FMO DATABASE

FMODB ID: 4972N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-358063.200145
FMO2-HF: Nuclear repulsion	331052.583882
FMO2-HF: Total energy	-27010.616264
FMO2-MP2: Total energy	-27087.801507

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.
-5.815	-2.335	0.96	-1.518	-2.921	-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 : -0.044 / q_NPA : -0.037

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	-0.926	-0.973	2.948	-4.345	-1.815	0.358	-1.192	-1.695	-0.004
4	C	19	GLY	0	-0.021	0.014	2.656	-0.385	0.703	0.580	-0.615	-1.053	-0.002
5	C	20	SER	0	0.004	0.000	3.366	0.680	0.542	0.022	0.289	-0.173	0.000
6	C	21	ASP	-1	-0.970	-0.982	5.360	-1.814	-1.814	0.000	0.000	0.000	0.000
7	C	22	ALA	0	-0.006	-0.005	7.072	0.156	0.156	0.000	0.000	0.000	0.000
8	C	23	GLU	-1	-0.876	-0.942	8.473	-0.482	-0.482	0.000	0.000	0.000	0.000
9	C	24	ILE	0	-0.016	-0.033	12.113	0.032	0.032	0.000	0.000	0.000	0.000
10	C	25	GLY	0	-0.015	-0.010	13.810	0.016	0.016	0.000	0.000	0.000	0.000
11	C	26	MET	0	-0.023	0.001	9.720	0.000	0.000	0.000	0.000	0.000	0.000
12	C	27	SER	0	-0.015	-0.012	8.216	0.030	0.030	0.000	0.000	0.000	0.000
13	C	28	PRO	0	0.017	0.014	10.942	0.032	0.032	0.000	0.000	0.000	0.000
14	C	29	TRP	0	0.031	0.017	9.788	0.048	0.048	0.000	0.000	0.000	0.000
15	C	30	GLN	0	0.019	0.027	5.781	-0.030	-0.030	0.000	0.000	0.000	0.000
16	C	31	VAL	0	-0.020	-0.003	10.445	-0.022	-0.022	0.000	0.000	0.000	0.000
17	C	32	MET	0	0.001	0.001	9.071	0.044	0.044	0.000	0.000	0.000	0.000
18	C	33	LEU	0	0.038	0.024	11.617	-0.068	-0.068	0.000	0.000	0.000	0.000
19	C	34	PHE	0	-0.006	-0.030	12.936	0.078	0.078	0.000	0.000	0.000	0.000
20	C	35	ARG	1	0.938	0.966	15.780	-0.370	-0.370	0.000	0.000	0.000	0.000
21	C	36	LYS	1	0.868	0.939	18.784	-0.202	-0.202	0.000	0.000	0.000	0.000
22	C	36	SER	0	0.008	-0.026	21.409	-0.020	-0.020	0.000	0.000	0.000	0.000
23	C	37	PRO	0	0.063	0.049	21.392	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	38	GLN	0	0.004	0.009	16.847	0.001	0.001	0.000	0.000	0.000	0.000
25	C	39	GLU	-1	-0.842	-0.918	14.614	0.494	0.494	0.000	0.000	0.000	0.000
26	C	40	LEU	0	-0.078	-0.030	8.884	-0.041	-0.041	0.000	0.000	0.000	0.000
27	C	41	LEU	0	0.046	0.029	11.734	0.102	0.102	0.000	0.000	0.000	0.000
28	C	42	CYS	0	-0.135	-0.085	9.733	0.246	0.246	0.000	0.000	0.000	0.000
29	C	43	GLY	0	0.013	0.025	7.600	-0.035	-0.035	0.000	0.000	0.000	0.000
30	C	44	ALA	0	-0.040	-0.034	8.668	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	45	SER	0	0.026	0.010	9.694	-0.016	-0.016	0.000	0.000	0.000	0.000
32	C	46	LEU	0	-0.034	-0.005	12.160	0.012	0.012	0.000	0.000	0.000	0.000
33	C	47	ILE	0	-0.011	-0.006	15.652	-0.020	-0.020	0.000	0.000	0.000	0.000
34	C	48	SER	0	-0.001	-0.015	17.669	-0.008	-0.008	0.000	0.000	0.000	0.000
35	C	49	ASP	-1	-0.867	-0.936	19.903	0.051	0.051	0.000	0.000	0.000	0.000
36	C	50	ARG	1	0.878	0.939	22.454	-0.070	-0.070	0.000	0.000	0.000	0.000
37	C	51	TRP	0	0.019	0.013	20.209	0.013	0.013	0.000	0.000	0.000	0.000
38	C	52	VAL	0	-0.005	0.007	14.693	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	53	LEU	0	-0.024	-0.010	14.113	-0.001	-0.001	0.000	0.000	0.000	0.000
40	C	54	THR	0	0.036	-0.007	12.134	0.048	0.048	0.000	0.000	0.000	0.000
41	C	55	ALA	0	0.030	0.031	11.538	-0.050	-0.050	0.000	0.000	0.000	0.000
42	C	56	ALA	0	0.094	0.028	13.464	0.020	0.020	0.000	0.000	0.000	0.000
43	C	57	HIS	0	-0.002	-0.004	11.165	-0.022	-0.022	0.000	0.000	0.000	0.000
44	C	59	LEU	0	-0.010	0.021	14.890	0.000	0.000	0.000	0.000	0.000	0.000
45	C	60	LEU	0	-0.004	-0.006	18.278	-0.023	-0.023	0.000	0.000	0.000	0.000
46	C	60	TYR	0	0.026	0.000	17.925	-0.005	-0.005	0.000	0.000	0.000	0.000
47	C	60	PRO	0	0.067	0.029	20.057	0.014	0.014	0.000	0.000	0.000	0.000
48	C	60	PRO	0	-0.056	-0.020	21.006	-0.004	-0.004	0.000	0.000	0.000	0.000
49	C	60	TRP	0	-0.024	-0.022	13.564	0.043	0.043	0.000	0.000	0.000	0.000
50	C	60	ASP	-1	-0.960	-0.962	21.056	0.308	0.308	0.000	0.000	0.000	0.000
51	C	60	LYS	1	0.868	0.935	15.344	-0.626	-0.626	0.000	0.000	0.000	0.000
52	C	60	ASN	0	0.017	0.001	21.299	0.002	0.002	0.000	0.000	0.000	0.000
53	C	60	PHE	0	-0.032	-0.015	19.175	-0.011	-0.011	0.000	0.000	0.000	0.000
54	C	60	THR	0	0.008	-0.007	22.311	-0.009	-0.009	0.000	0.000	0.000	0.000
55	C	61	GLU	-1	-0.886	-0.946	23.346	0.186	0.186	0.000	0.000	0.000	0.000
56	C	62	ASN	0	-0.059	-0.034	23.696	-0.008	-0.008	0.000	0.000	0.000	0.000
57	C	63	ASP	-1	-0.855	-0.918	22.748	0.220	0.220	0.000	0.000	0.000	0.000
58	C	64	LEU	0	-0.037	0.001	17.511	0.023	0.023	0.000	0.000	0.000	0.000
59	C	65	LEU	0	-0.013	0.001	19.344	-0.030	-0.030	0.000	0.000	0.000	0.000
60	C	66	VAL	0	-0.014	-0.013	15.292	0.037	0.037	0.000	0.000	0.000	0.000
61	C	67	ARG	1	0.809	0.908	14.708	-0.188	-0.188	0.000	0.000	0.000	0.000
62	C	68	ILE	0	0.050	0.012	14.356	0.009	0.009	0.000	0.000	0.000	0.000
63	C	69	GLY	0	0.034	0.010	14.847	-0.007	-0.007	0.000	0.000	0.000	0.000
64	C	70	LYS	1	0.926	0.984	12.253	0.043	0.043	0.000	0.000	0.000	0.000
65	C	71	HIS	0	0.000	0.015	9.028	0.061	0.061	0.000	0.000	0.000	0.000
66	C	72	SER	0	0.016	0.006	9.793	0.060	0.060	0.000	0.000	0.000	0.000

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