FMO DATABASE

FMODB ID: 667YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-760322.660185
FMO2-HF: Nuclear repulsion	720017.751256
FMO2-HF: Total energy	-40304.908929
FMO2-MP2: Total energy	-40420.372404

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.
-5.571	0.756	3.385	-3.87	-5.842	-0.005

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 : 0.017 / 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	C	69	ALA	0	0.003	0.013	3.770	0.096	2.365	-0.020	-1.304	-0.945	0.002
4	C	70	THR	0	0.013	0.002	6.197	-0.154	-0.154	0.000	0.000	0.000	0.000
5	C	71	PHE	0	-0.029	-0.014	9.981	0.231	0.231	0.000	0.000	0.000	0.000
6	C	72	GLN	0	-0.003	-0.029	12.201	0.049	0.049	0.000	0.000	0.000	0.000
7	C	73	PHE	0	0.015	0.014	15.970	0.059	0.059	0.000	0.000	0.000	0.000
8	C	74	THR	0	0.012	0.011	18.684	0.002	0.002	0.000	0.000	0.000	0.000
9	C	85	VAL	0	0.018	-0.004	24.019	0.009	0.009	0.000	0.000	0.000	0.000
10	C	86	LEU	0	0.015	0.003	18.578	-0.034	-0.034	0.000	0.000	0.000	0.000
11	C	87	SER	0	-0.024	0.012	15.445	-0.001	-0.001	0.000	0.000	0.000	0.000
12	C	88	PRO	0	0.007	-0.008	16.063	0.022	0.022	0.000	0.000	0.000	0.000
13	C	89	PRO	0	-0.014	-0.003	12.429	-0.070	-0.070	0.000	0.000	0.000	0.000
14	C	90	CYS	0	-0.033	0.000	8.554	0.063	0.063	0.000	0.000	0.000	0.000
15	C	91	PHE	0	0.015	-0.016	7.836	-0.168	-0.168	0.000	0.000	0.000	0.000
16	C	92	VAL	0	0.042	0.032	2.467	-0.674	-0.109	0.324	-0.148	-0.741	-0.001
17	C	93	ARG	1	0.801	0.887	2.615	-3.902	-2.101	3.019	-1.687	-3.133	-0.003
18	C	94	ASN	0	-0.014	-0.020	4.710	-0.363	-0.314	-0.001	-0.015	-0.034	0.000
19	C	95	LEU	0	0.037	0.049	7.665	-0.242	-0.242	0.000	0.000	0.000	0.000
20	C	96	PRO	0	-0.006	0.000	8.923	-0.111	-0.111	0.000	0.000	0.000	0.000
21	C	97	TRP	0	0.052	0.009	6.934	-0.327	-0.327	0.000	0.000	0.000	0.000
22	C	98	LYS	1	0.819	0.912	11.233	0.113	0.113	0.000	0.000	0.000	0.000
23	C	99	ILE	0	0.003	0.010	14.501	-0.064	-0.064	0.000	0.000	0.000	0.000
24	C	100	MET	0	-0.040	-0.013	16.623	0.080	0.080	0.000	0.000	0.000	0.000
25	C	101	VAL	0	-0.015	-0.009	20.001	-0.037	-0.037	0.000	0.000	0.000	0.000
26	C	102	MET	0	-0.010	0.011	23.021	0.031	0.031	0.000	0.000	0.000	0.000
27	C	115	VAL	0	0.006	0.016	28.056	0.008	0.008	0.000	0.000	0.000	0.000
28	C	116	GLY	0	-0.060	-0.040	25.309	-0.020	-0.020	0.000	0.000	0.000	0.000
29	C	117	PHE	0	-0.020	-0.018	17.561	0.007	0.007	0.000	0.000	0.000	0.000
30	C	118	PHE	0	-0.001	-0.008	18.741	-0.030	-0.030	0.000	0.000	0.000	0.000
31	C	119	LEU	0	0.006	0.025	10.949	-0.029	-0.029	0.000	0.000	0.000	0.000
32	C	120	GLN	0	0.010	-0.012	15.054	0.005	0.005	0.000	0.000	0.000	0.000
33	C	121	CYS	0	-0.060	-0.040	9.722	-0.025	-0.025	0.000	0.000	0.000	0.000
34	C	122	ASN	0	0.031	-0.017	12.176	0.121	0.121	0.000	0.000	0.000	0.000
35	C	123	ALA	0	0.007	0.011	13.929	0.027	0.027	0.000	0.000	0.000	0.000
36	C	124	GLU	-1	-0.859	-0.898	17.245	-0.047	-0.047	0.000	0.000	0.000	0.000
37	C	125	SER	0	0.018	-0.013	17.030	0.072	0.072	0.000	0.000	0.000	0.000
38	C	126	ASP	-1	-0.922	-0.947	19.145	0.099	0.099	0.000	0.000	0.000	0.000
39	C	127	SER	0	-0.010	0.015	17.483	-0.005	-0.005	0.000	0.000	0.000	0.000
40	C	128	THR	0	-0.030	-0.036	19.720	-0.022	-0.022	0.000	0.000	0.000	0.000
41	C	129	SER	0	-0.019	-0.014	17.974	-0.032	-0.032	0.000	0.000	0.000	0.000
42	C	130	TRP	0	-0.022	0.025	11.931	0.025	0.025	0.000	0.000	0.000	0.000
43	C	131	SER	0	0.016	-0.012	13.201	-0.084	-0.084	0.000	0.000	0.000	0.000
44	C	132	CYS	0	-0.057	-0.021	7.346	0.040	0.040	0.000	0.000	0.000	0.000
45	C	133	HIS	0	-0.041	-0.013	9.625	0.013	0.013	0.000	0.000	0.000	0.000
46	C	134	ALA	0	0.021	0.010	7.956	-0.323	-0.323	0.000	0.000	0.000	0.000
47	C	135	GLN	0	0.045	0.028	8.623	0.597	0.597	0.000	0.000	0.000	0.000
48	C	136	ALA	0	0.037	0.000	9.373	-0.485	-0.485	0.000	0.000	0.000	0.000
49	C	137	VAL	0	-0.063	-0.041	11.768	0.299	0.299	0.000	0.000	0.000	0.000
50	C	138	LEU	0	0.026	0.036	14.381	-0.024	-0.024	0.000	0.000	0.000	0.000
51	C	139	LYS	1	0.917	0.953	16.923	0.695	0.695	0.000	0.000	0.000	0.000
52	C	140	ILE	0	0.017	0.023	19.269	0.011	0.011	0.000	0.000	0.000	0.000
53	C	141	ILE	0	-0.064	-0.036	18.829	0.006	0.006	0.000	0.000	0.000	0.000
54	C	142	ASN	0	0.033	0.030	22.729	0.010	0.010	0.000	0.000	0.000	0.000
55	C	150	PHE	0	0.003	-0.003	23.664	-0.017	-0.017	0.000	0.000	0.000	0.000
56	C	151	SER	0	0.035	-0.005	18.390	-0.001	-0.001	0.000	0.000	0.000	0.000
57	C	152	ARG	1	0.811	0.932	19.465	0.488	0.488	0.000	0.000	0.000	0.000
58	C	153	ARG	1	0.940	0.971	14.698	0.920	0.920	0.000	0.000	0.000	0.000
59	C	154	ILE	0	-0.010	0.010	14.035	0.131	0.131	0.000	0.000	0.000	0.000
60	C	155	SER	0	0.028	0.002	13.096	-0.260	-0.260	0.000	0.000	0.000	0.000
61	C	156	HIS	1	0.744	0.897	12.917	0.682	0.682	0.000	0.000	0.000	0.000
62	C	157	LEU	0	0.058	0.039	12.448	-0.135	-0.135	0.000	0.000	0.000	0.000
63	C	158	PHE	0	-0.014	-0.012	11.322	0.078	0.078	0.000	0.000	0.000	0.000
64	C	159	PHE	0	0.068	0.023	13.628	0.074	0.074	0.000	0.000	0.000	0.000
65	C	160	HIS	0	0.103	0.053	16.106	-0.033	-0.033	0.000	0.000	0.000	0.000
66	C	161	LYS	1	0.835	0.933	18.968	0.159	0.159	0.000	0.000	0.000	0.000
67	C	162	GLU	-1	-0.869	-0.946	18.565	-0.288	-0.288	0.000	0.000	0.000	0.000
68	C	163	ASN	0	-0.015	0.005	15.921	-0.084	-0.084	0.000	0.000	0.000	0.000
69	C	164	ASP	-1	-0.773	-0.915	15.671	-0.443	-0.443	0.000	0.000	0.000	0.000
70	C	165	TRP	0	-0.016	-0.006	15.894	0.031	0.031	0.000	0.000	0.000	0.000
71	C	166	GLY	0	0.040	0.004	16.830	-0.086	-0.086	0.000	0.000	0.000	0.000
72	C	167	PHE	0	-0.031	-0.010	19.296	0.035	0.035	0.000	0.000	0.000	0.000
73	C	168	SER	0	0.051	0.015	22.834	0.005	0.005	0.000	0.000	0.000	0.000
74	C	169	ASN	0	-0.013	-0.020	25.883	0.019	0.019	0.000	0.000	0.000	0.000
75	C	170	PHE	0	-0.032	-0.003	20.198	-0.004	-0.004	0.000	0.000	0.000	0.000
76	C	171	MET	0	0.011	0.007	25.164	-0.017	-0.017	0.000	0.000	0.000	0.000
77	C	172	ALA	0	0.066	0.049	28.183	0.015	0.015	0.000	0.000	0.000	0.000
78	C	173	TRP	0	0.040	0.008	29.131	-0.011	-0.011	0.000	0.000	0.000	0.000
79	C	174	SER	0	-0.039	-0.025	32.154	0.004	0.004	0.000	0.000	0.000	0.000
80	C	175	GLU	-1	-0.967	-0.977	30.291	-0.293	-0.293	0.000	0.000	0.000	0.000
81	C	176	VAL	0	-0.018	-0.013	26.936	0.002	0.002	0.000	0.000	0.000	0.000
82	C	188	LYS	1	0.970	0.982	27.214	0.179	0.179	0.000	0.000	0.000	0.000
83	C	189	VAL	0	0.022	-0.002	24.781	-0.002	-0.002	0.000	0.000	0.000	0.000
84	C	190	THR	0	-0.068	-0.018	20.506	-0.007	-0.007	0.000	0.000	0.000	0.000
85	C	191	PHE	0	0.050	0.016	19.184	-0.011	-0.011	0.000	0.000	0.000	0.000
86	C	192	GLU	-1	-0.859	-0.937	14.906	-0.806	-0.806	0.000	0.000	0.000	0.000
87	C	193	VAL	0	0.010	0.004	11.486	0.014	0.014	0.000	0.000	0.000	0.000
88	C	194	PHE	0	-0.032	0.005	6.826	0.163	0.163	0.000	0.000	0.000	0.000
89	C	195	VAL	0	0.003	0.015	6.835	0.176	0.176	0.000	0.000	0.000	0.000
90	C	196	GLN	0	-0.033	-0.037	4.487	0.177	0.273	-0.001	-0.026	-0.069	0.000
91	C	197	ALA	0	0.013	-0.003	3.916	1.343	1.821	0.001	-0.190	-0.288	0.000
92	C	198	ASP	-1	-0.799	-0.869	3.348	-3.710	-2.641	0.063	-0.500	-0.632	-0.003
93	C	199	ALA	0	-0.062	-0.050	5.466	0.500	0.500	0.000	0.000	0.000	0.000
94	C	200	PRO	0	-0.008	-0.010	5.801	-0.310	-0.310	0.000	0.000	0.000	0.000
95	C	201	HIS	0	0.042	0.011	8.638	0.227	0.227	0.000	0.000	0.000	0.000
96	C	202	GLY	0	0.050	0.008	12.333	-0.036	-0.036	0.000	0.000	0.000	0.000
97	C	203	VAL	0	-0.072	-0.022	10.508	-0.031	-0.031	0.000	0.000	0.000	0.000
98	C	204	ALA	0	-0.010	-0.002	13.817	0.075	0.075	0.000	0.000	0.000	0.000

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