FMO DATABASE

FMODB ID: 82JGY

Calculation Name: 4NJ7-D-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NJ7

Chain ID: D

ChEMBL ID:

UniProt ID: P93022

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	77
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-473393.136169
FMO2-HF: Nuclear repulsion	443685.163694
FMO2-HF: Total energy	-29707.972475
FMO2-MP2: Total energy	-29795.350012

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(D:1039:ACE )

Summations of interaction energy for fragment #1(D:1039:ACE )

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.
0.031	0.905	-0.004	-0.472	-0.398	-0.001

Interaction energy analysis for fragmet #1(D:1039:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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

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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	D	1041	THR	0	0.070	0.048	3.869	0.645	1.519	-0.004	-0.472	-0.398	-0.001
4	D	1042	ALA	0	-0.022	-0.005	7.206	0.152	0.152	0.000	0.000	0.000	0.000
5	D	1043	VAL	0	0.034	0.017	10.372	0.043	0.043	0.000	0.000	0.000	0.000
6	D	1044	GLN	0	-0.047	-0.030	13.750	0.021	0.021	0.000	0.000	0.000	0.000
7	D	1045	LYS	1	1.001	1.006	16.876	0.137	0.137	0.000	0.000	0.000	0.000
8	D	1046	ARG	1	0.996	0.997	20.540	0.078	0.078	0.000	0.000	0.000	0.000
9	D	1047	GLY	0	-0.021	-0.016	23.267	0.000	0.000	0.000	0.000	0.000	0.000
10	D	1048	SER	0	-0.020	-0.001	21.197	0.002	0.002	0.000	0.000	0.000	0.000
11	D	1049	VAL	0	0.021	0.018	17.429	0.004	0.004	0.000	0.000	0.000	0.000
12	D	1050	GLY	0	-0.013	-0.002	15.650	-0.015	-0.015	0.000	0.000	0.000	0.000
13	D	1051	ARG	1	0.911	0.951	13.414	0.331	0.331	0.000	0.000	0.000	0.000
14	D	1052	SER	0	0.031	0.007	7.793	0.058	0.058	0.000	0.000	0.000	0.000
15	D	1053	ILE	0	-0.014	0.004	9.101	0.038	0.038	0.000	0.000	0.000	0.000
16	D	1054	ASP	-1	-0.831	-0.926	6.309	-2.312	-2.312	0.000	0.000	0.000	0.000
17	D	1055	VAL	0	0.024	-0.014	7.452	0.403	0.403	0.000	0.000	0.000	0.000
18	D	1056	ASN	0	0.025	0.015	7.044	0.399	0.399	0.000	0.000	0.000	0.000
19	D	1057	ARG	1	0.865	0.953	10.207	0.682	0.682	0.000	0.000	0.000	0.000
20	D	1058	TYR	0	-0.113	-0.125	12.007	0.083	0.083	0.000	0.000	0.000	0.000
21	D	1059	ARG	1	0.892	0.957	14.679	0.219	0.219	0.000	0.000	0.000	0.000
22	D	1060	GLY	0	0.052	0.012	17.439	0.022	0.022	0.000	0.000	0.000	0.000
23	D	1061	TYR	0	-0.012	-0.033	16.850	-0.029	-0.029	0.000	0.000	0.000	0.000
24	D	1062	ASP	-1	-0.898	-0.943	19.241	-0.172	-0.172	0.000	0.000	0.000	0.000
25	D	1063	GLU	-1	-0.838	-0.926	17.650	-0.301	-0.301	0.000	0.000	0.000	0.000
26	D	1064	LEU	0	0.011	0.017	13.681	-0.003	-0.003	0.000	0.000	0.000	0.000
27	D	1065	ARG	1	0.941	0.969	17.225	0.192	0.192	0.000	0.000	0.000	0.000
28	D	1066	HIS	0	-0.037	0.000	20.203	0.020	0.020	0.000	0.000	0.000	0.000
29	D	1067	ASP	-1	-0.788	-0.829	16.045	-0.360	-0.360	0.000	0.000	0.000	0.000
30	D	1068	LEU	0	0.014	0.006	14.580	0.007	0.007	0.000	0.000	0.000	0.000
31	D	1069	ALA	0	0.021	0.001	18.430	0.018	0.018	0.000	0.000	0.000	0.000
32	D	1070	ARG	1	0.879	0.924	19.320	0.256	0.256	0.000	0.000	0.000	0.000
33	D	1071	MET	0	-0.087	-0.030	16.139	0.031	0.031	0.000	0.000	0.000	0.000
34	D	1072	PHE	0	-0.081	-0.037	16.518	0.007	0.007	0.000	0.000	0.000	0.000
35	D	1073	GLY	0	-0.010	-0.007	21.727	0.017	0.017	0.000	0.000	0.000	0.000
36	D	1074	ILE	0	-0.065	-0.032	23.511	0.014	0.014	0.000	0.000	0.000	0.000
37	D	1075	NME	0	0.006	0.016	25.389	0.001	0.001	0.000	0.000	0.000	0.000
38	D	1085	ACE	0	-0.004	-0.011	30.948	0.001	0.001	0.000	0.000	0.000	0.000
39	D	1086	TRP	0	-0.011	-0.018	24.840	-0.003	-0.003	0.000	0.000	0.000	0.000
40	D	1087	LYS	1	0.944	0.968	24.158	0.099	0.099	0.000	0.000	0.000	0.000
41	D	1088	LEU	0	0.039	0.032	17.854	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	1089	VAL	0	0.009	0.007	18.894	0.003	0.003	0.000	0.000	0.000	0.000
43	D	1090	TYR	0	-0.019	-0.057	13.954	-0.045	-0.045	0.000	0.000	0.000	0.000
44	D	1091	VAL	0	-0.056	-0.010	14.203	0.029	0.029	0.000	0.000	0.000	0.000
45	D	1092	ALA	0	0.047	0.036	13.724	-0.007	-0.007	0.000	0.000	0.000	0.000
46	D	1093	HIS	0	0.028	0.006	15.276	0.027	0.027	0.000	0.000	0.000	0.000
47	D	1094	GLU	-1	-0.936	-0.956	17.044	0.031	0.031	0.000	0.000	0.000	0.000
48	D	1095	ASN	0	-0.047	-0.039	17.118	-0.014	-0.014	0.000	0.000	0.000	0.000
49	D	1096	ALA	0	0.015	0.028	18.179	-0.008	-0.008	0.000	0.000	0.000	0.000
50	D	1097	ILE	0	-0.011	-0.021	18.414	-0.017	-0.017	0.000	0.000	0.000	0.000
51	D	1098	LEU	0	-0.001	0.003	18.377	0.013	0.013	0.000	0.000	0.000	0.000
52	D	1099	LEU	0	-0.018	-0.020	19.521	-0.021	-0.021	0.000	0.000	0.000	0.000
53	D	1100	VAL	0	-0.015	-0.003	16.673	-0.004	-0.004	0.000	0.000	0.000	0.000
54	D	1101	GLY	0	-0.063	-0.059	19.173	0.006	0.006	0.000	0.000	0.000	0.000
55	D	1102	ASP	-1	-0.908	-0.927	20.874	-0.108	-0.108	0.000	0.000	0.000	0.000
56	D	1103	ASP	-1	-0.852	-0.894	18.172	-0.142	-0.142	0.000	0.000	0.000	0.000
57	D	1104	PRO	0	0.057	0.027	19.474	-0.019	-0.019	0.000	0.000	0.000	0.000
58	D	1105	TRP	0	-0.006	0.010	13.904	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	1106	GLU	-1	-0.880	-0.964	15.086	-0.243	-0.243	0.000	0.000	0.000	0.000
60	D	1107	GLU	-1	-0.949	-0.965	14.170	-0.102	-0.102	0.000	0.000	0.000	0.000
61	D	1108	PHE	0	-0.003	-0.003	13.544	-0.031	-0.031	0.000	0.000	0.000	0.000
62	D	1109	VAL	0	-0.036	-0.035	10.221	-0.049	-0.049	0.000	0.000	0.000	0.000
63	D	1110	ASN	0	-0.044	-0.015	9.008	-0.125	-0.125	0.000	0.000	0.000	0.000
64	D	1111	CYS	0	-0.016	-0.006	10.349	0.086	0.086	0.000	0.000	0.000	0.000
65	D	1112	VAL	0	-0.062	0.009	8.981	0.037	0.037	0.000	0.000	0.000	0.000
66	D	1113	GLN	0	0.028	0.002	8.368	-0.111	-0.111	0.000	0.000	0.000	0.000
67	D	1114	SER	0	-0.084	-0.039	9.011	-0.054	-0.054	0.000	0.000	0.000	0.000
68	D	1115	ILE	0	0.056	0.022	11.605	0.037	0.037	0.000	0.000	0.000	0.000
69	D	1116	LYS	1	0.893	0.940	14.145	0.150	0.150	0.000	0.000	0.000	0.000
70	D	1117	ILE	0	0.005	0.003	17.552	0.005	0.005	0.000	0.000	0.000	0.000
71	D	1118	LEU	0	-0.022	0.000	20.598	0.013	0.013	0.000	0.000	0.000	0.000
72	D	1119	SER	0	0.003	-0.014	23.583	0.002	0.002	0.000	0.000	0.000	0.000
73	D	1120	SER	0	0.000	-0.030	27.198	0.000	0.000	0.000	0.000	0.000	0.000
74	D	1121	ALA	0	0.016	0.004	30.058	0.005	0.005	0.000	0.000	0.000	0.000
75	D	1122	GLU	-1	-0.925	-0.958	24.573	-0.098	-0.098	0.000	0.000	0.000	0.000
76	D	1123	VAL	0	-0.031	0.012	25.866	0.000	0.000	0.000	0.000	0.000	0.000
77	D	1124	NME	0	0.000	0.008	27.985	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1039:ACE )