FMO DATABASE

FMODB ID: Q1MVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-889014.689165
FMO2-HF: Nuclear repulsion	844555.405284
FMO2-HF: Total energy	-44459.283881
FMO2-MP2: Total energy	-44587.184047

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.
-12.62	-6.245	2.951	-3.882	-5.442	0.012

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 : -0.031 / q_NPA : -0.028

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	0.006	0.010	3.721	-1.282	0.671	-0.020	-1.050	-0.882	-0.001
4	B	70	THR	0	0.016	0.006	6.123	0.178	0.178	0.000	0.000	0.000	0.000
5	B	71	PHE	0	-0.027	0.002	9.800	0.068	0.068	0.000	0.000	0.000	0.000
6	B	72	GLN	0	0.039	-0.014	12.151	-0.045	-0.045	0.000	0.000	0.000	0.000
7	B	73	PHE	0	-0.001	-0.014	15.947	0.048	0.048	0.000	0.000	0.000	0.000
8	B	74	THR	0	0.014	-0.006	18.609	-0.009	-0.009	0.000	0.000	0.000	0.000
9	B	75	VAL	0	0.022	0.028	22.196	0.017	0.017	0.000	0.000	0.000	0.000
10	B	76	GLU	-1	-0.859	-0.917	24.589	-0.096	-0.096	0.000	0.000	0.000	0.000
11	B	77	ARG	1	0.795	0.873	27.976	0.074	0.074	0.000	0.000	0.000	0.000
12	B	78	PHE	0	0.100	0.057	27.470	0.007	0.007	0.000	0.000	0.000	0.000
13	B	79	SER	0	-0.037	-0.035	29.826	0.005	0.005	0.000	0.000	0.000	0.000
14	B	80	ARG	1	0.869	0.940	32.403	0.084	0.084	0.000	0.000	0.000	0.000
15	B	81	LEU	0	0.020	0.010	33.123	0.005	0.005	0.000	0.000	0.000	0.000
16	B	82	SER	0	-0.007	0.006	31.156	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	83	GLU	-1	-0.869	-0.940	27.268	-0.087	-0.087	0.000	0.000	0.000	0.000
18	B	84	SER	0	-0.005	-0.039	22.802	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	85	VAL	0	-0.032	0.000	24.282	0.008	0.008	0.000	0.000	0.000	0.000
20	B	86	LEU	0	0.020	0.015	18.347	-0.014	-0.014	0.000	0.000	0.000	0.000
21	B	87	SER	0	0.027	0.041	15.688	-0.018	-0.018	0.000	0.000	0.000	0.000
22	B	88	PRO	0	-0.020	-0.017	15.863	0.042	0.042	0.000	0.000	0.000	0.000
23	B	89	PRO	0	-0.024	-0.008	13.082	-0.029	-0.029	0.000	0.000	0.000	0.000
24	B	90	CYS	0	-0.031	-0.001	8.417	-0.044	-0.044	0.000	0.000	0.000	0.000
25	B	91	PHE	0	0.046	0.010	7.767	0.039	0.039	0.000	0.000	0.000	0.000
26	B	92	VAL	0	0.016	0.031	2.901	-0.904	0.054	0.439	-0.413	-0.985	0.005
27	B	93	ARG	1	0.848	0.909	2.649	-11.492	-8.470	2.533	-2.265	-3.289	0.008
28	B	94	ASN	0	-0.006	-0.011	4.762	-1.647	-1.604	0.000	-0.032	-0.011	0.000
29	B	95	LEU	0	0.037	0.037	7.615	-0.520	-0.520	0.000	0.000	0.000	0.000
30	B	96	PRO	0	-0.002	0.002	8.890	0.104	0.104	0.000	0.000	0.000	0.000
31	B	97	TRP	0	-0.008	-0.033	7.228	-0.373	-0.373	0.000	0.000	0.000	0.000
32	B	98	LYS	1	0.822	0.919	11.378	-0.312	-0.312	0.000	0.000	0.000	0.000
33	B	99	ILE	0	-0.010	0.009	14.515	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	100	MET	0	-0.029	-0.015	16.717	0.019	0.019	0.000	0.000	0.000	0.000
35	B	101	VAL	0	0.001	-0.002	20.079	-0.023	-0.023	0.000	0.000	0.000	0.000
36	B	102	MET	0	0.036	0.013	23.136	0.007	0.007	0.000	0.000	0.000	0.000
37	B	103	PRO	0	0.021	0.018	26.749	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	104	ARG	1	0.946	0.980	29.795	0.034	0.034	0.000	0.000	0.000	0.000
39	B	115	VAL	0	-0.007	-0.004	25.243	0.003	0.003	0.000	0.000	0.000	0.000
40	B	116	GLY	0	-0.029	-0.001	25.586	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	117	PHE	0	-0.032	-0.016	17.531	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	118	PHE	0	-0.007	-0.026	19.512	-0.014	-0.014	0.000	0.000	0.000	0.000
43	B	119	LEU	0	-0.003	0.006	11.876	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	120	GLN	0	0.086	0.023	15.654	0.006	0.006	0.000	0.000	0.000	0.000
45	B	121	CYS	0	-0.065	-0.049	10.349	0.060	0.060	0.000	0.000	0.000	0.000
46	B	122	ASN	0	0.008	-0.010	13.035	0.024	0.024	0.000	0.000	0.000	0.000
47	B	123	ALA	0	0.030	0.018	14.738	-0.022	-0.022	0.000	0.000	0.000	0.000
48	B	124	GLU	-1	-0.868	-0.917	17.814	0.256	0.256	0.000	0.000	0.000	0.000
49	B	125	SER	0	-0.034	-0.028	17.764	0.070	0.070	0.000	0.000	0.000	0.000
50	B	126	ASP	-1	-0.868	-0.918	19.918	0.237	0.237	0.000	0.000	0.000	0.000
51	B	127	SER	0	-0.017	-0.029	21.938	-0.016	-0.016	0.000	0.000	0.000	0.000
52	B	128	THR	0	0.017	-0.016	20.829	0.030	0.030	0.000	0.000	0.000	0.000
53	B	129	SER	0	-0.065	-0.023	19.906	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	130	TRP	0	0.013	0.049	12.771	0.066	0.066	0.000	0.000	0.000	0.000
55	B	131	SER	0	-0.006	-0.035	13.707	-0.079	-0.079	0.000	0.000	0.000	0.000
56	B	132	CYS	0	-0.063	-0.034	7.813	0.216	0.216	0.000	0.000	0.000	0.000
57	B	133	HIS	0	-0.045	-0.024	10.230	-0.247	-0.247	0.000	0.000	0.000	0.000
58	B	134	ALA	0	0.043	0.027	8.401	0.093	0.093	0.000	0.000	0.000	0.000
59	B	135	GLN	0	0.097	0.060	9.149	0.067	0.067	0.000	0.000	0.000	0.000
60	B	136	ALA	0	0.017	-0.007	9.961	-0.235	-0.235	0.000	0.000	0.000	0.000
61	B	137	VAL	0	-0.030	-0.005	12.270	0.149	0.149	0.000	0.000	0.000	0.000
62	B	138	LEU	0	0.002	0.017	14.729	-0.035	-0.035	0.000	0.000	0.000	0.000
63	B	139	LYS	1	0.864	0.896	16.596	0.669	0.669	0.000	0.000	0.000	0.000
64	B	140	ILE	0	-0.024	0.002	19.187	0.001	0.001	0.000	0.000	0.000	0.000
65	B	141	ILE	0	0.001	-0.011	19.161	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	142	ASN	0	-0.033	-0.006	23.166	0.045	0.045	0.000	0.000	0.000	0.000
67	B	150	PHE	0	0.016	0.007	22.313	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	151	SER	0	0.042	0.032	18.982	-0.044	-0.044	0.000	0.000	0.000	0.000
69	B	152	ARG	1	0.839	0.912	19.300	0.215	0.215	0.000	0.000	0.000	0.000
70	B	153	ARG	1	0.878	0.942	14.637	0.405	0.405	0.000	0.000	0.000	0.000
71	B	154	ILE	0	-0.040	-0.014	14.514	0.073	0.073	0.000	0.000	0.000	0.000
72	B	155	SER	0	0.030	0.006	13.944	-0.122	-0.122	0.000	0.000	0.000	0.000
73	B	156	HIS	1	0.762	0.909	13.535	-0.106	-0.106	0.000	0.000	0.000	0.000
74	B	157	LEU	0	0.079	0.044	12.964	0.034	0.034	0.000	0.000	0.000	0.000
75	B	158	PHE	0	-0.037	-0.018	11.950	-0.042	-0.042	0.000	0.000	0.000	0.000
76	B	159	PHE	0	0.050	0.014	14.228	0.101	0.101	0.000	0.000	0.000	0.000
77	B	160	HIS	0	0.006	0.009	16.589	-0.070	-0.070	0.000	0.000	0.000	0.000
78	B	161	LYS	1	0.904	0.982	19.522	-0.215	-0.215	0.000	0.000	0.000	0.000
79	B	162	GLU	-1	-0.848	-0.928	19.500	0.134	0.134	0.000	0.000	0.000	0.000
80	B	163	ASN	0	-0.009	-0.009	16.556	0.014	0.014	0.000	0.000	0.000	0.000
81	B	164	ASP	-1	-0.851	-0.945	16.511	0.112	0.112	0.000	0.000	0.000	0.000
82	B	165	TRP	0	-0.024	-0.002	16.484	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	166	GLY	0	0.021	0.007	17.923	-0.037	-0.037	0.000	0.000	0.000	0.000
84	B	167	PHE	0	-0.031	-0.004	19.905	0.020	0.020	0.000	0.000	0.000	0.000
85	B	168	SER	0	0.057	0.024	23.396	0.002	0.002	0.000	0.000	0.000	0.000
86	B	169	ASN	0	-0.027	-0.015	26.445	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	170	PHE	0	-0.021	-0.008	20.747	-0.004	-0.004	0.000	0.000	0.000	0.000
88	B	171	MET	0	-0.020	-0.023	25.504	-0.023	-0.023	0.000	0.000	0.000	0.000
89	B	172	ALA	0	0.046	0.030	28.525	0.012	0.012	0.000	0.000	0.000	0.000
90	B	173	TRP	0	0.042	0.028	28.131	-0.009	-0.009	0.000	0.000	0.000	0.000
91	B	174	SER	0	-0.084	-0.063	32.242	0.003	0.003	0.000	0.000	0.000	0.000
92	B	175	GLU	-1	-0.907	-0.922	30.969	-0.118	-0.118	0.000	0.000	0.000	0.000
93	B	189	VAL	0	-0.016	-0.022	25.939	-0.009	-0.009	0.000	0.000	0.000	0.000
94	B	190	THR	0	-0.009	0.011	21.028	0.010	0.010	0.000	0.000	0.000	0.000
95	B	191	PHE	0	0.017	0.002	19.021	-0.013	-0.013	0.000	0.000	0.000	0.000
96	B	192	GLU	-1	-0.782	-0.878	14.709	-0.738	-0.738	0.000	0.000	0.000	0.000
97	B	193	VAL	0	0.021	0.005	11.242	0.056	0.056	0.000	0.000	0.000	0.000
98	B	194	PHE	0	-0.033	0.005	7.153	0.149	0.149	0.000	0.000	0.000	0.000
99	B	195	VAL	0	-0.016	-0.028	7.064	0.231	0.231	0.000	0.000	0.000	0.000
100	B	196	GLN	0	-0.005	-0.012	5.036	0.116	0.116	0.000	0.000	0.000	0.000
101	B	197	ALA	0	0.003	0.001	4.340	0.993	1.244	-0.001	-0.072	-0.178	0.000
102	B	198	ASP	-1	-0.815	-0.882	4.160	1.260	1.408	0.000	-0.050	-0.097	0.000
103	B	199	ALA	0	-0.062	-0.047	6.056	0.458	0.458	0.000	0.000	0.000	0.000
104	B	200	PRO	0	-0.004	-0.003	6.235	-0.410	-0.410	0.000	0.000	0.000	0.000
105	B	201	HIS	0	0.024	0.016	9.126	-0.113	-0.113	0.000	0.000	0.000	0.000
106	B	202	GLY	0	0.017	0.001	12.832	-0.030	-0.030	0.000	0.000	0.000	0.000
107	B	203	VAL	0	-0.049	-0.023	11.013	-0.032	-0.032	0.000	0.000	0.000	0.000
108	B	204	ALA	0	0.002	0.012	14.365	-0.005	-0.005	0.000	0.000	0.000	0.000

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