FMO DATABASE

FMODB ID: YY2Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-245506.22648
FMO2-HF: Nuclear repulsion	221707.242769
FMO2-HF: Total energy	-23798.983711
FMO2-MP2: Total energy	-23861.968849

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.
-7.056	-2.946	2.283	-2.062	-4.33	-0.014

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 : 0.011 / q_NPA : -0.003

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	0.080	0.042	2.998	-3.455	0.193	1.412	-1.799	-3.261	-0.011
4	I	4	GLY	0	-0.020	-0.013	4.670	0.321	0.345	-0.001	-0.006	-0.016	0.000
5	I	5	MET	0	-0.104	-0.056	7.265	0.369	0.369	0.000	0.000	0.000	0.000
6	I	6	GLY	0	0.055	0.036	8.296	0.130	0.130	0.000	0.000	0.000	0.000
7	I	7	LYS	1	0.867	0.927	5.179	-0.920	-0.920	0.000	0.000	0.000	0.000
8	I	8	VAL	0	-0.018	0.002	2.523	-0.509	-0.071	0.872	-0.257	-1.053	-0.003
9	I	9	PRO	0	0.025	0.028	5.605	-0.129	-0.129	0.000	0.000	0.000	0.000
10	I	10	CYS	0	-0.010	0.014	6.193	-0.413	-0.413	0.000	0.000	0.000	0.000
11	I	11	PRO	0	-0.028	0.000	11.528	0.072	0.072	0.000	0.000	0.000	0.000
12	I	12	ASP	-1	-0.847	-0.920	14.708	-0.193	-0.193	0.000	0.000	0.000	0.000
13	I	13	GLY	0	-0.009	-0.004	17.914	0.016	0.016	0.000	0.000	0.000	0.000
14	I	14	GLU	-1	-0.958	-0.983	16.696	-0.337	-0.337	0.000	0.000	0.000	0.000
15	I	15	VAL	0	-0.067	-0.039	11.385	-0.023	-0.023	0.000	0.000	0.000	0.000
16	I	16	GLY	0	0.061	0.015	12.958	-0.048	-0.048	0.000	0.000	0.000	0.000
17	I	17	TYR	0	-0.066	-0.037	7.133	-0.022	-0.022	0.000	0.000	0.000	0.000
18	I	18	THR	0	0.007	0.000	6.620	0.148	0.148	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.764	-0.890	6.750	-0.758	-0.758	0.000	0.000	0.000	0.000
20	I	21	CYS	0	0.040	0.017	8.694	0.119	0.119	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.065	0.035	12.373	0.028	0.028	0.000	0.000	0.000	0.000
22	I	23	GLU	-1	-0.866	-0.929	12.263	-0.152	-0.152	0.000	0.000	0.000	0.000
23	I	24	LYS	1	0.769	0.874	11.464	0.162	0.162	0.000	0.000	0.000	0.000
24	I	25	ILE	0	0.023	0.012	6.977	-0.012	-0.012	0.000	0.000	0.000	0.000
25	I	26	CYS	0	-0.024	-0.016	9.896	0.089	0.089	0.000	0.000	0.000	0.000
26	I	27	LEU	0	0.016	-0.002	10.064	-0.123	-0.123	0.000	0.000	0.000	0.000
27	I	28	TYR	0	0.015	0.007	10.937	0.080	0.080	0.000	0.000	0.000	0.000
28	I	29	GLY	0	0.072	0.051	12.431	0.042	0.042	0.000	0.000	0.000	0.000
29	I	30	GLN	0	-0.064	-0.034	14.853	0.067	0.067	0.000	0.000	0.000	0.000
30	I	31	SER	0	-0.045	-0.031	15.604	-0.001	-0.001	0.000	0.000	0.000	0.000
31	I	33	ASN	0	-0.067	-0.049	16.495	0.007	0.007	0.000	0.000	0.000	0.000
32	I	34	ASP	-1	-0.878	-0.935	16.851	-0.104	-0.104	0.000	0.000	0.000	0.000
33	I	35	GLY	0	0.021	0.011	17.377	-0.015	-0.015	0.000	0.000	0.000	0.000
34	I	36	GLN	0	-0.116	-0.069	16.823	-0.010	-0.010	0.000	0.000	0.000	0.000
35	I	38	SER	0	-0.006	0.004	18.031	0.010	0.010	0.000	0.000	0.000	0.000
36	I	39	GLY	0	-0.007	0.014	18.850	0.019	0.019	0.000	0.000	0.000	0.000
37	I	40	ASP	-1	-0.892	-0.941	19.376	-0.289	-0.289	0.000	0.000	0.000	0.000
38	I	41	PRO	0	-0.048	-0.016	15.519	-0.006	-0.006	0.000	0.000	0.000	0.000
39	I	42	LYS	1	0.865	0.931	16.533	0.320	0.320	0.000	0.000	0.000	0.000
40	I	43	PRO	0	-0.004	-0.008	16.112	-0.005	-0.005	0.000	0.000	0.000	0.000
41	I	44	SER	0	-0.011	-0.019	16.749	-0.045	-0.045	0.000	0.000	0.000	0.000
42	I	45	SER	0	-0.024	-0.009	18.871	0.027	0.027	0.000	0.000	0.000	0.000
43	I	46	GLU	-1	-0.911	-0.968	20.833	-0.265	-0.265	0.000	0.000	0.000	0.000
44	I	47	PHE	0	-0.079	-0.021	23.677	0.021	0.021	0.000	0.000	0.000	0.000
45	I	48	GLU	-1	-0.966	-0.979	23.330	-0.230	-0.230	0.000	0.000	0.000	0.000
46	I	49	GLU	-1	-0.961	-0.980	18.879	-0.362	-0.362	0.000	0.000	0.000	0.000
47	I	50	PHE	0	-0.037	-0.026	23.424	0.017	0.017	0.000	0.000	0.000	0.000
48	I	51	GLU	-1	-0.919	-0.952	24.896	-0.197	-0.197	0.000	0.000	0.000	0.000
49	I	52	ILE	0	-0.104	-0.062	27.242	0.013	0.013	0.000	0.000	0.000	0.000
50	I	53	ASP	-1	-0.922	-0.957	27.728	-0.140	-0.140	0.000	0.000	0.000	0.000
51	I	54	GLU	-1	-1.034	-1.006	28.758	-0.100	-0.100	0.000	0.000	0.000	0.000
52	I	55	GLU	-1	-0.957	-0.981	22.245	-0.215	-0.215	0.000	0.000	0.000	0.000
53	I	56	GLU	-1	-0.892	-0.935	24.955	-0.144	-0.144	0.000	0.000	0.000	0.000
54	I	57	LYS	1	0.850	0.918	26.572	0.089	0.089	0.000	0.000	0.000	0.000

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