FMO DATABASE

FMODB ID: 8577Y

Calculation Name: 2J4U-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J4U

Chain ID: S

ChEMBL ID:

UniProt ID: P06996

Base Structure: X-ray

Registration Date: 2023-06-22

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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-202783.754581
FMO2-HF: Nuclear repulsion	183651.70152
FMO2-HF: Total energy	-19132.053061
FMO2-MP2: Total energy	-19184.801588

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(S:1001:ALA)

Summations of interaction energy for fragment #1(S:1001:ALA)

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.
-1.955	-2.001	7.988	-2.86	-5.081	0.002

Interaction energy analysis for fragmet #1(S:1001:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : -0.011

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	S	1003	LYS	1	1.010	1.017	3.824	-0.317	1.455	0.018	-0.947	-0.843	-0.002
4	S	1004	LYS	1	0.915	0.945	6.302	0.561	0.561	0.000	0.000	0.000	0.000
5	S	1005	SER	0	0.037	0.025	7.389	0.150	0.150	0.000	0.000	0.000	0.000
6	S	1006	VAL	0	0.047	0.035	5.692	-0.091	-0.091	0.000	0.000	0.000	0.000
7	S	1007	ARG	1	0.888	0.923	2.100	-0.483	-1.801	4.118	-0.894	-1.905	0.002
8	S	1008	TRP	0	-0.012	0.000	5.592	-0.085	-0.085	0.000	0.000	0.000	0.000
9	S	1045	CYS	0	-0.161	-0.081	6.673	0.015	0.015	0.000	0.000	0.000	0.000
10	S	1010	THR	0	0.035	0.049	8.236	-0.040	-0.040	0.000	0.000	0.000	0.000
11	S	1011	THR	0	0.030	0.074	11.066	-0.027	-0.027	0.000	0.000	0.000	0.000
12	S	1012	SER	0	0.018	0.007	13.906	0.013	0.013	0.000	0.000	0.000	0.000
13	S	1013	PRO	0	0.018	0.022	16.011	0.014	0.014	0.000	0.000	0.000	0.000
14	S	1014	ALA	0	0.003	-0.008	18.393	0.008	0.008	0.000	0.000	0.000	0.000
15	S	1015	GLU	-1	-0.771	-0.908	14.677	0.132	0.132	0.000	0.000	0.000	0.000
16	S	1016	SER	0	0.000	0.014	13.073	0.018	0.018	0.000	0.000	0.000	0.000
17	S	1017	LYS	1	0.880	0.955	15.816	-0.086	-0.086	0.000	0.000	0.000	0.000
18	S	1018	LYS	1	0.970	0.957	16.973	-0.126	-0.126	0.000	0.000	0.000	0.000
19	S	1019	CYS	0	-0.033	-0.002	5.375	-0.150	-0.150	0.000	0.000	0.000	0.000
20	S	1020	ALA	0	0.023	0.014	12.630	0.057	0.057	0.000	0.000	0.000	0.000
21	S	1021	GLN	0	0.069	-0.038	13.235	0.051	0.051	0.000	0.000	0.000	0.000
22	S	1022	TRP	0	0.083	0.034	12.405	-0.009	-0.009	0.000	0.000	0.000	0.000
23	S	1023	GLN	0	0.100	0.059	9.496	-0.034	-0.034	0.000	0.000	0.000	0.000
24	S	1024	ARG	1	0.857	0.915	9.318	-0.689	-0.689	0.000	0.000	0.000	0.000
25	S	1025	ARG	1	0.882	0.960	14.399	-0.179	-0.179	0.000	0.000	0.000	0.000
26	S	1026	MET	0	0.014	0.085	10.498	-0.030	-0.030	0.000	0.000	0.000	0.000
27	S	1027	LYS	1	0.912	0.964	11.966	-0.390	-0.390	0.000	0.000	0.000	0.000
28	S	1028	LYS	1	0.798	0.925	14.583	-0.193	-0.193	0.000	0.000	0.000	0.000
29	S	1029	VAL	0	0.169	0.076	18.372	-0.008	-0.008	0.000	0.000	0.000	0.000
30	S	1030	ARG	1	0.914	0.934	13.866	-0.116	-0.116	0.000	0.000	0.000	0.000
31	S	1031	GLY	0	0.169	0.108	13.707	0.028	0.028	0.000	0.000	0.000	0.000
32	S	1032	PRO	0	0.018	-0.019	13.801	0.003	0.003	0.000	0.000	0.000	0.000
33	S	1033	SER	0	-0.083	-0.052	9.264	0.016	0.016	0.000	0.000	0.000	0.000
34	S	1034	VAL	0	0.022	0.038	8.225	-0.049	-0.049	0.000	0.000	0.000	0.000
35	S	1035	THR	0	-0.018	-0.013	2.752	-0.174	0.301	0.168	-0.183	-0.459	-0.001
36	S	1037	VAL	0	-0.077	-0.039	1.941	0.154	-0.813	3.685	-0.829	-1.890	0.003
37	S	1038	LYN	0	0.103	0.033	5.281	-0.060	-0.068	-0.001	-0.007	0.016	0.000
38	S	1039	LYS	1	0.913	0.967	5.146	0.306	0.306	0.000	0.000	0.000	0.000
39	S	1040	THR	0	0.082	0.010	10.851	0.009	0.009	0.000	0.000	0.000	0.000
40	S	1041	SER	0	-0.047	-0.048	13.634	0.017	0.017	0.000	0.000	0.000	0.000
41	S	1042	ARG	1	1.096	1.037	12.780	-0.039	-0.039	0.000	0.000	0.000	0.000
42	S	1043	PHE	0	-0.055	0.002	12.764	0.000	0.000	0.000	0.000	0.000	0.000
43	S	1044	GLU	-1	-0.845	-0.961	8.865	-0.132	-0.132	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(S:1001:ALA)