FMO DATABASE

FMODB ID: R1J68

Calculation Name: 1YZE-A-Xray310

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZE

Chain ID: A

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	115
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-926840.264718
FMO2-HF: Nuclear repulsion	881598.46031
FMO2-HF: Total energy	-45241.804408
FMO2-MP2: Total energy	-45372.664136

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:64:ACE )

Summations of interaction energy for fragment #1(A:64: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.
-0.28	2.305	0.137	-1.079	-1.643	-0.002

Interaction energy analysis for fragmet #1(A:64:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / 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	A	66	ARG	1	0.895	0.969	3.698	-1.462	-0.154	0.002	-0.630	-0.680	0.000
4	A	67	SER	0	0.060	0.010	5.800	-0.002	-0.002	0.000	0.000	0.000	0.000
5	A	68	GLU	-1	-0.877	-0.927	8.867	0.054	0.054	0.000	0.000	0.000	0.000
6	A	69	ALA	0	-0.027	-0.026	7.949	0.113	0.113	0.000	0.000	0.000	0.000
7	A	70	THR	0	0.041	0.033	10.120	-0.069	-0.069	0.000	0.000	0.000	0.000
8	A	71	PHE	0	-0.020	-0.012	11.248	0.082	0.082	0.000	0.000	0.000	0.000
9	A	72	GLN	0	0.056	0.000	13.326	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	73	PHE	0	-0.011	-0.004	16.288	0.038	0.038	0.000	0.000	0.000	0.000
11	A	74	THR	0	-0.033	-0.028	18.231	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	75	VAL	0	-0.022	0.012	21.714	0.004	0.004	0.000	0.000	0.000	0.000
13	A	76	GLU	-1	-0.777	-0.935	24.083	0.132	0.132	0.000	0.000	0.000	0.000
14	A	77	ARG	1	0.837	0.923	26.975	-0.081	-0.081	0.000	0.000	0.000	0.000
15	A	78	PHE	0	0.058	0.039	26.354	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	79	SER	0	-0.027	-0.021	29.489	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	80	ARG	1	0.921	0.938	33.173	-0.065	-0.065	0.000	0.000	0.000	0.000
18	A	81	LEU	0	0.024	0.034	31.146	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	82	SER	0	-0.045	-0.037	30.207	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	83	GLU	-1	-0.840	-0.918	25.415	0.096	0.096	0.000	0.000	0.000	0.000
21	A	84	SER	0	-0.014	0.000	20.554	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	85	VAL	0	0.022	0.010	21.929	0.008	0.008	0.000	0.000	0.000	0.000
23	A	86	LEU	0	0.007	0.012	17.113	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	87	SER	0	0.025	0.024	14.217	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	88	PRO	0	0.001	-0.012	12.887	0.007	0.007	0.000	0.000	0.000	0.000
26	A	89	PRO	0	0.009	0.011	8.842	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	90	CYS	0	-0.053	-0.015	7.569	0.233	0.233	0.000	0.000	0.000	0.000
28	A	91	PHE	0	0.033	-0.006	3.096	-0.280	0.016	0.096	-0.150	-0.242	-0.001
29	A	92	VAL	0	0.001	0.011	4.157	0.443	0.636	0.002	-0.056	-0.138	0.000
30	A	93	ARG	1	0.875	0.954	5.312	0.266	0.309	0.000	-0.006	-0.038	0.000
31	A	94	ASN	0	-0.039	-0.041	3.375	0.229	0.856	0.037	-0.231	-0.432	-0.001
32	A	95	LEU	0	0.040	0.050	4.386	0.264	0.382	0.000	-0.006	-0.113	0.000
33	A	96	PRO	0	-0.013	0.020	6.274	0.266	0.266	0.000	0.000	0.000	0.000
34	A	97	TRP	0	0.066	-0.006	7.446	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	98	LYS	1	0.815	0.913	10.340	-0.153	-0.153	0.000	0.000	0.000	0.000
36	A	99	ILE	0	0.018	0.020	13.366	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	100	MET	0	-0.013	0.001	16.576	0.000	0.000	0.000	0.000	0.000	0.000
38	A	101	VAL	0	-0.029	-0.003	19.841	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	102	MET	0	0.028	0.012	23.168	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	103	PRO	0	0.042	0.029	26.626	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	104	ARG	1	0.929	0.967	30.277	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	105	NME	0	0.077	0.047	28.712	0.004	0.004	0.000	0.000	0.000	0.000
43	A	114	ACE	0	-0.040	-0.091	32.524	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	115	VAL	0	0.016	0.014	26.773	0.004	0.004	0.000	0.000	0.000	0.000
45	A	116	GLY	0	0.043	0.021	26.590	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	117	PHE	0	-0.030	-0.032	18.847	0.009	0.009	0.000	0.000	0.000	0.000
47	A	118	PHE	0	-0.040	-0.025	20.535	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	119	LEU	0	-0.016	0.006	13.063	0.023	0.023	0.000	0.000	0.000	0.000
49	A	120	GLN	0	0.072	0.022	15.092	0.009	0.009	0.000	0.000	0.000	0.000
50	A	121	CYS	0	-0.053	-0.020	11.531	0.049	0.049	0.000	0.000	0.000	0.000
51	A	122	ASN	0	0.037	-0.011	11.238	0.017	0.017	0.000	0.000	0.000	0.000
52	A	123	ALA	0	-0.013	-0.008	12.380	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	124	GLU	-1	-0.938	-0.955	13.184	0.179	0.179	0.000	0.000	0.000	0.000
54	A	125	SER	0	-0.070	-0.027	13.667	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	126	ASP	-1	-0.878	-0.917	15.471	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	127	SER	0	-0.024	-0.013	16.091	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	128	THR	0	-0.015	-0.052	18.161	0.011	0.011	0.000	0.000	0.000	0.000
58	A	129	SER	0	-0.010	0.002	18.715	0.009	0.009	0.000	0.000	0.000	0.000
59	A	130	TRP	0	-0.018	0.026	13.851	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	131	SER	0	0.032	-0.008	15.383	0.032	0.032	0.000	0.000	0.000	0.000
61	A	132	CYS	0	-0.072	-0.022	11.725	-0.041	-0.041	0.000	0.000	0.000	0.000
62	A	133	HIS	0	0.010	0.017	14.216	0.050	0.050	0.000	0.000	0.000	0.000
63	A	134	ALA	0	0.038	0.026	13.326	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	135	GLN	0	-0.019	-0.003	15.297	0.009	0.009	0.000	0.000	0.000	0.000
65	A	136	ALA	0	0.019	0.000	15.500	0.010	0.010	0.000	0.000	0.000	0.000
66	A	137	VAL	0	-0.040	-0.012	17.251	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	138	LEU	0	-0.003	0.005	18.126	0.020	0.020	0.000	0.000	0.000	0.000
68	A	139	LYS	1	0.932	0.950	20.176	-0.127	-0.127	0.000	0.000	0.000	0.000
69	A	140	ILE	0	0.010	0.037	21.556	0.016	0.016	0.000	0.000	0.000	0.000
70	A	141	ILE	0	0.015	-0.010	23.040	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	142	NME	0	-0.059	-0.013	24.277	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	149	ACE	0	0.017	-0.002	30.681	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	150	PHE	0	0.050	0.009	24.608	0.003	0.003	0.000	0.000	0.000	0.000
74	A	151	SER	0	-0.038	-0.015	22.679	0.010	0.010	0.000	0.000	0.000	0.000
75	A	152	ARG	1	0.900	0.948	23.423	-0.060	-0.060	0.000	0.000	0.000	0.000
76	A	153	ARG	1	0.922	0.968	21.647	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	154	ILE	0	-0.013	0.001	18.174	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	155	SER	0	0.027	-0.017	19.798	0.003	0.003	0.000	0.000	0.000	0.000
79	A	156	HIS	1	0.778	0.913	18.381	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	157	LEU	0	0.101	0.067	17.749	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	158	PHE	0	-0.078	-0.026	15.159	0.011	0.011	0.000	0.000	0.000	0.000
82	A	159	PHE	0	0.081	0.005	16.752	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	160	HIS	0	0.003	0.010	18.101	0.020	0.020	0.000	0.000	0.000	0.000
84	A	161	LYS	1	0.955	0.976	19.893	0.025	0.025	0.000	0.000	0.000	0.000
85	A	162	GLU	-1	-0.890	-0.928	20.791	0.004	0.004	0.000	0.000	0.000	0.000
86	A	163	ASN	0	0.043	0.007	16.147	0.015	0.015	0.000	0.000	0.000	0.000
87	A	164	ASP	-1	-0.827	-0.925	16.757	0.100	0.100	0.000	0.000	0.000	0.000
88	A	165	TRP	0	-0.023	-0.015	18.834	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	166	GLY	0	0.010	-0.007	19.892	0.017	0.017	0.000	0.000	0.000	0.000
90	A	167	PHE	0	-0.046	-0.006	22.448	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	168	SER	0	0.053	0.023	25.837	0.005	0.005	0.000	0.000	0.000	0.000
92	A	169	ASN	0	-0.016	-0.017	28.101	0.005	0.005	0.000	0.000	0.000	0.000
93	A	170	PHE	0	-0.050	-0.015	23.661	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	171	MET	0	0.015	-0.005	27.998	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	172	ALA	0	0.024	0.014	30.741	0.001	0.001	0.000	0.000	0.000	0.000
96	A	173	TRP	0	-0.024	0.041	29.121	0.002	0.002	0.000	0.000	0.000	0.000
97	A	174	NME	0	-0.047	-0.021	33.763	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	187	ACE	0	0.015	-0.004	32.122	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	188	LYS	1	0.886	0.957	25.278	-0.133	-0.133	0.000	0.000	0.000	0.000
100	A	189	VAL	0	0.009	0.007	25.639	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	190	THR	0	0.025	0.035	20.617	0.007	0.007	0.000	0.000	0.000	0.000
102	A	191	PHE	0	0.021	0.030	19.950	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	192	GLU	-1	-0.914	-0.969	17.162	0.192	0.192	0.000	0.000	0.000	0.000
104	A	193	VAL	0	-0.005	0.000	14.137	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	194	PHE	0	-0.016	0.013	13.738	0.040	0.040	0.000	0.000	0.000	0.000
106	A	195	VAL	0	0.011	0.004	10.180	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	196	GLN	0	-0.024	-0.025	11.629	0.014	0.014	0.000	0.000	0.000	0.000
108	A	197	ALA	0	0.010	-0.006	10.362	0.003	0.003	0.000	0.000	0.000	0.000
109	A	198	ASP	-1	-0.868	-0.939	12.354	-0.212	-0.212	0.000	0.000	0.000	0.000
110	A	199	ALA	0	-0.051	-0.049	11.461	-0.037	-0.037	0.000	0.000	0.000	0.000
111	A	200	PRO	0	0.014	-0.002	9.571	0.049	0.049	0.000	0.000	0.000	0.000
112	A	201	HIS	0	0.011	0.005	12.786	-0.054	-0.054	0.000	0.000	0.000	0.000
113	A	202	GLY	0	0.030	0.015	15.192	0.032	0.032	0.000	0.000	0.000	0.000
114	A	203	VAL	0	-0.032	-0.031	11.222	0.030	0.030	0.000	0.000	0.000	0.000
115	A	204	NME	0	-0.007	0.024	12.947	-0.032	-0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:ACE )