FMO DATABASE

FMODB ID: J3NL9

Calculation Name: 2VVY-A-Xray372

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: 2023-06-19

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1441276.943754
FMO2-HF: Nuclear repulsion	1381123.980551
FMO2-HF: Total energy	-60152.963203
FMO2-MP2: Total energy	-60322.2858

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:8:HIS)

Summations of interaction energy for fragment #1(A:8:HIS)

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.
-0.466	1.542	-0.027	-0.888	-1.092	0.003

Interaction energy analysis for fragmet #1(A:8:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / 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	10	PHE	0	0.049	0.030	3.794	-0.793	1.025	-0.028	-0.853	-0.937	0.003
4	A	11	SER	0	0.018	-0.016	6.399	0.611	0.611	0.000	0.000	0.000	0.000
5	A	12	PRO	0	-0.016	0.007	8.048	-0.195	-0.195	0.000	0.000	0.000	0.000
6	A	13	GLN	0	-0.021	0.001	11.846	0.051	0.051	0.000	0.000	0.000	0.000
7	A	14	HIS	0	0.042	-0.017	13.995	0.028	0.028	0.000	0.000	0.000	0.000
8	A	15	CYS	0	-0.081	-0.036	11.440	0.119	0.119	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.020	-0.007	13.879	0.041	0.041	0.000	0.000	0.000	0.000
10	A	17	CYS	0	-0.053	0.000	15.480	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	18	ASP	-1	-0.778	-0.890	18.761	0.267	0.267	0.000	0.000	0.000	0.000
12	A	19	ARG	1	0.811	0.905	22.023	-0.143	-0.143	0.000	0.000	0.000	0.000
13	A	20	LEU	0	0.027	0.022	20.960	0.001	0.001	0.000	0.000	0.000	0.000
14	A	21	THR	0	-0.027	-0.013	24.054	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	22	SER	0	-0.007	-0.028	25.586	0.002	0.002	0.000	0.000	0.000	0.000
16	A	23	ILE	0	-0.021	-0.003	26.232	0.013	0.013	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.886	-0.930	26.303	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	25	ASP	-1	-0.888	-0.945	21.859	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	26	VAL	0	-0.026	-0.010	22.060	0.020	0.020	0.000	0.000	0.000	0.000
20	A	27	ARG	1	0.952	0.983	23.180	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	28	GLN	0	-0.015	-0.015	16.046	0.016	0.016	0.000	0.000	0.000	0.000
22	A	29	CYS	0	-0.019	0.011	18.415	0.027	0.027	0.000	0.000	0.000	0.000
23	A	30	LEU	0	0.055	0.010	18.481	0.039	0.039	0.000	0.000	0.000	0.000
24	A	31	THR	0	-0.009	-0.015	17.731	0.023	0.023	0.000	0.000	0.000	0.000
25	A	32	GLU	-1	-0.822	-0.908	14.224	0.069	0.069	0.000	0.000	0.000	0.000
26	A	33	TYR	0	0.004	0.009	14.638	0.058	0.058	0.000	0.000	0.000	0.000
27	A	34	ILE	0	0.037	0.029	16.315	0.065	0.065	0.000	0.000	0.000	0.000
28	A	35	TYR	0	0.001	0.012	10.446	0.051	0.051	0.000	0.000	0.000	0.000
29	A	36	TRP	0	-0.021	-0.018	10.164	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.016	-0.026	13.005	0.128	0.128	0.000	0.000	0.000	0.000
31	A	38	SER	0	-0.009	0.011	14.016	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	39	TYR	0	-0.013	-0.030	7.824	-0.054	-0.054	0.000	0.000	0.000	0.000
33	A	40	ALA	0	-0.002	0.002	8.607	0.193	0.193	0.000	0.000	0.000	0.000
34	A	41	TYR	0	0.047	0.037	9.248	0.423	0.423	0.000	0.000	0.000	0.000
35	A	42	ARG	1	0.762	0.867	10.720	-0.937	-0.937	0.000	0.000	0.000	0.000
36	A	43	ASN	0	-0.041	-0.024	6.226	-0.082	-0.082	0.000	0.000	0.000	0.000
37	A	44	ARG	1	0.833	0.932	3.949	-1.596	-1.406	0.001	-0.035	-0.155	0.000
38	A	45	GLN	0	-0.004	0.002	8.392	-0.539	-0.539	0.000	0.000	0.000	0.000
39	A	47	ALA	0	0.005	0.000	14.012	-0.063	-0.063	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.031	0.047	16.787	-0.055	-0.055	0.000	0.000	0.000	0.000
41	A	49	GLN	0	-0.008	-0.033	18.798	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	50	LEU	0	-0.022	0.003	19.344	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	51	TYR	0	0.069	0.005	14.778	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	52	SER	0	0.005	0.018	19.247	0.017	0.017	0.000	0.000	0.000	0.000
45	A	53	THR	0	-0.050	-0.025	21.918	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	54	LEU	0	-0.011	0.017	19.588	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	55	LEU	0	-0.004	0.006	18.177	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	56	SER	0	-0.047	-0.033	22.308	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	57	PHE	0	0.020	-0.009	25.206	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	58	ARG	1	0.837	0.910	25.159	-0.307	-0.307	0.000	0.000	0.000	0.000
51	A	59	ASP	-1	-0.902	-0.954	27.014	0.234	0.234	0.000	0.000	0.000	0.000
52	A	60	ASP	-1	-0.850	-0.924	29.922	0.150	0.150	0.000	0.000	0.000	0.000
53	A	61	ALA	0	-0.018	-0.007	28.709	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.780	-0.890	29.868	0.223	0.223	0.000	0.000	0.000	0.000
55	A	63	LEU	0	-0.087	-0.026	32.645	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	64	VAL	0	-0.035	-0.019	34.094	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	65	PHE	0	-0.029	-0.027	31.450	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	66	ILE	0	-0.038	-0.013	35.053	0.000	0.000	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.837	-0.901	32.926	0.202	0.202	0.000	0.000	0.000	0.000
60	A	68	ILE	0	0.031	0.001	27.350	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	69	ARG	1	0.892	0.962	27.391	-0.262	-0.262	0.000	0.000	0.000	0.000
62	A	70	GLU	-1	-0.822	-0.919	29.636	0.196	0.196	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.024	0.025	31.956	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	72	VAL	0	-0.022	-0.008	25.599	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.728	0.852	28.554	-0.201	-0.201	0.000	0.000	0.000	0.000
66	A	74	ASN	0	-0.085	-0.037	29.924	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	75	MET	0	0.013	0.020	29.991	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	76	PRO	0	0.064	0.051	30.523	0.011	0.011	0.000	0.000	0.000	0.000
69	A	77	TRP	0	-0.004	-0.022	26.000	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	78	ASP	-1	-0.944	-0.965	27.044	0.106	0.106	0.000	0.000	0.000	0.000
71	A	79	ASP	-1	-0.875	-0.944	28.597	0.057	0.057	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.009	-0.013	26.945	0.003	0.003	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.803	0.875	29.865	-0.041	-0.041	0.000	0.000	0.000	0.000
74	A	82	ASP	-1	-0.860	-0.928	33.337	0.082	0.082	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.022	-0.008	30.408	0.008	0.008	0.000	0.000	0.000	0.000
76	A	84	ALA	0	-0.036	-0.025	32.127	0.004	0.004	0.000	0.000	0.000	0.000
77	A	85	GLU	-1	-0.856	-0.918	33.367	0.060	0.060	0.000	0.000	0.000	0.000
78	A	86	ILE	0	0.008	0.008	34.600	0.002	0.002	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.003	-0.017	30.202	0.003	0.003	0.000	0.000	0.000	0.000
80	A	88	ARG	1	0.826	0.909	34.521	-0.063	-0.063	0.000	0.000	0.000	0.000
81	A	89	CYS	0	-0.062	-0.018	37.797	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	90	TYR	0	-0.046	-0.029	36.528	0.001	0.001	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.061	-0.033	34.048	0.000	0.000	0.000	0.000	0.000	0.000
84	A	92	PRO	0	0.007	0.011	38.015	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.945	-0.961	40.812	0.053	0.053	0.000	0.000	0.000	0.000
86	A	94	GLU	-1	-0.808	-0.898	37.143	0.052	0.052	0.000	0.000	0.000	0.000
87	A	95	GLN	0	-0.100	-0.044	38.123	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	96	LYS	1	0.830	0.915	34.205	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	97	THR	0	-0.048	-0.069	37.419	0.000	0.000	0.000	0.000	0.000	0.000
90	A	98	ILE	0	0.005	-0.016	32.722	0.005	0.005	0.000	0.000	0.000	0.000
91	A	99	ARG	1	0.944	0.994	32.722	-0.117	-0.117	0.000	0.000	0.000	0.000
92	A	100	GLU	-1	-0.729	-0.832	33.084	0.099	0.099	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.010	-0.002	29.644	0.007	0.007	0.000	0.000	0.000	0.000
94	A	102	SER	0	-0.019	-0.026	28.555	0.009	0.009	0.000	0.000	0.000	0.000
95	A	103	ALA	0	0.025	0.027	28.275	0.017	0.017	0.000	0.000	0.000	0.000
96	A	104	ILE	0	0.030	0.025	28.184	0.014	0.014	0.000	0.000	0.000	0.000
97	A	105	ILE	0	-0.008	-0.005	23.457	0.009	0.009	0.000	0.000	0.000	0.000
98	A	106	GLY	0	0.007	0.001	24.331	0.022	0.022	0.000	0.000	0.000	0.000
99	A	107	LEU	0	-0.006	-0.008	25.135	0.024	0.024	0.000	0.000	0.000	0.000
100	A	108	CYS	0	-0.044	-0.015	23.905	0.009	0.009	0.000	0.000	0.000	0.000
101	A	109	ALA	0	0.018	0.004	20.584	0.014	0.014	0.000	0.000	0.000	0.000
102	A	110	TYR	0	-0.001	0.000	20.712	0.035	0.035	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.018	0.007	22.567	0.021	0.021	0.000	0.000	0.000	0.000
104	A	112	ALA	0	-0.015	-0.011	18.461	0.005	0.005	0.000	0.000	0.000	0.000
105	A	113	THR	0	-0.045	-0.040	17.774	0.024	0.024	0.000	0.000	0.000	0.000
106	A	114	TYR	0	-0.082	-0.037	18.960	0.025	0.025	0.000	0.000	0.000	0.000
107	A	115	TRP	0	0.007	-0.006	21.010	0.008	0.008	0.000	0.000	0.000	0.000
108	A	116	GLY	0	-0.019	0.026	16.578	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.020	-0.010	15.102	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-0.890	-0.931	11.165	1.264	1.264	0.000	0.000	0.000	0.000
111	A	119	ASP	-1	-0.793	-0.888	8.510	0.826	0.826	0.000	0.000	0.000	0.000
112	A	120	HIS	1	0.791	0.883	9.301	-0.562	-0.562	0.000	0.000	0.000	0.000
113	A	121	PRO	0	0.045	0.029	12.010	0.040	0.040	0.000	0.000	0.000	0.000
114	A	122	THR	0	-0.020	-0.032	14.982	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	123	SER	0	0.036	-0.001	18.574	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	124	ASN	0	0.035	0.026	21.391	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	125	SER	0	-0.010	-0.002	17.175	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	126	LEU	0	-0.029	-0.019	16.084	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	127	ASN	0	0.007	-0.015	19.885	-0.019	-0.019	0.000	0.000	0.000	0.000
120	A	128	ALA	0	0.018	0.021	21.700	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	129	LEU	0	-0.048	-0.018	18.176	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	130	PHE	0	-0.028	-0.027	20.547	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	131	VAL	0	0.036	0.031	24.669	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	132	MET	0	-0.001	-0.004	22.562	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	133	LEU	0	-0.077	-0.048	22.518	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	134	GLU	-1	-0.822	-0.883	26.749	0.038	0.038	0.000	0.000	0.000	0.000
127	A	135	MET	0	-0.034	-0.003	29.641	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	136	LEU	0	-0.052	-0.006	27.189	0.002	0.002	0.000	0.000	0.000	0.000
129	A	137	ASN	0	0.014	-0.005	30.364	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	138	TYR	0	-0.008	-0.040	31.395	0.004	0.004	0.000	0.000	0.000	0.000
131	A	139	VAL	0	-0.001	-0.001	32.442	0.001	0.001	0.000	0.000	0.000	0.000
132	A	140	ASP	-1	-0.735	-0.855	31.700	0.070	0.070	0.000	0.000	0.000	0.000
133	A	141	TYR	0	0.028	-0.011	25.991	0.007	0.007	0.000	0.000	0.000	0.000
134	A	142	ASN	0	0.033	0.002	29.786	0.003	0.003	0.000	0.000	0.000	0.000
135	A	143	ILE	0	-0.006	0.007	32.429	0.003	0.003	0.000	0.000	0.000	0.000
136	A	144	ILE	0	0.037	0.029	27.536	0.004	0.004	0.000	0.000	0.000	0.000
137	A	145	PHE	0	0.039	0.012	26.992	0.013	0.013	0.000	0.000	0.000	0.000
138	A	146	ARG	1	0.839	0.911	29.060	-0.051	-0.051	0.000	0.000	0.000	0.000
139	A	147	ARG	1	0.813	0.895	28.538	-0.164	-0.164	0.000	0.000	0.000	0.000
140	A	148	MET	0	-0.019	0.006	22.651	0.012	0.012	0.000	0.000	0.000	0.000
141	A	149	ASN	0	-0.026	-0.004	25.912	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:HIS)