FMO DATABASE

FMODB ID: R5M88

Calculation Name: 1YZE-B-Xray372

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: 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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-889495.727935
FMO2-HF: Nuclear repulsion	845037.454446
FMO2-HF: Total energy	-44458.27349
FMO2-MP2: Total energy	-44586.286508

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:67:SER)

Summations of interaction energy for fragment #1(B:67: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.
-1.157	2.711	5.673	-3.852	-5.69	-0.007

Interaction energy analysis for fragmet #1(B:67:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.033

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	B	69	ALA	0	0.004	0.009	3.797	1.689	3.406	-0.022	-0.887	-0.808	0.001
4	B	70	THR	0	0.027	0.015	6.728	-0.321	-0.321	0.000	0.000	0.000	0.000
5	B	71	PHE	0	-0.027	-0.003	9.758	0.151	0.151	0.000	0.000	0.000	0.000
6	B	72	GLN	0	0.070	0.001	12.463	-0.077	-0.077	0.000	0.000	0.000	0.000
7	B	73	PHE	0	-0.021	-0.015	16.192	0.021	0.021	0.000	0.000	0.000	0.000
8	B	74	THR	0	0.044	-0.006	18.639	-0.008	-0.008	0.000	0.000	0.000	0.000
9	B	75	VAL	0	-0.007	0.021	22.309	0.009	0.009	0.000	0.000	0.000	0.000
10	B	76	GLU	-1	-0.898	-0.957	24.511	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	77	ARG	1	0.854	0.924	27.955	0.091	0.091	0.000	0.000	0.000	0.000
12	B	78	PHE	0	0.114	0.064	26.842	0.004	0.004	0.000	0.000	0.000	0.000
13	B	79	SER	0	-0.112	-0.068	29.680	0.012	0.012	0.000	0.000	0.000	0.000
14	B	80	ARG	1	0.939	0.972	32.275	0.094	0.094	0.000	0.000	0.000	0.000
15	B	81	LEU	0	0.010	-0.003	32.818	0.006	0.006	0.000	0.000	0.000	0.000
16	B	82	SER	0	-0.014	0.006	30.558	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	83	GLU	-1	-0.872	-0.942	27.132	-0.129	-0.129	0.000	0.000	0.000	0.000
18	B	84	SER	0	-0.001	-0.036	22.322	0.001	0.001	0.000	0.000	0.000	0.000
19	B	85	VAL	0	-0.019	0.002	23.744	0.008	0.008	0.000	0.000	0.000	0.000
20	B	86	LEU	0	0.013	0.016	17.573	-0.016	-0.016	0.000	0.000	0.000	0.000
21	B	87	SER	0	0.034	0.039	15.374	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	88	PRO	0	-0.007	-0.019	15.849	0.004	0.004	0.000	0.000	0.000	0.000
23	B	89	PRO	0	-0.028	-0.011	12.526	-0.036	-0.036	0.000	0.000	0.000	0.000
24	B	90	CYS	0	-0.025	0.010	8.380	0.062	0.062	0.000	0.000	0.000	0.000
25	B	91	PHE	0	0.054	0.011	7.177	-0.106	-0.106	0.000	0.000	0.000	0.000
26	B	92	VAL	0	0.028	0.040	1.950	-0.139	-0.418	2.037	-0.388	-1.370	-0.005
27	B	93	ARG	1	0.874	0.931	2.340	-4.544	-2.714	3.658	-2.371	-3.117	-0.003
28	B	94	ASN	0	-0.001	-0.012	4.031	0.245	0.352	0.002	-0.055	-0.055	0.000
29	B	95	LEU	0	0.021	0.028	6.702	0.121	0.121	0.000	0.000	0.000	0.000
30	B	96	PRO	0	0.027	0.005	7.916	-0.098	-0.098	0.000	0.000	0.000	0.000
31	B	97	TRP	0	-0.005	-0.018	6.301	-0.044	-0.044	0.000	0.000	0.000	0.000
32	B	98	LYS	1	0.921	0.977	10.561	0.264	0.264	0.000	0.000	0.000	0.000
33	B	99	ILE	0	-0.006	0.015	13.882	-0.029	-0.029	0.000	0.000	0.000	0.000
34	B	100	MET	0	-0.029	-0.024	16.242	0.040	0.040	0.000	0.000	0.000	0.000
35	B	101	VAL	0	-0.005	-0.001	19.454	-0.011	-0.011	0.000	0.000	0.000	0.000
36	B	102	MET	0	0.031	0.009	22.638	0.011	0.011	0.000	0.000	0.000	0.000
37	B	103	PRO	0	0.032	0.004	26.178	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	104	ARG	1	0.941	0.978	29.110	0.102	0.102	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.003	-0.019	24.977	0.005	0.005	0.000	0.000	0.000	0.000
40	B	116	GLY	0	-0.045	0.002	25.031	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	117	PHE	0	-0.001	-0.012	17.102	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	118	PHE	0	0.003	-0.020	18.845	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	119	LEU	0	0.002	0.005	10.993	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	120	GLN	0	0.085	0.021	14.835	0.030	0.030	0.000	0.000	0.000	0.000
45	B	121	CYS	0	-0.087	-0.053	9.497	-0.049	-0.049	0.000	0.000	0.000	0.000
46	B	122	ASN	0	0.016	0.002	12.227	0.048	0.048	0.000	0.000	0.000	0.000
47	B	123	ALA	0	0.004	-0.010	13.747	0.024	0.024	0.000	0.000	0.000	0.000
48	B	124	GLU	-1	-0.984	-0.972	16.781	-0.115	-0.115	0.000	0.000	0.000	0.000
49	B	125	SER	0	-0.036	-0.039	16.721	0.000	0.000	0.000	0.000	0.000	0.000
50	B	126	ASP	-1	-0.882	-0.918	18.988	-0.080	-0.080	0.000	0.000	0.000	0.000
51	B	127	SER	0	-0.005	-0.023	21.361	0.005	0.005	0.000	0.000	0.000	0.000
52	B	128	THR	0	0.015	-0.005	20.377	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	129	SER	0	-0.062	-0.033	19.920	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	130	TRP	0	0.013	0.060	12.560	0.016	0.016	0.000	0.000	0.000	0.000
55	B	131	SER	0	-0.015	-0.050	13.766	-0.004	-0.004	0.000	0.000	0.000	0.000
56	B	132	CYS	0	-0.048	-0.027	7.758	-0.064	-0.064	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.028	0.002	10.232	-0.131	-0.131	0.000	0.000	0.000	0.000
58	B	134	ALA	0	0.066	0.043	8.526	-0.054	-0.054	0.000	0.000	0.000	0.000
59	B	135	GLN	0	0.059	0.043	9.145	0.186	0.186	0.000	0.000	0.000	0.000
60	B	136	ALA	0	0.024	-0.001	9.780	-0.275	-0.275	0.000	0.000	0.000	0.000
61	B	137	VAL	0	-0.024	-0.003	11.992	0.171	0.171	0.000	0.000	0.000	0.000
62	B	138	LEU	0	-0.011	0.015	14.304	-0.018	-0.018	0.000	0.000	0.000	0.000
63	B	139	LYS	1	0.928	0.937	16.923	0.439	0.439	0.000	0.000	0.000	0.000
64	B	140	ILE	0	-0.028	0.001	19.069	0.000	0.000	0.000	0.000	0.000	0.000
65	B	141	ILE	0	0.003	-0.014	19.728	0.005	0.005	0.000	0.000	0.000	0.000
66	B	142	ASN	0	-0.014	0.004	23.389	0.032	0.032	0.000	0.000	0.000	0.000
67	B	150	PHE	0	0.019	0.016	22.252	0.000	0.000	0.000	0.000	0.000	0.000
68	B	151	SER	0	0.033	0.022	18.418	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	152	ARG	1	0.859	0.941	18.875	0.242	0.242	0.000	0.000	0.000	0.000
70	B	153	ARG	1	0.896	0.935	14.146	0.384	0.384	0.000	0.000	0.000	0.000
71	B	154	ILE	0	-0.034	-0.007	14.458	0.071	0.071	0.000	0.000	0.000	0.000
72	B	155	SER	0	0.023	0.001	13.939	-0.094	-0.094	0.000	0.000	0.000	0.000
73	B	156	HIS	1	0.801	0.932	13.538	0.311	0.311	0.000	0.000	0.000	0.000
74	B	157	LEU	0	0.088	0.044	12.978	-0.054	-0.054	0.000	0.000	0.000	0.000
75	B	158	PHE	0	-0.044	-0.018	12.393	0.017	0.017	0.000	0.000	0.000	0.000
76	B	159	PHE	0	0.051	0.004	14.267	0.034	0.034	0.000	0.000	0.000	0.000
77	B	160	HIS	0	-0.021	-0.002	16.567	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	161	LYS	1	0.896	0.975	19.157	0.074	0.074	0.000	0.000	0.000	0.000
79	B	162	GLU	-1	-0.871	-0.935	19.409	-0.150	-0.150	0.000	0.000	0.000	0.000
80	B	163	ASN	0	0.002	0.015	16.094	-0.036	-0.036	0.000	0.000	0.000	0.000
81	B	164	ASP	-1	-0.849	-0.946	15.733	-0.260	-0.260	0.000	0.000	0.000	0.000
82	B	165	TRP	0	-0.014	0.005	16.385	0.028	0.028	0.000	0.000	0.000	0.000
83	B	166	GLY	0	0.011	-0.001	17.449	-0.039	-0.039	0.000	0.000	0.000	0.000
84	B	167	PHE	0	-0.028	-0.004	19.461	0.033	0.033	0.000	0.000	0.000	0.000
85	B	168	SER	0	0.051	0.018	23.094	0.003	0.003	0.000	0.000	0.000	0.000
86	B	169	ASN	0	-0.017	-0.007	25.961	0.008	0.008	0.000	0.000	0.000	0.000
87	B	170	PHE	0	-0.032	-0.026	20.467	0.001	0.001	0.000	0.000	0.000	0.000
88	B	171	MET	0	-0.035	-0.035	25.224	-0.009	-0.009	0.000	0.000	0.000	0.000
89	B	172	ALA	0	0.055	0.039	28.289	0.003	0.003	0.000	0.000	0.000	0.000
90	B	173	TRP	0	0.040	0.052	28.069	-0.007	-0.007	0.000	0.000	0.000	0.000
91	B	174	SER	0	-0.101	-0.070	32.005	0.003	0.003	0.000	0.000	0.000	0.000
92	B	175	GLU	-1	-0.898	-0.920	30.990	-0.106	-0.106	0.000	0.000	0.000	0.000
93	B	189	VAL	0	-0.017	-0.020	26.140	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	190	THR	0	0.000	0.023	21.107	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	191	PHE	0	-0.018	-0.007	18.864	-0.009	-0.009	0.000	0.000	0.000	0.000
96	B	192	GLU	-1	-0.863	-0.932	14.892	-0.480	-0.480	0.000	0.000	0.000	0.000
97	B	193	VAL	0	0.019	0.005	11.097	0.021	0.021	0.000	0.000	0.000	0.000
98	B	194	PHE	0	-0.016	0.010	6.217	0.095	0.095	0.000	0.000	0.000	0.000
99	B	195	VAL	0	-0.028	-0.029	6.582	0.177	0.177	0.000	0.000	0.000	0.000
100	B	196	GLN	0	-0.009	-0.018	4.414	-0.261	-0.169	-0.001	-0.022	-0.068	0.000
101	B	197	ALA	0	-0.022	-0.011	4.328	0.954	1.213	-0.001	-0.071	-0.187	0.000
102	B	198	ASP	-1	-0.863	-0.932	4.141	0.770	0.912	0.000	-0.058	-0.085	0.000
103	B	199	ALA	0	-0.078	-0.057	6.079	-0.142	-0.142	0.000	0.000	0.000	0.000
104	B	200	PRO	0	-0.016	-0.005	6.285	-0.100	-0.100	0.000	0.000	0.000	0.000
105	B	201	HIS	0	0.037	0.020	9.162	0.058	0.058	0.000	0.000	0.000	0.000
106	B	202	GLY	0	0.025	0.005	12.863	-0.050	-0.050	0.000	0.000	0.000	0.000
107	B	203	VAL	0	-0.050	-0.021	11.094	-0.026	-0.026	0.000	0.000	0.000	0.000
108	B	204	ALA	0	0.000	0.009	14.341	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:67:SER)