FMO DATABASE

FMODB ID: YY1Q2

Calculation Name: 1VGG-A-Xray372

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: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1471294.732098
FMO2-HF: Nuclear repulsion	1410228.567491
FMO2-HF: Total energy	-61066.164608
FMO2-MP2: Total energy	-61246.371623

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.
-24.727	-19.878	19.196	-10.455	-13.592	-0.086

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 : 0 / q_Mulliken : -0.055 / q_NPA : -0.024

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	-0.034	-0.029	2.547	-3.420	-0.064	0.834	-1.694	-2.495	-0.004
4	A	4	LYS	1	0.817	0.895	5.217	0.995	1.062	-0.001	-0.006	-0.060	0.000
5	A	5	LEU	0	-0.016	-0.016	8.590	0.165	0.165	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.010	-0.003	11.029	-0.017	-0.017	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.025	-0.025	14.306	0.041	0.041	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.012	0.002	17.678	0.007	0.007	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.842	-0.889	20.139	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.788	0.881	23.141	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.045	0.029	26.224	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.897	-0.946	29.201	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.040	-0.036	30.408	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.021	0.011	29.459	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	ASN	0	0.007	0.004	28.499	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.003	0.003	23.319	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.010	-0.012	23.526	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.014	0.028	16.393	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.041	0.004	18.557	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.009	0.029	13.888	0.069	0.069	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.025	0.015	17.674	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.053	-0.037	18.708	0.027	0.027	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.088	0.033	20.831	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.017	0.010	23.425	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.868	0.918	25.228	-0.098	-0.098	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.005	-0.001	22.657	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.054	-0.029	25.173	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.897	-0.943	27.167	0.070	0.070	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.701	-0.805	28.843	0.099	0.099	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.004	-0.014	24.434	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	HIS	0	-0.005	0.022	28.988	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.914	-0.969	31.528	0.063	0.063	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.030	0.000	31.026	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.034	-0.022	28.980	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.011	-0.016	33.290	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.051	-0.026	36.409	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.077	-0.029	35.009	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.032	-0.019	36.382	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.034	0.026	38.636	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.004	-0.017	40.942	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.043	0.004	33.589	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.869	0.944	35.588	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.001	-0.015	29.764	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.038	0.032	28.879	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.035	-0.013	24.801	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.016	0.009	22.313	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.019	-0.012	19.470	0.014	0.014	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.038	0.030	16.039	-0.030	-0.030	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.795	-0.873	17.452	0.119	0.119	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.006	-0.005	14.727	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.016	-0.003	15.694	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.049	0.015	18.400	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.858	0.914	21.270	-0.051	-0.051	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.827	0.910	13.427	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.007	0.010	18.697	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.007	-0.001	18.506	0.016	0.016	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.806	0.896	20.892	-0.095	-0.095	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.850	0.871	23.710	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.007	-0.009	26.505	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.014	-0.001	29.250	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	THR	0	-0.032	-0.040	31.870	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.802	-0.888	33.556	0.030	0.030	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.755	-0.843	32.184	0.041	0.041	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.055	0.034	31.245	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.030	-0.005	29.325	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.035	-0.012	27.750	0.007	0.007	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.953	-0.971	26.601	0.029	0.029	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.002	0.003	24.904	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.006	0.005	23.535	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.015	-0.010	21.844	0.010	0.010	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.841	0.901	20.940	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.025	-0.027	19.553	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.016	-0.005	17.170	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.036	-0.016	16.155	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.017	0.000	15.907	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.015	-0.005	13.254	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.008	0.028	11.606	0.019	0.019	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.028	-0.001	10.440	0.055	0.055	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.050	0.019	11.400	-0.041	-0.041	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.030	-0.042	13.398	0.045	0.045	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.005	0.017	13.519	0.005	0.005	0.000	0.000	0.000	0.000
82	A	82	PHE	0	-0.024	-0.014	16.354	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.013	-0.009	19.739	0.015	0.015	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.003	0.011	21.748	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.006	-0.003	25.032	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.003	-0.004	27.225	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.057	0.006	30.594	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.887	-0.949	33.587	0.026	0.026	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.019	-0.002	35.762	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.001	0.006	34.375	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.034	0.013	32.247	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.063	0.019	28.138	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.027	-0.015	30.251	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.006	0.002	32.781	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.053	0.027	30.178	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.017	-0.014	26.168	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.059	-0.021	29.081	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.084	0.039	30.995	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.023	-0.014	25.389	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.915	0.943	25.723	-0.115	-0.115	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.014	0.010	27.334	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.023	0.017	26.866	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.021	0.003	26.770	0.014	0.014	0.000	0.000	0.000	0.000
104	A	104	GLH	0	-0.013	-0.042	24.067	0.004	0.004	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.061	-0.022	22.117	0.027	0.027	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.025	-0.003	17.755	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.904	0.938	11.550	-0.668	-0.668	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.005	-0.012	19.633	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.063	-0.035	13.210	0.049	0.049	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.038	0.012	17.967	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.034	-0.024	20.743	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.053	-0.036	22.824	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.074	0.030	25.916	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	ASN	0	-0.033	-0.010	24.208	-0.015	-0.015	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.028	0.005	23.801	0.005	0.005	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.019	0.009	18.688	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.910	0.953	16.470	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.010	0.007	12.430	0.024	0.024	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.014	0.018	7.984	-0.076	-0.076	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.013	-0.011	7.527	0.220	0.220	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.034	0.019	2.829	-0.442	-1.433	3.666	-1.030	-1.646	0.003
122	A	122	GLU	-1	-0.810	-0.887	3.056	-0.797	0.043	0.080	-0.239	-0.682	0.000
123	A	123	GLU	-1	-0.810	-0.918	1.853	-21.847	-20.610	14.598	-7.439	-8.396	-0.085
124	A	124	GLY	0	0.025	0.017	3.611	0.860	1.049	0.020	-0.031	-0.179	0.000
125	A	125	GLU	-1	-0.888	-0.914	6.793	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.058	-0.028	6.590	0.346	0.346	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.811	0.873	5.858	-0.180	-0.180	0.000	0.000	0.000	0.000
128	A	128	ALA	0	-0.030	-0.009	6.230	0.036	0.036	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.010	0.007	7.628	0.134	0.134	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.052	-0.022	4.492	-0.082	0.069	-0.001	-0.016	-0.134	0.000
131	A	131	GLY	0	-0.001	-0.006	9.040	-0.124	-0.124	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.024	-0.007	12.374	-0.016	-0.016	0.000	0.000	0.000	0.000
133	A	133	MET	0	-0.008	-0.003	13.551	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.784	-0.875	17.513	0.076	0.076	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.005	0.011	20.774	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	136	PHE	0	-0.040	-0.032	22.000	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	137	THR	0	0.021	0.017	22.012	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.006	-0.002	24.206	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	LEU	0	0.008	-0.011	27.589	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	140	GLY	0	0.003	0.007	30.427	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	141	VAL	0	-0.064	-0.035	31.672	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.752	-0.817	34.104	0.025	0.025	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.793	-0.893	36.875	0.010	0.010	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.816	-0.931	40.592	0.021	0.021	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.007	0.014	43.163	0.001	0.001	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.884	-0.952	37.738	0.011	0.011	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.046	-0.020	38.644	0.003	0.003	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.033	-0.024	40.538	0.002	0.002	0.000	0.000	0.000	0.000
149	A	149	TRP	0	0.027	0.019	39.973	0.001	0.001	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.810	0.855	36.527	-0.028	-0.028	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.771	0.884	40.025	-0.019	-0.019	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.772	-0.846	42.543	0.019	0.019	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.033	0.022	38.798	0.001	0.001	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.012	-0.018	37.701	0.001	0.001	0.000	0.000	0.000	0.000
155	A	155	ARG	1	0.789	0.887	41.808	-0.026	-0.026	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.803	0.863	45.018	-0.017	-0.017	0.000	0.000	0.000	0.000
157	A	157	LEU	0	-0.006	0.004	39.246	0.000	0.000	0.000	0.000	0.000	0.000
158	A	158	GLY	0	0.007	0.017	43.266	0.001	0.001	0.000	0.000	0.000	0.000
159	A	159	TYR	0	0.007	0.007	37.901	0.002	0.002	0.000	0.000	0.000	0.000
160	A	160	LYS	1	0.857	0.917	38.891	-0.040	-0.040	0.000	0.000	0.000	0.000
161	A	161	LEU	0	0.085	0.063	43.653	-0.002	-0.002	0.000	0.000	0.000	0.000

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