FMO DATABASE

FMODB ID: 5J6VZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1795251.120472
FMO2-HF: Nuclear repulsion	1729018.833873
FMO2-HF: Total energy	-66232.286598
FMO2-MP2: Total energy	-66426.110155

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.
-10.513	-3.251	8.613	-5.029	-10.846	-0.042

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 : -0.054 / q_NPA : -0.028

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	-0.015	-0.009	3.897	-1.575	-0.297	-0.003	-0.462	-0.813	0.003
4	A	4	VAL	0	0.024	0.002	5.395	0.588	0.676	-0.001	-0.005	-0.081	0.000
5	A	5	ALA	0	-0.001	0.005	8.567	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.039	-0.050	11.621	0.064	0.064	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.044	0.025	15.000	0.003	0.003	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.719	-0.788	16.510	-0.430	-0.430	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.020	0.029	20.445	0.014	0.014	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.018	-0.001	24.042	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.021	-0.013	19.799	0.016	0.016	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.072	-0.036	20.981	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.018	0.008	17.194	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.014	-0.014	16.460	-0.102	-0.102	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.004	0.012	14.460	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.054	0.004	12.363	-0.074	-0.074	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.030	-0.016	11.655	-0.128	-0.128	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.053	-0.029	12.693	-0.043	-0.043	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.006	0.004	8.085	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.008	-0.002	8.050	-0.390	-0.390	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.940	0.978	8.364	0.382	0.382	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.001	0.002	9.801	0.044	0.044	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.021	-0.008	4.436	0.138	0.192	-0.001	-0.003	-0.050	0.000
24	A	24	ALA	0	-0.070	-0.044	5.504	-0.185	-0.185	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.060	-0.040	7.152	0.253	0.253	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.024	-0.005	9.714	0.142	0.142	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.919	-0.964	12.799	-0.175	-0.175	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.930	-0.966	15.765	-0.198	-0.198	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.024	-0.026	12.882	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.877	-0.920	17.439	-0.253	-0.253	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.008	-0.025	17.471	0.034	0.034	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.925	0.980	14.458	0.235	0.235	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.040	-0.041	16.822	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.045	-0.008	17.473	0.023	0.023	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.068	-0.037	11.579	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.013	-0.014	16.007	0.027	0.027	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.792	-0.934	14.742	-0.158	-0.158	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.887	-0.928	13.502	0.149	0.149	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.781	-0.857	12.484	-0.038	-0.038	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.035	-0.030	10.357	-0.094	-0.094	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.857	0.930	8.799	-0.154	-0.154	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.005	0.006	7.963	0.094	0.094	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.015	-0.002	6.835	0.170	0.170	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.924	0.989	4.350	-0.432	-0.247	-0.001	-0.051	-0.133	0.000
45	A	45	ASN	0	-0.063	-0.027	2.420	-4.848	-3.001	3.064	-1.987	-2.925	-0.019
46	A	46	VAL	0	-0.032	-0.015	2.404	-2.572	-1.041	2.974	-1.312	-3.193	-0.025
47	A	47	ARG	1	0.967	0.986	2.411	-2.133	0.062	2.562	-1.228	-3.529	-0.002
48	A	48	VAL	0	0.001	0.003	3.603	0.451	0.535	0.019	0.019	-0.122	0.001
49	A	49	ILE	0	-0.063	-0.024	6.087	0.078	0.078	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.010	-0.013	9.040	0.175	0.175	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.043	0.035	12.559	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.042	-0.008	14.551	0.063	0.063	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.010	0.005	18.199	0.023	0.023	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.006	-0.006	21.180	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.052	0.028	23.754	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.009	0.000	27.146	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.064	0.035	27.524	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.064	0.029	28.386	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.016	-0.013	26.447	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.054	0.017	23.301	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.844	-0.923	24.014	-0.148	-0.148	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.942	0.976	25.814	0.149	0.149	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.049	-0.019	20.738	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.038	-0.036	18.353	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.877	-0.898	21.511	-0.211	-0.211	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.032	-0.011	22.709	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.829	0.905	25.943	0.120	0.120	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.061	-0.040	25.790	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.028	0.029	29.790	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.829	-0.915	32.986	-0.111	-0.111	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.011	0.000	34.576	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.769	-0.860	35.553	-0.089	-0.089	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.034	-0.019	36.651	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.006	0.001	37.777	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	TYR	0	0.015	-0.020	33.128	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.944	0.976	36.266	0.096	0.096	0.000	0.000	0.000	0.000
77	A	77	TYR	0	0.006	0.009	32.916	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.034	-0.016	29.993	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.864	0.949	25.739	0.210	0.210	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.029	0.007	31.343	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.029	-0.020	29.272	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.011	-0.001	33.739	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.706	-0.835	32.335	-0.098	-0.098	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.943	-0.958	31.821	-0.081	-0.081	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.901	0.916	31.846	0.090	0.090	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.737	-0.846	28.682	-0.156	-0.156	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.011	-0.018	27.428	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.947	-0.971	26.899	-0.118	-0.118	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.063	0.015	25.785	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.033	0.000	23.029	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.912	0.936	21.964	0.100	0.100	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.022	0.002	22.225	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.026	-0.025	20.925	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.000	0.015	17.919	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.797	-0.895	17.521	-0.188	-0.188	0.000	0.000	0.000	0.000
96	A	96	GLY	0	-0.003	0.000	18.880	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.008	-0.011	14.460	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.793	0.911	12.237	0.259	0.259	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.942	0.964	14.504	0.160	0.160	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.761	0.879	16.475	0.255	0.255	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.032	-0.042	11.876	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.045	0.001	10.323	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.016	0.001	8.659	-0.081	-0.081	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.026	-0.009	6.165	-0.421	-0.421	0.000	0.000	0.000	0.000
105	A	105	ILE	0	0.000	-0.005	9.220	0.191	0.191	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.035	-0.021	11.069	-0.147	-0.147	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.014	-0.013	13.061	0.078	0.078	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.024	0.029	16.264	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.024	-0.041	19.715	0.025	0.025	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.091	-0.074	22.131	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.047	0.024	25.741	0.007	0.007	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.006	0.008	28.785	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.043	-0.007	32.222	0.000	0.000	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.029	0.018	34.214	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.831	0.885	30.422	0.082	0.082	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.019	0.016	28.128	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.059	-0.017	26.087	0.010	0.010	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.025	0.002	19.784	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	119	CYS	0	-0.044	0.002	19.793	0.038	0.038	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.019	-0.003	15.019	-0.044	-0.044	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.027	-0.013	16.261	0.058	0.058	0.000	0.000	0.000	0.000
122	A	122	THR	0	0.007	-0.035	12.957	-0.084	-0.084	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.755	-0.849	10.075	-0.100	-0.100	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.073	-0.028	13.105	0.053	0.053	0.000	0.000	0.000	0.000
125	A	125	ASN	0	-0.013	-0.013	16.527	0.002	0.002	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.897	0.941	17.602	0.075	0.075	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.051	-0.034	17.131	0.030	0.030	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.011	-0.013	21.133	-0.027	-0.027	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.017	-0.011	19.791	0.021	0.021	0.000	0.000	0.000	0.000
130	A	130	THR	0	0.051	0.030	25.246	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.062	-0.045	26.629	0.002	0.002	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.783	-0.890	27.449	-0.100	-0.100	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.029	-0.007	30.041	0.009	0.009	0.000	0.000	0.000	0.000
134	A	134	TYR	0	0.034	0.016	31.704	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.008	0.001	32.263	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	ASN	0	0.039	0.005	34.373	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.024	-0.006	30.672	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.014	-0.009	33.842	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	139	THR	0	0.008	-0.006	37.191	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	PHE	0	-0.034	-0.011	34.103	0.001	0.001	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.921	-0.952	35.716	-0.085	-0.085	0.000	0.000	0.000	0.000
142	A	142	ASN	0	0.026	0.006	34.284	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.012	-0.007	30.293	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.966	0.996	27.239	0.162	0.162	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.847	-0.935	28.644	-0.132	-0.132	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.846	0.908	28.123	0.132	0.132	0.000	0.000	0.000	0.000
147	A	147	GLN	0	-0.025	-0.009	24.760	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.929	0.958	24.127	0.162	0.162	0.000	0.000	0.000	0.000
149	A	149	ASN	0	0.002	0.000	23.990	-0.014	-0.014	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.023	0.002	23.711	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	151	ILE	0	-0.024	-0.012	18.601	-0.018	-0.018	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.851	-0.890	19.370	-0.187	-0.187	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.770	0.868	20.397	0.121	0.121	0.000	0.000	0.000	0.000
154	A	154	GLY	0	0.007	-0.008	18.852	0.007	0.007	0.000	0.000	0.000	0.000
155	A	155	ILE	0	0.006	0.014	14.210	-0.023	-0.023	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.927	0.957	16.084	0.118	0.118	0.000	0.000	0.000	0.000
157	A	157	ARG	1	0.823	0.902	18.059	0.120	0.120	0.000	0.000	0.000	0.000
158	A	158	PHE	0	0.039	0.012	8.906	0.047	0.047	0.000	0.000	0.000	0.000
159	A	159	LEU	0	0.032	0.013	12.280	0.021	0.021	0.000	0.000	0.000	0.000
160	A	160	GLU	-1	-0.859	-0.912	14.516	-0.027	-0.027	0.000	0.000	0.000	0.000
161	A	161	ILE	0	-0.030	-0.018	13.923	0.061	0.061	0.000	0.000	0.000	0.000
162	A	162	LEU	0	0.000	0.012	7.706	0.064	0.064	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.872	0.919	11.538	0.179	0.179	0.000	0.000	0.000	0.000
164	A	164	LYS	1	0.830	0.920	13.488	0.029	0.029	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.782	-0.840	13.093	0.055	0.055	0.000	0.000	0.000	0.000
166	A	166	TYR	0	-0.019	-0.038	8.114	-0.058	-0.058	0.000	0.000	0.000	0.000
167	A	167	PHE	0	-0.010	0.009	6.510	0.203	0.203	0.000	0.000	0.000	0.000

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