FMO DATABASE

FMODB ID: K3YQ3

Calculation Name: 1ETS-L-Xray372

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: 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	OptAll
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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-125092.956055
FMO2-HF: Nuclear repulsion	110574.009778
FMO2-HF: Total energy	-14518.946277
FMO2-MP2: Total energy	-14561.040904

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:1:THR)

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

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.
0.153	1.713	-0.017	-0.745	-0.798	0.002

Interaction energy analysis for fragmet #1(L:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.025

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	GLY	0	0.009	0.003	3.868	-0.091	1.469	-0.017	-0.745	-0.798	0.002
4	L	1	ALA	0	-0.043	-0.022	6.257	-0.080	-0.080	0.000	0.000	0.000	0.000
5	L	1	GLY	0	0.037	0.028	10.084	0.026	0.026	0.000	0.000	0.000	0.000
6	L	1	GLU	-1	-0.934	-0.964	11.968	0.175	0.175	0.000	0.000	0.000	0.000
7	L	1	ALA	0	0.016	-0.011	11.089	-0.035	-0.035	0.000	0.000	0.000	0.000
8	L	1	ASP	-1	-0.850	-0.904	10.790	0.952	0.952	0.000	0.000	0.000	0.000
9	L	1	CYS	0	-0.034	-0.023	12.112	0.030	0.030	0.000	0.000	0.000	0.000
10	L	2	GLY	0	0.018	0.024	14.565	-0.021	-0.021	0.000	0.000	0.000	0.000
11	L	3	LEU	0	-0.024	-0.020	14.657	-0.002	-0.002	0.000	0.000	0.000	0.000
12	L	4	ARG	1	0.840	0.884	14.318	-0.278	-0.278	0.000	0.000	0.000	0.000
13	L	5	PRO	0	-0.001	-0.018	11.101	-0.004	-0.004	0.000	0.000	0.000	0.000
14	L	6	LEU	0	-0.057	-0.036	13.095	-0.011	-0.011	0.000	0.000	0.000	0.000
15	L	7	PHE	0	0.048	0.029	15.969	-0.055	-0.055	0.000	0.000	0.000	0.000
16	L	8	GLU	-1	-0.681	-0.823	17.156	0.483	0.483	0.000	0.000	0.000	0.000
17	L	9	LYS	1	0.740	0.871	11.076	-0.997	-0.997	0.000	0.000	0.000	0.000
18	L	10	LYS	1	0.834	0.925	14.181	-0.530	-0.530	0.000	0.000	0.000	0.000
19	L	11	GLN	0	-0.063	-0.027	16.659	-0.044	-0.044	0.000	0.000	0.000	0.000
20	L	12	VAL	0	-0.038	-0.004	19.731	-0.043	-0.043	0.000	0.000	0.000	0.000
21	L	13	GLN	0	-0.028	-0.026	21.321	0.013	0.013	0.000	0.000	0.000	0.000
22	L	14	ASP	-1	-0.837	-0.917	23.604	0.277	0.277	0.000	0.000	0.000	0.000
23	L	14	GLN	0	-0.054	-0.045	25.292	-0.010	-0.010	0.000	0.000	0.000	0.000
24	L	14	THR	0	0.001	0.010	27.749	-0.013	-0.013	0.000	0.000	0.000	0.000
25	L	14	GLU	-1	-0.770	-0.864	23.725	0.309	0.309	0.000	0.000	0.000	0.000
26	L	14	LYS	1	0.843	0.907	27.812	-0.159	-0.159	0.000	0.000	0.000	0.000
27	L	14	GLU	-1	-0.888	-0.957	30.902	0.153	0.153	0.000	0.000	0.000	0.000
28	L	14	LEU	0	-0.026	-0.001	27.483	-0.009	-0.009	0.000	0.000	0.000	0.000
29	L	14	PHE	0	-0.001	-0.004	25.886	-0.010	-0.010	0.000	0.000	0.000	0.000
30	L	14	GLU	-1	-0.831	-0.900	31.679	0.130	0.130	0.000	0.000	0.000	0.000
31	L	14	SER	0	-0.018	-0.024	33.845	-0.008	-0.008	0.000	0.000	0.000	0.000
32	L	14	TYR	0	-0.060	-0.034	28.759	0.000	0.000	0.000	0.000	0.000	0.000
33	L	14	ILE	0	-0.047	-0.020	34.451	-0.005	-0.005	0.000	0.000	0.000	0.000
34	L	14	GLU	-1	-0.971	-0.964	37.007	0.100	0.100	0.000	0.000	0.000	0.000
35	L	14	GLY	0	-0.021	-0.007	38.547	-0.007	-0.007	0.000	0.000	0.000	0.000
36	L	15	ARG	1	0.917	0.962	37.701	-0.083	-0.083	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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