FMO DATABASE

FMODB ID: 4JZVN

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	OptH
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	-1793914.222261
FMO2-HF: Nuclear repulsion	1727683.047255
FMO2-HF: Total energy	-66231.175005
FMO2-MP2: Total energy	-66425.05886

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.
-12.756	-4.214	7.93	-5.325	-11.144	-0.039

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 : -0.056 / q_NPA : -0.031

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	-0.018	-0.010	3.734	-1.525	-0.010	0.009	-0.571	-0.952	0.003
4	A	4	VAL	0	0.023	0.001	5.125	0.530	0.626	-0.001	-0.006	-0.089	0.000
5	A	5	ALA	0	0.002	0.007	8.269	-0.015	-0.015	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.027	-0.048	11.342	0.053	0.053	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.031	0.027	14.727	0.014	0.014	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.704	-0.785	16.420	-0.478	-0.478	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.054	0.035	20.399	0.026	0.026	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.023	0.006	23.995	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.030	-0.017	19.721	0.019	0.019	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.062	-0.027	20.916	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.012	0.007	17.166	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.048	0.005	16.405	-0.100	-0.100	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.015	0.013	14.392	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.048	0.001	12.299	-0.087	-0.087	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.026	-0.013	11.594	-0.130	-0.130	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.043	-0.024	12.695	-0.043	-0.043	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.001	0.000	7.997	-0.052	-0.052	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.005	-0.002	7.994	-0.390	-0.390	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.941	0.976	8.405	0.396	0.396	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.007	0.002	9.817	0.048	0.048	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.019	-0.010	4.456	0.126	0.181	-0.001	-0.003	-0.050	0.000
24	A	24	ALA	0	-0.077	-0.046	5.524	-0.198	-0.198	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.057	-0.020	7.171	0.263	0.263	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.026	-0.016	9.726	0.139	0.139	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.912	-0.963	12.819	-0.209	-0.209	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.923	-0.963	15.782	-0.224	-0.224	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.041	-0.035	12.934	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.910	-0.944	17.476	-0.272	-0.272	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.002	-0.025	17.407	0.035	0.035	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.938	0.982	14.538	0.297	0.297	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.041	-0.019	16.862	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.035	-0.007	17.466	0.024	0.024	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.067	-0.034	11.784	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.020	0.015	16.046	0.034	0.034	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.873	-0.966	14.769	-0.240	-0.240	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.918	-0.955	13.516	0.036	0.036	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.794	-0.898	12.502	-0.229	-0.229	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.026	-0.025	10.387	-0.136	-0.136	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.930	0.970	8.818	-0.128	-0.128	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.001	0.011	7.970	0.018	0.018	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.021	-0.010	6.860	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.932	0.981	4.378	-0.344	-0.170	-0.001	-0.046	-0.127	0.000
45	A	45	ASN	0	-0.050	-0.013	2.417	-4.856	-2.786	2.011	-1.515	-2.565	-0.018
46	A	46	VAL	0	-0.020	-0.007	2.447	-3.613	-1.284	2.414	-1.721	-3.022	-0.023
47	A	47	ARG	1	0.963	0.991	2.487	-2.663	-0.447	3.476	-1.498	-4.195	-0.002
48	A	48	VAL	0	0.002	-0.002	3.585	0.401	0.488	0.023	0.035	-0.144	0.001
49	A	49	ILE	0	-0.066	-0.026	5.973	0.139	0.139	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.014	-0.018	8.842	0.166	0.166	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.050	0.044	12.336	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.049	-0.013	14.526	0.067	0.067	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.008	0.004	18.065	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.011	-0.005	20.992	0.019	0.019	0.000	0.000	0.000	0.000
55	A	55	PRO	0	0.086	0.037	23.499	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.012	0.017	27.000	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.083	0.034	27.270	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.063	0.030	28.141	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.027	-0.025	26.215	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.053	0.022	23.115	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.879	-0.950	23.781	-0.154	-0.154	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.932	0.973	25.588	0.147	0.147	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.063	-0.027	20.530	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.037	-0.036	18.183	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.900	-0.912	21.285	-0.194	-0.194	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.043	-0.022	22.645	0.010	0.010	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.940	0.966	25.689	0.122	0.122	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.065	-0.037	25.730	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.009	0.006	29.528	0.008	0.008	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.869	-0.929	32.714	-0.114	-0.114	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.006	-0.004	34.286	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.785	-0.883	35.271	-0.104	-0.104	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.035	-0.018	36.569	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.008	0.002	37.522	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	TYR	0	0.031	-0.013	32.982	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.948	0.976	36.116	0.099	0.099	0.000	0.000	0.000	0.000
77	A	77	TYR	0	0.005	0.007	32.795	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.038	-0.023	29.935	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.834	0.912	25.713	0.224	0.224	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.031	0.003	31.198	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.039	-0.023	29.130	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.012	0.011	33.485	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.709	-0.855	32.205	-0.124	-0.124	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.949	-0.953	31.545	-0.102	-0.102	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.890	0.913	31.551	0.102	0.102	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.728	-0.846	28.447	-0.176	-0.176	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.008	-0.023	27.129	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.970	-0.987	26.606	-0.138	-0.138	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.055	0.015	25.451	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.029	0.001	22.755	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.908	0.945	21.674	0.128	0.128	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.005	0.011	21.952	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.027	-0.025	20.663	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.000	0.014	17.639	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.827	-0.933	17.258	-0.241	-0.241	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.003	0.005	18.592	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.006	-0.009	14.238	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.793	0.923	12.244	0.389	0.389	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.955	0.972	14.139	0.159	0.159	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.811	0.915	16.126	0.252	0.252	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.035	-0.047	11.505	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.034	0.005	10.720	-0.056	-0.056	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.014	0.004	8.459	-0.081	-0.081	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.031	-0.022	6.033	-0.480	-0.480	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.003	-0.003	9.183	0.217	0.217	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.040	-0.021	10.779	-0.136	-0.136	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.001	-0.006	13.148	0.074	0.074	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.023	0.028	15.962	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.023	-0.039	19.417	0.021	0.021	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.104	-0.072	22.073	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.054	0.026	25.670	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.017	0.007	28.725	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.036	-0.010	32.165	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.025	0.018	34.142	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.841	0.905	30.337	0.111	0.111	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.020	0.011	28.060	-0.013	-0.013	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.060	-0.014	25.865	0.008	0.008	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.027	0.000	19.763	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	119	CYS	0	-0.081	-0.013	20.565	0.027	0.027	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.004	-0.003	14.876	-0.042	-0.042	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.015	-0.006	16.006	0.058	0.058	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.006	-0.050	12.856	-0.084	-0.084	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.765	-0.857	10.254	-0.269	-0.269	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.082	-0.032	13.226	0.072	0.072	0.000	0.000	0.000	0.000
125	A	125	ASN	0	-0.013	-0.009	16.536	0.023	0.023	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.931	0.970	17.595	0.118	0.118	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.091	-0.076	16.973	0.040	0.040	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.007	-0.021	21.123	-0.028	-0.028	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.016	-0.007	19.811	0.023	0.023	0.000	0.000	0.000	0.000
130	A	130	THR	0	0.059	0.035	25.171	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.067	-0.047	26.532	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.792	-0.902	27.364	-0.138	-0.138	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.042	-0.016	29.936	0.011	0.011	0.000	0.000	0.000	0.000
134	A	134	TYR	0	0.034	0.014	31.622	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.003	-0.002	32.213	0.002	0.002	0.000	0.000	0.000	0.000
136	A	136	ASN	0	0.029	0.009	34.297	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.014	-0.013	30.671	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.015	-0.002	33.783	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	THR	0	0.006	-0.010	37.136	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	PHE	0	-0.030	-0.006	34.464	0.001	0.001	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.924	-0.958	35.644	-0.100	-0.100	0.000	0.000	0.000	0.000
142	A	142	ASN	0	0.028	0.015	34.006	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.022	-0.016	30.340	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.993	1.003	28.689	0.159	0.159	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.858	-0.939	28.562	-0.149	-0.149	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.869	0.924	28.058	0.152	0.152	0.000	0.000	0.000	0.000
147	A	147	GLN	0	-0.028	-0.010	24.405	-0.027	-0.027	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.976	0.989	24.121	0.189	0.189	0.000	0.000	0.000	0.000
149	A	149	ASN	0	0.007	0.008	23.897	-0.018	-0.018	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.020	0.002	23.625	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	151	ILE	0	-0.011	-0.007	18.546	-0.023	-0.023	0.000	0.000	0.000	0.000
152	A	152	GLU	-1	-0.876	-0.922	19.277	-0.239	-0.239	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.773	0.868	20.296	0.160	0.160	0.000	0.000	0.000	0.000
154	A	154	GLY	0	0.011	-0.007	18.765	0.002	0.002	0.000	0.000	0.000	0.000
155	A	155	ILE	0	0.017	0.018	14.103	-0.034	-0.034	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.945	0.975	15.980	0.188	0.188	0.000	0.000	0.000	0.000
157	A	157	ARG	1	0.815	0.884	17.955	0.199	0.199	0.000	0.000	0.000	0.000
158	A	158	PHE	0	0.039	0.018	8.871	0.040	0.040	0.000	0.000	0.000	0.000
159	A	159	LEU	0	0.033	0.012	12.273	-0.011	-0.011	0.000	0.000	0.000	0.000
160	A	160	GLU	-1	-0.888	-0.915	14.412	-0.115	-0.115	0.000	0.000	0.000	0.000
161	A	161	ILE	0	-0.063	-0.036	13.818	0.062	0.062	0.000	0.000	0.000	0.000
162	A	162	LEU	0	0.003	0.017	7.825	0.053	0.053	0.000	0.000	0.000	0.000
163	A	163	LYS	1	0.891	0.927	11.604	0.287	0.287	0.000	0.000	0.000	0.000
164	A	164	LYS	1	0.887	0.963	13.560	0.159	0.159	0.000	0.000	0.000	0.000
165	A	165	GLU	-1	-0.765	-0.824	13.030	-0.080	-0.080	0.000	0.000	0.000	0.000
166	A	166	TYR	0	-0.016	-0.023	8.112	-0.056	-0.056	0.000	0.000	0.000	0.000
167	A	167	PHE	0	-0.019	0.000	6.442	0.172	0.172	0.000	0.000	0.000	0.000

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