FMO DATABASE

FMODB ID: 6399Z

Calculation Name: 2A9U-A-Xray307

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 8

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2A9U

Chain ID: A

ChEMBL ID: CHEMBL2157854

UniProt ID: P40818

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1093470.735693
FMO2-HF: Nuclear repulsion	1037936.747411
FMO2-HF: Total energy	-55533.988282
FMO2-MP2: Total energy	-55698.58584

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(A:5:ACE )

Summations of interaction energy for fragment #1(A:5:ACE )

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.
1.318	2.305	-0.005	-0.465	-0.517	-0.001

Interaction energy analysis for fragmet #1(A:5:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.000

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	A	7	VAL	0	0.021	0.033	3.848	0.730	1.717	-0.005	-0.465	-0.517	-0.001
4	A	8	PRO	0	0.008	0.004	6.505	-0.015	-0.015	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.955	0.966	10.147	0.383	0.383	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.896	-0.936	12.867	-0.139	-0.139	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.031	-0.022	14.974	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	12	TYR	0	0.033	0.002	17.946	0.004	0.004	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.045	-0.012	20.931	0.016	0.016	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.033	-0.040	22.693	0.015	0.015	0.000	0.000	0.000	0.000
11	A	15	SER	0	0.024	0.025	22.939	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	16	SER	0	0.022	0.009	24.773	0.009	0.009	0.000	0.000	0.000	0.000
13	A	17	LEU	0	0.110	0.043	22.617	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.980	0.997	25.485	0.040	0.040	0.000	0.000	0.000	0.000
15	A	19	ASP	-1	-0.952	-0.971	27.975	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	20	LEU	0	0.037	0.008	21.914	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	21	ASN	0	0.059	0.011	26.521	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.901	0.978	28.538	0.058	0.058	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.884	0.943	26.277	0.102	0.102	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.047	-0.025	26.903	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.913	-0.939	29.572	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.024	-0.005	33.298	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.936	0.977	35.657	0.047	0.047	0.000	0.000	0.000	0.000
24	A	28	PRO	0	0.096	0.040	38.832	0.000	0.000	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.914	-0.961	40.813	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	30	LYS	1	0.873	0.950	35.731	0.052	0.052	0.000	0.000	0.000	0.000
27	A	31	ILE	0	0.004	0.020	35.702	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	32	SER	0	0.011	0.010	37.512	0.002	0.002	0.000	0.000	0.000	0.000
29	A	33	THR	0	0.082	0.009	39.169	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.997	1.006	35.775	0.045	0.045	0.000	0.000	0.000	0.000
31	A	35	SER	0	-0.018	-0.014	34.811	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	36	TYR	0	0.065	0.026	35.735	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	37	VAL	0	0.006	0.016	38.180	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	38	HIS	0	0.005	-0.003	33.155	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	39	SER	0	-0.046	-0.021	33.889	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.005	-0.005	34.923	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.035	0.018	35.530	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.949	0.983	27.875	0.113	0.113	0.000	0.000	0.000	0.000
39	A	43	ILE	0	-0.044	-0.028	33.758	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	44	PHE	0	0.050	0.021	35.992	0.000	0.000	0.000	0.000	0.000	0.000
41	A	45	LYS	1	0.972	0.990	30.536	0.091	0.091	0.000	0.000	0.000	0.000
42	A	46	THR	0	-0.030	-0.017	32.636	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	47	ALA	0	0.009	0.010	34.583	0.000	0.000	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.821	-0.867	38.032	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	49	GLU	-1	-0.914	-0.961	32.140	-0.095	-0.095	0.000	0.000	0.000	0.000
46	A	50	CYS	0	-0.026	-0.009	35.364	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	51	ARG	1	0.892	0.949	37.497	0.055	0.055	0.000	0.000	0.000	0.000
48	A	52	LEU	0	-0.093	-0.051	38.326	0.003	0.003	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.916	-0.948	35.965	-0.078	-0.078	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.839	0.924	38.380	0.052	0.052	0.000	0.000	0.000	0.000
51	A	55	ASP	-1	-0.796	-0.880	37.000	-0.071	-0.071	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.857	-0.953	40.000	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.810	-0.864	40.739	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	58	ARG	1	0.935	0.963	32.171	0.091	0.091	0.000	0.000	0.000	0.000
55	A	59	ALA	0	0.007	0.002	38.744	0.000	0.000	0.000	0.000	0.000	0.000
56	A	60	TYR	0	0.018	0.019	40.551	0.002	0.002	0.000	0.000	0.000	0.000
57	A	61	VAL	0	0.000	0.000	38.497	0.001	0.001	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.072	-0.034	35.410	0.000	0.000	0.000	0.000	0.000	0.000
59	A	63	TYR	0	-0.004	-0.068	39.365	0.001	0.001	0.000	0.000	0.000	0.000
60	A	64	MET	0	0.069	0.048	42.633	0.002	0.002	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.938	0.980	35.993	0.071	0.071	0.000	0.000	0.000	0.000
62	A	66	TYR	0	-0.011	-0.003	39.892	0.000	0.000	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.042	0.018	41.684	0.002	0.002	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.052	-0.034	43.275	0.003	0.003	0.000	0.000	0.000	0.000
65	A	69	VAL	0	-0.036	-0.021	39.288	0.001	0.001	0.000	0.000	0.000	0.000
66	A	70	TYR	0	-0.031	-0.040	42.637	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	ASN	0	0.028	-0.005	45.197	0.003	0.003	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.023	0.011	42.764	0.002	0.002	0.000	0.000	0.000	0.000
69	A	73	ILE	0	-0.003	-0.027	42.344	0.002	0.002	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.913	0.979	45.661	0.036	0.036	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.901	0.946	48.876	0.034	0.034	0.000	0.000	0.000	0.000
72	A	76	ARG	1	0.834	0.922	41.727	0.043	0.043	0.000	0.000	0.000	0.000
73	A	77	PRO	0	0.034	0.002	48.967	0.000	0.000	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.807	-0.903	44.710	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	79	PHE	0	-0.001	0.006	45.373	0.000	0.000	0.000	0.000	0.000	0.000
76	A	80	LYS	1	0.942	0.964	47.769	0.028	0.028	0.000	0.000	0.000	0.000
77	A	81	GLN	0	0.004	0.007	50.156	0.000	0.000	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.027	-0.012	47.097	0.000	0.000	0.000	0.000	0.000	0.000
79	A	83	GLN	0	0.000	0.003	47.906	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.843	-0.916	49.190	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	85	TYR	0	-0.013	-0.005	40.619	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	86	PHE	0	-0.002	-0.022	41.722	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.047	0.048	44.720	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	88	SER	0	-0.008	0.005	45.996	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	ILE	0	-0.079	-0.025	39.881	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.034	-0.022	40.873	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	91	GLY	0	0.056	0.047	42.830	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	92	PRO	0	0.016	-0.015	45.275	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	93	GLY	0	0.014	0.011	48.061	0.000	0.000	0.000	0.000	0.000	0.000
90	A	94	ASN	0	-0.017	-0.020	42.604	0.000	0.000	0.000	0.000	0.000	0.000
91	A	95	ILE	0	-0.032	-0.017	45.273	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	96	LYS	1	0.969	0.990	46.930	0.032	0.032	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.981	1.002	44.443	0.048	0.048	0.000	0.000	0.000	0.000
94	A	98	ALA	0	-0.027	-0.011	44.327	0.000	0.000	0.000	0.000	0.000	0.000
95	A	99	VAL	0	-0.018	-0.015	45.891	0.000	0.000	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.912	-0.956	49.244	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	101	GLU	-1	-0.838	-0.905	45.346	-0.046	-0.046	0.000	0.000	0.000	0.000
98	A	102	ALA	0	-0.027	-0.011	46.587	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	103	GLU	-1	-0.888	-0.949	47.675	-0.035	-0.035	0.000	0.000	0.000	0.000
100	A	104	ARG	1	0.846	0.912	46.663	0.044	0.044	0.000	0.000	0.000	0.000
101	A	105	LEU	0	-0.072	-0.052	44.281	0.000	0.000	0.000	0.000	0.000	0.000
102	A	106	SER	0	-0.012	0.007	48.349	0.000	0.000	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.825	-0.906	49.837	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	108	SER	0	-0.066	-0.041	48.784	0.001	0.001	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.006	-0.023	45.053	0.000	0.000	0.000	0.000	0.000	0.000
106	A	110	LYS	1	0.845	0.926	49.224	0.035	0.035	0.000	0.000	0.000	0.000
107	A	111	LEU	0	0.052	0.031	52.275	0.001	0.001	0.000	0.000	0.000	0.000
108	A	112	ARG	1	0.877	0.945	44.848	0.049	0.049	0.000	0.000	0.000	0.000
109	A	113	TYR	0	-0.072	-0.085	43.940	0.000	0.000	0.000	0.000	0.000	0.000
110	A	114	GLU	-1	-0.962	-0.967	50.395	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	115	GLU	-1	-0.843	-0.916	52.298	-0.036	-0.036	0.000	0.000	0.000	0.000
112	A	116	ALA	0	0.036	0.028	49.315	0.000	0.000	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.867	-0.930	51.379	-0.037	-0.037	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.009	-0.018	53.030	0.001	0.001	0.000	0.000	0.000	0.000
115	A	119	ARG	1	0.850	0.922	52.062	0.036	0.036	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.868	0.929	49.774	0.040	0.040	0.000	0.000	0.000	0.000
117	A	121	LYS	1	0.871	0.929	53.481	0.032	0.032	0.000	0.000	0.000	0.000
118	A	122	LEU	0	-0.003	0.002	56.684	0.001	0.001	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.873	-0.935	52.942	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	124	GLU	-1	-0.777	-0.850	55.065	-0.030	-0.030	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.906	0.954	56.824	0.026	0.026	0.000	0.000	0.000	0.000
122	A	126	ASP	-1	-0.893	-0.948	59.516	-0.025	-0.025	0.000	0.000	0.000	0.000
123	A	127	ARG	1	0.788	0.874	55.010	0.030	0.030	0.000	0.000	0.000	0.000
124	A	128	GLN	0	-0.100	-0.075	58.119	0.002	0.002	0.000	0.000	0.000	0.000
125	A	129	GLU	-1	-0.900	-0.955	61.097	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	130	GLU	-1	-0.855	-0.926	61.648	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	131	ALA	0	-0.033	-0.008	60.449	0.001	0.001	0.000	0.000	0.000	0.000
128	A	132	GLN	0	-0.030	-0.017	62.473	0.001	0.001	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.902	0.942	65.370	0.023	0.023	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.016	0.004	62.206	0.001	0.001	0.000	0.000	0.000	0.000
131	A	135	GLN	0	-0.003	-0.006	65.379	0.000	0.000	0.000	0.000	0.000	0.000
132	A	136	GLN	0	0.001	-0.012	67.032	0.001	0.001	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.955	0.985	69.914	0.018	0.018	0.000	0.000	0.000	0.000
134	A	138	ARG	1	0.838	0.918	65.387	0.019	0.019	0.000	0.000	0.000	0.000
135	A	139	GLN	0	-0.040	-0.004	70.380	0.000	0.000	0.000	0.000	0.000	0.000
136	A	140	NME	0	0.022	0.022	73.392	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ACE )