FMO DATABASE

FMODB ID: YY1Z2

Calculation Name: 1YZE-A-Xray372

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: 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	OptAll
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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-898264.383104
FMO2-HF: Nuclear repulsion	853704.674132
FMO2-HF: Total energy	-44559.708972
FMO2-MP2: Total energy	-44688.172983

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:65:TRP)

Summations of interaction energy for fragment #1(A:65:TRP)

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.
-16.15	-14.495	12.129	-5.415	-8.367	-0.03

Interaction energy analysis for fragmet #1(A:65:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.007

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	67	SER	0	0.021	-0.031	3.516	-0.861	-0.052	0.044	0.186	-1.038	0.005
4	A	68	GLU	-1	-0.812	-0.875	6.047	1.137	1.137	0.000	0.000	0.000	0.000
5	A	69	ALA	0	-0.024	-0.020	7.943	0.773	0.773	0.000	0.000	0.000	0.000
6	A	70	THR	0	0.018	0.015	10.038	-0.214	-0.214	0.000	0.000	0.000	0.000
7	A	71	PHE	0	-0.016	-0.005	12.206	0.088	0.088	0.000	0.000	0.000	0.000
8	A	72	GLN	0	-0.014	-0.029	14.250	-0.106	-0.106	0.000	0.000	0.000	0.000
9	A	73	PHE	0	0.018	0.010	17.550	0.003	0.003	0.000	0.000	0.000	0.000
10	A	74	THR	0	-0.011	-0.013	19.898	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	75	VAL	0	-0.019	0.007	23.561	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	76	GLU	-1	-0.708	-0.856	25.838	0.177	0.177	0.000	0.000	0.000	0.000
13	A	77	ARG	1	0.871	0.928	28.781	-0.132	-0.132	0.000	0.000	0.000	0.000
14	A	78	PHE	0	0.046	0.031	28.784	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	79	SER	0	0.009	0.006	31.084	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	80	ARG	1	0.891	0.929	34.678	-0.135	-0.135	0.000	0.000	0.000	0.000
17	A	81	LEU	0	-0.004	0.014	32.673	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	82	SER	0	-0.030	-0.031	32.402	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	83	GLU	-1	-0.844	-0.916	27.834	0.192	0.192	0.000	0.000	0.000	0.000
20	A	84	SER	0	-0.013	-0.006	22.657	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	85	VAL	0	0.012	0.000	24.138	0.026	0.026	0.000	0.000	0.000	0.000
22	A	86	LEU	0	0.006	0.010	19.018	0.029	0.029	0.000	0.000	0.000	0.000
23	A	87	SER	0	-0.001	0.006	15.797	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	88	PRO	0	0.030	0.001	15.396	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	89	PRO	0	0.013	0.024	11.028	0.092	0.092	0.000	0.000	0.000	0.000
26	A	90	CYS	0	-0.052	-0.014	9.741	0.138	0.138	0.000	0.000	0.000	0.000
27	A	91	PHE	0	0.042	0.021	4.505	-0.117	-0.025	-0.001	-0.008	-0.083	0.000
28	A	92	VAL	0	-0.004	0.010	4.311	1.841	2.074	0.001	-0.053	-0.181	0.000
29	A	93	ARG	1	0.848	0.926	2.572	-3.010	-2.306	0.664	-0.492	-0.876	0.000
30	A	94	ASN	0	0.016	-0.001	1.866	-14.724	-15.042	11.380	-5.013	-6.048	-0.035
31	A	95	LEU	0	0.042	0.047	3.454	-1.209	-1.074	0.041	-0.035	-0.141	0.000
32	A	96	PRO	0	0.002	0.006	6.867	0.965	0.965	0.000	0.000	0.000	0.000
33	A	97	TRP	0	0.052	0.003	7.459	-0.586	-0.586	0.000	0.000	0.000	0.000
34	A	98	LYS	1	0.784	0.881	11.247	-0.592	-0.592	0.000	0.000	0.000	0.000
35	A	99	ILE	0	-0.014	-0.001	14.645	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	100	MET	0	0.006	0.011	17.792	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	101	VAL	0	-0.030	-0.014	21.059	0.004	0.004	0.000	0.000	0.000	0.000
38	A	102	MET	0	0.050	0.025	24.556	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	103	PRO	0	0.038	0.018	28.087	0.005	0.005	0.000	0.000	0.000	0.000
40	A	104	ARG	1	0.959	1.001	29.862	-0.175	-0.175	0.000	0.000	0.000	0.000
41	A	115	VAL	0	-0.026	-0.009	27.588	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	116	GLY	0	-0.028	-0.013	27.730	0.006	0.006	0.000	0.000	0.000	0.000
43	A	117	PHE	0	-0.065	-0.045	20.069	0.002	0.002	0.000	0.000	0.000	0.000
44	A	118	PHE	0	-0.019	-0.017	21.011	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	119	LEU	0	-0.012	0.008	13.383	0.024	0.024	0.000	0.000	0.000	0.000
46	A	120	GLN	0	0.002	-0.022	16.015	-0.049	-0.049	0.000	0.000	0.000	0.000
47	A	121	CYS	0	-0.075	-0.039	11.010	0.201	0.201	0.000	0.000	0.000	0.000
48	A	122	ASN	0	0.035	0.000	11.476	-0.109	-0.109	0.000	0.000	0.000	0.000
49	A	123	ALA	0	0.008	0.018	12.933	-0.100	-0.100	0.000	0.000	0.000	0.000
50	A	124	GLU	-1	-0.838	-0.906	14.153	0.447	0.447	0.000	0.000	0.000	0.000
51	A	125	SER	0	-0.073	-0.019	13.833	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	126	ASP	-1	-0.881	-0.944	15.895	0.057	0.057	0.000	0.000	0.000	0.000
53	A	127	SER	0	-0.037	-0.006	15.616	0.004	0.004	0.000	0.000	0.000	0.000
54	A	128	THR	0	0.013	-0.028	17.755	0.040	0.040	0.000	0.000	0.000	0.000
55	A	129	SER	0	-0.055	-0.029	15.725	0.004	0.004	0.000	0.000	0.000	0.000
56	A	130	TRP	0	-0.030	0.015	12.351	0.058	0.058	0.000	0.000	0.000	0.000
57	A	131	SER	0	0.033	-0.014	12.986	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	132	CYS	0	-0.053	-0.014	9.418	0.136	0.136	0.000	0.000	0.000	0.000
59	A	133	HIS	0	-0.009	0.015	11.670	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	134	ALA	0	0.021	0.010	11.816	0.137	0.137	0.000	0.000	0.000	0.000
61	A	135	GLN	0	-0.016	0.000	13.491	-0.224	-0.224	0.000	0.000	0.000	0.000
62	A	136	ALA	0	0.017	0.004	14.593	0.159	0.159	0.000	0.000	0.000	0.000
63	A	137	VAL	0	-0.037	-0.024	16.729	-0.120	-0.120	0.000	0.000	0.000	0.000
64	A	138	LEU	0	0.030	0.029	18.233	0.036	0.036	0.000	0.000	0.000	0.000
65	A	139	LYS	1	0.848	0.890	20.109	-0.646	-0.646	0.000	0.000	0.000	0.000
66	A	140	ILE	0	-0.004	0.015	22.523	0.019	0.019	0.000	0.000	0.000	0.000
67	A	141	ILE	0	-0.014	-0.002	22.976	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	150	PHE	0	0.100	0.047	24.412	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	151	SER	0	-0.084	-0.055	23.055	0.033	0.033	0.000	0.000	0.000	0.000
70	A	152	ARG	1	0.844	0.929	23.746	-0.341	-0.341	0.000	0.000	0.000	0.000
71	A	153	ARG	1	0.883	0.936	19.677	-0.478	-0.478	0.000	0.000	0.000	0.000
72	A	154	ILE	0	-0.018	-0.005	17.934	-0.051	-0.051	0.000	0.000	0.000	0.000
73	A	155	SER	0	0.030	-0.008	18.320	0.066	0.066	0.000	0.000	0.000	0.000
74	A	156	HIS	1	0.759	0.892	17.279	-0.569	-0.569	0.000	0.000	0.000	0.000
75	A	157	LEU	0	0.095	0.055	15.323	0.085	0.085	0.000	0.000	0.000	0.000
76	A	158	PHE	0	-0.026	-0.011	13.590	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	159	PHE	0	0.055	0.004	14.712	0.000	0.000	0.000	0.000	0.000	0.000
78	A	160	HIS	0	0.018	0.029	16.543	0.021	0.021	0.000	0.000	0.000	0.000
79	A	161	LYS	1	0.938	0.970	18.761	-0.186	-0.186	0.000	0.000	0.000	0.000
80	A	162	GLU	-1	-0.890	-0.925	19.778	0.328	0.328	0.000	0.000	0.000	0.000
81	A	163	ASN	0	0.075	0.018	16.641	0.112	0.112	0.000	0.000	0.000	0.000
82	A	164	ASP	-1	-0.812	-0.898	16.867	0.515	0.515	0.000	0.000	0.000	0.000
83	A	165	TRP	0	-0.016	-0.020	19.056	-0.036	-0.036	0.000	0.000	0.000	0.000
84	A	166	GLY	0	0.009	-0.005	20.103	0.058	0.058	0.000	0.000	0.000	0.000
85	A	167	PHE	0	-0.038	-0.007	22.616	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	168	SER	0	0.032	-0.007	26.244	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	169	ASN	0	-0.001	-0.008	28.669	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	170	PHE	0	-0.010	0.003	24.067	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	171	MET	0	-0.001	0.001	28.416	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	172	ALA	0	0.043	0.037	31.379	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	173	TRP	0	0.016	0.009	30.282	0.008	0.008	0.000	0.000	0.000	0.000
92	A	188	LYS	1	0.809	0.886	27.455	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	189	VAL	0	-0.031	-0.014	27.026	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	190	THR	0	0.020	0.020	21.976	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	191	PHE	0	0.033	0.027	21.621	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	192	GLU	-1	-0.808	-0.904	17.855	0.627	0.627	0.000	0.000	0.000	0.000
97	A	193	VAL	0	0.007	-0.004	14.577	-0.062	-0.062	0.000	0.000	0.000	0.000
98	A	194	PHE	0	-0.023	0.013	12.148	0.106	0.106	0.000	0.000	0.000	0.000
99	A	195	VAL	0	0.015	-0.005	10.272	-0.173	-0.173	0.000	0.000	0.000	0.000
100	A	196	GLN	0	-0.006	-0.015	10.614	0.227	0.227	0.000	0.000	0.000	0.000
101	A	197	ALA	0	0.035	0.018	8.217	-0.237	-0.237	0.000	0.000	0.000	0.000
102	A	198	ASP	-1	-0.838	-0.908	8.929	0.765	0.765	0.000	0.000	0.000	0.000
103	A	199	ALA	0	-0.011	-0.024	7.353	0.200	0.200	0.000	0.000	0.000	0.000
104	A	200	PRO	0	-0.012	-0.020	6.367	-0.051	-0.051	0.000	0.000	0.000	0.000
105	A	201	HIS	0	0.012	0.017	9.184	-0.109	-0.109	0.000	0.000	0.000	0.000
106	A	202	GLY	0	0.054	0.033	11.924	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	203	VAL	0	-0.023	0.003	8.401	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:65:TRP)