FMO DATABASE

FMODB ID: 8271Y

Calculation Name: 2XXN-A-Xray372

Preferred Name: Ubiquitin carboxyl-terminal hydrolase 7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2XXN

Chain ID: A

ChEMBL ID: CHEMBL2157850

UniProt ID: Q93009

Base Structure: X-ray

Registration Date: 2023-03-14

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1389248.378276
FMO2-HF: Nuclear repulsion	1330056.887835
FMO2-HF: Total energy	-59191.49044
FMO2-MP2: Total energy	-59363.509906

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:63:THR)

Summations of interaction energy for fragment #1(A:63:THR)

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.
-14.329	-7.576	9.397	-5.564	-10.586	-0.009

Interaction energy analysis for fragmet #1(A:63:THR)

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 : -0.015

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	65	TRP	0	0.022	0.026	2.148	-14.316	-9.318	7.585	-4.665	-7.918	-0.005
4	A	66	ARG	1	0.845	0.929	2.292	-1.878	-0.156	1.766	-1.008	-2.480	-0.004
5	A	67	SER	0	0.070	0.014	3.417	0.646	0.679	0.046	0.109	-0.188	0.000
6	A	68	GLU	-1	-0.867	-0.930	6.778	-0.472	-0.472	0.000	0.000	0.000	0.000
7	A	69	ALA	0	-0.029	-0.011	6.836	-0.305	-0.305	0.000	0.000	0.000	0.000
8	A	70	THR	0	0.032	0.015	8.556	0.034	0.034	0.000	0.000	0.000	0.000
9	A	71	PHE	0	-0.039	-0.015	10.591	0.111	0.111	0.000	0.000	0.000	0.000
10	A	72	GLN	0	0.012	-0.020	12.436	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	73	PHE	0	-0.005	-0.008	15.728	0.072	0.072	0.000	0.000	0.000	0.000
12	A	74	THR	0	0.005	-0.003	18.418	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	75	VAL	0	-0.031	-0.003	21.677	0.020	0.020	0.000	0.000	0.000	0.000
14	A	76	GLU	-1	-0.773	-0.887	24.689	0.160	0.160	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.833	0.906	27.389	-0.162	-0.162	0.000	0.000	0.000	0.000
16	A	78	PHE	0	0.055	0.026	27.361	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	79	SER	0	-0.060	-0.069	30.362	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	80	ARG	1	0.856	0.917	33.310	-0.094	-0.094	0.000	0.000	0.000	0.000
19	A	81	LEU	0	-0.026	0.015	28.087	0.002	0.002	0.000	0.000	0.000	0.000
20	A	82	SER	0	-0.010	-0.017	31.904	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	83	GLU	-1	-0.947	-0.978	30.531	0.121	0.121	0.000	0.000	0.000	0.000
22	A	84	SER	0	-0.050	-0.027	26.066	0.002	0.002	0.000	0.000	0.000	0.000
23	A	85	VAL	0	0.008	0.013	23.613	0.011	0.011	0.000	0.000	0.000	0.000
24	A	86	LEU	0	0.002	-0.017	20.341	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	87	SER	0	-0.018	-0.001	15.666	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	88	PRO	0	0.029	-0.002	14.531	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	89	PRO	0	-0.005	0.008	12.234	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	90	CYS	0	-0.051	-0.007	8.944	0.244	0.244	0.000	0.000	0.000	0.000
29	A	91	PHE	0	0.033	0.008	6.437	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	92	VAL	0	0.009	0.016	6.160	-0.194	-0.194	0.000	0.000	0.000	0.000
31	A	93	ARG	1	0.859	0.936	6.006	1.079	1.079	0.000	0.000	0.000	0.000
32	A	94	ASN	0	-0.036	-0.044	5.910	0.781	0.781	0.000	0.000	0.000	0.000
33	A	95	LEU	0	0.023	0.023	8.072	0.087	0.087	0.000	0.000	0.000	0.000
34	A	96	PRO	0	-0.005	0.012	10.198	0.017	0.017	0.000	0.000	0.000	0.000
35	A	97	TRP	0	0.012	-0.018	10.474	-0.148	-0.148	0.000	0.000	0.000	0.000
36	A	98	LYS	1	0.892	0.939	13.456	-0.323	-0.323	0.000	0.000	0.000	0.000
37	A	99	ILE	0	-0.001	0.006	16.117	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.012	0.004	18.471	0.031	0.031	0.000	0.000	0.000	0.000
39	A	101	VAL	0	0.003	0.008	22.094	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	102	MET	0	0.047	0.033	24.987	0.007	0.007	0.000	0.000	0.000	0.000
41	A	103	PRO	0	0.002	0.031	28.683	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	104	ARG	1	0.859	0.922	30.015	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	105	PHE	0	0.012	-0.005	33.946	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	106	TYR	0	0.061	0.032	34.686	0.003	0.003	0.000	0.000	0.000	0.000
45	A	107	PRO	0	0.041	0.019	40.016	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	108	ASP	-1	-0.886	-0.937	43.598	0.021	0.021	0.000	0.000	0.000	0.000
47	A	109	ARG	1	0.835	0.909	41.354	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	110	PRO	0	0.027	0.023	41.641	0.002	0.002	0.000	0.000	0.000	0.000
49	A	111	HIS	0	0.012	0.007	42.563	0.005	0.005	0.000	0.000	0.000	0.000
50	A	112	GLN	0	-0.033	-0.027	39.368	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	113	LYS	1	0.928	0.992	35.589	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	114	SER	0	0.018	0.004	32.610	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	115	VAL	0	0.006	0.002	27.514	0.008	0.008	0.000	0.000	0.000	0.000
54	A	116	GLY	0	-0.017	-0.009	28.480	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	117	PHE	0	-0.021	-0.018	20.068	0.014	0.014	0.000	0.000	0.000	0.000
56	A	118	PHE	0	-0.007	-0.015	22.645	-0.021	-0.021	0.000	0.000	0.000	0.000
57	A	119	LEU	0	0.000	0.013	15.090	0.020	0.020	0.000	0.000	0.000	0.000
58	A	120	GLN	0	0.031	-0.003	18.137	0.010	0.010	0.000	0.000	0.000	0.000
59	A	121	CYS	0	-0.039	-0.017	14.337	0.045	0.045	0.000	0.000	0.000	0.000
60	A	122	ASN	0	0.017	-0.024	15.499	0.044	0.044	0.000	0.000	0.000	0.000
61	A	123	ALA	0	0.048	0.020	16.929	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	124	GLU	-1	-0.930	-0.941	16.984	0.494	0.494	0.000	0.000	0.000	0.000
63	A	125	SER	0	-0.054	-0.013	18.550	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	126	ASP	-1	-0.858	-0.925	20.526	0.173	0.173	0.000	0.000	0.000	0.000
65	A	127	SER	0	-0.073	-0.033	20.826	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	128	THR	0	0.012	-0.021	22.815	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	129	SER	0	-0.050	-0.023	21.608	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	130	TRP	0	-0.029	0.011	17.060	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	131	SER	0	-0.002	-0.007	17.927	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	132	CYS	0	-0.037	-0.019	13.323	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	133	HIS	0	0.032	0.035	16.124	0.042	0.042	0.000	0.000	0.000	0.000
72	A	134	ALA	0	0.010	0.003	14.454	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	135	GLN	0	0.068	0.068	15.622	0.061	0.061	0.000	0.000	0.000	0.000
74	A	136	ALA	0	0.026	0.002	15.686	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	137	VAL	0	-0.036	-0.006	17.284	0.015	0.015	0.000	0.000	0.000	0.000
76	A	138	LEU	0	-0.014	0.001	18.218	0.011	0.011	0.000	0.000	0.000	0.000
77	A	139	LYS	1	0.885	0.906	18.619	0.070	0.070	0.000	0.000	0.000	0.000
78	A	140	ILE	0	-0.002	0.019	21.440	0.020	0.020	0.000	0.000	0.000	0.000
79	A	141	ILE	0	-0.009	-0.023	19.822	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	142	ASN	0	-0.039	-0.034	23.840	0.009	0.009	0.000	0.000	0.000	0.000
81	A	143	TYR	0	-0.024	-0.047	26.360	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	144	ARG	1	0.856	0.937	27.353	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	145	ASP	-1	-0.815	-0.917	29.499	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	146	ASP	-1	-0.888	-0.929	24.114	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	147	GLU	-1	-0.935	-0.962	25.290	-0.082	-0.082	0.000	0.000	0.000	0.000
86	A	148	LYS	1	0.794	0.897	27.776	0.005	0.005	0.000	0.000	0.000	0.000
87	A	149	SER	0	-0.057	-0.021	24.239	0.014	0.014	0.000	0.000	0.000	0.000
88	A	150	PHE	0	-0.023	0.004	25.920	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	151	SER	0	-0.040	-0.026	22.474	0.001	0.001	0.000	0.000	0.000	0.000
90	A	152	ARG	1	0.844	0.940	23.734	0.010	0.010	0.000	0.000	0.000	0.000
91	A	153	ARG	1	0.957	0.976	22.155	0.144	0.144	0.000	0.000	0.000	0.000
92	A	154	ILE	0	-0.018	-0.003	19.680	0.013	0.013	0.000	0.000	0.000	0.000
93	A	155	SER	0	-0.043	-0.057	20.229	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	156	HIS	1	0.798	0.907	19.883	0.030	0.030	0.000	0.000	0.000	0.000
95	A	157	LEU	0	0.081	0.048	19.323	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	158	PHE	0	-0.048	-0.020	17.602	0.023	0.023	0.000	0.000	0.000	0.000
97	A	159	PHE	0	0.073	0.007	19.476	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	160	HIS	0	0.067	0.037	21.379	0.003	0.003	0.000	0.000	0.000	0.000
99	A	161	LYS	1	0.921	0.965	23.638	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	162	GLU	-1	-0.896	-0.920	24.499	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	163	ASN	0	-0.008	-0.009	20.827	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	164	ASP	-1	-0.889	-0.945	20.459	0.108	0.108	0.000	0.000	0.000	0.000
103	A	165	TRP	0	0.025	-0.004	21.713	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	166	GLY	0	0.001	0.001	22.206	0.005	0.005	0.000	0.000	0.000	0.000
105	A	167	PHE	0	-0.033	-0.011	24.382	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	168	SER	0	0.075	0.024	27.626	0.011	0.011	0.000	0.000	0.000	0.000
107	A	169	ASN	0	-0.014	-0.003	30.294	0.007	0.007	0.000	0.000	0.000	0.000
108	A	170	PHE	0	0.000	0.005	24.453	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	171	MET	0	0.066	0.032	29.264	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	172	ALA	0	0.053	0.041	31.618	0.007	0.007	0.000	0.000	0.000	0.000
111	A	173	TRP	0	0.030	-0.019	30.740	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	174	SER	0	-0.011	-0.003	34.512	0.003	0.003	0.000	0.000	0.000	0.000
113	A	175	GLU	-1	-0.939	-0.966	34.611	0.010	0.010	0.000	0.000	0.000	0.000
114	A	176	VAL	0	-0.005	-0.003	29.248	0.000	0.000	0.000	0.000	0.000	0.000
115	A	177	THR	0	-0.040	-0.050	32.097	0.004	0.004	0.000	0.000	0.000	0.000
116	A	178	ASP	-1	-0.819	-0.884	34.194	0.026	0.026	0.000	0.000	0.000	0.000
117	A	179	PRO	0	0.021	-0.008	35.093	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	180	GLU	-1	-0.977	-0.983	35.607	0.016	0.016	0.000	0.000	0.000	0.000
119	A	181	LYS	1	0.814	0.901	34.315	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	182	GLY	0	0.001	0.016	32.055	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	183	PHE	0	-0.006	-0.007	27.472	0.000	0.000	0.000	0.000	0.000	0.000
122	A	184	ILE	0	-0.057	-0.006	28.201	0.009	0.009	0.000	0.000	0.000	0.000
123	A	185	ASP	-1	-0.830	-0.890	29.228	0.060	0.060	0.000	0.000	0.000	0.000
124	A	186	ASP	-1	-0.895	-0.947	29.848	0.116	0.116	0.000	0.000	0.000	0.000
125	A	187	ASP	-1	-0.805	-0.886	31.206	0.102	0.102	0.000	0.000	0.000	0.000
126	A	188	LYS	1	0.833	0.921	26.217	-0.129	-0.129	0.000	0.000	0.000	0.000
127	A	189	VAL	0	0.034	0.022	25.558	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	190	THR	0	0.008	0.013	20.192	0.026	0.026	0.000	0.000	0.000	0.000
129	A	191	PHE	0	0.003	0.006	20.540	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	192	GLU	-1	-0.784	-0.884	15.872	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	193	VAL	0	0.006	0.004	14.608	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	194	PHE	0	-0.024	0.003	11.818	0.043	0.043	0.000	0.000	0.000	0.000
133	A	195	VAL	0	0.005	-0.005	11.047	0.005	0.005	0.000	0.000	0.000	0.000
134	A	196	GLN	0	-0.048	-0.045	11.264	-0.035	-0.035	0.000	0.000	0.000	0.000
135	A	197	ALA	0	0.014	0.011	10.339	0.082	0.082	0.000	0.000	0.000	0.000
136	A	198	ASP	-1	-0.866	-0.925	10.931	-0.569	-0.569	0.000	0.000	0.000	0.000
137	A	199	ALA	0	-0.074	-0.052	10.949	0.015	0.015	0.000	0.000	0.000	0.000
138	A	200	PRO	0	0.001	0.005	10.992	0.030	0.030	0.000	0.000	0.000	0.000
139	A	201	HIS	0	0.006	0.005	13.982	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	202	GLY	0	0.028	0.004	17.134	0.032	0.032	0.000	0.000	0.000	0.000
141	A	203	VAL	0	-0.030	-0.022	13.036	0.031	0.031	0.000	0.000	0.000	0.000
142	A	204	ALA	0	-0.018	0.001	13.003	0.051	0.051	0.000	0.000	0.000	0.000
143	A	205	TRP	0	0.014	0.011	15.123	-0.049	-0.049	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:THR)