FMO DATABASE

FMODB ID: 7GLNK

Calculation Name: 3VBC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VBC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JIP3

Base Structure: X-ray

Registration Date: 2023-06-20

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1272391.571241
FMO2-HF: Nuclear repulsion	1217924.318599
FMO2-HF: Total energy	-54467.252642
FMO2-MP2: Total energy	-54624.477863

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:325:LEU)

Summations of interaction energy for fragment #1(A:325: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.
-2.706	-0.102	0.031	-1.347	-1.288	0.004

Interaction energy analysis for fragmet #1(A:325:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.013

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	327	PRO	0	0.005	0.013	3.382	-2.343	0.261	0.031	-1.347	-1.288	0.004
4	A	328	LEU	0	-0.061	-0.036	4.970	0.628	0.628	0.000	0.000	0.000	0.000
5	A	329	ILE	0	0.027	0.031	5.840	-0.026	-0.026	0.000	0.000	0.000	0.000
6	A	330	LYS	1	0.819	0.888	5.755	0.185	0.185	0.000	0.000	0.000	0.000
7	A	331	VAL	0	0.001	-0.005	9.701	0.022	0.022	0.000	0.000	0.000	0.000
8	A	332	LEU	0	-0.008	0.006	13.342	0.032	0.032	0.000	0.000	0.000	0.000
9	A	333	VAL	0	-0.022	-0.012	15.731	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	334	VAL	0	0.001	0.008	19.170	0.021	0.021	0.000	0.000	0.000	0.000
11	A	335	TYR	0	0.008	-0.007	22.049	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	336	PRO	0	0.021	0.021	25.339	0.010	0.010	0.000	0.000	0.000	0.000
13	A	337	SER	0	-0.021	-0.019	29.019	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	338	GLU	-1	-0.802	-0.910	30.478	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	339	ILE	0	0.045	0.006	32.858	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	340	CYS	0	-0.037	-0.020	34.162	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	341	PHE	0	0.035	0.021	27.565	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	342	HIS	0	0.032	0.022	27.911	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	343	HIS	0	0.031	0.014	28.793	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	344	THR	0	-0.001	0.001	28.088	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	345	VAL	0	0.004	0.012	24.204	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	346	CYS	0	-0.022	-0.002	24.328	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	347	ARG	1	0.888	0.939	24.248	0.136	0.136	0.000	0.000	0.000	0.000
24	A	348	PHE	0	0.029	0.008	20.190	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	349	THR	0	-0.030	-0.022	19.993	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	350	ASP	-1	-0.792	-0.879	19.436	-0.194	-0.194	0.000	0.000	0.000	0.000
27	A	351	PHE	0	-0.026	-0.010	20.301	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	352	LEU	0	0.038	0.011	16.108	-0.033	-0.033	0.000	0.000	0.000	0.000
29	A	353	GLN	0	0.024	0.027	15.523	-0.039	-0.039	0.000	0.000	0.000	0.000
30	A	354	ASN	0	-0.049	-0.046	16.170	-0.064	-0.064	0.000	0.000	0.000	0.000
31	A	355	TYR	0	-0.067	-0.027	18.841	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	356	CYS	0	-0.050	-0.027	16.060	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	357	ARG	1	0.817	0.924	11.734	0.437	0.437	0.000	0.000	0.000	0.000
34	A	358	SER	0	0.037	0.011	11.251	-0.120	-0.120	0.000	0.000	0.000	0.000
35	A	359	GLU	-1	-0.831	-0.911	7.906	-0.096	-0.096	0.000	0.000	0.000	0.000
36	A	360	VAL	0	-0.057	-0.026	11.743	0.001	0.001	0.000	0.000	0.000	0.000
37	A	361	ILE	0	-0.018	0.004	11.196	0.036	0.036	0.000	0.000	0.000	0.000
38	A	362	LEU	0	0.031	0.005	15.510	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	363	GLH	0	0.010	-0.035	19.335	0.013	0.013	0.000	0.000	0.000	0.000
40	A	364	ALA	0	-0.036	-0.023	22.326	0.011	0.011	0.000	0.000	0.000	0.000
41	A	365	TRP	0	-0.025	-0.014	17.613	0.000	0.000	0.000	0.000	0.000	0.000
42	A	366	GLN	0	0.038	0.020	14.949	0.027	0.027	0.000	0.000	0.000	0.000
43	A	367	ALA	0	0.028	0.014	20.506	0.011	0.011	0.000	0.000	0.000	0.000
44	A	368	ALA	0	0.027	0.018	22.597	0.002	0.002	0.000	0.000	0.000	0.000
45	A	369	ALA	0	0.069	0.034	19.423	0.006	0.006	0.000	0.000	0.000	0.000
46	A	370	ILE	0	-0.021	-0.011	21.381	0.003	0.003	0.000	0.000	0.000	0.000
47	A	371	ALA	0	-0.047	-0.020	23.584	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	372	GLU	-1	-0.967	-0.982	23.398	0.124	0.124	0.000	0.000	0.000	0.000
49	A	373	MET	0	-0.067	-0.025	17.903	0.007	0.007	0.000	0.000	0.000	0.000
50	A	374	GLY	0	0.050	0.038	23.517	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	375	PRO	0	0.007	-0.016	23.972	0.004	0.004	0.000	0.000	0.000	0.000
52	A	376	VAL	0	0.040	0.021	23.246	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	377	GLN	0	0.051	0.040	20.254	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	378	TRP	0	0.014	0.001	18.101	0.005	0.005	0.000	0.000	0.000	0.000
55	A	379	LEU	0	0.007	-0.002	18.260	0.001	0.001	0.000	0.000	0.000	0.000
56	A	380	THR	0	-0.005	-0.015	18.289	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	381	THR	0	-0.030	-0.010	14.585	0.015	0.015	0.000	0.000	0.000	0.000
58	A	382	GLN	0	0.011	-0.005	13.773	0.005	0.005	0.000	0.000	0.000	0.000
59	A	383	LYS	1	0.816	0.916	13.584	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	384	GLN	0	-0.092	-0.055	12.869	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	385	ALA	0	-0.013	-0.008	9.641	0.000	0.000	0.000	0.000	0.000	0.000
62	A	386	ALA	0	-0.013	0.011	8.728	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	387	ASP	-1	-0.811	-0.900	6.827	-0.562	-0.562	0.000	0.000	0.000	0.000
64	A	388	LYS	1	0.770	0.870	9.759	0.337	0.337	0.000	0.000	0.000	0.000
65	A	389	VAL	0	-0.016	-0.008	13.431	0.024	0.024	0.000	0.000	0.000	0.000
66	A	390	VAL	0	-0.017	-0.010	16.493	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	391	PHE	0	0.011	0.015	19.524	0.015	0.015	0.000	0.000	0.000	0.000
68	A	392	LEU	0	-0.025	-0.013	23.122	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	393	LEU	0	0.003	-0.010	24.938	0.013	0.013	0.000	0.000	0.000	0.000
70	A	394	PRO	0	-0.007	0.003	28.716	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	395	SER	0	-0.038	-0.023	31.928	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	417	GLN	0	-0.067	-0.032	30.834	0.003	0.003	0.000	0.000	0.000	0.000
73	A	418	ASP	-1	-0.814	-0.900	28.582	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	419	LEU	0	0.029	0.014	23.698	0.002	0.002	0.000	0.000	0.000	0.000
75	A	420	PHE	0	-0.008	0.021	25.717	0.000	0.000	0.000	0.000	0.000	0.000
76	A	421	PRO	0	0.019	0.001	26.724	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	422	LEU	0	-0.009	0.006	26.062	0.002	0.002	0.000	0.000	0.000	0.000
78	A	423	ALA	0	0.033	0.012	22.430	0.005	0.005	0.000	0.000	0.000	0.000
79	A	424	PHE	0	0.025	0.005	23.844	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	425	ASN	0	-0.060	-0.035	26.051	0.005	0.005	0.000	0.000	0.000	0.000
81	A	426	LEU	0	0.009	0.008	22.986	0.003	0.003	0.000	0.000	0.000	0.000
82	A	427	PHE	0	-0.003	-0.017	19.469	0.004	0.004	0.000	0.000	0.000	0.000
83	A	428	CYS	0	-0.032	-0.006	22.510	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	429	SER	0	-0.006	-0.010	23.365	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	430	ASP	-1	-0.822	-0.876	19.370	0.001	0.001	0.000	0.000	0.000	0.000
86	A	431	PHE	0	-0.048	-0.012	21.039	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	432	SER	0	0.013	0.009	22.803	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	433	SER	0	-0.009	-0.001	19.720	0.004	0.004	0.000	0.000	0.000	0.000
89	A	434	GLN	0	0.036	-0.001	19.292	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	435	THR	0	-0.059	-0.025	16.560	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	436	HIS	0	0.018	0.005	12.136	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	437	LEU	0	0.028	0.021	15.692	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	438	HIS	0	0.018	0.001	16.263	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	439	LYS	1	0.858	0.958	11.401	0.035	0.035	0.000	0.000	0.000	0.000
95	A	440	TYR	0	-0.035	-0.044	15.630	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	441	LEU	0	0.001	-0.003	16.928	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	442	VAL	0	0.002	0.004	20.542	0.012	0.012	0.000	0.000	0.000	0.000
98	A	443	VAL	0	-0.029	-0.016	21.765	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	444	TYR	0	-0.033	-0.015	24.902	0.013	0.013	0.000	0.000	0.000	0.000
100	A	445	LEU	0	0.031	-0.001	26.557	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	446	GLY	0	0.026	0.016	29.575	0.007	0.007	0.000	0.000	0.000	0.000
102	A	447	GLY	0	-0.001	-0.010	32.551	0.001	0.001	0.000	0.000	0.000	0.000
103	A	448	ALA	0	-0.039	-0.025	33.662	0.001	0.001	0.000	0.000	0.000	0.000
104	A	449	ASP	-1	-0.918	-0.954	35.705	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	450	LEU	0	0.012	0.004	31.094	0.003	0.003	0.000	0.000	0.000	0.000
106	A	451	LYS	1	0.967	0.981	35.438	0.016	0.016	0.000	0.000	0.000	0.000
107	A	452	GLY	0	-0.052	-0.012	34.822	0.003	0.003	0.000	0.000	0.000	0.000
108	A	453	ASP	-1	-0.811	-0.897	35.024	-0.041	-0.041	0.000	0.000	0.000	0.000
109	A	454	TYR	0	-0.007	-0.030	29.942	0.004	0.004	0.000	0.000	0.000	0.000
110	A	455	ASN	0	0.000	-0.019	30.578	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	456	ALA	0	0.015	0.014	28.797	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	457	LEU	0	0.022	0.003	25.529	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	458	SER	0	-0.057	-0.030	26.904	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	459	VAL	0	-0.024	-0.004	25.467	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	460	CYS	0	-0.028	0.014	22.697	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	461	PRO	0	0.008	0.006	20.681	0.004	0.004	0.000	0.000	0.000	0.000
117	A	462	GLN	0	-0.026	-0.012	23.679	0.006	0.006	0.000	0.000	0.000	0.000
118	A	463	TYR	0	-0.003	-0.005	21.384	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	464	HIS	0	0.021	0.002	26.069	0.008	0.008	0.000	0.000	0.000	0.000
120	A	465	LEU	0	-0.023	0.010	23.560	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	466	MET	0	-0.014	-0.032	25.142	0.014	0.014	0.000	0.000	0.000	0.000
122	A	467	LYS	1	0.937	0.971	27.876	0.098	0.098	0.000	0.000	0.000	0.000
123	A	468	ASP	-1	-0.782	-0.880	26.201	-0.158	-0.158	0.000	0.000	0.000	0.000
124	A	469	ALA	0	-0.014	-0.011	23.634	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	470	THR	0	0.046	0.013	22.016	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	471	ALA	0	0.003	0.021	21.548	-0.029	-0.029	0.000	0.000	0.000	0.000
127	A	472	PHE	0	0.044	0.013	18.479	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	473	HIS	0	0.042	0.020	15.435	-0.027	-0.027	0.000	0.000	0.000	0.000
129	A	474	THR	0	-0.031	-0.026	16.609	-0.056	-0.056	0.000	0.000	0.000	0.000
130	A	475	GLU	-1	-0.853	-0.899	16.695	-0.348	-0.348	0.000	0.000	0.000	0.000
131	A	476	LEU	0	0.009	-0.001	14.049	-0.016	-0.016	0.000	0.000	0.000	0.000
132	A	477	LEU	0	0.013	0.004	12.482	-0.095	-0.095	0.000	0.000	0.000	0.000
133	A	478	LYS	1	0.838	0.921	12.047	0.199	0.199	0.000	0.000	0.000	0.000
134	A	479	ALA	0	0.005	0.007	9.813	-0.027	-0.027	0.000	0.000	0.000	0.000
135	A	480	THR	0	-0.065	-0.040	7.476	-0.128	-0.128	0.000	0.000	0.000	0.000
136	A	481	GLN	0	-0.081	-0.023	7.567	-0.205	-0.205	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:325:LEU)