FMO DATABASE

FMODB ID: K9NY3

Calculation Name: 2HNT-C-Xray372

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2HNT

Chain ID: C

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	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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-358517.552683
FMO2-HF: Nuclear repulsion	331508.133762
FMO2-HF: Total energy	-27009.418921
FMO2-MP2: Total energy	-27086.769501

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(C:16:ILE)

Summations of interaction energy for fragment #1(C:16:ILE)

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.
-5.187	-2.117	1.633	-1.368	-3.334	-0.006

Interaction energy analysis for fragmet #1(C:16:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.028

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	C	18	GLU	-1	-0.937	-0.980	3.069	-4.190	-1.670	0.345	-1.161	-1.704	-0.003
4	C	19	GLY	0	0.000	0.030	2.432	-0.361	0.635	1.261	-0.894	-1.364	-0.003
5	C	20	SER	0	-0.032	-0.013	3.209	1.161	0.645	0.028	0.687	-0.198	0.000
6	C	21	ASP	-1	-0.930	-0.972	5.145	-1.897	-1.827	-0.001	0.000	-0.068	0.000
7	C	22	ALA	0	0.000	-0.005	7.323	0.168	0.168	0.000	0.000	0.000	0.000
8	C	23	GLU	-1	-0.867	-0.978	8.699	-0.462	-0.462	0.000	0.000	0.000	0.000
9	C	24	ILE	0	-0.005	-0.018	12.295	0.039	0.039	0.000	0.000	0.000	0.000
10	C	25	GLY	0	-0.015	-0.012	13.906	0.015	0.015	0.000	0.000	0.000	0.000
11	C	26	MET	0	-0.028	0.046	10.044	-0.005	-0.005	0.000	0.000	0.000	0.000
12	C	27	SER	0	-0.027	-0.016	8.099	0.030	0.030	0.000	0.000	0.000	0.000
13	C	28	PRO	0	0.022	0.005	11.013	0.039	0.039	0.000	0.000	0.000	0.000
14	C	29	TRP	0	0.030	0.028	9.758	0.036	0.036	0.000	0.000	0.000	0.000
15	C	30	GLN	0	0.014	0.018	6.185	0.047	0.047	0.000	0.000	0.000	0.000
16	C	31	VAL	0	-0.038	-0.011	10.730	-0.032	-0.032	0.000	0.000	0.000	0.000
17	C	32	MET	0	0.018	0.006	9.664	0.034	0.034	0.000	0.000	0.000	0.000
18	C	33	LEU	0	0.045	0.028	12.073	-0.080	-0.080	0.000	0.000	0.000	0.000
19	C	34	PHE	0	-0.007	-0.034	13.130	0.083	0.083	0.000	0.000	0.000	0.000
20	C	35	ARG	1	1.007	1.022	15.850	-0.389	-0.389	0.000	0.000	0.000	0.000
21	C	36	LYS	1	0.873	0.938	18.865	-0.212	-0.212	0.000	0.000	0.000	0.000
22	C	36	SER	0	0.004	-0.016	21.469	-0.020	-0.020	0.000	0.000	0.000	0.000
23	C	37	PRO	0	0.075	0.043	21.377	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	38	GLN	0	-0.049	-0.018	16.857	0.008	0.008	0.000	0.000	0.000	0.000
25	C	39	GLU	-1	-0.903	-0.966	14.397	0.571	0.571	0.000	0.000	0.000	0.000
26	C	40	LEU	0	-0.092	-0.032	8.648	-0.046	-0.046	0.000	0.000	0.000	0.000
27	C	41	LEU	0	0.061	0.044	11.823	0.113	0.113	0.000	0.000	0.000	0.000
28	C	42	CYS	0	-0.136	-0.088	9.880	0.256	0.256	0.000	0.000	0.000	0.000
29	C	43	GLY	0	0.003	0.016	8.275	-0.025	-0.025	0.000	0.000	0.000	0.000
30	C	44	ALA	0	-0.035	-0.031	9.354	-0.016	-0.016	0.000	0.000	0.000	0.000
31	C	45	SER	0	0.038	0.015	10.090	-0.013	-0.013	0.000	0.000	0.000	0.000
32	C	46	LEU	0	-0.052	-0.006	12.430	0.007	0.007	0.000	0.000	0.000	0.000
33	C	47	ILE	0	-0.017	-0.008	15.882	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	48	SER	0	-0.004	-0.014	17.771	-0.012	-0.012	0.000	0.000	0.000	0.000
35	C	49	ASP	-1	-0.871	-0.936	20.132	0.065	0.065	0.000	0.000	0.000	0.000
36	C	50	ARG	1	0.905	0.950	22.709	-0.088	-0.088	0.000	0.000	0.000	0.000
37	C	51	TRP	0	-0.005	0.003	20.529	0.012	0.012	0.000	0.000	0.000	0.000
38	C	52	VAL	0	-0.012	-0.006	15.118	-0.005	-0.005	0.000	0.000	0.000	0.000
39	C	53	LEU	0	-0.005	0.000	14.396	-0.005	-0.005	0.000	0.000	0.000	0.000
40	C	54	THR	0	0.039	-0.004	12.700	0.062	0.062	0.000	0.000	0.000	0.000
41	C	55	ALA	0	0.028	0.035	12.075	-0.057	-0.057	0.000	0.000	0.000	0.000
42	C	56	ALA	0	0.092	0.019	13.866	0.021	0.021	0.000	0.000	0.000	0.000
43	C	57	HIS	0	0.005	-0.001	11.979	-0.019	-0.019	0.000	0.000	0.000	0.000
44	C	59	LEU	0	-0.033	0.003	15.378	0.000	0.000	0.000	0.000	0.000	0.000
45	C	60	LEU	0	-0.001	-0.001	18.817	-0.025	-0.025	0.000	0.000	0.000	0.000
46	C	60	TYR	0	0.045	0.002	17.949	-0.011	-0.011	0.000	0.000	0.000	0.000
47	C	60	PRO	0	0.054	0.030	20.679	0.012	0.012	0.000	0.000	0.000	0.000
48	C	60	PRO	0	-0.057	-0.029	21.433	-0.004	-0.004	0.000	0.000	0.000	0.000
49	C	60	TRP	0	-0.054	-0.028	14.007	0.041	0.041	0.000	0.000	0.000	0.000
50	C	60	ASP	-1	-0.973	-0.972	21.207	0.328	0.328	0.000	0.000	0.000	0.000
51	C	60	LYS	1	0.921	0.968	15.628	-0.647	-0.647	0.000	0.000	0.000	0.000
52	C	60	ASN	0	0.024	-0.003	21.566	0.003	0.003	0.000	0.000	0.000	0.000
53	C	60	PHE	0	-0.024	-0.004	19.123	-0.014	-0.014	0.000	0.000	0.000	0.000
54	C	60	THR	0	0.016	0.012	22.600	-0.010	-0.010	0.000	0.000	0.000	0.000
55	C	61	GLU	-1	-0.884	-0.955	23.942	0.199	0.199	0.000	0.000	0.000	0.000
56	C	62	ASN	0	-0.045	-0.025	24.154	-0.006	-0.006	0.000	0.000	0.000	0.000
57	C	63	ASP	-1	-0.896	-0.953	22.749	0.246	0.246	0.000	0.000	0.000	0.000
58	C	64	LEU	0	-0.041	-0.008	18.171	0.026	0.026	0.000	0.000	0.000	0.000
59	C	65	LEU	0	-0.045	-0.023	19.574	-0.033	-0.033	0.000	0.000	0.000	0.000
60	C	66	VAL	0	0.015	0.008	15.725	0.041	0.041	0.000	0.000	0.000	0.000
61	C	67	ARG	1	0.874	0.941	15.089	-0.212	-0.212	0.000	0.000	0.000	0.000
62	C	68	ILE	0	0.036	0.012	14.610	0.014	0.014	0.000	0.000	0.000	0.000
63	C	69	GLY	0	0.045	0.013	14.737	-0.008	-0.008	0.000	0.000	0.000	0.000
64	C	70	LYS	1	0.913	0.985	11.816	-0.026	-0.026	0.000	0.000	0.000	0.000
65	C	71	HIS	0	-0.012	0.005	8.583	0.083	0.083	0.000	0.000	0.000	0.000
66	C	72	SER	0	0.008	0.004	10.055	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:16:ILE)