FMO DATABASE

FMODB ID: 52M7Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-358076.837526
FMO2-HF: Nuclear repulsion	331065.245466
FMO2-HF: Total energy	-27011.592061
FMO2-MP2: Total energy	-27088.584872

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.
-6.146	-3.092	1.877	-1.598	-3.335	-0.012

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 : -0.040 / q_NPA : -0.035

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].
3	C	18	GLU	-1	-0.929	-0.963	2.894	-5.066	-2.449	0.285	-1.335	-1.567	-0.008
4	C	19	GLY	0	-0.018	0.006	2.394	-0.894	0.157	1.528	-1.188	-1.392	-0.003
5	C	20	SER	0	-0.033	-0.022	3.113	1.404	0.679	0.065	0.926	-0.267	-0.001
6	C	21	ASP	-1	-0.948	-0.968	5.072	-1.692	-1.581	-0.001	-0.001	-0.109	0.000
7	C	22	ALA	0	0.013	0.005	6.703	0.088	0.088	0.000	0.000	0.000	0.000
8	C	23	GLU	-1	-0.858	-0.940	8.266	-0.412	-0.412	0.000	0.000	0.000	0.000
9	C	24	ILE	0	-0.042	-0.040	11.851	0.024	0.024	0.000	0.000	0.000	0.000
10	C	25	GLY	0	0.016	0.011	13.425	0.030	0.030	0.000	0.000	0.000	0.000
11	C	26	MET	0	-0.035	0.011	9.575	-0.025	-0.025	0.000	0.000	0.000	0.000
12	C	27	SER	0	-0.005	-0.014	8.264	0.018	0.018	0.000	0.000	0.000	0.000
13	C	28	PRO	0	-0.004	0.005	10.957	0.039	0.039	0.000	0.000	0.000	0.000
14	C	29	TRP	0	0.038	0.018	9.948	0.049	0.049	0.000	0.000	0.000	0.000
15	C	30	GLN	0	0.011	0.026	6.236	-0.057	-0.057	0.000	0.000	0.000	0.000
16	C	31	VAL	0	-0.017	-0.014	10.091	-0.012	-0.012	0.000	0.000	0.000	0.000
17	C	32	MET	0	-0.028	-0.006	9.301	0.045	0.045	0.000	0.000	0.000	0.000
18	C	33	LEU	0	0.018	0.015	11.378	-0.064	-0.064	0.000	0.000	0.000	0.000
19	C	34	PHE	0	0.011	-0.027	13.067	0.066	0.066	0.000	0.000	0.000	0.000
20	C	35	ARG	1	0.937	0.963	16.110	-0.359	-0.359	0.000	0.000	0.000	0.000
21	C	36	LYS	1	0.827	0.908	19.187	-0.188	-0.188	0.000	0.000	0.000	0.000
22	C	36	SER	0	-0.019	0.002	21.663	-0.030	-0.030	0.000	0.000	0.000	0.000
23	C	37	PRO	0	0.044	0.033	21.397	0.001	0.001	0.000	0.000	0.000	0.000
24	C	38	GLN	0	0.019	-0.007	17.160	0.005	0.005	0.000	0.000	0.000	0.000
25	C	39	GLU	-1	-0.814	-0.891	15.298	0.456	0.456	0.000	0.000	0.000	0.000
26	C	40	LEU	0	-0.035	-0.018	9.340	-0.056	-0.056	0.000	0.000	0.000	0.000
27	C	41	LEU	0	0.018	0.017	12.076	0.106	0.106	0.000	0.000	0.000	0.000
28	C	42	CYS	0	-0.096	-0.056	9.700	0.219	0.219	0.000	0.000	0.000	0.000
29	C	43	GLY	0	0.030	0.036	7.352	-0.102	-0.102	0.000	0.000	0.000	0.000
30	C	44	ALA	0	-0.023	-0.021	8.400	0.012	0.012	0.000	0.000	0.000	0.000
31	C	45	SER	0	0.004	0.008	9.818	-0.035	-0.035	0.000	0.000	0.000	0.000
32	C	46	LEU	0	-0.033	-0.017	11.995	0.013	0.013	0.000	0.000	0.000	0.000
33	C	47	ILE	0	-0.037	-0.025	15.438	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	48	SER	0	-0.011	-0.034	17.818	-0.008	-0.008	0.000	0.000	0.000	0.000
35	C	49	ASP	-1	-0.834	-0.908	20.333	0.041	0.041	0.000	0.000	0.000	0.000
36	C	50	ARG	1	0.862	0.936	22.789	-0.058	-0.058	0.000	0.000	0.000	0.000
37	C	51	TRP	0	0.003	0.019	20.584	0.015	0.015	0.000	0.000	0.000	0.000
38	C	52	VAL	0	0.014	0.002	14.657	-0.011	-0.011	0.000	0.000	0.000	0.000
39	C	53	LEU	0	0.004	0.015	14.292	0.005	0.005	0.000	0.000	0.000	0.000
40	C	54	THR	0	0.014	-0.019	11.602	0.036	0.036	0.000	0.000	0.000	0.000
41	C	55	ALA	0	0.039	0.032	11.973	-0.048	-0.048	0.000	0.000	0.000	0.000
42	C	56	ALA	0	0.053	0.013	13.687	0.015	0.015	0.000	0.000	0.000	0.000
43	C	57	HIS	0	0.033	0.011	11.154	-0.031	-0.031	0.000	0.000	0.000	0.000
44	C	59	LEU	0	-0.017	0.008	14.689	-0.016	-0.016	0.000	0.000	0.000	0.000
45	C	60	LEU	0	-0.008	-0.005	18.348	-0.018	-0.018	0.000	0.000	0.000	0.000
46	C	60	TYR	0	-0.003	-0.025	18.073	0.003	0.003	0.000	0.000	0.000	0.000
47	C	60	PRO	0	0.053	0.019	20.268	0.017	0.017	0.000	0.000	0.000	0.000
48	C	60	PRO	0	-0.044	-0.018	21.378	-0.005	-0.005	0.000	0.000	0.000	0.000
49	C	60	TRP	0	-0.002	0.001	13.820	0.021	0.021	0.000	0.000	0.000	0.000
50	C	60	ASP	-1	-0.931	-0.957	20.154	0.318	0.318	0.000	0.000	0.000	0.000
51	C	60	LYS	1	0.860	0.945	16.540	-0.501	-0.501	0.000	0.000	0.000	0.000
52	C	60	ASN	0	0.022	-0.007	20.680	-0.012	-0.012	0.000	0.000	0.000	0.000
53	C	60	PHE	0	-0.044	-0.009	19.614	-0.012	-0.012	0.000	0.000	0.000	0.000
54	C	60	THR	0	-0.001	-0.021	22.181	-0.008	-0.008	0.000	0.000	0.000	0.000
55	C	61	GLU	-1	-0.893	-0.964	23.112	0.177	0.177	0.000	0.000	0.000	0.000
56	C	62	ASN	0	-0.049	-0.023	24.196	-0.015	-0.015	0.000	0.000	0.000	0.000
57	C	63	ASP	-1	-0.859	-0.882	22.742	0.202	0.202	0.000	0.000	0.000	0.000
58	C	64	LEU	0	0.021	-0.001	17.526	0.035	0.035	0.000	0.000	0.000	0.000
59	C	65	LEU	0	-0.032	-0.018	18.952	-0.033	-0.033	0.000	0.000	0.000	0.000
60	C	66	VAL	0	0.002	0.005	15.543	0.037	0.037	0.000	0.000	0.000	0.000
61	C	67	ARG	1	0.813	0.909	14.403	-0.180	-0.180	0.000	0.000	0.000	0.000
62	C	68	ILE	0	0.067	0.022	13.792	0.015	0.015	0.000	0.000	0.000	0.000
63	C	69	GLY	0	0.026	0.022	14.132	-0.007	-0.007	0.000	0.000	0.000	0.000
64	C	70	LYS	1	0.819	0.909	12.225	0.063	0.063	0.000	0.000	0.000	0.000
65	C	71	HIS	0	0.053	0.035	8.712	0.073	0.073	0.000	0.000	0.000	0.000
66	C	72	SER	0	-0.008	-0.012	9.150	0.180	0.180	0.000	0.000	0.000	0.000

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