FMO DATABASE

FMODB ID: 22RNR

Calculation Name: 1YZE-C-Xray372

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: 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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-761041.93675
FMO2-HF: Nuclear repulsion	720737.799255
FMO2-HF: Total energy	-40304.137495
FMO2-MP2: Total energy	-40419.678869

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:67:SER)

Summations of interaction energy for fragment #1(C: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.
-2.08	0.084000000000002	11.511	-6.218	-7.457	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.044

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	69	ALA	0	0.006	0.015	3.819	0.103	2.072	-0.023	-1.064	-0.882	0.001
4	C	70	THR	0	0.020	0.010	6.438	-0.071	-0.071	0.000	0.000	0.000	0.000
5	C	71	PHE	0	-0.045	-0.023	10.214	0.039	0.039	0.000	0.000	0.000	0.000
6	C	72	GLN	0	0.025	0.001	12.375	0.031	0.031	0.000	0.000	0.000	0.000
7	C	73	PHE	0	-0.001	0.007	16.135	-0.018	-0.018	0.000	0.000	0.000	0.000
8	C	74	THR	0	0.030	0.021	18.807	0.027	0.027	0.000	0.000	0.000	0.000
9	C	85	VAL	0	0.026	0.003	23.957	0.001	0.001	0.000	0.000	0.000	0.000
10	C	86	LEU	0	0.006	-0.007	18.384	-0.016	-0.016	0.000	0.000	0.000	0.000
11	C	87	SER	0	-0.012	0.028	15.517	0.015	0.015	0.000	0.000	0.000	0.000
12	C	88	PRO	0	-0.015	-0.021	16.037	-0.018	-0.018	0.000	0.000	0.000	0.000
13	C	89	PRO	0	-0.014	0.003	12.366	-0.022	-0.022	0.000	0.000	0.000	0.000
14	C	90	CYS	0	-0.014	0.008	8.596	-0.014	-0.014	0.000	0.000	0.000	0.000
15	C	91	PHE	0	0.015	-0.016	7.737	-0.101	-0.101	0.000	0.000	0.000	0.000
16	C	92	VAL	0	0.051	0.038	2.397	-1.183	-0.611	0.430	-0.188	-0.814	-0.001
17	C	93	ARG	1	0.787	0.885	2.261	2.670	0.292	11.026	-3.965	-4.683	-0.001
18	C	94	ASN	0	0.007	-0.012	4.720	0.268	0.302	-0.001	-0.017	-0.016	0.000
19	C	95	LEU	0	0.023	0.035	7.439	0.280	0.280	0.000	0.000	0.000	0.000
20	C	96	PRO	0	-0.016	-0.001	8.766	-0.198	-0.198	0.000	0.000	0.000	0.000
21	C	97	TRP	0	0.043	0.007	6.897	0.079	0.079	0.000	0.000	0.000	0.000
22	C	98	LYS	1	0.831	0.923	11.179	0.500	0.500	0.000	0.000	0.000	0.000
23	C	99	ILE	0	0.003	0.005	14.491	-0.010	-0.010	0.000	0.000	0.000	0.000
24	C	100	MET	0	-0.032	-0.010	16.670	0.043	0.043	0.000	0.000	0.000	0.000
25	C	101	VAL	0	-0.017	-0.007	20.023	0.005	0.005	0.000	0.000	0.000	0.000
26	C	102	MET	0	-0.037	-0.004	23.076	0.010	0.010	0.000	0.000	0.000	0.000
27	C	115	VAL	0	-0.014	-0.001	28.077	-0.002	-0.002	0.000	0.000	0.000	0.000
28	C	116	GLY	0	-0.024	-0.011	25.286	0.000	0.000	0.000	0.000	0.000	0.000
29	C	117	PHE	0	-0.008	-0.013	17.449	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	118	PHE	0	0.010	-0.007	18.757	0.015	0.015	0.000	0.000	0.000	0.000
31	C	119	LEU	0	-0.007	0.019	10.948	-0.011	-0.011	0.000	0.000	0.000	0.000
32	C	120	GLN	0	0.047	0.005	15.035	-0.046	-0.046	0.000	0.000	0.000	0.000
33	C	121	CYS	0	-0.055	-0.028	9.920	-0.085	-0.085	0.000	0.000	0.000	0.000
34	C	122	ASN	0	0.022	-0.020	12.176	0.047	0.047	0.000	0.000	0.000	0.000
35	C	123	ALA	0	0.001	0.008	13.924	0.056	0.056	0.000	0.000	0.000	0.000
36	C	124	GLU	-1	-0.869	-0.924	16.703	-0.413	-0.413	0.000	0.000	0.000	0.000
37	C	125	SER	0	0.001	-0.020	17.183	-0.025	-0.025	0.000	0.000	0.000	0.000
38	C	126	ASP	-1	-0.901	-0.940	19.146	-0.247	-0.247	0.000	0.000	0.000	0.000
39	C	127	SER	0	-0.031	0.012	17.411	0.014	0.014	0.000	0.000	0.000	0.000
40	C	128	THR	0	-0.018	-0.033	19.722	-0.012	-0.012	0.000	0.000	0.000	0.000
41	C	129	SER	0	-0.029	-0.026	17.802	0.012	0.012	0.000	0.000	0.000	0.000
42	C	130	TRP	0	-0.024	0.030	11.999	-0.023	-0.023	0.000	0.000	0.000	0.000
43	C	131	SER	0	-0.006	-0.017	13.203	0.028	0.028	0.000	0.000	0.000	0.000
44	C	132	CYS	0	-0.028	-0.016	7.197	-0.143	-0.143	0.000	0.000	0.000	0.000
45	C	133	HIS	0	-0.025	0.006	9.609	0.035	0.035	0.000	0.000	0.000	0.000
46	C	134	ALA	0	0.014	0.010	8.042	-0.223	-0.223	0.000	0.000	0.000	0.000
47	C	135	GLN	0	0.056	0.034	8.655	0.262	0.262	0.000	0.000	0.000	0.000
48	C	136	ALA	0	0.025	-0.005	9.407	-0.254	-0.254	0.000	0.000	0.000	0.000
49	C	137	VAL	0	-0.054	-0.032	11.742	0.132	0.132	0.000	0.000	0.000	0.000
50	C	138	LEU	0	0.022	0.031	14.447	-0.034	-0.034	0.000	0.000	0.000	0.000
51	C	139	LYS	1	0.921	0.959	16.923	0.183	0.183	0.000	0.000	0.000	0.000
52	C	140	ILE	0	0.019	0.018	19.454	-0.020	-0.020	0.000	0.000	0.000	0.000
53	C	141	ILE	0	-0.070	-0.039	19.203	0.020	0.020	0.000	0.000	0.000	0.000
54	C	142	ASN	0	0.037	0.030	22.954	0.020	0.020	0.000	0.000	0.000	0.000
55	C	150	PHE	0	-0.002	0.000	23.894	0.001	0.001	0.000	0.000	0.000	0.000
56	C	151	SER	0	0.030	-0.005	18.777	-0.026	-0.026	0.000	0.000	0.000	0.000
57	C	152	ARG	1	0.814	0.941	19.506	0.164	0.164	0.000	0.000	0.000	0.000
58	C	153	ARG	1	0.943	0.969	14.794	0.058	0.058	0.000	0.000	0.000	0.000
59	C	154	ILE	0	-0.004	0.009	13.965	0.033	0.033	0.000	0.000	0.000	0.000
60	C	155	SER	0	0.030	0.005	13.171	-0.033	-0.033	0.000	0.000	0.000	0.000
61	C	156	HIS	1	0.742	0.895	12.899	0.445	0.445	0.000	0.000	0.000	0.000
62	C	157	LEU	0	0.072	0.042	12.434	-0.101	-0.101	0.000	0.000	0.000	0.000
63	C	158	PHE	0	-0.015	-0.011	11.488	0.045	0.045	0.000	0.000	0.000	0.000
64	C	159	PHE	0	0.042	0.011	13.623	-0.006	-0.006	0.000	0.000	0.000	0.000
65	C	160	HIS	0	0.097	0.043	16.102	-0.006	-0.006	0.000	0.000	0.000	0.000
66	C	161	LYS	1	0.888	0.943	18.964	0.210	0.210	0.000	0.000	0.000	0.000
67	C	162	GLU	-1	-0.877	-0.934	18.614	-0.231	-0.231	0.000	0.000	0.000	0.000
68	C	163	ASN	0	-0.022	0.008	15.914	-0.047	-0.047	0.000	0.000	0.000	0.000
69	C	164	ASP	-1	-0.797	-0.926	15.658	-0.437	-0.437	0.000	0.000	0.000	0.000
70	C	165	TRP	0	-0.006	-0.004	15.882	0.038	0.038	0.000	0.000	0.000	0.000
71	C	166	GLY	0	0.033	0.005	16.808	-0.044	-0.044	0.000	0.000	0.000	0.000
72	C	167	PHE	0	-0.026	-0.004	19.108	0.035	0.035	0.000	0.000	0.000	0.000
73	C	168	SER	0	0.048	0.017	22.810	-0.003	-0.003	0.000	0.000	0.000	0.000
74	C	169	ASN	0	-0.025	-0.031	25.860	0.012	0.012	0.000	0.000	0.000	0.000
75	C	170	PHE	0	-0.024	0.005	20.361	0.007	0.007	0.000	0.000	0.000	0.000
76	C	171	MET	0	0.039	0.005	25.138	0.008	0.008	0.000	0.000	0.000	0.000
77	C	172	ALA	0	0.064	0.046	28.199	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	173	TRP	0	0.032	0.000	28.931	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	174	SER	0	-0.046	-0.026	32.284	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	175	GLU	-1	-1.003	-0.988	30.804	-0.071	-0.071	0.000	0.000	0.000	0.000
81	C	176	VAL	0	0.013	0.000	27.162	0.002	0.002	0.000	0.000	0.000	0.000
82	C	188	LYS	1	0.935	0.946	27.164	0.105	0.105	0.000	0.000	0.000	0.000
83	C	189	VAL	0	0.057	0.032	24.915	0.009	0.009	0.000	0.000	0.000	0.000
84	C	190	THR	0	-0.066	-0.014	21.021	-0.019	-0.019	0.000	0.000	0.000	0.000
85	C	191	PHE	0	0.036	0.007	19.178	0.018	0.018	0.000	0.000	0.000	0.000
86	C	192	GLU	-1	-0.884	-0.972	14.976	-0.204	-0.204	0.000	0.000	0.000	0.000
87	C	193	VAL	0	0.007	0.006	11.409	0.026	0.026	0.000	0.000	0.000	0.000
88	C	194	PHE	0	-0.020	0.010	7.323	-0.119	-0.119	0.000	0.000	0.000	0.000
89	C	195	VAL	0	0.006	0.016	6.730	0.178	0.178	0.000	0.000	0.000	0.000
90	C	196	GLN	0	-0.028	-0.026	4.729	-1.213	-1.074	-0.001	-0.028	-0.109	0.000
91	C	197	ALA	0	0.011	-0.007	3.886	0.700	1.087	0.000	-0.131	-0.257	0.000
92	C	198	ASP	-1	-0.824	-0.892	3.341	-3.149	-1.708	0.080	-0.825	-0.696	-0.005
93	C	199	ALA	0	-0.071	-0.052	5.471	-0.306	-0.306	0.000	0.000	0.000	0.000
94	C	200	PRO	0	-0.009	-0.004	5.819	0.062	0.062	0.000	0.000	0.000	0.000
95	C	201	HIS	0	0.050	0.012	8.647	0.096	0.096	0.000	0.000	0.000	0.000
96	C	202	GLY	0	0.041	0.003	12.344	-0.033	-0.033	0.000	0.000	0.000	0.000
97	C	203	VAL	0	-0.059	-0.012	10.666	-0.002	-0.002	0.000	0.000	0.000	0.000
98	C	204	ALA	0	-0.013	-0.006	13.832	0.024	0.024	0.000	0.000	0.000	0.000

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