FMO DATABASE

FMODB ID: M377Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1437401.293854
FMO2-HF: Nuclear repulsion	1375516.321245
FMO2-HF: Total energy	-61884.972609
FMO2-MP2: Total energy	-62059.323116

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.
-249.122	-245.986	28.158	-14.219	-17.074	-0.162

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 : 0.853 / q_NPA : 0.920

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	-0.787	-0.885	1.783	-126.766	-126.290	26.414	-13.669	-13.221	-0.150
4	A	12	LEU	0	0.021	0.014	2.272	5.505	6.592	1.345	-0.012	-2.420	-0.009
5	A	13	CYS	0	0.024	0.016	3.975	6.490	6.892	0.003	-0.092	-0.313	0.000
6	A	14	GLU	-1	-0.907	-0.953	5.921	-26.304	-26.304	0.000	0.000	0.000	0.000
7	A	15	SER	0	-0.030	-0.011	6.570	3.686	3.686	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.026	-0.014	6.651	2.964	2.964	0.000	0.000	0.000	0.000
9	A	17	LEU	0	0.023	0.012	9.822	2.385	2.385	0.000	0.000	0.000	0.000
10	A	18	THR	0	-0.046	-0.022	11.752	2.043	2.043	0.000	0.000	0.000	0.000
11	A	19	TRP	0	0.045	0.020	12.879	1.124	1.124	0.000	0.000	0.000	0.000
12	A	20	ILE	0	0.002	0.010	13.228	1.364	1.364	0.000	0.000	0.000	0.000
13	A	21	GLN	0	-0.018	-0.018	15.257	1.133	1.133	0.000	0.000	0.000	0.000
14	A	22	THR	0	-0.072	-0.046	17.537	1.039	1.039	0.000	0.000	0.000	0.000
15	A	23	PHE	0	0.011	0.002	16.949	0.882	0.882	0.000	0.000	0.000	0.000
16	A	24	ASN	0	-0.064	-0.020	21.242	0.763	0.763	0.000	0.000	0.000	0.000
17	A	25	VAL	0	-0.042	-0.025	20.517	0.628	0.628	0.000	0.000	0.000	0.000
18	A	26	ASP	-1	-0.942	-0.959	23.353	-10.793	-10.793	0.000	0.000	0.000	0.000
19	A	27	ALA	0	-0.012	0.001	22.173	0.006	0.006	0.000	0.000	0.000	0.000
20	A	28	PRO	0	0.023	-0.004	21.941	-0.378	-0.378	0.000	0.000	0.000	0.000
21	A	29	CYS	0	-0.011	-0.017	17.179	-0.285	-0.285	0.000	0.000	0.000	0.000
22	A	30	GLN	0	-0.006	0.006	16.955	-0.621	-0.621	0.000	0.000	0.000	0.000
23	A	31	THR	0	-0.037	-0.025	14.004	-1.324	-1.324	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.063	0.012	9.568	0.705	0.705	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.801	-0.892	12.609	-16.730	-16.730	0.000	0.000	0.000	0.000
26	A	34	ASP	-1	-0.839	-0.882	15.493	-15.470	-15.470	0.000	0.000	0.000	0.000
27	A	35	LEU	0	-0.020	-0.019	12.445	0.767	0.767	0.000	0.000	0.000	0.000
28	A	36	THR	0	-0.020	0.007	13.127	0.723	0.723	0.000	0.000	0.000	0.000
29	A	37	ASN	0	0.017	-0.006	15.215	0.376	0.376	0.000	0.000	0.000	0.000
30	A	38	GLY	0	0.014	-0.003	17.144	0.727	0.727	0.000	0.000	0.000	0.000
31	A	39	VAL	0	0.021	0.008	18.111	0.204	0.204	0.000	0.000	0.000	0.000
32	A	40	VAL	0	0.060	0.037	17.064	0.274	0.274	0.000	0.000	0.000	0.000
33	A	41	MET	0	-0.006	-0.004	13.343	-0.145	-0.145	0.000	0.000	0.000	0.000
34	A	42	ALA	0	-0.001	0.003	17.238	0.286	0.286	0.000	0.000	0.000	0.000
35	A	43	GLN	0	0.047	0.012	20.639	0.087	0.087	0.000	0.000	0.000	0.000
36	A	44	VAL	0	0.016	0.011	16.896	0.289	0.289	0.000	0.000	0.000	0.000
37	A	45	LEU	0	-0.034	-0.016	17.718	0.149	0.149	0.000	0.000	0.000	0.000
38	A	46	GLN	0	-0.028	-0.010	20.615	0.293	0.293	0.000	0.000	0.000	0.000
39	A	47	LYS	1	0.813	0.901	22.343	11.996	11.996	0.000	0.000	0.000	0.000
40	A	48	ILE	0	-0.043	-0.013	18.054	0.186	0.186	0.000	0.000	0.000	0.000
41	A	49	ASP	-1	-0.790	-0.880	22.670	-9.797	-9.797	0.000	0.000	0.000	0.000
42	A	50	PRO	0	0.004	0.009	25.452	0.068	0.068	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.046	-0.023	27.910	0.275	0.275	0.000	0.000	0.000	0.000
44	A	52	TYR	0	-0.074	-0.052	24.392	0.088	0.088	0.000	0.000	0.000	0.000
45	A	53	PHE	0	-0.046	-0.024	21.267	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	54	ASP	-1	-0.717	-0.860	25.986	-9.035	-9.035	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.935	-0.971	28.666	-8.744	-8.744	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.064	-0.042	30.644	0.074	0.074	0.000	0.000	0.000	0.000
49	A	57	TRP	0	0.008	0.000	21.916	-0.253	-0.253	0.000	0.000	0.000	0.000
50	A	58	LEU	0	0.027	-0.005	24.290	-0.243	-0.243	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.009	0.007	26.953	-0.042	-0.042	0.000	0.000	0.000	0.000
52	A	60	ARG	1	0.792	0.907	24.724	10.101	10.101	0.000	0.000	0.000	0.000
53	A	61	ILE	0	-0.067	-0.037	21.825	-0.155	-0.155	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.846	0.937	25.029	10.099	10.099	0.000	0.000	0.000	0.000
55	A	63	THR	0	0.067	0.016	24.544	-0.411	-0.411	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.896	-0.923	25.628	-10.459	-10.459	0.000	0.000	0.000	0.000
57	A	65	VAL	0	-0.077	-0.040	21.864	0.126	0.126	0.000	0.000	0.000	0.000
58	A	66	GLY	0	0.026	0.012	24.915	0.173	0.173	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.881	-0.945	22.431	-12.900	-12.900	0.000	0.000	0.000	0.000
60	A	68	ASN	0	-0.029	-0.013	23.278	-0.246	-0.246	0.000	0.000	0.000	0.000
61	A	69	TRP	0	0.105	0.027	19.033	0.030	0.030	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.922	0.968	19.863	11.506	11.506	0.000	0.000	0.000	0.000
63	A	71	LEU	0	-0.029	-0.009	22.143	0.051	0.051	0.000	0.000	0.000	0.000
64	A	72	LYS	1	0.911	0.972	17.279	15.722	15.722	0.000	0.000	0.000	0.000
65	A	73	ILE	0	0.017	0.024	16.772	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.040	-0.009	18.640	0.102	0.102	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.025	-0.036	20.431	0.643	0.643	0.000	0.000	0.000	0.000
68	A	76	LEU	0	0.037	0.020	14.183	0.118	0.118	0.000	0.000	0.000	0.000
69	A	77	LYS	1	0.862	0.930	17.200	12.883	12.883	0.000	0.000	0.000	0.000
70	A	78	LYS	1	0.837	0.921	18.898	11.291	11.291	0.000	0.000	0.000	0.000
71	A	79	ILE	0	0.039	0.035	16.834	0.266	0.266	0.000	0.000	0.000	0.000
72	A	80	LEU	0	-0.003	0.009	14.112	0.019	0.019	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.787	0.864	17.170	10.608	10.608	0.000	0.000	0.000	0.000
74	A	82	GLY	0	0.039	0.014	20.630	0.304	0.304	0.000	0.000	0.000	0.000
75	A	83	ILE	0	-0.004	0.001	14.908	0.175	0.175	0.000	0.000	0.000	0.000
76	A	84	LEU	0	-0.039	-0.024	17.058	0.186	0.186	0.000	0.000	0.000	0.000
77	A	85	ASP	-1	-0.794	-0.873	19.954	-10.265	-10.265	0.000	0.000	0.000	0.000
78	A	86	TYR	0	-0.029	-0.027	20.979	0.105	0.105	0.000	0.000	0.000	0.000
79	A	87	ASN	0	0.025	0.007	19.263	0.389	0.389	0.000	0.000	0.000	0.000
80	A	88	HIS	0	-0.042	-0.010	21.919	0.069	0.069	0.000	0.000	0.000	0.000
81	A	89	GLU	-1	-0.936	-0.959	24.775	-9.196	-9.196	0.000	0.000	0.000	0.000
82	A	90	ILE	0	-0.058	-0.023	25.748	0.342	0.342	0.000	0.000	0.000	0.000
83	A	91	LEU	0	-0.054	-0.004	20.829	0.141	0.141	0.000	0.000	0.000	0.000
84	A	92	GLY	0	0.011	0.008	25.030	0.139	0.139	0.000	0.000	0.000	0.000
85	A	93	GLN	0	-0.087	-0.056	22.736	-0.236	-0.236	0.000	0.000	0.000	0.000
86	A	94	GLN	0	0.002	0.005	20.473	-0.171	-0.171	0.000	0.000	0.000	0.000
87	A	95	ILE	0	-0.020	-0.012	15.055	-0.384	-0.384	0.000	0.000	0.000	0.000
88	A	96	ASN	0	-0.062	-0.034	13.387	0.666	0.666	0.000	0.000	0.000	0.000
89	A	97	ASP	-1	-0.866	-0.951	12.885	-14.692	-14.692	0.000	0.000	0.000	0.000
90	A	98	PHE	0	-0.044	-0.010	13.214	0.311	0.311	0.000	0.000	0.000	0.000
91	A	99	THR	0	-0.049	-0.032	8.936	0.059	0.059	0.000	0.000	0.000	0.000
92	A	100	LEU	0	0.019	0.014	10.755	-0.568	-0.568	0.000	0.000	0.000	0.000
93	A	101	PRO	0	0.004	0.006	8.800	-0.627	-0.627	0.000	0.000	0.000	0.000
94	A	102	ASP	-1	-0.802	-0.889	9.357	-15.260	-15.260	0.000	0.000	0.000	0.000
95	A	103	VAL	0	0.010	-0.023	11.118	-0.547	-0.547	0.000	0.000	0.000	0.000
96	A	104	ASN	0	-0.047	-0.048	13.084	1.093	1.093	0.000	0.000	0.000	0.000
97	A	105	LEU	0	0.040	0.028	9.837	0.361	0.361	0.000	0.000	0.000	0.000
98	A	106	ILE	0	-0.027	0.010	9.529	-0.390	-0.390	0.000	0.000	0.000	0.000
99	A	107	GLY	0	-0.009	-0.017	11.830	0.202	0.202	0.000	0.000	0.000	0.000
100	A	108	GLU	-1	-0.954	-0.985	15.306	-14.199	-14.199	0.000	0.000	0.000	0.000
101	A	109	HIS	0	-0.076	-0.047	12.484	-0.146	-0.146	0.000	0.000	0.000	0.000
102	A	110	SER	0	-0.038	-0.029	12.369	-0.847	-0.847	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.872	-0.931	6.430	-31.171	-31.171	0.000	0.000	0.000	0.000
104	A	112	ALA	0	0.070	0.018	6.450	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	113	ALA	0	-0.049	-0.017	2.475	-3.687	-2.903	0.398	-0.421	-0.762	-0.002
106	A	114	GLU	-1	-0.783	-0.882	3.409	-24.233	-23.886	-0.001	-0.019	-0.326	-0.001
107	A	115	LEU	0	0.018	-0.002	6.280	1.508	1.508	0.000	0.000	0.000	0.000
108	A	116	GLY	0	0.032	0.006	4.563	1.472	1.512	-0.001	-0.006	-0.032	0.000
109	A	117	ARG	1	0.846	0.905	5.009	27.265	27.265	0.000	0.000	0.000	0.000
110	A	118	MET	0	-0.026	-0.012	6.594	1.858	1.858	0.000	0.000	0.000	0.000
111	A	119	LEU	0	0.026	0.009	8.572	1.483	1.483	0.000	0.000	0.000	0.000
112	A	120	GLN	0	-0.011	-0.003	5.654	-0.589	-0.589	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.015	0.007	9.495	1.301	1.301	0.000	0.000	0.000	0.000
114	A	122	ILE	0	0.024	0.011	12.384	1.028	1.028	0.000	0.000	0.000	0.000
115	A	123	LEU	0	0.016	0.007	11.880	0.755	0.755	0.000	0.000	0.000	0.000
116	A	124	GLY	0	-0.006	-0.003	13.505	0.721	0.721	0.000	0.000	0.000	0.000
117	A	125	CYS	0	-0.024	-0.019	15.223	0.928	0.928	0.000	0.000	0.000	0.000
118	A	126	ALA	0	0.021	0.017	17.301	0.623	0.623	0.000	0.000	0.000	0.000
119	A	127	VAL	0	-0.028	-0.027	16.674	0.589	0.589	0.000	0.000	0.000	0.000
120	A	128	ASN	0	-0.082	-0.059	18.036	0.683	0.683	0.000	0.000	0.000	0.000
121	A	129	CYS	0	-0.008	0.039	21.190	0.455	0.455	0.000	0.000	0.000	0.000
122	A	130	GLU	-1	-0.932	-0.975	23.516	-9.067	-9.067	0.000	0.000	0.000	0.000
123	A	131	GLN	0	-0.045	-0.047	25.271	0.253	0.253	0.000	0.000	0.000	0.000
124	A	132	LYS	1	0.957	1.001	22.284	10.937	10.937	0.000	0.000	0.000	0.000
125	A	133	GLN	0	-0.020	-0.025	22.961	-0.597	-0.597	0.000	0.000	0.000	0.000
126	A	134	GLU	-1	-0.899	-0.923	24.842	-10.923	-10.923	0.000	0.000	0.000	0.000
127	A	135	TYR	0	0.047	0.012	19.780	-0.490	-0.490	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.006	-0.005	18.767	-0.680	-0.680	0.000	0.000	0.000	0.000
129	A	137	GLN	0	-0.005	-0.003	20.896	-0.317	-0.317	0.000	0.000	0.000	0.000
130	A	138	ALA	0	0.000	-0.001	21.016	-0.149	-0.149	0.000	0.000	0.000	0.000
131	A	139	ILE	0	0.013	-0.003	15.840	-0.539	-0.539	0.000	0.000	0.000	0.000
132	A	140	MET	0	-0.012	-0.005	18.290	-0.710	-0.710	0.000	0.000	0.000	0.000
133	A	141	MET	0	-0.028	-0.004	20.391	0.095	0.095	0.000	0.000	0.000	0.000
134	A	142	MET	0	-0.045	-0.008	14.295	0.035	0.035	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.915	-0.954	16.579	-17.954	-17.954	0.000	0.000	0.000	0.000
136	A	144	GLU	-1	-0.947	-0.981	19.319	-11.561	-11.561	0.000	0.000	0.000	0.000
137	A	145	SER	0	-0.058	-0.026	20.600	0.390	0.390	0.000	0.000	0.000	0.000
138	A	146	VAL	0	0.034	0.012	16.621	0.162	0.162	0.000	0.000	0.000	0.000
139	A	147	GLN	0	-0.023	-0.019	19.124	0.249	0.249	0.000	0.000	0.000	0.000
140	A	148	HIS	0	0.023	0.020	22.508	0.487	0.487	0.000	0.000	0.000	0.000
141	A	149	VAL	0	-0.012	0.018	19.793	0.395	0.395	0.000	0.000	0.000	0.000
142	A	150	VAL	0	0.001	0.002	19.384	0.220	0.220	0.000	0.000	0.000	0.000
143	A	151	MET	0	-0.006	0.001	22.022	0.453	0.453	0.000	0.000	0.000	0.000
144	A	152	THR	0	-0.023	-0.029	25.133	0.588	0.588	0.000	0.000	0.000	0.000
145	A	153	ALA	0	0.005	0.003	22.498	0.296	0.296	0.000	0.000	0.000	0.000
146	A	154	ILE	0	-0.027	-0.020	23.904	0.302	0.302	0.000	0.000	0.000	0.000
147	A	155	GLN	0	-0.043	-0.048	26.372	0.640	0.640	0.000	0.000	0.000	0.000
148	A	156	GLU	-1	-0.967	-0.969	27.114	-10.095	-10.095	0.000	0.000	0.000	0.000
149	A	157	LEU	0	-0.093	-0.037	24.100	0.063	0.063	0.000	0.000	0.000	0.000
150	A	158	MET	0	-0.098	-0.022	28.724	0.282	0.282	0.000	0.000	0.000	0.000

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