FMO DATABASE

FMODB ID: YV842

Calculation Name: 3WVA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVA

Chain ID: A

ChEMBL ID:

UniProt ID: Q58649

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1790047.317369
FMO2-HF: Nuclear repulsion	1723814.374666
FMO2-HF: Total energy	-66232.942703
FMO2-MP2: Total energy	-66426.694491

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:MET)

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

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.
-9.175	-3.295	9.764	-4.928	-10.717	-0.046

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.027

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	THR	0	-0.009	-0.007	3.883	-1.752	-0.557	-0.008	-0.440	-0.747	0.003
4	A	4	VAL	0	0.014	0.001	5.736	0.617	0.617	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.011	0.008	8.801	-0.098	-0.098	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.041	-0.040	11.972	0.070	0.070	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.043	0.027	15.302	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.726	-0.796	16.913	-0.369	-0.369	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.036	0.004	20.917	0.009	0.009	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.021	0.004	24.518	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.011	-0.015	20.213	0.015	0.015	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.049	-0.031	21.054	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.020	0.013	17.374	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.038	0.003	16.538	-0.104	-0.104	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.001	0.022	14.751	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.048	0.004	12.616	-0.060	-0.060	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.003	-0.009	11.720	-0.141	-0.141	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.031	-0.019	12.824	-0.048	-0.048	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.003	0.006	8.283	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.022	0.004	8.026	-0.369	-0.369	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.849	0.927	8.464	0.339	0.339	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.016	0.013	9.929	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.038	-0.018	4.464	0.110	0.165	-0.001	-0.003	-0.050	0.000
24	A	24	ALA	0	-0.007	-0.007	5.706	-0.103	-0.103	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.051	-0.015	7.126	0.222	0.222	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.037	-0.015	9.630	0.106	0.106	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.905	-0.961	12.890	-0.184	-0.184	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.904	-0.956	15.806	-0.189	-0.189	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.015	-0.031	13.131	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.910	-0.939	17.770	-0.234	-0.234	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.031	-0.001	17.630	0.031	0.031	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.868	0.957	14.499	0.222	0.222	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.013	-0.040	17.033	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.075	-0.022	17.538	0.026	0.026	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.052	-0.028	11.631	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.009	-0.019	15.973	0.017	0.017	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.788	-0.931	14.727	-0.144	-0.144	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.847	-0.903	13.469	0.217	0.217	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.790	-0.849	12.454	0.106	0.106	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.003	-0.004	10.206	-0.059	-0.059	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.849	0.921	8.866	-0.261	-0.261	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.015	0.002	7.898	0.124	0.124	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.010	-0.006	6.934	0.390	0.390	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.833	0.923	4.312	-0.240	-0.042	-0.001	-0.047	-0.151	0.000
45	A	45	ASN	0	-0.060	-0.027	2.457	-5.290	-3.625	4.135	-2.549	-3.251	-0.020
46	A	46	VAL	0	-0.009	-0.001	2.491	-1.134	-0.388	2.737	-0.568	-2.915	-0.023
47	A	47	ARG	1	0.955	0.972	2.348	-2.220	-0.340	2.890	-1.287	-3.483	-0.006
48	A	48	VAL	0	-0.008	0.005	3.745	0.498	0.639	0.012	-0.034	-0.120	0.000
49	A	49	ILE	0	-0.040	-0.018	6.182	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.001	-0.017	9.363	0.165	0.165	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.030	0.025	12.839	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.028	0.011	14.755	0.054	0.054	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.020	0.009	18.387	0.026	0.026	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.005	-0.008	21.364	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.049	0.019	23.918	0.019	0.019	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.010	-0.004	27.393	0.016	0.016	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.067	0.033	27.977	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.032	0.011	28.560	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.022	-0.006	26.810	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.040	0.005	23.698	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.796	-0.886	24.215	-0.136	-0.136	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.942	0.964	25.884	0.146	0.146	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.009	0.003	20.830	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.028	-0.006	18.861	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.821	-0.864	21.795	-0.202	-0.202	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.038	-0.013	23.287	0.013	0.013	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.787	0.874	26.507	0.105	0.105	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.035	-0.026	26.309	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.026	0.041	30.304	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.789	-0.898	33.345	-0.102	-0.102	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.041	-0.023	35.210	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.773	-0.853	36.251	-0.073	-0.073	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.017	-0.014	37.104	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.007	-0.004	38.230	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.002	-0.010	33.430	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.925	0.958	36.991	0.093	0.093	0.000	0.000	0.000	0.000
77	A	77	TYR	0	0.012	0.012	32.991	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.022	-0.009	30.063	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.862	0.954	26.246	0.188	0.188	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.008	-0.002	31.850	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.022	-0.028	29.763	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.046	0.013	34.339	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.717	-0.849	32.733	-0.070	-0.070	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.928	-0.943	32.173	-0.056	-0.056	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.912	0.929	32.207	0.074	0.074	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.775	-0.875	29.172	-0.128	-0.128	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.007	-0.015	27.872	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.926	-0.953	27.643	-0.087	-0.087	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.051	0.003	26.234	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.023	-0.003	23.809	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.898	0.919	22.335	0.064	0.064	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.015	0.009	22.299	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.031	-0.018	21.124	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.020	0.022	18.087	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.788	-0.890	17.723	-0.122	-0.122	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.000	0.000	19.111	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.014	-0.016	15.071	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.794	0.893	12.560	0.102	0.102	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.851	0.921	15.274	0.180	0.180	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.733	0.843	17.317	0.250	0.250	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.020	-0.023	12.160	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.033	-0.005	10.713	-0.045	-0.045	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.015	0.009	8.996	-0.041	-0.041	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.015	0.003	6.429	-0.291	-0.291	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.008	-0.009	9.475	0.150	0.150	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.045	-0.034	11.373	-0.147	-0.147	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.015	-0.012	13.785	0.069	0.069	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.033	0.028	16.763	-0.031	-0.031	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.045	-0.041	20.217	0.027	0.027	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.054	-0.053	22.609	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.064	0.016	26.303	0.009	0.009	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.030	0.008	29.372	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.033	-0.006	32.839	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.029	0.014	34.750	0.004	0.004	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.802	0.883	30.729	0.054	0.054	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.024	0.023	29.109	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.049	-0.028	26.636	0.011	0.011	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.008	-0.002	20.208	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	119	CYS	0	-0.036	0.008	20.212	0.033	0.033	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.018	-0.012	15.396	-0.040	-0.040	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.027	-0.004	16.357	0.051	0.051	0.000	0.000	0.000	0.000
122	A	122	THR	0	0.027	-0.012	13.237	-0.074	-0.074	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.759	-0.857	10.321	0.102	0.102	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.069	-0.031	13.149	0.036	0.036	0.000	0.000	0.000	0.000
125	A	125	ASN	0	-0.047	-0.014	16.742	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.892	0.933	17.857	0.022	0.022	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.053	-0.039	17.480	0.014	0.014	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.008	-0.013	21.522	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.009	-0.006	20.223	0.017	0.017	0.000	0.000	0.000	0.000
130	A	130	THR	0	0.037	0.019	25.734	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.021	-0.024	27.102	0.004	0.004	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.820	-0.894	27.949	-0.062	-0.062	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.015	-0.013	30.294	0.006	0.006	0.000	0.000	0.000	0.000
134	A	134	TYR	0	0.016	0.004	32.329	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.017	0.019	32.740	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	ASN	0	0.035	0.006	34.869	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.027	-0.012	31.138	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.036	-0.021	34.216	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	139	THR	0	0.019	0.003	37.753	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	PHE	0	-0.029	-0.012	34.154	0.001	0.001	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.889	-0.937	35.807	-0.073	-0.073	0.000	0.000	0.000	0.000
142	A	142	ASN	0	0.002	-0.011	34.565	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.015	0.017	30.562	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.935	0.966	26.826	0.154	0.154	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.834	-0.926	28.632	-0.117	-0.117	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.829	0.906	28.450	0.111	0.111	0.000	0.000	0.000	0.000
147	A	147	GLN	0	-0.011	0.003	25.018	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.890	0.943	23.777	0.148	0.148	0.000	0.000	0.000	0.000
149	A	149	ASN	0	0.004	-0.010	24.033	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.040	0.009	23.903	0.003	0.003	0.000	0.000	0.000	0.000
151	A	151	ILE	0	-0.030	-0.019	18.711	-0.011	-0.011	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.856	-0.898	19.433	-0.149	-0.149	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.800	0.883	20.466	0.085	0.085	0.000	0.000	0.000	0.000
154	A	154	GLY	0	0.016	0.002	19.085	0.014	0.014	0.000	0.000	0.000	0.000
155	A	155	ILE	0	-0.011	0.000	14.334	-0.012	-0.012	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.910	0.950	16.063	0.064	0.064	0.000	0.000	0.000	0.000
157	A	157	ARG	1	0.846	0.914	18.003	0.050	0.050	0.000	0.000	0.000	0.000
158	A	158	PHE	0	0.051	0.015	9.053	0.051	0.051	0.000	0.000	0.000	0.000
159	A	159	LEU	0	0.029	0.011	12.333	0.054	0.054	0.000	0.000	0.000	0.000
160	A	160	GLU	-1	-0.847	-0.905	14.474	0.062	0.062	0.000	0.000	0.000	0.000
161	A	161	ILE	0	-0.071	-0.038	14.075	0.057	0.057	0.000	0.000	0.000	0.000
162	A	162	LEU	0	0.010	0.010	7.862	0.069	0.069	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.860	0.908	11.727	0.063	0.063	0.000	0.000	0.000	0.000
164	A	164	LYS	1	0.813	0.914	13.633	-0.081	-0.081	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.731	-0.821	13.445	0.152	0.152	0.000	0.000	0.000	0.000
166	A	166	TYR	0	-0.016	-0.034	8.181	-0.069	-0.069	0.000	0.000	0.000	0.000
167	A	167	PHE	0	-0.004	0.015	6.525	0.235	0.235	0.000	0.000	0.000	0.000

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