FMO DATABASE

FMODB ID: Q1R5Y

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	OptHSide
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	-124706.717211
FMO2-HF: Nuclear repulsion	110188.028958
FMO2-HF: Total energy	-14518.688253
FMO2-MP2: Total energy	-14560.807515

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.
-1.411	1.15	-0.017	-1.325	-1.219	0.006

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 : 0.010 / q_NPA : 0.003

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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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	0.016	0.015	3.778	-0.396	2.165	-0.017	-1.325	-1.219	0.006
4	L	1	ALA	0	-0.036	-0.024	5.755	-0.238	-0.238	0.000	0.000	0.000	0.000
5	L	1	GLY	0	0.032	0.024	9.541	0.171	0.171	0.000	0.000	0.000	0.000
6	L	1	GLU	-1	-0.951	-0.975	11.737	-0.515	-0.515	0.000	0.000	0.000	0.000
7	L	1	ALA	0	0.013	0.000	10.713	-0.037	-0.037	0.000	0.000	0.000	0.000
8	L	1	ASP	-1	-0.881	-0.930	11.029	-0.265	-0.265	0.000	0.000	0.000	0.000
9	L	1	CYS	0	-0.056	-0.038	12.229	0.039	0.039	0.000	0.000	0.000	0.000
10	L	2	GLY	0	0.027	0.015	14.417	0.001	0.001	0.000	0.000	0.000	0.000
11	L	3	LEU	0	0.000	0.020	14.123	0.039	0.039	0.000	0.000	0.000	0.000
12	L	4	ARG	1	0.814	0.852	14.015	-0.122	-0.122	0.000	0.000	0.000	0.000
13	L	5	PRO	0	0.008	-0.023	11.082	-0.007	-0.007	0.000	0.000	0.000	0.000
14	L	6	LEU	0	-0.063	-0.049	13.036	-0.009	-0.009	0.000	0.000	0.000	0.000
15	L	7	PHE	0	0.043	0.024	15.845	-0.006	-0.006	0.000	0.000	0.000	0.000
16	L	8	GLU	-1	-0.683	-0.824	16.657	0.133	0.133	0.000	0.000	0.000	0.000
17	L	9	LYS	1	0.799	0.909	10.278	0.086	0.086	0.000	0.000	0.000	0.000
18	L	10	LYS	1	0.882	0.959	14.746	-0.521	-0.521	0.000	0.000	0.000	0.000
19	L	11	GLN	0	-0.052	-0.025	16.871	-0.008	-0.008	0.000	0.000	0.000	0.000
20	L	12	VAL	0	-0.053	-0.004	19.668	-0.012	-0.012	0.000	0.000	0.000	0.000
21	L	13	GLN	0	-0.015	-0.025	21.320	-0.009	-0.009	0.000	0.000	0.000	0.000
22	L	14	ASP	-1	-0.867	-0.927	23.261	0.165	0.165	0.000	0.000	0.000	0.000
23	L	14	GLN	0	-0.025	-0.033	24.951	-0.019	-0.019	0.000	0.000	0.000	0.000
24	L	14	THR	0	0.019	0.025	27.777	-0.011	-0.011	0.000	0.000	0.000	0.000
25	L	14	GLU	-1	-0.820	-0.892	23.577	0.089	0.089	0.000	0.000	0.000	0.000
26	L	14	LYS	1	0.830	0.898	27.904	-0.055	-0.055	0.000	0.000	0.000	0.000
27	L	14	GLU	-1	-0.902	-0.950	31.079	0.069	0.069	0.000	0.000	0.000	0.000
28	L	14	LEU	0	0.027	0.014	27.449	-0.009	-0.009	0.000	0.000	0.000	0.000
29	L	14	PHE	0	-0.033	-0.012	25.810	-0.013	-0.013	0.000	0.000	0.000	0.000
30	L	14	GLU	-1	-0.839	-0.908	31.685	0.030	0.030	0.000	0.000	0.000	0.000
31	L	14	SER	0	-0.003	-0.015	33.896	-0.005	-0.005	0.000	0.000	0.000	0.000
32	L	14	TYR	0	-0.076	-0.037	28.865	-0.006	-0.006	0.000	0.000	0.000	0.000
33	L	14	ILE	0	-0.029	-0.012	34.149	-0.006	-0.006	0.000	0.000	0.000	0.000
34	L	14	GLU	-1	-0.965	-0.963	36.696	0.016	0.016	0.000	0.000	0.000	0.000
35	L	14	GLY	0	-0.040	-0.018	38.329	0.000	0.000	0.000	0.000	0.000	0.000
36	L	15	ARG	1	0.909	0.957	37.585	0.020	0.020	0.000	0.000	0.000	0.000

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