FMO DATABASE

FMODB ID: 9QN72

Calculation Name: 2HPP-P-Xray547

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name: d-phenylalanyl-n-[(3s)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-l-prolinamide

Ligand 3-letter code: 0G7

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HPP

Chain ID: P

ChEMBL ID: CHEMBL4471

UniProt ID: P00735

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-509444.446748
FMO2-HF: Nuclear repulsion	477128.921115
FMO2-HF: Total energy	-32315.525633
FMO2-MP2: Total energy	-32405.541234

3D Structure Molmil

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(P:379:CYS)

Summations of interaction energy for fragment #1(P:379:CYS)

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.
11.98	18.67	2.875	-0.581	-8.984	-0.017

Interaction energy analysis for fragmet #1(P:379:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.125 / q_NPA : -0.056

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	P	303	PRO	0	0.042	0.011	2.247	0.486	1.428	2.248	1.420	-4.610	-0.006
4	P	304	ASP	-1	-0.783	-0.875	3.332	10.095	10.807	0.036	0.203	-0.952	-0.004
5	P	305	ARG	1	0.902	0.937	4.806	-13.742	-13.420	-0.001	-0.007	-0.313	0.000
74	P	376	LEU	0	-0.049	-0.015	5.340	-2.135	-2.010	-0.002	-0.006	-0.117	0.000
75	P	377	ASN	0	-0.018	-0.011	3.070	5.094	9.683	0.594	-2.191	-2.992	-0.007
6	P	306	GLY	0	0.011	0.021	5.757	-1.468	-1.468	0.000	0.000	0.000	0.000
7	P	307	ARG	1	0.792	0.878	7.341	-5.304	-5.304	0.000	0.000	0.000	0.000
8	P	308	GLU	-1	-0.874	-0.922	9.329	-1.450	-1.450	0.000	0.000	0.000	0.000
9	P	309	TYR	0	-0.024	-0.002	7.242	-1.105	-1.105	0.000	0.000	0.000	0.000
10	P	310	ARG	1	0.871	0.920	9.790	4.332	4.332	0.000	0.000	0.000	0.000
11	P	311	GLY	0	0.003	0.004	10.539	0.213	0.213	0.000	0.000	0.000	0.000
12	P	312	ARG	1	0.951	0.971	11.510	5.344	5.344	0.000	0.000	0.000	0.000
13	P	313	LEU	0	-0.003	0.010	9.627	0.354	0.354	0.000	0.000	0.000	0.000
14	P	314	ALA	0	0.021	0.011	12.834	0.546	0.546	0.000	0.000	0.000	0.000
15	P	315	VAL	0	-0.044	-0.021	14.914	0.478	0.478	0.000	0.000	0.000	0.000
16	P	316	THR	0	0.039	-0.021	14.593	-0.655	-0.655	0.000	0.000	0.000	0.000
17	P	317	THR	0	-0.004	-0.018	12.157	-0.540	-0.540	0.000	0.000	0.000	0.000
18	P	318	SER	0	-0.071	-0.043	14.401	-0.001	-0.001	0.000	0.000	0.000	0.000
19	P	319	GLY	0	-0.037	-0.017	17.347	0.101	0.101	0.000	0.000	0.000	0.000
20	P	320	SER	0	-0.001	0.001	18.999	0.014	0.014	0.000	0.000	0.000	0.000
21	P	321	ARG	1	0.874	0.929	19.210	2.053	2.053	0.000	0.000	0.000	0.000
22	P	322	CYS	0	-0.003	0.008	13.324	-0.226	-0.226	0.000	0.000	0.000	0.000
23	P	323	LEU	0	-0.005	0.014	19.940	-0.109	-0.109	0.000	0.000	0.000	0.000
24	P	324	ALA	0	-0.023	-0.032	22.020	-0.065	-0.065	0.000	0.000	0.000	0.000
25	P	325	TRP	0	0.008	-0.011	16.249	0.353	0.353	0.000	0.000	0.000	0.000
26	P	326	SER	0	-0.042	-0.019	22.695	0.137	0.137	0.000	0.000	0.000	0.000
27	P	327	SER	0	-0.031	-0.017	25.853	0.081	0.081	0.000	0.000	0.000	0.000
28	P	328	GLU	-1	-0.938	-0.973	27.789	-0.614	-0.614	0.000	0.000	0.000	0.000
29	P	329	GLN	0	0.036	0.003	28.680	0.018	0.018	0.000	0.000	0.000	0.000
30	P	330	ALA	0	0.031	0.036	23.644	0.060	0.060	0.000	0.000	0.000	0.000
31	P	331	LYS	1	0.879	0.920	24.806	0.626	0.626	0.000	0.000	0.000	0.000
32	P	332	ALA	0	-0.043	-0.017	26.947	0.093	0.093	0.000	0.000	0.000	0.000
33	P	333	LEU	0	0.039	0.027	24.270	0.097	0.097	0.000	0.000	0.000	0.000
34	P	334	SER	0	-0.002	0.019	21.968	0.067	0.067	0.000	0.000	0.000	0.000
35	P	335	LYS	1	0.740	0.860	24.589	0.114	0.114	0.000	0.000	0.000	0.000
36	P	336	ASP	-1	-0.810	-0.884	27.431	-0.011	-0.011	0.000	0.000	0.000	0.000
37	P	337	GLN	0	-0.036	-0.014	21.092	0.119	0.119	0.000	0.000	0.000	0.000
38	P	338	ASP	-1	-0.936	-0.962	22.436	0.370	0.370	0.000	0.000	0.000	0.000
39	P	339	PHE	0	-0.004	0.001	19.907	-0.043	-0.043	0.000	0.000	0.000	0.000
40	P	340	ASN	0	0.065	0.016	17.021	-0.235	-0.235	0.000	0.000	0.000	0.000
41	P	341	PRO	0	-0.025	-0.010	19.139	-0.267	-0.267	0.000	0.000	0.000	0.000
42	P	342	ALA	0	-0.045	-0.021	16.839	0.006	0.006	0.000	0.000	0.000	0.000
43	P	343	VAL	0	-0.020	0.007	14.181	-0.542	-0.542	0.000	0.000	0.000	0.000
44	P	344	PRO	0	-0.034	-0.014	16.367	0.083	0.083	0.000	0.000	0.000	0.000
45	P	345	LEU	0	0.051	0.024	17.680	-0.433	-0.433	0.000	0.000	0.000	0.000
46	P	346	ALA	0	-0.039	-0.009	17.599	0.135	0.135	0.000	0.000	0.000	0.000
47	P	347	GLU	-1	-0.902	-0.964	19.122	-3.105	-3.105	0.000	0.000	0.000	0.000
48	P	348	ASN	0	-0.051	-0.038	19.721	0.092	0.092	0.000	0.000	0.000	0.000
49	P	349	PHE	0	-0.010	0.001	14.930	-0.245	-0.245	0.000	0.000	0.000	0.000
50	P	350	CYS	0	-0.032	-0.002	10.820	0.269	0.269	0.000	0.000	0.000	0.000
51	P	351	ARG	1	0.797	0.891	12.425	3.536	3.536	0.000	0.000	0.000	0.000
52	P	352	ASN	0	0.010	0.006	9.665	0.166	0.166	0.000	0.000	0.000	0.000
53	P	353	PRO	0	-0.031	-0.026	12.637	0.321	0.321	0.000	0.000	0.000	0.000
54	P	354	ASP	-1	-0.797	-0.883	15.562	0.322	0.322	0.000	0.000	0.000	0.000
55	P	355	GLY	0	-0.034	-0.014	12.436	0.236	0.236	0.000	0.000	0.000	0.000
56	P	356	ASP	-1	-0.801	-0.870	12.415	2.382	2.382	0.000	0.000	0.000	0.000
57	P	357	GLU	-1	-0.937	-0.965	10.390	4.486	4.486	0.000	0.000	0.000	0.000
58	P	358	GLU	-1	-0.894	-0.942	9.068	4.865	4.865	0.000	0.000	0.000	0.000
59	P	359	GLY	0	-0.021	-0.017	7.558	-0.203	-0.203	0.000	0.000	0.000	0.000
60	P	360	ALA	0	-0.062	-0.035	7.972	0.133	0.133	0.000	0.000	0.000	0.000
61	P	361	TRP	0	0.032	0.010	9.950	-0.372	-0.372	0.000	0.000	0.000	0.000
62	P	363	TYR	0	0.053	0.005	16.832	0.240	0.240	0.000	0.000	0.000	0.000
63	P	364	VAL	0	-0.034	-0.038	19.450	-0.271	-0.271	0.000	0.000	0.000	0.000
64	P	365	ALA	0	-0.042	-0.021	22.114	-0.016	-0.016	0.000	0.000	0.000	0.000
65	P	366	ASP	-1	-0.887	-0.947	25.301	-0.603	-0.603	0.000	0.000	0.000	0.000
66	P	367	GLN	0	-0.065	-0.022	27.337	0.126	0.126	0.000	0.000	0.000	0.000
67	P	368	PRO	0	-0.026	-0.031	25.918	-0.026	-0.026	0.000	0.000	0.000	0.000
68	P	369	GLY	0	0.022	0.016	22.963	0.069	0.069	0.000	0.000	0.000	0.000
69	P	370	ASP	-1	-0.856	-0.903	22.305	-0.545	-0.545	0.000	0.000	0.000	0.000
70	P	371	PHE	0	-0.048	-0.042	15.608	-0.222	-0.222	0.000	0.000	0.000	0.000
71	P	372	GLU	-1	-0.760	-0.817	16.334	-1.214	-1.214	0.000	0.000	0.000	0.000
72	P	373	TYR	0	0.002	-0.033	10.943	-0.413	-0.413	0.000	0.000	0.000	0.000
73	P	375	ASN	0	0.003	0.009	8.900	-0.552	-0.552	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:379:CYS)