FMO DATABASE

FMODB ID: K38G3

Calculation Name: 1YZE-B-Xray372

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZE

Chain ID: B

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-887227.541323
FMO2-HF: Nuclear repulsion	842767.638637
FMO2-HF: Total energy	-44459.902687
FMO2-MP2: Total energy	-44587.710545

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(B:67:SER)

Summations of interaction energy for fragment #1(B: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.
-19.614	-13.091	6.711	-5.468	-7.766	0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.026

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	B	69	ALA	0	0.015	0.008	3.775	-1.162	0.566	-0.014	-0.933	-0.781	0.000
4	B	70	THR	0	0.002	0.001	6.322	0.203	0.203	0.000	0.000	0.000	0.000
5	B	71	PHE	0	-0.019	0.004	9.968	0.080	0.080	0.000	0.000	0.000	0.000
6	B	72	GLN	0	0.037	-0.011	12.293	-0.037	-0.037	0.000	0.000	0.000	0.000
7	B	73	PHE	0	-0.009	-0.008	16.073	0.043	0.043	0.000	0.000	0.000	0.000
8	B	74	THR	0	0.023	-0.003	18.733	-0.020	-0.020	0.000	0.000	0.000	0.000
9	B	75	VAL	0	0.016	0.028	22.506	0.018	0.018	0.000	0.000	0.000	0.000
10	B	76	GLU	-1	-0.807	-0.894	25.025	-0.104	-0.104	0.000	0.000	0.000	0.000
11	B	77	ARG	1	0.760	0.847	28.107	0.083	0.083	0.000	0.000	0.000	0.000
12	B	78	PHE	0	0.063	0.034	27.613	0.008	0.008	0.000	0.000	0.000	0.000
13	B	79	SER	0	-0.055	-0.013	29.932	0.003	0.003	0.000	0.000	0.000	0.000
14	B	80	ARG	1	0.880	0.930	32.252	0.090	0.090	0.000	0.000	0.000	0.000
15	B	81	LEU	0	0.023	0.011	33.276	0.006	0.006	0.000	0.000	0.000	0.000
16	B	82	SER	0	-0.011	0.005	31.115	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	83	GLU	-1	-0.802	-0.910	27.248	-0.094	-0.094	0.000	0.000	0.000	0.000
18	B	84	SER	0	-0.007	-0.010	22.987	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	85	VAL	0	-0.017	-0.006	24.030	0.005	0.005	0.000	0.000	0.000	0.000
20	B	86	LEU	0	-0.003	-0.003	18.415	-0.008	-0.008	0.000	0.000	0.000	0.000
21	B	87	SER	0	0.007	0.012	15.569	-0.015	-0.015	0.000	0.000	0.000	0.000
22	B	88	PRO	0	0.013	-0.010	15.744	0.041	0.041	0.000	0.000	0.000	0.000
23	B	89	PRO	0	-0.023	0.010	12.771	-0.037	-0.037	0.000	0.000	0.000	0.000
24	B	90	CYS	0	-0.011	0.017	8.371	-0.049	-0.049	0.000	0.000	0.000	0.000
25	B	91	PHE	0	0.027	-0.006	7.421	0.105	0.105	0.000	0.000	0.000	0.000
26	B	92	VAL	0	0.030	0.024	3.044	-1.322	-0.224	0.262	-0.425	-0.935	0.004
27	B	93	ARG	1	0.805	0.897	2.576	-17.646	-14.497	6.452	-3.877	-5.725	0.025
28	B	94	ASN	0	-0.007	-0.004	4.278	-2.305	-2.120	0.012	-0.122	-0.074	0.001
29	B	95	LEU	0	0.031	0.029	7.144	-0.613	-0.613	0.000	0.000	0.000	0.000
30	B	96	PRO	0	0.003	0.006	8.451	0.114	0.114	0.000	0.000	0.000	0.000
31	B	97	TRP	0	0.018	-0.022	7.022	-0.377	-0.377	0.000	0.000	0.000	0.000
32	B	98	LYS	1	0.784	0.885	11.239	-0.282	-0.282	0.000	0.000	0.000	0.000
33	B	99	ILE	0	-0.016	0.007	14.347	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	100	MET	0	-0.012	0.000	16.669	0.034	0.034	0.000	0.000	0.000	0.000
35	B	101	VAL	0	-0.009	-0.009	19.978	-0.022	-0.022	0.000	0.000	0.000	0.000
36	B	102	MET	0	0.041	0.015	23.261	0.011	0.011	0.000	0.000	0.000	0.000
37	B	103	PRO	0	0.018	0.018	26.960	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	104	ARG	1	0.956	0.986	29.250	0.036	0.036	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.007	-0.011	25.263	0.003	0.003	0.000	0.000	0.000	0.000
40	B	116	GLY	0	-0.048	-0.007	25.905	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	117	PHE	0	-0.040	-0.032	17.858	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	118	PHE	0	-0.002	-0.006	19.440	-0.014	-0.014	0.000	0.000	0.000	0.000
43	B	119	LEU	0	0.004	0.005	11.806	-0.041	-0.041	0.000	0.000	0.000	0.000
44	B	120	GLN	0	0.039	0.014	15.729	0.009	0.009	0.000	0.000	0.000	0.000
45	B	121	CYS	0	-0.054	-0.038	10.254	0.050	0.050	0.000	0.000	0.000	0.000
46	B	122	ASN	0	0.008	-0.014	12.505	0.049	0.049	0.000	0.000	0.000	0.000
47	B	123	ALA	0	0.006	0.015	14.313	-0.016	-0.016	0.000	0.000	0.000	0.000
48	B	124	GLU	-1	-0.821	-0.903	17.709	0.244	0.244	0.000	0.000	0.000	0.000
49	B	125	SER	0	-0.010	-0.012	17.036	0.082	0.082	0.000	0.000	0.000	0.000
50	B	126	ASP	-1	-0.903	-0.925	19.199	0.252	0.252	0.000	0.000	0.000	0.000
51	B	127	SER	0	-0.043	-0.034	21.216	-0.019	-0.019	0.000	0.000	0.000	0.000
52	B	128	THR	0	0.011	-0.027	20.419	0.029	0.029	0.000	0.000	0.000	0.000
53	B	129	SER	0	-0.039	-0.011	19.610	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	130	TRP	0	0.017	0.052	12.710	0.079	0.079	0.000	0.000	0.000	0.000
55	B	131	SER	0	-0.002	-0.026	13.659	-0.078	-0.078	0.000	0.000	0.000	0.000
56	B	132	CYS	0	-0.025	-0.008	7.527	0.247	0.247	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.024	-0.005	10.007	-0.269	-0.269	0.000	0.000	0.000	0.000
58	B	134	ALA	0	0.028	0.014	8.308	0.156	0.156	0.000	0.000	0.000	0.000
59	B	135	GLN	0	0.071	0.054	9.361	0.057	0.057	0.000	0.000	0.000	0.000
60	B	136	ALA	0	0.035	0.006	10.041	-0.243	-0.243	0.000	0.000	0.000	0.000
61	B	137	VAL	0	-0.047	-0.026	12.346	0.148	0.148	0.000	0.000	0.000	0.000
62	B	138	LEU	0	0.015	0.024	14.881	-0.055	-0.055	0.000	0.000	0.000	0.000
63	B	139	LYS	1	0.847	0.895	16.789	0.665	0.665	0.000	0.000	0.000	0.000
64	B	140	ILE	0	0.000	0.012	19.431	0.008	0.008	0.000	0.000	0.000	0.000
65	B	141	ILE	0	0.007	0.006	19.301	0.002	0.002	0.000	0.000	0.000	0.000
66	B	142	ASN	0	-0.045	-0.027	23.370	0.050	0.050	0.000	0.000	0.000	0.000
67	B	150	PHE	0	0.029	0.014	22.865	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	151	SER	0	0.017	-0.008	19.469	-0.048	-0.048	0.000	0.000	0.000	0.000
69	B	152	ARG	1	0.808	0.925	19.976	0.197	0.197	0.000	0.000	0.000	0.000
70	B	153	ARG	1	0.903	0.954	14.999	0.338	0.338	0.000	0.000	0.000	0.000
71	B	154	ILE	0	-0.024	-0.007	14.674	0.072	0.072	0.000	0.000	0.000	0.000
72	B	155	SER	0	0.000	-0.021	13.832	-0.127	-0.127	0.000	0.000	0.000	0.000
73	B	156	HIS	1	0.759	0.904	13.471	-0.131	-0.131	0.000	0.000	0.000	0.000
74	B	157	LEU	0	0.051	0.025	12.937	0.039	0.039	0.000	0.000	0.000	0.000
75	B	158	PHE	0	-0.008	0.003	11.682	-0.055	-0.055	0.000	0.000	0.000	0.000
76	B	159	PHE	0	0.030	-0.004	13.869	0.114	0.114	0.000	0.000	0.000	0.000
77	B	160	HIS	0	0.013	0.010	16.419	-0.077	-0.077	0.000	0.000	0.000	0.000
78	B	161	LYS	1	0.918	0.986	19.433	-0.220	-0.220	0.000	0.000	0.000	0.000
79	B	162	GLU	-1	-0.855	-0.925	19.262	0.160	0.160	0.000	0.000	0.000	0.000
80	B	163	ASN	0	0.007	0.002	16.598	0.009	0.009	0.000	0.000	0.000	0.000
81	B	164	ASP	-1	-0.857	-0.938	16.147	0.101	0.101	0.000	0.000	0.000	0.000
82	B	165	TRP	0	-0.002	-0.013	16.484	0.011	0.011	0.000	0.000	0.000	0.000
83	B	166	GLY	0	0.012	-0.002	17.880	-0.039	-0.039	0.000	0.000	0.000	0.000
84	B	167	PHE	0	-0.020	-0.008	20.050	0.018	0.018	0.000	0.000	0.000	0.000
85	B	168	SER	0	0.039	0.013	23.652	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	169	ASN	0	-0.015	-0.013	26.694	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	170	PHE	0	-0.031	-0.011	20.750	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	171	MET	0	-0.001	0.003	25.586	-0.023	-0.023	0.000	0.000	0.000	0.000
89	B	172	ALA	0	0.059	0.034	28.718	0.010	0.010	0.000	0.000	0.000	0.000
90	B	173	TRP	0	0.012	-0.006	28.123	-0.009	-0.009	0.000	0.000	0.000	0.000
91	B	174	SER	0	-0.065	-0.055	32.479	0.004	0.004	0.000	0.000	0.000	0.000
92	B	175	GLU	-1	-0.920	-0.914	30.942	-0.121	-0.121	0.000	0.000	0.000	0.000
93	B	189	VAL	0	-0.005	-0.017	26.409	-0.008	-0.008	0.000	0.000	0.000	0.000
94	B	190	THR	0	-0.016	0.008	21.326	0.008	0.008	0.000	0.000	0.000	0.000
95	B	191	PHE	0	0.023	0.000	19.319	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	192	GLU	-1	-0.796	-0.891	14.760	-0.740	-0.740	0.000	0.000	0.000	0.000
97	B	193	VAL	0	0.007	0.004	11.097	0.063	0.063	0.000	0.000	0.000	0.000
98	B	194	PHE	0	-0.005	0.018	7.631	0.084	0.084	0.000	0.000	0.000	0.000
99	B	195	VAL	0	-0.010	-0.020	7.108	0.328	0.328	0.000	0.000	0.000	0.000
100	B	196	GLN	0	-0.017	-0.020	5.302	-0.190	-0.190	0.000	0.000	0.000	0.000
101	B	197	ALA	0	0.036	0.017	4.365	0.971	1.185	-0.001	-0.058	-0.155	0.000
102	B	198	ASP	-1	-0.834	-0.892	4.089	1.501	1.650	0.000	-0.053	-0.096	0.000
103	B	199	ALA	0	-0.029	-0.032	5.621	0.656	0.656	0.000	0.000	0.000	0.000
104	B	200	PRO	0	-0.032	-0.012	6.157	-0.415	-0.415	0.000	0.000	0.000	0.000
105	B	201	HIS	0	0.013	0.001	9.090	-0.124	-0.124	0.000	0.000	0.000	0.000
106	B	202	GLY	0	0.033	0.010	12.845	-0.030	-0.030	0.000	0.000	0.000	0.000
107	B	203	VAL	0	-0.052	-0.019	10.659	-0.055	-0.055	0.000	0.000	0.000	0.000
108	B	204	ALA	0	-0.012	0.005	13.881	-0.021	-0.021	0.000	0.000	0.000	0.000

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