FMO DATABASE

FMODB ID: GNRM1

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	OptH
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1389522.053464
FMO2-HF: Nuclear repulsion	1330330.974494
FMO2-HF: Total energy	-59191.07897
FMO2-MP2: Total energy	-59363.055051

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.
-10.565	-13.267	23.123	-8.647	-11.773	-0.015

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 : -0.003 / 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	A	65	TRP	0	0.027	0.041	1.842	-11.900	-16.229	21.007	-7.730	-8.948	-0.010
4	A	66	ARG	1	0.858	0.940	2.229	-0.499	1.137	2.067	-1.059	-2.643	-0.005
5	A	67	SER	0	0.056	0.008	3.396	0.799	0.790	0.049	0.142	-0.182	0.000
6	A	68	GLU	-1	-0.881	-0.943	6.778	-0.646	-0.646	0.000	0.000	0.000	0.000
7	A	69	ALA	0	-0.023	-0.014	6.698	-0.426	-0.426	0.000	0.000	0.000	0.000
8	A	70	THR	0	0.033	0.021	8.494	0.113	0.113	0.000	0.000	0.000	0.000
9	A	71	PHE	0	-0.044	-0.019	10.510	0.092	0.092	0.000	0.000	0.000	0.000
10	A	72	GLN	0	0.020	-0.008	12.335	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	73	PHE	0	-0.008	-0.013	15.611	0.068	0.068	0.000	0.000	0.000	0.000
12	A	74	THR	0	0.019	0.007	18.298	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	75	VAL	0	-0.037	-0.006	21.561	0.021	0.021	0.000	0.000	0.000	0.000
14	A	76	GLU	-1	-0.885	-0.962	24.564	0.148	0.148	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.924	0.959	27.267	-0.137	-0.137	0.000	0.000	0.000	0.000
16	A	78	PHE	0	0.046	0.023	27.173	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	79	SER	0	-0.052	-0.050	30.238	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	80	ARG	1	0.862	0.922	33.186	-0.075	-0.075	0.000	0.000	0.000	0.000
19	A	81	LEU	0	-0.032	0.008	27.743	0.003	0.003	0.000	0.000	0.000	0.000
20	A	82	SER	0	-0.030	-0.027	31.769	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	83	GLU	-1	-0.924	-0.964	30.029	0.093	0.093	0.000	0.000	0.000	0.000
22	A	84	SER	0	-0.056	-0.036	25.940	0.005	0.005	0.000	0.000	0.000	0.000
23	A	85	VAL	0	0.025	0.028	23.457	0.013	0.013	0.000	0.000	0.000	0.000
24	A	86	LEU	0	-0.007	-0.030	19.942	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	87	SER	0	-0.018	0.005	15.574	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	88	PRO	0	0.034	0.003	14.414	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	89	PRO	0	-0.006	0.008	12.164	-0.046	-0.046	0.000	0.000	0.000	0.000
28	A	90	CYS	0	-0.045	-0.004	8.727	0.198	0.198	0.000	0.000	0.000	0.000
29	A	91	PHE	0	0.023	0.001	6.505	-0.132	-0.132	0.000	0.000	0.000	0.000
30	A	92	VAL	0	0.014	0.014	6.034	-0.446	-0.446	0.000	0.000	0.000	0.000
31	A	93	ARG	1	0.857	0.933	5.942	1.516	1.516	0.000	0.000	0.000	0.000
32	A	94	ASN	0	-0.031	-0.044	6.047	0.702	0.702	0.000	0.000	0.000	0.000
33	A	95	LEU	0	0.011	0.017	7.980	0.181	0.181	0.000	0.000	0.000	0.000
34	A	96	PRO	0	-0.004	0.015	10.100	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	97	TRP	0	0.015	-0.016	10.356	-0.090	-0.090	0.000	0.000	0.000	0.000
36	A	98	LYS	1	0.875	0.931	13.318	-0.235	-0.235	0.000	0.000	0.000	0.000
37	A	99	ILE	0	0.003	0.011	15.980	-0.060	-0.060	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.017	0.001	18.341	0.039	0.039	0.000	0.000	0.000	0.000
39	A	101	VAL	0	0.001	0.007	21.961	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	102	MET	0	0.035	0.025	24.857	0.012	0.012	0.000	0.000	0.000	0.000
41	A	103	PRO	0	0.008	0.033	28.551	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	104	ARG	1	0.863	0.926	30.236	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	105	PHE	0	0.005	-0.006	33.821	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	106	TYR	0	0.061	0.031	34.510	0.001	0.001	0.000	0.000	0.000	0.000
45	A	107	PRO	0	0.047	0.017	39.894	0.000	0.000	0.000	0.000	0.000	0.000
46	A	108	ASP	-1	-0.883	-0.930	43.461	0.000	0.000	0.000	0.000	0.000	0.000
47	A	109	ARG	1	0.829	0.904	41.242	0.008	0.008	0.000	0.000	0.000	0.000
48	A	110	PRO	0	0.029	0.025	41.524	0.001	0.001	0.000	0.000	0.000	0.000
49	A	111	HIS	0	0.004	0.006	42.442	0.005	0.005	0.000	0.000	0.000	0.000
50	A	112	GLN	0	-0.032	-0.029	39.156	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	113	LYS	1	0.944	0.992	35.469	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	114	SER	0	0.006	-0.003	32.393	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	115	VAL	0	0.011	0.004	27.399	0.009	0.009	0.000	0.000	0.000	0.000
54	A	116	GLY	0	-0.023	-0.014	28.360	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	117	PHE	0	-0.021	-0.015	20.017	0.013	0.013	0.000	0.000	0.000	0.000
56	A	118	PHE	0	-0.001	-0.013	22.527	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	119	LEU	0	0.009	0.014	14.894	0.016	0.016	0.000	0.000	0.000	0.000
58	A	120	GLN	0	0.053	0.006	18.021	0.019	0.019	0.000	0.000	0.000	0.000
59	A	121	CYS	0	-0.034	-0.010	14.144	0.030	0.030	0.000	0.000	0.000	0.000
60	A	122	ASN	0	0.017	-0.024	15.606	0.058	0.058	0.000	0.000	0.000	0.000
61	A	123	ALA	0	0.019	0.004	16.870	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	124	GLU	-1	-0.914	-0.936	17.505	0.427	0.427	0.000	0.000	0.000	0.000
63	A	125	SER	0	-0.049	-0.005	18.630	0.006	0.006	0.000	0.000	0.000	0.000
64	A	126	ASP	-1	-0.856	-0.926	20.518	0.124	0.124	0.000	0.000	0.000	0.000
65	A	127	SER	0	-0.082	-0.036	20.885	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	128	THR	0	-0.005	-0.028	22.724	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	129	SER	0	-0.041	-0.024	21.638	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	130	TRP	0	-0.025	0.015	16.932	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	131	SER	0	-0.008	-0.010	17.839	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	132	CYS	0	-0.024	-0.016	13.227	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	133	HIS	0	0.032	0.038	16.055	0.046	0.046	0.000	0.000	0.000	0.000
72	A	134	ALA	0	0.007	0.004	14.416	-0.073	-0.073	0.000	0.000	0.000	0.000
73	A	135	GLN	0	0.040	0.040	15.572	0.082	0.082	0.000	0.000	0.000	0.000
74	A	136	ALA	0	0.027	0.004	15.643	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	137	VAL	0	-0.034	-0.006	17.217	0.034	0.034	0.000	0.000	0.000	0.000
76	A	138	LEU	0	-0.017	-0.001	18.140	0.002	0.002	0.000	0.000	0.000	0.000
77	A	139	LYS	1	0.926	0.952	18.925	0.165	0.165	0.000	0.000	0.000	0.000
78	A	140	ILE	0	-0.002	0.016	21.348	0.017	0.017	0.000	0.000	0.000	0.000
79	A	141	ILE	0	-0.006	-0.023	19.822	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	142	ASN	0	-0.047	-0.035	23.761	0.015	0.015	0.000	0.000	0.000	0.000
81	A	143	TYR	0	-0.012	-0.018	26.294	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	144	ARG	1	0.889	0.962	27.281	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	145	ASP	-1	-0.821	-0.921	29.490	-0.059	-0.059	0.000	0.000	0.000	0.000
84	A	146	ASP	-1	-0.897	-0.931	24.170	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	147	GLU	-1	-0.939	-0.965	25.247	-0.116	-0.116	0.000	0.000	0.000	0.000
86	A	148	LYS	1	0.824	0.913	27.738	0.035	0.035	0.000	0.000	0.000	0.000
87	A	149	SER	0	-0.047	-0.015	24.196	0.014	0.014	0.000	0.000	0.000	0.000
88	A	150	PHE	0	-0.022	0.007	25.855	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	151	SER	0	-0.037	-0.028	22.468	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	152	ARG	1	0.850	0.945	23.663	0.067	0.067	0.000	0.000	0.000	0.000
91	A	153	ARG	1	0.966	0.980	21.777	0.203	0.203	0.000	0.000	0.000	0.000
92	A	154	ILE	0	-0.022	-0.002	19.385	0.021	0.021	0.000	0.000	0.000	0.000
93	A	155	SER	0	-0.028	-0.040	20.183	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	156	HIS	1	0.815	0.927	19.828	0.120	0.120	0.000	0.000	0.000	0.000
95	A	157	LEU	0	0.068	0.040	19.262	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	158	PHE	0	-0.049	-0.017	17.551	0.029	0.029	0.000	0.000	0.000	0.000
97	A	159	PHE	0	0.076	0.001	19.399	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	160	HIS	0	0.046	0.028	21.295	0.003	0.003	0.000	0.000	0.000	0.000
99	A	161	LYS	1	0.908	0.957	23.547	0.017	0.017	0.000	0.000	0.000	0.000
100	A	162	GLU	-1	-0.898	-0.931	24.402	-0.056	-0.056	0.000	0.000	0.000	0.000
101	A	163	ASN	0	0.015	0.014	20.598	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	164	ASP	-1	-0.896	-0.950	20.369	0.030	0.030	0.000	0.000	0.000	0.000
103	A	165	TRP	0	0.026	-0.004	21.554	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	166	GLY	0	-0.002	-0.001	22.099	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	167	PHE	0	-0.041	-0.012	23.962	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	168	SER	0	0.076	0.024	27.522	0.012	0.012	0.000	0.000	0.000	0.000
107	A	169	ASN	0	-0.003	0.007	30.180	0.010	0.010	0.000	0.000	0.000	0.000
108	A	170	PHE	0	-0.010	-0.003	24.583	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	171	MET	0	0.069	0.027	29.162	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	172	ALA	0	0.062	0.044	31.518	0.007	0.007	0.000	0.000	0.000	0.000
111	A	173	TRP	0	0.033	-0.015	30.535	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	174	SER	0	-0.024	-0.016	34.399	0.003	0.003	0.000	0.000	0.000	0.000
113	A	175	GLU	-1	-0.938	-0.967	34.748	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	176	VAL	0	-0.014	-0.005	29.193	0.000	0.000	0.000	0.000	0.000	0.000
115	A	177	THR	0	-0.052	-0.047	31.995	0.004	0.004	0.000	0.000	0.000	0.000
116	A	178	ASP	-1	-0.814	-0.895	34.086	0.006	0.006	0.000	0.000	0.000	0.000
117	A	179	PRO	0	0.019	-0.005	35.009	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	180	GLU	-1	-0.975	-0.981	35.521	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	181	LYS	1	0.824	0.916	33.940	0.005	0.005	0.000	0.000	0.000	0.000
120	A	182	GLY	0	-0.004	0.008	31.981	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	183	PHE	0	-0.010	-0.012	27.359	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	184	ILE	0	-0.059	-0.005	28.106	0.007	0.007	0.000	0.000	0.000	0.000
123	A	185	ASP	-1	-0.887	-0.950	29.064	0.044	0.044	0.000	0.000	0.000	0.000
124	A	186	ASP	-1	-0.898	-0.950	29.748	0.097	0.097	0.000	0.000	0.000	0.000
125	A	187	ASP	-1	-0.810	-0.900	31.097	0.077	0.077	0.000	0.000	0.000	0.000
126	A	188	LYS	1	0.876	0.953	25.865	-0.115	-0.115	0.000	0.000	0.000	0.000
127	A	189	VAL	0	0.037	0.024	25.323	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	190	THR	0	0.003	0.011	20.098	0.026	0.026	0.000	0.000	0.000	0.000
129	A	191	PHE	0	-0.007	-0.005	20.407	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	192	GLU	-1	-0.831	-0.939	15.791	-0.104	-0.104	0.000	0.000	0.000	0.000
131	A	193	VAL	0	0.001	0.004	14.489	-0.016	-0.016	0.000	0.000	0.000	0.000
132	A	194	PHE	0	-0.015	0.009	11.782	0.021	0.021	0.000	0.000	0.000	0.000
133	A	195	VAL	0	0.008	-0.006	10.969	0.023	0.023	0.000	0.000	0.000	0.000
134	A	196	GLN	0	-0.040	-0.030	11.226	-0.069	-0.069	0.000	0.000	0.000	0.000
135	A	197	ALA	0	0.013	0.009	10.293	0.115	0.115	0.000	0.000	0.000	0.000
136	A	198	ASP	-1	-0.858	-0.920	10.898	-0.715	-0.715	0.000	0.000	0.000	0.000
137	A	199	ALA	0	-0.079	-0.058	10.904	-0.020	-0.020	0.000	0.000	0.000	0.000
138	A	200	PRO	0	0.005	0.009	10.937	0.054	0.054	0.000	0.000	0.000	0.000
139	A	201	HIS	0	0.010	0.006	13.919	0.006	0.006	0.000	0.000	0.000	0.000
140	A	202	GLY	0	0.024	0.002	17.074	0.028	0.028	0.000	0.000	0.000	0.000
141	A	203	VAL	0	-0.028	-0.017	13.014	0.033	0.033	0.000	0.000	0.000	0.000
142	A	204	ALA	0	-0.016	-0.002	12.959	0.059	0.059	0.000	0.000	0.000	0.000
143	A	205	TRP	0	0.011	0.011	15.074	-0.044	-0.044	0.000	0.000	0.000	0.000

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