FMO DATABASE

FMODB ID: YY1V2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1089518.397068
FMO2-HF: Nuclear repulsion	1034155.32871
FMO2-HF: Total energy	-55363.068358
FMO2-MP2: Total energy	-55527.133468

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.
0.806	2.035	-0.015	-0.526	-0.688	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 : -0.011 / q_NPA : -0.021

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	0.008	0.004	3.837	1.379	2.608	-0.015	-0.526	-0.688	0.002
4	A	9	LYS	1	0.954	0.965	6.192	-0.534	-0.534	0.000	0.000	0.000	0.000
5	A	10	GLU	-1	-0.895	-0.936	8.919	-0.021	-0.021	0.000	0.000	0.000	0.000
6	A	11	LEU	0	-0.030	-0.022	12.011	0.026	0.026	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.033	0.001	13.424	0.013	0.013	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.045	-0.012	16.771	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.033	-0.040	18.539	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	15	SER	0	0.025	0.026	19.296	0.001	0.001	0.000	0.000	0.000	0.000
11	A	16	SER	0	0.022	0.009	21.420	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	17	LEU	0	0.110	0.044	18.469	0.006	0.006	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.980	0.996	21.294	0.014	0.014	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.954	-0.972	23.642	0.015	0.015	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.037	0.007	16.801	0.005	0.005	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.059	0.011	21.516	0.000	0.000	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.901	0.978	23.408	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.884	0.943	20.870	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.046	-0.024	21.166	0.001	0.001	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.912	-0.939	23.765	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	26	VAL	0	0.024	-0.005	27.217	0.004	0.004	0.000	0.000	0.000	0.000
22	A	27	LYS	1	0.935	0.978	29.595	0.013	0.013	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.095	0.040	33.004	0.000	0.000	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.915	-0.964	34.891	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.874	0.951	30.417	0.015	0.015	0.000	0.000	0.000	0.000
26	A	31	ILE	0	0.004	0.021	29.921	0.000	0.000	0.000	0.000	0.000	0.000
27	A	32	SER	0	0.010	0.010	32.182	0.001	0.001	0.000	0.000	0.000	0.000
28	A	33	THR	0	0.082	0.010	33.650	0.002	0.002	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.998	1.006	31.295	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	35	SER	0	-0.020	-0.016	29.275	0.003	0.003	0.000	0.000	0.000	0.000
31	A	36	TYR	0	0.066	0.027	30.193	0.002	0.002	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.007	0.015	32.562	0.002	0.002	0.000	0.000	0.000	0.000
33	A	38	HIS	0	0.003	-0.003	27.935	0.005	0.005	0.000	0.000	0.000	0.000
34	A	39	SER	0	-0.045	-0.021	28.239	0.005	0.005	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.011	-0.007	29.274	0.004	0.004	0.000	0.000	0.000	0.000
36	A	41	LEU	0	0.036	0.018	30.444	0.002	0.002	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.954	0.984	22.058	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	43	ILE	0	-0.048	-0.029	28.356	0.003	0.003	0.000	0.000	0.000	0.000
39	A	44	PHE	0	0.055	0.022	30.314	0.001	0.001	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.973	0.991	25.768	-0.073	-0.073	0.000	0.000	0.000	0.000
41	A	46	THR	0	-0.034	-0.019	27.159	0.005	0.005	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.011	0.010	29.198	0.001	0.001	0.000	0.000	0.000	0.000
43	A	48	GLU	-1	-0.817	-0.867	32.790	0.035	0.035	0.000	0.000	0.000	0.000
44	A	49	GLU	-1	-0.918	-0.962	27.157	0.078	0.078	0.000	0.000	0.000	0.000
45	A	50	CYS	0	-0.025	-0.009	29.954	0.000	0.000	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.890	0.948	32.235	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.090	-0.050	33.642	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.915	-0.948	30.978	0.059	0.059	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.839	0.924	33.562	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.797	-0.880	31.523	0.041	0.041	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.860	-0.954	34.688	0.026	0.026	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.807	-0.863	34.986	0.026	0.026	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.937	0.964	26.428	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.005	0.001	32.955	0.000	0.000	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.022	0.020	34.913	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.003	-0.002	32.400	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.064	-0.031	29.453	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	63	TYR	0	-0.009	-0.070	33.466	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	64	MET	0	0.068	0.049	36.847	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	65	LYS	1	0.939	0.980	29.819	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	66	TYR	0	-0.011	-0.003	34.278	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	67	VAL	0	0.039	0.017	35.831	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	68	THR	0	-0.056	-0.036	37.137	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.034	-0.020	33.333	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	70	TYR	0	-0.023	-0.037	36.679	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	71	ASN	0	0.022	-0.007	39.415	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	72	LEU	0	-0.022	0.012	36.700	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	73	ILE	0	-0.004	-0.027	36.690	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.919	0.981	39.923	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.897	0.944	43.226	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	76	ARG	1	0.833	0.923	36.130	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	77	PRO	0	0.034	0.002	43.363	0.001	0.001	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.807	-0.903	39.535	0.006	0.006	0.000	0.000	0.000	0.000
74	A	79	PHE	0	-0.002	0.006	40.022	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.942	0.963	42.546	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	81	GLN	0	0.005	0.007	45.385	0.000	0.000	0.000	0.000	0.000	0.000
77	A	82	GLN	0	-0.027	-0.011	42.468	0.001	0.001	0.000	0.000	0.000	0.000
78	A	83	GLN	0	0.000	0.004	43.154	0.002	0.002	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.844	-0.917	44.319	0.011	0.011	0.000	0.000	0.000	0.000
80	A	85	TYR	0	-0.013	-0.005	36.565	0.001	0.001	0.000	0.000	0.000	0.000
81	A	86	PHE	0	-0.001	-0.021	36.905	0.002	0.002	0.000	0.000	0.000	0.000
82	A	87	HIS	0	0.048	0.048	39.844	0.002	0.002	0.000	0.000	0.000	0.000
83	A	88	SER	0	-0.009	0.004	41.692	0.001	0.001	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.077	-0.025	35.354	0.002	0.002	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.036	-0.022	35.727	0.002	0.002	0.000	0.000	0.000	0.000
86	A	91	GLY	0	0.053	0.045	37.918	0.002	0.002	0.000	0.000	0.000	0.000
87	A	92	PRO	0	0.019	-0.014	40.548	0.000	0.000	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.012	0.010	43.298	0.000	0.000	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.016	-0.020	37.903	0.001	0.001	0.000	0.000	0.000	0.000
90	A	95	ILE	0	-0.028	-0.016	40.179	0.000	0.000	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.964	0.988	41.540	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.984	1.003	39.466	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	98	ALA	0	-0.029	-0.011	38.797	0.000	0.000	0.000	0.000	0.000	0.000
94	A	99	VAL	0	-0.018	-0.016	40.340	0.000	0.000	0.000	0.000	0.000	0.000
95	A	100	GLU	-1	-0.911	-0.956	43.551	0.018	0.018	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.838	-0.904	40.014	0.027	0.027	0.000	0.000	0.000	0.000
97	A	102	ALA	0	-0.025	-0.010	40.735	0.000	0.000	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.893	-0.951	41.886	0.014	0.014	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.849	0.913	41.383	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	105	LEU	0	-0.072	-0.052	38.655	0.000	0.000	0.000	0.000	0.000	0.000
101	A	106	SER	0	-0.009	0.007	42.678	0.000	0.000	0.000	0.000	0.000	0.000
102	A	107	GLU	-1	-0.829	-0.907	43.954	0.014	0.014	0.000	0.000	0.000	0.000
103	A	108	SER	0	-0.063	-0.040	43.300	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	109	LEU	0	-0.008	-0.023	39.263	0.000	0.000	0.000	0.000	0.000	0.000
105	A	110	LYS	1	0.846	0.925	43.455	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.052	0.031	46.381	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	112	ARG	1	0.876	0.944	39.431	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	113	TYR	0	-0.071	-0.084	38.059	0.000	0.000	0.000	0.000	0.000	0.000
109	A	114	GLU	-1	-0.961	-0.967	44.624	0.012	0.012	0.000	0.000	0.000	0.000
110	A	115	GLU	-1	-0.843	-0.916	46.958	0.017	0.017	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.034	0.027	43.814	0.000	0.000	0.000	0.000	0.000	0.000
112	A	117	GLU	-1	-0.865	-0.929	45.833	0.011	0.011	0.000	0.000	0.000	0.000
113	A	118	VAL	0	-0.009	-0.018	47.381	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	119	ARG	1	0.852	0.922	46.910	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	120	LYS	1	0.866	0.929	44.134	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	121	LYS	1	0.872	0.929	48.146	-0.010	-0.010	0.000	0.000	0.000	0.000
117	A	122	LEU	0	-0.003	0.003	51.251	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	123	GLU	-1	-0.873	-0.935	48.015	0.016	0.016	0.000	0.000	0.000	0.000
119	A	124	GLU	-1	-0.777	-0.850	49.958	0.009	0.009	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.906	0.954	51.805	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	126	ASP	-1	-0.892	-0.948	54.719	0.010	0.010	0.000	0.000	0.000	0.000
122	A	127	ARG	1	0.785	0.873	50.418	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.097	-0.074	53.103	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	129	GLU	-1	-0.901	-0.954	56.385	0.008	0.008	0.000	0.000	0.000	0.000
125	A	130	GLU	-1	-0.854	-0.926	57.289	0.009	0.009	0.000	0.000	0.000	0.000
126	A	131	ALA	0	-0.035	-0.009	56.123	0.000	0.000	0.000	0.000	0.000	0.000
127	A	132	GLN	0	-0.028	-0.017	58.193	0.000	0.000	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.901	0.942	60.782	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	134	LEU	0	-0.016	0.003	58.403	0.000	0.000	0.000	0.000	0.000	0.000
130	A	135	GLN	0	-0.006	-0.008	61.283	0.000	0.000	0.000	0.000	0.000	0.000
131	A	136	GLN	0	0.004	-0.011	63.025	0.000	0.000	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.944	0.985	66.000	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	138	ARG	1	0.834	0.919	61.791	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	139	GLN	0	0.003	0.022	66.291	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:6:SER)