.877	0.000
5	A	17	ALA	0	0.008	-0.002	7.510	0.525	0.525	0.000	0.000	0.000	0.000
6	A	18	SER	0	-0.062	-0.041	8.275	-0.197	-0.197	0.000	0.000	0.000	0.000
7	A	19	ALA	0	0.048	-0.003	9.640	-0.053	-0.053	0.000	0.000	0.000	0.000
8	A	20	GLU	-1	-0.872	-0.918	10.470	-0.369	-0.369	0.000	0.000	0.000	0.000
9	A	21	ASP	-1	-0.786	-0.860	12.156	-0.875	-0.875	0.000	0.000	0.000	0.000
10	A	22	ILE	0	0.034	0.016	7.422	0.077	0.077	0.000	0.000	0.000	0.000
11	A	23	SER	0	-0.087	-0.059	11.726	0.124	0.124	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.819	0.901	14.130	0.483	0.483	0.000	0.000	0.000	0.000
13	A	25	VAL	0	0.070	0.045	13.804	0.055	0.055	0.000	0.000	0.000	0.000
14	A	26	ARG	1	0.905	0.972	9.792	0.618	0.618	0.000	0.000	0.000	0.000
15	A	27	ALA	0	-0.056	-0.030	16.147	0.051	0.051	0.000	0.000	0.000	0.000
16	A	28	GLU	-1	-0.940	-0.976	19.037	-0.348	-0.348	0.000	0.000	0.000	0.000
17	A	29	LEU	0	-0.063	-0.017	17.012	0.017	0.017	0.000	0.000	0.000	0.000
18	A	30	LEU	0	-0.009	-0.007	19.950	0.030	0.030	0.000	0.000	0.000	0.000
19	A	31	THR	0	-0.020	0.001	20.434	0.021	0.021	0.000	0.000	0.000	0.000
20	A	32	CYS	0	-0.073	-0.046	19.397	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	33	PRO	0	0.050	0.025	18.910	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	34	GLU	-1	-0.930	-0.965	18.663	-0.100	-0.100	0.000	0.000	0.000	0.000
23	A	35	LEU	0	-0.079	-0.025	15.970	0.036	0.036	0.000	0.000	0.000	0.000
24	A	36	ASN	0	0.061	0.020	13.193	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	37	THR	0	0.061	0.022	9.900	0.058	0.058	0.000	0.000	0.000	0.000
26	A	38	SER	0	-0.039	-0.016	8.966	-0.166	-0.166	0.000	0.000	0.000	0.000
27	A	39	LEU	0	-0.070	-0.031	9.578	0.042	0.042	0.000	0.000	0.000	0.000
28	A	40	ALA	0	-0.023	-0.015	12.109	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	41	GLY	0	0.033	0.021	9.372	-0.040	-0.040	0.000	0.000	0.000	0.000
30	A	42	THR	0	-0.019	-0.018	7.451	0.369	0.369	0.000	0.000	0.000	0.000
31	A	43	ILE	0	-0.033	-0.019	10.300	-0.114	-0.114	0.000	0.000	0.000	0.000
32	A	44	ILE	0	-0.022	-0.019	8.088	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	45	GLU	-1	-0.898	-0.960	12.255	-0.647	-0.647	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.027	-0.018	15.945	0.011	0.011	0.000	0.000	0.000	0.000
35	A	47	ASP	-1	-0.799	-0.883	19.302	-0.322	-0.322	0.000	0.000	0.000	0.000
36	A	48	LYS	1	0.785	0.864	22.937	0.225	0.225	0.000	0.000	0.000	0.000
37	A	49	ASN	0	-0.088	-0.038	25.752	0.008	0.008	0.000	0.000	0.000	0.000
38	A	50	TYR	0	0.022	0.000	18.301	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	51	ALA	0	0.020	0.017	17.696	0.001	0.001	0.000	0.000	0.000	0.000
40	A	52	LYS	1	0.905	0.957	13.094	0.838	0.838	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.004	-0.010	11.785	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	54	ILE	0	0.021	0.022	4.811	0.041	0.041	0.000	0.000	0.000	0.000
43	A	55	LEU	0	0.009	0.000	8.128	0.010	0.010	0.000	0.000	0.000	0.000
44	A	56	ILE	0	0.015	0.014	2.203	-1.408	-0.505	2.697	-0.740	-2.859	0.001
45	A	57	THR	0	-0.030	-0.034	4.898	0.414	0.497	-0.001	-0.003	-0.079	0.000
46	A	58	THR	0	0.095	0.021	5.509	0.248	0.248	0.000	0.000	0.000	0.000
47	A	59	SER	0	0.015	-0.016	7.586	-0.068	-0.068	0.000	0.000	0.000	0.000
48	A	60	GLU	-1	-0.987	-0.989	10.547	0.283	0.283	0.000	0.000	0.000	0.000
49	A	61	MET	0	-0.050	0.013	9.866	-0.082	-0.082	0.000	0.000	0.000	0.000
50	A	62	VAL	0	-0.033	-0.013	12.323	-0.042	-0.042	0.000	0.000	0.000	0.000
51	A	63	ALA	0	-0.061	-0.031	14.473	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	64	ASP	-1	-0.841	-0.933	17.317	0.080	0.080	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.922	-0.954	17.057	0.166	0.166	0.000	0.000	0.000	0.000
54	A	66	GLN	0	-0.102	-0.065	17.746	0.017	0.017	0.000	0.000	0.000	0.000
55	A	67	GLY	0	-0.026	-0.003	13.567	0.003	0.003	0.000	0.000	0.000	0.000
56	A	68	LEU	0	0.013	0.021	13.221	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.000	-0.001	10.324	0.026	0.026	0.000	0.000	0.000	0.000
58	A	70	PHE	0	-0.006	-0.001	14.026	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	71	ASP	-1	-0.816	-0.926	15.749	-0.158	-0.158	0.000	0.000	0.000	0.000
60	A	72	ALA	0	-0.038	-0.019	17.372	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	73	PHE	0	0.031	0.020	12.838	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	74	ILE	0	0.020	0.029	13.627	-0.068	-0.068	0.000	0.000	0.000	0.000
63	A	75	PHE	0	-0.034	-0.024	15.050	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	76	ALA	0	-0.015	-0.009	15.423	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	77	ALA	0	0.076	0.040	12.752	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	78	ALA	0	-0.015	-0.014	14.713	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.051	-0.039	17.546	0.008	0.008	0.000	0.000	0.000	0.000
68	A	80	TYR	0	0.004	0.005	13.533	0.005	0.005	0.000	0.000	0.000	0.000
69	A	81	VAL	0	0.040	0.013	15.352	0.020	0.020	0.000	0.000	0.000	0.000
70	A	82	ALA	0	-0.007	-0.008	17.322	0.023	0.023	0.000	0.000	0.000	0.000
71	A	83	GLN	0	0.025	0.024	20.888	0.035	0.035	0.000	0.000	0.000	0.000
72	A	84	ALA	0	0.030	0.018	18.313	0.021	0.021	0.000	0.000	0.000	0.000
73	A	85	SER	0	-0.062	-0.033	20.306	0.016	0.016	0.000	0.000	0.000	0.000
74	A	86	ILE	0	-0.092	-0.053	22.142	0.028	0.028	0.000	0.000	0.000	0.000
75	A	87	ASN	0	0.009	-0.002	22.278	0.015	0.015	0.000	0.000	0.000	0.000
76	A	88	LYS	1	0.933	0.966	24.068	0.197	0.197	0.000	0.000	0.000	0.000
77	A	89	GLU	-1	-0.898	-0.945	25.833	-0.149	-0.149	0.000	0.000	0.000	0.000
78	A	90	PHE	0	-0.027	-0.009	26.824	0.005	0.005	0.000	0.000	0.000	0.000
79	A	91	SER	0	-0.008	-0.023	25.622	0.001	0.001	0.000	0.000	0.000	0.000
80	A	92	VAL	0	-0.006	0.013	26.767	0.002	0.002	0.000	0.000	0.000	0.000
81	A	93	ILE	0	0.005	0.002	23.628	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.037	-0.023	27.313	0.013	0.013	0.000	0.000	0.000	0.000
83	A	95	GLY	0	0.013	0.004	28.952	0.013	0.013	0.000	0.000	0.000	0.000
84	A	96	SER	0	-0.046	-0.013	25.270	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	97	LYS	1	0.938	0.973	26.693	0.154	0.154	0.000	0.000	0.000	0.000
86	A	98	CYS	0	-0.021	-0.005	22.185	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	99	PHE	0	-0.043	-0.020	22.995	0.029	0.029	0.000	0.000	0.000	0.000
88	A	100	PHE	0	0.061	0.018	18.349	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	101	TYR	0	-0.099	-0.067	19.602	0.032	0.032	0.000	0.000	0.000	0.000
90	A	102	ALA	0	0.021	0.002	17.250	0.022	0.022	0.000	0.000	0.000	0.000
91	A	103	PRO	0	-0.006	0.022	16.460	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	104	LEU	0	0.026	-0.001	9.970	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	105	LYS	1	0.936	0.964	11.039	0.062	0.062	0.000	0.000	0.000	0.000
94	A	106	LEU	0	-0.021	-0.012	7.822	-0.043	-0.043	0.000	0.000	0.000	0.000
95	A	107	GLY	0	-0.042	-0.020	5.597	0.095	0.095	0.000	0.000	0.000	0.000
96	A	108	ASP	-1	-0.887	-0.928	4.779	-0.481	-0.402	-0.001	-0.002	-0.076	0.000
97	A	109	VAL	0	-0.003	-0.002	3.539	-0.319	0.044	0.008	-0.054	-0.317	0.000
98	A	110	LEU	0	-0.048	-0.016	5.510	0.155	0.155	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.907	-0.962	8.811	-1.492	-1.492	0.000	0.000	0.000	0.000
100	A	112	LEU	0	-0.060	-0.037	10.905	0.199	0.199	0.000	0.000	0.000	0.000
101	A	113	GLU	-1	-0.800	-0.875	14.021	-0.648	-0.648	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.031	-0.022	17.041	0.057	0.057	0.000	0.000	0.000	0.000
103	A	115	HIS	0	0.024	0.013	20.058	0.023	0.023	0.000	0.000	0.000	0.000
104	A	116	ALA	0	-0.039	-0.009	23.563	0.022	0.022	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.011	-0.011	26.419	0.006	0.006	0.000	0.000	0.000	0.000
106	A	118	PHE	0	0.001	-0.001	29.860	0.003	0.003	0.000	0.000	0.000	0.000
107	A	119	ASP	-1	-0.761	-0.894	32.089	-0.134	-0.134	0.000	0.000	0.000	0.000
108	A	120	GLU	-1	-0.920	-0.925	33.661	-0.178	-0.178	0.000	0.000	0.000	0.000
109	A	121	THR	0	-0.104	-0.055	35.444	0.009	0.009	0.000	0.000	0.000	0.000
110	A	122	SER	0	-0.018	0.005	35.691	0.006	0.006	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.856	0.906	33.934	0.111	0.111	0.000	0.000	0.000	0.000
112	A	124	LYS	1	0.850	0.932	32.550	0.125	0.125	0.000	0.000	0.000	0.000
113	A	125	ARG	1	0.858	0.917	29.088	0.206	0.206	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.848	-0.906	28.979	-0.169	-0.169	0.000	0.000	0.000	0.000
115	A	127	VAL	0	0.004	0.005	22.829	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	128	LYS	1	0.862	0.939	23.638	0.263	0.263	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.021	0.009	18.128	-0.021	-0.021	0.000	0.000	0.000	0.000
118	A	130	VAL	0	-0.028	-0.017	17.931	0.047	0.047	0.000	0.000	0.000	0.000
119	A	131	GLY	0	0.037	0.016	14.718	-0.055	-0.055	0.000	0.000	0.000	0.000
120	A	132	HIS	0	0.008	-0.006	13.256	0.139	0.139	0.000	0.000	0.000	0.000
121	A	133	VAL	0	0.043	0.036	8.819	-0.116	-0.116	0.000	0.000	0.000	0.000
122	A	134	LYS	1	0.972	0.982	7.374	0.704	0.704	0.000	0.000	0.000	0.000
123	A	135	GLU	-1	-0.899	-0.956	11.087	-0.391	-0.391	0.000	0.000	0.000	0.000
124	A	136	ILE	0	-0.021	0.005	14.257	0.055	0.055	0.000	0.000	0.000	0.000
125	A	137	LYS	1	0.843	0.912	14.967	0.247	0.247	0.000	0.000	0.000	0.000
126	A	138	MET	0	-0.002	0.004	13.209	0.047	0.047	0.000	0.000	0.000	0.000
127	A	139	PHE	0	-0.013	-0.014	16.451	0.042	0.042	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.772	-0.853	18.223	-0.298	-0.298	0.000	0.000	0.000	0.000
129	A	141	GLY	0	-0.002	-0.002	21.202	0.030	0.030	0.000	0.000	0.000	0.000
130	A	142	THR	0	-0.069	-0.026	23.242	-0.020	-0.020	0.000	0.000	0.000	0.000
131	A	143	ILE	0	0.010	0.001	21.473	0.021	0.021	0.000	0.000	0.000	0.000
132	A	144	GLN	0	-0.024	-0.020	25.689	0.006	0.006	0.000	0.000	0.000	0.000
133	A	145	VAL	0	0.031	0.020	25.075	0.007	0.007	0.000	0.000	0.000	0.000
134	A	146	VAL	0	-0.016	-0.012	28.089	0.008	0.008	0.000	0.000	0.000	0.000
135	A	147	SER	0	-0.007	-0.005	29.858	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	148	THR	0	-0.058	-0.051	31.494	0.007	0.007	0.000	0.000	0.000	0.000
137	A	149	ASP	-1	-0.851	-0.921	32.892	-0.118	-0.118	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.808	-0.880	34.449	-0.075	-0.075	0.000	0.000	0.000	0.000
139	A	151	HIS	0	0.048	0.045	28.497	0.001	0.001	0.000	0.000	0.000	0.000
140	A	152	ILE	0	0.040	0.012	31.255	0.008	0.008	0.000	0.000	0.000	0.000
141	A	153	PHE	0	-0.052	-0.023	30.090	0.005	0.005	0.000	0.000	0.000	0.000
142	A	154	LYS	1	0.793	0.889	35.052	0.078	0.078	0.000	0.000	0.000	0.000

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