FMO DATABASE

FMODB ID: 43M3N

Calculation Name: 1E0F-I-Xray372

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1E0F

Chain ID: I

ChEMBL ID: CHEMBL204

UniProt ID: P00734

Base Structure: X-ray

Registration Date: 2023-06-21

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-244959.594915
FMO2-HF: Nuclear repulsion	221161.387128
FMO2-HF: Total energy	-23798.207787
FMO2-MP2: Total energy	-23861.230357

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(I:1:ILE)

Summations of interaction energy for fragment #1(I:1: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.
-7.259	-2.855	0.383	-1.659	-3.128	-0.003

Interaction energy analysis for fragmet #1(I:1:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.001

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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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	I	3	PHE	0	0.049	0.031	3.568	-3.503	0.306	0.098	-1.508	-2.399	-0.002
4	I	4	GLY	0	-0.011	0.007	4.786	0.357	0.394	-0.001	-0.005	-0.031	0.000
5	I	5	MET	0	-0.077	-0.061	6.847	0.275	0.275	0.000	0.000	0.000	0.000
6	I	6	GLY	0	0.105	0.070	7.635	0.112	0.112	0.000	0.000	0.000	0.000
7	I	7	LYS	1	0.842	0.908	4.956	-0.904	-0.904	0.000	0.000	0.000	0.000
8	I	8	VAL	0	-0.020	0.003	2.901	-0.505	0.053	0.286	-0.146	-0.698	-0.001
9	I	9	PRO	0	0.019	0.017	5.958	-0.112	-0.112	0.000	0.000	0.000	0.000
10	I	10	CYS	0	-0.013	0.012	6.398	-0.505	-0.505	0.000	0.000	0.000	0.000
11	I	11	PRO	0	-0.033	-0.002	11.486	0.067	0.067	0.000	0.000	0.000	0.000
12	I	12	ASP	-1	-0.881	-0.957	14.494	-0.243	-0.243	0.000	0.000	0.000	0.000
13	I	13	GLY	0	-0.024	-0.013	17.642	0.014	0.014	0.000	0.000	0.000	0.000
14	I	14	GLU	-1	-0.964	-0.975	16.935	-0.329	-0.329	0.000	0.000	0.000	0.000
15	I	15	VAL	0	-0.062	-0.043	11.513	-0.035	-0.035	0.000	0.000	0.000	0.000
16	I	16	GLY	0	0.049	0.007	13.301	-0.043	-0.043	0.000	0.000	0.000	0.000
17	I	17	TYR	0	-0.025	-0.013	7.295	-0.021	-0.021	0.000	0.000	0.000	0.000
18	I	18	THR	0	0.002	-0.005	7.579	0.143	0.143	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.815	-0.921	6.772	-0.817	-0.817	0.000	0.000	0.000	0.000
20	I	21	CYS	0	0.048	-0.001	8.574	0.144	0.144	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.046	0.025	12.340	0.036	0.036	0.000	0.000	0.000	0.000
22	I	23	GLU	-1	-0.950	-0.985	11.949	-0.139	-0.139	0.000	0.000	0.000	0.000
23	I	24	LYS	1	0.881	0.949	11.360	0.233	0.233	0.000	0.000	0.000	0.000
24	I	25	ILE	0	0.029	0.008	7.667	-0.008	-0.008	0.000	0.000	0.000	0.000
25	I	26	CYS	0	-0.033	0.015	10.434	0.089	0.089	0.000	0.000	0.000	0.000
26	I	27	LEU	0	-0.018	-0.021	10.939	-0.110	-0.110	0.000	0.000	0.000	0.000
27	I	28	TYR	0	0.006	-0.003	11.554	0.094	0.094	0.000	0.000	0.000	0.000
28	I	29	GLY	0	0.073	0.058	12.937	0.044	0.044	0.000	0.000	0.000	0.000
29	I	30	GLN	0	-0.016	-0.006	15.222	0.077	0.077	0.000	0.000	0.000	0.000
30	I	31	SER	0	-0.033	-0.034	15.698	-0.009	-0.009	0.000	0.000	0.000	0.000
31	I	33	ASN	0	-0.005	-0.004	16.532	0.006	0.006	0.000	0.000	0.000	0.000
32	I	34	ASP	-1	-0.923	-0.951	16.981	-0.136	-0.136	0.000	0.000	0.000	0.000
33	I	35	GLY	0	0.013	0.005	17.614	-0.014	-0.014	0.000	0.000	0.000	0.000
34	I	36	GLN	0	-0.129	-0.065	16.838	-0.014	-0.014	0.000	0.000	0.000	0.000
35	I	38	SER	0	-0.024	-0.013	18.403	0.008	0.008	0.000	0.000	0.000	0.000
36	I	39	GLY	0	-0.002	0.027	19.127	0.022	0.022	0.000	0.000	0.000	0.000
37	I	40	ASP	-1	-0.950	-0.992	19.615	-0.316	-0.316	0.000	0.000	0.000	0.000
38	I	41	PRO	0	-0.066	-0.033	15.799	-0.006	-0.006	0.000	0.000	0.000	0.000
39	I	42	LYS	1	0.926	0.987	16.962	0.348	0.348	0.000	0.000	0.000	0.000
40	I	43	PRO	0	0.019	-0.009	16.800	-0.006	-0.006	0.000	0.000	0.000	0.000
41	I	44	SER	0	0.002	-0.018	17.294	-0.057	-0.057	0.000	0.000	0.000	0.000
42	I	45	SER	0	-0.019	-0.010	19.537	0.029	0.029	0.000	0.000	0.000	0.000
43	I	46	GLU	-1	-0.914	-0.967	21.517	-0.274	-0.274	0.000	0.000	0.000	0.000
44	I	47	PHE	0	-0.058	-0.001	23.951	0.021	0.021	0.000	0.000	0.000	0.000
45	I	48	GLU	-1	-0.991	-0.991	23.600	-0.229	-0.229	0.000	0.000	0.000	0.000
46	I	49	GLU	-1	-0.973	-0.987	18.550	-0.363	-0.363	0.000	0.000	0.000	0.000
47	I	50	PHE	0	-0.023	-0.014	23.427	0.018	0.018	0.000	0.000	0.000	0.000
48	I	51	GLU	-1	-0.911	-0.948	24.372	-0.207	-0.207	0.000	0.000	0.000	0.000
49	I	52	ILE	0	-0.118	-0.079	27.037	0.013	0.013	0.000	0.000	0.000	0.000
50	I	53	ASP	-1	-0.958	-0.991	27.472	-0.144	-0.144	0.000	0.000	0.000	0.000
51	I	54	GLU	-1	-1.004	-0.964	28.276	-0.092	-0.092	0.000	0.000	0.000	0.000
52	I	55	GLU	-1	-0.936	-0.968	22.490	-0.206	-0.206	0.000	0.000	0.000	0.000
53	I	56	GLU	-1	-0.948	-0.969	25.272	-0.131	-0.131	0.000	0.000	0.000	0.000
54	I	57	LYS	1	0.904	0.945	26.644	0.069	0.069	0.000	0.000	0.000	0.000

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