FMO DATABASE

FMODB ID: 53YJZ

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	OptHSide
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	-900248.636422
FMO2-HF: Nuclear repulsion	855689.438204
FMO2-HF: Total energy	-44559.198218
FMO2-MP2: Total energy	-44687.729721

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.
-10.69	-7.283	5.49	-2.93	-5.97	-0.025

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 : 0.018 / q_NPA : 0.003

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	0.053	0.002	3.532	-1.717	-0.873	0.018	0.154	-1.017	0.004
4	A	68	GLU	-1	-0.868	-0.932	5.611	0.861	0.861	0.000	0.000	0.000	0.000
5	A	69	ALA	0	-0.018	-0.013	8.089	0.769	0.769	0.000	0.000	0.000	0.000
6	A	70	THR	0	0.025	0.014	10.071	-0.244	-0.244	0.000	0.000	0.000	0.000
7	A	71	PHE	0	-0.009	-0.001	12.472	0.098	0.098	0.000	0.000	0.000	0.000
8	A	72	GLN	0	0.020	-0.022	14.449	-0.113	-0.113	0.000	0.000	0.000	0.000
9	A	73	PHE	0	-0.007	-0.002	17.942	0.018	0.018	0.000	0.000	0.000	0.000
10	A	74	THR	0	-0.021	-0.027	19.976	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	75	VAL	0	0.001	0.022	23.541	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	76	GLU	-1	-0.708	-0.861	26.031	0.216	0.216	0.000	0.000	0.000	0.000
13	A	77	ARG	1	0.870	0.929	29.044	-0.143	-0.143	0.000	0.000	0.000	0.000
14	A	78	PHE	0	0.068	0.046	28.831	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	79	SER	0	0.004	-0.019	31.389	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	80	ARG	1	0.915	0.955	35.020	-0.139	-0.139	0.000	0.000	0.000	0.000
17	A	81	LEU	0	0.002	0.019	32.914	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	82	SER	0	-0.046	-0.035	32.413	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	83	GLU	-1	-0.842	-0.921	27.611	0.199	0.199	0.000	0.000	0.000	0.000
20	A	84	SER	0	-0.013	0.000	22.703	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	85	VAL	0	0.024	0.008	24.020	0.021	0.021	0.000	0.000	0.000	0.000
22	A	86	LEU	0	0.004	0.015	19.137	0.026	0.026	0.000	0.000	0.000	0.000
23	A	87	SER	0	0.015	0.026	16.063	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	88	PRO	0	0.010	-0.013	14.975	0.001	0.001	0.000	0.000	0.000	0.000
25	A	89	PRO	0	0.013	0.010	10.826	0.078	0.078	0.000	0.000	0.000	0.000
26	A	90	CYS	0	-0.063	-0.017	9.645	0.271	0.271	0.000	0.000	0.000	0.000
27	A	91	PHE	0	0.049	0.005	4.773	-0.136	-0.066	-0.001	-0.004	-0.066	0.000
28	A	92	VAL	0	0.007	0.025	4.636	2.219	2.385	-0.001	-0.019	-0.146	0.000
29	A	93	ARG	1	0.863	0.944	3.010	-2.591	-1.956	0.127	-0.201	-0.562	0.000
30	A	94	ASN	0	0.017	-0.010	2.016	-9.211	-7.638	5.339	-2.801	-4.111	-0.029
31	A	95	LEU	0	0.021	0.042	3.992	-0.798	-0.679	0.008	-0.059	-0.068	0.000
32	A	96	PRO	0	-0.006	0.013	7.351	0.778	0.778	0.000	0.000	0.000	0.000
33	A	97	TRP	0	0.058	0.002	7.571	-0.464	-0.464	0.000	0.000	0.000	0.000
34	A	98	LYS	1	0.815	0.904	11.728	-0.470	-0.470	0.000	0.000	0.000	0.000
35	A	99	ILE	0	0.004	0.013	15.049	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	100	MET	0	0.000	0.004	18.160	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	101	VAL	0	-0.046	-0.012	21.474	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	102	MET	0	0.024	0.003	24.808	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	103	PRO	0	0.025	0.025	28.299	0.003	0.003	0.000	0.000	0.000	0.000
40	A	104	ARG	1	0.999	1.003	30.266	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	115	VAL	0	-0.025	-0.018	28.043	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	116	GLY	0	-0.039	-0.031	27.813	0.007	0.007	0.000	0.000	0.000	0.000
43	A	117	PHE	0	-0.036	-0.035	20.114	0.007	0.007	0.000	0.000	0.000	0.000
44	A	118	PHE	0	-0.022	-0.021	21.282	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	119	LEU	0	-0.015	0.003	13.823	0.028	0.028	0.000	0.000	0.000	0.000
46	A	120	GLN	0	-0.001	-0.032	16.392	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	121	CYS	0	-0.069	-0.029	11.084	0.170	0.170	0.000	0.000	0.000	0.000
48	A	122	ASN	0	0.017	-0.012	11.410	-0.106	-0.106	0.000	0.000	0.000	0.000
49	A	123	ALA	0	-0.002	0.009	13.131	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	124	GLU	-1	-0.860	-0.931	14.164	0.350	0.350	0.000	0.000	0.000	0.000
51	A	125	SER	0	-0.059	-0.016	14.167	-0.056	-0.056	0.000	0.000	0.000	0.000
52	A	126	ASP	-1	-0.870	-0.912	16.114	0.028	0.028	0.000	0.000	0.000	0.000
53	A	127	SER	0	-0.017	-0.008	15.763	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	128	THR	0	-0.010	-0.043	17.902	0.034	0.034	0.000	0.000	0.000	0.000
55	A	129	SER	0	-0.039	-0.015	16.536	0.010	0.010	0.000	0.000	0.000	0.000
56	A	130	TRP	0	-0.024	0.019	12.474	0.026	0.026	0.000	0.000	0.000	0.000
57	A	131	SER	0	0.031	-0.009	13.247	0.004	0.004	0.000	0.000	0.000	0.000
58	A	132	CYS	0	-0.066	-0.027	9.650	0.080	0.080	0.000	0.000	0.000	0.000
59	A	133	HIS	0	0.008	0.019	12.028	0.030	0.030	0.000	0.000	0.000	0.000
60	A	134	ALA	0	0.017	0.014	11.611	0.073	0.073	0.000	0.000	0.000	0.000
61	A	135	GLN	0	-0.007	-0.003	13.394	-0.165	-0.165	0.000	0.000	0.000	0.000
62	A	136	ALA	0	0.015	0.002	14.884	0.105	0.105	0.000	0.000	0.000	0.000
63	A	137	VAL	0	-0.035	-0.010	16.599	-0.102	-0.102	0.000	0.000	0.000	0.000
64	A	138	LEU	0	0.005	0.007	18.340	0.056	0.056	0.000	0.000	0.000	0.000
65	A	139	LYS	1	0.885	0.909	20.633	-0.604	-0.604	0.000	0.000	0.000	0.000
66	A	140	ILE	0	0.003	0.028	22.489	0.029	0.029	0.000	0.000	0.000	0.000
67	A	141	ILE	0	-0.030	-0.023	23.103	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	150	PHE	0	0.091	0.044	24.197	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	151	SER	0	-0.071	-0.056	23.052	0.029	0.029	0.000	0.000	0.000	0.000
70	A	152	ARG	1	0.842	0.920	23.640	-0.306	-0.306	0.000	0.000	0.000	0.000
71	A	153	ARG	1	0.897	0.948	19.642	-0.392	-0.392	0.000	0.000	0.000	0.000
72	A	154	ILE	0	-0.028	-0.002	17.965	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	155	SER	0	0.042	-0.009	18.202	0.054	0.054	0.000	0.000	0.000	0.000
74	A	156	HIS	1	0.759	0.899	17.264	-0.426	-0.426	0.000	0.000	0.000	0.000
75	A	157	LEU	0	0.102	0.069	15.417	0.060	0.060	0.000	0.000	0.000	0.000
76	A	158	PHE	0	-0.053	-0.024	14.101	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	159	PHE	0	0.080	0.012	15.254	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	160	HIS	0	0.011	0.014	16.979	0.029	0.029	0.000	0.000	0.000	0.000
79	A	161	LYS	1	0.950	0.976	19.278	-0.125	-0.125	0.000	0.000	0.000	0.000
80	A	162	GLU	-1	-0.896	-0.929	20.183	0.251	0.251	0.000	0.000	0.000	0.000
81	A	163	ASN	0	0.047	0.007	16.396	0.077	0.077	0.000	0.000	0.000	0.000
82	A	164	ASP	-1	-0.802	-0.893	17.003	0.432	0.432	0.000	0.000	0.000	0.000
83	A	165	TRP	0	-0.018	-0.017	19.096	-0.038	-0.038	0.000	0.000	0.000	0.000
84	A	166	GLY	0	0.012	-0.004	20.122	0.052	0.052	0.000	0.000	0.000	0.000
85	A	167	PHE	0	-0.038	0.000	22.638	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	168	SER	0	0.055	0.028	26.227	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	169	ASN	0	-0.019	-0.015	28.815	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	170	PHE	0	-0.020	-0.003	24.245	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	171	MET	0	0.014	0.003	28.717	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	172	ALA	0	0.029	0.035	31.683	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	173	TRP	0	0.008	0.004	30.577	0.005	0.005	0.000	0.000	0.000	0.000
92	A	188	LYS	1	0.792	0.879	27.013	-0.242	-0.242	0.000	0.000	0.000	0.000
93	A	189	VAL	0	-0.025	-0.019	27.216	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	190	THR	0	0.015	0.026	22.114	0.003	0.003	0.000	0.000	0.000	0.000
95	A	191	PHE	0	0.023	0.038	21.512	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	192	GLU	-1	-0.825	-0.903	18.032	0.636	0.636	0.000	0.000	0.000	0.000
97	A	193	VAL	0	0.000	0.001	14.903	-0.071	-0.071	0.000	0.000	0.000	0.000
98	A	194	PHE	0	-0.025	0.009	12.082	0.106	0.106	0.000	0.000	0.000	0.000
99	A	195	VAL	0	0.015	0.005	10.092	-0.150	-0.150	0.000	0.000	0.000	0.000
100	A	196	GLN	0	-0.006	-0.011	10.703	0.204	0.204	0.000	0.000	0.000	0.000
101	A	197	ALA	0	0.017	-0.002	8.152	-0.165	-0.165	0.000	0.000	0.000	0.000
102	A	198	ASP	-1	-0.859	-0.933	9.391	0.479	0.479	0.000	0.000	0.000	0.000
103	A	199	ALA	0	-0.040	-0.040	7.660	0.067	0.067	0.000	0.000	0.000	0.000
104	A	200	PRO	0	0.021	0.008	6.810	0.007	0.007	0.000	0.000	0.000	0.000
105	A	201	HIS	0	-0.003	0.000	9.759	-0.077	-0.077	0.000	0.000	0.000	0.000
106	A	202	GLY	0	0.048	0.033	12.399	0.002	0.002	0.000	0.000	0.000	0.000
107	A	203	VAL	0	-0.027	-0.006	8.622	-0.034	-0.034	0.000	0.000	0.000	0.000

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