FMO DATABASE

FMODB ID: Z2QKN

Calculation Name: 1YZE-B-Xray310

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZE

Chain ID: B

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	116
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-915047.726628
FMO2-HF: Nuclear repulsion	869905.779103
FMO2-HF: Total energy	-45141.947525
FMO2-MP2: Total energy	-45272.16327

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(B:66:ACE )

Summations of interaction energy for fragment #1(B: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.
0.113	2.012	2.257	-2.007	-2.148	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.004

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

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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	B	68	GLU	-1	-0.846	-0.921	3.850	-0.555	0.748	-0.006	-0.607	-0.690	-0.002
4	B	69	ALA	0	0.000	0.005	5.601	0.241	0.241	0.000	0.000	0.000	0.000
5	B	70	THR	0	0.030	0.017	7.495	-0.081	-0.081	0.000	0.000	0.000	0.000
6	B	71	PHE	0	-0.022	-0.001	10.141	0.082	0.082	0.000	0.000	0.000	0.000
7	B	72	GLN	0	0.068	0.000	12.599	-0.040	-0.040	0.000	0.000	0.000	0.000
8	B	73	PHE	0	-0.011	-0.009	16.244	0.031	0.031	0.000	0.000	0.000	0.000
9	B	74	THR	0	0.041	-0.008	18.621	-0.019	-0.019	0.000	0.000	0.000	0.000
10	B	75	VAL	0	-0.012	0.015	22.218	0.006	0.006	0.000	0.000	0.000	0.000
11	B	76	GLU	-1	-0.892	-0.955	24.450	0.073	0.073	0.000	0.000	0.000	0.000
12	B	77	ARG	1	0.814	0.883	27.751	-0.068	-0.068	0.000	0.000	0.000	0.000
13	B	78	PHE	0	0.149	0.081	27.319	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	79	SER	0	-0.050	-0.032	29.868	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	80	ARG	1	0.807	0.898	32.520	-0.031	-0.031	0.000	0.000	0.000	0.000
16	B	81	LEU	0	-0.003	0.007	31.002	0.001	0.001	0.000	0.000	0.000	0.000
17	B	82	SER	0	0.018	0.021	26.562	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	83	GLU	-1	-0.833	-0.907	27.523	0.070	0.070	0.000	0.000	0.000	0.000
19	B	84	SER	0	-0.041	-0.030	21.806	0.006	0.006	0.000	0.000	0.000	0.000
20	B	85	VAL	0	0.034	0.028	24.020	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	86	LEU	0	0.004	0.002	17.593	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	87	SER	0	0.017	0.030	15.131	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	88	PRO	0	0.000	-0.016	15.111	0.011	0.011	0.000	0.000	0.000	0.000
24	B	89	PRO	0	-0.028	-0.011	11.557	-0.015	-0.015	0.000	0.000	0.000	0.000
25	B	90	CYS	0	-0.025	0.009	8.108	0.101	0.101	0.000	0.000	0.000	0.000
26	B	91	PHE	0	0.051	0.011	5.769	-0.148	-0.148	0.000	0.000	0.000	0.000
27	B	92	VAL	0	0.004	0.029	2.728	0.213	0.954	0.231	-0.396	-0.575	-0.002
28	B	93	ARG	1	0.875	0.938	2.074	1.153	0.886	2.026	-1.012	-0.747	0.005
29	B	94	ASN	0	-0.004	-0.014	3.862	-0.391	-0.269	0.006	0.008	-0.136	0.000
30	B	95	LEU	0	0.022	0.029	5.842	-0.193	-0.193	0.000	0.000	0.000	0.000
31	B	96	PRO	0	0.029	0.007	7.388	0.155	0.155	0.000	0.000	0.000	0.000
32	B	97	TRP	0	-0.005	-0.019	6.808	-0.179	-0.179	0.000	0.000	0.000	0.000
33	B	98	LYS	1	0.926	0.980	10.589	-0.178	-0.178	0.000	0.000	0.000	0.000
34	B	99	ILE	0	-0.005	0.015	13.968	-0.038	-0.038	0.000	0.000	0.000	0.000
35	B	100	MET	0	-0.024	-0.021	16.643	0.009	0.009	0.000	0.000	0.000	0.000
36	B	101	VAL	0	-0.006	0.003	19.873	-0.015	-0.015	0.000	0.000	0.000	0.000
37	B	102	MET	0	0.030	0.005	23.130	0.004	0.004	0.000	0.000	0.000	0.000
38	B	103	PRO	0	0.013	-0.016	26.676	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	104	ARG	1	0.931	0.965	30.163	-0.013	-0.013	0.000	0.000	0.000	0.000
40	B	105	NME	0	0.014	0.023	29.778	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	114	ACE	0	-0.028	-0.022	31.847	0.000	0.000	0.000	0.000	0.000	0.000
42	B	115	VAL	0	0.060	-0.018	25.859	0.002	0.002	0.000	0.000	0.000	0.000
43	B	116	GLY	0	-0.010	0.033	25.922	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	117	PHE	0	0.002	-0.011	17.919	0.008	0.008	0.000	0.000	0.000	0.000
45	B	118	PHE	0	0.007	-0.018	19.875	-0.014	-0.014	0.000	0.000	0.000	0.000
46	B	119	LEU	0	-0.002	0.004	12.216	0.015	0.015	0.000	0.000	0.000	0.000
47	B	120	GLN	0	0.088	0.021	15.425	-0.030	-0.030	0.000	0.000	0.000	0.000
48	B	121	CYS	0	-0.081	-0.050	10.173	0.016	0.016	0.000	0.000	0.000	0.000
49	B	122	ASN	0	0.012	0.000	12.252	0.021	0.021	0.000	0.000	0.000	0.000
50	B	123	ALA	0	0.001	-0.012	13.728	-0.025	-0.025	0.000	0.000	0.000	0.000
51	B	124	GLU	-1	-0.984	-0.971	16.478	0.187	0.187	0.000	0.000	0.000	0.000
52	B	125	SER	0	-0.050	-0.049	16.397	0.011	0.011	0.000	0.000	0.000	0.000
53	B	126	ASP	-1	-0.843	-0.913	18.643	0.066	0.066	0.000	0.000	0.000	0.000
54	B	127	SER	0	-0.010	-0.001	21.700	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	128	THR	0	0.021	-0.020	19.594	-0.013	-0.013	0.000	0.000	0.000	0.000
56	B	129	SER	0	-0.107	-0.039	18.964	0.004	0.004	0.000	0.000	0.000	0.000
57	B	130	TRP	0	0.023	0.054	13.344	-0.015	-0.015	0.000	0.000	0.000	0.000
58	B	131	SER	0	-0.039	-0.058	14.476	-0.012	-0.012	0.000	0.000	0.000	0.000
59	B	132	CYS	0	-0.048	-0.031	9.663	-0.019	-0.019	0.000	0.000	0.000	0.000
60	B	133	HIS	0	-0.025	0.002	12.398	0.078	0.078	0.000	0.000	0.000	0.000
61	B	134	ALA	0	0.069	0.045	10.592	-0.096	-0.096	0.000	0.000	0.000	0.000
62	B	135	GLN	0	0.054	0.042	12.042	0.097	0.097	0.000	0.000	0.000	0.000
63	B	136	ALA	0	0.026	-0.001	12.352	-0.027	-0.027	0.000	0.000	0.000	0.000
64	B	137	VAL	0	-0.019	-0.002	14.310	0.014	0.014	0.000	0.000	0.000	0.000
65	B	138	LEU	0	-0.019	0.013	16.480	0.015	0.015	0.000	0.000	0.000	0.000
66	B	139	LYS	1	0.936	0.938	18.374	0.024	0.024	0.000	0.000	0.000	0.000
67	B	140	ILE	0	-0.020	0.002	20.299	0.013	0.013	0.000	0.000	0.000	0.000
68	B	141	ILE	0	0.006	-0.017	20.548	-0.007	-0.007	0.000	0.000	0.000	0.000
69	B	142	ASN	0	-0.055	-0.029	24.262	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	143	NME	0	0.004	0.068	27.156	0.001	0.001	0.000	0.000	0.000	0.000
71	B	149	ACE	0	0.018	-0.015	28.160	0.000	0.000	0.000	0.000	0.000	0.000
72	B	150	PHE	0	0.025	0.011	24.076	0.001	0.001	0.000	0.000	0.000	0.000
73	B	151	SER	0	0.028	0.033	21.255	0.003	0.003	0.000	0.000	0.000	0.000
74	B	152	ARG	1	0.849	0.936	21.207	0.026	0.026	0.000	0.000	0.000	0.000
75	B	153	ARG	1	0.902	0.937	18.166	0.146	0.146	0.000	0.000	0.000	0.000
76	B	154	ILE	0	-0.038	-0.009	16.025	0.008	0.008	0.000	0.000	0.000	0.000
77	B	155	SER	0	0.024	0.001	16.821	-0.034	-0.034	0.000	0.000	0.000	0.000
78	B	156	HIS	1	0.801	0.931	16.184	0.095	0.095	0.000	0.000	0.000	0.000
79	B	157	LEU	0	0.092	0.046	15.444	-0.032	-0.032	0.000	0.000	0.000	0.000
80	B	158	PHE	0	-0.045	-0.017	13.668	0.026	0.026	0.000	0.000	0.000	0.000
81	B	159	PHE	0	0.062	0.007	15.587	-0.014	-0.014	0.000	0.000	0.000	0.000
82	B	160	HIS	0	-0.005	0.013	17.436	0.011	0.011	0.000	0.000	0.000	0.000
83	B	161	LYS	1	0.893	0.974	19.687	0.018	0.018	0.000	0.000	0.000	0.000
84	B	162	GLU	-1	-0.868	-0.935	20.644	-0.038	-0.038	0.000	0.000	0.000	0.000
85	B	163	ASN	0	0.003	0.017	16.602	-0.016	-0.016	0.000	0.000	0.000	0.000
86	B	164	ASP	-1	-0.852	-0.947	16.394	0.048	0.048	0.000	0.000	0.000	0.000
87	B	165	TRP	0	-0.008	0.007	17.529	-0.013	-0.013	0.000	0.000	0.000	0.000
88	B	166	GLY	0	0.008	-0.001	18.657	0.007	0.007	0.000	0.000	0.000	0.000
89	B	167	PHE	0	-0.027	-0.004	20.932	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	168	SER	0	0.052	0.019	24.443	0.007	0.007	0.000	0.000	0.000	0.000
91	B	169	ASN	0	-0.021	-0.010	27.125	0.007	0.007	0.000	0.000	0.000	0.000
92	B	170	PHE	0	-0.034	-0.027	21.877	-0.005	-0.005	0.000	0.000	0.000	0.000
93	B	171	MET	0	-0.051	-0.027	26.488	-0.005	-0.005	0.000	0.000	0.000	0.000
94	B	172	ALA	0	0.048	0.039	29.490	0.003	0.003	0.000	0.000	0.000	0.000
95	B	173	TRP	0	0.009	0.044	28.774	0.002	0.002	0.000	0.000	0.000	0.000
96	B	174	SER	0	-0.120	-0.080	32.851	0.002	0.002	0.000	0.000	0.000	0.000
97	B	175	GLU	-1	-0.870	-0.913	31.939	0.001	0.001	0.000	0.000	0.000	0.000
98	B	176	NME	0	-0.017	-0.001	30.603	0.003	0.003	0.000	0.000	0.000	0.000
99	B	188	ACE	0	-0.005	-0.051	26.907	0.001	0.001	0.000	0.000	0.000	0.000
100	B	189	VAL	0	0.015	-0.008	26.040	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	190	THR	0	-0.009	0.025	21.320	0.002	0.002	0.000	0.000	0.000	0.000
102	B	191	PHE	0	-0.018	-0.007	19.468	-0.013	-0.013	0.000	0.000	0.000	0.000
103	B	192	GLU	-1	-0.862	-0.932	15.840	0.009	0.009	0.000	0.000	0.000	0.000
104	B	193	VAL	0	0.022	0.006	12.159	-0.021	-0.021	0.000	0.000	0.000	0.000
105	B	194	PHE	0	-0.017	0.010	9.600	0.038	0.038	0.000	0.000	0.000	0.000
106	B	195	VAL	0	-0.026	-0.028	7.870	-0.009	-0.009	0.000	0.000	0.000	0.000
107	B	196	GLN	0	-0.009	-0.019	7.969	-0.055	-0.055	0.000	0.000	0.000	0.000
108	B	197	ALA	0	-0.026	-0.013	6.592	0.153	0.153	0.000	0.000	0.000	0.000
109	B	198	ASP	-1	-0.861	-0.931	8.114	-0.853	-0.853	0.000	0.000	0.000	0.000
110	B	199	ALA	0	-0.070	-0.052	7.994	-0.051	-0.051	0.000	0.000	0.000	0.000
111	B	200	PRO	0	-0.016	-0.004	7.512	0.095	0.095	0.000	0.000	0.000	0.000
112	B	201	HIS	0	0.038	0.020	10.381	0.033	0.033	0.000	0.000	0.000	0.000
113	B	202	GLY	0	0.024	0.002	13.755	0.029	0.029	0.000	0.000	0.000	0.000
114	B	203	VAL	0	-0.067	-0.029	10.424	0.034	0.034	0.000	0.000	0.000	0.000
115	B	204	ALA	0	0.020	-0.003	13.408	0.003	0.003	0.000	0.000	0.000	0.000
116	B	205	NME	0	-0.010	0.018	16.206	0.004	0.004	0.000	0.000	0.000	0.000

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