FMO DATABASE

FMODB ID: 7GR3K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-466870.04746
FMO2-HF: Nuclear repulsion	437502.868791
FMO2-HF: Total energy	-29367.178669
FMO2-MP2: Total energy	-29453.375215

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.
-13.429	-4.318	6.282	-4.431	-10.964	0

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 : 0.012 / q_NPA : -0.002

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	D	1042	ALA	0	0.021	0.009	3.864	0.585	2.261	-0.008	-0.790	-0.879	0.005
4	D	1043	VAL	0	0.024	0.008	5.547	0.451	0.451	0.000	0.000	0.000	0.000
5	D	1044	GLN	0	-0.007	-0.013	8.347	0.121	0.121	0.000	0.000	0.000	0.000
6	D	1045	LYS	1	0.949	0.978	11.717	0.102	0.102	0.000	0.000	0.000	0.000
7	D	1046	ARG	1	0.892	0.930	15.325	0.278	0.278	0.000	0.000	0.000	0.000
8	D	1047	GLY	0	0.014	0.009	18.549	0.036	0.036	0.000	0.000	0.000	0.000
9	D	1048	SER	0	-0.037	-0.024	15.367	0.053	0.053	0.000	0.000	0.000	0.000
10	D	1049	VAL	0	0.023	0.025	11.677	-0.067	-0.067	0.000	0.000	0.000	0.000
11	D	1050	GLY	0	0.009	0.014	10.442	0.007	0.007	0.000	0.000	0.000	0.000
12	D	1051	ARG	1	0.882	0.915	7.144	-0.457	-0.457	0.000	0.000	0.000	0.000
13	D	1052	SER	0	-0.020	-0.022	2.357	-1.517	-0.723	0.756	-0.499	-1.051	0.002
14	D	1053	ILE	0	-0.014	0.005	2.976	-1.738	0.457	0.949	-0.866	-2.278	-0.003
15	D	1054	ASP	-1	-0.762	-0.857	2.683	-3.773	0.274	4.544	-2.204	-6.387	-0.006
16	D	1055	VAL	0	0.028	-0.001	3.964	-1.428	-1.029	0.041	-0.072	-0.369	0.002
17	D	1056	ASN	0	0.014	-0.004	6.057	-0.441	-0.441	0.000	0.000	0.000	0.000
18	D	1057	ARG	1	0.792	0.893	5.117	-2.466	-2.466	0.000	0.000	0.000	0.000
19	D	1058	TYR	0	-0.091	-0.058	7.859	-0.064	-0.064	0.000	0.000	0.000	0.000
20	D	1059	ARG	1	0.879	0.908	11.766	-0.583	-0.583	0.000	0.000	0.000	0.000
21	D	1060	GLY	0	0.050	0.026	14.436	-0.082	-0.082	0.000	0.000	0.000	0.000
22	D	1061	TYR	0	0.000	-0.020	14.143	0.087	0.087	0.000	0.000	0.000	0.000
23	D	1062	ASP	-1	-0.840	-0.906	15.539	0.074	0.074	0.000	0.000	0.000	0.000
24	D	1063	GLU	-1	-0.816	-0.874	13.820	0.553	0.553	0.000	0.000	0.000	0.000
25	D	1064	LEU	0	0.027	0.020	9.642	0.074	0.074	0.000	0.000	0.000	0.000
26	D	1065	ARG	1	0.813	0.881	12.924	0.044	0.044	0.000	0.000	0.000	0.000
27	D	1066	HIS	0	-0.024	-0.019	15.762	-0.019	-0.019	0.000	0.000	0.000	0.000
28	D	1067	ASP	-1	-0.807	-0.862	9.232	1.171	1.171	0.000	0.000	0.000	0.000
29	D	1068	LEU	0	0.018	-0.003	8.819	-0.004	-0.004	0.000	0.000	0.000	0.000
30	D	1069	ALA	0	0.018	0.011	12.387	-0.044	-0.044	0.000	0.000	0.000	0.000
31	D	1070	ARG	1	0.836	0.906	11.415	-0.763	-0.763	0.000	0.000	0.000	0.000
32	D	1071	MET	0	-0.040	-0.004	8.000	-0.030	-0.030	0.000	0.000	0.000	0.000
33	D	1072	PHE	0	-0.037	-0.023	10.509	-0.038	-0.038	0.000	0.000	0.000	0.000
34	D	1073	GLY	0	-0.015	0.006	14.853	-0.045	-0.045	0.000	0.000	0.000	0.000
35	D	1074	ILE	0	-0.058	-0.021	17.447	-0.033	-0.033	0.000	0.000	0.000	0.000
36	D	1086	TRP	0	-0.003	0.010	19.410	-0.003	-0.003	0.000	0.000	0.000	0.000
37	D	1087	LYS	1	0.889	0.944	20.746	0.171	0.171	0.000	0.000	0.000	0.000
38	D	1088	LEU	0	0.029	0.019	13.625	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	1089	VAL	0	0.017	0.006	15.944	0.026	0.026	0.000	0.000	0.000	0.000
40	D	1090	TYR	0	-0.050	-0.067	11.756	-0.121	-0.121	0.000	0.000	0.000	0.000
41	D	1091	VAL	0	-0.042	-0.004	12.352	0.130	0.130	0.000	0.000	0.000	0.000
42	D	1092	ALA	0	0.059	0.048	11.825	-0.247	-0.247	0.000	0.000	0.000	0.000
43	D	1093	HIS	0	0.056	0.021	13.082	-0.198	-0.198	0.000	0.000	0.000	0.000
44	D	1094	GLU	-1	-0.870	-0.926	14.005	-0.599	-0.599	0.000	0.000	0.000	0.000
45	D	1095	ASN	0	-0.048	-0.035	16.118	-0.118	-0.118	0.000	0.000	0.000	0.000
46	D	1096	ALA	0	-0.007	-0.001	17.254	0.060	0.060	0.000	0.000	0.000	0.000
47	D	1097	ILE	0	-0.036	-0.027	16.996	-0.077	-0.077	0.000	0.000	0.000	0.000
48	D	1098	LEU	0	0.034	0.024	16.966	0.081	0.081	0.000	0.000	0.000	0.000
49	D	1099	LEU	0	-0.008	-0.009	17.166	-0.038	-0.038	0.000	0.000	0.000	0.000
50	D	1100	VAL	0	-0.025	-0.017	13.642	-0.019	-0.019	0.000	0.000	0.000	0.000
51	D	1101	GLY	0	-0.032	-0.042	16.170	0.082	0.082	0.000	0.000	0.000	0.000
52	D	1102	ASP	-1	-0.894	-0.920	18.479	-0.249	-0.249	0.000	0.000	0.000	0.000
53	D	1103	ASP	-1	-0.836	-0.875	16.493	-0.458	-0.458	0.000	0.000	0.000	0.000
54	D	1104	PRO	0	0.026	0.018	17.925	0.036	0.036	0.000	0.000	0.000	0.000
55	D	1105	TRP	0	-0.017	0.000	10.857	-0.124	-0.124	0.000	0.000	0.000	0.000
56	D	1106	GLU	-1	-0.860	-0.948	13.454	-0.148	-0.148	0.000	0.000	0.000	0.000
57	D	1107	GLU	-1	-0.912	-0.947	13.608	-0.416	-0.416	0.000	0.000	0.000	0.000
58	D	1108	PHE	0	0.022	0.005	10.271	-0.170	-0.170	0.000	0.000	0.000	0.000
59	D	1109	VAL	0	-0.045	-0.040	8.944	-0.254	-0.254	0.000	0.000	0.000	0.000
60	D	1110	ASN	0	-0.067	-0.039	8.180	-0.313	-0.313	0.000	0.000	0.000	0.000
61	D	1111	CYS	0	-0.021	-0.002	10.076	-0.113	-0.113	0.000	0.000	0.000	0.000
62	D	1112	VAL	0	-0.052	-0.005	7.122	-0.092	-0.092	0.000	0.000	0.000	0.000
63	D	1113	GLN	0	-0.009	-0.009	7.068	-0.963	-0.963	0.000	0.000	0.000	0.000
64	D	1114	SER	0	-0.122	-0.073	7.254	-0.636	-0.636	0.000	0.000	0.000	0.000
65	D	1115	ILE	0	0.051	0.029	8.316	0.375	0.375	0.000	0.000	0.000	0.000
66	D	1116	LYS	1	0.849	0.917	10.741	1.118	1.118	0.000	0.000	0.000	0.000
67	D	1117	ILE	0	0.012	0.020	13.488	0.072	0.072	0.000	0.000	0.000	0.000
68	D	1118	LEU	0	0.012	0.008	16.053	0.007	0.007	0.000	0.000	0.000	0.000
69	D	1119	SER	0	-0.013	-0.047	19.263	0.039	0.039	0.000	0.000	0.000	0.000
70	D	1120	SER	0	-0.002	-0.056	22.676	-0.020	-0.020	0.000	0.000	0.000	0.000
71	D	1121	ALA	0	0.018	0.023	25.564	0.001	0.001	0.000	0.000	0.000	0.000
72	D	1122	GLU	-1	-0.813	-0.860	20.521	-0.274	-0.274	0.000	0.000	0.000	0.000
73	D	1123	VAL	0	-0.028	0.008	22.740	-0.018	-0.018	0.000	0.000	0.000	0.000

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