FMO DATABASE

FMODB ID: 9GJ72

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1269211.781063
FMO2-HF: Nuclear repulsion	1214745.234656
FMO2-HF: Total energy	-54466.546407
FMO2-MP2: Total energy	-54623.747485

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.
-3.261	-1.351	0.023	-0.88	-1.053	0

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 : -0.002 / q_NPA : -0.022

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

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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].
3	A	327	PRO	0	0.012	0.026	3.400	-2.057	-0.147	0.023	-0.880	-1.053
4	A	328	LEU	0	-0.065	-0.030	4.973	0.740	0.740	0.000	0.000	0.000
5	A	329	ILE	0	0.017	0.015	6.015	-0.196	-0.196	0.000	0.000	0.000
6	A	330	LYS	1	0.890	0.946	6.408	0.566	0.566	0.000	0.000	0.000
7	A	331	VAL	0	0.008	0.000	10.066	0.002	0.002	0.000	0.000	0.000
8	A	332	LEU	0	-0.009	0.011	13.634	0.055	0.055	0.000	0.000	0.000
9	A	333	VAL	0	-0.021	-0.017	15.941	-0.007	-0.007	0.000	0.000	0.000
10	A	334	VAL	0	-0.006	0.009	19.431	0.025	0.025	0.000	0.000	0.000
11	A	335	TYR	0	0.005	-0.017	22.402	-0.006	-0.006	0.000	0.000	0.000
12	A	336	PRO	0	0.018	0.005	25.776	0.008	0.008	0.000	0.000	0.000
13	A	337	SER	0	0.000	-0.011	29.432	-0.001	-0.001	0.000	0.000	0.000
14	A	338	GLU	-1	-0.861	-0.936	30.613	-0.073	-0.073	0.000	0.000	0.000
15	A	339	ILE	0	0.060	0.007	33.015	-0.004	-0.004	0.000	0.000	0.000
16	A	340	CYS	0	-0.033	-0.021	34.455	-0.001	-0.001	0.000	0.000	0.000
17	A	341	PHE	0	0.011	0.022	27.994	-0.002	-0.002	0.000	0.000	0.000
18	A	342	HIS	0	0.046	0.021	28.236	-0.011	-0.011	0.000	0.000	0.000
19	A	343	HIS	0	0.014	0.002	29.310	-0.002	-0.002	0.000	0.000	0.000
20	A	344	THR	0	-0.008	-0.007	28.227	-0.004	-0.004	0.000	0.000	0.000
21	A	345	VAL	0	0.019	0.018	24.559	-0.014	-0.014	0.000	0.000	0.000
22	A	346	CYS	0	-0.030	-0.005	24.595	-0.009	-0.009	0.000	0.000	0.000
23	A	347	ARG	1	0.971	0.991	24.766	0.124	0.124	0.000	0.000	0.000
24	A	348	PHE	0	0.022	0.000	20.522	-0.011	-0.011	0.000	0.000	0.000
25	A	349	THR	0	-0.018	-0.009	20.402	-0.019	-0.019	0.000	0.000	0.000
26	A	350	ASP	-1	-0.880	-0.939	19.842	-0.154	-0.154	0.000	0.000	0.000
27	A	351	PHE	0	-0.020	-0.020	20.794	-0.016	-0.016	0.000	0.000	0.000
28	A	352	LEU	0	-0.001	-0.013	16.748	-0.024	-0.024	0.000	0.000	0.000
29	A	353	GLN	0	0.009	0.012	15.913	-0.029	-0.029	0.000	0.000	0.000
30	A	354	ASN	0	-0.071	-0.031	16.236	-0.027	-0.027	0.000	0.000	0.000
31	A	355	TYR	0	-0.083	-0.042	18.495	-0.013	-0.013	0.000	0.000	0.000
32	A	356	CYS	0	-0.038	-0.017	16.157	-0.010	-0.010	0.000	0.000	0.000
33	A	357	ARG	1	0.906	0.980	11.824	0.330	0.330	0.000	0.000	0.000
34	A	358	SER	0	0.008	0.003	11.742	-0.123	-0.123	0.000	0.000	0.000
35	A	359	GLU	-1	-0.859	-0.944	8.314	-0.282	-0.282	0.000	0.000	0.000
36	A	360	VAL	0	-0.022	-0.012	12.011	-0.036	-0.036	0.000	0.000	0.000
37	A	361	ILE	0	-0.039	-0.014	11.711	0.047	0.047	0.000	0.000	0.000
38	A	362	LEU	0	0.035	0.002	15.781	-0.008	-0.008	0.000	0.000	0.000
39	A	363	GLH	0	0.003	-0.052	19.467	0.014	0.014	0.000	0.000	0.000
40	A	364	ALA	0	-0.041	-0.021	22.209	0.015	0.015	0.000	0.000	0.000
41	A	365	TRP	0	-0.029	-0.016	17.419	0.010	0.010	0.000	0.000	0.000
42	A	366	GLN	0	0.011	0.009	14.990	0.024	0.024	0.000	0.000	0.000
43	A	367	ALA	0	0.042	0.021	20.542	0.001	0.001	0.000	0.000	0.000
44	A	368	ALA	0	0.026	0.011	22.422	0.000	0.000	0.000	0.000	0.000
45	A	369	ALA	0	0.055	0.028	19.143	0.003	0.003	0.000	0.000	0.000
46	A	370	ILE	0	0.001	-0.004	21.151	-0.004	-0.004	0.000	0.000	0.000
47	A	371	ALA	0	-0.059	-0.024	23.442	-0.002	-0.002	0.000	0.000	0.000
48	A	372	GLU	-1	-0.962	-0.973	23.200	0.057	0.057	0.000	0.000	0.000
49	A	373	MET	0	-0.089	-0.027	18.202	0.001	0.001	0.000	0.000	0.000
50	A	374	GLY	0	0.042	0.029	23.572	-0.004	-0.004	0.000	0.000	0.000
51	A	375	PRO	0	0.016	-0.022	24.048	-0.006	-0.006	0.000	0.000	0.000
52	A	376	VAL	0	0.030	0.013	23.496	-0.011	-0.011	0.000	0.000	0.000
53	A	377	GLN	0	0.056	0.022	20.209	-0.028	-0.028	0.000	0.000	0.000
54	A	378	TRP	0	0.021	-0.002	18.288	-0.018	-0.018	0.000	0.000	0.000
55	A	379	LEU	0	0.017	0.004	18.447	-0.018	-0.018	0.000	0.000	0.000
56	A	380	THR	0	-0.001	0.005	18.249	-0.030	-0.030	0.000	0.000	0.000
57	A	381	THR	0	-0.022	-0.012	14.786	-0.017	-0.017	0.000	0.000	0.000
58	A	382	GLN	0	0.005	-0.003	14.028	-0.053	-0.053	0.000	0.000	0.000
59	A	383	LYS	1	0.899	0.978	13.542	0.160	0.160	0.000	0.000	0.000
60	A	384	GLN	0	-0.102	-0.063	12.760	-0.049	-0.049	0.000	0.000	0.000
61	A	385	ALA	0	-0.022	0.001	9.583	-0.048	-0.048	0.000	0.000	0.000
62	A	386	ALA	0	-0.037	-0.005	8.749	-0.111	-0.111	0.000	0.000	0.000
63	A	387	ASP	-1	-0.812	-0.900	7.106	-1.279	-1.279	0.000	0.000	0.000
64	A	388	LYS	1	0.824	0.912	10.058	0.594	0.594	0.000	0.000	0.000
65	A	389	VAL	0	-0.020	-0.011	13.746	0.022	0.022	0.000	0.000	0.000
66	A	390	VAL	0	-0.008	-0.004	16.752	0.004	0.004	0.000	0.000	0.000
67	A	391	PHE	0	-0.001	0.008	19.655	0.019	0.019	0.000	0.000	0.000
68	A	392	LEU	0	-0.020	-0.015	23.185	-0.003	-0.003	0.000	0.000	0.000
69	A	393	LEU	0	0.005	-0.016	25.118	0.014	0.014	0.000	0.000	0.000
70	A	394	PRO	0	-0.013	0.005	28.831	-0.005	-0.005	0.000	0.000	0.000
71	A	395	SER	0	-0.048	-0.033	31.955	-0.001	-0.001	0.000	0.000	0.000
72	A	417	GLN	0	-0.016	0.008	30.719	0.004	0.004	0.000	0.000	0.000
73	A	418	ASP	-1	-0.825	-0.884	28.658	-0.070	-0.070	0.000	0.000	0.000
74	A	419	LEU	0	0.036	0.019	23.359	0.000	0.000	0.000	0.000	0.000
75	A	420	PHE	0	-0.022	0.009	25.984	-0.008	-0.008	0.000	0.000	0.000
76	A	421	PRO	0	0.023	0.010	27.039	-0.007	-0.007	0.000	0.000	0.000
77	A	422	LEU	0	0.018	0.003	26.389	-0.001	-0.001	0.000	0.000	0.000
78	A	423	ALA	0	0.035	0.011	22.625	-0.003	-0.003	0.000	0.000	0.000
79	A	424	PHE	0	0.007	0.000	24.077	-0.010	-0.010	0.000	0.000	0.000
80	A	425	ASN	0	-0.074	-0.036	26.273	-0.005	-0.005	0.000	0.000	0.000
81	A	426	LEU	0	-0.004	-0.008	23.123	0.000	0.000	0.000	0.000	0.000
82	A	427	PHE	0	0.012	-0.009	19.476	-0.010	-0.010	0.000	0.000	0.000
83	A	428	CYS	0	-0.023	0.006	22.749	-0.009	-0.009	0.000	0.000	0.000
84	A	429	SER	0	0.015	0.000	24.394	-0.002	-0.002	0.000	0.000	0.000
85	A	430	ASP	-1	-0.911	-0.959	19.988	-0.198	-0.198	0.000	0.000	0.000
86	A	431	PHE	0	-0.086	-0.033	21.109	-0.021	-0.021	0.000	0.000	0.000
87	A	432	SER	0	0.013	0.000	22.271	-0.009	-0.009	0.000	0.000	0.000
88	A	433	SER	0	-0.022	0.006	19.777	-0.003	-0.003	0.000	0.000	0.000
89	A	434	GLN	0	0.038	0.004	20.361	-0.028	-0.028	0.000	0.000	0.000
90	A	435	THR	0	-0.097	-0.043	16.718	-0.021	-0.021	0.000	0.000	0.000
91	A	436	HIS	0	0.009	0.007	12.795	-0.079	-0.079	0.000	0.000	0.000
92	A	437	LEU	0	0.045	0.024	15.842	0.019	0.019	0.000	0.000	0.000
93	A	438	HIS	0	0.029	0.005	16.638	-0.040	-0.040	0.000	0.000	0.000
94	A	439	LYS	1	0.912	0.978	11.959	0.419	0.419	0.000	0.000	0.000
95	A	440	TYR	0	0.007	-0.001	16.130	-0.014	-0.014	0.000	0.000	0.000
96	A	441	LEU	0	0.004	0.000	17.114	0.009	0.009	0.000	0.000	0.000
97	A	442	VAL	0	0.023	0.014	20.823	0.010	0.010	0.000	0.000	0.000
98	A	443	VAL	0	-0.023	-0.012	22.045	-0.005	-0.005	0.000	0.000	0.000
99	A	444	TYR	0	-0.043	-0.011	25.095	0.013	0.013	0.000	0.000	0.000
100	A	445	LEU	0	0.009	-0.018	26.476	-0.004	-0.004	0.000	0.000	0.000
101	A	446	GLY	0	0.036	0.026	29.684	0.005	0.005	0.000	0.000	0.000
102	A	447	GLY	0	0.017	0.012	32.554	-0.001	-0.001	0.000	0.000	0.000
103	A	448	ALA	0	-0.012	-0.030	33.842	0.002	0.002	0.000	0.000	0.000
104	A	449	ASP	-1	-0.929	-0.952	35.965	-0.072	-0.072	0.000	0.000	0.000
105	A	450	LEU	0	-0.017	0.001	31.115	0.001	0.001	0.000	0.000	0.000
106	A	451	LYS	1	1.001	0.995	35.625	0.058	0.058	0.000	0.000	0.000
107	A	452	GLY	0	-0.072	-0.036	35.087	0.002	0.002	0.000	0.000	0.000
108	A	453	ASP	-1	-0.874	-0.914	35.350	-0.082	-0.082	0.000	0.000	0.000
109	A	454	TYR	0	-0.004	-0.036	29.880	0.000	0.000	0.000	0.000	0.000
110	A	455	ASN	0	0.065	0.019	30.805	-0.008	-0.008	0.000	0.000	0.000
111	A	456	ALA	0	0.034	0.022	28.775	-0.004	-0.004	0.000	0.000	0.000
112	A	457	LEU	0	0.040	0.014	25.540	-0.010	-0.010	0.000	0.000	0.000
113	A	458	SER	0	-0.074	-0.032	27.364	-0.011	-0.011	0.000	0.000	0.000
114	A	459	VAL	0	-0.021	-0.008	25.842	-0.002	-0.002	0.000	0.000	0.000
115	A	460	CYS	0	-0.052	0.001	23.073	-0.014	-0.014	0.000	0.000	0.000
116	A	461	PRO	0	0.010	0.018	20.973	0.015	0.015	0.000	0.000	0.000
117	A	462	GLN	0	-0.026	-0.032	24.061	0.011	0.011	0.000	0.000	0.000
118	A	463	TYR	0	-0.017	-0.003	21.333	-0.011	-0.011	0.000	0.000	0.000
119	A	464	HIS	0	0.022	0.007	26.118	0.011	0.011	0.000	0.000	0.000
120	A	465	LEU	0	-0.036	0.022	23.463	-0.002	-0.002	0.000	0.000	0.000
121	A	466	MET	0	-0.005	-0.033	25.061	0.012	0.012	0.000	0.000	0.000
122	A	467	LYS	1	0.942	0.965	28.202	0.116	0.116	0.000	0.000	0.000
123	A	468	ASP	-1	-0.792	-0.881	26.103	-0.191	-0.191	0.000	0.000	0.000
124	A	469	ALA	0	-0.023	-0.021	24.009	-0.022	-0.022	0.000	0.000	0.000
125	A	470	THR	0	0.045	0.014	22.417	-0.024	-0.024	0.000	0.000	0.000
126	A	471	ALA	0	0.015	0.013	21.816	-0.030	-0.030	0.000	0.000	0.000
127	A	472	PHE	0	0.043	0.008	18.931	-0.029	-0.029	0.000	0.000	0.000
128	A	473	HIS	0	0.048	0.017	16.086	-0.054	-0.054	0.000	0.000	0.000
129	A	474	THR	0	-0.035	-0.020	16.932	-0.056	-0.056	0.000	0.000	0.000
130	A	475	GLU	-1	-0.931	-0.974	16.952	-0.489	-0.489	0.000	0.000	0.000
131	A	476	LEU	0	0.010	0.002	14.102	-0.050	-0.050	0.000	0.000	0.000
132	A	477	LEU	0	0.017	0.009	12.630	-0.118	-0.118	0.000	0.000	0.000
133	A	478	LYS	1	0.852	0.932	12.391	0.307	0.307	0.000	0.000	0.000
134	A	479	ALA	0	0.006	-0.002	10.476	-0.041	-0.041	0.000	0.000	0.000
135	A	480	THR	0	-0.089	-0.023	7.857	-0.181	-0.181	0.000	0.000	0.000
136	A	481	GLN	0	-0.031	-0.002	8.339	-0.235	-0.235	0.000	0.000	0.000

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