FMO DATABASE

FMODB ID: GNGL1

Calculation Name: 1VMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VMO

Chain ID: A

ChEMBL ID:

UniProt ID: P41366

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	OptHSide
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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1620849.591893
FMO2-HF: Nuclear repulsion	1556888.653976
FMO2-HF: Total energy	-63960.937917
FMO2-MP2: Total energy	-64144.727587

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:ARG)

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

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.
54.755	61.27	4.33	-3.509	-7.336	-0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.961

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	ARG	1	0.820	0.879	3.339	21.664	23.880	0.074	-0.972	-1.318	-0.002
4	A	4	GLU	-1	-0.809	-0.882	2.460	-47.707	-45.966	2.497	-1.467	-2.770	-0.018
5	A	5	TYR	0	-0.019	-0.036	2.308	4.643	6.013	1.642	-0.654	-2.358	-0.006
6	A	6	THR	0	0.011	-0.010	5.522	-1.917	-1.917	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.011	-0.001	8.311	1.478	1.478	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.027	-0.019	7.870	-1.581	-1.581	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.009	0.005	10.232	1.176	1.176	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.013	-0.016	13.635	-0.450	-0.450	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.000	-0.006	15.962	0.293	0.293	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.015	-0.015	19.774	-0.234	-0.234	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.026	-0.001	22.321	0.083	0.083	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.026	0.006	21.913	-0.470	-0.470	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.040	0.041	22.557	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.085	-0.056	20.322	-1.150	-1.150	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.019	0.022	20.855	-0.684	-0.684	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.086	0.038	20.056	-0.057	-0.057	0.000	0.000	0.000	0.000
19	A	19	LYN	0	-0.035	-0.002	14.398	-0.460	-0.460	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.054	-0.053	11.602	-0.448	-0.448	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.062	0.043	12.361	0.020	0.020	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.004	0.008	7.834	-1.732	-1.732	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.849	0.936	4.276	33.481	33.680	-0.001	-0.025	-0.174	0.000
24	A	24	GLN	0	0.035	0.034	5.948	-1.645	-1.645	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.003	-0.035	3.160	-2.353	-1.364	0.118	-0.391	-0.716	-0.004
26	A	26	CYS	0	-0.002	0.030	7.872	0.559	0.559	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.048	0.035	9.751	-3.392	-3.392	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.050	-0.040	10.528	-1.277	-1.277	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.018	0.004	12.671	0.885	0.885	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.003	-0.004	12.321	-1.996	-1.996	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.095	0.041	14.327	0.479	0.479	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.011	-0.014	15.906	-0.122	-0.122	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.065	0.036	18.848	0.773	0.773	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.021	-0.018	18.767	-0.921	-0.921	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.023	0.025	20.337	0.564	0.564	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.012	-0.015	21.054	-0.669	-0.669	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.797	0.914	22.610	11.842	11.842	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.059	0.028	24.271	-0.142	-0.142	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.740	-0.848	27.402	-8.784	-8.784	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.030	-0.005	30.872	0.078	0.078	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.081	0.052	33.665	0.055	0.055	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.055	-0.035	35.751	0.076	0.076	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.047	0.007	38.053	-0.118	-0.118	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.026	0.000	40.667	0.068	0.068	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.796	0.884	35.005	8.135	8.135	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.875	-0.925	36.709	-7.609	-7.609	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.945	-0.969	33.644	-8.499	-8.499	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.003	-0.012	29.991	-0.128	-0.128	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.017	0.012	26.004	-0.115	-0.115	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.053	-0.006	22.751	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.027	-0.002	22.945	-0.231	-0.231	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.014	-0.014	19.367	-0.489	-0.489	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.011	0.020	16.903	0.399	0.399	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.830	0.894	16.560	13.033	13.033	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.014	-0.003	13.087	0.563	0.563	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.962	0.988	16.523	12.299	12.299	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.023	-0.013	16.468	0.436	0.436	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.751	-0.847	15.021	-18.179	-18.179	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.007	-0.004	18.414	-0.079	-0.079	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.079	-0.043	14.654	-0.042	-0.042	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.000	-0.023	16.461	0.113	0.113	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.041	-0.006	10.431	-0.613	-0.613	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.738	-0.857	13.258	-13.783	-13.783	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.040	-0.041	10.810	-1.079	-1.079	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.001	0.014	12.851	0.100	0.100	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.042	-0.019	15.469	0.204	0.204	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.082	0.042	18.881	0.040	0.040	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.904	0.961	22.357	9.888	9.888	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.010	0.006	25.021	0.470	0.470	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.039	0.025	26.248	-0.334	-0.334	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.039	-0.036	27.797	0.033	0.033	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.047	-0.028	19.208	-0.146	-0.146	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.033	0.036	25.768	0.186	0.186	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.009	0.005	25.794	-0.240	-0.240	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.065	-0.050	19.630	-0.114	-0.114	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.050	0.054	24.167	0.325	0.325	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.071	-0.067	23.231	-0.578	-0.578	0.000	0.000	0.000	0.000
78	A	79	CYS	0	-0.026	-0.009	21.263	-0.559	-0.559	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.006	0.006	24.767	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.014	-0.018	26.241	0.183	0.183	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.066	-0.004	22.834	-0.310	-0.310	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.001	-0.026	17.281	-0.502	-0.502	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.014	0.004	16.954	0.442	0.442	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.061	-0.047	17.016	-0.801	-0.801	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.040	-0.020	17.587	-0.226	-0.226	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.061	0.025	16.232	0.176	0.176	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.009	0.006	20.409	0.104	0.104	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.057	0.018	20.698	-0.042	-0.042	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.886	0.966	23.813	9.354	9.354	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.069	0.035	25.910	-0.263	-0.263	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.860	-0.914	28.024	-8.941	-8.941	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.854	0.924	29.461	9.307	9.307	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.048	0.040	29.783	0.052	0.052	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.005	-0.008	32.086	0.203	0.203	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.012	-0.002	32.006	-0.221	-0.221	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.005	0.011	31.538	-0.192	-0.192	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.076	0.036	31.233	-0.231	-0.231	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.812	-0.902	27.460	-10.117	-10.117	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.874	-0.944	28.051	-9.356	-9.356	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.064	-0.052	25.545	0.095	0.095	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.016	0.021	24.425	-0.557	-0.557	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.048	-0.037	22.053	0.174	0.174	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.012	-0.016	24.171	-0.118	-0.118	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.050	-0.041	25.687	-0.184	-0.184	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.049	-0.019	19.089	-0.315	-0.315	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.013	0.011	23.609	0.491	0.491	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.013	-0.008	17.155	-0.575	-0.575	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.881	0.945	21.709	11.475	11.475	0.000	0.000	0.000	0.000
109	A	111	SER	0	0.004	-0.018	20.195	0.225	0.225	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.801	-0.892	22.657	-11.074	-11.074	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.777	-0.859	25.423	-10.672	-10.672	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.004	0.025	26.914	0.273	0.273	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.026	-0.027	26.079	-0.456	-0.456	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.020	-0.008	23.561	0.267	0.267	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.009	-0.025	25.493	-0.436	-0.436	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.032	0.021	25.672	0.113	0.113	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.865	-0.928	26.487	-9.169	-9.169	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.044	-0.028	28.017	-0.082	-0.082	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.025	0.030	28.886	0.300	0.300	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.085	-0.061	30.364	-0.224	-0.224	0.000	0.000	0.000	0.000
121	A	123	TRP	0	0.112	0.062	32.223	0.111	0.111	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.066	0.038	31.324	-0.294	-0.294	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.856	0.909	30.874	8.594	8.594	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.022	0.010	25.985	-0.184	-0.184	0.000	0.000	0.000	0.000
125	A	127	GLY	0	-0.003	0.018	26.402	0.271	0.271	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.026	-0.023	24.437	0.005	0.005	0.000	0.000	0.000	0.000
127	A	129	TRP	0	-0.016	-0.003	22.473	-0.383	-0.383	0.000	0.000	0.000	0.000
128	A	130	SER	0	0.018	0.028	17.625	0.028	0.028	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.937	0.957	16.825	14.834	14.834	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.866	0.903	17.768	11.928	11.928	0.000	0.000	0.000	0.000
131	A	133	CYS	0	-0.051	-0.013	8.529	1.238	1.238	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.934	0.977	13.491	17.955	17.955	0.000	0.000	0.000	0.000
133	A	135	ILE	0	0.038	0.026	12.106	-1.913	-1.913	0.000	0.000	0.000	0.000
134	A	136	CYS	0	-0.030	-0.001	8.111	-3.590	-3.590	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.073	0.040	7.964	-1.267	-1.267	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.028	0.004	8.972	1.088	1.088	0.000	0.000	0.000	0.000
137	A	139	GLN	0	0.020	-0.005	8.684	-2.241	-2.241	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.019	0.009	10.551	0.377	0.377	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.848	0.937	14.156	14.196	14.196	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.019	-0.017	16.363	0.563	0.563	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.793	-0.905	19.329	-12.156	-12.156	0.000	0.000	0.000	0.000
142	A	144	SER	0	0.015	0.023	22.374	0.298	0.298	0.000	0.000	0.000	0.000
143	A	145	PRO	0	-0.020	0.013	19.174	0.313	0.313	0.000	0.000	0.000	0.000
144	A	146	GLN	0	-0.009	-0.029	22.127	0.049	0.049	0.000	0.000	0.000	0.000
145	A	147	GLY	0	0.012	0.015	24.410	0.359	0.359	0.000	0.000	0.000	0.000
146	A	148	LEU	0	0.016	-0.005	27.253	0.023	0.023	0.000	0.000	0.000	0.000
147	A	149	ARG	1	0.814	0.876	29.392	8.507	8.507	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.903	-0.957	30.427	-8.625	-8.625	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.868	-0.935	28.438	-9.620	-9.620	0.000	0.000	0.000	0.000
150	A	152	THR	0	-0.106	-0.038	24.002	-0.321	-0.321	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.028	0.001	24.103	0.209	0.209	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.042	-0.004	18.013	-0.577	-0.577	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.012	-0.011	20.256	0.529	0.529	0.000	0.000	0.000	0.000
154	A	156	ASN	0	-0.022	-0.017	17.072	-0.320	-0.320	0.000	0.000	0.000	0.000
155	A	157	VAL	0	0.006	-0.002	14.751	-0.376	-0.376	0.000	0.000	0.000	0.000
156	A	158	ARG	1	0.813	0.933	10.214	21.592	21.592	0.000	0.000	0.000	0.000
157	A	159	PHE	0	0.054	0.027	11.025	-0.793	-0.793	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.035	-0.010	6.427	-0.983	-0.983	0.000	0.000	0.000	0.000
159	A	163	LYS	1	0.884	0.929	8.206	33.948	33.948	0.000	0.000	0.000	0.000

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