FMO DATABASE

FMODB ID: 14YNZ

Calculation Name: 2A9U-A-Xray372

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: 2023-03-13

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1094014.570485
FMO2-HF: Nuclear repulsion	1038650.068491
FMO2-HF: Total energy	-55364.501994
FMO2-MP2: Total energy	-55528.551219

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:6:SER)

Summations of interaction energy for fragment #1(A:6:SER)

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.
0.966	2.293	-0.01	-0.577	-0.74	0.002

Interaction energy analysis for fragmet #1(A:6:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.011

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	8	PRO	0	0.003	-0.002	3.865	-0.451	0.876	-0.010	-0.577	-0.740	0.002
4	A	9	LYS	1	0.888	0.945	5.575	0.876	0.876	0.000	0.000	0.000	0.000
5	A	10	GLU	-1	-0.887	-0.935	8.435	-0.096	-0.096	0.000	0.000	0.000	0.000
6	A	11	LEU	0	-0.005	-0.009	11.766	0.046	0.046	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.034	0.001	13.041	0.061	0.061	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.007	0.012	16.314	0.021	0.021	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.054	-0.079	18.096	0.007	0.007	0.000	0.000	0.000	0.000
10	A	15	SER	0	0.042	0.035	18.416	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	16	SER	0	0.017	0.006	20.519	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	17	LEU	0	0.092	0.050	18.283	0.016	0.016	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.992	0.995	20.693	0.146	0.146	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.801	-0.865	22.951	-0.101	-0.101	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.024	0.016	16.344	0.021	0.021	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.083	0.028	20.782	0.005	0.005	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.832	0.921	22.856	0.118	0.118	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.796	0.899	20.792	0.137	0.137	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.039	-0.026	20.708	0.003	0.003	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.825	-0.885	23.449	-0.091	-0.091	0.000	0.000	0.000	0.000
21	A	26	VAL	0	0.025	0.002	26.912	0.008	0.008	0.000	0.000	0.000	0.000
22	A	27	LYS	1	0.899	0.950	29.424	0.056	0.056	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.043	0.015	32.828	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.836	-0.918	34.982	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.814	0.895	29.300	0.090	0.090	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.027	0.015	29.660	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	32	SER	0	0.049	0.024	31.689	0.007	0.007	0.000	0.000	0.000	0.000
28	A	33	THR	0	0.026	-0.025	32.904	0.001	0.001	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.999	0.998	31.597	0.053	0.053	0.000	0.000	0.000	0.000
30	A	35	SER	0	-0.009	-0.005	28.751	0.000	0.000	0.000	0.000	0.000	0.000
31	A	36	TYR	0	0.049	0.022	29.722	0.003	0.003	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.011	0.014	32.307	0.005	0.005	0.000	0.000	0.000	0.000
33	A	38	HIS	0	0.022	0.010	27.604	0.009	0.009	0.000	0.000	0.000	0.000
34	A	39	SER	0	-0.049	-0.032	28.054	0.006	0.006	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.016	-0.002	29.077	0.008	0.008	0.000	0.000	0.000	0.000
36	A	41	LEU	0	0.031	0.014	30.451	0.006	0.006	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.966	0.987	22.037	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	43	ILE	0	-0.039	-0.011	28.098	0.009	0.009	0.000	0.000	0.000	0.000
39	A	44	PHE	0	0.045	0.022	30.209	0.006	0.006	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.832	0.902	25.349	-0.074	-0.074	0.000	0.000	0.000	0.000
41	A	46	THR	0	-0.015	-0.023	27.061	0.008	0.008	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.011	0.013	29.248	0.006	0.006	0.000	0.000	0.000	0.000
43	A	48	GLU	-1	-0.733	-0.819	32.916	0.044	0.044	0.000	0.000	0.000	0.000
44	A	49	GLU	-1	-0.817	-0.890	27.581	0.087	0.087	0.000	0.000	0.000	0.000
45	A	50	CYS	0	-0.060	-0.025	30.285	0.006	0.006	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.860	0.922	32.335	-0.050	-0.050	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.086	-0.047	33.423	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.872	-0.927	30.476	0.101	0.101	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.829	0.900	33.247	-0.056	-0.056	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.728	-0.827	31.968	0.068	0.068	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.786	-0.882	34.864	0.044	0.044	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.790	-0.850	35.472	0.047	0.047	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.808	0.862	27.987	-0.091	-0.091	0.000	0.000	0.000	0.000
54	A	59	ALA	0	-0.002	-0.004	32.902	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.012	0.019	34.953	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	61	VAL	0	0.015	0.012	32.750	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.044	-0.026	29.334	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	63	TYR	0	0.002	-0.036	33.471	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	64	MET	0	0.073	0.044	36.806	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	65	LYS	1	0.924	0.980	29.743	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	66	TYR	0	0.011	0.002	34.284	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	67	VAL	0	0.035	0.017	35.850	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	68	THR	0	-0.061	-0.036	37.124	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.033	-0.021	33.274	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	70	TYR	0	0.006	-0.022	36.683	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	71	ASN	0	0.014	-0.006	39.421	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	72	LEU	0	-0.040	-0.001	36.421	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.005	-0.018	36.476	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.906	0.977	39.742	0.000	0.000	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.902	0.953	43.119	0.013	0.013	0.000	0.000	0.000	0.000
71	A	76	ARG	1	0.834	0.921	35.773	0.035	0.035	0.000	0.000	0.000	0.000
72	A	77	PRO	0	0.052	0.012	43.315	0.001	0.001	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.786	-0.865	38.956	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	79	PHE	0	-0.002	-0.016	39.142	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.892	0.936	42.111	0.016	0.016	0.000	0.000	0.000	0.000
76	A	81	GLN	0	0.005	0.020	44.752	0.001	0.001	0.000	0.000	0.000	0.000
77	A	82	GLN	0	-0.005	-0.008	41.617	0.002	0.002	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.011	0.012	42.599	0.001	0.001	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.848	-0.927	43.626	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	85	TYR	0	0.003	0.021	35.825	0.001	0.001	0.000	0.000	0.000	0.000
81	A	86	PHE	0	0.001	-0.017	36.334	0.000	0.000	0.000	0.000	0.000	0.000
82	A	87	HIS	0	0.045	0.021	39.232	0.002	0.002	0.000	0.000	0.000	0.000
83	A	88	SER	0	-0.023	-0.021	41.096	0.004	0.004	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.076	-0.027	34.729	0.002	0.002	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.033	-0.019	35.452	0.002	0.002	0.000	0.000	0.000	0.000
86	A	91	GLY	0	0.073	0.055	37.457	0.004	0.004	0.000	0.000	0.000	0.000
87	A	92	PRO	0	0.012	-0.013	39.949	0.001	0.001	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.016	0.012	43.008	0.000	0.000	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.016	-0.019	37.234	0.004	0.004	0.000	0.000	0.000	0.000
90	A	95	ILE	0	-0.014	-0.007	39.838	0.001	0.001	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.813	0.895	41.468	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.881	0.932	39.086	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	98	ALA	0	-0.004	-0.008	38.629	0.002	0.002	0.000	0.000	0.000	0.000
94	A	99	VAL	0	-0.014	-0.010	40.249	0.000	0.000	0.000	0.000	0.000	0.000
95	A	100	GLU	-1	-0.797	-0.878	43.537	0.022	0.022	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.820	-0.887	40.125	0.039	0.039	0.000	0.000	0.000	0.000
97	A	102	ALA	0	-0.029	-0.014	40.725	0.002	0.002	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.891	-0.944	41.958	0.018	0.018	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.822	0.872	41.506	-0.036	-0.036	0.000	0.000	0.000	0.000
100	A	105	LEU	0	-0.078	-0.039	38.791	0.002	0.002	0.000	0.000	0.000	0.000
101	A	106	SER	0	-0.006	-0.014	42.890	0.001	0.001	0.000	0.000	0.000	0.000
102	A	107	GLU	-1	-0.786	-0.857	44.355	0.022	0.022	0.000	0.000	0.000	0.000
103	A	108	SER	0	-0.033	-0.021	43.329	0.000	0.000	0.000	0.000	0.000	0.000
104	A	109	LEU	0	-0.029	-0.022	39.292	0.001	0.001	0.000	0.000	0.000	0.000
105	A	110	LYS	1	0.832	0.894	43.426	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.048	0.028	46.504	0.000	0.000	0.000	0.000	0.000	0.000
107	A	112	ARG	1	0.832	0.901	39.297	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	113	TYR	0	-0.090	-0.075	38.626	0.000	0.000	0.000	0.000	0.000	0.000
109	A	114	GLU	-1	-0.943	-0.963	45.057	0.024	0.024	0.000	0.000	0.000	0.000
110	A	115	GLU	-1	-0.853	-0.901	47.686	0.039	0.039	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.057	0.024	44.355	0.000	0.000	0.000	0.000	0.000	0.000
112	A	117	GLU	-1	-0.841	-0.898	46.374	0.030	0.030	0.000	0.000	0.000	0.000
113	A	118	VAL	0	-0.016	-0.017	47.936	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	119	ARG	1	0.795	0.872	46.962	-0.041	-0.041	0.000	0.000	0.000	0.000
115	A	120	LYS	1	0.857	0.916	44.624	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	121	LYS	1	0.856	0.917	48.646	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	122	LEU	0	-0.004	0.006	51.978	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	123	GLU	-1	-0.815	-0.907	48.259	0.041	0.041	0.000	0.000	0.000	0.000
119	A	124	GLU	-1	-0.789	-0.844	50.160	0.032	0.032	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.779	0.877	51.978	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	126	ASP	-1	-0.820	-0.910	55.205	0.028	0.028	0.000	0.000	0.000	0.000
122	A	127	ARG	1	0.808	0.878	50.459	-0.034	-0.034	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.089	-0.063	53.409	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	129	GLU	-1	-0.809	-0.885	56.523	0.024	0.024	0.000	0.000	0.000	0.000
125	A	130	GLU	-1	-0.828	-0.892	57.708	0.027	0.027	0.000	0.000	0.000	0.000
126	A	131	ALA	0	-0.023	-0.005	56.278	0.000	0.000	0.000	0.000	0.000	0.000
127	A	132	GLN	0	0.007	0.004	58.408	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.815	0.874	61.052	-0.026	-0.026	0.000	0.000	0.000	0.000
129	A	134	LEU	0	-0.021	-0.007	58.660	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	135	GLN	0	-0.008	-0.008	61.433	0.001	0.001	0.000	0.000	0.000	0.000
131	A	136	GLN	0	-0.027	-0.025	63.230	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.960	0.996	65.929	-0.025	-0.025	0.000	0.000	0.000	0.000
133	A	138	ARG	1	0.847	0.926	62.057	-0.025	-0.025	0.000	0.000	0.000	0.000
134	A	139	GLN	0	-0.035	-0.011	66.675	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER)