FMO DATABASE

FMODB ID: Z63JN

Calculation Name: 2HNT-E-Xray372

Preferred Name: Thrombin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2HNT

Chain ID: E

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	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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-324878.398299
FMO2-HF: Nuclear repulsion	297487.817443
FMO2-HF: Total energy	-27390.580855
FMO2-MP2: Total energy	-27470.065478

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(E:80:GLU)

Summations of interaction energy for fragment #1(E:80:GLU)

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.
-50.628	-45.88	0.939	-2.443	-3.244	0.013

Interaction energy analysis for fragmet #1(E:80:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.888 / q_NPA : -0.949

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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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	E	82	ILE	0	0.066	0.062	2.503	-3.952	0.636	0.938	-2.411	-3.115	0.013
4	E	83	SER	0	-0.072	-0.075	4.851	-6.270	-6.257	-0.001	-0.003	-0.008	0.000
5	E	84	MET	0	0.020	0.028	8.286	-0.335	-0.335	0.000	0.000	0.000	0.000
6	E	85	LEU	0	0.038	0.010	11.755	-0.402	-0.402	0.000	0.000	0.000	0.000
7	E	86	GLU	-1	-0.954	-0.986	14.498	13.977	13.977	0.000	0.000	0.000	0.000
8	E	87	LYS	1	0.941	0.964	17.848	-13.154	-13.154	0.000	0.000	0.000	0.000
9	E	88	ILE	0	0.027	0.022	17.688	0.986	0.986	0.000	0.000	0.000	0.000
10	E	89	TYR	0	-0.051	-0.027	20.068	-1.062	-1.062	0.000	0.000	0.000	0.000
11	E	90	ILE	0	0.064	0.045	21.456	0.635	0.635	0.000	0.000	0.000	0.000
12	E	91	HIS	0	0.034	0.058	24.326	-0.630	-0.630	0.000	0.000	0.000	0.000
13	E	92	PRO	0	0.017	-0.014	26.920	-0.098	-0.098	0.000	0.000	0.000	0.000
14	E	93	ARG	1	0.864	0.909	30.210	-9.342	-9.342	0.000	0.000	0.000	0.000
15	E	94	TYR	0	0.056	0.041	24.332	-0.225	-0.225	0.000	0.000	0.000	0.000
16	E	95	ASN	0	-0.028	-0.008	28.814	-0.321	-0.321	0.000	0.000	0.000	0.000
17	E	96	TRP	0	0.015	0.016	27.234	0.002	0.002	0.000	0.000	0.000	0.000
18	E	97	ARG	1	0.903	0.953	28.748	-8.904	-8.904	0.000	0.000	0.000	0.000
19	E	97	GLU	-1	-0.994	-0.984	32.236	8.651	8.651	0.000	0.000	0.000	0.000
20	E	98	ASN	0	0.049	0.008	31.357	0.177	0.177	0.000	0.000	0.000	0.000
21	E	99	LEU	0	0.019	0.008	24.887	0.135	0.135	0.000	0.000	0.000	0.000
22	E	100	ASP	-1	-0.825	-0.900	27.827	10.321	10.321	0.000	0.000	0.000	0.000
23	E	101	ARG	1	0.815	0.885	27.687	-9.818	-9.818	0.000	0.000	0.000	0.000
24	E	102	ASP	-1	-0.903	-0.938	22.693	14.080	14.080	0.000	0.000	0.000	0.000
25	E	103	ILE	0	-0.018	-0.010	21.634	0.590	0.590	0.000	0.000	0.000	0.000
26	E	104	ALA	0	0.048	0.000	19.061	-0.639	-0.639	0.000	0.000	0.000	0.000
27	E	105	LEU	0	-0.034	-0.010	18.590	0.779	0.779	0.000	0.000	0.000	0.000
28	E	106	MET	0	0.040	0.000	13.250	-0.442	-0.442	0.000	0.000	0.000	0.000
29	E	107	LYS	1	0.947	0.989	15.321	-13.115	-13.115	0.000	0.000	0.000	0.000
30	E	108	LEU	0	-0.017	-0.021	10.308	-0.109	-0.109	0.000	0.000	0.000	0.000
31	E	109	LYS	1	0.936	0.982	13.829	-17.067	-17.067	0.000	0.000	0.000	0.000
32	E	110	LYS	1	0.968	0.964	11.128	-22.877	-22.877	0.000	0.000	0.000	0.000
33	E	111	PRO	0	0.027	0.025	12.547	1.734	1.734	0.000	0.000	0.000	0.000
34	E	112	VAL	0	-0.019	-0.040	7.794	0.186	0.186	0.000	0.000	0.000	0.000
35	E	113	ALA	0	0.023	0.016	9.328	-1.435	-1.435	0.000	0.000	0.000	0.000
36	E	114	PHE	0	0.006	-0.019	8.631	1.904	1.904	0.000	0.000	0.000	0.000
37	E	115	SER	0	0.018	-0.001	6.308	-0.806	-0.806	0.000	0.000	0.000	0.000
38	E	116	ASP	-1	-0.850	-0.911	9.357	19.895	19.895	0.000	0.000	0.000	0.000
39	E	117	TYR	0	-0.047	-0.029	5.180	0.978	0.978	0.000	0.000	0.000	0.000
40	E	118	ILE	0	-0.106	-0.029	3.718	2.608	2.755	0.002	-0.029	-0.121	0.000
41	E	119	HIS	0	0.038	-0.002	7.805	-2.344	-2.344	0.000	0.000	0.000	0.000
42	E	120	PRO	0	-0.037	-0.003	11.491	0.587	0.587	0.000	0.000	0.000	0.000
43	E	121	VAL	0	0.017	0.021	14.217	0.042	0.042	0.000	0.000	0.000	0.000
44	E	122	CYS	0	-0.040	-0.021	16.675	-0.224	-0.224	0.000	0.000	0.000	0.000
45	E	123	LEU	0	-0.001	-0.001	20.214	0.275	0.275	0.000	0.000	0.000	0.000
46	E	124	PRO	0	0.017	0.007	22.779	-0.175	-0.175	0.000	0.000	0.000	0.000
47	E	125	ASP	-1	-0.822	-0.866	26.130	10.340	10.340	0.000	0.000	0.000	0.000
48	E	126	ARG	1	0.982	0.965	29.607	-8.265	-8.265	0.000	0.000	0.000	0.000
49	E	127	GLU	-1	-0.892	-0.951	32.864	8.611	8.611	0.000	0.000	0.000	0.000
50	E	128	THR	0	-0.019	-0.033	26.946	-0.134	-0.134	0.000	0.000	0.000	0.000
51	E	129	ALA	0	-0.006	-0.013	29.236	0.181	0.181	0.000	0.000	0.000	0.000
52	E	129	ALA	0	-0.027	-0.017	30.336	-0.031	-0.031	0.000	0.000	0.000	0.000
53	E	129	SER	0	-0.033	-0.033	33.175	-0.065	-0.065	0.000	0.000	0.000	0.000
54	E	129	LEU	0	-0.027	0.011	27.564	-0.024	-0.024	0.000	0.000	0.000	0.000
55	E	130	LEU	0	-0.029	-0.011	28.764	0.178	0.178	0.000	0.000	0.000	0.000
56	E	131	GLN	0	0.033	0.002	30.862	-0.198	-0.198	0.000	0.000	0.000	0.000
57	E	132	ALA	0	0.029	0.030	32.164	0.243	0.243	0.000	0.000	0.000	0.000
58	E	133	GLY	0	-0.013	-0.007	32.916	-0.208	-0.208	0.000	0.000	0.000	0.000
59	E	134	TYR	0	-0.085	-0.030	29.942	0.072	0.072	0.000	0.000	0.000	0.000
60	E	135	LYS	1	0.934	0.960	26.260	-11.001	-11.001	0.000	0.000	0.000	0.000
61	E	136	GLY	0	0.069	0.045	23.883	0.029	0.029	0.000	0.000	0.000	0.000
62	E	137	ARG	1	0.917	0.956	18.175	-16.080	-16.080	0.000	0.000	0.000	0.000
63	E	138	VAL	0	0.009	-0.002	18.393	0.280	0.280	0.000	0.000	0.000	0.000
64	E	139	THR	0	-0.017	-0.012	13.362	-0.228	-0.228	0.000	0.000	0.000	0.000
65	E	140	GLY	0	-0.004	-0.027	12.074	0.179	0.179	0.000	0.000	0.000	0.000
66	E	141	TRP	0	0.020	0.022	6.889	0.531	0.531	0.000	0.000	0.000	0.000
67	E	142	GLY	0	0.024	0.042	11.941	0.166	0.166	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:80:GLU)