FMO DATABASE

FMODB ID: R9RZ8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-324694.842106
FMO2-HF: Nuclear repulsion	297303.072751
FMO2-HF: Total energy	-27391.769355
FMO2-MP2: Total energy	-27471.129866

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.
-52.32	-46.513	0.415	-3	-3.222	0.018

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 : -0.899 / q_NPA : -0.946

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	0.080	0.072	2.713	-4.374	1.261	0.413	-2.967	-3.081	0.018
4	E	83	SER	0	-0.072	-0.055	5.367	-7.489	-7.487	-0.001	-0.001	0.000	0.000
5	E	84	MET	0	0.024	0.017	9.014	-0.350	-0.350	0.000	0.000	0.000	0.000
6	E	85	LEU	0	0.037	0.011	12.343	-0.418	-0.418	0.000	0.000	0.000	0.000
7	E	86	GLU	-1	-0.875	-0.932	14.949	13.958	13.958	0.000	0.000	0.000	0.000
8	E	87	LYS	1	0.923	0.955	18.328	-13.341	-13.341	0.000	0.000	0.000	0.000
9	E	88	ILE	0	0.025	0.021	17.234	1.015	1.015	0.000	0.000	0.000	0.000
10	E	89	TYR	0	-0.052	-0.025	20.191	-0.998	-0.998	0.000	0.000	0.000	0.000
11	E	90	ILE	0	0.065	0.043	21.508	0.662	0.662	0.000	0.000	0.000	0.000
12	E	91	HIS	0	0.049	0.047	24.254	-0.675	-0.675	0.000	0.000	0.000	0.000
13	E	92	PRO	0	0.000	-0.013	26.888	-0.101	-0.101	0.000	0.000	0.000	0.000
14	E	93	ARG	1	0.902	0.936	30.153	-9.286	-9.286	0.000	0.000	0.000	0.000
15	E	94	TYR	0	-0.003	0.009	23.881	-0.298	-0.298	0.000	0.000	0.000	0.000
16	E	95	ASN	0	-0.028	-0.010	28.899	-0.315	-0.315	0.000	0.000	0.000	0.000
17	E	96	TRP	0	0.022	0.018	27.433	0.013	0.013	0.000	0.000	0.000	0.000
18	E	97	ARG	1	0.904	0.958	28.932	-8.904	-8.904	0.000	0.000	0.000	0.000
19	E	97	GLU	-1	-0.938	-0.960	32.433	8.715	8.715	0.000	0.000	0.000	0.000
20	E	98	ASN	0	-0.006	-0.020	31.699	0.246	0.246	0.000	0.000	0.000	0.000
21	E	99	LEU	0	0.031	0.013	25.322	0.117	0.117	0.000	0.000	0.000	0.000
22	E	100	ASP	-1	-0.794	-0.881	28.061	10.203	10.203	0.000	0.000	0.000	0.000
23	E	101	ARG	1	0.757	0.855	27.816	-9.863	-9.863	0.000	0.000	0.000	0.000
24	E	102	ASP	-1	-0.855	-0.909	22.769	14.075	14.075	0.000	0.000	0.000	0.000
25	E	103	ILE	0	-0.010	-0.007	21.435	0.591	0.591	0.000	0.000	0.000	0.000
26	E	104	ALA	0	0.024	-0.012	19.359	-0.609	-0.609	0.000	0.000	0.000	0.000
27	E	105	LEU	0	-0.042	-0.009	18.738	0.772	0.772	0.000	0.000	0.000	0.000
28	E	106	MET	0	0.045	0.003	12.845	-0.576	-0.576	0.000	0.000	0.000	0.000
29	E	107	LYS	1	0.857	0.925	15.768	-13.586	-13.586	0.000	0.000	0.000	0.000
30	E	108	LEU	0	0.018	-0.001	11.011	-0.006	-0.006	0.000	0.000	0.000	0.000
31	E	109	LYS	1	0.932	0.972	14.569	-17.577	-17.577	0.000	0.000	0.000	0.000
32	E	110	LYS	1	0.973	0.976	12.212	-22.169	-22.169	0.000	0.000	0.000	0.000
33	E	111	PRO	0	0.004	0.010	12.880	1.809	1.809	0.000	0.000	0.000	0.000
34	E	112	VAL	0	-0.005	-0.008	7.772	0.055	0.055	0.000	0.000	0.000	0.000
35	E	113	ALA	0	0.003	0.015	9.340	-1.476	-1.476	0.000	0.000	0.000	0.000
36	E	114	PHE	0	-0.011	-0.016	8.629	1.767	1.767	0.000	0.000	0.000	0.000
37	E	115	SER	0	0.037	0.011	6.163	-0.612	-0.612	0.000	0.000	0.000	0.000
38	E	116	ASP	-1	-0.876	-0.929	9.351	20.175	20.175	0.000	0.000	0.000	0.000
39	E	117	TYR	0	-0.032	-0.019	5.191	0.951	0.951	0.000	0.000	0.000	0.000
40	E	118	ILE	0	-0.085	-0.033	3.643	2.629	2.799	0.003	-0.032	-0.141	0.000
41	E	119	HIS	0	0.033	-0.005	7.807	-2.464	-2.464	0.000	0.000	0.000	0.000
42	E	120	PRO	0	-0.054	-0.002	11.495	0.612	0.612	0.000	0.000	0.000	0.000
43	E	121	VAL	0	0.027	0.020	14.225	-0.013	-0.013	0.000	0.000	0.000	0.000
44	E	122	CYS	0	-0.037	-0.019	16.683	-0.210	-0.210	0.000	0.000	0.000	0.000
45	E	123	LEU	0	0.029	0.018	20.452	0.282	0.282	0.000	0.000	0.000	0.000
46	E	124	PRO	0	-0.020	-0.008	22.932	-0.183	-0.183	0.000	0.000	0.000	0.000
47	E	125	ASP	-1	-0.794	-0.878	26.304	10.157	10.157	0.000	0.000	0.000	0.000
48	E	126	ARG	1	0.962	0.967	29.726	-8.215	-8.215	0.000	0.000	0.000	0.000
49	E	127	GLU	-1	-0.876	-0.949	33.027	8.613	8.613	0.000	0.000	0.000	0.000
50	E	128	THR	0	-0.012	-0.016	26.919	-0.066	-0.066	0.000	0.000	0.000	0.000
51	E	129	ALA	0	-0.025	-0.012	29.514	0.176	0.176	0.000	0.000	0.000	0.000
52	E	129	ALA	0	-0.006	-0.004	30.518	-0.031	-0.031	0.000	0.000	0.000	0.000
53	E	129	SER	0	-0.053	-0.050	32.792	-0.037	-0.037	0.000	0.000	0.000	0.000
54	E	129	LEU	0	0.000	0.019	27.357	-0.028	-0.028	0.000	0.000	0.000	0.000
55	E	130	LEU	0	-0.065	-0.036	27.701	0.171	0.171	0.000	0.000	0.000	0.000
56	E	131	GLN	0	0.026	0.014	31.047	-0.445	-0.445	0.000	0.000	0.000	0.000
57	E	132	ALA	0	0.044	0.041	32.368	0.245	0.245	0.000	0.000	0.000	0.000
58	E	133	GLY	0	-0.010	-0.007	33.119	-0.205	-0.205	0.000	0.000	0.000	0.000
59	E	134	TYR	0	-0.091	-0.050	30.198	0.122	0.122	0.000	0.000	0.000	0.000
60	E	135	LYS	1	0.920	0.955	26.658	-10.728	-10.728	0.000	0.000	0.000	0.000
61	E	136	GLY	0	0.080	0.054	24.108	0.031	0.031	0.000	0.000	0.000	0.000
62	E	137	ARG	1	0.915	0.960	18.532	-15.971	-15.971	0.000	0.000	0.000	0.000
63	E	138	VAL	0	0.033	0.007	18.598	0.283	0.283	0.000	0.000	0.000	0.000
64	E	139	THR	0	-0.033	-0.027	13.675	-0.150	-0.150	0.000	0.000	0.000	0.000
65	E	140	GLY	0	-0.009	-0.026	12.615	0.191	0.191	0.000	0.000	0.000	0.000
66	E	141	TRP	0	0.019	0.022	7.033	0.572	0.572	0.000	0.000	0.000	0.000
67	E	142	GLY	0	0.026	0.043	12.590	0.241	0.241	0.000	0.000	0.000	0.000

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