FMO DATABASE

FMODB ID: 7GRRK

Calculation Name: 5J8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J8E

Chain ID: A

ChEMBL ID:

UniProt ID: Q86VS8

Base Structure: X-ray

Registration Date: 2023-06-20

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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1440461.412533
FMO2-HF: Nuclear repulsion	1378576.211011
FMO2-HF: Total energy	-61885.201521
FMO2-MP2: Total energy	-62059.522255

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:9:ARG)

Summations of interaction energy for fragment #1(A:9:ARG)

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.
-255.369	-258.054	33.897	-15.349	-15.862	-0.156

Interaction energy analysis for fragmet #1(A:9:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / q_NPA : 0.917

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	11	GLU	-1	-0.789	-0.868	1.749	-133.441	-137.982	31.196	-14.291	-12.363	-0.148
4	A	12	LEU	0	0.008	0.019	2.654	5.471	6.907	0.228	-0.271	-1.393	-0.002
5	A	13	CYS	0	0.021	0.014	4.552	6.511	6.770	-0.001	-0.041	-0.218	0.000
6	A	14	GLU	-1	-0.909	-0.958	6.282	-26.485	-26.485	0.000	0.000	0.000	0.000
7	A	15	SER	0	-0.039	-0.026	6.542	3.565	3.565	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.024	-0.015	7.244	3.040	3.040	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.016	0.012	10.250	2.297	2.297	0.000	0.000	0.000	0.000
10	A	18	THR	0	-0.034	-0.016	12.067	2.080	2.080	0.000	0.000	0.000	0.000
11	A	19	TRP	0	0.037	0.018	13.154	1.076	1.076	0.000	0.000	0.000	0.000
12	A	20	ILE	0	-0.007	0.000	13.435	1.353	1.353	0.000	0.000	0.000	0.000
13	A	21	GLN	0	-0.020	-0.018	15.223	1.184	1.184	0.000	0.000	0.000	0.000
14	A	22	THR	0	-0.047	-0.029	17.867	1.105	1.105	0.000	0.000	0.000	0.000
15	A	23	PHE	0	0.027	0.017	17.204	0.898	0.898	0.000	0.000	0.000	0.000
16	A	24	ASN	0	-0.071	-0.029	21.523	0.812	0.812	0.000	0.000	0.000	0.000
17	A	25	VAL	0	-0.056	-0.032	20.881	0.598	0.598	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.871	-0.923	23.707	-10.782	-10.782	0.000	0.000	0.000	0.000
19	A	27	ALA	0	0.001	0.004	22.199	0.030	0.030	0.000	0.000	0.000	0.000
20	A	28	PRO	0	0.005	-0.007	21.922	-0.388	-0.388	0.000	0.000	0.000	0.000
21	A	29	CYS	0	-0.003	-0.019	17.855	-0.264	-0.264	0.000	0.000	0.000	0.000
22	A	30	GLN	0	0.001	0.008	16.902	-0.672	-0.672	0.000	0.000	0.000	0.000
23	A	31	THR	0	-0.046	-0.036	13.951	-1.257	-1.257	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.067	0.012	9.602	0.680	0.680	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.755	-0.853	12.405	-16.256	-16.256	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.861	-0.888	15.372	-15.347	-15.347	0.000	0.000	0.000	0.000
27	A	35	LEU	0	0.008	0.004	12.600	0.828	0.828	0.000	0.000	0.000	0.000
28	A	36	THR	0	-0.022	-0.017	12.630	0.865	0.865	0.000	0.000	0.000	0.000
29	A	37	ASN	0	-0.006	-0.012	14.901	0.871	0.871	0.000	0.000	0.000	0.000
30	A	38	GLY	0	0.008	-0.005	17.009	0.739	0.739	0.000	0.000	0.000	0.000
31	A	39	VAL	0	0.010	-0.001	17.977	0.080	0.080	0.000	0.000	0.000	0.000
32	A	40	VAL	0	0.046	0.032	17.317	0.254	0.254	0.000	0.000	0.000	0.000
33	A	41	MET	0	-0.006	-0.002	13.336	-0.213	-0.213	0.000	0.000	0.000	0.000
34	A	42	ALA	0	-0.002	0.004	17.381	0.253	0.253	0.000	0.000	0.000	0.000
35	A	43	GLN	0	-0.003	-0.014	20.805	0.080	0.080	0.000	0.000	0.000	0.000
36	A	44	VAL	0	-0.001	0.001	17.048	0.256	0.256	0.000	0.000	0.000	0.000
37	A	45	LEU	0	-0.027	-0.015	17.787	0.173	0.173	0.000	0.000	0.000	0.000
38	A	46	GLN	0	-0.060	-0.038	20.835	0.345	0.345	0.000	0.000	0.000	0.000
39	A	47	LYS	1	0.830	0.914	22.803	12.045	12.045	0.000	0.000	0.000	0.000
40	A	48	ILE	0	-0.042	-0.009	18.087	0.138	0.138	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.761	-0.861	22.658	-9.937	-9.937	0.000	0.000	0.000	0.000
42	A	50	PRO	0	0.020	0.012	25.531	0.057	0.057	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.058	-0.021	28.204	0.304	0.304	0.000	0.000	0.000	0.000
44	A	52	TYR	0	-0.076	-0.051	24.297	0.107	0.107	0.000	0.000	0.000	0.000
45	A	53	PHE	0	-0.040	-0.026	21.360	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	54	ASP	-1	-0.694	-0.834	26.215	-8.949	-8.949	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.915	-0.962	28.760	-8.781	-8.781	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.078	-0.051	30.679	0.064	0.064	0.000	0.000	0.000	0.000
49	A	57	TRP	0	-0.014	-0.002	22.006	-0.268	-0.268	0.000	0.000	0.000	0.000
50	A	58	LEU	0	0.024	0.002	24.498	-0.224	-0.224	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.027	-0.013	26.963	-0.084	-0.084	0.000	0.000	0.000	0.000
52	A	60	ARG	1	0.830	0.932	24.587	10.137	10.137	0.000	0.000	0.000	0.000
53	A	61	ILE	0	-0.049	-0.021	21.708	-0.119	-0.119	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.823	0.908	24.340	10.279	10.279	0.000	0.000	0.000	0.000
55	A	63	THR	0	0.073	0.005	24.267	-0.431	-0.431	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.888	-0.897	25.340	-10.321	-10.321	0.000	0.000	0.000	0.000
57	A	65	VAL	0	-0.091	-0.051	21.155	0.149	0.149	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.045	0.015	24.090	0.151	0.151	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.875	-0.942	22.034	-12.580	-12.580	0.000	0.000	0.000	0.000
60	A	68	ASN	0	-0.035	-0.006	22.535	-0.309	-0.309	0.000	0.000	0.000	0.000
61	A	69	TRP	0	0.078	0.015	18.536	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.914	0.965	19.341	11.608	11.608	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.029	-0.010	21.577	0.043	0.043	0.000	0.000	0.000	0.000
64	A	72	LYS	1	0.892	0.967	16.499	15.760	15.760	0.000	0.000	0.000	0.000
65	A	73	ILE	0	0.007	0.018	16.363	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.048	-0.015	18.149	0.136	0.136	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.035	-0.030	20.098	0.700	0.700	0.000	0.000	0.000	0.000
68	A	76	LEU	0	0.036	0.018	13.956	0.118	0.118	0.000	0.000	0.000	0.000
69	A	77	LYS	1	0.871	0.934	16.983	12.761	12.761	0.000	0.000	0.000	0.000
70	A	78	LYS	1	0.851	0.926	18.623	11.174	11.174	0.000	0.000	0.000	0.000
71	A	79	ILE	0	0.028	0.033	16.692	0.293	0.293	0.000	0.000	0.000	0.000
72	A	80	LEU	0	-0.001	0.004	14.048	0.005	0.005	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.786	0.866	17.052	10.575	10.575	0.000	0.000	0.000	0.000
74	A	82	GLY	0	0.044	0.011	20.622	0.272	0.272	0.000	0.000	0.000	0.000
75	A	83	ILE	0	-0.009	0.000	14.682	0.158	0.158	0.000	0.000	0.000	0.000
76	A	84	LEU	0	-0.035	-0.020	17.354	0.149	0.149	0.000	0.000	0.000	0.000
77	A	85	ASP	-1	-0.813	-0.876	19.884	-10.268	-10.268	0.000	0.000	0.000	0.000
78	A	86	TYR	0	-0.019	-0.032	20.912	0.114	0.114	0.000	0.000	0.000	0.000
79	A	87	ASN	0	0.004	-0.009	19.168	0.275	0.275	0.000	0.000	0.000	0.000
80	A	88	HIS	0	-0.053	-0.016	21.720	0.002	0.002	0.000	0.000	0.000	0.000
81	A	89	GLU	-1	-0.911	-0.949	25.006	-9.158	-9.158	0.000	0.000	0.000	0.000
82	A	90	ILE	0	-0.047	-0.012	25.772	0.317	0.317	0.000	0.000	0.000	0.000
83	A	91	LEU	0	-0.034	0.000	20.675	0.110	0.110	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.014	0.011	24.912	0.075	0.075	0.000	0.000	0.000	0.000
85	A	93	GLN	0	-0.113	-0.072	22.990	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	94	GLN	0	-0.013	-0.001	20.191	-0.161	-0.161	0.000	0.000	0.000	0.000
87	A	95	ILE	0	-0.017	-0.007	15.127	-0.424	-0.424	0.000	0.000	0.000	0.000
88	A	96	ASN	0	-0.043	-0.027	13.301	0.743	0.743	0.000	0.000	0.000	0.000
89	A	97	ASP	-1	-0.858	-0.937	12.830	-14.622	-14.622	0.000	0.000	0.000	0.000
90	A	98	PHE	0	-0.037	-0.017	13.263	0.107	0.107	0.000	0.000	0.000	0.000
91	A	99	THR	0	-0.083	-0.049	9.243	-0.160	-0.160	0.000	0.000	0.000	0.000
92	A	100	LEU	0	0.049	0.029	9.949	-1.058	-1.058	0.000	0.000	0.000	0.000
93	A	101	PRO	0	0.003	0.015	8.664	-0.660	-0.660	0.000	0.000	0.000	0.000
94	A	102	ASP	-1	-0.789	-0.892	9.031	-15.219	-15.219	0.000	0.000	0.000	0.000
95	A	103	VAL	0	-0.010	-0.033	10.889	-0.416	-0.416	0.000	0.000	0.000	0.000
96	A	104	ASN	0	-0.059	-0.046	12.972	1.310	1.310	0.000	0.000	0.000	0.000
97	A	105	LEU	0	0.032	0.025	9.501	0.352	0.352	0.000	0.000	0.000	0.000
98	A	106	ILE	0	-0.024	0.004	9.071	-0.139	-0.139	0.000	0.000	0.000	0.000
99	A	107	GLY	0	0.008	-0.006	11.395	0.255	0.255	0.000	0.000	0.000	0.000
100	A	108	GLU	-1	-0.937	-0.984	15.162	-13.835	-13.835	0.000	0.000	0.000	0.000
101	A	109	HIS	0	-0.074	-0.047	12.072	-0.141	-0.141	0.000	0.000	0.000	0.000
102	A	110	SER	0	-0.060	-0.044	12.224	-0.778	-0.778	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.856	-0.920	5.969	-30.295	-30.295	0.000	0.000	0.000	0.000
104	A	112	ALA	0	0.091	0.028	6.578	0.224	0.224	0.000	0.000	0.000	0.000
105	A	113	ALA	0	-0.064	-0.031	1.954	-4.305	-4.372	2.474	-1.045	-1.362	-0.004
106	A	114	GLU	-1	-0.782	-0.869	3.025	-24.236	-24.057	0.001	0.308	-0.488	-0.002
107	A	115	LEU	0	0.024	-0.001	5.793	1.329	1.329	0.000	0.000	0.000	0.000
108	A	116	GLY	0	0.033	0.019	4.295	1.233	1.282	-0.001	-0.009	-0.038	0.000
109	A	117	ARG	1	0.847	0.896	5.171	26.285	26.285	0.000	0.000	0.000	0.000
110	A	118	MET	0	-0.025	-0.010	6.575	1.780	1.780	0.000	0.000	0.000	0.000
111	A	119	LEU	0	0.024	0.006	8.655	1.583	1.583	0.000	0.000	0.000	0.000
112	A	120	GLN	0	-0.007	-0.003	5.975	-0.579	-0.579	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.028	0.001	9.624	1.364	1.364	0.000	0.000	0.000	0.000
114	A	122	ILE	0	0.040	0.020	12.447	1.058	1.058	0.000	0.000	0.000	0.000
115	A	123	LEU	0	0.020	0.010	12.067	0.801	0.801	0.000	0.000	0.000	0.000
116	A	124	GLY	0	0.001	-0.004	13.543	0.738	0.738	0.000	0.000	0.000	0.000
117	A	125	CYS	0	-0.019	-0.014	15.249	0.945	0.945	0.000	0.000	0.000	0.000
118	A	126	ALA	0	0.016	0.014	17.477	0.661	0.661	0.000	0.000	0.000	0.000
119	A	127	VAL	0	-0.028	-0.021	16.918	0.520	0.520	0.000	0.000	0.000	0.000
120	A	128	ASN	0	-0.066	-0.058	18.339	0.750	0.750	0.000	0.000	0.000	0.000
121	A	129	CYS	0	-0.002	0.022	21.485	0.465	0.465	0.000	0.000	0.000	0.000
122	A	130	GLU	-1	-0.928	-0.969	23.891	-9.136	-9.136	0.000	0.000	0.000	0.000
123	A	131	GLN	0	-0.024	-0.038	25.622	0.179	0.179	0.000	0.000	0.000	0.000
124	A	132	LYS	1	0.859	0.956	22.497	11.176	11.176	0.000	0.000	0.000	0.000
125	A	133	GLN	0	0.002	-0.011	23.030	-0.710	-0.710	0.000	0.000	0.000	0.000
126	A	134	GLU	-1	-0.902	-0.922	24.955	-10.956	-10.956	0.000	0.000	0.000	0.000
127	A	135	TYR	0	0.028	0.001	19.941	-0.463	-0.463	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.009	-0.001	19.174	-0.711	-0.711	0.000	0.000	0.000	0.000
129	A	137	GLN	0	0.004	-0.012	21.085	-0.344	-0.344	0.000	0.000	0.000	0.000
130	A	138	ALA	0	0.004	-0.001	21.076	-0.166	-0.166	0.000	0.000	0.000	0.000
131	A	139	ILE	0	0.003	-0.009	16.090	-0.542	-0.542	0.000	0.000	0.000	0.000
132	A	140	MET	0	-0.021	-0.011	18.592	-0.683	-0.683	0.000	0.000	0.000	0.000
133	A	141	MET	0	-0.015	0.007	20.993	0.101	0.101	0.000	0.000	0.000	0.000
134	A	142	MET	0	-0.051	-0.006	14.378	0.008	0.008	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.884	-0.942	16.675	-18.141	-18.141	0.000	0.000	0.000	0.000
136	A	144	GLU	-1	-0.927	-0.968	19.369	-11.649	-11.649	0.000	0.000	0.000	0.000
137	A	145	SER	0	-0.049	-0.019	20.562	0.370	0.370	0.000	0.000	0.000	0.000
138	A	146	VAL	0	0.020	0.008	16.540	0.115	0.115	0.000	0.000	0.000	0.000
139	A	147	GLN	0	-0.022	-0.013	19.116	0.422	0.422	0.000	0.000	0.000	0.000
140	A	148	HIS	0	-0.008	0.003	22.308	0.499	0.499	0.000	0.000	0.000	0.000
141	A	149	VAL	0	-0.005	0.016	19.847	0.414	0.414	0.000	0.000	0.000	0.000
142	A	150	VAL	0	-0.003	-0.002	19.179	0.218	0.218	0.000	0.000	0.000	0.000
143	A	151	MET	0	-0.016	-0.007	21.826	0.486	0.486	0.000	0.000	0.000	0.000
144	A	152	THR	0	-0.035	-0.035	25.073	0.579	0.579	0.000	0.000	0.000	0.000
145	A	153	ALA	0	-0.005	-0.008	22.426	0.320	0.320	0.000	0.000	0.000	0.000
146	A	154	ILE	0	-0.034	-0.017	23.722	0.219	0.219	0.000	0.000	0.000	0.000
147	A	155	GLN	0	-0.029	-0.036	26.190	0.664	0.664	0.000	0.000	0.000	0.000
148	A	156	GLU	-1	-0.945	-0.964	26.921	-10.209	-10.209	0.000	0.000	0.000	0.000
149	A	157	LEU	0	-0.083	-0.030	24.107	-0.014	-0.014	0.000	0.000	0.000	0.000
150	A	158	MET	0	-0.115	-0.032	28.717	0.236	0.236	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ARG)