FMO DATABASE

FMODB ID: 9G6N2

Calculation Name: 4NJ7-D-Xray372

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: 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	OptH
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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-464698.149196
FMO2-HF: Nuclear repulsion	435332.140407
FMO2-HF: Total energy	-29366.008788
FMO2-MP2: Total energy	-29452.314853

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:1040:TYR)

Summations of interaction energy for fragment #1(D:1040:TYR)

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.
-5.134	3.788	3.627	-3.641	-8.907	-0.011

Interaction energy analysis for fragmet #1(D:1040:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.030

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	1042	ALA	0	-0.028	-0.009	3.741	-0.319	1.342	-0.026	-0.752	-0.883	-0.001
4	D	1043	VAL	0	0.036	0.019	5.817	0.392	0.392	0.000	0.000	0.000	0.000
5	D	1044	GLN	0	-0.046	-0.029	8.770	-0.064	-0.064	0.000	0.000	0.000	0.000
6	D	1045	LYS	1	0.999	1.005	11.931	0.386	0.386	0.000	0.000	0.000	0.000
7	D	1046	ARG	1	0.995	0.997	15.425	0.245	0.245	0.000	0.000	0.000	0.000
8	D	1047	GLY	0	-0.021	-0.017	18.360	0.018	0.018	0.000	0.000	0.000	0.000
9	D	1048	SER	0	-0.021	-0.001	15.497	0.027	0.027	0.000	0.000	0.000	0.000
10	D	1049	VAL	0	0.021	0.018	11.863	-0.011	-0.011	0.000	0.000	0.000	0.000
11	D	1050	GLY	0	-0.012	-0.002	10.663	-0.013	-0.013	0.000	0.000	0.000	0.000
12	D	1051	ARG	1	0.911	0.952	6.903	1.043	1.043	0.000	0.000	0.000	0.000
13	D	1052	SER	0	0.033	0.007	2.463	-0.653	0.289	0.621	-0.548	-1.015	0.001
14	D	1053	ILE	0	-0.010	0.006	2.981	-2.924	-1.000	0.527	-0.626	-1.825	-0.006
15	D	1054	ASP	-1	-0.854	-0.936	2.905	-0.310	3.754	2.468	-1.675	-4.857	-0.006
16	D	1055	VAL	0	0.037	-0.007	4.105	-1.389	-1.058	0.037	-0.040	-0.327	0.001
17	D	1056	ASN	0	0.027	0.017	6.281	-0.645	-0.645	0.000	0.000	0.000	0.000
18	D	1057	ARG	1	0.863	0.950	5.234	-0.840	-0.840	0.000	0.000	0.000	0.000
19	D	1058	TYR	0	-0.113	-0.125	7.609	-0.245	-0.245	0.000	0.000	0.000	0.000
20	D	1059	ARG	1	0.892	0.958	11.606	-0.132	-0.132	0.000	0.000	0.000	0.000
21	D	1060	GLY	0	0.052	0.012	14.719	0.013	0.013	0.000	0.000	0.000	0.000
22	D	1061	TYR	0	-0.009	-0.031	14.028	-0.037	-0.037	0.000	0.000	0.000	0.000
23	D	1062	ASP	-1	-0.899	-0.943	15.827	-0.066	-0.066	0.000	0.000	0.000	0.000
24	D	1063	GLU	-1	-0.841	-0.928	13.588	0.096	0.096	0.000	0.000	0.000	0.000
25	D	1064	LEU	0	0.011	0.018	9.499	-0.064	-0.064	0.000	0.000	0.000	0.000
26	D	1065	ARG	1	0.945	0.970	12.854	0.009	0.009	0.000	0.000	0.000	0.000
27	D	1066	HIS	0	-0.041	-0.002	15.439	-0.035	-0.035	0.000	0.000	0.000	0.000
28	D	1067	ASP	-1	-0.787	-0.829	9.610	-0.590	-0.590	0.000	0.000	0.000	0.000
29	D	1068	LEU	0	0.019	0.007	9.136	-0.076	-0.076	0.000	0.000	0.000	0.000
30	D	1069	ALA	0	0.012	-0.004	12.483	-0.021	-0.021	0.000	0.000	0.000	0.000
31	D	1070	ARG	1	0.878	0.928	12.198	0.362	0.362	0.000	0.000	0.000	0.000
32	D	1071	MET	0	-0.091	-0.031	8.537	0.005	0.005	0.000	0.000	0.000	0.000
33	D	1072	PHE	0	-0.081	-0.038	10.522	-0.036	-0.036	0.000	0.000	0.000	0.000
34	D	1073	GLY	0	-0.007	-0.001	15.172	0.032	0.032	0.000	0.000	0.000	0.000
35	D	1074	ILE	0	-0.052	-0.019	17.828	0.035	0.035	0.000	0.000	0.000	0.000
36	D	1086	TRP	0	-0.019	-0.022	19.930	-0.005	-0.005	0.000	0.000	0.000	0.000
37	D	1087	LYS	1	0.932	0.956	20.550	0.157	0.157	0.000	0.000	0.000	0.000
38	D	1088	LEU	0	0.037	0.029	13.539	-0.033	-0.033	0.000	0.000	0.000	0.000
39	D	1089	VAL	0	0.007	0.006	15.755	0.041	0.041	0.000	0.000	0.000	0.000
40	D	1090	TYR	0	-0.010	-0.055	11.696	-0.118	-0.118	0.000	0.000	0.000	0.000
41	D	1091	VAL	0	-0.073	-0.028	12.336	0.027	0.027	0.000	0.000	0.000	0.000
42	D	1092	ALA	0	0.029	0.036	12.846	-0.015	-0.015	0.000	0.000	0.000	0.000
43	D	1093	HIS	0	0.042	0.021	14.077	-0.006	-0.006	0.000	0.000	0.000	0.000
44	D	1094	GLU	-1	-0.878	-0.926	15.031	-0.021	-0.021	0.000	0.000	0.000	0.000
45	D	1095	ASN	0	-0.020	-0.018	16.579	-0.038	-0.038	0.000	0.000	0.000	0.000
46	D	1096	ALA	0	-0.029	-0.012	17.667	-0.024	-0.024	0.000	0.000	0.000	0.000
47	D	1097	ILE	0	-0.013	-0.024	17.143	-0.020	-0.020	0.000	0.000	0.000	0.000
48	D	1098	LEU	0	0.015	0.011	16.911	0.023	0.023	0.000	0.000	0.000	0.000
49	D	1099	LEU	0	-0.025	-0.023	17.063	-0.045	-0.045	0.000	0.000	0.000	0.000
50	D	1100	VAL	0	-0.011	-0.001	13.681	0.019	0.019	0.000	0.000	0.000	0.000
51	D	1101	GLY	0	-0.061	-0.060	16.275	-0.008	-0.008	0.000	0.000	0.000	0.000
52	D	1102	ASP	-1	-0.911	-0.929	18.035	-0.027	-0.027	0.000	0.000	0.000	0.000
53	D	1103	ASP	-1	-0.847	-0.891	16.506	0.034	0.034	0.000	0.000	0.000	0.000
54	D	1104	PRO	0	0.051	0.024	17.967	-0.002	-0.002	0.000	0.000	0.000	0.000
55	D	1105	TRP	0	-0.008	0.009	11.057	-0.058	-0.058	0.000	0.000	0.000	0.000
56	D	1106	GLU	-1	-0.884	-0.968	13.474	0.427	0.427	0.000	0.000	0.000	0.000
57	D	1107	GLU	-1	-0.948	-0.964	13.647	0.225	0.225	0.000	0.000	0.000	0.000
58	D	1108	PHE	0	0.004	0.002	10.434	0.000	0.000	0.000	0.000	0.000	0.000
59	D	1109	VAL	0	-0.045	-0.040	8.770	-0.021	-0.021	0.000	0.000	0.000	0.000
60	D	1110	ASN	0	-0.047	-0.017	8.316	0.360	0.360	0.000	0.000	0.000	0.000
61	D	1111	CYS	0	-0.019	-0.006	10.749	0.011	0.011	0.000	0.000	0.000	0.000
62	D	1112	VAL	0	-0.063	0.013	6.991	-0.163	-0.163	0.000	0.000	0.000	0.000
63	D	1113	GLN	0	0.029	0.002	7.500	0.000	0.000	0.000	0.000	0.000	0.000
64	D	1114	SER	0	-0.091	-0.043	7.180	-0.514	-0.514	0.000	0.000	0.000	0.000
65	D	1115	ILE	0	0.064	0.026	8.752	0.232	0.232	0.000	0.000	0.000	0.000
66	D	1116	LYS	1	0.886	0.936	10.733	0.427	0.427	0.000	0.000	0.000	0.000
67	D	1117	ILE	0	0.009	0.004	13.557	0.063	0.063	0.000	0.000	0.000	0.000
68	D	1118	LEU	0	-0.022	0.002	16.080	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	1119	SER	0	-0.014	-0.022	19.405	0.027	0.027	0.000	0.000	0.000	0.000
70	D	1120	SER	0	0.014	-0.027	22.769	-0.001	-0.001	0.000	0.000	0.000	0.000
71	D	1121	ALA	0	0.002	0.003	25.979	0.008	0.008	0.000	0.000	0.000	0.000
72	D	1122	GLU	-1	-0.921	-0.954	20.362	-0.287	-0.287	0.000	0.000	0.000	0.000
73	D	1123	VAL	0	-0.012	0.022	22.694	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1040:TYR)