FMO DATABASE

FMODB ID: 76QVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-162828.875613
FMO2-HF: Nuclear repulsion	144278.634931
FMO2-HF: Total energy	-18550.240682
FMO2-MP2: Total energy	-18601.269798

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.
-31.249	-27.247	-0.01	-1.717	-2.275	-0.004

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 : 0.941 / q_NPA : 0.955

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	0.018	0.004	3.546	1.985	5.589	-0.022	-1.654	-1.928	-0.004
4	P	8	CYS	0	-0.017	-0.018	3.691	0.406	0.804	0.012	-0.063	-0.347	0.000
5	P	9	CYS	0	-0.024	0.002	5.471	0.960	0.960	0.000	0.000	0.000	0.000
6	P	10	ILE	0	0.003	0.007	8.511	0.993	0.993	0.000	0.000	0.000	0.000
7	P	11	LEU	0	-0.027	-0.005	11.122	0.949	0.949	0.000	0.000	0.000	0.000
8	P	12	ASP	-1	-0.754	-0.864	14.288	-13.137	-13.137	0.000	0.000	0.000	0.000
9	P	13	GLU	-1	-0.944	-0.978	15.169	-15.211	-15.211	0.000	0.000	0.000	0.000
10	P	14	ARG	1	0.768	0.876	16.236	12.961	12.961	0.000	0.000	0.000	0.000
11	P	15	PHE	0	-0.056	-0.035	16.696	0.405	0.405	0.000	0.000	0.000	0.000
12	P	16	GLY	0	0.033	0.045	12.776	-0.672	-0.672	0.000	0.000	0.000	0.000
13	P	17	SER	0	0.010	-0.010	7.366	0.626	0.626	0.000	0.000	0.000	0.000
14	P	18	TYR	0	-0.017	-0.021	9.985	0.204	0.204	0.000	0.000	0.000	0.000
15	P	19	CYS	0	-0.015	-0.008	8.977	-4.430	-4.430	0.000	0.000	0.000	0.000
16	P	20	PRO	0	0.017	0.021	8.545	2.487	2.487	0.000	0.000	0.000	0.000
17	P	21	THR	0	0.065	0.024	11.522	-0.258	-0.258	0.000	0.000	0.000	0.000
18	P	22	THR	0	0.044	-0.004	14.079	-0.579	-0.579	0.000	0.000	0.000	0.000
19	P	23	CYS	0	0.003	0.012	15.631	0.593	0.593	0.000	0.000	0.000	0.000
20	P	24	GLY	0	0.050	0.035	14.708	0.279	0.279	0.000	0.000	0.000	0.000
21	P	25	ILE	0	-0.035	-0.019	10.254	-0.446	-0.446	0.000	0.000	0.000	0.000
22	P	26	ALA	0	-0.007	-0.004	13.716	0.135	0.135	0.000	0.000	0.000	0.000
23	P	27	ASP	-1	-0.869	-0.936	17.274	-14.730	-14.730	0.000	0.000	0.000	0.000
24	P	28	PHE	0	-0.063	-0.030	11.740	0.119	0.119	0.000	0.000	0.000	0.000
25	P	29	LEU	0	-0.005	-0.017	14.981	0.206	0.206	0.000	0.000	0.000	0.000
26	P	30	ASN	0	0.018	0.021	16.031	0.842	0.842	0.000	0.000	0.000	0.000
27	P	31	ASN	0	0.010	0.007	17.774	1.116	1.116	0.000	0.000	0.000	0.000
28	P	32	TYR	0	-0.035	-0.016	14.719	0.221	0.221	0.000	0.000	0.000	0.000
29	P	33	GLN	0	0.006	-0.002	17.150	0.589	0.589	0.000	0.000	0.000	0.000
30	P	34	THR	0	0.021	0.000	19.523	0.596	0.596	0.000	0.000	0.000	0.000
31	P	35	SER	0	-0.073	-0.023	19.517	0.793	0.793	0.000	0.000	0.000	0.000
32	P	36	VAL	0	0.046	0.008	17.584	0.355	0.355	0.000	0.000	0.000	0.000
33	P	37	ASP	-1	-0.840	-0.906	20.897	-11.348	-11.348	0.000	0.000	0.000	0.000
34	P	38	LYS	1	0.929	0.960	23.834	11.503	11.503	0.000	0.000	0.000	0.000
35	P	39	ASP	-1	-0.908	-0.953	22.466	-12.594	-12.594	0.000	0.000	0.000	0.000
36	P	40	LEU	0	-0.048	-0.023	21.736	0.292	0.292	0.000	0.000	0.000	0.000
37	P	41	ARG	1	0.917	0.954	25.505	11.365	11.365	0.000	0.000	0.000	0.000
38	P	42	THR	0	-0.089	-0.035	28.415	0.550	0.550	0.000	0.000	0.000	0.000
39	P	43	LEU	0	-0.024	-0.018	25.469	0.354	0.354	0.000	0.000	0.000	0.000
40	P	44	GLU	-1	-0.922	-0.974	27.409	-10.851	-10.851	0.000	0.000	0.000	0.000
41	P	45	GLY	0	-0.042	-0.012	30.889	0.328	0.328	0.000	0.000	0.000	0.000
42	P	46	ILE	0	-0.082	-0.036	31.901	0.314	0.314	0.000	0.000	0.000	0.000
43	P	47	LEU	0	-0.049	-0.025	30.560	0.241	0.241	0.000	0.000	0.000	0.000
44	P	48	TYR	0	-0.037	-0.001	29.154	0.240	0.240	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)