FMO DATABASE

FMODB ID: ZYLVN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-758001.415793
FMO2-HF: Nuclear repulsion	717696.087025
FMO2-HF: Total energy	-40305.328768
FMO2-MP2: Total energy	-40420.713009

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.
-7.817	0.052	3.513	-5.194	-6.187	-0.008

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 : -0.001 / q_NPA : 0.000

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	0.005	0.007	3.859	-0.486	1.925	-0.021	-1.455	-0.935	0.004
4	C	70	THR	0	0.008	-0.001	6.832	-0.123	-0.123	0.000	0.000	0.000	0.000
5	C	71	PHE	0	-0.020	-0.001	10.409	0.100	0.100	0.000	0.000	0.000	0.000
6	C	72	GLN	0	0.006	-0.027	12.948	0.019	0.019	0.000	0.000	0.000	0.000
7	C	73	PHE	0	0.000	0.005	16.603	-0.001	-0.001	0.000	0.000	0.000	0.000
8	C	74	THR	0	-0.002	0.002	19.241	0.018	0.018	0.000	0.000	0.000	0.000
9	C	85	VAL	0	0.023	-0.001	24.307	0.004	0.004	0.000	0.000	0.000	0.000
10	C	86	LEU	0	0.000	-0.008	18.703	-0.022	-0.022	0.000	0.000	0.000	0.000
11	C	87	SER	0	-0.009	0.005	15.538	0.007	0.007	0.000	0.000	0.000	0.000
12	C	88	PRO	0	0.015	-0.003	16.371	0.006	0.006	0.000	0.000	0.000	0.000
13	C	89	PRO	0	-0.016	0.002	12.660	-0.047	-0.047	0.000	0.000	0.000	0.000
14	C	90	CYS	0	-0.013	0.014	9.014	0.005	0.005	0.000	0.000	0.000	0.000
15	C	91	PHE	0	0.023	-0.005	8.042	-0.121	-0.121	0.000	0.000	0.000	0.000
16	C	92	VAL	0	0.028	0.017	2.775	-1.241	-0.533	0.221	-0.314	-0.615	-0.003
17	C	93	ARG	1	0.820	0.897	2.577	-2.987	-0.404	3.150	-2.387	-3.347	-0.003
18	C	94	ASN	0	-0.010	-0.012	4.052	0.023	0.144	0.001	-0.038	-0.084	0.000
19	C	95	LEU	0	0.039	0.045	6.928	0.028	0.028	0.000	0.000	0.000	0.000
20	C	96	PRO	0	-0.011	0.001	8.131	-0.229	-0.229	0.000	0.000	0.000	0.000
21	C	97	TRP	0	0.038	-0.004	6.449	-0.076	-0.076	0.000	0.000	0.000	0.000
22	C	98	LYS	1	0.782	0.873	10.914	0.366	0.366	0.000	0.000	0.000	0.000
23	C	99	ILE	0	-0.010	0.013	14.230	-0.017	-0.017	0.000	0.000	0.000	0.000
24	C	100	MET	0	-0.026	-0.006	16.589	0.053	0.053	0.000	0.000	0.000	0.000
25	C	101	VAL	0	-0.004	-0.009	19.933	-0.012	-0.012	0.000	0.000	0.000	0.000
26	C	102	MET	0	-0.021	-0.002	23.197	0.017	0.017	0.000	0.000	0.000	0.000
27	C	115	VAL	0	0.038	0.022	28.303	0.006	0.006	0.000	0.000	0.000	0.000
28	C	116	GLY	0	-0.056	-0.014	25.449	-0.011	-0.011	0.000	0.000	0.000	0.000
29	C	117	PHE	0	-0.040	-0.026	17.935	0.005	0.005	0.000	0.000	0.000	0.000
30	C	118	PHE	0	-0.015	-0.013	18.781	0.003	0.003	0.000	0.000	0.000	0.000
31	C	119	LEU	0	-0.009	0.008	11.054	-0.016	-0.016	0.000	0.000	0.000	0.000
32	C	120	GLN	0	0.027	0.007	15.049	-0.035	-0.035	0.000	0.000	0.000	0.000
33	C	121	CYS	0	-0.059	-0.033	9.696	-0.077	-0.077	0.000	0.000	0.000	0.000
34	C	122	ASN	0	0.035	-0.007	11.921	0.090	0.090	0.000	0.000	0.000	0.000
35	C	123	ALA	0	0.040	0.019	13.723	0.051	0.051	0.000	0.000	0.000	0.000
36	C	124	GLU	-1	-0.870	-0.898	16.931	-0.246	-0.246	0.000	0.000	0.000	0.000
37	C	125	SER	0	0.002	-0.011	16.488	0.031	0.031	0.000	0.000	0.000	0.000
38	C	126	ASP	-1	-0.923	-0.949	18.496	-0.089	-0.089	0.000	0.000	0.000	0.000
39	C	127	SER	0	-0.019	-0.004	17.703	0.002	0.002	0.000	0.000	0.000	0.000
40	C	128	THR	0	-0.011	-0.028	19.341	-0.018	-0.018	0.000	0.000	0.000	0.000
41	C	129	SER	0	-0.025	-0.014	18.093	-0.010	-0.010	0.000	0.000	0.000	0.000
42	C	130	TRP	0	-0.053	0.008	12.311	-0.016	-0.016	0.000	0.000	0.000	0.000
43	C	131	SER	0	0.027	-0.007	13.335	-0.031	-0.031	0.000	0.000	0.000	0.000
44	C	132	CYS	0	-0.038	-0.016	7.184	-0.069	-0.069	0.000	0.000	0.000	0.000
45	C	133	HIS	0	-0.026	0.002	9.390	0.037	0.037	0.000	0.000	0.000	0.000
46	C	134	ALA	0	0.039	0.018	7.645	-0.323	-0.323	0.000	0.000	0.000	0.000
47	C	135	GLN	0	0.044	0.038	8.548	0.466	0.466	0.000	0.000	0.000	0.000
48	C	136	ALA	0	0.019	-0.004	9.245	-0.334	-0.334	0.000	0.000	0.000	0.000
49	C	137	VAL	0	-0.041	-0.036	11.700	0.181	0.181	0.000	0.000	0.000	0.000
50	C	138	LEU	0	0.047	0.052	14.318	-0.011	-0.011	0.000	0.000	0.000	0.000
51	C	139	LYS	1	0.841	0.907	16.775	0.302	0.302	0.000	0.000	0.000	0.000
52	C	140	ILE	0	0.027	0.027	19.444	-0.009	-0.009	0.000	0.000	0.000	0.000
53	C	141	ILE	0	-0.038	-0.005	19.350	0.014	0.014	0.000	0.000	0.000	0.000
54	C	142	ASN	0	-0.018	-0.008	23.144	0.026	0.026	0.000	0.000	0.000	0.000
55	C	150	PHE	0	0.030	0.012	23.658	-0.004	-0.004	0.000	0.000	0.000	0.000
56	C	151	SER	0	0.036	-0.001	18.375	-0.012	-0.012	0.000	0.000	0.000	0.000
57	C	152	ARG	1	0.796	0.918	19.301	0.275	0.275	0.000	0.000	0.000	0.000
58	C	153	ARG	1	0.913	0.955	14.693	0.392	0.392	0.000	0.000	0.000	0.000
59	C	154	ILE	0	-0.014	0.003	13.887	0.063	0.063	0.000	0.000	0.000	0.000
60	C	155	SER	0	0.019	-0.006	12.634	-0.129	-0.129	0.000	0.000	0.000	0.000
61	C	156	HIS	1	0.755	0.907	12.674	0.552	0.552	0.000	0.000	0.000	0.000
62	C	157	LEU	0	0.035	0.020	12.198	-0.125	-0.125	0.000	0.000	0.000	0.000
63	C	158	PHE	0	0.004	0.002	11.167	0.057	0.057	0.000	0.000	0.000	0.000
64	C	159	PHE	0	0.072	0.016	13.456	0.027	0.027	0.000	0.000	0.000	0.000
65	C	160	HIS	0	0.092	0.055	16.033	-0.023	-0.023	0.000	0.000	0.000	0.000
66	C	161	LYS	1	0.807	0.904	18.941	0.190	0.190	0.000	0.000	0.000	0.000
67	C	162	GLU	-1	-0.872	-0.933	18.536	-0.243	-0.243	0.000	0.000	0.000	0.000
68	C	163	ASN	0	0.013	0.011	16.134	-0.063	-0.063	0.000	0.000	0.000	0.000
69	C	164	ASP	-1	-0.796	-0.919	15.820	-0.447	-0.447	0.000	0.000	0.000	0.000
70	C	165	TRP	0	-0.005	-0.008	15.839	0.029	0.029	0.000	0.000	0.000	0.000
71	C	166	GLY	0	0.032	0.003	17.094	-0.052	-0.052	0.000	0.000	0.000	0.000
72	C	167	PHE	0	-0.031	-0.011	19.289	0.032	0.032	0.000	0.000	0.000	0.000
73	C	168	SER	0	0.065	0.016	22.865	0.000	0.000	0.000	0.000	0.000	0.000
74	C	169	ASN	0	-0.012	-0.009	26.035	0.014	0.014	0.000	0.000	0.000	0.000
75	C	170	PHE	0	-0.016	-0.004	20.106	0.000	0.000	0.000	0.000	0.000	0.000
76	C	171	MET	0	0.018	0.008	25.295	-0.007	-0.007	0.000	0.000	0.000	0.000
77	C	172	ALA	0	0.047	0.034	28.116	0.001	0.001	0.000	0.000	0.000	0.000
78	C	173	TRP	0	0.033	-0.010	29.552	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	174	SER	0	-0.055	-0.022	32.687	0.002	0.002	0.000	0.000	0.000	0.000
80	C	175	GLU	-1	-0.924	-0.952	30.383	-0.143	-0.143	0.000	0.000	0.000	0.000
81	C	176	VAL	0	-0.025	-0.009	27.408	0.002	0.002	0.000	0.000	0.000	0.000
82	C	188	LYS	1	0.981	0.986	28.177	0.113	0.113	0.000	0.000	0.000	0.000
83	C	189	VAL	0	0.014	0.004	25.163	0.005	0.005	0.000	0.000	0.000	0.000
84	C	190	THR	0	-0.029	0.000	21.204	-0.011	-0.011	0.000	0.000	0.000	0.000
85	C	191	PHE	0	0.027	0.006	19.774	0.010	0.010	0.000	0.000	0.000	0.000
86	C	192	GLU	-1	-0.858	-0.936	15.494	-0.329	-0.329	0.000	0.000	0.000	0.000
87	C	193	VAL	0	0.018	0.003	11.219	0.016	0.016	0.000	0.000	0.000	0.000
88	C	194	PHE	0	-0.009	0.022	7.216	-0.095	-0.095	0.000	0.000	0.000	0.000
89	C	195	VAL	0	-0.010	-0.018	6.817	0.166	0.166	0.000	0.000	0.000	0.000
90	C	196	GLN	0	-0.039	-0.037	4.312	-0.557	-0.504	-0.001	-0.025	-0.027	0.000
91	C	197	ALA	0	0.031	0.011	3.718	0.883	1.487	0.003	-0.275	-0.332	0.001
92	C	198	ASP	-1	-0.819	-0.890	3.034	-3.666	-2.319	0.161	-0.696	-0.811	-0.007
93	C	199	ALA	0	-0.047	-0.040	5.087	0.135	0.177	-0.001	-0.004	-0.036	0.000
94	C	200	PRO	0	-0.017	-0.009	6.157	-0.203	-0.203	0.000	0.000	0.000	0.000
95	C	201	HIS	0	0.015	0.000	8.917	0.173	0.173	0.000	0.000	0.000	0.000
96	C	202	GLY	0	0.033	0.011	12.602	-0.043	-0.043	0.000	0.000	0.000	0.000
97	C	203	VAL	0	-0.014	0.002	11.066	-0.027	-0.027	0.000	0.000	0.000	0.000
98	C	204	ALA	0	-0.011	0.008	14.263	0.026	0.026	0.000	0.000	0.000	0.000

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