FMO DATABASE

FMODB ID: 53L3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-245047.272121
FMO2-HF: Nuclear repulsion	221248.724233
FMO2-HF: Total energy	-23798.547888
FMO2-MP2: Total energy	-23861.552317

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.
-7.766	-3.064	0.973	-1.897	-3.778	-0.008

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 : 0.004 / q_NPA : -0.005

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	0.044	0.032	3.167	-4.005	0.104	0.581	-1.723	-2.967	-0.007
4	I	4	GLY	0	-0.018	-0.009	4.805	0.379	0.408	-0.001	-0.004	-0.024	0.000
5	I	5	MET	0	-0.102	-0.070	7.462	0.302	0.302	0.000	0.000	0.000	0.000
6	I	6	GLY	0	0.104	0.061	7.653	0.104	0.104	0.000	0.000	0.000	0.000
7	I	7	LYS	1	0.851	0.916	4.900	-0.823	-0.823	0.000	0.000	0.000	0.000
8	I	8	VAL	0	-0.007	0.007	2.879	-0.548	0.016	0.393	-0.170	-0.787	-0.001
9	I	9	PRO	0	0.031	0.022	5.844	-0.098	-0.098	0.000	0.000	0.000	0.000
10	I	10	CYS	0	-0.022	0.010	6.298	-0.497	-0.497	0.000	0.000	0.000	0.000
11	I	11	PRO	0	-0.021	0.002	11.519	0.068	0.068	0.000	0.000	0.000	0.000
12	I	12	ASP	-1	-0.852	-0.927	14.522	-0.240	-0.240	0.000	0.000	0.000	0.000
13	I	13	GLY	0	-0.025	-0.014	17.655	0.015	0.015	0.000	0.000	0.000	0.000
14	I	14	GLU	-1	-0.963	-0.977	16.955	-0.345	-0.345	0.000	0.000	0.000	0.000
15	I	15	VAL	0	-0.057	-0.036	11.470	-0.033	-0.033	0.000	0.000	0.000	0.000
16	I	16	GLY	0	0.046	0.009	13.221	-0.041	-0.041	0.000	0.000	0.000	0.000
17	I	17	TYR	0	-0.037	-0.016	7.103	-0.022	-0.022	0.000	0.000	0.000	0.000
18	I	18	THR	0	0.014	-0.002	7.201	0.146	0.146	0.000	0.000	0.000	0.000
19	I	20	ASP	-1	-0.772	-0.892	6.957	-0.881	-0.881	0.000	0.000	0.000	0.000
20	I	21	CYS	0	0.017	-0.006	8.620	0.135	0.135	0.000	0.000	0.000	0.000
21	I	22	GLY	0	0.061	0.036	12.425	0.034	0.034	0.000	0.000	0.000	0.000
22	I	23	GLU	-1	-0.898	-0.951	12.022	-0.152	-0.152	0.000	0.000	0.000	0.000
23	I	24	LYS	1	0.813	0.904	11.370	0.183	0.183	0.000	0.000	0.000	0.000
24	I	25	ILE	0	0.025	0.005	7.411	-0.011	-0.011	0.000	0.000	0.000	0.000
25	I	26	CYS	0	-0.021	0.006	10.389	0.086	0.086	0.000	0.000	0.000	0.000
26	I	27	LEU	0	-0.010	-0.015	10.470	-0.108	-0.108	0.000	0.000	0.000	0.000
27	I	28	TYR	0	0.010	-0.001	11.419	0.085	0.085	0.000	0.000	0.000	0.000
28	I	29	GLY	0	0.075	0.057	12.807	0.044	0.044	0.000	0.000	0.000	0.000
29	I	30	GLN	0	-0.045	-0.023	15.206	0.071	0.071	0.000	0.000	0.000	0.000
30	I	31	SER	0	-0.008	-0.015	15.618	-0.019	-0.019	0.000	0.000	0.000	0.000
31	I	33	ASN	0	-0.056	-0.047	16.498	0.005	0.005	0.000	0.000	0.000	0.000
32	I	34	ASP	-1	-0.913	-0.946	17.048	-0.135	-0.135	0.000	0.000	0.000	0.000
33	I	35	GLY	0	-0.002	-0.001	17.665	-0.011	-0.011	0.000	0.000	0.000	0.000
34	I	36	GLN	0	-0.121	-0.064	16.820	-0.013	-0.013	0.000	0.000	0.000	0.000
35	I	38	SER	0	-0.011	-0.004	18.368	0.017	0.017	0.000	0.000	0.000	0.000
36	I	39	GLY	0	-0.002	0.025	19.035	0.022	0.022	0.000	0.000	0.000	0.000
37	I	40	ASP	-1	-0.939	-0.989	19.488	-0.300	-0.300	0.000	0.000	0.000	0.000
38	I	41	PRO	0	-0.092	-0.041	15.520	-0.005	-0.005	0.000	0.000	0.000	0.000
39	I	42	LYS	1	0.931	0.989	16.820	0.338	0.338	0.000	0.000	0.000	0.000
40	I	43	PRO	0	0.031	-0.003	16.563	-0.007	-0.007	0.000	0.000	0.000	0.000
41	I	44	SER	0	-0.003	-0.015	17.122	-0.050	-0.050	0.000	0.000	0.000	0.000
42	I	45	SER	0	-0.028	-0.012	19.356	0.027	0.027	0.000	0.000	0.000	0.000
43	I	46	GLU	-1	-0.903	-0.967	21.563	-0.264	-0.264	0.000	0.000	0.000	0.000
44	I	47	PHE	0	-0.072	-0.008	23.989	0.022	0.022	0.000	0.000	0.000	0.000
45	I	48	GLU	-1	-0.989	-0.991	23.791	-0.216	-0.216	0.000	0.000	0.000	0.000
46	I	49	GLU	-1	-0.972	-0.985	18.906	-0.354	-0.354	0.000	0.000	0.000	0.000
47	I	50	PHE	0	-0.016	-0.013	23.682	0.017	0.017	0.000	0.000	0.000	0.000
48	I	51	GLU	-1	-0.920	-0.951	24.798	-0.195	-0.195	0.000	0.000	0.000	0.000
49	I	52	ILE	0	-0.121	-0.078	27.237	0.012	0.012	0.000	0.000	0.000	0.000
50	I	53	ASP	-1	-0.923	-0.970	27.612	-0.142	-0.142	0.000	0.000	0.000	0.000
51	I	54	GLU	-1	-1.021	-0.978	28.411	-0.093	-0.093	0.000	0.000	0.000	0.000
52	I	55	GLU	-1	-0.962	-0.983	22.541	-0.209	-0.209	0.000	0.000	0.000	0.000
53	I	56	GLU	-1	-0.934	-0.962	25.202	-0.132	-0.132	0.000	0.000	0.000	0.000
54	I	57	LYS	1	0.905	0.947	26.658	0.071	0.071	0.000	0.000	0.000	0.000

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