FMO DATABASE

FMODB ID: 82QZY

Calculation Name: 4JPB-W-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JPB

Chain ID: W

ChEMBL ID:

UniProt ID: Q56310

Base Structure: X-ray

Registration Date: 2023-03-14

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1294724.737441
FMO2-HF: Nuclear repulsion	1240311.541654
FMO2-HF: Total energy	-54413.195786
FMO2-MP2: Total energy	-54574.98363

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(W:8:LEU)

Summations of interaction energy for fragment #1(W:8:LEU)

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.
-8.078	-4.038	6.103	-4.004	-6.14	-0.001

Interaction energy analysis for fragmet #1(W:8:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.005

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	W	10	GLU	-1	-0.850	-0.900	3.366	-2.431	0.747	0.080	-1.464	-1.794	0.001
4	W	11	PHE	0	-0.015	-0.015	4.477	-0.136	-0.069	-0.001	-0.007	-0.060	0.000
5	W	12	GLU	-1	-0.808	-0.882	7.478	-0.328	-0.328	0.000	0.000	0.000	0.000
6	W	13	VAL	0	0.017	0.014	10.801	-0.005	-0.005	0.000	0.000	0.000	0.000
7	W	14	LEU	0	0.003	0.012	13.795	0.029	0.029	0.000	0.000	0.000	0.000
8	W	15	SER	0	-0.006	-0.024	16.928	0.023	0.023	0.000	0.000	0.000	0.000
9	W	16	PHE	0	0.012	-0.021	18.710	-0.001	-0.001	0.000	0.000	0.000	0.000
10	W	17	GLU	-1	-0.795	-0.907	22.330	0.013	0.013	0.000	0.000	0.000	0.000
11	W	18	ILE	0	-0.049	-0.035	25.110	-0.010	-0.010	0.000	0.000	0.000	0.000
12	W	19	ASP	-1	-0.789	-0.897	27.982	0.008	0.008	0.000	0.000	0.000	0.000
13	W	20	GLU	-1	-0.967	-0.961	28.620	0.039	0.039	0.000	0.000	0.000	0.000
14	W	21	GLN	0	-0.013	0.000	24.194	0.008	0.008	0.000	0.000	0.000	0.000
15	W	22	ALA	0	0.009	0.007	21.219	-0.013	-0.013	0.000	0.000	0.000	0.000
16	W	23	LEU	0	-0.048	-0.028	19.682	0.015	0.015	0.000	0.000	0.000	0.000
17	W	24	ALA	0	0.042	0.010	16.031	-0.009	-0.009	0.000	0.000	0.000	0.000
18	W	25	PHE	0	-0.012	-0.006	16.262	0.018	0.018	0.000	0.000	0.000	0.000
19	W	26	ASP	-1	-0.740	-0.851	13.752	-0.374	-0.374	0.000	0.000	0.000	0.000
20	W	27	VAL	0	0.020	0.000	13.587	0.040	0.040	0.000	0.000	0.000	0.000
21	W	28	ASP	-1	-0.938	-0.965	13.516	-0.634	-0.634	0.000	0.000	0.000	0.000
22	W	29	ASN	0	-0.055	-0.033	16.605	-0.008	-0.008	0.000	0.000	0.000	0.000
23	W	30	ILE	0	-0.052	-0.022	18.865	0.043	0.043	0.000	0.000	0.000	0.000
24	W	31	GLU	-1	-0.836	-0.889	21.322	-0.203	-0.203	0.000	0.000	0.000	0.000
25	W	32	MET	0	-0.050	-0.033	24.614	0.006	0.006	0.000	0.000	0.000	0.000
26	W	33	VAL	0	-0.011	-0.007	23.609	0.003	0.003	0.000	0.000	0.000	0.000
27	W	34	ILE	0	-0.031	-0.008	26.568	0.001	0.001	0.000	0.000	0.000	0.000
28	W	35	GLU	-1	-0.903	-0.949	30.320	-0.056	-0.056	0.000	0.000	0.000	0.000
29	W	36	LYS	1	0.834	0.926	32.902	0.038	0.038	0.000	0.000	0.000	0.000
30	W	37	SER	0	-0.072	-0.026	35.065	0.004	0.004	0.000	0.000	0.000	0.000
31	W	38	ASP	-1	-0.877	-0.955	38.122	-0.048	-0.048	0.000	0.000	0.000	0.000
32	W	39	ILE	0	-0.051	-0.029	36.015	-0.005	-0.005	0.000	0.000	0.000	0.000
33	W	40	THR	0	-0.003	0.020	39.642	0.004	0.004	0.000	0.000	0.000	0.000
34	W	41	PRO	0	0.033	0.021	41.310	-0.002	-0.002	0.000	0.000	0.000	0.000
35	W	42	VAL	0	0.035	0.008	40.743	0.000	0.000	0.000	0.000	0.000	0.000
36	W	43	PRO	0	-0.012	-0.003	43.045	0.002	0.002	0.000	0.000	0.000	0.000
37	W	44	LYS	1	0.908	0.947	45.044	0.027	0.027	0.000	0.000	0.000	0.000
38	W	45	SER	0	0.019	0.019	39.792	0.000	0.000	0.000	0.000	0.000	0.000
39	W	46	ARG	1	0.885	0.931	32.787	0.059	0.059	0.000	0.000	0.000	0.000
40	W	47	HIS	0	0.021	0.003	34.961	-0.003	-0.003	0.000	0.000	0.000	0.000
41	W	48	PHE	0	0.024	0.012	33.275	0.002	0.002	0.000	0.000	0.000	0.000
42	W	49	VAL	0	-0.045	-0.020	34.408	-0.005	-0.005	0.000	0.000	0.000	0.000
43	W	50	GLU	-1	-0.727	-0.851	35.889	-0.036	-0.036	0.000	0.000	0.000	0.000
44	W	51	GLY	0	-0.043	-0.028	37.193	0.003	0.003	0.000	0.000	0.000	0.000
45	W	52	VAL	0	-0.044	-0.012	37.061	-0.005	-0.005	0.000	0.000	0.000	0.000
46	W	53	ILE	0	0.031	0.024	33.218	0.004	0.004	0.000	0.000	0.000	0.000
47	W	54	ASN	0	-0.015	-0.010	37.367	-0.008	-0.008	0.000	0.000	0.000	0.000
48	W	55	LEU	0	0.055	0.024	31.652	0.002	0.002	0.000	0.000	0.000	0.000
49	W	56	ARG	1	0.912	0.947	33.676	0.103	0.103	0.000	0.000	0.000	0.000
50	W	57	GLY	0	0.018	0.012	36.086	-0.003	-0.003	0.000	0.000	0.000	0.000
51	W	58	ARG	1	0.782	0.872	29.129	0.147	0.147	0.000	0.000	0.000	0.000
52	W	59	ILE	0	0.005	-0.005	36.672	0.002	0.002	0.000	0.000	0.000	0.000
53	W	60	ILE	0	0.006	0.014	31.152	-0.005	-0.005	0.000	0.000	0.000	0.000
54	W	61	PRO	0	0.005	0.008	32.431	0.008	0.008	0.000	0.000	0.000	0.000
55	W	62	VAL	0	0.001	-0.001	32.529	-0.007	-0.007	0.000	0.000	0.000	0.000
56	W	63	VAL	0	-0.024	-0.019	30.005	0.008	0.008	0.000	0.000	0.000	0.000
57	W	64	ASN	0	0.018	-0.004	31.056	-0.002	-0.002	0.000	0.000	0.000	0.000
58	W	65	LEU	0	0.043	0.018	23.904	0.004	0.004	0.000	0.000	0.000	0.000
59	W	66	ALA	0	0.037	0.025	28.413	0.006	0.006	0.000	0.000	0.000	0.000
60	W	67	LYS	1	0.755	0.874	30.166	0.038	0.038	0.000	0.000	0.000	0.000
61	W	68	ILE	0	-0.012	0.003	27.557	0.002	0.002	0.000	0.000	0.000	0.000
62	W	69	LEU	0	-0.011	-0.001	24.118	0.002	0.002	0.000	0.000	0.000	0.000
63	W	70	GLY	0	-0.001	0.010	27.983	0.010	0.010	0.000	0.000	0.000	0.000
64	W	71	ILE	0	-0.077	-0.026	26.527	0.009	0.009	0.000	0.000	0.000	0.000
65	W	72	SER	0	0.055	0.020	30.597	-0.004	-0.004	0.000	0.000	0.000	0.000
66	W	73	PHE	0	-0.004	-0.020	31.307	-0.003	-0.003	0.000	0.000	0.000	0.000
67	W	74	ASP	-1	-0.764	-0.890	33.463	-0.010	-0.010	0.000	0.000	0.000	0.000
68	W	75	GLU	-1	-0.825	-0.922	35.589	-0.035	-0.035	0.000	0.000	0.000	0.000
69	W	76	GLN	0	-0.036	-0.010	37.707	-0.006	-0.006	0.000	0.000	0.000	0.000
70	W	77	LYS	1	0.735	0.859	32.986	0.000	0.000	0.000	0.000	0.000	0.000
71	W	78	MET	0	-0.018	0.012	30.494	-0.005	-0.005	0.000	0.000	0.000	0.000
72	W	79	LYS	1	0.902	0.948	31.894	0.034	0.034	0.000	0.000	0.000	0.000
73	W	80	SER	0	-0.010	0.000	27.967	-0.005	-0.005	0.000	0.000	0.000	0.000
74	W	81	ILE	0	-0.012	-0.006	29.250	0.003	0.003	0.000	0.000	0.000	0.000
75	W	82	ILE	0	0.014	0.008	22.474	-0.007	-0.007	0.000	0.000	0.000	0.000
76	W	83	VAL	0	-0.033	-0.007	25.904	0.004	0.004	0.000	0.000	0.000	0.000
77	W	84	ALA	0	0.013	0.008	22.794	-0.016	-0.016	0.000	0.000	0.000	0.000
78	W	85	ARG	1	0.787	0.873	23.343	0.199	0.199	0.000	0.000	0.000	0.000
79	W	86	THR	0	-0.032	-0.005	21.500	-0.019	-0.019	0.000	0.000	0.000	0.000
80	W	87	LYS	1	0.789	0.887	21.930	0.217	0.217	0.000	0.000	0.000	0.000
81	W	88	ASP	-1	-0.881	-0.945	24.977	-0.153	-0.153	0.000	0.000	0.000	0.000
82	W	89	VAL	0	-0.009	0.006	27.584	0.006	0.006	0.000	0.000	0.000	0.000
83	W	90	GLU	-1	-0.748	-0.856	27.197	-0.158	-0.158	0.000	0.000	0.000	0.000
84	W	91	VAL	0	-0.035	-0.025	27.859	0.014	0.014	0.000	0.000	0.000	0.000
85	W	92	GLY	0	0.039	0.025	27.763	-0.010	-0.010	0.000	0.000	0.000	0.000
86	W	93	PHE	0	0.015	-0.013	25.763	0.013	0.013	0.000	0.000	0.000	0.000
87	W	94	LEU	0	-0.033	-0.010	27.811	-0.003	-0.003	0.000	0.000	0.000	0.000
88	W	95	VAL	0	-0.005	-0.017	25.309	0.005	0.005	0.000	0.000	0.000	0.000
89	W	96	ASP	-1	-0.807	-0.910	28.525	-0.025	-0.025	0.000	0.000	0.000	0.000
90	W	97	ARG	1	0.890	0.943	26.156	0.039	0.039	0.000	0.000	0.000	0.000
91	W	98	VAL	0	0.056	0.033	22.201	0.002	0.002	0.000	0.000	0.000	0.000
92	W	99	LEU	0	-0.104	-0.041	20.898	0.010	0.010	0.000	0.000	0.000	0.000
93	W	100	GLY	0	0.035	0.014	19.483	0.004	0.004	0.000	0.000	0.000	0.000
94	W	101	VAL	0	-0.001	0.018	14.327	0.004	0.004	0.000	0.000	0.000	0.000
95	W	102	LEU	0	-0.004	0.001	12.501	0.021	0.021	0.000	0.000	0.000	0.000
96	W	103	ARG	1	0.760	0.859	7.191	0.611	0.611	0.000	0.000	0.000	0.000
97	W	104	ILE	0	-0.016	-0.012	7.634	0.127	0.127	0.000	0.000	0.000	0.000
98	W	105	THR	0	0.031	0.008	1.980	-2.218	-1.983	4.364	-1.875	-2.723	-0.001
99	W	106	GLU	-1	-0.859	-0.946	3.992	-0.978	-0.769	0.000	-0.045	-0.164	0.000
100	W	107	ASN	0	-0.051	-0.024	2.375	-1.492	-1.141	1.660	-0.613	-1.399	-0.001
101	W	108	GLN	0	-0.032	-0.016	5.674	-0.213	-0.213	0.000	0.000	0.000	0.000
102	W	109	LEU	0	-0.028	-0.002	8.107	-0.184	-0.184	0.000	0.000	0.000	0.000
103	W	110	ASP	-1	-0.811	-0.878	9.977	0.535	0.535	0.000	0.000	0.000	0.000
104	W	111	LEU	0	0.036	0.011	10.449	-0.078	-0.078	0.000	0.000	0.000	0.000
105	W	112	THR	0	-0.052	-0.037	14.484	-0.029	-0.029	0.000	0.000	0.000	0.000
106	W	113	ASN	0	-0.053	-0.030	18.036	-0.027	-0.027	0.000	0.000	0.000	0.000
107	W	114	VAL	0	-0.030	-0.023	20.312	-0.015	-0.015	0.000	0.000	0.000	0.000
108	W	115	SER	0	-0.011	-0.019	22.648	-0.018	-0.018	0.000	0.000	0.000	0.000
109	W	116	ASP	-1	-0.829	-0.897	23.220	0.098	0.098	0.000	0.000	0.000	0.000
110	W	117	LYS	1	0.821	0.913	24.821	-0.036	-0.036	0.000	0.000	0.000	0.000
111	W	118	PHE	0	0.010	0.007	21.743	-0.010	-0.010	0.000	0.000	0.000	0.000
112	W	119	GLY	0	0.044	0.022	23.058	-0.015	-0.015	0.000	0.000	0.000	0.000
113	W	120	LYS	1	0.923	0.944	16.641	-0.039	-0.039	0.000	0.000	0.000	0.000
114	W	121	LYS	1	0.844	0.931	19.428	0.009	0.009	0.000	0.000	0.000	0.000
115	W	122	SER	0	-0.020	-0.009	18.338	-0.014	-0.014	0.000	0.000	0.000	0.000
116	W	123	LYS	1	0.816	0.900	12.765	0.291	0.291	0.000	0.000	0.000	0.000
117	W	124	GLY	0	0.039	0.020	13.234	0.054	0.054	0.000	0.000	0.000	0.000
118	W	125	LEU	0	-0.045	-0.015	14.463	-0.054	-0.054	0.000	0.000	0.000	0.000
119	W	126	VAL	0	0.018	0.013	11.535	0.074	0.074	0.000	0.000	0.000	0.000
120	W	127	LYS	1	0.846	0.906	12.189	-0.535	-0.535	0.000	0.000	0.000	0.000
121	W	128	THR	0	0.030	-0.005	12.116	0.033	0.033	0.000	0.000	0.000	0.000
122	W	129	ASP	-1	-0.890	-0.934	14.377	0.089	0.089	0.000	0.000	0.000	0.000
123	W	130	GLY	0	-0.023	-0.008	17.026	0.002	0.002	0.000	0.000	0.000	0.000
124	W	131	ARG	1	0.821	0.915	18.537	-0.039	-0.039	0.000	0.000	0.000	0.000
125	W	132	LEU	0	-0.029	-0.017	17.170	-0.004	-0.004	0.000	0.000	0.000	0.000
126	W	133	ILE	0	0.014	0.017	16.383	-0.026	-0.026	0.000	0.000	0.000	0.000
127	W	134	ILE	0	-0.019	-0.012	16.254	0.020	0.020	0.000	0.000	0.000	0.000
128	W	135	TYR	0	-0.068	-0.049	10.329	-0.036	-0.036	0.000	0.000	0.000	0.000
129	W	136	LEU	0	0.004	-0.007	15.614	0.018	0.018	0.000	0.000	0.000	0.000
130	W	137	ASP	-1	-0.854	-0.931	16.087	-0.249	-0.249	0.000	0.000	0.000	0.000
131	W	138	ILE	0	0.015	0.008	18.093	0.022	0.022	0.000	0.000	0.000	0.000
132	W	139	ASP	-1	-0.724	-0.871	18.772	-0.246	-0.246	0.000	0.000	0.000	0.000
133	W	140	LYS	1	0.839	0.921	19.833	0.096	0.096	0.000	0.000	0.000	0.000
134	W	141	ILE	0	-0.002	-0.012	21.736	0.021	0.021	0.000	0.000	0.000	0.000
135	W	142	ILE	0	0.029	0.008	23.926	0.016	0.016	0.000	0.000	0.000	0.000
136	W	143	GLU	-1	-0.878	-0.935	22.819	-0.142	-0.142	0.000	0.000	0.000	0.000
137	W	144	GLU	-1	-0.908	-0.931	26.155	-0.031	-0.031	0.000	0.000	0.000	0.000
138	W	145	ILE	0	-0.059	-0.020	28.097	0.009	0.009	0.000	0.000	0.000	0.000
139	W	146	THR	0	-0.029	-0.014	28.880	0.006	0.006	0.000	0.000	0.000	0.000
140	W	147	VAL	0	-0.018	0.007	30.631	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(W:8:LEU)