FMO DATABASE

FMODB ID: VRNQ1

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	OptHSide
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	-1091673.886445
FMO2-HF: Nuclear repulsion	1036309.732954
FMO2-HF: Total energy	-55364.153491
FMO2-MP2: Total energy	-55528.240449

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.
1.048	2.486	-0.017	-0.643	-0.778	0.003

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 : 0.003 / 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	-0.009	-0.004	3.837	-0.450	0.988	-0.017	-0.643	-0.778	0.003
4	A	9	LYS	1	0.916	0.955	5.477	0.868	0.868	0.000	0.000	0.000	0.000
5	A	10	GLU	-1	-0.887	-0.928	8.346	-0.143	-0.143	0.000	0.000	0.000	0.000
6	A	11	LEU	0	-0.021	-0.024	11.533	0.029	0.029	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.035	-0.001	12.847	0.070	0.070	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.030	0.001	16.093	0.028	0.028	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.022	-0.056	17.807	0.017	0.017	0.000	0.000	0.000	0.000
10	A	15	SER	0	0.028	0.027	18.526	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	16	SER	0	0.010	0.001	20.647	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	17	LEU	0	0.109	0.048	18.279	0.008	0.008	0.000	0.000	0.000	0.000
13	A	18	LYS	1	1.005	1.008	20.780	0.162	0.162	0.000	0.000	0.000	0.000
14	A	19	ASP	-1	-0.843	-0.895	23.163	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.024	0.009	16.503	0.022	0.022	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.068	0.016	21.028	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.819	0.920	23.048	0.140	0.140	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.841	0.920	20.793	0.158	0.158	0.000	0.000	0.000	0.000
19	A	24	THR	0	-0.038	-0.017	20.900	0.005	0.005	0.000	0.000	0.000	0.000
20	A	25	GLU	-1	-0.829	-0.877	23.571	-0.125	-0.125	0.000	0.000	0.000	0.000
21	A	26	VAL	0	0.042	0.005	27.173	0.008	0.008	0.000	0.000	0.000	0.000
22	A	27	LYS	1	0.889	0.953	29.494	0.085	0.085	0.000	0.000	0.000	0.000
23	A	28	PRO	0	0.074	0.028	32.805	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.863	-0.934	34.678	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.794	0.889	29.506	0.123	0.123	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.006	0.020	29.677	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	32	SER	0	0.022	0.021	31.779	0.008	0.008	0.000	0.000	0.000	0.000
28	A	33	THR	0	0.053	-0.011	33.225	0.001	0.001	0.000	0.000	0.000	0.000
29	A	34	LYS	1	1.005	1.004	31.178	0.069	0.069	0.000	0.000	0.000	0.000
30	A	35	SER	0	-0.018	-0.017	28.838	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	36	TYR	0	0.067	0.025	29.752	0.002	0.002	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.010	0.016	32.147	0.006	0.006	0.000	0.000	0.000	0.000
33	A	38	HIS	0	0.007	0.001	27.419	0.008	0.008	0.000	0.000	0.000	0.000
34	A	39	SER	0	-0.051	-0.028	27.834	0.004	0.004	0.000	0.000	0.000	0.000
35	A	40	ALA	0	-0.010	-0.007	28.871	0.008	0.008	0.000	0.000	0.000	0.000
36	A	41	LEU	0	0.032	0.014	30.060	0.007	0.007	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.967	0.995	21.751	0.022	0.022	0.000	0.000	0.000	0.000
38	A	43	ILE	0	-0.050	-0.028	27.929	0.008	0.008	0.000	0.000	0.000	0.000
39	A	44	PHE	0	0.047	0.020	29.995	0.006	0.006	0.000	0.000	0.000	0.000
40	A	45	LYS	1	0.894	0.936	25.647	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	46	THR	0	-0.024	-0.018	26.721	0.008	0.008	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.026	0.017	28.899	0.006	0.006	0.000	0.000	0.000	0.000
43	A	48	GLU	-1	-0.755	-0.826	32.535	0.039	0.039	0.000	0.000	0.000	0.000
44	A	49	GLU	-1	-0.849	-0.907	26.902	0.080	0.080	0.000	0.000	0.000	0.000
45	A	50	CYS	0	-0.060	-0.029	29.977	0.005	0.005	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.867	0.922	32.061	-0.044	-0.044	0.000	0.000	0.000	0.000
47	A	52	LEU	0	-0.088	-0.050	33.358	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	ASP	-1	-0.916	-0.945	30.843	0.097	0.097	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.790	0.879	33.416	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.752	-0.852	31.315	0.058	0.058	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.824	-0.907	34.649	0.035	0.035	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.807	-0.872	35.145	0.034	0.034	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.891	0.928	27.081	-0.069	-0.069	0.000	0.000	0.000	0.000
54	A	59	ALA	0	0.003	0.003	32.921	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	60	TYR	0	0.016	0.018	34.781	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	61	VAL	0	0.005	0.004	32.465	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.055	-0.027	29.215	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	63	TYR	0	0.005	-0.041	33.297	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	64	MET	0	0.076	0.051	36.626	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	65	LYS	1	0.934	0.981	29.586	0.015	0.015	0.000	0.000	0.000	0.000
61	A	66	TYR	0	0.004	0.000	33.950	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	67	VAL	0	0.040	0.016	35.550	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	68	THR	0	-0.061	-0.036	36.874	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.037	-0.022	33.005	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	70	TYR	0	-0.015	-0.021	36.397	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	71	ASN	0	0.024	-0.005	39.067	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	72	LEU	0	-0.025	0.009	36.454	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	73	ILE	0	0.003	-0.022	36.308	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	74	LYS	1	0.923	0.989	39.555	0.011	0.011	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.906	0.949	42.827	0.024	0.024	0.000	0.000	0.000	0.000
71	A	76	ARG	1	0.845	0.927	35.707	0.052	0.052	0.000	0.000	0.000	0.000
72	A	77	PRO	0	0.050	0.007	42.969	0.002	0.002	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.815	-0.890	38.951	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	79	PHE	0	0.018	0.003	39.236	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.874	0.934	42.046	0.026	0.026	0.000	0.000	0.000	0.000
76	A	81	GLN	0	0.019	0.015	44.898	0.002	0.002	0.000	0.000	0.000	0.000
77	A	82	GLN	0	-0.029	-0.012	41.792	0.003	0.003	0.000	0.000	0.000	0.000
78	A	83	GLN	0	0.005	0.010	42.562	0.001	0.001	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.853	-0.927	43.749	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	85	TYR	0	-0.006	0.010	35.654	0.000	0.000	0.000	0.000	0.000	0.000
81	A	86	PHE	0	-0.001	-0.019	36.234	0.000	0.000	0.000	0.000	0.000	0.000
82	A	87	HIS	0	0.051	0.031	39.276	0.002	0.002	0.000	0.000	0.000	0.000
83	A	88	SER	0	-0.018	-0.010	41.003	0.004	0.004	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.078	-0.027	34.723	0.002	0.002	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.042	-0.020	35.202	0.002	0.002	0.000	0.000	0.000	0.000
86	A	91	GLY	0	0.055	0.043	37.369	0.005	0.005	0.000	0.000	0.000	0.000
87	A	92	PRO	0	0.021	-0.013	39.994	0.001	0.001	0.000	0.000	0.000	0.000
88	A	93	GLY	0	0.014	0.012	42.778	0.000	0.000	0.000	0.000	0.000	0.000
89	A	94	ASN	0	-0.028	-0.023	37.146	0.005	0.005	0.000	0.000	0.000	0.000
90	A	95	ILE	0	-0.011	-0.007	39.727	0.000	0.000	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.837	0.912	41.125	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.907	0.950	38.618	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	98	ALA	0	-0.028	-0.012	38.430	0.001	0.001	0.000	0.000	0.000	0.000
94	A	99	VAL	0	-0.010	-0.018	40.026	0.000	0.000	0.000	0.000	0.000	0.000
95	A	100	GLU	-1	-0.799	-0.882	43.274	0.015	0.015	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.818	-0.882	39.776	0.033	0.033	0.000	0.000	0.000	0.000
97	A	102	ALA	0	-0.027	-0.013	40.497	0.001	0.001	0.000	0.000	0.000	0.000
98	A	103	GLU	-1	-0.891	-0.946	41.714	0.010	0.010	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.831	0.886	40.953	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	105	LEU	0	-0.075	-0.054	38.511	0.002	0.002	0.000	0.000	0.000	0.000
101	A	106	SER	0	0.007	0.010	42.581	0.001	0.001	0.000	0.000	0.000	0.000
102	A	107	GLU	-1	-0.790	-0.867	43.910	0.013	0.013	0.000	0.000	0.000	0.000
103	A	108	SER	0	-0.047	-0.022	43.335	0.001	0.001	0.000	0.000	0.000	0.000
104	A	109	LEU	0	-0.017	-0.027	39.218	0.001	0.001	0.000	0.000	0.000	0.000
105	A	110	LYS	1	0.819	0.894	43.500	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.053	0.033	46.457	0.000	0.000	0.000	0.000	0.000	0.000
107	A	112	ARG	1	0.882	0.936	39.263	-0.040	-0.040	0.000	0.000	0.000	0.000
108	A	113	TYR	0	-0.084	-0.083	38.327	0.000	0.000	0.000	0.000	0.000	0.000
109	A	114	GLU	-1	-0.955	-0.961	44.799	0.016	0.016	0.000	0.000	0.000	0.000
110	A	115	GLU	-1	-0.856	-0.923	47.389	0.033	0.033	0.000	0.000	0.000	0.000
111	A	116	ALA	0	0.028	0.020	44.072	0.001	0.001	0.000	0.000	0.000	0.000
112	A	117	GLU	-1	-0.823	-0.884	46.123	0.020	0.020	0.000	0.000	0.000	0.000
113	A	118	VAL	0	0.006	-0.013	47.677	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	119	ARG	1	0.817	0.908	46.888	-0.035	-0.035	0.000	0.000	0.000	0.000
115	A	120	LYS	1	0.873	0.923	44.635	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	121	LYS	1	0.818	0.888	48.450	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	122	LEU	0	-0.006	0.004	51.597	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	123	GLU	-1	-0.828	-0.916	48.340	0.035	0.035	0.000	0.000	0.000	0.000
119	A	124	GLU	-1	-0.765	-0.828	50.296	0.024	0.024	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.794	0.874	52.129	-0.021	-0.021	0.000	0.000	0.000	0.000
121	A	126	ASP	-1	-0.848	-0.919	55.028	0.023	0.023	0.000	0.000	0.000	0.000
122	A	127	ARG	1	0.792	0.861	50.640	-0.026	-0.026	0.000	0.000	0.000	0.000
123	A	128	GLN	0	-0.081	-0.062	53.588	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	129	GLU	-1	-0.820	-0.887	56.716	0.019	0.019	0.000	0.000	0.000	0.000
125	A	130	GLU	-1	-0.822	-0.896	57.612	0.023	0.023	0.000	0.000	0.000	0.000
126	A	131	ALA	0	-0.029	-0.007	56.373	0.000	0.000	0.000	0.000	0.000	0.000
127	A	132	GLN	0	-0.005	-0.007	58.480	0.000	0.000	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.838	0.888	60.983	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	134	LEU	0	-0.027	-0.006	58.592	0.000	0.000	0.000	0.000	0.000	0.000
130	A	135	GLN	0	-0.028	-0.022	61.579	0.001	0.001	0.000	0.000	0.000	0.000
131	A	136	GLN	0	-0.045	-0.030	63.321	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.956	0.985	66.106	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	138	ARG	1	0.846	0.928	61.783	-0.021	-0.021	0.000	0.000	0.000	0.000
134	A	139	GLN	0	0.018	0.032	66.890	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)