FMO DATABASE

FMODB ID: 9Y5V2

Calculation Name: 1VMO-A-Xray315

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: 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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1621467.477303
FMO2-HF: Nuclear repulsion	1557508.057394
FMO2-HF: Total energy	-63959.419909
FMO2-MP2: Total energy	-64143.338451

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.
29.596	36.344	4.267	-3.714	-7.302	-0.029

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 : 0.961 / q_NPA : 0.971

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	0.848	0.927	3.178	21.211	23.816	0.135	-1.274	-1.466	-0.003
4	A	4	GLU	-1	-0.947	-0.968	2.596	-52.083	-50.119	2.190	-1.448	-2.706	-0.017
5	A	5	TYR	0	-0.002	-0.034	2.211	5.437	6.639	1.851	-0.675	-2.378	-0.006
6	A	6	THR	0	0.020	-0.007	5.523	-2.087	-2.087	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.016	-0.003	8.414	1.567	1.567	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.030	-0.017	8.125	-1.397	-1.397	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.013	0.003	10.445	1.168	1.168	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.005	-0.029	13.848	-0.283	-0.283	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.015	-0.003	16.194	0.299	0.299	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.033	-0.022	19.794	-0.208	-0.208	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.015	0.025	22.338	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.024	0.005	21.945	-0.463	-0.463	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.047	0.039	22.602	-0.056	-0.056	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.130	-0.071	20.393	-1.109	-1.109	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.012	0.013	20.939	-0.625	-0.625	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.058	0.025	20.139	-0.058	-0.058	0.000	0.000	0.000	0.000
19	A	19	LYN	0	-0.029	-0.002	14.540	-0.584	-0.584	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.068	-0.054	11.645	-0.341	-0.341	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.057	0.039	12.341	0.008	0.008	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.000	0.004	7.764	-1.590	-1.590	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.826	0.917	4.674	31.138	31.297	0.000	-0.016	-0.144	0.000
24	A	24	GLN	0	0.075	0.049	6.024	-1.202	-1.202	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.000	-0.030	3.094	-1.942	-1.124	0.091	-0.301	-0.608	-0.003
26	A	57	CYS	0	0.019	0.038	7.847	0.558	0.558	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.041	0.026	9.666	-3.315	-3.315	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.027	-0.043	10.547	-1.319	-1.319	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.017	-0.006	12.718	0.837	0.837	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.054	-0.059	12.291	-0.997	-0.997	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.073	0.032	14.338	0.543	0.543	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.009	-0.004	15.869	-0.207	-0.207	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.040	0.024	18.830	0.788	0.788	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.024	-0.024	18.766	-0.883	-0.883	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.027	0.028	20.354	0.568	0.568	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.016	-0.019	21.101	-0.640	-0.640	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.864	0.965	22.713	11.724	11.724	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.077	0.035	24.343	-0.131	-0.131	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.816	-0.924	27.480	-8.917	-8.917	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.057	-0.017	30.955	0.113	0.113	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.081	0.050	33.737	0.053	0.053	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.065	-0.046	35.822	0.092	0.092	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.061	0.013	38.138	-0.113	-0.113	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.030	-0.002	40.755	0.068	0.068	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.834	0.914	35.299	7.934	7.934	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.861	-0.921	36.685	-7.533	-7.533	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.950	-0.971	33.741	-8.381	-8.381	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.012	-0.001	30.052	-0.144	-0.144	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.022	0.005	26.148	-0.127	-0.127	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.043	-0.002	22.730	-0.042	-0.042	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.031	0.001	23.055	-0.272	-0.272	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.019	-0.019	19.459	-0.485	-0.485	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.013	0.022	17.001	0.391	0.391	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.882	0.953	16.606	12.739	12.739	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.008	-0.005	13.079	0.569	0.569	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.952	0.987	16.525	12.086	12.086	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.013	-0.007	16.421	0.483	0.483	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.758	-0.852	14.877	-17.741	-17.741	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.012	-0.008	18.342	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.084	-0.048	14.608	-0.067	-0.067	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.002	-0.023	16.429	0.118	0.118	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.049	-0.010	10.677	-0.592	-0.592	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.849	-0.942	13.295	-13.723	-13.723	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.010	-0.024	10.719	-1.259	-1.259	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.030	-0.002	12.939	0.163	0.163	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.039	-0.014	15.445	0.225	0.225	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.063	0.025	18.980	0.055	0.055	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.880	0.935	22.392	9.675	9.675	0.000	0.000	0.000	0.000
69	A	70	TRP	0	-0.028	-0.011	25.000	0.463	0.463	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.064	0.037	26.339	-0.344	-0.344	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.053	-0.044	27.839	0.042	0.042	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.055	-0.027	19.437	-0.157	-0.157	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.043	0.038	25.822	0.190	0.190	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.023	-0.008	25.825	-0.329	-0.329	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.051	-0.042	19.649	-0.118	-0.118	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.056	0.055	24.186	0.322	0.322	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.070	-0.069	23.057	-0.580	-0.580	0.000	0.000	0.000	0.000
78	A	110	CYS	0	-0.053	-0.018	21.388	-0.513	-0.513	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.008	0.006	24.741	0.008	0.008	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.003	-0.007	26.124	0.081	0.081	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.027	-0.003	23.027	-0.342	-0.342	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.008	-0.026	17.624	-0.339	-0.339	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.010	0.003	17.244	0.448	0.448	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.033	-0.027	17.111	-0.786	-0.786	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.052	-0.025	17.727	-0.195	-0.195	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.045	0.021	16.431	0.213	0.213	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.008	0.017	20.602	0.156	0.156	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.069	0.013	20.586	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.895	0.964	23.887	9.270	9.270	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.021	0.010	25.982	-0.123	-0.123	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.826	-0.916	28.097	-8.809	-8.809	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.863	0.930	29.737	9.129	9.129	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.047	0.045	30.126	0.039	0.039	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.011	-0.020	32.139	0.198	0.198	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.029	-0.009	32.072	-0.219	-0.219	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.020	0.022	31.615	-0.179	-0.179	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.092	0.048	31.312	-0.218	-0.218	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.832	-0.925	27.696	-9.880	-9.880	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.864	-0.934	28.114	-9.191	-9.191	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.074	-0.057	25.516	0.065	0.065	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.012	0.023	24.474	-0.557	-0.557	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.050	-0.039	22.183	0.160	0.160	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.021	0.002	24.273	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.020	-0.023	25.804	-0.123	-0.123	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.052	-0.017	19.215	-0.310	-0.310	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.001	0.012	23.648	0.451	0.451	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.013	-0.006	17.097	-0.571	-0.571	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.943	0.986	21.856	11.473	11.473	0.000	0.000	0.000	0.000
109	A	111	SER	0	0.000	0.009	20.939	0.317	0.317	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.821	-0.919	22.724	-10.681	-10.681	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.858	-0.917	25.507	-10.519	-10.519	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.011	0.021	26.981	0.277	0.277	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.027	-0.032	26.200	-0.466	-0.466	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.014	-0.013	23.289	0.267	0.267	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.026	-0.029	25.518	-0.423	-0.423	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.032	0.026	25.716	0.103	0.103	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.880	-0.947	26.530	-9.071	-9.071	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.036	-0.019	28.089	-0.065	-0.065	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.010	0.027	28.713	0.307	0.307	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.114	-0.076	30.442	-0.221	-0.221	0.000	0.000	0.000	0.000
121	A	123	TRP	0	0.108	0.071	32.313	0.096	0.096	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.084	0.039	31.419	-0.288	-0.288	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.838	0.894	30.959	8.583	8.583	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.025	0.018	26.173	-0.195	-0.195	0.000	0.000	0.000	0.000
125	A	127	GLY	0	-0.015	0.000	26.527	0.246	0.246	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.023	-0.026	24.750	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	129	TRP	0	0.001	0.007	22.559	-0.372	-0.372	0.000	0.000	0.000	0.000
128	A	130	SER	0	0.012	0.017	17.871	0.003	0.003	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.934	0.961	17.273	14.868	14.868	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.896	0.920	17.936	11.812	11.812	0.000	0.000	0.000	0.000
131	A	161	CYS	0	-0.046	-0.011	8.711	1.213	1.213	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.920	0.981	13.484	18.151	18.151	0.000	0.000	0.000	0.000
133	A	135	ILE	0	0.024	0.017	12.168	-1.880	-1.880	0.000	0.000	0.000	0.000
134	A	162	CYS	0	-0.028	-0.008	8.177	-3.826	-3.826	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.062	0.034	7.966	-1.229	-1.229	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.025	0.000	9.003	1.085	1.085	0.000	0.000	0.000	0.000
137	A	139	GLN	0	0.024	0.012	8.578	-2.172	-2.172	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.021	0.011	10.656	0.377	0.377	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.908	0.967	14.270	14.380	14.380	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.001	-0.008	16.429	0.545	0.545	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.858	-0.951	19.403	-11.591	-11.591	0.000	0.000	0.000	0.000
142	A	144	SER	0	0.028	0.047	22.455	0.282	0.282	0.000	0.000	0.000	0.000
143	A	145	PRO	0	0.003	0.023	19.352	0.294	0.294	0.000	0.000	0.000	0.000
144	A	146	GLN	0	-0.002	-0.027	22.111	0.094	0.094	0.000	0.000	0.000	0.000
145	A	147	GLY	0	0.017	0.023	24.399	0.359	0.359	0.000	0.000	0.000	0.000
146	A	148	LEU	0	0.022	-0.003	27.240	0.079	0.079	0.000	0.000	0.000	0.000
147	A	149	ARG	1	0.871	0.928	29.372	8.316	8.316	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.955	-0.985	30.546	-8.487	-8.487	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.813	-0.897	28.503	-9.538	-9.538	0.000	0.000	0.000	0.000
150	A	152	THR	0	-0.114	-0.046	23.957	-0.327	-0.327	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.033	0.001	24.232	0.189	0.189	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.054	-0.004	18.106	-0.589	-0.589	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.032	0.002	20.313	0.498	0.498	0.000	0.000	0.000	0.000
154	A	156	ASN	0	-0.001	-0.017	16.960	-0.109	-0.109	0.000	0.000	0.000	0.000
155	A	157	VAL	0	-0.006	-0.001	14.228	-0.377	-0.377	0.000	0.000	0.000	0.000
156	A	158	ARG	1	0.824	0.941	10.125	20.905	20.905	0.000	0.000	0.000	0.000
157	A	159	PHE	0	0.045	0.020	11.080	-0.687	-0.687	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.038	-0.018	6.560	-1.013	-1.013	0.000	0.000	0.000	0.000
159	A	163	LYS	0	0.167	0.107	8.313	11.657	11.657	0.000	0.000	0.000	0.000

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