FMO DATABASE

FMODB ID: 52R7Z

Calculation Name: 1JFI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JFI

Chain ID: B

ChEMBL ID:

UniProt ID: Q14919

Base Structure: X-ray

Registration Date: 2023-06-22

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905040.297131
FMO2-HF: Nuclear repulsion	850865.311919
FMO2-HF: Total energy	-54174.985212
FMO2-MP2: Total energy	-54331.81259

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(B:109:ASP)

Summations of interaction energy for fragment #1(B:109:ASP)

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.
-15.003	-10.952	1.23	-2.236	-3.046	0.008

Interaction energy analysis for fragmet #1(B:109:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.984 / q_NPA : -0.996

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	B	111	LEU	0	-0.065	-0.027	2.285	-11.902	-7.829	1.230	-2.215	-3.088	0.008
4	B	112	THR	0	0.029	0.007	4.179	-3.516	-3.538	0.000	-0.021	0.042	0.000
5	B	113	ILE	0	-0.017	-0.004	7.757	-0.545	-0.545	0.000	0.000	0.000	0.000
6	B	114	PRO	0	0.044	0.013	10.931	-0.879	-0.879	0.000	0.000	0.000	0.000
7	B	115	ARG	1	0.905	0.913	13.092	-18.147	-18.147	0.000	0.000	0.000	0.000
8	B	116	ALA	0	-0.023	-0.014	15.474	-0.902	-0.902	0.000	0.000	0.000	0.000
9	B	117	ALA	0	0.013	0.011	15.749	-0.871	-0.871	0.000	0.000	0.000	0.000
10	B	118	ILE	0	0.087	0.040	14.523	-0.828	-0.828	0.000	0.000	0.000	0.000
11	B	119	ASN	0	-0.025	-0.012	18.109	-0.815	-0.815	0.000	0.000	0.000	0.000
12	B	120	LYS	1	0.796	0.886	20.824	-12.885	-12.885	0.000	0.000	0.000	0.000
13	B	121	MET	0	0.062	0.041	20.619	-0.405	-0.405	0.000	0.000	0.000	0.000
14	B	122	ILE	0	0.009	0.003	20.791	-0.602	-0.602	0.000	0.000	0.000	0.000
15	B	123	LYS	1	0.898	0.959	23.977	-10.481	-10.481	0.000	0.000	0.000	0.000
16	B	124	GLU	-1	-0.810	-0.899	25.077	11.294	11.294	0.000	0.000	0.000	0.000
17	B	125	THR	0	-0.007	0.004	25.157	-0.297	-0.297	0.000	0.000	0.000	0.000
18	B	126	LEU	0	-0.057	-0.032	26.420	-0.348	-0.348	0.000	0.000	0.000	0.000
19	B	127	PRO	0	0.015	0.005	29.193	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	128	ASN	0	-0.101	-0.050	31.525	-0.134	-0.134	0.000	0.000	0.000	0.000
21	B	129	VAL	0	0.086	0.043	29.213	-0.202	-0.202	0.000	0.000	0.000	0.000
22	B	130	ARG	1	0.898	0.956	28.822	-8.556	-8.556	0.000	0.000	0.000	0.000
23	B	131	VAL	0	0.059	0.029	23.482	-0.054	-0.054	0.000	0.000	0.000	0.000
24	B	132	ALA	0	0.029	0.017	24.836	0.170	0.170	0.000	0.000	0.000	0.000
25	B	133	ASN	0	0.037	-0.002	20.418	0.712	0.712	0.000	0.000	0.000	0.000
26	B	134	ASP	-1	-0.868	-0.928	20.028	14.382	14.382	0.000	0.000	0.000	0.000
27	B	135	ALA	0	0.053	0.018	19.405	0.567	0.567	0.000	0.000	0.000	0.000
28	B	136	ARG	1	0.831	0.906	19.237	-12.302	-12.302	0.000	0.000	0.000	0.000
29	B	137	GLU	-1	-0.785	-0.881	13.579	20.571	20.571	0.000	0.000	0.000	0.000
30	B	138	LEU	0	0.033	0.042	14.941	1.018	1.018	0.000	0.000	0.000	0.000
31	B	139	VAL	0	0.012	0.010	15.879	0.463	0.463	0.000	0.000	0.000	0.000
32	B	140	VAL	0	-0.005	-0.005	11.552	0.299	0.299	0.000	0.000	0.000	0.000
33	B	141	ASN	0	0.002	-0.011	10.629	2.867	2.867	0.000	0.000	0.000	0.000
34	B	142	CYS	0	-0.016	0.001	11.806	0.458	0.458	0.000	0.000	0.000	0.000
35	B	143	CYS	0	-0.090	-0.044	12.591	-0.162	-0.162	0.000	0.000	0.000	0.000
36	B	144	THR	0	0.022	0.010	6.744	0.037	0.037	0.000	0.000	0.000	0.000
37	B	145	GLU	-1	-0.929	-0.951	9.745	18.952	18.952	0.000	0.000	0.000	0.000
38	B	146	PHE	0	0.021	0.005	11.460	-0.232	-0.232	0.000	0.000	0.000	0.000
39	B	147	ILE	0	-0.004	-0.002	9.471	-0.445	-0.445	0.000	0.000	0.000	0.000
40	B	148	HIS	0	0.044	0.035	5.713	-1.749	-1.749	0.000	0.000	0.000	0.000
41	B	149	LEU	0	-0.001	0.022	10.775	-0.704	-0.704	0.000	0.000	0.000	0.000
42	B	150	ILE	0	-0.014	-0.014	14.374	-0.733	-0.733	0.000	0.000	0.000	0.000
43	B	151	SER	0	-0.032	-0.037	11.651	-0.535	-0.535	0.000	0.000	0.000	0.000
44	B	152	SER	0	-0.035	-0.027	12.544	-0.112	-0.112	0.000	0.000	0.000	0.000
45	B	153	GLU	-1	-0.826	-0.886	14.585	13.246	13.246	0.000	0.000	0.000	0.000
46	B	154	ALA	0	-0.017	-0.018	16.631	-0.762	-0.762	0.000	0.000	0.000	0.000
47	B	155	ASN	0	-0.021	-0.030	14.974	-0.247	-0.247	0.000	0.000	0.000	0.000
48	B	156	GLU	-1	-0.880	-0.920	17.128	13.697	13.697	0.000	0.000	0.000	0.000
49	B	157	ILE	0	-0.050	-0.024	20.043	-0.664	-0.664	0.000	0.000	0.000	0.000
50	B	158	CYS	0	-0.034	0.000	19.583	-0.560	-0.560	0.000	0.000	0.000	0.000
51	B	159	ASN	0	0.005	0.017	18.829	-0.448	-0.448	0.000	0.000	0.000	0.000
52	B	160	LYS	1	0.894	0.937	22.456	-13.473	-13.473	0.000	0.000	0.000	0.000
53	B	161	SER	0	-0.090	-0.035	24.249	-0.466	-0.466	0.000	0.000	0.000	0.000
54	B	162	GLU	-1	-0.859	-0.950	26.509	10.755	10.755	0.000	0.000	0.000	0.000
55	B	163	LYS	1	0.815	0.933	23.951	-11.379	-11.379	0.000	0.000	0.000	0.000
56	B	164	LYS	1	0.954	0.968	19.515	-15.154	-15.154	0.000	0.000	0.000	0.000
57	B	165	THR	0	-0.046	-0.032	18.195	0.863	0.863	0.000	0.000	0.000	0.000
58	B	166	ILE	0	0.051	0.032	14.680	-0.859	-0.859	0.000	0.000	0.000	0.000
59	B	167	SER	0	-0.023	-0.015	18.663	0.051	0.051	0.000	0.000	0.000	0.000
60	B	168	PRO	0	0.008	-0.036	20.926	0.096	0.096	0.000	0.000	0.000	0.000
61	B	169	GLU	-1	-0.879	-0.913	22.045	11.083	11.083	0.000	0.000	0.000	0.000
62	B	170	HIS	0	0.061	0.039	20.444	0.384	0.384	0.000	0.000	0.000	0.000
63	B	171	VAL	0	0.028	0.011	17.680	0.129	0.129	0.000	0.000	0.000	0.000
64	B	172	ILE	0	-0.022	-0.008	20.259	-0.133	-0.133	0.000	0.000	0.000	0.000
65	B	173	GLN	0	-0.062	-0.054	23.662	-0.094	-0.094	0.000	0.000	0.000	0.000
66	B	174	ALA	0	0.060	0.023	19.610	-0.255	-0.255	0.000	0.000	0.000	0.000
67	B	175	LEU	0	0.010	0.005	19.625	-0.027	-0.027	0.000	0.000	0.000	0.000
68	B	176	GLU	-1	-0.935	-0.971	22.505	10.144	10.144	0.000	0.000	0.000	0.000
69	B	177	SER	0	-0.099	-0.064	23.594	-0.409	-0.409	0.000	0.000	0.000	0.000
70	B	178	LEU	0	-0.022	-0.010	18.419	-0.036	-0.036	0.000	0.000	0.000	0.000
71	B	179	GLY	0	-0.035	0.004	22.935	-0.073	-0.073	0.000	0.000	0.000	0.000
72	B	180	PHE	0	-0.040	-0.037	19.687	-0.072	-0.072	0.000	0.000	0.000	0.000
73	B	181	GLY	0	0.095	0.043	24.686	0.019	0.019	0.000	0.000	0.000	0.000
74	B	182	SER	0	-0.075	-0.037	27.588	-0.127	-0.127	0.000	0.000	0.000	0.000
75	B	183	TYR	0	-0.001	-0.003	21.737	0.004	0.004	0.000	0.000	0.000	0.000
76	B	184	ILE	0	-0.011	-0.007	25.753	0.032	0.032	0.000	0.000	0.000	0.000
77	B	185	SER	0	-0.013	0.002	27.156	-0.228	-0.228	0.000	0.000	0.000	0.000
78	B	186	GLU	-1	-0.873	-0.946	26.871	10.803	10.803	0.000	0.000	0.000	0.000
79	B	187	VAL	0	-0.021	-0.007	22.717	0.264	0.264	0.000	0.000	0.000	0.000
80	B	188	LYS	1	0.924	0.967	25.135	-9.901	-9.901	0.000	0.000	0.000	0.000
81	B	189	GLU	-1	-0.918	-0.958	27.829	9.811	9.811	0.000	0.000	0.000	0.000
82	B	190	VAL	0	0.041	0.021	22.550	-0.035	-0.035	0.000	0.000	0.000	0.000
83	B	191	LEU	0	0.007	0.010	24.088	0.111	0.111	0.000	0.000	0.000	0.000
84	B	192	GLN	0	0.058	0.021	25.604	0.115	0.115	0.000	0.000	0.000	0.000
85	B	193	GLU	-1	-0.887	-0.930	26.013	11.466	11.466	0.000	0.000	0.000	0.000
86	B	194	CYS	0	0.000	0.003	23.579	0.156	0.156	0.000	0.000	0.000	0.000
87	B	195	LYS	1	0.899	0.954	25.974	-10.692	-10.692	0.000	0.000	0.000	0.000
88	B	196	THR	0	-0.060	-0.040	28.520	-0.387	-0.387	0.000	0.000	0.000	0.000
89	B	197	VAL	0	-0.004	-0.001	26.156	-0.312	-0.312	0.000	0.000	0.000	0.000
90	B	198	ALA	0	0.015	0.009	26.476	-0.118	-0.118	0.000	0.000	0.000	0.000
91	B	199	LEU	0	-0.012	-0.017	28.309	-0.249	-0.249	0.000	0.000	0.000	0.000
92	B	200	LYS	1	0.934	0.949	31.999	-9.603	-9.603	0.000	0.000	0.000	0.000
93	B	201	ARG	1	0.961	0.988	25.285	-12.238	-12.238	0.000	0.000	0.000	0.000
94	B	202	ARG	1	0.947	0.985	30.111	-10.076	-10.076	0.000	0.000	0.000	0.000
95	B	203	LYS	1	0.955	0.967	32.163	-8.910	-8.910	0.000	0.000	0.000	0.000
96	B	204	ALA	0	-0.025	-0.007	33.149	-0.261	-0.261	0.000	0.000	0.000	0.000
97	B	205	SER	0	0.054	0.028	31.438	-0.094	-0.094	0.000	0.000	0.000	0.000
98	B	206	SER	0	0.000	0.008	34.024	-0.223	-0.223	0.000	0.000	0.000	0.000
99	B	207	ARG	1	0.957	0.977	36.975	-8.377	-8.377	0.000	0.000	0.000	0.000
100	B	208	LEU	0	-0.023	0.001	34.194	-0.187	-0.187	0.000	0.000	0.000	0.000
101	B	209	GLU	-1	-0.927	-0.970	34.066	9.277	9.277	0.000	0.000	0.000	0.000
102	B	210	ASN	0	-0.073	-0.040	38.479	-0.261	-0.261	0.000	0.000	0.000	0.000
103	B	211	LEU	0	-0.082	-0.047	41.623	-0.173	-0.173	0.000	0.000	0.000	0.000
104	B	212	GLY	0	0.011	0.023	42.343	-0.080	-0.080	0.000	0.000	0.000	0.000
105	B	213	ILE	0	-0.019	-0.012	43.232	-0.116	-0.116	0.000	0.000	0.000	0.000
106	B	214	PRO	0	0.045	0.026	44.753	0.128	0.128	0.000	0.000	0.000	0.000
107	B	215	GLU	-1	-0.898	-0.968	41.702	7.591	7.591	0.000	0.000	0.000	0.000
108	B	216	GLU	-1	-0.931	-0.951	44.856	6.273	6.273	0.000	0.000	0.000	0.000
109	B	217	GLU	-1	-0.801	-0.903	48.271	6.238	6.238	0.000	0.000	0.000	0.000
110	B	218	LEU	0	-0.050	-0.011	41.820	0.025	0.025	0.000	0.000	0.000	0.000
111	B	219	LEU	0	0.010	0.006	44.262	0.033	0.033	0.000	0.000	0.000	0.000
112	B	220	ARG	1	0.797	0.877	45.796	-6.123	-6.123	0.000	0.000	0.000	0.000
113	B	221	GLN	0	0.017	0.001	46.539	-0.022	-0.022	0.000	0.000	0.000	0.000
114	B	222	GLN	0	-0.024	-0.014	39.773	-0.057	-0.057	0.000	0.000	0.000	0.000
115	B	223	GLN	0	-0.007	-0.022	45.216	0.039	0.039	0.000	0.000	0.000	0.000
116	B	224	GLU	-1	-0.842	-0.891	47.527	6.048	6.048	0.000	0.000	0.000	0.000
117	B	225	LEU	0	-0.056	-0.040	44.477	-0.082	-0.082	0.000	0.000	0.000	0.000
118	B	226	PHE	0	-0.005	-0.005	41.073	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	227	ALA	0	-0.025	-0.019	46.793	-0.034	-0.034	0.000	0.000	0.000	0.000
120	B	228	LYS	1	0.973	0.998	48.668	-6.591	-6.591	0.000	0.000	0.000	0.000
121	B	229	ALA	0	-0.017	-0.006	46.803	-0.068	-0.068	0.000	0.000	0.000	0.000
122	B	230	ARG	1	0.945	0.968	46.885	-6.696	-6.696	0.000	0.000	0.000	0.000
123	B	231	GLN	0	0.007	0.001	50.078	-0.010	-0.010	0.000	0.000	0.000	0.000
124	B	232	GLN	0	0.059	0.045	49.316	0.050	0.050	0.000	0.000	0.000	0.000
125	B	233	GLN	0	-0.039	-0.040	47.458	-0.099	-0.099	0.000	0.000	0.000	0.000
126	B	234	ALA	0	-0.002	0.018	50.918	-0.012	-0.012	0.000	0.000	0.000	0.000
127	B	235	GLU	-1	-0.952	-0.975	53.832	5.542	5.542	0.000	0.000	0.000	0.000
128	B	236	LEU	0	-0.008	-0.004	50.679	-0.057	-0.057	0.000	0.000	0.000	0.000
129	B	237	ALA	0	0.016	0.027	52.190	0.002	0.002	0.000	0.000	0.000	0.000
130	B	238	GLN	0	-0.001	-0.028	54.078	-0.031	-0.031	0.000	0.000	0.000	0.000
131	B	239	GLN	0	-0.028	-0.028	57.578	-0.035	-0.035	0.000	0.000	0.000	0.000
132	B	240	GLU	-1	-0.961	-0.969	53.055	6.015	6.015	0.000	0.000	0.000	0.000
133	B	241	TRP	0	-0.078	-0.037	52.281	-0.031	-0.031	0.000	0.000	0.000	0.000
134	B	242	LEU	0	-0.076	-0.023	58.412	-0.084	-0.084	0.000	0.000	0.000	0.000
135	B	243	GLN	0	-0.048	-0.013	58.838	-0.140	-0.140	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:109:ASP)