FMO DATABASE

FMODB ID: K37M3

Calculation Name: 1ETS-L-Xray319

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name: 1-[n-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-d-phenylalanyl]piperidine

ligand 3-letter code: MID

PDB ID: 1ETS

Chain ID: L

ChEMBL ID: CHEMBL4471

UniProt ID: P00735

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	37
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-126181.940507
FMO2-HF: Nuclear repulsion	111512.539545
FMO2-HF: Total energy	-14669.400962
FMO2-MP2: Total energy	-14711.92559

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(L:0:ACE )

Summations of interaction energy for fragment #1(L:0:ACE )

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.
1.1	1.746	-0.004	-0.213	-0.43	0.001

Interaction energy analysis for fragmet #1(L:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.013

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	L	1	PHE	0	0.010	0.005	3.822	1.087	1.733	-0.004	-0.213	-0.430	0.001
4	L	1	GLY	0	0.013	0.014	6.574	-0.101	-0.101	0.000	0.000	0.000	0.000
5	L	1	ALA	0	-0.032	-0.020	10.249	0.087	0.087	0.000	0.000	0.000	0.000
6	L	1	GLY	0	0.032	0.021	13.048	-0.016	-0.016	0.000	0.000	0.000	0.000
7	L	1	GLU	-1	-0.968	-0.983	14.632	-0.211	-0.211	0.000	0.000	0.000	0.000
8	L	1	ALA	0	0.007	0.002	12.883	0.028	0.028	0.000	0.000	0.000	0.000
9	L	1	ASP	-1	-0.962	-0.974	12.326	-0.129	-0.129	0.000	0.000	0.000	0.000
10	L	1	CYS	0	-0.026	-0.029	14.298	-0.043	-0.043	0.000	0.000	0.000	0.000
11	L	2	GLY	0	0.002	0.004	16.402	0.021	0.021	0.000	0.000	0.000	0.000
12	L	3	LEU	0	0.032	0.033	14.249	0.018	0.018	0.000	0.000	0.000	0.000
13	L	4	ARG	1	0.799	0.880	15.660	0.058	0.058	0.000	0.000	0.000	0.000
14	L	5	PRO	0	-0.034	-0.047	12.007	0.015	0.015	0.000	0.000	0.000	0.000
15	L	6	LEU	0	-0.040	-0.037	13.763	0.035	0.035	0.000	0.000	0.000	0.000
16	L	7	PHE	0	0.047	0.033	16.064	0.017	0.017	0.000	0.000	0.000	0.000
17	L	8	GLU	-1	-0.696	-0.846	17.067	-0.091	-0.091	0.000	0.000	0.000	0.000
18	L	9	LYS	1	0.891	0.951	10.279	0.341	0.341	0.000	0.000	0.000	0.000
19	L	10	LYS	1	0.890	0.961	13.821	0.120	0.120	0.000	0.000	0.000	0.000
20	L	11	GLN	0	-0.041	-0.019	15.720	0.027	0.027	0.000	0.000	0.000	0.000
21	L	12	VAL	0	-0.056	-0.010	18.878	0.007	0.007	0.000	0.000	0.000	0.000
22	L	13	GLN	0	0.002	-0.002	21.049	-0.003	-0.003	0.000	0.000	0.000	0.000
23	L	14	ASP	-1	-0.880	-0.932	23.894	-0.073	-0.073	0.000	0.000	0.000	0.000
24	L	14	GLN	0	-0.028	-0.037	25.369	0.003	0.003	0.000	0.000	0.000	0.000
25	L	14	THR	0	0.069	0.042	29.004	0.003	0.003	0.000	0.000	0.000	0.000
26	L	14	GLU	-1	-0.848	-0.922	24.352	-0.053	-0.053	0.000	0.000	0.000	0.000
27	L	14	LYS	1	0.929	0.954	28.693	0.022	0.022	0.000	0.000	0.000	0.000
28	L	14	GLU	-1	-0.874	-0.931	31.551	-0.039	-0.039	0.000	0.000	0.000	0.000
29	L	14	LEU	0	0.018	0.008	28.993	0.002	0.002	0.000	0.000	0.000	0.000
30	L	14	PHE	0	-0.067	-0.019	26.604	0.004	0.004	0.000	0.000	0.000	0.000
31	L	14	GLU	-1	-0.963	-0.976	32.405	-0.018	-0.018	0.000	0.000	0.000	0.000
32	L	14	SER	0	-0.003	-0.019	35.032	0.001	0.001	0.000	0.000	0.000	0.000
33	L	14	TYR	0	-0.076	-0.037	29.712	0.000	0.000	0.000	0.000	0.000	0.000
34	L	14	ILE	0	-0.051	-0.025	34.255	0.002	0.002	0.000	0.000	0.000	0.000
35	L	14	GLU	-1	-0.964	-0.968	37.213	-0.017	-0.017	0.000	0.000	0.000	0.000
36	L	14	GLY	0	-0.058	-0.030	39.139	0.000	0.000	0.000	0.000	0.000	0.000
37	L	15	ARG	0	-0.040	-0.010	38.341	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(L:0:ACE )