FMO DATABASE

FMODB ID: 894GY

Calculation Name: 3BVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q38184

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	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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1257928.479839
FMO2-HF: Nuclear repulsion	1203661.266276
FMO2-HF: Total energy	-54267.213563
FMO2-MP2: Total energy	-54426.697186

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-325.988	-327.2	43.848	-19.926	-22.712	-0.227

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.875

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	5	VAL	0	0.017	0.006	3.251	-8.078	-6.156	0.017	-0.758	-1.181	0.001
4	A	6	ALA	0	0.037	0.042	5.299	5.806	5.871	-0.001	-0.004	-0.061	0.000
5	A	7	ILE	0	-0.001	0.003	8.861	-1.641	-1.641	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.042	-0.063	10.833	2.040	2.040	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.017	-0.016	13.587	0.389	0.389	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.769	0.863	16.793	14.668	14.668	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.006	0.027	20.262	-0.064	-0.064	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.045	-0.026	23.756	-0.164	-0.164	0.000	0.000	0.000	0.000
11	A	13	THR	0	-0.060	-0.023	26.733	0.441	0.441	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.066	0.009	27.548	-0.365	-0.365	0.000	0.000	0.000	0.000
13	A	15	ASN	0	-0.051	-0.017	29.402	-0.203	-0.203	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.056	0.000	24.956	-0.478	-0.478	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.008	0.004	27.855	-0.174	-0.174	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.899	-0.942	30.210	-8.980	-8.980	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.812	-0.909	25.465	-12.184	-12.184	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.024	-0.011	26.489	0.001	0.001	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.032	-0.030	18.468	-0.425	-0.425	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.006	-0.008	22.505	-0.479	-0.479	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.008	-0.018	19.796	-0.731	-0.731	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.879	-0.939	19.368	-14.169	-14.169	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.820	-0.879	19.735	-13.577	-13.577	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.062	-0.051	16.512	-1.649	-1.649	0.000	0.000	0.000	0.000
25	A	27	ILE	0	0.042	0.019	15.283	-1.491	-1.491	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.822	-0.875	14.919	-17.221	-17.221	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.904	0.949	15.124	16.051	16.051	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.024	-0.016	10.596	-1.123	-1.123	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.007	-0.009	10.506	-2.788	-2.788	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.831	0.898	10.454	15.054	15.054	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.031	-0.009	7.831	-0.934	-0.934	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.021	0.001	6.379	-1.657	-1.657	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.919	-0.968	6.490	-22.727	-22.727	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.053	-0.024	8.842	0.338	0.338	0.000	0.000	0.000	0.000
35	A	37	MET	0	-0.067	-0.019	5.360	2.535	2.535	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.028	-0.001	5.919	-2.408	-2.408	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.063	-0.040	2.751	-12.953	-8.925	3.244	-1.806	-5.465	-0.018
38	A	40	GLN	0	0.024	0.011	3.719	5.450	6.057	0.004	-0.139	-0.472	0.000
39	A	41	VAL	0	0.029	0.014	5.505	-3.584	-3.584	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.042	-0.024	7.329	0.899	0.899	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.822	-0.889	9.073	-17.611	-17.611	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.033	-0.021	11.269	-1.881	-1.881	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.089	-0.054	11.919	0.887	0.887	0.000	0.000	0.000	0.000
44	A	46	THR	0	0.034	0.006	15.874	-0.414	-0.414	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.756	-0.845	19.100	-14.662	-14.662	0.000	0.000	0.000	0.000
46	A	48	ALA	0	0.009	-0.018	21.817	0.122	0.122	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.011	0.010	24.431	0.524	0.524	0.000	0.000	0.000	0.000
48	A	50	PHE	0	0.034	0.017	24.243	0.356	0.356	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.028	0.009	24.821	-0.508	-0.508	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.044	0.016	22.735	-0.260	-0.260	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.071	-0.038	23.310	-0.317	-0.317	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.860	0.917	25.101	11.951	11.951	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.062	0.027	19.786	-0.444	-0.444	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.821	-0.877	22.411	-12.587	-12.587	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.751	0.857	19.152	16.051	16.051	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.010	0.007	22.450	-0.517	-0.517	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.007	-0.002	18.360	-0.382	-0.382	0.000	0.000	0.000	0.000
58	A	60	MET	0	0.000	0.006	16.386	-1.377	-1.377	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.002	-0.009	18.007	-1.134	-1.134	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.809	0.896	15.602	17.950	17.950	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.011	0.008	11.565	-0.512	-0.512	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.043	-0.028	14.315	-1.201	-1.201	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.028	-0.018	16.403	-0.073	-0.073	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.802	-0.889	13.856	-19.261	-19.261	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.060	-0.013	10.374	-1.480	-1.480	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.957	-0.980	11.964	-19.423	-19.423	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.071	-0.038	14.228	1.070	1.070	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.886	0.944	9.940	23.773	23.773	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.016	0.016	8.975	-1.167	-1.167	0.000	0.000	0.000	0.000
70	A	72	PHE	0	-0.046	-0.030	6.355	0.281	0.281	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.783	-0.872	1.692	-115.636	-120.256	20.337	-8.098	-7.619	-0.103
72	A	74	THR	0	0.008	-0.013	2.116	-16.917	-16.125	5.063	-2.370	-3.486	-0.026
73	A	75	VAL	0	-0.018	0.004	4.561	7.123	7.201	-0.001	-0.034	-0.044	0.000
74	A	76	LEU	0	0.027	0.012	5.498	-0.437	-0.437	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.010	-0.004	8.503	3.042	3.042	0.000	0.000	0.000	0.000
76	A	78	TYR	0	0.043	0.029	12.177	-0.376	-0.376	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.895	0.935	14.545	15.000	15.000	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.057	0.034	15.035	0.124	0.124	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.843	-0.908	16.902	-14.529	-14.529	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.790	0.901	16.736	15.358	15.358	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.053	0.043	13.412	0.429	0.429	0.000	0.000	0.000	0.000
82	A	84	SER	0	0.028	0.006	16.901	0.945	0.945	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.934	0.969	20.184	12.064	12.064	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.014	-0.014	22.783	0.632	0.632	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.079	0.041	21.566	-0.791	-0.791	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.989	0.998	20.954	11.321	11.321	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.837	-0.891	21.077	-14.043	-14.043	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.021	-0.033	16.704	-0.986	-0.986	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.013	-0.004	16.373	-1.323	-1.323	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.004	0.006	16.791	-0.845	-0.845	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.010	-0.001	14.684	-0.675	-0.675	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.039	0.018	10.912	-1.467	-1.467	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.888	0.968	11.836	14.321	14.321	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.892	-0.958	13.837	-18.154	-18.154	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.050	-0.019	13.973	0.778	0.778	0.000	0.000	0.000	0.000
96	A	98	PHE	0	0.011	0.001	9.116	-0.491	-0.491	0.000	0.000	0.000	0.000
97	A	99	THR	0	0.043	0.004	9.214	-1.975	-1.975	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.924	0.973	10.263	17.278	17.278	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.039	-0.020	11.495	1.738	1.738	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.792	0.889	8.392	24.495	24.495	0.000	0.000	0.000	0.000
101	A	103	ILE	0	-0.015	0.021	5.629	-5.103	-5.103	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.811	-0.898	1.685	-106.234	-110.574	15.188	-6.689	-4.160	-0.081
103	A	105	PHE	0	-0.017	-0.033	4.751	4.319	4.358	-0.001	-0.003	-0.034	0.000
104	A	106	ILE	0	0.014	0.008	4.130	0.615	0.742	-0.001	-0.013	-0.113	0.000
105	A	107	SER	0	-0.038	-0.037	8.207	1.655	1.655	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.001	-0.002	11.113	1.131	1.131	0.000	0.000	0.000	0.000
107	A	109	ASN	0	-0.105	-0.066	12.630	1.194	1.194	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.746	-0.854	15.155	-17.552	-17.552	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.071	-0.028	12.734	0.580	0.580	0.000	0.000	0.000	0.000
110	A	112	ILE	0	-0.016	0.004	11.313	-0.616	-0.616	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.762	-0.871	5.793	-49.023	-49.023	0.000	0.000	0.000	0.000
112	A	114	THR	0	0.005	0.003	6.288	2.110	2.110	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.027	-0.016	4.210	2.978	3.068	-0.001	-0.012	-0.077	0.000
114	A	116	SER	0	-0.041	-0.021	6.340	5.182	5.182	0.000	0.000	0.000	0.000
115	A	117	ALA	0	0.048	0.011	9.329	1.171	1.171	0.000	0.000	0.000	0.000
116	A	118	MET	0	-0.006	-0.007	12.844	1.786	1.786	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.031	0.029	11.536	1.374	1.374	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.018	-0.004	10.883	1.666	1.666	0.000	0.000	0.000	0.000
119	A	121	LEU	0	-0.017	0.005	12.506	1.537	1.537	0.000	0.000	0.000	0.000
120	A	122	PHE	0	0.019	0.000	14.845	1.178	1.178	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.002	0.003	12.385	1.078	1.078	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.034	-0.024	15.792	1.026	1.026	0.000	0.000	0.000	0.000
123	A	125	ILE	0	-0.007	-0.008	18.045	0.993	0.993	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.003	0.006	18.027	0.763	0.763	0.000	0.000	0.000	0.000
125	A	127	SER	0	0.002	-0.010	19.132	0.496	0.496	0.000	0.000	0.000	0.000
126	A	128	ALA	0	-0.019	-0.004	21.054	0.595	0.595	0.000	0.000	0.000	0.000
127	A	129	ILE	0	0.002	0.000	23.772	0.607	0.607	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.022	0.002	23.799	0.296	0.296	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.881	-0.922	25.439	-12.078	-12.078	0.000	0.000	0.000	0.000
130	A	132	PHE	0	0.023	0.011	27.165	0.475	0.475	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.896	-0.943	27.067	-11.493	-11.493	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.770	0.855	25.146	12.251	12.251	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.966	-0.968	31.260	-9.412	-9.412	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.049	-0.016	33.259	0.371	0.371	0.000	0.000	0.000	0.000
135	A	137	GLU	-1	-0.934	-0.940	33.175	-9.407	-9.407	0.000	0.000	0.000	0.000
136	A	138	TYR	0	-0.200	-0.124	31.719	0.321	0.321	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)