FMO DATABASE

FMODB ID: 436JN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-900941.569292
FMO2-HF: Nuclear repulsion	856383.373098
FMO2-HF: Total energy	-44558.196195
FMO2-MP2: Total energy	-44686.838152

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.
-4.53	-2.883	2.264	0.709	-4.616	-0.006

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 : 0.012 / q_NPA : -0.002

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	0.050	0.003	3.066	1.022	-0.573	0.012	2.788	-1.205	0.003
4	A	68	GLU	-1	-0.872	-0.927	5.304	0.843	0.969	-0.001	-0.002	-0.122	0.000
5	A	69	ALA	0	-0.027	-0.024	7.556	0.707	0.707	0.000	0.000	0.000	0.000
6	A	70	THR	0	0.037	0.032	10.071	-0.283	-0.283	0.000	0.000	0.000	0.000
7	A	71	PHE	0	-0.021	-0.012	12.426	0.105	0.105	0.000	0.000	0.000	0.000
8	A	72	GLN	0	0.056	0.000	14.449	-0.115	-0.115	0.000	0.000	0.000	0.000
9	A	73	PHE	0	-0.015	-0.005	17.942	0.029	0.029	0.000	0.000	0.000	0.000
10	A	74	THR	0	-0.026	-0.025	19.976	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	75	VAL	0	-0.018	0.014	23.541	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	76	GLU	-1	-0.776	-0.935	26.031	0.270	0.270	0.000	0.000	0.000	0.000
13	A	77	ARG	1	0.832	0.915	29.044	-0.194	-0.194	0.000	0.000	0.000	0.000
14	A	78	PHE	0	0.069	0.042	28.039	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	79	SER	0	-0.028	-0.022	31.389	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	80	ARG	1	0.925	0.942	35.021	-0.175	-0.175	0.000	0.000	0.000	0.000
17	A	81	LEU	0	0.028	0.037	33.076	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	82	SER	0	-0.048	-0.037	32.309	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	83	GLU	-1	-0.838	-0.919	27.544	0.265	0.265	0.000	0.000	0.000	0.000
20	A	84	SER	0	-0.012	0.003	22.782	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	85	VAL	0	0.024	0.011	23.852	0.025	0.025	0.000	0.000	0.000	0.000
22	A	86	LEU	0	0.006	0.011	19.001	0.031	0.031	0.000	0.000	0.000	0.000
23	A	87	SER	0	0.022	0.022	16.219	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	88	PRO	0	0.002	-0.012	15.208	0.025	0.025	0.000	0.000	0.000	0.000
25	A	89	PRO	0	0.010	0.010	10.930	0.081	0.081	0.000	0.000	0.000	0.000
26	A	90	CYS	0	-0.053	-0.015	9.645	0.265	0.265	0.000	0.000	0.000	0.000
27	A	91	PHE	0	0.036	-0.004	4.815	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	92	VAL	0	0.011	0.016	4.640	2.114	2.290	-0.001	-0.018	-0.156	0.000
29	A	93	ARG	1	0.878	0.956	3.039	-2.612	-1.977	0.124	-0.189	-0.569	0.000
30	A	94	ASN	0	-0.026	-0.035	2.194	-5.253	-3.079	2.121	-1.805	-2.490	-0.009
31	A	95	LEU	0	0.034	0.048	4.011	-1.165	-1.034	0.009	-0.065	-0.074	0.000
32	A	96	PRO	0	-0.010	0.022	7.449	0.805	0.805	0.000	0.000	0.000	0.000
33	A	97	TRP	0	0.065	-0.006	7.483	-0.644	-0.644	0.000	0.000	0.000	0.000
34	A	98	LYS	1	0.813	0.912	11.794	-0.931	-0.931	0.000	0.000	0.000	0.000
35	A	99	ILE	0	0.015	0.019	15.101	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	100	MET	0	-0.012	0.001	18.160	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	101	VAL	0	-0.029	-0.005	21.484	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	102	MET	0	0.024	0.014	24.808	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	103	PRO	0	0.040	0.030	28.299	0.000	0.000	0.000	0.000	0.000	0.000
40	A	104	ARG	1	0.995	0.998	30.268	-0.210	-0.210	0.000	0.000	0.000	0.000
41	A	115	VAL	0	-0.030	-0.018	28.223	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	116	GLY	0	-0.022	-0.032	27.813	0.006	0.006	0.000	0.000	0.000	0.000
43	A	117	PHE	0	-0.032	-0.034	20.042	0.011	0.011	0.000	0.000	0.000	0.000
44	A	118	PHE	0	-0.040	-0.026	21.357	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	119	LEU	0	-0.011	0.009	13.714	0.030	0.030	0.000	0.000	0.000	0.000
46	A	120	GLN	0	0.070	0.021	16.326	0.021	0.021	0.000	0.000	0.000	0.000
47	A	121	CYS	0	-0.061	-0.023	10.984	0.217	0.217	0.000	0.000	0.000	0.000
48	A	122	ASN	0	0.045	-0.007	11.774	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	123	ALA	0	-0.014	-0.008	13.143	-0.084	-0.084	0.000	0.000	0.000	0.000
50	A	124	GLU	-1	-0.937	-0.955	14.614	0.497	0.497	0.000	0.000	0.000	0.000
51	A	125	SER	0	-0.071	-0.027	14.274	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	126	ASP	-1	-0.879	-0.918	16.205	0.228	0.228	0.000	0.000	0.000	0.000
53	A	127	SER	0	-0.022	-0.013	15.602	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	128	THR	0	-0.015	-0.052	17.915	0.027	0.027	0.000	0.000	0.000	0.000
55	A	129	SER	0	-0.010	0.002	17.138	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	130	TRP	0	-0.017	0.027	12.426	0.049	0.049	0.000	0.000	0.000	0.000
57	A	131	SER	0	0.029	-0.008	13.237	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	132	CYS	0	-0.070	-0.022	9.597	0.135	0.135	0.000	0.000	0.000	0.000
59	A	133	HIS	0	0.011	0.018	12.019	0.028	0.028	0.000	0.000	0.000	0.000
60	A	134	ALA	0	0.031	0.023	11.602	0.081	0.081	0.000	0.000	0.000	0.000
61	A	135	GLN	0	-0.014	-0.001	13.379	-0.182	-0.182	0.000	0.000	0.000	0.000
62	A	136	ALA	0	0.018	0.001	14.867	0.105	0.105	0.000	0.000	0.000	0.000
63	A	137	VAL	0	-0.043	-0.013	16.585	-0.112	-0.112	0.000	0.000	0.000	0.000
64	A	138	LEU	0	0.003	0.007	18.550	0.056	0.056	0.000	0.000	0.000	0.000
65	A	139	LYS	1	0.930	0.951	20.677	-0.595	-0.595	0.000	0.000	0.000	0.000
66	A	140	ILE	0	0.015	0.042	22.489	0.037	0.037	0.000	0.000	0.000	0.000
67	A	141	ILE	0	-0.047	-0.032	24.060	-0.036	-0.036	0.000	0.000	0.000	0.000
68	A	150	PHE	0	0.072	0.017	23.711	0.005	0.005	0.000	0.000	0.000	0.000
69	A	151	SER	0	-0.042	-0.027	22.961	0.037	0.037	0.000	0.000	0.000	0.000
70	A	152	ARG	1	0.905	0.952	23.627	-0.367	-0.367	0.000	0.000	0.000	0.000
71	A	153	ARG	1	0.922	0.968	19.914	-0.437	-0.437	0.000	0.000	0.000	0.000
72	A	154	ILE	0	-0.013	0.000	17.789	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	155	SER	0	0.029	-0.017	18.185	0.051	0.051	0.000	0.000	0.000	0.000
74	A	156	HIS	1	0.777	0.912	17.251	-0.597	-0.597	0.000	0.000	0.000	0.000
75	A	157	LEU	0	0.100	0.067	15.386	0.076	0.076	0.000	0.000	0.000	0.000
76	A	158	PHE	0	-0.067	-0.018	14.112	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	159	PHE	0	0.084	0.004	15.250	0.006	0.006	0.000	0.000	0.000	0.000
78	A	160	HIS	0	0.001	0.007	16.979	0.036	0.036	0.000	0.000	0.000	0.000
79	A	161	LYS	1	0.954	0.976	19.283	-0.240	-0.240	0.000	0.000	0.000	0.000
80	A	162	GLU	-1	-0.890	-0.929	20.185	0.357	0.357	0.000	0.000	0.000	0.000
81	A	163	ASN	0	0.035	0.006	16.243	0.102	0.102	0.000	0.000	0.000	0.000
82	A	164	ASP	-1	-0.828	-0.926	17.005	0.622	0.622	0.000	0.000	0.000	0.000
83	A	165	TRP	0	-0.027	-0.019	19.100	-0.051	-0.051	0.000	0.000	0.000	0.000
84	A	166	GLY	0	0.014	-0.005	20.119	0.057	0.057	0.000	0.000	0.000	0.000
85	A	167	PHE	0	-0.043	-0.003	22.634	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	168	SER	0	0.081	0.035	26.223	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	169	ASN	0	-0.031	-0.018	28.813	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	170	PHE	0	-0.050	-0.013	24.206	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	171	MET	0	0.011	-0.009	28.713	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	172	ALA	0	0.028	0.030	31.683	0.000	0.000	0.000	0.000	0.000	0.000
91	A	173	TRP	0	-0.003	0.001	30.760	0.003	0.003	0.000	0.000	0.000	0.000
92	A	188	LYS	1	0.937	0.990	27.077	-0.295	-0.295	0.000	0.000	0.000	0.000
93	A	189	VAL	0	-0.050	-0.036	27.073	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	190	THR	0	0.034	0.039	22.116	0.006	0.006	0.000	0.000	0.000	0.000
95	A	191	PHE	0	0.008	0.028	21.378	-0.026	-0.026	0.000	0.000	0.000	0.000
96	A	192	GLU	-1	-0.913	-0.967	17.950	0.693	0.693	0.000	0.000	0.000	0.000
97	A	193	VAL	0	-0.006	-0.001	14.725	-0.076	-0.076	0.000	0.000	0.000	0.000
98	A	194	PHE	0	-0.017	0.013	11.501	0.117	0.117	0.000	0.000	0.000	0.000
99	A	195	VAL	0	0.010	0.004	9.994	-0.155	-0.155	0.000	0.000	0.000	0.000
100	A	196	GLN	0	-0.025	-0.026	10.540	0.222	0.222	0.000	0.000	0.000	0.000
101	A	197	ALA	0	0.009	-0.006	8.130	-0.134	-0.134	0.000	0.000	0.000	0.000
102	A	198	ASP	-1	-0.864	-0.938	9.367	0.641	0.641	0.000	0.000	0.000	0.000
103	A	199	ALA	0	-0.057	-0.052	7.642	0.142	0.142	0.000	0.000	0.000	0.000
104	A	200	PRO	0	0.012	-0.003	6.934	-0.044	-0.044	0.000	0.000	0.000	0.000
105	A	201	HIS	0	0.012	0.004	9.750	-0.053	-0.053	0.000	0.000	0.000	0.000
106	A	202	GLY	0	0.038	0.027	12.397	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	203	VAL	0	-0.042	-0.013	9.108	-0.021	-0.021	0.000	0.000	0.000	0.000

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