FMO DATABASE

FMODB ID: V2161

Calculation Name: 1VGG-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VGG

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJC3

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	161
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1468338.127105
FMO2-HF: Nuclear repulsion	1407272.654327
FMO2-HF: Total energy	-61065.472778
FMO2-MP2: Total energy	-61245.750769

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:1:MET )

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

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.
-115.394	-111.262	26.105	-14.742	-15.495	-0.152

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.779 / q_NPA : 0.886

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	3	LEU	0	-0.011	-0.003	2.749	1.696	4.339	0.382	-1.083	-1.942	-0.004
4	A	4	LYS	1	0.929	0.972	5.220	42.806	42.864	0.000	-0.008	-0.051	0.000
5	A	5	LEU	0	-0.003	-0.004	8.480	0.947	0.947	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.008	-0.011	10.939	0.662	0.662	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.043	-0.025	14.009	0.654	0.654	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.006	0.012	17.354	-0.161	-0.161	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.874	-0.918	19.771	-11.669	-11.669	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.828	0.896	22.955	10.945	10.945	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.036	0.034	25.947	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.893	-0.953	28.880	-10.071	-10.071	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.032	-0.010	30.028	-0.170	-0.170	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.047	-0.010	29.168	0.157	0.157	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.016	-0.002	27.800	-0.371	-0.371	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.007	0.004	22.661	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.001	-0.007	23.627	0.058	0.058	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.001	0.014	16.096	-0.108	-0.108	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.032	0.002	18.854	0.045	0.045	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.010	0.030	14.171	-0.934	-0.934	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.014	0.009	17.975	0.679	0.679	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.053	-0.036	18.860	-0.620	-0.620	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.072	0.030	20.949	0.530	0.530	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.059	0.016	23.711	-0.035	-0.035	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.856	0.928	25.366	9.534	9.534	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.012	-0.012	23.048	0.207	0.207	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.043	-0.027	25.384	0.104	0.104	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.897	-0.948	27.467	-8.822	-8.822	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.701	-0.802	29.197	-9.274	-9.274	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.022	-0.022	24.849	0.168	0.168	0.000	0.000	0.000	0.000
31	A	31	HIS	0	0.003	0.037	29.370	-0.070	-0.070	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.915	-0.970	31.706	-8.127	-8.127	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.020	-0.009	31.477	0.244	0.244	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.052	-0.030	29.337	0.157	0.157	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.027	-0.019	33.667	0.191	0.191	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.042	-0.009	36.685	0.306	0.306	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.075	-0.026	35.526	0.165	0.165	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.023	-0.016	36.692	0.145	0.145	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.020	0.018	39.004	-0.075	-0.075	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.011	-0.010	41.132	0.020	0.020	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.037	0.006	33.671	-0.073	-0.073	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.887	0.947	35.634	8.245	8.245	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.015	-0.012	29.907	-0.194	-0.194	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.034	0.027	29.007	0.176	0.176	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.035	-0.008	24.797	-0.287	-0.287	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.016	0.006	22.393	0.105	0.105	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.012	-0.013	19.756	-0.283	-0.283	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.011	0.011	15.529	0.455	0.455	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.827	-0.891	17.574	-13.390	-13.390	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.014	0.003	14.669	-0.524	-0.524	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.022	-0.005	15.909	-0.453	-0.453	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.067	0.023	18.572	0.453	0.453	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.905	0.942	20.843	11.934	11.934	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.848	0.937	14.088	19.268	19.268	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.001	0.001	19.098	-0.203	-0.203	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.032	0.019	19.057	0.015	0.015	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.796	0.891	21.311	12.531	12.531	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.848	0.891	24.224	9.798	9.798	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.013	-0.028	26.881	0.334	0.334	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.026	0.000	29.520	-0.281	-0.281	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.031	-0.022	32.087	0.123	0.123	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.788	-0.881	33.691	-8.407	-8.407	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.737	-0.856	32.125	-9.740	-9.740	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.046	0.036	31.596	-0.305	-0.305	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.058	-0.019	29.825	-0.377	-0.377	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.016	-0.007	28.076	-0.480	-0.480	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.948	-0.969	26.818	-10.377	-10.377	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.001	0.008	25.060	-0.521	-0.521	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.002	-0.004	23.743	-0.632	-0.632	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.005	-0.015	22.061	-0.728	-0.728	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.856	0.919	21.259	11.599	11.599	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.017	-0.019	19.674	-1.257	-1.257	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.017	-0.006	17.431	-1.046	-1.046	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.035	-0.006	16.453	-1.058	-1.058	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.008	0.005	16.094	-1.166	-1.166	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.020	-0.019	13.325	-1.555	-1.555	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.009	0.028	11.726	-2.073	-2.073	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.011	-0.008	10.658	-2.187	-2.187	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.024	0.005	11.526	1.636	1.636	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.012	-0.033	13.496	0.260	0.260	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.003	0.033	13.715	0.618	0.618	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.019	-0.014	16.601	0.389	0.389	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.015	-0.012	20.025	-0.319	-0.319	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.011	0.012	21.965	0.311	0.311	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.004	-0.003	25.372	-0.171	-0.171	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.017	-0.020	27.425	0.274	0.274	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.042	-0.002	30.772	-0.039	-0.039	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.903	-0.970	33.746	-8.076	-8.076	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.015	0.003	35.661	0.180	0.180	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.017	0.022	34.314	0.122	0.122	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.036	0.000	32.258	-0.257	-0.257	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.069	0.022	27.986	0.084	0.084	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.035	-0.009	30.142	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.022	-0.008	32.491	0.108	0.108	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.057	0.018	30.118	0.116	0.116	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.002	-0.003	26.111	-0.155	-0.155	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.045	-0.014	29.263	-0.275	-0.275	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.087	0.038	31.365	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.034	-0.008	25.332	-0.178	-0.178	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.908	0.934	26.265	9.621	9.621	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.001	0.014	27.361	-0.122	-0.122	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.018	0.025	27.243	0.139	0.139	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.035	0.006	27.068	-0.334	-0.334	0.000	0.000	0.000	0.000
104	A	104	GLH	0	-0.040	-0.059	24.405	-0.144	-0.144	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.058	-0.022	22.531	-0.702	-0.702	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.022	0.003	18.167	0.128	0.128	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.951	0.964	12.263	17.118	17.118	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.000	-0.007	20.039	-0.154	-0.154	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.086	-0.067	13.751	-0.206	-0.206	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.035	0.005	18.004	0.026	0.026	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.014	0.002	20.557	0.108	0.108	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.050	-0.023	22.391	0.348	0.348	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.082	0.035	25.387	-0.059	-0.059	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.043	0.003	24.168	0.473	0.473	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.012	-0.014	23.122	-0.356	-0.356	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.038	0.030	18.325	-0.172	-0.172	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.932	0.968	15.526	14.232	14.232	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.021	0.010	11.838	0.159	0.159	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.010	0.020	7.471	-0.965	-0.965	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.008	-0.001	7.444	0.641	0.641	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.016	0.007	2.872	-2.839	-3.253	2.742	-0.817	-1.511	0.002
122	A	122	GLU	-1	-0.852	-0.931	3.070	-33.680	-32.759	0.080	-0.298	-0.703	-0.001
123	A	123	GLU	-1	-0.789	-0.908	1.762	-152.338	-151.754	22.877	-12.464	-10.997	-0.148
124	A	124	GLY	0	-0.003	0.013	3.519	10.005	10.193	0.024	-0.057	-0.154	-0.001
125	A	125	GLU	-1	-0.890	-0.939	6.757	-21.782	-21.782	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.037	-0.017	6.758	6.184	6.184	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.829	0.890	5.958	22.849	22.849	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.028	-0.002	6.088	2.961	2.961	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.035	0.013	7.849	-1.226	-1.226	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.074	-0.048	4.266	0.321	0.473	0.000	-0.015	-0.137	0.000
131	A	131	GLY	0	0.013	0.005	8.900	1.125	1.125	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.031	-0.008	12.132	-0.625	-0.625	0.000	0.000	0.000	0.000
133	A	133	MET	0	-0.021	-0.014	12.776	0.496	0.496	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.801	-0.902	16.850	-11.874	-11.874	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.020	0.013	20.322	0.414	0.414	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.051	-0.037	21.560	-0.485	-0.485	0.000	0.000	0.000	0.000
137	A	137	THR	0	0.022	0.012	21.476	0.016	0.016	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.016	-0.008	23.896	0.262	0.262	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.021	-0.002	27.229	-0.077	-0.077	0.000	0.000	0.000	0.000
140	A	140	GLY	0	-0.005	0.004	30.228	0.221	0.221	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.075	-0.037	31.636	-0.223	-0.223	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.770	-0.852	33.982	-7.714	-7.714	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.799	-0.896	36.640	-6.983	-6.983	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.899	-0.994	40.264	-6.828	-6.828	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.052	-0.008	43.041	0.079	0.079	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.866	-0.933	38.305	-7.579	-7.579	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.037	-0.002	38.959	-0.072	-0.072	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.040	-0.035	40.561	0.017	0.017	0.000	0.000	0.000	0.000
149	A	149	TRP	0	0.028	0.018	39.823	0.092	0.092	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.819	0.886	36.421	7.711	7.711	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.874	0.934	39.592	6.758	6.758	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.790	-0.884	42.092	-6.309	-6.309	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.012	0.013	38.008	0.053	0.053	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.018	-0.024	37.374	0.014	0.014	0.000	0.000	0.000	0.000
155	A	155	ARG	1	0.837	0.928	41.385	6.706	6.706	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.844	0.912	44.827	6.278	6.278	0.000	0.000	0.000	0.000
157	A	157	LEU	0	-0.047	-0.020	39.126	0.016	0.016	0.000	0.000	0.000	0.000
158	A	158	GLY	0	0.028	0.032	43.256	-0.006	-0.006	0.000	0.000	0.000	0.000
159	A	159	TYR	0	-0.045	-0.021	37.925	-0.048	-0.048	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.846	0.914	38.947	7.191	7.191	0.000	0.000	0.000	0.000
161	A	161	LEU	-1	-0.845	-0.913	43.710	-6.161	-6.161	0.000	0.000	0.000	0.000

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