FMO DATABASE

FMODB ID: M376Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-464910.118915
FMO2-HF: Nuclear repulsion	435543.361206
FMO2-HF: Total energy	-29366.75771
FMO2-MP2: Total energy	-29452.966289

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.
-12.642	-3.12	4.481	-4.282	-9.722	0.002

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 : 0.010 / q_NPA : -0.001

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	-0.029	-0.005	3.758	-0.164	2.312	-0.028	-1.225	-1.222	0.004
4	D	1043	VAL	0	0.027	0.009	5.919	0.182	0.182	0.000	0.000	0.000	0.000
5	D	1044	GLN	0	-0.004	-0.013	8.917	0.080	0.080	0.000	0.000	0.000	0.000
6	D	1045	LYS	1	0.970	0.987	12.048	0.018	0.018	0.000	0.000	0.000	0.000
7	D	1046	ARG	1	0.922	0.944	15.553	0.212	0.212	0.000	0.000	0.000	0.000
8	D	1047	GLY	0	-0.018	-0.017	18.465	0.029	0.029	0.000	0.000	0.000	0.000
9	D	1048	SER	0	-0.024	0.005	15.645	0.038	0.038	0.000	0.000	0.000	0.000
10	D	1049	VAL	0	0.026	0.019	12.133	-0.060	-0.060	0.000	0.000	0.000	0.000
11	D	1050	GLY	0	-0.004	0.001	10.733	0.027	0.027	0.000	0.000	0.000	0.000
12	D	1051	ARG	1	0.874	0.918	7.195	-0.626	-0.626	0.000	0.000	0.000	0.000
13	D	1052	SER	0	-0.003	-0.010	2.549	-1.202	-0.338	0.416	-0.420	-0.861	0.001
14	D	1053	ILE	0	0.017	0.022	3.085	-1.394	0.404	0.341	-0.578	-1.560	-0.004
15	D	1054	ASP	-1	-0.824	-0.911	2.732	-2.617	1.248	3.707	-2.025	-5.548	-0.001
16	D	1055	VAL	0	0.021	-0.014	4.098	-1.402	-1.066	0.046	-0.028	-0.355	0.002
17	D	1056	ASN	0	0.019	0.003	5.903	-0.467	-0.467	0.000	0.000	0.000	0.000
18	D	1057	ARG	1	0.860	0.948	4.792	-2.571	-2.388	-0.001	-0.006	-0.176	0.000
19	D	1058	TYR	0	-0.100	-0.071	7.479	-0.079	-0.079	0.000	0.000	0.000	0.000
20	D	1059	ARG	1	0.924	0.965	11.532	-0.499	-0.499	0.000	0.000	0.000	0.000
21	D	1060	GLY	0	0.054	0.020	14.734	-0.080	-0.080	0.000	0.000	0.000	0.000
22	D	1061	TYR	0	-0.008	-0.028	14.064	0.084	0.084	0.000	0.000	0.000	0.000
23	D	1062	ASP	-1	-0.871	-0.929	15.839	0.094	0.094	0.000	0.000	0.000	0.000
24	D	1063	GLU	-1	-0.847	-0.917	13.671	0.530	0.530	0.000	0.000	0.000	0.000
25	D	1064	LEU	0	0.021	0.019	9.929	0.065	0.065	0.000	0.000	0.000	0.000
26	D	1065	ARG	1	0.911	0.948	13.034	0.030	0.030	0.000	0.000	0.000	0.000
27	D	1066	HIS	0	-0.062	-0.020	15.619	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	1067	ASP	-1	-0.780	-0.856	9.536	1.047	1.047	0.000	0.000	0.000	0.000
29	D	1068	LEU	0	0.011	-0.004	9.200	0.012	0.012	0.000	0.000	0.000	0.000
30	D	1069	ALA	0	0.020	0.003	12.651	-0.024	-0.024	0.000	0.000	0.000	0.000
31	D	1070	ARG	1	0.816	0.898	11.941	-0.697	-0.697	0.000	0.000	0.000	0.000
32	D	1071	MET	0	-0.032	0.003	8.589	-0.014	-0.014	0.000	0.000	0.000	0.000
33	D	1072	PHE	0	-0.078	-0.038	10.874	-0.021	-0.021	0.000	0.000	0.000	0.000
34	D	1073	GLY	0	-0.009	-0.001	15.298	-0.044	-0.044	0.000	0.000	0.000	0.000
35	D	1074	ILE	0	-0.043	-0.013	17.769	-0.042	-0.042	0.000	0.000	0.000	0.000
36	D	1086	TRP	0	-0.012	-0.019	19.971	-0.002	-0.002	0.000	0.000	0.000	0.000
37	D	1087	LYS	1	0.904	0.947	20.732	0.130	0.130	0.000	0.000	0.000	0.000
38	D	1088	LEU	0	0.038	0.029	13.542	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	1089	VAL	0	0.020	0.010	15.955	0.015	0.015	0.000	0.000	0.000	0.000
40	D	1090	TYR	0	-0.017	-0.058	11.650	-0.105	-0.105	0.000	0.000	0.000	0.000
41	D	1091	VAL	0	-0.050	-0.017	12.363	0.106	0.106	0.000	0.000	0.000	0.000
42	D	1092	ALA	0	0.051	0.044	12.603	-0.177	-0.177	0.000	0.000	0.000	0.000
43	D	1093	HIS	0	0.044	0.028	13.400	-0.158	-0.158	0.000	0.000	0.000	0.000
44	D	1094	GLU	-1	-0.878	-0.927	14.339	-0.553	-0.553	0.000	0.000	0.000	0.000
45	D	1095	ASN	0	-0.039	-0.033	16.290	-0.094	-0.094	0.000	0.000	0.000	0.000
46	D	1096	ALA	0	-0.027	-0.005	17.376	0.037	0.037	0.000	0.000	0.000	0.000
47	D	1097	ILE	0	-0.011	-0.024	17.203	-0.061	-0.061	0.000	0.000	0.000	0.000
48	D	1098	LEU	0	0.016	0.013	16.937	0.075	0.075	0.000	0.000	0.000	0.000
49	D	1099	LEU	0	-0.030	-0.021	17.086	-0.027	-0.027	0.000	0.000	0.000	0.000
50	D	1100	VAL	0	-0.022	-0.006	13.650	-0.016	-0.016	0.000	0.000	0.000	0.000
51	D	1101	GLY	0	-0.051	-0.058	16.296	0.062	0.062	0.000	0.000	0.000	0.000
52	D	1102	ASP	-1	-0.923	-0.940	18.054	-0.207	-0.207	0.000	0.000	0.000	0.000
53	D	1103	ASP	-1	-0.851	-0.884	16.507	-0.403	-0.403	0.000	0.000	0.000	0.000
54	D	1104	PRO	0	0.054	0.034	17.984	0.037	0.037	0.000	0.000	0.000	0.000
55	D	1105	TRP	0	0.001	0.005	10.842	-0.107	-0.107	0.000	0.000	0.000	0.000
56	D	1106	GLU	-1	-0.878	-0.959	13.488	-0.158	-0.158	0.000	0.000	0.000	0.000
57	D	1107	GLU	-1	-0.924	-0.956	13.659	-0.398	-0.398	0.000	0.000	0.000	0.000
58	D	1108	PHE	0	0.011	0.002	10.175	-0.155	-0.155	0.000	0.000	0.000	0.000
59	D	1109	VAL	0	-0.045	-0.038	8.822	-0.203	-0.203	0.000	0.000	0.000	0.000
60	D	1110	ASN	0	-0.079	-0.044	8.224	-0.366	-0.366	0.000	0.000	0.000	0.000
61	D	1111	CYS	0	-0.012	0.003	10.196	-0.109	-0.109	0.000	0.000	0.000	0.000
62	D	1112	VAL	0	-0.048	0.014	7.010	-0.097	-0.097	0.000	0.000	0.000	0.000
63	D	1113	GLN	0	-0.015	-0.014	7.178	-0.711	-0.711	0.000	0.000	0.000	0.000
64	D	1114	SER	0	-0.088	-0.049	7.180	-0.483	-0.483	0.000	0.000	0.000	0.000
65	D	1115	ILE	0	0.054	0.022	8.581	0.290	0.290	0.000	0.000	0.000	0.000
66	D	1116	LYS	1	0.847	0.923	10.895	0.911	0.911	0.000	0.000	0.000	0.000
67	D	1117	ILE	0	0.019	0.009	13.709	0.053	0.053	0.000	0.000	0.000	0.000
68	D	1118	LEU	0	-0.012	0.004	16.245	0.015	0.015	0.000	0.000	0.000	0.000
69	D	1119	SER	0	-0.007	-0.040	19.559	0.032	0.032	0.000	0.000	0.000	0.000
70	D	1120	SER	0	-0.004	-0.034	22.925	-0.018	-0.018	0.000	0.000	0.000	0.000
71	D	1121	ALA	0	0.003	0.006	26.139	-0.005	-0.005	0.000	0.000	0.000	0.000
72	D	1122	GLU	-1	-0.823	-0.868	20.676	-0.208	-0.208	0.000	0.000	0.000	0.000
73	D	1123	VAL	0	-0.006	0.023	22.763	-0.024	-0.024	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

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