FMO DATABASE

FMODB ID: R5Z48

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

Total energy (hartree)

FMO2-HF: Electronic energy	-124618.494907
FMO2-HF: Nuclear repulsion	110100.260513
FMO2-HF: Total energy	-14518.234394
FMO2-MP2: Total energy	-14560.320071

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.
-0.214	1.162	-0.02	-0.591	-0.764	0.001

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 : -0.020 / q_NPA : -0.029

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

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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	0.007	0.010	3.837	0.155	1.531	-0.020	-0.591	-0.764	0.001
4	L	1	ALA	0	-0.031	-0.019	6.068	0.020	0.020	0.000	0.000	0.000	0.000
5	L	1	GLY	0	0.031	0.021	9.850	-0.020	-0.020	0.000	0.000	0.000	0.000
6	L	1	GLU	-1	-0.968	-0.984	11.845	0.056	0.056	0.000	0.000	0.000	0.000
7	L	1	ALA	0	0.008	0.003	10.766	-0.009	-0.009	0.000	0.000	0.000	0.000
8	L	1	ASP	-1	-0.962	-0.974	11.151	0.903	0.903	0.000	0.000	0.000	0.000
9	L	1	CYS	0	-0.027	-0.029	12.251	-0.022	-0.022	0.000	0.000	0.000	0.000
10	L	2	GLY	0	0.000	0.003	14.438	0.020	0.020	0.000	0.000	0.000	0.000
11	L	3	LEU	0	0.033	0.033	13.967	-0.018	-0.018	0.000	0.000	0.000	0.000
12	L	4	ARG	1	0.798	0.880	14.033	-0.343	-0.343	0.000	0.000	0.000	0.000
13	L	5	PRO	0	-0.032	-0.046	11.152	0.066	0.066	0.000	0.000	0.000	0.000
14	L	6	LEU	0	-0.040	-0.037	13.048	0.014	0.014	0.000	0.000	0.000	0.000
15	L	7	PHE	0	0.046	0.033	15.852	-0.076	-0.076	0.000	0.000	0.000	0.000
16	L	8	GLU	-1	-0.702	-0.849	16.557	0.585	0.585	0.000	0.000	0.000	0.000
17	L	9	LYS	1	0.894	0.952	9.700	-1.566	-1.566	0.000	0.000	0.000	0.000
18	L	10	LYS	1	0.894	0.963	14.778	-0.617	-0.617	0.000	0.000	0.000	0.000
19	L	11	GLN	0	-0.040	-0.018	16.898	-0.020	-0.020	0.000	0.000	0.000	0.000
20	L	12	VAL	0	-0.055	-0.010	19.749	-0.062	-0.062	0.000	0.000	0.000	0.000
21	L	13	GLN	0	-0.002	-0.004	21.342	0.015	0.015	0.000	0.000	0.000	0.000
22	L	14	ASP	-1	-0.875	-0.929	23.275	0.316	0.316	0.000	0.000	0.000	0.000
23	L	14	GLN	0	-0.026	-0.036	24.962	-0.022	-0.022	0.000	0.000	0.000	0.000
24	L	14	THR	0	0.067	0.042	27.994	-0.010	-0.010	0.000	0.000	0.000	0.000
25	L	14	GLU	-1	-0.848	-0.923	23.810	0.359	0.359	0.000	0.000	0.000	0.000
26	L	14	LYS	1	0.932	0.954	27.919	-0.217	-0.217	0.000	0.000	0.000	0.000
27	L	14	GLU	-1	-0.872	-0.929	31.098	0.158	0.158	0.000	0.000	0.000	0.000
28	L	14	LEU	0	0.021	0.010	27.448	-0.008	-0.008	0.000	0.000	0.000	0.000
29	L	14	PHE	0	-0.066	-0.020	26.130	-0.014	-0.014	0.000	0.000	0.000	0.000
30	L	14	GLU	-1	-0.959	-0.973	31.709	0.156	0.156	0.000	0.000	0.000	0.000
31	L	14	SER	0	0.001	-0.016	33.836	-0.010	-0.010	0.000	0.000	0.000	0.000
32	L	14	TYR	0	-0.080	-0.039	28.398	-0.010	-0.010	0.000	0.000	0.000	0.000
33	L	14	ILE	0	-0.056	-0.030	33.995	-0.007	-0.007	0.000	0.000	0.000	0.000
34	L	14	GLU	-1	-0.939	-0.952	36.727	0.123	0.123	0.000	0.000	0.000	0.000
35	L	14	GLY	0	-0.039	-0.017	38.367	-0.010	-0.010	0.000	0.000	0.000	0.000
36	L	15	ARG	1	0.907	0.957	37.620	-0.099	-0.099	0.000	0.000	0.000	0.000

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