FMO DATABASE

FMODB ID: QYQRY

Calculation Name: 2HNT-E-Xray372

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2HNT

Chain ID: E

ChEMBL ID: CHEMBL204

UniProt ID: P00734

Base Structure: X-ray

Registration Date: 2023-09-20

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-324602.191194
FMO2-HF: Nuclear repulsion	297209.590828
FMO2-HF: Total energy	-27392.600366
FMO2-MP2: Total energy	-27471.812886

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(E:80:GLU)

Summations of interaction energy for fragment #1(E:80:GLU)

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.
-62.095	-56.507	1.083	-3.132	-3.539	0.021

Interaction energy analysis for fragmet #1(E:80:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.880 / q_NPA : -0.938

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	E	82	ILE	0	0.084	0.051	2.551	-10.600	-5.236	1.075	-3.078	-3.361	0.021
4	E	83	SER	0	-0.041	-0.026	4.985	-8.964	-8.964	-0.001	-0.007	0.008	0.000
5	E	84	MET	0	0.016	0.017	8.596	-0.919	-0.919	0.000	0.000	0.000	0.000
6	E	85	LEU	0	0.055	0.030	11.815	-0.327	-0.327	0.000	0.000	0.000	0.000
7	E	86	GLU	-1	-0.915	-0.951	14.529	14.008	14.008	0.000	0.000	0.000	0.000
8	E	87	LYS	1	0.964	0.977	18.117	-13.407	-13.407	0.000	0.000	0.000	0.000
9	E	88	ILE	0	0.016	0.013	16.519	0.952	0.952	0.000	0.000	0.000	0.000
10	E	89	TYR	0	-0.034	-0.011	19.601	-1.035	-1.035	0.000	0.000	0.000	0.000
11	E	90	ILE	0	0.070	0.030	21.183	0.666	0.666	0.000	0.000	0.000	0.000
12	E	91	HIS	0	0.055	0.035	23.877	-0.591	-0.591	0.000	0.000	0.000	0.000
13	E	92	PRO	0	0.000	-0.007	26.777	-0.139	-0.139	0.000	0.000	0.000	0.000
14	E	93	ARG	1	0.920	0.951	30.050	-9.417	-9.417	0.000	0.000	0.000	0.000
15	E	94	TYR	0	-0.019	-0.008	23.880	-0.278	-0.278	0.000	0.000	0.000	0.000
16	E	95	ASN	0	-0.038	-0.029	29.011	-0.199	-0.199	0.000	0.000	0.000	0.000
17	E	96	TRP	0	0.040	0.009	27.417	-0.133	-0.133	0.000	0.000	0.000	0.000
18	E	97	ARG	1	0.843	0.939	29.122	-9.180	-9.180	0.000	0.000	0.000	0.000
19	E	97	GLU	-1	-0.893	-0.942	32.191	8.557	8.557	0.000	0.000	0.000	0.000
20	E	98	ASN	0	0.015	-0.002	32.101	0.298	0.298	0.000	0.000	0.000	0.000
21	E	99	LEU	0	0.003	0.014	25.456	0.140	0.140	0.000	0.000	0.000	0.000
22	E	100	ASP	-1	-0.775	-0.867	27.864	10.287	10.287	0.000	0.000	0.000	0.000
23	E	101	ARG	1	0.745	0.837	27.622	-9.991	-9.991	0.000	0.000	0.000	0.000
24	E	102	ASP	-1	-0.839	-0.900	22.715	14.285	14.285	0.000	0.000	0.000	0.000
25	E	103	ILE	0	-0.034	-0.010	21.428	0.450	0.450	0.000	0.000	0.000	0.000
26	E	104	ALA	0	0.009	-0.002	19.016	-0.501	-0.501	0.000	0.000	0.000	0.000
27	E	105	LEU	0	-0.021	-0.005	18.234	0.568	0.568	0.000	0.000	0.000	0.000
28	E	106	MET	0	0.024	-0.002	12.915	-0.507	-0.507	0.000	0.000	0.000	0.000
29	E	107	LYS	1	0.872	0.943	15.136	-14.060	-14.060	0.000	0.000	0.000	0.000
30	E	108	LEU	0	0.059	0.013	10.729	-0.126	-0.126	0.000	0.000	0.000	0.000
31	E	109	LYS	1	0.856	0.923	14.066	-18.511	-18.511	0.000	0.000	0.000	0.000
32	E	110	LYS	1	0.962	0.969	12.604	-22.367	-22.367	0.000	0.000	0.000	0.000
33	E	111	PRO	0	0.037	0.021	12.859	1.705	1.705	0.000	0.000	0.000	0.000
34	E	112	VAL	0	-0.022	-0.017	7.206	1.174	1.174	0.000	0.000	0.000	0.000
35	E	113	ALA	0	0.020	0.026	9.662	-1.346	-1.346	0.000	0.000	0.000	0.000
36	E	114	PHE	0	0.000	-0.012	8.710	1.648	1.648	0.000	0.000	0.000	0.000
37	E	115	SER	0	0.011	-0.002	6.561	-0.472	-0.472	0.000	0.000	0.000	0.000
38	E	116	ASP	-1	-0.876	-0.940	9.608	20.792	20.792	0.000	0.000	0.000	0.000
39	E	117	TYR	0	-0.024	-0.007	5.191	0.767	0.767	0.000	0.000	0.000	0.000
40	E	118	ILE	0	-0.066	-0.027	3.454	2.844	3.068	0.009	-0.047	-0.186	0.000
41	E	119	HIS	0	0.016	0.000	7.483	-2.566	-2.566	0.000	0.000	0.000	0.000
42	E	120	PRO	0	-0.027	0.003	11.288	0.783	0.783	0.000	0.000	0.000	0.000
43	E	121	VAL	0	0.019	0.009	14.028	-0.277	-0.277	0.000	0.000	0.000	0.000
44	E	122	CYS	0	-0.023	-0.014	16.637	-0.179	-0.179	0.000	0.000	0.000	0.000
45	E	123	LEU	0	0.019	0.013	20.431	0.169	0.169	0.000	0.000	0.000	0.000
46	E	124	PRO	0	-0.021	-0.002	22.767	-0.226	-0.226	0.000	0.000	0.000	0.000
47	E	125	ASP	-1	-0.765	-0.854	26.102	10.119	10.119	0.000	0.000	0.000	0.000
48	E	126	ARG	1	0.827	0.864	29.408	-8.383	-8.383	0.000	0.000	0.000	0.000
49	E	127	GLU	-1	-0.762	-0.851	32.627	8.508	8.508	0.000	0.000	0.000	0.000
50	E	128	THR	0	-0.025	-0.024	26.924	-0.044	-0.044	0.000	0.000	0.000	0.000
51	E	129	ALA	0	-0.034	-0.018	29.492	0.139	0.139	0.000	0.000	0.000	0.000
52	E	129	ALA	0	-0.012	-0.008	30.380	-0.025	-0.025	0.000	0.000	0.000	0.000
53	E	129	SER	0	-0.045	-0.040	32.609	-0.105	-0.105	0.000	0.000	0.000	0.000
54	E	129	LEU	0	-0.005	-0.002	27.461	0.010	0.010	0.000	0.000	0.000	0.000
55	E	130	LEU	0	-0.049	-0.014	27.386	0.226	0.226	0.000	0.000	0.000	0.000
56	E	131	GLN	0	0.004	0.007	30.944	-0.428	-0.428	0.000	0.000	0.000	0.000
57	E	132	ALA	0	0.018	0.001	32.619	0.265	0.265	0.000	0.000	0.000	0.000
58	E	133	GLY	0	0.003	0.000	32.908	-0.154	-0.154	0.000	0.000	0.000	0.000
59	E	134	TYR	0	-0.074	-0.034	30.062	0.138	0.138	0.000	0.000	0.000	0.000
60	E	135	LYS	1	0.935	0.964	26.729	-10.505	-10.505	0.000	0.000	0.000	0.000
61	E	136	GLY	0	0.068	0.052	24.247	0.171	0.171	0.000	0.000	0.000	0.000
62	E	137	ARG	1	0.904	0.936	18.634	-16.035	-16.035	0.000	0.000	0.000	0.000
63	E	138	VAL	0	0.028	0.016	18.276	0.255	0.255	0.000	0.000	0.000	0.000
64	E	139	THR	0	-0.009	-0.009	13.558	-0.339	-0.339	0.000	0.000	0.000	0.000
65	E	140	GLY	0	-0.003	-0.005	12.521	0.254	0.254	0.000	0.000	0.000	0.000
66	E	141	TRP	0	0.013	0.009	7.449	0.417	0.417	0.000	0.000	0.000	0.000
67	E	142	GLY	0	0.010	0.021	12.530	-0.354	-0.354	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:80:GLU)