FMO DATABASE

FMODB ID: 2N93R

Calculation Name: 1JY2-P-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: P

ChEMBL ID:

UniProt ID: P02672

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	44
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-162923.341522
FMO2-HF: Nuclear repulsion	144372.90442
FMO2-HF: Total energy	-18550.437101
FMO2-MP2: Total energy	-18601.442868

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(P:5:ARG)

Summations of interaction energy for fragment #1(P:5:ARG)

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.
-30.515	-25.913	0.05	-2.165	-2.488	-0.005

Interaction energy analysis for fragmet #1(P:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.978 / q_NPA : 0.984

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	P	7	ASN	0	0.002	-0.006	3.096	1.546	5.690	0.000	-2.077	-2.068	-0.005
4	P	8	CYS	0	-0.007	-0.008	3.846	1.322	1.780	0.050	-0.088	-0.420	0.000
5	P	9	CYS	0	-0.022	0.000	5.478	1.808	1.808	0.000	0.000	0.000	0.000
6	P	10	ILE	0	0.006	0.012	8.527	1.051	1.051	0.000	0.000	0.000	0.000
7	P	11	LEU	0	-0.020	0.001	11.131	1.086	1.086	0.000	0.000	0.000	0.000
8	P	12	ASP	-1	-0.773	-0.859	14.300	-13.574	-13.574	0.000	0.000	0.000	0.000
9	P	13	GLU	-1	-0.931	-0.972	14.806	-15.878	-15.878	0.000	0.000	0.000	0.000
10	P	14	ARG	1	0.769	0.861	15.887	13.401	13.401	0.000	0.000	0.000	0.000
11	P	15	PHE	0	-0.057	-0.038	16.300	0.414	0.414	0.000	0.000	0.000	0.000
12	P	16	GLY	0	0.039	0.048	12.135	-0.717	-0.717	0.000	0.000	0.000	0.000
13	P	17	SER	0	0.005	-0.014	7.501	0.554	0.554	0.000	0.000	0.000	0.000
14	P	18	TYR	0	-0.010	-0.014	9.974	0.270	0.270	0.000	0.000	0.000	0.000
15	P	19	CYS	0	-0.031	-0.024	8.051	-5.038	-5.038	0.000	0.000	0.000	0.000
16	P	20	PRO	0	0.019	0.028	8.070	2.653	2.653	0.000	0.000	0.000	0.000
17	P	21	THR	0	0.058	0.013	11.000	-0.329	-0.329	0.000	0.000	0.000	0.000
18	P	22	THR	0	0.044	0.002	13.476	-0.638	-0.638	0.000	0.000	0.000	0.000
19	P	23	CYS	0	0.002	0.009	14.975	0.436	0.436	0.000	0.000	0.000	0.000
20	P	24	GLY	0	0.065	0.045	14.214	0.295	0.295	0.000	0.000	0.000	0.000
21	P	25	ILE	0	-0.036	-0.024	9.489	-0.439	-0.439	0.000	0.000	0.000	0.000
22	P	26	ALA	0	-0.007	-0.001	13.213	0.197	0.197	0.000	0.000	0.000	0.000
23	P	27	ASP	-1	-0.874	-0.936	16.788	-15.105	-15.105	0.000	0.000	0.000	0.000
24	P	28	PHE	0	-0.059	-0.032	11.386	0.128	0.128	0.000	0.000	0.000	0.000
25	P	29	LEU	0	-0.002	-0.012	14.653	0.285	0.285	0.000	0.000	0.000	0.000
26	P	30	ASN	0	0.001	0.011	15.642	0.978	0.978	0.000	0.000	0.000	0.000
27	P	31	ASN	0	0.010	0.009	17.477	1.110	1.110	0.000	0.000	0.000	0.000
28	P	32	TYR	0	-0.010	-0.002	14.665	0.339	0.339	0.000	0.000	0.000	0.000
29	P	33	GLN	0	0.003	-0.005	16.890	0.604	0.604	0.000	0.000	0.000	0.000
30	P	34	THR	0	0.012	-0.009	19.245	0.622	0.622	0.000	0.000	0.000	0.000
31	P	35	SER	0	-0.034	-0.010	19.400	0.610	0.610	0.000	0.000	0.000	0.000
32	P	36	VAL	0	0.010	-0.003	17.414	0.410	0.410	0.000	0.000	0.000	0.000
33	P	37	ASP	-1	-0.828	-0.887	20.750	-11.297	-11.297	0.000	0.000	0.000	0.000
34	P	38	LYS	1	0.947	0.977	23.646	11.773	11.773	0.000	0.000	0.000	0.000
35	P	39	ASP	-1	-0.908	-0.954	22.314	-12.615	-12.615	0.000	0.000	0.000	0.000
36	P	40	LEU	0	-0.036	-0.019	21.532	0.324	0.324	0.000	0.000	0.000	0.000
37	P	41	ARG	1	0.884	0.915	25.354	11.504	11.504	0.000	0.000	0.000	0.000
38	P	42	THR	0	-0.079	-0.034	28.222	0.526	0.526	0.000	0.000	0.000	0.000
39	P	43	LEU	0	-0.026	-0.017	25.281	0.349	0.349	0.000	0.000	0.000	0.000
40	P	44	GLU	-1	-0.869	-0.925	28.145	-10.662	-10.662	0.000	0.000	0.000	0.000
41	P	45	GLY	0	-0.043	-0.009	30.783	0.321	0.321	0.000	0.000	0.000	0.000
42	P	46	ILE	0	-0.088	-0.041	31.702	0.311	0.311	0.000	0.000	0.000	0.000
43	P	47	LEU	0	-0.051	-0.023	30.412	0.239	0.239	0.000	0.000	0.000	0.000
44	P	48	TYR	0	-0.102	-0.052	28.881	0.311	0.311	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(P:5:ARG)