FMO DATABASE

FMODB ID: 63QKZ

Calculation Name: 1YZE-C-Xray310

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZE

Chain ID: C

ChEMBL ID: CHEMBL2157850

UniProt ID: Q93009

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	108
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-790636.260862
FMO2-HF: Nuclear repulsion	749477.416607
FMO2-HF: Total energy	-41158.844255
FMO2-MP2: Total energy	-41277.142477

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(C:66:ACE )

Summations of interaction energy for fragment #1(C:66: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.
0.464	3.327	0.017	-1.225	-1.655	-0.003

Interaction energy analysis for fragmet #1(C:66:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.005

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	C	68	GLU	-1	-0.817	-0.913	3.837	-1.461	0.642	-0.006	-1.037	-1.060	-0.004
4	C	69	ALA	0	0.002	0.013	5.378	0.451	0.451	0.000	0.000	0.000	0.000
5	C	70	THR	0	0.021	0.011	7.524	-0.114	-0.114	0.000	0.000	0.000	0.000
6	C	71	PHE	0	-0.042	-0.022	11.260	0.081	0.081	0.000	0.000	0.000	0.000
7	C	72	GLN	0	0.023	-0.001	13.007	-0.024	-0.024	0.000	0.000	0.000	0.000
8	C	73	PHE	0	-0.001	0.001	16.681	0.022	0.022	0.000	0.000	0.000	0.000
9	C	74	THR	0	-0.001	-0.004	19.247	-0.013	-0.013	0.000	0.000	0.000	0.000
10	C	75	NME	0	0.025	0.027	22.979	-0.007	-0.007	0.000	0.000	0.000	0.000
11	C	84	ACE	0	-0.009	-0.015	25.287	0.002	0.002	0.000	0.000	0.000	0.000
12	C	85	VAL	0	0.024	0.006	24.191	-0.004	-0.004	0.000	0.000	0.000	0.000
13	C	86	LEU	0	0.013	0.006	18.735	-0.007	-0.007	0.000	0.000	0.000	0.000
14	C	87	SER	0	-0.011	0.029	15.805	0.000	0.000	0.000	0.000	0.000	0.000
15	C	88	PRO	0	-0.018	-0.021	15.602	-0.002	-0.002	0.000	0.000	0.000	0.000
16	C	89	PRO	0	-0.011	0.005	12.021	-0.017	-0.017	0.000	0.000	0.000	0.000
17	C	90	CYS	0	-0.017	0.007	8.858	0.097	0.097	0.000	0.000	0.000	0.000
18	C	91	PHE	0	0.016	-0.015	6.786	-0.106	-0.106	0.000	0.000	0.000	0.000
19	C	92	VAL	0	0.042	0.032	3.709	-0.001	0.247	0.005	-0.062	-0.192	0.000
20	C	93	ARG	1	0.793	0.896	3.202	1.952	2.269	0.018	-0.116	-0.218	0.001
21	C	94	ASN	0	-0.003	-0.016	4.693	0.353	0.548	0.000	-0.010	-0.185	0.000
22	C	95	LEU	0	0.025	0.035	6.698	0.020	0.020	0.000	0.000	0.000	0.000
23	C	96	PRO	0	-0.016	-0.001	8.755	0.037	0.037	0.000	0.000	0.000	0.000
24	C	97	TRP	0	0.043	0.007	7.712	-0.066	-0.066	0.000	0.000	0.000	0.000
25	C	98	LYS	1	0.830	0.922	11.730	0.009	0.009	0.000	0.000	0.000	0.000
26	C	99	ILE	0	0.007	0.006	15.062	-0.028	-0.028	0.000	0.000	0.000	0.000
27	C	100	MET	0	-0.031	-0.009	17.516	0.017	0.017	0.000	0.000	0.000	0.000
28	C	101	VAL	0	-0.023	-0.008	20.887	-0.010	-0.010	0.000	0.000	0.000	0.000
29	C	102	MET	0	-0.005	-0.005	24.034	0.003	0.003	0.000	0.000	0.000	0.000
30	C	103	NME	0	0.012	0.062	27.644	0.002	0.002	0.000	0.000	0.000	0.000
31	C	114	ACE	0	0.001	-0.012	31.793	0.000	0.000	0.000	0.000	0.000	0.000
32	C	115	VAL	0	-0.059	-0.032	29.403	0.001	0.001	0.000	0.000	0.000	0.000
33	C	116	GLY	0	-0.023	-0.022	26.828	-0.005	-0.005	0.000	0.000	0.000	0.000
34	C	117	PHE	0	0.010	-0.010	18.718	0.006	0.006	0.000	0.000	0.000	0.000
35	C	118	PHE	0	0.020	-0.005	20.525	-0.010	-0.010	0.000	0.000	0.000	0.000
36	C	119	LEU	0	-0.009	0.018	12.744	0.013	0.013	0.000	0.000	0.000	0.000
37	C	120	GLN	0	0.045	0.004	16.515	-0.015	-0.015	0.000	0.000	0.000	0.000
38	C	121	CYS	0	-0.047	-0.025	11.362	-0.007	-0.007	0.000	0.000	0.000	0.000
39	C	122	ASN	0	0.018	-0.022	12.917	0.022	0.022	0.000	0.000	0.000	0.000
40	C	123	ALA	0	0.001	0.009	14.427	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	124	GLU	-1	-0.869	-0.924	16.700	0.020	0.020	0.000	0.000	0.000	0.000
42	C	125	SER	0	0.000	-0.020	17.016	0.003	0.003	0.000	0.000	0.000	0.000
43	C	126	ASP	-1	-0.902	-0.941	19.126	-0.019	-0.019	0.000	0.000	0.000	0.000
44	C	127	SER	0	-0.032	0.012	18.157	-0.012	-0.012	0.000	0.000	0.000	0.000
45	C	128	THR	0	-0.016	-0.032	20.710	-0.006	-0.006	0.000	0.000	0.000	0.000
46	C	129	SER	0	-0.030	-0.026	19.056	0.000	0.000	0.000	0.000	0.000	0.000
47	C	130	TRP	0	-0.025	0.030	14.142	-0.027	-0.027	0.000	0.000	0.000	0.000
48	C	131	SER	0	-0.004	-0.018	15.439	0.004	0.004	0.000	0.000	0.000	0.000
49	C	132	CYS	0	-0.030	-0.015	10.294	-0.060	-0.060	0.000	0.000	0.000	0.000
50	C	133	HIS	0	-0.023	0.007	13.132	0.093	0.093	0.000	0.000	0.000	0.000
51	C	134	ALA	0	0.018	0.012	11.452	-0.113	-0.113	0.000	0.000	0.000	0.000
52	C	135	GLN	0	0.046	0.030	12.443	0.131	0.131	0.000	0.000	0.000	0.000
53	C	136	ALA	0	0.027	-0.005	12.629	-0.051	-0.051	0.000	0.000	0.000	0.000
54	C	137	VAL	0	-0.053	-0.033	14.529	0.031	0.031	0.000	0.000	0.000	0.000
55	C	138	LEU	0	0.019	0.030	16.535	0.013	0.013	0.000	0.000	0.000	0.000
56	C	139	LYS	1	0.918	0.958	18.757	0.032	0.032	0.000	0.000	0.000	0.000
57	C	140	ILE	0	0.028	0.024	20.960	0.010	0.010	0.000	0.000	0.000	0.000
58	C	141	ILE	0	-0.055	-0.037	20.237	-0.005	-0.005	0.000	0.000	0.000	0.000
59	C	142	ASN	0	0.058	0.026	24.103	-0.005	-0.005	0.000	0.000	0.000	0.000
60	C	143	NME	0	-0.011	0.006	27.661	0.006	0.006	0.000	0.000	0.000	0.000
61	C	149	ACE	0	0.007	0.003	25.899	0.001	0.001	0.000	0.000	0.000	0.000
62	C	150	PHE	0	-0.045	-0.019	25.036	-0.005	-0.005	0.000	0.000	0.000	0.000
63	C	151	SER	0	0.033	0.000	21.050	0.004	0.004	0.000	0.000	0.000	0.000
64	C	152	ARG	1	0.824	0.948	21.773	0.058	0.058	0.000	0.000	0.000	0.000
65	C	153	ARG	1	0.940	0.967	18.614	0.146	0.146	0.000	0.000	0.000	0.000
66	C	154	ILE	0	-0.009	0.007	16.619	0.015	0.015	0.000	0.000	0.000	0.000
67	C	155	SER	0	0.028	0.005	17.078	-0.033	-0.033	0.000	0.000	0.000	0.000
68	C	156	HIS	1	0.743	0.895	16.604	0.196	0.196	0.000	0.000	0.000	0.000
69	C	157	LEU	0	0.073	0.041	16.062	-0.047	-0.047	0.000	0.000	0.000	0.000
70	C	158	PHE	0	-0.016	-0.010	14.600	0.033	0.033	0.000	0.000	0.000	0.000
71	C	159	PHE	0	0.048	0.012	16.362	-0.014	-0.014	0.000	0.000	0.000	0.000
72	C	160	HIS	0	0.093	0.043	18.499	0.006	0.006	0.000	0.000	0.000	0.000
73	C	161	LYS	1	0.888	0.943	20.782	0.090	0.090	0.000	0.000	0.000	0.000
74	C	162	GLU	-1	-0.877	-0.935	21.309	-0.112	-0.112	0.000	0.000	0.000	0.000
75	C	163	ASN	0	-0.021	0.010	17.891	-0.018	-0.018	0.000	0.000	0.000	0.000
76	C	164	ASP	-1	-0.800	-0.926	17.292	-0.074	-0.074	0.000	0.000	0.000	0.000
77	C	165	TRP	0	-0.002	-0.003	18.570	-0.003	-0.003	0.000	0.000	0.000	0.000
78	C	166	GLY	0	0.032	0.005	19.078	-0.006	-0.006	0.000	0.000	0.000	0.000
79	C	167	PHE	0	-0.028	-0.004	21.562	0.002	0.002	0.000	0.000	0.000	0.000
80	C	168	SER	0	0.031	0.008	25.075	0.008	0.008	0.000	0.000	0.000	0.000
81	C	169	ASN	0	-0.014	-0.026	28.038	0.005	0.005	0.000	0.000	0.000	0.000
82	C	170	PHE	0	-0.031	0.001	22.383	-0.003	-0.003	0.000	0.000	0.000	0.000
83	C	171	MET	0	0.028	0.008	27.089	-0.001	-0.001	0.000	0.000	0.000	0.000
84	C	172	ALA	0	0.075	0.049	29.909	0.001	0.001	0.000	0.000	0.000	0.000
85	C	173	TRP	0	0.027	-0.002	29.991	0.001	0.001	0.000	0.000	0.000	0.000
86	C	174	SER	0	-0.058	-0.032	33.581	0.002	0.002	0.000	0.000	0.000	0.000
87	C	175	GLU	-1	-0.993	-0.990	32.501	-0.019	-0.019	0.000	0.000	0.000	0.000
88	C	176	VAL	0	0.044	0.011	28.339	0.002	0.002	0.000	0.000	0.000	0.000
89	C	177	NME	0	-0.045	-0.016	30.429	0.002	0.002	0.000	0.000	0.000	0.000
90	C	187	ACE	0	0.038	0.012	32.873	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	188	LYS	1	0.895	0.929	27.439	-0.041	-0.041	0.000	0.000	0.000	0.000
92	C	189	VAL	0	0.068	0.040	25.877	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	190	THR	0	-0.079	-0.019	21.535	-0.002	-0.002	0.000	0.000	0.000	0.000
94	C	191	PHE	0	0.062	0.020	20.238	-0.008	-0.008	0.000	0.000	0.000	0.000
95	C	192	GLU	-1	-0.887	-0.975	16.215	0.002	0.002	0.000	0.000	0.000	0.000
96	C	193	VAL	0	0.010	0.008	12.830	-0.020	-0.020	0.000	0.000	0.000	0.000
97	C	194	PHE	0	-0.020	0.009	9.812	0.030	0.030	0.000	0.000	0.000	0.000
98	C	195	VAL	0	0.009	0.018	8.346	-0.012	-0.012	0.000	0.000	0.000	0.000
99	C	196	GLN	0	-0.032	-0.028	8.418	-0.011	-0.011	0.000	0.000	0.000	0.000
100	C	197	ALA	0	0.004	-0.011	7.386	0.155	0.155	0.000	0.000	0.000	0.000
101	C	198	ASP	-1	-0.820	-0.893	7.441	-1.207	-1.207	0.000	0.000	0.000	0.000
102	C	199	ALA	0	-0.062	-0.046	7.970	-0.122	-0.122	0.000	0.000	0.000	0.000
103	C	200	PRO	0	-0.012	-0.006	8.108	0.118	0.118	0.000	0.000	0.000	0.000
104	C	201	HIS	0	0.048	0.010	11.035	0.051	0.051	0.000	0.000	0.000	0.000
105	C	202	GLY	0	0.043	0.003	14.432	0.022	0.022	0.000	0.000	0.000	0.000
106	C	203	VAL	0	-0.060	-0.013	11.284	0.030	0.030	0.000	0.000	0.000	0.000
107	C	204	ALA	0	0.011	-0.004	14.166	0.007	0.007	0.000	0.000	0.000	0.000
108	C	205	NME	0	-0.028	-0.003	17.057	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:66:ACE )