FMO DATABASE

FMODB ID: 3JV5L

Calculation Name: 3BPV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BPV

Chain ID: A

ChEMBL ID:

UniProt ID: O26413

Base Structure: X-ray

Registration Date: 2023-09-23

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1270877.661013
FMO2-HF: Nuclear repulsion	1213884.283477
FMO2-HF: Total energy	-56993.377536
FMO2-MP2: Total energy	-57161.014846

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-5.42	-1.165	4.306	-2.169	-6.393	-0.01

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.010

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	7	LEU	0	0.118	0.057	2.484	-3.547	-1.249	1.303	-1.521	-2.081	-0.011
4	A	8	LYS	1	0.981	0.984	4.970	-0.282	-0.120	-0.001	-0.013	-0.148	0.000
5	A	9	GLY	0	-0.009	0.001	2.396	-0.162	0.032	1.377	-0.749	-0.822	0.003
6	A	10	LEU	0	0.052	0.019	2.514	-0.785	0.104	1.490	0.259	-2.638	-0.002
7	A	11	LEU	0	0.051	0.023	4.051	0.126	0.249	0.004	-0.015	-0.112	0.000
8	A	12	SER	0	-0.035	-0.036	6.234	0.146	0.146	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.046	-0.017	2.907	-0.517	0.072	0.133	-0.130	-0.592	0.000
10	A	14	ILE	0	0.067	0.041	6.951	0.028	0.028	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.047	0.021	9.613	0.050	0.050	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.907	0.961	6.067	-0.198	-0.198	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.021	-0.008	11.621	0.013	0.013	0.000	0.000	0.000	0.000
14	A	18	HIS	1	0.834	0.906	13.512	0.119	0.119	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.876	0.918	13.457	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.025	-0.015	15.294	0.011	0.011	0.000	0.000	0.000	0.000
17	A	21	PHE	0	0.018	0.006	17.508	0.004	0.004	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.034	0.016	19.377	0.008	0.008	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.020	-0.005	20.606	0.007	0.007	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.873	0.932	21.287	0.056	0.056	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.788	-0.859	23.512	-0.084	-0.084	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.006	-0.005	24.944	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.058	0.039	26.420	0.007	0.007	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.015	0.000	27.362	0.007	0.007	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.016	-0.010	29.814	0.003	0.003	0.000	0.000	0.000	0.000
26	A	30	ASN	0	-0.023	-0.008	28.850	0.004	0.004	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.041	0.037	26.007	0.006	0.006	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.003	-0.012	21.858	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.797	-0.895	17.336	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	34	ALA	0	0.031	0.012	20.464	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	35	GLN	0	-0.038	-0.040	21.590	0.001	0.001	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.061	0.035	22.904	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	37	ALA	0	0.006	0.010	21.000	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.040	-0.027	23.121	0.002	0.002	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.025	0.021	26.033	0.000	0.000	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.018	0.000	24.072	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.715	0.850	25.333	0.015	0.015	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.008	-0.002	27.424	0.001	0.001	0.000	0.000	0.000	0.000
39	A	43	HIS	0	0.032	0.016	30.440	0.002	0.002	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.815	0.900	27.331	0.033	0.033	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.824	-0.882	30.969	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	46	PRO	0	0.041	0.029	32.969	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.072	0.031	35.908	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.080	-0.019	29.715	0.003	0.003	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.899	0.955	34.043	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.025	0.008	31.109	0.000	0.000	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.887	-0.940	30.186	0.025	0.025	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.743	-0.851	29.696	0.012	0.012	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.002	0.007	26.831	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.054	-0.051	25.846	0.001	0.001	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.033	-0.031	24.762	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	PHE	0	-0.009	0.002	22.968	0.000	0.000	0.000	0.000	0.000	0.000
53	A	57	PHE	0	-0.031	-0.032	20.819	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	58	HIS	0	-0.010	0.017	19.823	0.017	0.017	0.000	0.000	0.000	0.000
55	A	59	VAL	0	-0.029	0.000	18.828	0.017	0.017	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.811	-0.872	21.249	0.089	0.089	0.000	0.000	0.000	0.000
57	A	61	LYS	1	1.014	0.970	23.621	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.014	0.018	26.511	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.030	-0.055	21.175	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.010	0.026	24.513	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	65	ALA	0	-0.013	-0.004	26.121	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.933	0.963	26.565	-0.053	-0.053	0.000	0.000	0.000	0.000
63	A	67	THR	0	-0.057	-0.035	24.584	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.040	0.010	27.058	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.976	0.997	30.105	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.899	0.960	25.844	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.001	0.012	28.048	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.924	-0.964	31.485	0.008	0.008	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.966	-0.977	34.203	0.008	0.008	0.000	0.000	0.000	0.000
70	A	74	SER	0	-0.089	-0.047	32.507	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	GLY	0	0.012	0.021	34.965	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.050	-0.033	31.130	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.023	-0.023	31.514	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.884	-0.937	35.220	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.858	0.919	34.867	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.876	-0.923	38.051	0.002	0.002	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.074	-0.043	40.071	0.003	0.003	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.784	-0.922	39.886	0.010	0.010	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.008	-0.003	41.943	0.002	0.002	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.897	-0.934	42.305	0.008	0.008	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.018	-0.030	40.387	0.003	0.003	0.000	0.000	0.000	0.000
82	A	86	ARG	1	1.018	1.020	41.858	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.835	0.911	38.990	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.753	0.862	34.606	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	89	TYR	0	0.005	-0.008	36.063	0.000	0.000	0.000	0.000	0.000	0.000
86	A	90	ILE	0	0.018	0.021	36.027	0.001	0.001	0.000	0.000	0.000	0.000
87	A	91	LEU	0	-0.040	-0.019	31.554	0.001	0.001	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.868	-0.937	35.467	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.049	-0.012	32.698	0.001	0.001	0.000	0.000	0.000	0.000
90	A	94	THR	0	0.046	0.025	35.526	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.930	0.941	37.492	0.018	0.018	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.962	0.994	35.168	0.021	0.021	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.003	-0.011	34.077	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.858	-0.929	33.513	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.930	-0.971	35.079	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	100	ILE	0	-0.059	-0.024	30.994	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	101	ILE	0	0.006	0.010	29.626	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.016	0.006	29.806	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	103	LEU	0	0.003	0.005	30.295	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	104	ILE	0	0.002	0.001	25.175	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.001	-0.005	25.533	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.896	0.947	26.127	0.084	0.084	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.033	-0.018	22.807	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.832	-0.897	20.410	-0.120	-0.120	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.859	-0.912	21.513	-0.120	-0.120	0.000	0.000	0.000	0.000
106	A	110	ARG	1	0.817	0.867	23.026	0.086	0.086	0.000	0.000	0.000	0.000
107	A	111	TRP	0	-0.032	-0.016	13.539	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.797	-0.885	18.377	-0.216	-0.216	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.829	-0.912	19.243	-0.187	-0.187	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.070	-0.032	18.942	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.054	-0.021	12.433	-0.027	-0.027	0.000	0.000	0.000	0.000
112	A	116	PHE	0	-0.047	-0.030	15.482	-0.045	-0.045	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.896	0.950	17.403	0.243	0.243	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.941	-0.957	16.209	-0.313	-0.313	0.000	0.000	0.000	0.000
115	A	119	PHE	0	-0.075	-0.031	13.172	-0.036	-0.036	0.000	0.000	0.000	0.000
116	A	120	THR	0	-0.012	-0.032	18.787	0.038	0.038	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.844	-0.948	21.488	-0.202	-0.202	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.872	-0.941	23.485	-0.182	-0.182	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.833	-0.878	18.207	-0.352	-0.352	0.000	0.000	0.000	0.000
120	A	124	ARG	1	0.827	0.918	19.031	0.173	0.173	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.881	0.931	20.125	0.171	0.171	0.000	0.000	0.000	0.000
122	A	126	LEU	0	-0.026	-0.019	18.805	0.011	0.011	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.033	0.013	12.108	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.887	0.925	17.146	0.184	0.184	0.000	0.000	0.000	0.000
125	A	129	LYS	1	0.923	0.954	19.341	0.179	0.179	0.000	0.000	0.000	0.000
126	A	130	MET	0	-0.035	-0.013	15.385	0.022	0.022	0.000	0.000	0.000	0.000
127	A	131	CYS	0	0.019	0.008	15.633	0.004	0.004	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.930	0.978	16.598	0.148	0.148	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.982	0.990	19.354	0.209	0.209	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.002	-0.001	12.934	0.012	0.012	0.000	0.000	0.000	0.000
131	A	135	ALA	0	-0.014	-0.003	16.882	0.023	0.023	0.000	0.000	0.000	0.000
132	A	136	GLU	-1	-0.918	-0.973	18.254	-0.094	-0.094	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.832	-0.893	18.018	-0.057	-0.057	0.000	0.000	0.000	0.000
134	A	138	ALA	0	-0.023	-0.015	16.332	0.020	0.020	0.000	0.000	0.000	0.000
135	A	139	VAL	0	-0.037	-0.017	18.171	0.021	0.021	0.000	0.000	0.000	0.000
136	A	140	ARG	1	0.790	0.881	21.657	0.087	0.087	0.000	0.000	0.000	0.000
137	A	141	MET	0	-0.083	-0.023	15.857	0.018	0.018	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)