FMO DATABASE

FMODB ID: LL229

Calculation Name: 2VVY-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VVY

Chain ID: A

ChEMBL ID:

UniProt ID: P24772

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	142
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1446033.063558
FMO2-HF: Nuclear repulsion	1385729.241045
FMO2-HF: Total energy	-60303.822513
FMO2-MP2: Total energy	-60473.578153

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:7:ACE )

Summations of interaction energy for fragment #1(A:7: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.
1.209	2.233	-0.006	-0.456	-0.562	-0.001

Interaction energy analysis for fragmet #1(A:7:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.022

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	9	VAL	0	0.087	0.067	3.832	0.389	1.413	-0.006	-0.456	-0.562	-0.001
4	A	10	PHE	0	0.048	0.032	6.562	-0.082	-0.082	0.000	0.000	0.000	0.000
5	A	11	SER	0	0.006	-0.021	9.912	0.003	0.003	0.000	0.000	0.000	0.000
6	A	12	PRO	0	-0.010	0.012	11.441	0.025	0.025	0.000	0.000	0.000	0.000
7	A	13	GLN	0	-0.014	0.003	15.125	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	14	HIS	0	0.056	0.013	17.565	0.005	0.005	0.000	0.000	0.000	0.000
9	A	46	CYS	0	-0.093	-0.036	12.093	-0.054	-0.054	0.000	0.000	0.000	0.000
10	A	16	GLY	0	0.012	-0.015	16.271	0.021	0.021	0.000	0.000	0.000	0.000
11	A	17	CYS	0	-0.049	-0.009	17.512	0.017	0.017	0.000	0.000	0.000	0.000
12	A	18	ASP	-1	-0.831	-0.921	21.107	-0.092	-0.092	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.881	0.941	23.982	0.089	0.089	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.025	0.024	23.982	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	21	THR	0	0.003	0.005	26.966	0.008	0.008	0.000	0.000	0.000	0.000
16	A	22	SER	0	0.006	0.002	28.990	0.009	0.009	0.000	0.000	0.000	0.000
17	A	23	ILE	0	0.022	0.019	29.575	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	24	ASP	-1	-0.918	-0.972	30.310	-0.081	-0.081	0.000	0.000	0.000	0.000
19	A	25	ASP	-1	-0.928	-0.962	25.310	-0.130	-0.130	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.040	-0.011	25.437	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	27	ARG	1	0.957	0.982	26.309	0.078	0.078	0.000	0.000	0.000	0.000
22	A	28	GLN	0	-0.034	-0.059	19.890	0.012	0.012	0.000	0.000	0.000	0.000
23	A	29	CYS	0	-0.015	0.011	21.583	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	30	LEU	0	0.037	0.007	21.332	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	31	THR	0	0.009	0.008	21.046	0.003	0.003	0.000	0.000	0.000	0.000
26	A	32	GLU	-1	-0.820	-0.902	17.361	-0.247	-0.247	0.000	0.000	0.000	0.000
27	A	33	TYR	0	0.015	0.020	17.255	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	34	ILE	0	0.037	0.027	18.252	0.002	0.002	0.000	0.000	0.000	0.000
29	A	35	TYR	0	0.011	0.027	13.427	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	36	TRP	0	-0.041	-0.023	11.747	0.015	0.015	0.000	0.000	0.000	0.000
31	A	37	SER	0	-0.019	-0.034	14.280	0.011	0.011	0.000	0.000	0.000	0.000
32	A	38	SER	0	-0.026	0.001	15.575	0.026	0.026	0.000	0.000	0.000	0.000
33	A	39	TYR	0	-0.038	-0.057	9.774	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	40	ALA	0	-0.001	0.004	9.634	0.017	0.017	0.000	0.000	0.000	0.000
35	A	41	TYR	0	0.066	0.046	9.837	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	42	ARG	1	0.874	0.939	10.817	-0.092	-0.092	0.000	0.000	0.000	0.000
37	A	43	ASN	0	-0.087	-0.039	5.485	0.004	0.004	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.847	0.938	6.481	0.997	0.997	0.000	0.000	0.000	0.000
39	A	45	GLN	0	0.021	0.010	8.618	0.051	0.051	0.000	0.000	0.000	0.000
40	A	47	ALA	0	0.002	-0.004	15.050	0.023	0.023	0.000	0.000	0.000	0.000
41	A	48	GLY	0	0.040	0.051	17.700	0.014	0.014	0.000	0.000	0.000	0.000
42	A	49	GLN	0	-0.030	-0.039	20.184	0.013	0.013	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.009	0.013	21.592	0.008	0.008	0.000	0.000	0.000	0.000
44	A	51	TYR	0	0.070	-0.002	16.641	0.000	0.000	0.000	0.000	0.000	0.000
45	A	52	SER	0	-0.039	0.004	20.740	0.011	0.011	0.000	0.000	0.000	0.000
46	A	53	THR	0	0.017	0.007	22.833	0.010	0.010	0.000	0.000	0.000	0.000
47	A	54	LEU	0	-0.026	-0.005	21.200	0.005	0.005	0.000	0.000	0.000	0.000
48	A	55	LEU	0	-0.021	-0.004	18.783	0.007	0.007	0.000	0.000	0.000	0.000
49	A	56	SER	0	-0.048	-0.021	23.163	0.009	0.009	0.000	0.000	0.000	0.000
50	A	57	PHE	0	0.046	0.009	26.301	0.003	0.003	0.000	0.000	0.000	0.000
51	A	58	ARG	1	0.918	0.960	24.361	0.010	0.010	0.000	0.000	0.000	0.000
52	A	59	ASP	-1	-0.911	-0.952	27.660	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	60	ASP	-1	-0.865	-0.939	30.824	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	61	ALA	0	-0.022	-0.014	29.711	0.001	0.001	0.000	0.000	0.000	0.000
55	A	62	GLU	-1	-0.892	-0.952	30.352	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	63	LEU	0	-0.092	-0.029	33.094	0.002	0.002	0.000	0.000	0.000	0.000
57	A	64	VAL	0	-0.042	-0.021	35.169	0.001	0.001	0.000	0.000	0.000	0.000
58	A	65	PHE	0	-0.029	-0.029	32.420	0.001	0.001	0.000	0.000	0.000	0.000
59	A	66	ILE	0	-0.041	-0.017	35.820	0.003	0.003	0.000	0.000	0.000	0.000
60	A	67	ASP	-1	-0.817	-0.898	33.005	0.003	0.003	0.000	0.000	0.000	0.000
61	A	68	ILE	0	0.018	-0.006	27.886	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	69	ARG	1	0.905	0.966	26.976	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.816	-0.923	29.894	0.012	0.012	0.000	0.000	0.000	0.000
64	A	71	LEU	0	0.010	0.017	32.555	0.000	0.000	0.000	0.000	0.000	0.000
65	A	72	VAL	0	-0.029	-0.014	26.373	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	73	LYS	1	0.751	0.875	29.138	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	74	ASN	0	-0.082	-0.039	30.697	0.000	0.000	0.000	0.000	0.000	0.000
68	A	75	MET	0	0.003	0.018	31.034	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	76	PRO	0	0.078	0.052	31.793	0.001	0.001	0.000	0.000	0.000	0.000
70	A	77	TRP	0	-0.013	-0.028	27.576	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	78	ASP	-1	-0.939	-0.959	28.916	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	79	ASP	-1	-0.868	-0.942	30.578	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	80	VAL	0	-0.005	-0.009	29.537	0.000	0.000	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.838	0.900	32.230	0.037	0.037	0.000	0.000	0.000	0.000
75	A	82	ASP	-1	-0.850	-0.915	35.872	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	83	CYS	0	-0.037	-0.011	32.042	0.001	0.001	0.000	0.000	0.000	0.000
77	A	84	ALA	0	-0.035	-0.024	34.247	0.000	0.000	0.000	0.000	0.000	0.000
78	A	85	GLU	-1	-0.901	-0.961	35.483	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	86	ILE	0	0.001	0.009	36.016	0.001	0.001	0.000	0.000	0.000	0.000
80	A	87	ILE	0	-0.010	-0.020	31.993	0.001	0.001	0.000	0.000	0.000	0.000
81	A	88	ARG	1	0.908	0.967	36.502	0.031	0.031	0.000	0.000	0.000	0.000
82	A	89	CYS	0	-0.049	-0.013	39.675	0.002	0.002	0.000	0.000	0.000	0.000
83	A	90	TYR	0	-0.062	-0.031	37.953	0.002	0.002	0.000	0.000	0.000	0.000
84	A	91	ILE	0	-0.055	-0.034	35.761	0.000	0.000	0.000	0.000	0.000	0.000
85	A	92	PRO	0	0.014	0.020	39.808	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	93	ASP	-1	-0.944	-0.968	42.783	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	94	GLU	-1	-0.883	-0.953	40.259	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	95	GLN	0	-0.120	-0.060	40.719	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	96	LYS	1	0.917	0.975	36.062	0.040	0.040	0.000	0.000	0.000	0.000
90	A	97	THR	0	-0.030	-0.030	39.508	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	98	ILE	0	0.022	-0.007	34.795	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	99	ARG	1	0.959	0.987	34.615	0.021	0.021	0.000	0.000	0.000	0.000
93	A	100	GLU	-1	-0.783	-0.887	34.658	-0.028	-0.028	0.000	0.000	0.000	0.000
94	A	101	ILE	0	0.007	0.006	31.902	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	102	SER	0	-0.025	-0.019	30.374	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	103	ALA	0	0.033	0.029	29.828	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	104	ILE	0	0.025	0.019	30.217	0.000	0.000	0.000	0.000	0.000	0.000
98	A	105	ILE	0	-0.017	-0.016	25.466	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	106	GLY	0	0.004	0.000	25.908	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.002	-0.006	26.167	0.002	0.002	0.000	0.000	0.000	0.000
101	A	108	CYS	0	-0.032	0.001	25.536	0.003	0.003	0.000	0.000	0.000	0.000
102	A	109	ALA	0	0.035	0.008	21.706	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	110	TYR	0	-0.013	0.000	21.650	0.005	0.005	0.000	0.000	0.000	0.000
104	A	111	ALA	0	0.014	0.007	23.160	0.007	0.007	0.000	0.000	0.000	0.000
105	A	112	ALA	0	-0.001	-0.006	19.940	0.005	0.005	0.000	0.000	0.000	0.000
106	A	113	THR	0	-0.029	-0.019	17.886	0.000	0.000	0.000	0.000	0.000	0.000
107	A	114	TYR	0	-0.103	-0.047	19.513	0.016	0.016	0.000	0.000	0.000	0.000
108	A	115	TRP	0	0.004	-0.005	21.927	0.011	0.011	0.000	0.000	0.000	0.000
109	A	116	GLY	0	-0.016	0.020	17.630	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	117	GLY	0	-0.028	-0.012	16.265	0.015	0.015	0.000	0.000	0.000	0.000
111	A	118	GLU	-1	-0.997	-1.012	10.588	0.299	0.299	0.000	0.000	0.000	0.000
112	A	119	ASP	-1	-0.774	-0.877	9.580	0.183	0.183	0.000	0.000	0.000	0.000
113	A	120	HIS	1	0.773	0.873	10.889	-0.120	-0.120	0.000	0.000	0.000	0.000
114	A	121	PRO	0	0.025	0.017	13.663	0.014	0.014	0.000	0.000	0.000	0.000
115	A	122	THR	0	-0.022	-0.025	16.781	0.008	0.008	0.000	0.000	0.000	0.000
116	A	123	SER	0	0.034	-0.003	20.373	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	124	ASN	0	0.051	0.031	23.617	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	125	SER	0	0.012	0.014	19.069	0.000	0.000	0.000	0.000	0.000	0.000
119	A	126	LEU	0	-0.048	-0.028	19.201	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	127	ASN	0	0.000	-0.024	22.175	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	128	ALA	0	0.014	0.020	23.472	0.000	0.000	0.000	0.000	0.000	0.000
122	A	129	LEU	0	-0.040	-0.018	20.997	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	130	PHE	0	-0.018	-0.026	24.197	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	131	VAL	0	0.044	0.035	27.525	0.002	0.002	0.000	0.000	0.000	0.000
125	A	132	MET	0	-0.008	-0.009	25.023	0.000	0.000	0.000	0.000	0.000	0.000
126	A	133	LEU	0	-0.087	-0.051	26.083	0.000	0.000	0.000	0.000	0.000	0.000
127	A	134	GLU	-1	-0.879	-0.916	29.762	-0.040	-0.040	0.000	0.000	0.000	0.000
128	A	135	MET	0	-0.035	-0.006	32.238	0.003	0.003	0.000	0.000	0.000	0.000
129	A	136	LEU	0	-0.063	-0.011	29.644	0.001	0.001	0.000	0.000	0.000	0.000
130	A	137	ASN	0	0.049	0.036	33.463	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	138	TYR	0	-0.015	-0.048	34.750	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	139	VAL	0	0.012	0.007	35.790	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	140	ASP	-1	-0.743	-0.878	34.499	-0.043	-0.043	0.000	0.000	0.000	0.000
134	A	141	TYR	0	-0.002	-0.019	28.839	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	142	ASN	0	0.041	-0.003	32.748	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	143	ILE	0	-0.044	-0.004	35.441	0.000	0.000	0.000	0.000	0.000	0.000
137	A	144	ILE	0	0.005	0.008	29.825	0.000	0.000	0.000	0.000	0.000	0.000
138	A	145	PHE	0	0.048	0.009	29.993	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	146	ARG	1	0.899	0.953	31.650	0.050	0.050	0.000	0.000	0.000	0.000
140	A	147	ARG	1	0.796	0.889	30.465	0.047	0.047	0.000	0.000	0.000	0.000
141	A	148	MET	0	-0.052	-0.017	25.208	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	149	ASN	-1	-0.906	-0.946	28.266	-0.074	-0.074	0.000	0.000	0.000	0.000

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