FMO DATABASE

FMODB ID: VKML1

Calculation Name: 1E0F-I-Xray540

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E0F

Chain ID: I

ChEMBL ID: CHEMBL204

UniProt ID: P00734

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-245496.543766
FMO2-HF: Nuclear repulsion	221707.242769
FMO2-HF: Total energy	-23789.300996
FMO2-MP2: Total energy	-23852.042582

3D Structure Molmil

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.
-7.837	-5.676	0	-1.069	-1.093	0.002

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 : 0.091 / q_NPA : -0.015

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

Sort

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].
4	I	2	ARG	1	0.881	1.053	3.806	-2.598	-2.067	0.011	-0.208	-0.334	0.001
5	I	3	PHE	0	0.160	-0.075	3.885	-0.153	1.291	-0.011	-0.808	-0.625	0.001
6	I	3	PHE	0	-0.084	0.090	4.276	-0.958	-0.816	0.001	-0.039	-0.105	0.000
7	I	4	GLY	0	0.000	-0.112	6.634	0.507	0.507	0.000	0.000	0.000	0.000
8	I	5	MET	0	0.001	-0.018	8.358	0.114	0.114	0.000	0.000	0.000	0.000
9	I	5	MET	0	-0.136	0.061	7.532	0.360	0.360	0.000	0.000	0.000	0.000
10	I	6	GLY	0	0.083	-0.061	9.463	0.204	0.204	0.000	0.000	0.000	0.000
11	I	7	LYS	0	-0.004	-0.017	6.080	-0.030	-0.030	0.000	0.000	0.000	0.000
12	I	7	LYS	1	0.876	1.055	5.505	-1.126	-1.126	0.000	0.000	0.000	0.000
13	I	8	VAL	0	0.019	-0.090	6.635	0.533	0.533	0.000	0.000	0.000	0.000
14	I	8	VAL	0	-0.077	0.099	4.513	-0.179	-0.135	-0.001	-0.014	-0.029	0.000
15	I	9	PRO	0	0.072	-0.080	7.487	-0.172	-0.172	0.000	0.000	0.000	0.000
16	I	10	CYS	0	0.088	-0.022	11.317	-0.095	-0.095	0.000	0.000	0.000	0.000
17	I	10	CYS	0	-0.153	0.237	11.041	0.069	0.069	0.000	0.000	0.000	0.000
18	I	11	PRO	0	-0.040	-0.106	13.525	0.099	0.099	0.000	0.000	0.000	0.000
19	I	12	ASP	0	0.111	0.007	16.685	-0.055	-0.055	0.000	0.000	0.000	0.000
20	I	12	ASP	-1	-0.949	-0.827	20.587	-0.263	-0.263	0.000	0.000	0.000	0.000
21	I	13	GLY	0	-0.020	-0.116	19.908	0.029	0.029	0.000	0.000	0.000	0.000
22	I	14	GLU	0	0.079	-0.008	18.814	-0.035	-0.035	0.000	0.000	0.000	0.000
23	I	14	GLU	-1	-1.011	-0.850	18.869	-0.432	-0.432	0.000	0.000	0.000	0.000
24	I	15	VAL	0	0.031	-0.156	15.336	-0.002	-0.002	0.000	0.000	0.000	0.000
25	I	15	VAL	0	-0.115	0.125	13.538	0.001	0.001	0.000	0.000	0.000	0.000
26	I	16	GLY	0	0.064	-0.111	15.120	-0.065	-0.065	0.000	0.000	0.000	0.000
27	I	17	TYR	0	0.078	-0.004	10.844	0.036	0.036	0.000	0.000	0.000	0.000
28	I	17	TYR	0	-0.129	0.065	9.257	0.023	0.023	0.000	0.000	0.000	0.000
29	I	18	THR	0	0.043	-0.049	9.672	0.164	0.164	0.000	0.000	0.000	0.000
30	I	18	THR	0	-0.065	0.040	8.523	0.108	0.108	0.000	0.000	0.000	0.000
31	I	19	CYS	0	0.030	-0.086	8.357	-0.639	-0.639	0.000	0.000	0.000	0.000
32	I	20	ASP	0	0.154	-0.100	9.609	-0.090	-0.090	0.000	0.000	0.000	0.000
33	I	20	ASP	-1	-0.890	-0.793	8.368	-1.315	-1.315	0.000	0.000	0.000	0.000
34	I	21	CYS	0	0.135	-0.066	10.781	0.104	0.104	0.000	0.000	0.000	0.000
35	I	21	CYS	0	-0.231	0.199	15.001	0.023	0.023	0.000	0.000	0.000	0.000
36	I	22	GLY	0	0.031	-0.101	14.293	0.027	0.027	0.000	0.000	0.000	0.000
37	I	23	GLU	0	-0.004	-0.028	14.121	0.057	0.057	0.000	0.000	0.000	0.000
38	I	23	GLU	-1	-0.865	-0.789	15.429	-0.325	-0.325	0.000	0.000	0.000	0.000
39	I	24	LYS	0	-0.003	-0.126	13.607	-0.085	-0.085	0.000	0.000	0.000	0.000
40	I	24	LYS	1	0.794	0.993	15.970	0.372	0.372	0.000	0.000	0.000	0.000
41	I	25	ILE	0	0.111	-0.071	11.091	0.063	0.063	0.000	0.000	0.000	0.000
42	I	25	ILE	0	-0.090	0.092	8.910	-0.049	-0.049	0.000	0.000	0.000	0.000
43	I	26	CYS	0	0.012	-0.129	12.015	0.095	0.095	0.000	0.000	0.000	0.000
44	I	26	CYS	0	-0.169	0.218	14.261	0.036	0.036	0.000	0.000	0.000	0.000
45	I	27	LEU	0	0.087	-0.091	12.336	-0.191	-0.191	0.000	0.000	0.000	0.000
46	I	27	LEU	0	-0.043	0.093	11.757	-0.003	-0.003	0.000	0.000	0.000	0.000
47	I	28	TYR	0	0.159	-0.069	12.929	0.129	0.129	0.000	0.000	0.000	0.000
48	I	28	TYR	0	-0.135	0.095	13.183	-0.016	-0.016	0.000	0.000	0.000	0.000
49	I	29	GLY	0	0.038	-0.073	14.496	0.055	0.055	0.000	0.000	0.000	0.000
50	I	30	GLN	0	0.082	0.006	16.955	0.095	0.095	0.000	0.000	0.000	0.000
51	I	30	GLN	0	-0.158	0.072	16.856	0.004	0.004	0.000	0.000	0.000	0.000
52	I	31	SER	0	0.035	-0.095	17.668	-0.053	-0.053	0.000	0.000	0.000	0.000
53	I	31	SER	0	-0.045	0.072	20.590	0.030	0.030	0.000	0.000	0.000	0.000
54	I	32	CYS	0	0.201	-0.108	17.078	0.029	0.029	0.000	0.000	0.000	0.000
55	I	33	ASN	0	0.034	-0.071	18.500	0.002	0.002	0.000	0.000	0.000	0.000
56	I	33	ASN	0	-0.198	0.029	22.243	-0.001	-0.001	0.000	0.000	0.000	0.000
57	I	34	ASP	0	0.133	-0.086	18.884	0.019	0.019	0.000	0.000	0.000	0.000
58	I	34	ASP	-1	-0.990	-0.854	19.683	-0.214	-0.214	0.000	0.000	0.000	0.000
59	I	35	GLY	0	0.038	-0.101	19.495	-0.023	-0.023	0.000	0.000	0.000	0.000
60	I	36	GLN	0	0.094	0.055	18.967	0.004	0.004	0.000	0.000	0.000	0.000
61	I	36	GLN	0	-0.176	0.011	19.179	-0.012	-0.012	0.000	0.000	0.000	0.000
62	I	37	CYS	0	0.069	-0.124	18.625	0.018	0.018	0.000	0.000	0.000	0.000
63	I	38	SER	0	0.011	-0.088	20.042	0.032	0.032	0.000	0.000	0.000	0.000
64	I	38	SER	0	0.029	0.099	21.492	-0.014	-0.014	0.000	0.000	0.000	0.000
65	I	39	GLY	0	-0.031	-0.092	20.779	0.030	0.030	0.000	0.000	0.000	0.000
66	I	40	ASP	0	0.078	-0.014	21.153	-0.039	-0.039	0.000	0.000	0.000	0.000
67	I	40	ASP	-1	-0.965	-0.815	23.617	-0.396	-0.396	0.000	0.000	0.000	0.000
68	I	41	PRO	0	-0.048	-0.126	17.367	-0.008	-0.008	0.000	0.000	0.000	0.000
69	I	42	LYS	0	0.056	0.026	18.478	0.037	0.037	0.000	0.000	0.000	0.000
70	I	42	LYS	1	0.818	1.016	21.333	0.424	0.424	0.000	0.000	0.000	0.000
71	I	43	PRO	0	-0.024	-0.122	18.027	-0.005	-0.005	0.000	0.000	0.000	0.000
72	I	44	SER	0	0.039	0.014	18.452	-0.090	-0.090	0.000	0.000	0.000	0.000
73	I	44	SER	0	-0.021	0.068	20.382	0.010	0.010	0.000	0.000	0.000	0.000
74	I	45	SER	0	-0.013	-0.109	20.416	0.026	0.026	0.000	0.000	0.000	0.000
75	I	45	SER	0	-0.008	0.093	21.503	0.012	0.012	0.000	0.000	0.000	0.000
76	I	46	GLU	0	-0.017	-0.098	22.014	-0.048	-0.048	0.000	0.000	0.000	0.000
77	I	46	GLU	-1	-0.940	-0.855	25.263	-0.343	-0.343	0.000	0.000	0.000	0.000
78	I	47	PHE	0	0.038	-0.109	24.799	0.017	0.017	0.000	0.000	0.000	0.000
79	I	47	PHE	0	-0.116	0.078	26.292	0.012	0.012	0.000	0.000	0.000	0.000
80	I	48	GLU	0	0.122	-0.082	24.356	-0.043	-0.043	0.000	0.000	0.000	0.000
81	I	48	GLU	-1	-1.043	-0.875	24.883	-0.285	-0.285	0.000	0.000	0.000	0.000
82	I	49	GLU	0	0.064	-0.126	23.334	0.022	0.022	0.000	0.000	0.000	0.000
83	I	49	GLU	-1	-1.028	-0.867	20.241	-0.521	-0.521	0.000	0.000	0.000	0.000
84	I	50	PHE	0	0.093	-0.080	24.658	0.015	0.015	0.000	0.000	0.000	0.000
85	I	50	PHE	0	-0.154	0.045	28.262	0.004	0.004	0.000	0.000	0.000	0.000
86	I	51	GLU	0	0.024	-0.116	27.088	-0.018	-0.018	0.000	0.000	0.000	0.000
87	I	51	GLU	-1	-0.955	-0.838	26.217	-0.250	-0.250	0.000	0.000	0.000	0.000
88	I	52	ILE	0	-0.055	-0.118	28.758	0.016	0.016	0.000	0.000	0.000	0.000
89	I	52	ILE	0	-0.101	0.066	29.744	0.001	0.001	0.000	0.000	0.000	0.000
90	I	53	ASP	0	0.120	-0.104	30.477	0.012	0.012	0.000	0.000	0.000	0.000
91	I	53	ASP	-1	-0.978	-0.849	29.551	-0.195	-0.195	0.000	0.000	0.000	0.000
92	I	54	GLU	0	0.096	-0.104	30.512	-0.008	-0.008	0.000	0.000	0.000	0.000
93	I	54	GLU	-1	-1.098	-0.896	32.416	-0.120	-0.120	0.000	0.000	0.000	0.000
94	I	55	GLU	0	0.058	-0.131	27.250	0.009	0.009	0.000	0.000	0.000	0.000
95	I	55	GLU	-1	-1.034	-0.855	24.184	-0.279	-0.279	0.000	0.000	0.000	0.000
96	I	56	GLU	0	0.049	-0.094	27.369	0.004	0.004	0.000	0.000	0.000	0.000
97	I	56	GLU	-1	-0.957	-0.848	26.476	-0.187	-0.187	0.000	0.000	0.000	0.000
98	I	57	LYS	0	-0.061	-0.124	28.106	0.013	0.013	0.000	0.000	0.000	0.000
99	I	57	LYS	1	0.913	0.951	28.913	0.086	0.086	0.000	0.000	0.000	0.000

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