FMO DATABASE

FMODB ID: JQ9Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1271090.225164
FMO2-HF: Nuclear repulsion	1214097.871815
FMO2-HF: Total energy	-56992.353349
FMO2-MP2: Total energy	-57160.059637

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.
-5.195	-1.631	5.141	-2.265	-6.442	-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 : 0.005 / q_NPA : -0.007

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	0.127	0.062	2.325	-3.089	-1.703	2.512	-1.595	-2.304	-0.011
4	A	8	LYS	1	1.001	1.000	4.771	-0.350	-0.173	-0.001	-0.016	-0.160	0.000
5	A	9	GLY	0	-0.022	-0.021	2.479	-0.257	0.039	1.320	-0.751	-0.865	0.003
6	A	10	LEU	0	0.058	0.022	2.538	-0.920	0.127	1.169	0.223	-2.439	-0.002
7	A	11	LEU	0	0.044	0.019	3.984	0.226	0.349	0.007	-0.010	-0.121	0.000
8	A	12	SER	0	-0.035	-0.028	6.208	0.180	0.180	0.000	0.000	0.000	0.000
9	A	13	ILE	0	-0.044	-0.016	2.834	-0.438	0.097	0.134	-0.116	-0.553	0.000
10	A	14	ILE	0	0.060	0.040	6.966	0.043	0.043	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.058	0.028	9.603	0.062	0.062	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.880	0.954	5.977	-0.250	-0.250	0.000	0.000	0.000	0.000
13	A	17	SER	0	-0.011	-0.006	11.635	0.019	0.019	0.000	0.000	0.000	0.000
14	A	18	HIS	1	0.827	0.893	13.512	0.137	0.137	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.958	0.963	12.686	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	20	VAL	0	-0.038	-0.022	15.207	0.013	0.013	0.000	0.000	0.000	0.000
17	A	21	PHE	0	0.015	0.005	17.521	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	ILE	0	0.036	0.021	19.388	0.009	0.009	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.027	-0.011	20.623	0.007	0.007	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.858	0.927	21.029	0.050	0.050	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.825	-0.901	23.405	-0.088	-0.088	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.012	-0.010	24.667	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.055	0.037	26.436	0.007	0.007	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.019	-0.001	27.385	0.007	0.007	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.028	-0.016	29.787	0.003	0.003	0.000	0.000	0.000	0.000
26	A	30	ASN	0	-0.018	-0.005	28.889	0.003	0.003	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.001	0.019	26.062	0.005	0.005	0.000	0.000	0.000	0.000
28	A	32	THR	0	0.000	-0.017	21.868	0.000	0.000	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.859	-0.922	17.346	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	34	ALA	0	0.033	0.006	20.449	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	35	GLN	0	-0.043	-0.038	21.564	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.061	0.038	22.824	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	37	ALA	0	0.014	0.013	20.997	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	38	CYS	0	-0.035	-0.022	23.111	0.001	0.001	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.029	0.023	26.081	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.015	-0.002	24.028	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.713	0.837	25.031	0.026	0.026	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.007	-0.002	27.400	0.001	0.001	0.000	0.000	0.000	0.000
39	A	43	HIS	0	0.029	0.014	30.310	0.003	0.003	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.879	0.949	27.166	0.051	0.051	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.894	-0.917	30.673	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	46	PRO	0	0.042	0.031	32.924	0.004	0.004	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.075	0.023	35.887	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	ILE	0	-0.054	-0.009	29.761	0.004	0.004	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.962	0.976	34.068	0.001	0.001	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.013	-0.006	31.124	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.883	-0.938	30.299	0.023	0.023	0.000	0.000	0.000	0.000
48	A	52	GLU	-1	-0.776	-0.890	29.802	0.005	0.005	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.011	0.011	26.749	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.051	-0.059	25.924	0.001	0.001	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.032	-0.021	24.879	0.008	0.008	0.000	0.000	0.000	0.000
52	A	56	PHE	0	-0.016	-0.001	22.824	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	57	PHE	0	-0.032	-0.030	20.595	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	58	HIS	0	-0.014	0.016	19.868	0.018	0.018	0.000	0.000	0.000	0.000
55	A	59	VAL	0	-0.023	0.003	18.858	0.019	0.019	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.825	-0.861	21.237	0.100	0.100	0.000	0.000	0.000	0.000
57	A	61	LYS	1	1.021	0.967	23.480	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.008	0.007	26.459	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.006	-0.056	21.174	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.005	0.030	24.447	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	65	ALA	0	-0.013	-0.006	26.053	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.920	0.956	26.667	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	67	THR	0	-0.048	-0.026	24.661	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.046	0.012	27.011	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.968	0.996	30.104	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.917	0.963	24.996	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.012	0.010	27.982	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.949	-0.973	31.464	0.008	0.008	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.949	-0.970	34.192	0.009	0.009	0.000	0.000	0.000	0.000
70	A	74	SER	0	-0.092	-0.041	32.574	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	GLY	0	0.012	0.021	34.958	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.035	-0.033	31.484	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.022	-0.021	31.671	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.907	-0.942	35.185	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	79	ARG	1	0.874	0.924	35.703	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.872	-0.922	38.155	0.001	0.001	0.000	0.000	0.000	0.000
77	A	81	GLN	0	-0.075	-0.050	40.176	0.003	0.003	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.827	-0.924	40.031	0.007	0.007	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.018	-0.007	42.040	0.002	0.002	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.927	-0.957	43.410	0.005	0.005	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.032	-0.029	40.753	0.004	0.004	0.000	0.000	0.000	0.000
82	A	86	ARG	1	1.039	1.025	41.986	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.812	0.899	38.901	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.786	0.897	34.785	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	89	TYR	0	0.023	0.007	36.109	0.000	0.000	0.000	0.000	0.000	0.000
86	A	90	ILE	0	0.017	0.022	36.123	0.001	0.001	0.000	0.000	0.000	0.000
87	A	91	LEU	0	-0.038	-0.015	31.622	0.002	0.002	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.866	-0.934	35.529	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	93	VAL	0	-0.051	-0.009	32.734	0.002	0.002	0.000	0.000	0.000	0.000
90	A	94	THR	0	0.068	0.029	35.517	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.959	0.968	37.455	0.022	0.022	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.974	1.006	35.061	0.021	0.021	0.000	0.000	0.000	0.000
93	A	97	GLY	0	-0.004	-0.015	34.052	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	98	GLU	-1	-0.902	-0.962	33.482	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.928	-0.976	35.044	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	100	ILE	0	-0.057	-0.019	30.622	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	101	ILE	0	0.015	0.015	29.672	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	102	PRO	0	0.016	0.001	29.776	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.006	0.002	30.273	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	104	ILE	0	0.002	0.002	25.132	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.004	-0.004	25.511	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.985	1.015	26.101	0.082	0.082	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.059	-0.036	22.734	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.817	-0.893	20.329	-0.139	-0.139	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.932	-0.955	21.493	-0.143	-0.143	0.000	0.000	0.000	0.000
106	A	110	ARG	1	0.875	0.916	23.013	0.096	0.096	0.000	0.000	0.000	0.000
107	A	111	TRP	0	-0.045	-0.023	13.586	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.947	-0.985	18.356	-0.233	-0.233	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.878	-0.935	19.231	-0.205	-0.205	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.093	-0.051	18.878	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	115	LEU	0	-0.063	-0.027	12.517	-0.029	-0.029	0.000	0.000	0.000	0.000
112	A	116	PHE	0	-0.048	-0.031	15.539	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.909	0.956	17.686	0.249	0.249	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.931	-0.949	16.261	-0.329	-0.329	0.000	0.000	0.000	0.000
115	A	119	PHE	0	-0.063	-0.028	13.451	-0.040	-0.040	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.010	0.009	18.802	0.042	0.042	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.818	-0.937	21.489	-0.231	-0.231	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.924	-0.967	23.479	-0.219	-0.219	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.888	-0.937	18.192	-0.424	-0.424	0.000	0.000	0.000	0.000
120	A	124	ARG	1	0.935	0.985	18.960	0.191	0.191	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.949	0.974	19.854	0.183	0.183	0.000	0.000	0.000	0.000
122	A	126	LEU	0	-0.008	-0.015	18.702	0.012	0.012	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.040	0.019	11.626	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.985	0.993	16.782	0.211	0.211	0.000	0.000	0.000	0.000
125	A	129	LYS	1	0.886	0.937	18.997	0.219	0.219	0.000	0.000	0.000	0.000
126	A	130	MET	0	-0.022	-0.006	15.127	0.019	0.019	0.000	0.000	0.000	0.000
127	A	131	CYS	0	0.018	0.009	14.971	0.001	0.001	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.950	0.982	16.283	0.189	0.189	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.975	0.988	18.961	0.268	0.268	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.010	-0.004	12.702	0.013	0.013	0.000	0.000	0.000	0.000
131	A	135	ALA	0	-0.008	0.001	16.607	0.026	0.026	0.000	0.000	0.000	0.000
132	A	136	GLU	-1	-0.921	-0.976	18.037	-0.125	-0.125	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.908	-0.965	17.799	-0.099	-0.099	0.000	0.000	0.000	0.000
134	A	138	ALA	0	-0.026	-0.020	16.224	0.022	0.022	0.000	0.000	0.000	0.000
135	A	139	VAL	0	-0.050	-0.016	18.025	0.023	0.023	0.000	0.000	0.000	0.000
136	A	140	ARG	1	0.838	0.936	21.529	0.125	0.125	0.000	0.000	0.000	0.000
137	A	141	MET	0	-0.048	-0.004	15.572	0.012	0.012	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

Support

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