FMO DATABASE

FMODB ID: 9Y662

Calculation Name: 2VVX-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VVX

Chain ID: A

ChEMBL ID:

UniProt ID: Q01220

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	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1688611.90747
FMO2-HF: Nuclear repulsion	1623101.917528
FMO2-HF: Total energy	-65509.989942
FMO2-MP2: Total energy	-65698.309688

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:39:ACE )

Summations of interaction energy for fragment #1(A:39:ACE )

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.
0.695	1.571	-0.005	-0.401	-0.47	-0.001

Interaction energy analysis for fragmet #1(A:39:ACE )

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 : -0.011

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	41	LYS	1	0.866	0.948	3.839	1.384	2.260	-0.005	-0.401	-0.470	-0.001
4	A	42	PRO	0	-0.041	-0.018	6.664	-0.034	-0.034	0.000	0.000	0.000	0.000
5	A	43	ASP	-1	-0.773	-0.854	10.046	-0.380	-0.380	0.000	0.000	0.000	0.000
6	A	44	TYR	0	-0.069	-0.093	11.225	0.042	0.042	0.000	0.000	0.000	0.000
7	A	45	LEU	0	-0.010	0.026	15.761	0.045	0.045	0.000	0.000	0.000	0.000
8	A	46	GLU	-1	-0.894	-0.972	18.082	-0.118	-0.118	0.000	0.000	0.000	0.000
9	A	47	TYR	0	-0.048	-0.003	13.054	0.010	0.010	0.000	0.000	0.000	0.000
10	A	48	ASP	-1	-0.875	-0.950	17.560	-0.075	-0.075	0.000	0.000	0.000	0.000
11	A	49	ASP	-1	-0.929	-0.950	16.363	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	50	LEU	0	-0.019	-0.040	16.194	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	51	LEU	0	-0.001	0.005	12.403	0.030	0.030	0.000	0.000	0.000	0.000
14	A	52	ASP	-1	-0.807	-0.917	14.656	0.052	0.052	0.000	0.000	0.000	0.000
15	A	53	ARG	1	0.899	0.962	8.817	0.004	0.004	0.000	0.000	0.000	0.000
16	A	54	ASP	-1	-0.781	-0.865	9.965	-0.218	-0.218	0.000	0.000	0.000	0.000
17	A	55	GLU	-1	-0.887	-0.962	10.659	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	56	MET	0	0.041	0.029	13.033	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	57	PHE	0	0.034	0.004	16.055	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	58	THR	0	0.043	0.024	11.267	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	59	ILE	0	0.011	0.018	14.409	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	60	LEU	0	-0.020	-0.015	16.243	0.008	0.008	0.000	0.000	0.000	0.000
23	A	61	GLU	-1	-0.959	-0.993	14.954	-0.307	-0.307	0.000	0.000	0.000	0.000
24	A	62	GLU	-1	-0.819	-0.926	13.264	-0.446	-0.446	0.000	0.000	0.000	0.000
25	A	63	TYR	0	0.027	0.031	17.663	0.020	0.020	0.000	0.000	0.000	0.000
26	A	64	PHE	0	-0.014	-0.031	20.761	0.015	0.015	0.000	0.000	0.000	0.000
27	A	65	MET	0	-0.043	0.001	16.952	0.011	0.011	0.000	0.000	0.000	0.000
28	A	66	TYR	0	-0.011	-0.053	16.474	0.033	0.033	0.000	0.000	0.000	0.000
29	A	67	ARG	1	0.749	0.847	22.412	0.104	0.104	0.000	0.000	0.000	0.000
30	A	68	GLY	0	0.020	-0.008	25.027	0.013	0.013	0.000	0.000	0.000	0.000
31	A	69	LEU	0	-0.089	-0.042	22.708	0.009	0.009	0.000	0.000	0.000	0.000
32	A	70	LEU	0	-0.014	-0.007	22.848	0.008	0.008	0.000	0.000	0.000	0.000
33	A	71	GLY	0	-0.034	-0.005	26.843	0.012	0.012	0.000	0.000	0.000	0.000
34	A	72	LEU	0	0.011	-0.011	27.412	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	73	ARG	1	0.880	0.952	29.523	0.071	0.071	0.000	0.000	0.000	0.000
36	A	74	ILE	0	0.036	0.008	24.670	0.001	0.001	0.000	0.000	0.000	0.000
37	A	75	LYS	1	0.862	0.942	22.227	0.127	0.127	0.000	0.000	0.000	0.000
38	A	76	TYR	0	0.013	0.008	22.953	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	77	GLY	0	0.021	0.022	21.089	0.011	0.011	0.000	0.000	0.000	0.000
40	A	78	ARG	1	0.921	0.935	22.155	0.054	0.054	0.000	0.000	0.000	0.000
41	A	79	LEU	0	0.017	0.030	17.273	0.006	0.006	0.000	0.000	0.000	0.000
42	A	80	PHE	0	0.063	0.016	18.415	0.008	0.008	0.000	0.000	0.000	0.000
43	A	81	ASN	0	-0.037	-0.018	22.592	0.007	0.007	0.000	0.000	0.000	0.000
44	A	82	GLU	-1	-0.829	-0.916	24.217	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	83	ILE	0	-0.011	-0.005	20.763	0.004	0.004	0.000	0.000	0.000	0.000
46	A	84	LYS	1	0.904	0.963	25.324	0.079	0.079	0.000	0.000	0.000	0.000
47	A	85	LYS	1	0.818	0.907	27.908	0.052	0.052	0.000	0.000	0.000	0.000
48	A	86	PHE	0	0.000	-0.011	25.150	0.005	0.005	0.000	0.000	0.000	0.000
49	A	87	ASP	-1	-0.795	-0.898	30.160	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	88	ASN	0	-0.043	-0.025	32.598	0.002	0.002	0.000	0.000	0.000	0.000
51	A	89	ASP	-1	-0.900	-0.936	32.803	-0.038	-0.038	0.000	0.000	0.000	0.000
52	A	90	ALA	0	-0.024	-0.021	32.983	0.002	0.002	0.000	0.000	0.000	0.000
53	A	91	GLU	-1	-0.973	-0.971	34.963	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	92	GLU	-1	-0.982	-0.985	38.174	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	93	GLN	0	-0.086	-0.036	36.176	0.001	0.001	0.000	0.000	0.000	0.000
56	A	94	PHE	0	-0.066	-0.062	33.913	0.001	0.001	0.000	0.000	0.000	0.000
57	A	95	GLY	0	0.046	0.047	39.067	0.000	0.000	0.000	0.000	0.000	0.000
58	A	96	THR	0	0.042	0.021	39.535	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	97	ILE	0	0.040	0.012	36.044	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	98	GLU	-1	-0.894	-0.969	39.244	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	99	GLU	-1	-0.937	-0.943	42.569	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	100	LEU	0	0.035	0.016	37.361	0.000	0.000	0.000	0.000	0.000	0.000
63	A	101	LYS	1	0.920	0.975	40.078	0.052	0.052	0.000	0.000	0.000	0.000
64	A	102	GLN	0	-0.090	-0.064	40.949	0.001	0.001	0.000	0.000	0.000	0.000
65	A	103	LYS	1	0.940	0.960	43.576	0.034	0.034	0.000	0.000	0.000	0.000
66	A	104	LEU	0	0.008	0.006	37.530	0.000	0.000	0.000	0.000	0.000	0.000
67	A	105	ARG	1	0.913	0.970	40.561	0.043	0.043	0.000	0.000	0.000	0.000
68	A	106	LEU	0	0.034	0.032	35.785	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	107	ASN	0	0.030	-0.009	37.375	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	108	SER	0	-0.051	-0.011	39.165	0.000	0.000	0.000	0.000	0.000	0.000
71	A	109	GLU	-1	-0.883	-0.951	38.963	-0.059	-0.059	0.000	0.000	0.000	0.000
72	A	110	GLU	-1	-0.834	-0.925	38.214	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	111	GLY	0	-0.040	0.000	37.666	0.000	0.000	0.000	0.000	0.000	0.000
74	A	112	ALA	0	-0.022	-0.030	32.411	0.000	0.000	0.000	0.000	0.000	0.000
75	A	113	ASP	-1	-0.889	-0.953	34.125	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	114	ASN	0	-0.006	-0.009	35.917	0.003	0.003	0.000	0.000	0.000	0.000
77	A	115	PHE	0	0.012	-0.008	30.145	0.001	0.001	0.000	0.000	0.000	0.000
78	A	116	ILE	0	-0.061	-0.033	30.159	0.000	0.000	0.000	0.000	0.000	0.000
79	A	117	ASP	-1	-0.918	-0.956	33.745	-0.041	-0.041	0.000	0.000	0.000	0.000
80	A	118	TYR	0	0.053	0.025	36.306	0.002	0.002	0.000	0.000	0.000	0.000
81	A	119	ILE	0	-0.012	-0.004	30.972	0.002	0.002	0.000	0.000	0.000	0.000
82	A	120	LYS	1	0.901	0.938	33.069	0.053	0.053	0.000	0.000	0.000	0.000
83	A	121	VAL	0	0.015	0.015	35.352	0.003	0.003	0.000	0.000	0.000	0.000
84	A	122	GLN	0	0.002	0.005	35.589	0.004	0.004	0.000	0.000	0.000	0.000
85	A	123	LYS	1	0.858	0.940	30.452	0.040	0.040	0.000	0.000	0.000	0.000
86	A	124	GLN	0	-0.103	-0.049	35.398	0.002	0.002	0.000	0.000	0.000	0.000
87	A	125	ASP	-1	-0.887	-0.937	38.566	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	126	ILE	0	-0.076	-0.021	35.934	0.002	0.002	0.000	0.000	0.000	0.000
89	A	127	VAL	0	-0.004	0.004	38.579	0.001	0.001	0.000	0.000	0.000	0.000
90	A	128	LYS	1	0.925	0.946	35.524	0.010	0.010	0.000	0.000	0.000	0.000
91	A	129	LEU	0	0.003	0.019	30.940	0.000	0.000	0.000	0.000	0.000	0.000
92	A	130	THR	0	-0.034	-0.020	33.126	0.003	0.003	0.000	0.000	0.000	0.000
93	A	131	VAL	0	0.036	-0.014	27.425	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	132	TYR	0	0.017	-0.006	29.728	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	133	ASP	-1	-0.691	-0.808	32.287	-0.032	-0.032	0.000	0.000	0.000	0.000
96	A	134	CYS	0	-0.089	-0.043	27.574	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	135	ILE	0	-0.014	-0.007	27.445	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	136	SER	0	0.090	0.040	29.141	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	137	MET	0	-0.038	0.000	28.139	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	138	ILE	0	0.005	-0.005	24.267	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	139	GLY	0	0.048	0.022	27.930	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	140	LEU	0	0.003	0.009	30.241	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	141	CYS	0	-0.067	-0.034	27.915	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	142	ALA	0	-0.041	-0.008	28.049	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	143	CYS	0	0.038	0.017	29.101	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	144	VAL	0	0.000	-0.003	31.936	0.001	0.001	0.000	0.000	0.000	0.000
107	A	145	VAL	0	-0.045	-0.026	27.008	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	146	ASP	-1	-0.793	-0.865	30.357	-0.090	-0.090	0.000	0.000	0.000	0.000
109	A	147	VAL	0	-0.059	-0.019	32.425	0.002	0.002	0.000	0.000	0.000	0.000
110	A	148	TRP	0	-0.002	-0.021	29.995	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	149	ARG	1	0.838	0.933	29.254	0.098	0.098	0.000	0.000	0.000	0.000
112	A	150	ASN	0	-0.064	-0.040	32.073	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	151	GLU	-1	-0.923	-0.946	35.583	-0.059	-0.059	0.000	0.000	0.000	0.000
114	A	152	LYS	1	0.889	0.944	33.371	0.076	0.076	0.000	0.000	0.000	0.000
115	A	153	LEU	0	-0.009	0.010	33.207	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	154	PHE	0	0.056	0.006	28.229	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	155	SER	0	-0.030	-0.013	27.077	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	156	ARG	1	0.867	0.935	27.541	0.071	0.071	0.000	0.000	0.000	0.000
119	A	157	TRP	0	0.093	0.048	19.811	0.005	0.005	0.000	0.000	0.000	0.000
120	A	158	LYS	1	0.910	0.966	21.688	0.174	0.174	0.000	0.000	0.000	0.000
121	A	159	TYR	0	-0.007	-0.011	25.013	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	160	CYS	0	0.027	0.033	25.457	0.009	0.009	0.000	0.000	0.000	0.000
123	A	161	LEU	0	0.029	0.038	20.079	0.005	0.005	0.000	0.000	0.000	0.000
124	A	162	ARG	1	0.909	0.953	23.579	0.102	0.102	0.000	0.000	0.000	0.000
125	A	163	ALA	0	0.040	0.016	25.905	0.008	0.008	0.000	0.000	0.000	0.000
126	A	164	ILE	0	0.033	0.006	22.719	0.007	0.007	0.000	0.000	0.000	0.000
127	A	165	LYS	1	0.916	0.965	19.556	0.153	0.153	0.000	0.000	0.000	0.000
128	A	166	LEU	0	-0.061	-0.012	24.569	0.009	0.009	0.000	0.000	0.000	0.000
129	A	167	PHE	0	-0.012	-0.025	27.956	0.007	0.007	0.000	0.000	0.000	0.000
130	A	168	ILE	0	-0.018	-0.018	24.488	0.007	0.007	0.000	0.000	0.000	0.000
131	A	169	ASN	0	0.017	0.021	24.388	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	170	ASP	-1	-0.779	-0.917	19.916	-0.054	-0.054	0.000	0.000	0.000	0.000
133	A	171	HIS	0	-0.036	-0.012	22.013	0.002	0.002	0.000	0.000	0.000	0.000
134	A	172	MET	0	-0.026	-0.025	24.544	0.004	0.004	0.000	0.000	0.000	0.000
135	A	173	LEU	0	0.012	0.006	19.327	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	174	ASP	-1	-0.857	-0.918	19.491	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	175	LYS	1	0.867	0.932	21.595	0.010	0.010	0.000	0.000	0.000	0.000
138	A	176	ILE	0	0.011	0.001	22.836	0.001	0.001	0.000	0.000	0.000	0.000
139	A	177	LYS	1	0.904	0.950	14.711	0.013	0.013	0.000	0.000	0.000	0.000
140	A	178	SER	0	-0.003	-0.001	21.003	0.006	0.006	0.000	0.000	0.000	0.000
141	A	179	ILE	0	-0.040	-0.011	23.190	0.003	0.003	0.000	0.000	0.000	0.000
142	A	180	LEU	0	0.005	-0.010	21.556	0.001	0.001	0.000	0.000	0.000	0.000
143	A	181	GLN	0	-0.037	-0.016	18.059	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	182	ASN	0	0.000	-0.001	22.438	0.007	0.007	0.000	0.000	0.000	0.000
145	A	183	ARG	1	0.924	0.961	26.123	0.037	0.037	0.000	0.000	0.000	0.000
146	A	184	LEU	0	0.016	0.007	20.878	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	185	VAL	0	0.025	0.025	24.113	0.002	0.002	0.000	0.000	0.000	0.000
148	A	186	TYR	0	-0.002	0.000	26.173	0.003	0.003	0.000	0.000	0.000	0.000
149	A	187	VAL	0	-0.010	0.000	26.913	0.000	0.000	0.000	0.000	0.000	0.000
150	A	188	GLU	-1	-0.841	-0.908	25.265	-0.014	-0.014	0.000	0.000	0.000	0.000
151	A	189	MET	0	-0.027	-0.026	27.970	0.002	0.002	0.000	0.000	0.000	0.000
152	A	190	SER	0	-0.041	-0.026	31.351	0.000	0.000	0.000	0.000	0.000	0.000
153	A	191	LYS	1	0.753	0.887	26.206	0.019	0.019	0.000	0.000	0.000	0.000
154	A	192	HIS	0	-0.070	-0.022	28.060	0.000	0.000	0.000	0.000	0.000	0.000
155	A	193	NME	0	-0.014	-0.001	33.015	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:39:ACE )