FMO DATABASE

FMODB ID: G5QL1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1267494.782338
FMO2-HF: Nuclear repulsion	1212441.705982
FMO2-HF: Total energy	-55053.076356
FMO2-MP2: Total energy	-55214.220751

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.
-4.004	2.365	3.289	-2.913	-6.745	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 : 0.003 / q_NPA : 0.000

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	-0.929	-0.941	3.446	-3.416	0.490	0.025	-1.852	-2.079	0.003
4	A	16	TYR	0	-0.087	-0.077	2.750	0.521	1.348	0.116	-0.139	-0.804	0.000
5	A	17	ALA	0	-0.003	0.000	7.621	0.502	0.502	0.000	0.000	0.000	0.000
6	A	18	SER	0	-0.052	-0.045	8.309	-0.214	-0.214	0.000	0.000	0.000	0.000
7	A	19	ALA	0	0.023	-0.011	9.813	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	20	GLU	-1	-0.864	-0.900	10.632	-0.356	-0.356	0.000	0.000	0.000	0.000
9	A	21	ASP	-1	-0.788	-0.858	11.988	-0.890	-0.890	0.000	0.000	0.000	0.000
10	A	22	ILE	0	0.053	0.019	7.032	0.073	0.073	0.000	0.000	0.000	0.000
11	A	23	SER	0	-0.089	-0.065	11.332	0.139	0.139	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.804	0.904	13.863	0.508	0.508	0.000	0.000	0.000	0.000
13	A	25	VAL	0	0.051	0.021	13.503	0.064	0.064	0.000	0.000	0.000	0.000
14	A	26	ARG	1	0.916	0.952	9.180	0.700	0.700	0.000	0.000	0.000	0.000
15	A	27	ALA	0	-0.053	-0.010	15.834	0.058	0.058	0.000	0.000	0.000	0.000
16	A	28	GLU	-1	-0.935	-0.967	18.789	-0.358	-0.358	0.000	0.000	0.000	0.000
17	A	29	LEU	0	-0.051	-0.011	16.901	0.016	0.016	0.000	0.000	0.000	0.000
18	A	30	LEU	0	-0.029	-0.008	19.729	0.032	0.032	0.000	0.000	0.000	0.000
19	A	31	THR	0	-0.002	0.003	20.255	0.021	0.021	0.000	0.000	0.000	0.000
20	A	32	CYS	0	-0.081	-0.053	19.379	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	33	PRO	0	0.047	0.024	18.540	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	34	GLU	-1	-0.923	-0.962	17.893	-0.092	-0.092	0.000	0.000	0.000	0.000
23	A	35	LEU	0	-0.082	-0.027	15.250	0.041	0.041	0.000	0.000	0.000	0.000
24	A	36	ASN	0	0.056	0.026	12.726	-0.052	-0.052	0.000	0.000	0.000	0.000
25	A	37	THR	0	0.061	0.021	9.111	0.082	0.082	0.000	0.000	0.000	0.000
26	A	38	SER	0	-0.050	-0.027	8.543	-0.131	-0.131	0.000	0.000	0.000	0.000
27	A	39	LEU	0	-0.055	-0.024	9.631	0.070	0.070	0.000	0.000	0.000	0.000
28	A	40	ALA	0	-0.023	-0.016	12.026	0.002	0.002	0.000	0.000	0.000	0.000
29	A	41	GLY	0	0.032	0.017	8.829	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	42	THR	0	-0.030	-0.018	6.487	0.439	0.439	0.000	0.000	0.000	0.000
31	A	43	ILE	0	-0.012	-0.016	9.466	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	44	ILE	0	-0.039	-0.022	7.667	-0.111	-0.111	0.000	0.000	0.000	0.000
33	A	45	GLU	-1	-0.821	-0.909	12.036	-0.658	-0.658	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.025	-0.025	15.767	0.016	0.016	0.000	0.000	0.000	0.000
35	A	47	ASP	-1	-0.827	-0.893	19.086	-0.318	-0.318	0.000	0.000	0.000	0.000
36	A	48	LYS	1	0.784	0.870	22.799	0.220	0.220	0.000	0.000	0.000	0.000
37	A	49	ASN	0	-0.055	-0.021	25.338	0.025	0.025	0.000	0.000	0.000	0.000
38	A	50	TYR	0	-0.047	-0.031	17.850	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	51	ALA	0	0.017	0.013	17.738	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	52	LYS	1	0.855	0.932	12.961	0.800	0.800	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.029	0.004	11.514	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	54	ILE	0	0.012	0.022	4.478	-0.025	0.085	-0.001	-0.013	-0.096	0.000
43	A	55	LEU	0	-0.001	-0.005	7.944	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	56	ILE	0	0.013	0.013	2.313	-1.329	-0.385	3.144	-0.835	-3.253	0.000
45	A	57	THR	0	-0.025	-0.031	4.496	0.295	0.398	-0.001	-0.008	-0.094	0.000
46	A	58	THR	0	0.077	0.011	5.435	0.386	0.386	0.000	0.000	0.000	0.000
47	A	59	SER	0	0.027	-0.009	7.851	-0.105	-0.105	0.000	0.000	0.000	0.000
48	A	60	GLU	-1	-0.991	-0.990	10.978	0.428	0.428	0.000	0.000	0.000	0.000
49	A	61	MET	0	-0.044	0.010	9.598	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	62	VAL	0	-0.016	-0.006	12.070	-0.049	-0.049	0.000	0.000	0.000	0.000
51	A	63	ALA	0	-0.059	-0.032	14.218	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	64	ASP	-1	-0.880	-0.944	17.136	0.144	0.144	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.893	-0.946	16.997	0.224	0.224	0.000	0.000	0.000	0.000
54	A	66	GLN	0	-0.099	-0.052	17.511	0.022	0.022	0.000	0.000	0.000	0.000
55	A	67	GLY	0	0.005	0.013	13.682	0.018	0.018	0.000	0.000	0.000	0.000
56	A	68	LEU	0	-0.021	-0.003	13.015	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	69	ILE	0	-0.022	-0.018	10.110	0.030	0.030	0.000	0.000	0.000	0.000
58	A	70	PHE	0	0.001	0.004	13.650	-0.047	-0.047	0.000	0.000	0.000	0.000
59	A	71	ASP	-1	-0.827	-0.935	15.579	-0.088	-0.088	0.000	0.000	0.000	0.000
60	A	72	ALA	0	-0.035	-0.016	17.386	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	73	PHE	0	0.024	0.012	12.828	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	74	ILE	0	-0.002	0.015	13.331	-0.066	-0.066	0.000	0.000	0.000	0.000
63	A	75	PHE	0	-0.020	-0.022	14.739	-0.049	-0.049	0.000	0.000	0.000	0.000
64	A	76	ALA	0	-0.008	0.001	15.482	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	77	ALA	0	0.065	0.032	12.690	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	78	ALA	0	-0.017	-0.002	14.759	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.018	-0.016	17.517	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	80	TYR	0	0.009	0.011	13.169	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	81	VAL	0	0.029	0.013	15.342	0.007	0.007	0.000	0.000	0.000	0.000
70	A	82	ALA	0	0.003	-0.004	17.274	0.017	0.017	0.000	0.000	0.000	0.000
71	A	83	GLN	0	0.013	0.015	20.927	0.025	0.025	0.000	0.000	0.000	0.000
72	A	84	ALA	0	0.043	0.024	18.036	0.019	0.019	0.000	0.000	0.000	0.000
73	A	85	SER	0	-0.063	-0.035	20.040	0.011	0.011	0.000	0.000	0.000	0.000
74	A	86	ILE	0	-0.089	-0.055	22.221	0.027	0.027	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.002	-0.012	22.170	0.024	0.024	0.000	0.000	0.000	0.000
76	A	88	LYS	1	0.918	0.955	23.832	0.197	0.197	0.000	0.000	0.000	0.000
77	A	89	GLU	-1	-0.872	-0.933	25.339	-0.140	-0.140	0.000	0.000	0.000	0.000
78	A	90	PHE	0	-0.046	-0.010	26.345	0.007	0.007	0.000	0.000	0.000	0.000
79	A	91	SER	0	-0.015	-0.030	24.813	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	92	VAL	0	0.001	0.012	26.300	0.007	0.007	0.000	0.000	0.000	0.000
81	A	93	ILE	0	0.010	0.001	23.696	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.025	-0.014	27.264	0.013	0.013	0.000	0.000	0.000	0.000
83	A	95	GLY	0	0.015	0.005	29.060	0.012	0.012	0.000	0.000	0.000	0.000
84	A	96	SER	0	-0.047	-0.015	25.330	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	97	LYS	1	0.918	0.966	26.864	0.128	0.128	0.000	0.000	0.000	0.000
86	A	98	CYS	0	-0.008	0.001	22.200	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	99	PHE	0	-0.038	-0.018	22.703	0.028	0.028	0.000	0.000	0.000	0.000
88	A	100	PHE	0	0.064	0.021	18.313	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	101	TYR	0	-0.098	-0.060	19.572	0.032	0.032	0.000	0.000	0.000	0.000
90	A	102	ALA	0	0.011	0.001	17.086	0.018	0.018	0.000	0.000	0.000	0.000
91	A	103	PRO	0	0.019	0.034	16.612	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	104	LEU	0	0.001	-0.008	9.684	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	105	LYS	1	0.837	0.902	10.216	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	106	LEU	0	-0.008	-0.008	7.563	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	107	GLY	0	-0.025	-0.011	5.965	0.037	0.037	0.000	0.000	0.000	0.000
96	A	108	ASP	-1	-0.840	-0.890	5.058	-0.231	-0.165	-0.001	-0.001	-0.064	0.000
97	A	109	VAL	0	0.013	0.007	3.530	-0.238	0.175	0.007	-0.065	-0.355	0.000
98	A	110	LEU	0	-0.021	-0.002	5.614	0.070	0.070	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.844	-0.935	8.482	-1.435	-1.435	0.000	0.000	0.000	0.000
100	A	112	LEU	0	-0.046	-0.029	10.512	0.202	0.202	0.000	0.000	0.000	0.000
101	A	113	GLU	-1	-0.783	-0.879	13.638	-0.631	-0.631	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.039	-0.019	16.825	0.059	0.059	0.000	0.000	0.000	0.000
103	A	115	HIS	0	0.008	-0.006	20.000	0.020	0.020	0.000	0.000	0.000	0.000
104	A	116	ALA	0	-0.015	-0.006	23.433	0.026	0.026	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.016	-0.014	26.342	0.006	0.006	0.000	0.000	0.000	0.000
106	A	118	PHE	0	-0.016	-0.003	29.744	0.003	0.003	0.000	0.000	0.000	0.000
107	A	119	ASP	-1	-0.743	-0.867	31.949	-0.123	-0.123	0.000	0.000	0.000	0.000
108	A	120	GLU	-1	-0.905	-0.936	32.945	-0.181	-0.181	0.000	0.000	0.000	0.000
109	A	121	THR	0	-0.120	-0.065	35.164	0.008	0.008	0.000	0.000	0.000	0.000
110	A	122	SER	0	-0.047	-0.030	35.068	0.009	0.009	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.860	0.909	33.742	0.101	0.101	0.000	0.000	0.000	0.000
112	A	124	LYS	1	0.838	0.935	32.186	0.115	0.115	0.000	0.000	0.000	0.000
113	A	125	ARG	1	0.856	0.916	29.105	0.197	0.197	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.819	-0.899	28.802	-0.155	-0.155	0.000	0.000	0.000	0.000
115	A	127	VAL	0	0.008	0.010	22.844	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	128	LYS	1	0.830	0.927	23.427	0.243	0.243	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.018	0.008	18.284	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	130	VAL	0	-0.027	-0.023	17.761	0.047	0.047	0.000	0.000	0.000	0.000
119	A	131	GLY	0	0.036	0.015	14.650	-0.058	-0.058	0.000	0.000	0.000	0.000
120	A	132	HIS	0	-0.027	-0.014	13.083	0.141	0.141	0.000	0.000	0.000	0.000
121	A	133	VAL	0	0.035	0.020	8.210	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	134	LYS	1	0.935	0.977	6.031	0.937	0.937	0.000	0.000	0.000	0.000
123	A	135	GLU	-1	-0.912	-0.963	11.053	-0.345	-0.345	0.000	0.000	0.000	0.000
124	A	136	ILE	0	-0.015	0.008	13.927	0.041	0.041	0.000	0.000	0.000	0.000
125	A	137	LYS	1	0.852	0.910	14.432	0.231	0.231	0.000	0.000	0.000	0.000
126	A	138	MET	0	0.000	0.016	12.883	0.042	0.042	0.000	0.000	0.000	0.000
127	A	139	PHE	0	-0.006	-0.015	16.112	0.044	0.044	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.779	-0.869	17.902	-0.279	-0.279	0.000	0.000	0.000	0.000
129	A	141	GLY	0	-0.002	-0.006	20.858	0.031	0.031	0.000	0.000	0.000	0.000
130	A	142	THR	0	-0.039	-0.009	23.461	-0.021	-0.021	0.000	0.000	0.000	0.000
131	A	143	ILE	0	0.013	0.005	21.421	0.023	0.023	0.000	0.000	0.000	0.000
132	A	144	GLN	0	-0.035	-0.028	25.686	0.002	0.002	0.000	0.000	0.000	0.000
133	A	145	VAL	0	0.059	0.039	24.898	0.011	0.011	0.000	0.000	0.000	0.000
134	A	146	VAL	0	-0.044	-0.026	27.713	0.010	0.010	0.000	0.000	0.000	0.000
135	A	147	SER	0	-0.016	-0.004	29.127	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	148	THR	0	-0.060	-0.052	30.773	0.007	0.007	0.000	0.000	0.000	0.000
137	A	149	ASP	-1	-0.826	-0.905	32.340	-0.111	-0.111	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.789	-0.855	33.865	-0.068	-0.068	0.000	0.000	0.000	0.000
139	A	151	HIS	0	0.071	0.045	27.973	0.000	0.000	0.000	0.000	0.000	0.000
140	A	152	ILE	0	0.017	0.009	30.608	0.007	0.007	0.000	0.000	0.000	0.000
141	A	153	PHE	0	-0.046	-0.024	29.732	0.005	0.005	0.000	0.000	0.000	0.000
142	A	154	LYS	1	0.770	0.865	34.562	0.069	0.069	0.000	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)