FMO DATABASE

FMODB ID: J36Z9

Calculation Name: 3VBC-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1278926.590533
FMO2-HF: Nuclear repulsion	1224269.976673
FMO2-HF: Total energy	-54656.61386
FMO2-MP2: Total energy	-54814.475525

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.
-3.354	-1.469	0.026	-0.876	-1.036	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 : -0.001 / q_NPA : -0.021

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].
3	A	327	PRO	0	0.013	0.028	3.400	-2.079	-0.194	0.026	-0.876	-1.036
4	A	328	LEU	0	-0.066	-0.030	4.973	0.757	0.757	0.000	0.000	0.000
5	A	329	ILE	0	0.017	0.014	6.015	-0.204	-0.204	0.000	0.000	0.000
6	A	330	LYS	1	0.890	0.946	6.408	0.598	0.598	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	-0.006	0.011	13.634	0.060	0.060	0.000	0.000	0.000
9	A	333	VAL	0	-0.021	-0.015	15.940	-0.006	-0.006	0.000	0.000	0.000
10	A	334	VAL	0	-0.009	0.007	19.431	0.026	0.026	0.000	0.000	0.000
11	A	335	TYR	0	0.005	-0.018	22.401	-0.006	-0.006	0.000	0.000	0.000
12	A	336	PRO	0	0.021	0.006	25.775	0.008	0.008	0.000	0.000	0.000
13	A	337	SER	0	0.006	-0.008	29.432	-0.001	-0.001	0.000	0.000	0.000
14	A	338	GLU	-1	-0.864	-0.936	30.613	-0.075	-0.075	0.000	0.000	0.000
15	A	339	ILE	0	0.061	0.007	33.015	-0.004	-0.004	0.000	0.000	0.000
16	A	340	CYS	0	-0.035	-0.021	34.455	-0.001	-0.001	0.000	0.000	0.000
17	A	341	PHE	0	0.010	0.021	27.994	-0.002	-0.002	0.000	0.000	0.000
18	A	342	HIS	0	0.047	0.021	28.236	-0.011	-0.011	0.000	0.000	0.000
19	A	343	HIS	0	0.018	0.003	29.310	-0.002	-0.002	0.000	0.000	0.000
20	A	344	THR	0	-0.011	-0.008	28.227	-0.004	-0.004	0.000	0.000	0.000
21	A	345	VAL	0	0.020	0.019	24.559	-0.014	-0.014	0.000	0.000	0.000
22	A	346	CYS	0	-0.029	-0.004	24.595	-0.009	-0.009	0.000	0.000	0.000
23	A	347	ARG	1	0.971	0.991	24.766	0.123	0.123	0.000	0.000	0.000
24	A	348	PHE	0	0.021	0.000	20.522	-0.011	-0.011	0.000	0.000	0.000
25	A	349	THR	0	-0.023	-0.011	20.402	-0.019	-0.019	0.000	0.000	0.000
26	A	350	ASP	-1	-0.874	-0.937	19.842	-0.150	-0.150	0.000	0.000	0.000
27	A	351	PHE	0	-0.028	-0.023	20.794	-0.016	-0.016	0.000	0.000	0.000
28	A	352	LEU	0	0.005	-0.011	16.749	-0.025	-0.025	0.000	0.000	0.000
29	A	353	GLN	0	0.009	0.014	15.913	-0.029	-0.029	0.000	0.000	0.000
30	A	354	ASN	0	-0.069	-0.030	16.236	-0.024	-0.024	0.000	0.000	0.000
31	A	355	TYR	0	-0.084	-0.043	18.495	-0.013	-0.013	0.000	0.000	0.000
32	A	356	CYS	0	-0.042	-0.018	16.157	-0.012	-0.012	0.000	0.000	0.000
33	A	357	ARG	1	0.908	0.981	11.824	0.316	0.316	0.000	0.000	0.000
34	A	358	SER	0	0.006	0.002	11.742	-0.125	-0.125	0.000	0.000	0.000
35	A	359	GLU	-1	-0.857	-0.944	8.314	-0.271	-0.271	0.000	0.000	0.000
36	A	360	VAL	0	-0.023	-0.012	12.011	-0.037	-0.037	0.000	0.000	0.000
37	A	361	ILE	0	-0.041	-0.014	11.711	0.049	0.049	0.000	0.000	0.000
38	A	362	LEU	0	0.038	0.003	15.781	-0.008	-0.008	0.000	0.000	0.000
39	A	363	GLH	0	0.002	-0.052	19.467	0.015	0.015	0.000	0.000	0.000
40	A	364	ALA	0	-0.043	-0.021	22.209	0.016	0.016	0.000	0.000	0.000
41	A	365	TRP	0	-0.028	-0.015	17.419	0.011	0.011	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	0.044	0.022	20.542	0.001	0.001	0.000	0.000	0.000
44	A	368	ALA	0	0.024	0.010	22.422	0.000	0.000	0.000	0.000	0.000
45	A	369	ALA	0	0.054	0.028	19.143	0.003	0.003	0.000	0.000	0.000
46	A	370	ILE	0	-0.001	-0.005	21.151	-0.005	-0.005	0.000	0.000	0.000
47	A	371	ALA	0	-0.056	-0.022	23.442	-0.002	-0.002	0.000	0.000	0.000
48	A	372	GLU	-1	-0.962	-0.973	23.199	0.055	0.055	0.000	0.000	0.000
49	A	373	MET	0	-0.092	-0.028	18.201	0.000	0.000	0.000	0.000	0.000
50	A	374	GLY	0	0.045	0.031	23.572	-0.005	-0.005	0.000	0.000	0.000
51	A	375	PRO	0	0.010	-0.024	24.047	-0.007	-0.007	0.000	0.000	0.000
52	A	376	VAL	0	0.031	0.014	23.495	-0.011	-0.011	0.000	0.000	0.000
53	A	377	GLN	0	0.056	0.022	20.208	-0.029	-0.029	0.000	0.000	0.000
54	A	378	TRP	0	0.023	-0.001	18.288	-0.019	-0.019	0.000	0.000	0.000
55	A	379	LEU	0	0.014	0.002	18.446	-0.020	-0.020	0.000	0.000	0.000
56	A	380	THR	0	0.000	0.006	18.248	-0.032	-0.032	0.000	0.000	0.000
57	A	381	THR	0	-0.021	-0.011	14.785	-0.019	-0.019	0.000	0.000	0.000
58	A	382	GLN	0	0.002	-0.005	14.027	-0.058	-0.058	0.000	0.000	0.000
59	A	383	LYS	1	0.899	0.978	13.541	0.169	0.169	0.000	0.000	0.000
60	A	384	GLN	0	-0.100	-0.061	12.759	-0.050	-0.050	0.000	0.000	0.000
61	A	385	ALA	0	-0.020	0.002	9.582	-0.054	-0.054	0.000	0.000	0.000
62	A	386	ALA	0	-0.041	-0.006	8.748	-0.119	-0.119	0.000	0.000	0.000
63	A	387	ASP	-1	-0.808	-0.898	7.106	-1.327	-1.327	0.000	0.000	0.000
64	A	388	LYS	1	0.820	0.911	10.058	0.612	0.612	0.000	0.000	0.000
65	A	389	VAL	0	-0.020	-0.011	13.746	0.025	0.025	0.000	0.000	0.000
66	A	390	VAL	0	-0.007	-0.003	16.752	0.006	0.006	0.000	0.000	0.000
67	A	391	PHE	0	-0.003	0.007	19.655	0.020	0.020	0.000	0.000	0.000
68	A	392	LEU	0	-0.019	-0.014	23.185	-0.002	-0.002	0.000	0.000	0.000
69	A	393	LEU	0	0.007	-0.016	25.118	0.015	0.015	0.000	0.000	0.000
70	A	394	PRO	0	-0.005	0.003	28.831	-0.005	-0.005	0.000	0.000	0.000
71	A	395	SER	0	-0.048	-0.048	31.955	0.000	0.000	0.000	0.000	0.000
72	A	396	NME	0	-0.032	0.010	32.240	-0.002	-0.002	0.000	0.000	0.000
73	A	416	ACE	0	-0.024	-0.018	34.281	0.001	0.001	0.000	0.000	0.000
74	A	417	GLN	0	0.017	0.027	30.725	0.003	0.003	0.000	0.000	0.000
75	A	418	ASP	-1	-0.833	-0.885	28.657	-0.073	-0.073	0.000	0.000	0.000
76	A	419	LEU	0	0.036	0.019	23.359	-0.001	-0.001	0.000	0.000	0.000
77	A	420	PHE	0	-0.017	0.014	25.984	-0.009	-0.009	0.000	0.000	0.000
78	A	421	PRO	0	0.012	0.006	27.039	-0.007	-0.007	0.000	0.000	0.000
79	A	422	LEU	0	0.019	0.003	26.389	-0.001	-0.001	0.000	0.000	0.000
80	A	423	ALA	0	0.037	0.012	22.624	-0.003	-0.003	0.000	0.000	0.000
81	A	424	PHE	0	-0.001	-0.002	24.076	-0.010	-0.010	0.000	0.000	0.000
82	A	425	ASN	0	-0.066	-0.033	26.272	-0.005	-0.005	0.000	0.000	0.000
83	A	426	LEU	0	-0.001	-0.007	23.123	0.000	0.000	0.000	0.000	0.000
84	A	427	PHE	0	0.006	-0.012	19.476	-0.011	-0.011	0.000	0.000	0.000
85	A	428	CYS	0	-0.019	0.007	22.749	-0.009	-0.009	0.000	0.000	0.000
86	A	429	SER	0	0.013	0.000	24.414	-0.002	-0.002	0.000	0.000	0.000
87	A	430	ASP	-1	-0.910	-0.959	19.988	-0.208	-0.208	0.000	0.000	0.000
88	A	431	PHE	0	-0.084	-0.032	21.109	-0.022	-0.022	0.000	0.000	0.000
89	A	432	SER	0	0.009	-0.002	22.272	-0.009	-0.009	0.000	0.000	0.000
90	A	433	SER	0	-0.021	0.006	19.777	-0.003	-0.003	0.000	0.000	0.000
91	A	434	GLN	0	0.040	0.005	20.361	-0.029	-0.029	0.000	0.000	0.000
92	A	435	THR	0	-0.098	-0.043	16.718	-0.022	-0.022	0.000	0.000	0.000
93	A	436	HIS	0	0.009	0.006	12.794	-0.084	-0.084	0.000	0.000	0.000
94	A	437	LEU	0	0.044	0.023	15.842	0.021	0.021	0.000	0.000	0.000
95	A	438	HIS	0	0.030	0.004	16.638	-0.041	-0.041	0.000	0.000	0.000
96	A	439	LYS	1	0.915	0.980	11.960	0.440	0.440	0.000	0.000	0.000
97	A	440	TYR	0	0.009	0.000	16.130	-0.013	-0.013	0.000	0.000	0.000
98	A	441	LEU	0	0.002	-0.001	17.114	0.010	0.010	0.000	0.000	0.000
99	A	442	VAL	0	0.022	0.014	20.823	0.011	0.011	0.000	0.000	0.000
100	A	443	VAL	0	-0.021	-0.013	22.043	-0.005	-0.005	0.000	0.000	0.000
101	A	444	TYR	0	-0.037	-0.012	25.095	0.014	0.014	0.000	0.000	0.000
102	A	445	LEU	0	0.012	-0.015	26.476	-0.004	-0.004	0.000	0.000	0.000
103	A	446	GLY	0	0.039	0.027	29.684	0.005	0.005	0.000	0.000	0.000
104	A	447	GLY	0	0.020	0.017	32.554	-0.001	-0.001	0.000	0.000	0.000
105	A	448	ALA	0	-0.011	-0.029	33.842	0.002	0.002	0.000	0.000	0.000
106	A	449	ASP	-1	-0.930	-0.953	35.965	-0.074	-0.074	0.000	0.000	0.000
107	A	450	LEU	0	-0.018	-0.001	31.116	0.001	0.001	0.000	0.000	0.000
108	A	451	LYS	1	1.005	0.997	35.625	0.060	0.060	0.000	0.000	0.000
109	A	452	GLY	0	-0.075	-0.036	35.086	0.002	0.002	0.000	0.000	0.000
110	A	453	ASP	-1	-0.873	-0.915	35.350	-0.085	-0.085	0.000	0.000	0.000
111	A	454	TYR	0	-0.008	-0.039	29.879	-0.001	-0.001	0.000	0.000	0.000
112	A	455	ASN	0	0.067	0.019	30.805	-0.008	-0.008	0.000	0.000	0.000
113	A	456	ALA	0	0.034	0.022	28.776	-0.005	-0.005	0.000	0.000	0.000
114	A	457	LEU	0	0.037	0.013	25.539	-0.011	-0.011	0.000	0.000	0.000
115	A	458	SER	0	-0.071	-0.030	27.364	-0.011	-0.011	0.000	0.000	0.000
116	A	459	VAL	0	-0.020	-0.008	25.844	-0.002	-0.002	0.000	0.000	0.000
117	A	460	CYS	0	-0.055	-0.001	23.073	-0.015	-0.015	0.000	0.000	0.000
118	A	461	PRO	0	0.012	0.019	20.973	0.015	0.015	0.000	0.000	0.000
119	A	462	GLN	0	-0.026	-0.031	24.062	0.012	0.012	0.000	0.000	0.000
120	A	463	TYR	0	-0.017	-0.004	21.333	-0.011	-0.011	0.000	0.000	0.000
121	A	464	HIS	0	0.033	0.010	26.118	0.012	0.012	0.000	0.000	0.000
122	A	465	LEU	0	-0.039	0.021	23.463	-0.002	-0.002	0.000	0.000	0.000
123	A	466	MET	0	-0.002	-0.033	25.062	0.012	0.012	0.000	0.000	0.000
124	A	467	LYS	1	0.941	0.965	28.202	0.117	0.117	0.000	0.000	0.000
125	A	468	ASP	-1	-0.792	-0.882	26.103	-0.193	-0.193	0.000	0.000	0.000
126	A	469	ALA	0	-0.023	-0.021	24.009	-0.023	-0.023	0.000	0.000	0.000
127	A	470	THR	0	0.044	0.014	22.417	-0.025	-0.025	0.000	0.000	0.000
128	A	471	ALA	0	0.018	0.014	21.816	-0.031	-0.031	0.000	0.000	0.000
129	A	472	PHE	0	0.038	0.005	18.931	-0.030	-0.030	0.000	0.000	0.000
130	A	473	HIS	0	0.048	0.018	16.086	-0.057	-0.057	0.000	0.000	0.000
131	A	474	THR	0	-0.032	-0.019	16.932	-0.057	-0.057	0.000	0.000	0.000
132	A	475	GLU	-1	-0.932	-0.974	16.952	-0.498	-0.498	0.000	0.000	0.000
133	A	476	LEU	0	0.002	0.000	14.102	-0.055	-0.055	0.000	0.000	0.000
134	A	477	LEU	0	0.023	0.011	12.629	-0.123	-0.123	0.000	0.000	0.000
135	A	478	LYS	1	0.854	0.932	12.391	0.310	0.310	0.000	0.000	0.000
136	A	479	ALA	0	0.004	-0.003	10.476	-0.046	-0.046	0.000	0.000	0.000
137	A	480	THR	0	-0.092	-0.025	7.857	-0.197	-0.197	0.000	0.000	0.000
138	A	481	GLN	0	-0.027	-0.007	8.339	-0.224	-0.224	0.000	0.000	0.000
139	A	1	NME	0	-0.005	0.005	8.753	-0.033	-0.033	0.000	0.000	0.000

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