FMO DATABASE

FMODB ID: N18RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1389173.189531
FMO2-HF: Nuclear repulsion	1329981.501007
FMO2-HF: Total energy	-59191.688524
FMO2-MP2: Total energy	-59363.723472

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.
-15.245	-8.315	11.819	-6.44	-12.309	-0.002

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 : 0.049 / q_NPA : 0.020

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	0.015	0.021	2.141	-15.905	-11.049	10.530	-5.477	-9.909	0.002
4	A	66	ARG	1	0.833	0.922	2.331	0.174	2.164	1.251	-1.030	-2.211	-0.004
5	A	67	SER	0	0.053	0.014	3.460	0.434	0.518	0.038	0.067	-0.189	0.000
6	A	68	GLU	-1	-0.857	-0.933	6.831	-0.595	-0.595	0.000	0.000	0.000	0.000
7	A	69	ALA	0	-0.022	-0.014	7.124	-0.487	-0.487	0.000	0.000	0.000	0.000
8	A	70	THR	0	0.033	0.023	8.894	0.147	0.147	0.000	0.000	0.000	0.000
9	A	71	PHE	0	-0.045	-0.021	10.626	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	72	GLN	0	0.013	-0.018	12.528	0.056	0.056	0.000	0.000	0.000	0.000
11	A	73	PHE	0	-0.007	-0.014	15.513	0.004	0.004	0.000	0.000	0.000	0.000
12	A	74	THR	0	0.003	-0.005	18.270	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	75	VAL	0	-0.019	0.008	21.444	0.013	0.013	0.000	0.000	0.000	0.000
14	A	76	GLU	-1	-0.773	-0.892	24.130	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.817	0.891	26.689	0.007	0.007	0.000	0.000	0.000	0.000
16	A	78	PHE	0	0.048	0.030	27.506	0.000	0.000	0.000	0.000	0.000	0.000
17	A	79	SER	0	-0.065	-0.077	29.893	0.000	0.000	0.000	0.000	0.000	0.000
18	A	80	ARG	1	0.854	0.917	32.830	0.017	0.017	0.000	0.000	0.000	0.000
19	A	81	LEU	0	-0.020	0.014	27.678	0.004	0.004	0.000	0.000	0.000	0.000
20	A	82	SER	0	-0.005	-0.011	31.432	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	83	GLU	-1	-0.937	-0.975	30.561	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	84	SER	0	-0.046	-0.024	25.993	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	85	VAL	0	-0.007	0.001	23.079	0.009	0.009	0.000	0.000	0.000	0.000
24	A	86	LEU	0	0.012	-0.013	19.790	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	87	SER	0	-0.003	0.005	15.093	0.006	0.006	0.000	0.000	0.000	0.000
26	A	88	PRO	0	0.027	-0.004	13.562	0.015	0.015	0.000	0.000	0.000	0.000
27	A	89	PRO	0	-0.004	0.021	12.092	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	90	CYS	0	-0.047	-0.013	8.966	-0.121	-0.121	0.000	0.000	0.000	0.000
29	A	91	PHE	0	0.021	0.007	6.333	0.037	0.037	0.000	0.000	0.000	0.000
30	A	92	VAL	0	0.010	0.016	6.300	-0.852	-0.852	0.000	0.000	0.000	0.000
31	A	93	ARG	1	0.852	0.940	6.133	1.257	1.257	0.000	0.000	0.000	0.000
32	A	94	ASN	0	-0.028	-0.040	5.613	0.992	0.992	0.000	0.000	0.000	0.000
33	A	95	LEU	0	0.023	0.033	7.829	0.121	0.121	0.000	0.000	0.000	0.000
34	A	96	PRO	0	-0.003	0.010	10.102	-0.152	-0.152	0.000	0.000	0.000	0.000
35	A	97	TRP	0	0.022	-0.017	10.452	0.040	0.040	0.000	0.000	0.000	0.000
36	A	98	LYS	1	0.843	0.908	13.048	0.036	0.036	0.000	0.000	0.000	0.000
37	A	99	ILE	0	-0.004	0.014	15.652	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.007	0.003	18.047	0.031	0.031	0.000	0.000	0.000	0.000
39	A	101	VAL	0	-0.003	0.001	21.623	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	102	MET	0	0.042	0.035	24.702	0.014	0.014	0.000	0.000	0.000	0.000
41	A	103	PRO	0	-0.006	0.022	28.403	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	104	ARG	1	0.861	0.920	30.200	0.074	0.074	0.000	0.000	0.000	0.000
43	A	105	PHE	0	0.027	0.005	33.938	0.000	0.000	0.000	0.000	0.000	0.000
44	A	106	TYR	0	0.050	0.027	35.045	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	107	PRO	0	0.030	0.018	40.199	0.001	0.001	0.000	0.000	0.000	0.000
46	A	108	ASP	-1	-0.867	-0.931	43.838	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	109	ARG	1	0.828	0.905	41.622	0.047	0.047	0.000	0.000	0.000	0.000
48	A	110	PRO	0	0.041	0.032	41.746	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	111	HIS	0	-0.005	-0.004	42.055	0.001	0.001	0.000	0.000	0.000	0.000
50	A	112	GLN	0	-0.029	-0.022	39.618	0.000	0.000	0.000	0.000	0.000	0.000
51	A	113	LYS	1	0.926	0.991	35.091	0.041	0.041	0.000	0.000	0.000	0.000
52	A	114	SER	0	-0.004	-0.006	33.084	0.001	0.001	0.000	0.000	0.000	0.000
53	A	115	VAL	0	0.001	0.002	27.754	0.004	0.004	0.000	0.000	0.000	0.000
54	A	116	GLY	0	-0.015	-0.002	28.728	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	117	PHE	0	-0.047	-0.027	20.344	0.003	0.003	0.000	0.000	0.000	0.000
56	A	118	PHE	0	0.001	-0.012	22.728	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	119	LEU	0	-0.003	0.013	15.231	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	120	GLN	0	0.025	-0.005	18.047	0.019	0.019	0.000	0.000	0.000	0.000
59	A	121	CYS	0	-0.023	-0.015	14.297	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	122	ASN	0	0.013	-0.021	15.488	0.055	0.055	0.000	0.000	0.000	0.000
61	A	123	ALA	0	0.040	0.020	16.790	0.022	0.022	0.000	0.000	0.000	0.000
62	A	124	GLU	-1	-0.909	-0.926	16.758	0.026	0.026	0.000	0.000	0.000	0.000
63	A	125	SER	0	-0.014	-0.011	18.619	0.024	0.024	0.000	0.000	0.000	0.000
64	A	126	ASP	-1	-0.874	-0.935	20.652	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	127	SER	0	-0.053	-0.018	20.674	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	128	THR	0	0.021	-0.020	22.468	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	129	SER	0	-0.054	-0.018	21.612	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	130	TRP	0	-0.040	0.012	17.287	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	131	SER	0	-0.006	-0.014	18.040	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	132	CYS	0	-0.033	-0.016	13.143	-0.027	-0.027	0.000	0.000	0.000	0.000
71	A	133	HIS	0	0.017	0.028	16.027	0.030	0.030	0.000	0.000	0.000	0.000
72	A	134	ALA	0	0.014	-0.003	14.453	-0.064	-0.064	0.000	0.000	0.000	0.000
73	A	135	GLN	0	0.079	0.073	15.638	0.074	0.074	0.000	0.000	0.000	0.000
74	A	136	ALA	0	0.016	0.001	15.706	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	137	VAL	0	-0.033	-0.021	17.585	0.048	0.048	0.000	0.000	0.000	0.000
76	A	138	LEU	0	0.000	0.027	18.493	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	139	LYS	1	0.872	0.898	18.785	0.273	0.273	0.000	0.000	0.000	0.000
78	A	140	ILE	0	-0.008	0.003	21.791	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	141	ILE	0	-0.001	-0.010	20.040	0.001	0.001	0.000	0.000	0.000	0.000
80	A	142	ASN	0	-0.035	-0.024	23.992	0.017	0.017	0.000	0.000	0.000	0.000
81	A	143	TYR	0	-0.041	-0.060	26.426	0.001	0.001	0.000	0.000	0.000	0.000
82	A	144	ARG	1	0.887	0.943	27.404	0.049	0.049	0.000	0.000	0.000	0.000
83	A	145	ASP	-1	-0.828	-0.920	29.199	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	146	ASP	-1	-0.894	-0.922	24.169	-0.114	-0.114	0.000	0.000	0.000	0.000
85	A	147	GLU	-1	-0.892	-0.933	25.634	-0.125	-0.125	0.000	0.000	0.000	0.000
86	A	148	LYS	1	0.778	0.885	27.697	0.076	0.076	0.000	0.000	0.000	0.000
87	A	149	SER	0	-0.078	-0.059	23.991	0.004	0.004	0.000	0.000	0.000	0.000
88	A	150	PHE	0	-0.013	0.010	25.462	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	151	SER	0	-0.037	-0.029	22.685	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	152	ARG	1	0.821	0.930	23.823	0.141	0.141	0.000	0.000	0.000	0.000
91	A	153	ARG	1	0.953	0.976	22.218	0.210	0.210	0.000	0.000	0.000	0.000
92	A	154	ILE	0	-0.021	-0.007	19.773	0.024	0.024	0.000	0.000	0.000	0.000
93	A	155	SER	0	-0.063	-0.061	20.235	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	156	HIS	1	0.791	0.896	19.875	0.208	0.208	0.000	0.000	0.000	0.000
95	A	157	LEU	0	0.074	0.041	19.231	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	158	PHE	0	-0.016	-0.003	17.585	0.020	0.020	0.000	0.000	0.000	0.000
97	A	159	PHE	0	0.054	-0.001	19.179	0.000	0.000	0.000	0.000	0.000	0.000
98	A	160	HIS	0	0.057	0.040	21.169	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	161	LYS	1	0.913	0.959	23.392	0.068	0.068	0.000	0.000	0.000	0.000
100	A	162	GLU	-1	-0.884	-0.912	24.159	-0.121	-0.121	0.000	0.000	0.000	0.000
101	A	163	ASN	0	0.013	0.000	20.887	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	164	ASP	-1	-0.904	-0.962	20.246	-0.136	-0.136	0.000	0.000	0.000	0.000
103	A	165	TRP	0	0.015	0.000	21.721	0.004	0.004	0.000	0.000	0.000	0.000
104	A	166	GLY	0	0.003	-0.003	22.394	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	167	PHE	0	-0.013	-0.004	24.697	0.011	0.011	0.000	0.000	0.000	0.000
106	A	168	SER	0	0.055	0.015	27.947	0.002	0.002	0.000	0.000	0.000	0.000
107	A	169	ASN	0	-0.005	-0.003	30.563	0.006	0.006	0.000	0.000	0.000	0.000
108	A	170	PHE	0	0.015	0.010	24.465	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	171	MET	0	0.045	0.029	29.373	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	172	ALA	0	0.044	0.028	32.060	0.003	0.003	0.000	0.000	0.000	0.000
111	A	173	TRP	0	0.012	-0.025	30.668	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	174	SER	0	0.002	0.012	34.547	0.000	0.000	0.000	0.000	0.000	0.000
113	A	175	GLU	-1	-0.883	-0.948	34.473	-0.073	-0.073	0.000	0.000	0.000	0.000
114	A	176	VAL	0	-0.021	-0.009	29.057	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	177	THR	0	-0.030	-0.045	31.755	0.003	0.003	0.000	0.000	0.000	0.000
116	A	178	ASP	-1	-0.824	-0.894	34.163	-0.042	-0.042	0.000	0.000	0.000	0.000
117	A	179	PRO	0	0.029	-0.005	34.739	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	180	GLU	-1	-0.933	-0.944	35.243	-0.042	-0.042	0.000	0.000	0.000	0.000
119	A	181	LYS	1	0.750	0.860	34.608	0.047	0.047	0.000	0.000	0.000	0.000
120	A	182	GLY	0	0.021	0.031	32.241	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	183	PHE	0	-0.028	-0.018	27.547	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	184	ILE	0	-0.046	-0.012	28.208	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	185	ASP	-1	-0.831	-0.879	29.134	-0.029	-0.029	0.000	0.000	0.000	0.000
124	A	186	ASP	-1	-0.887	-0.951	29.587	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	187	ASP	-1	-0.781	-0.861	30.963	-0.030	-0.030	0.000	0.000	0.000	0.000
126	A	188	LYS	1	0.809	0.913	25.934	0.013	0.013	0.000	0.000	0.000	0.000
127	A	189	VAL	0	0.046	0.028	25.360	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	190	THR	0	-0.004	0.007	20.035	0.003	0.003	0.000	0.000	0.000	0.000
129	A	191	PHE	0	0.033	0.023	20.658	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	192	GLU	-1	-0.791	-0.892	16.194	-0.291	-0.291	0.000	0.000	0.000	0.000
131	A	193	VAL	0	0.001	0.005	14.492	0.023	0.023	0.000	0.000	0.000	0.000
132	A	194	PHE	0	-0.008	0.014	11.925	-0.039	-0.039	0.000	0.000	0.000	0.000
133	A	195	VAL	0	0.002	-0.011	11.330	0.071	0.071	0.000	0.000	0.000	0.000
134	A	196	GLN	0	-0.037	-0.034	11.352	-0.078	-0.078	0.000	0.000	0.000	0.000
135	A	197	ALA	0	0.032	0.019	10.448	0.114	0.114	0.000	0.000	0.000	0.000
136	A	198	ASP	-1	-0.881	-0.940	11.094	-0.626	-0.626	0.000	0.000	0.000	0.000
137	A	199	ALA	0	-0.048	-0.033	11.111	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	200	PRO	0	-0.011	0.001	11.060	0.038	0.038	0.000	0.000	0.000	0.000
139	A	201	HIS	0	-0.003	-0.002	13.958	0.036	0.036	0.000	0.000	0.000	0.000
140	A	202	GLY	0	0.028	0.006	17.259	0.013	0.013	0.000	0.000	0.000	0.000
141	A	203	VAL	0	-0.019	-0.019	13.172	0.016	0.016	0.000	0.000	0.000	0.000
142	A	204	ALA	0	-0.025	-0.004	13.156	0.057	0.057	0.000	0.000	0.000	0.000
143	A	205	TRP	0	0.004	0.012	15.303	-0.031	-0.031	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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