FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VR761

Calculation Name: 4C0D-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0D

Chain ID: A

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2023-06-20

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 512
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -10227892.714227
FMO2-HF: Nuclear repulsion 10020874.962018
FMO2-HF: Total energy -207017.75221
FMO2-MP2: Total energy -207621.26318


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1842:TYR)


Summations of interaction energy for fragment #1(A:1842:TYR)
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.
-1.3370.2590.007-0.492-1.110.003
Interaction energy analysis for fragmet #1(A:1842:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / 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   
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].
3A1844ASP-1-0.762-0.8963.803-1.714-0.2780.008-0.483-0.9610.003
4A1845PRO0-0.024-0.0124.6852.0032.163-0.001-0.009-0.1490.000
5A1846PRO00.0470.0126.3450.0320.0320.0000.0000.0000.000
6A1847GLY00.0230.0118.150-0.391-0.3910.0000.0000.0000.000
7A1848LEU0-0.030-0.0149.794-0.251-0.2510.0000.0000.0000.000
8A1849ARG11.0281.00110.249-0.989-0.9890.0000.0000.0000.000
9A1850GLU-1-0.848-0.92612.0270.9460.9460.0000.0000.0000.000
10A1851LYS10.9120.97014.004-0.654-0.6540.0000.0000.0000.000
11A1852ALA00.0120.00014.696-0.088-0.0880.0000.0000.0000.000
12A1853GLU-1-0.906-0.96316.0680.3940.3940.0000.0000.0000.000
13A1854TYR0-0.079-0.04017.883-0.062-0.0620.0000.0000.0000.000
14A1855LEU00.0080.00419.246-0.042-0.0420.0000.0000.0000.000
15A1856LEU00.0280.01419.753-0.038-0.0380.0000.0000.0000.000
16A1857ARG10.9620.97421.579-0.303-0.3030.0000.0000.0000.000
17A1858GLU-1-0.911-0.96523.7620.1360.1360.0000.0000.0000.000
18A1859TRP0-0.030-0.01225.041-0.020-0.0200.0000.0000.0000.000
19A1860VAL0-0.037-0.02024.972-0.018-0.0180.0000.0000.0000.000
20A1861ASN0-0.046-0.02627.708-0.019-0.0190.0000.0000.0000.000
21A1862LEU0-0.021-0.01629.020-0.011-0.0110.0000.0000.0000.000
22A1863TYR0-0.039-0.01830.531-0.010-0.0100.0000.0000.0000.000
23A1864HIS0-0.054-0.02530.367-0.014-0.0140.0000.0000.0000.000
24A1865SER0-0.0120.01334.139-0.002-0.0020.0000.0000.0000.000
25A1866ALA00.0030.00535.804-0.006-0.0060.0000.0000.0000.000
26A1867ALA0-0.017-0.01436.6460.0000.0000.0000.0000.0000.000
27A1868ALA00.0500.02138.695-0.004-0.0040.0000.0000.0000.000
28A1869GLY00.0340.02439.2630.0010.0010.0000.0000.0000.000
29A1870ARG10.9780.97239.266-0.019-0.0190.0000.0000.0000.000
30A1871ASP-1-0.728-0.82238.9050.0390.0390.0000.0000.0000.000
31A1872SER00.015-0.00135.5730.0060.0060.0000.0000.0000.000
32A1873THR0-0.134-0.09534.7160.0010.0010.0000.0000.0000.000
33A1874LYS10.8990.94635.227-0.039-0.0390.0000.0000.0000.000
34A1875ALA00.0620.04332.7120.0050.0050.0000.0000.0000.000
35A1876PHE00.0160.01228.7810.0090.0090.0000.0000.0000.000
36A1877SER0-0.054-0.03830.3100.0030.0030.0000.0000.0000.000
37A1878ALA00.0240.00530.8290.0040.0040.0000.0000.0000.000
38A1879PHE00.0000.00423.3770.0100.0100.0000.0000.0000.000
39A1880VAL00.0360.01026.0610.0120.0120.0000.0000.0000.000
40A1881GLY00.0080.01426.0650.0040.0040.0000.0000.0000.000
41A1882GLN00.0490.01823.9620.0190.0190.0000.0000.0000.000
42A1883MET00.0100.01521.3190.0220.0220.0000.0000.0000.000
43A1884HIS0-0.069-0.04821.4260.0030.0030.0000.0000.0000.000
44A1885GLN0-0.038-0.01922.2150.0190.0190.0000.0000.0000.000
45A1886GLN0-0.041-0.01118.9900.0500.0500.0000.0000.0000.000
46A1887GLY0-0.059-0.03217.9880.0470.0470.0000.0000.0000.000
47A1888ILE0-0.001-0.00116.0570.0230.0230.0000.0000.0000.000
48A1889LEU0-0.023-0.02417.316-0.033-0.0330.0000.0000.0000.000
49A1890LYS10.9380.98617.057-0.165-0.1650.0000.0000.0000.000
50A1891THR00.0180.00814.409-0.031-0.0310.0000.0000.0000.000
51A1892ASP-1-0.816-0.91317.052-0.134-0.1340.0000.0000.0000.000
52A1893ASP-1-0.923-0.96710.718-0.437-0.4370.0000.0000.0000.000
53A1894LEU00.0510.00611.4650.0130.0130.0000.0000.0000.000
54A1895ILE00.0230.02813.8230.0500.0500.0000.0000.0000.000
55A1896THR0-0.028-0.02912.9710.0350.0350.0000.0000.0000.000
56A1897ARG10.8290.9266.5850.4960.4960.0000.0000.0000.000
57A1898PHE00.0270.02312.5710.0770.0770.0000.0000.0000.000
58A1899PHE00.0340.00315.4530.0200.0200.0000.0000.0000.000
59A1900ARG10.8410.9278.830-0.021-0.0210.0000.0000.0000.000
60A1901LEU00.0220.02510.1810.0010.0010.0000.0000.0000.000
61A1902CYS0-0.049-0.02014.0640.0220.0220.0000.0000.0000.000
62A1903THR0-0.004-0.02916.262-0.008-0.0080.0000.0000.0000.000
63A1904GLU-1-0.820-0.90210.860-0.062-0.0620.0000.0000.0000.000
64A1905MET0-0.0360.00615.2360.0360.0360.0000.0000.0000.000
65A1906CYS0-0.064-0.03417.591-0.006-0.0060.0000.0000.0000.000
66A1907VAL00.0140.00816.7340.0020.0020.0000.0000.0000.000
67A1908GLU-1-0.886-0.95414.7130.1090.1090.0000.0000.0000.000
68A1909ILE0-0.094-0.03818.1240.0070.0070.0000.0000.0000.000
69A1910SER0-0.031-0.03421.601-0.011-0.0110.0000.0000.0000.000
70A1911TYR00.013-0.00118.0430.0030.0030.0000.0000.0000.000
71A1912ARG10.9210.96617.596-0.255-0.2550.0000.0000.0000.000
72A1913ALA00.0050.01422.840-0.002-0.0020.0000.0000.0000.000
73A1914GLN0-0.022-0.01824.476-0.004-0.0040.0000.0000.0000.000
74A1915ALA00.0180.01023.382-0.005-0.0050.0000.0000.0000.000
75A1916GLU-1-0.944-0.97425.4920.0930.0930.0000.0000.0000.000
76A1917GLN0-0.040-0.02928.136-0.005-0.0050.0000.0000.0000.000
77A1918GLN0-0.053-0.03227.683-0.004-0.0040.0000.0000.0000.000
78A1919HIS0-0.040-0.01325.9450.0050.0050.0000.0000.0000.000
79A1920ASN0-0.0160.00230.475-0.002-0.0020.0000.0000.0000.000
80A1921PRO00.0370.01633.448-0.002-0.0020.0000.0000.0000.000
81A1922ALA0-0.035-0.01235.273-0.003-0.0030.0000.0000.0000.000
82A1923ALA0-0.0100.01334.1450.0000.0000.0000.0000.0000.000
83A1924ASN00.0410.00336.272-0.008-0.0080.0000.0000.0000.000
84A1925PRO00.0780.02534.0260.0030.0030.0000.0000.0000.000
85A1926THR0-0.046-0.02033.920-0.003-0.0030.0000.0000.0000.000
86A1927MET00.0030.00432.6210.0000.0000.0000.0000.0000.000
87A1928ILE00.0750.03729.4370.0040.0040.0000.0000.0000.000
88A1929ARG10.9630.97429.758-0.007-0.0070.0000.0000.0000.000
89A1930ALA0-0.0040.00630.831-0.002-0.0020.0000.0000.0000.000
90A1931LYS10.9690.99628.217-0.097-0.0970.0000.0000.0000.000
91A1932CYS0-0.0040.00426.3190.0060.0060.0000.0000.0000.000
92A1933TYR0-0.041-0.04127.298-0.005-0.0050.0000.0000.0000.000
93A1934HIS00.0460.04629.3970.0030.0030.0000.0000.0000.000
94A1935ASN0-0.002-0.01624.6080.0140.0140.0000.0000.0000.000
95A1936LEU0-0.0230.00423.056-0.003-0.0030.0000.0000.0000.000
96A1937ASP-1-0.794-0.87826.198-0.003-0.0030.0000.0000.0000.000
97A1938ALA00.0120.01527.118-0.004-0.0040.0000.0000.0000.000
98A1939PHE00.014-0.00320.1400.0010.0010.0000.0000.0000.000
99A1940VAL00.0290.01925.452-0.010-0.0100.0000.0000.0000.000
100A1941ARG10.9000.96227.215-0.013-0.0130.0000.0000.0000.000
101A1942LEU0-0.014-0.00723.448-0.004-0.0040.0000.0000.0000.000
102A1943ILE00.0190.00622.659-0.008-0.0080.0000.0000.0000.000
103A1944ALA00.0060.00426.238-0.009-0.0090.0000.0000.0000.000
104A1945LEU0-0.065-0.03229.762-0.004-0.0040.0000.0000.0000.000
105A1946LEU00.0270.01223.9770.0000.0000.0000.0000.0000.000
106A1947VAL0-0.016-0.00627.005-0.006-0.0060.0000.0000.0000.000
107A1948LYS10.8930.95428.9950.0180.0180.0000.0000.0000.000
108A1949HIS0-0.077-0.03031.5580.0000.0000.0000.0000.0000.000
109A1950SER0-0.0010.01727.6090.0050.0050.0000.0000.0000.000
110A1951GLY00.0140.01030.188-0.008-0.0080.0000.0000.0000.000
111A1952GLU-1-0.883-0.94431.996-0.016-0.0160.0000.0000.0000.000
112A1953ALA0-0.020-0.02035.479-0.004-0.0040.0000.0000.0000.000
113A1954THR0-0.001-0.00737.807-0.003-0.0030.0000.0000.0000.000
114A1955ASN00.0090.01333.024-0.001-0.0010.0000.0000.0000.000
115A1956THR00.0460.01833.292-0.003-0.0030.0000.0000.0000.000
116A1957VAL00.0220.00729.577-0.006-0.0060.0000.0000.0000.000
117A1958THR00.0170.00728.122-0.013-0.0130.0000.0000.0000.000
118A1959LYS10.8620.93227.4600.0360.0360.0000.0000.0000.000
119A1960ILE00.0270.01328.109-0.007-0.0070.0000.0000.0000.000
120A1961ASN00.0010.00424.775-0.021-0.0210.0000.0000.0000.000
121A1962LEU0-0.0030.00622.589-0.022-0.0220.0000.0000.0000.000
122A1963LEU00.0210.01623.516-0.008-0.0080.0000.0000.0000.000
123A1964ASN0-0.018-0.04423.690-0.016-0.0160.0000.0000.0000.000
124A1965LYS10.8570.96016.9200.1890.1890.0000.0000.0000.000
125A1966VAL00.012-0.00319.264-0.034-0.0340.0000.0000.0000.000
126A1967LEU0-0.011-0.00119.848-0.014-0.0140.0000.0000.0000.000
127A1968GLY00.0390.02119.032-0.016-0.0160.0000.0000.0000.000
128A1969ILE0-0.055-0.01614.716-0.060-0.0600.0000.0000.0000.000
129A1970VAL0-0.013-0.00615.661-0.039-0.0390.0000.0000.0000.000
130A1971VAL00.003-0.00117.747-0.007-0.0070.0000.0000.0000.000
131A1972GLY00.0000.00414.143-0.018-0.0180.0000.0000.0000.000
132A1973VAL0-0.004-0.01013.032-0.074-0.0740.0000.0000.0000.000
133A1974LEU0-0.021-0.00214.1150.0090.0090.0000.0000.0000.000
134A1975LEU0-0.035-0.03214.9620.0230.0230.0000.0000.0000.000
135A1976GLN00.0310.0288.129-0.103-0.1030.0000.0000.0000.000
136A1977ASP-1-0.786-0.91012.068-0.148-0.1480.0000.0000.0000.000
137A1978HIS0-0.007-0.01913.8930.0870.0870.0000.0000.0000.000
138A1979ASP-1-0.966-0.98412.155-0.610-0.6100.0000.0000.0000.000
139A1980VAL0-0.0330.00110.0660.0330.0330.0000.0000.0000.000
140A1981ARG10.9120.96412.6600.0830.0830.0000.0000.0000.000
141A1982GLN00.0000.00615.8960.0730.0730.0000.0000.0000.000
142A1983SER0-0.025-0.01518.4200.0080.0080.0000.0000.0000.000
143A1984GLU-1-0.982-0.99218.424-0.008-0.0080.0000.0000.0000.000
144A1985PHE0-0.046-0.01317.8380.0140.0140.0000.0000.0000.000
145A1986GLN0-0.005-0.00319.9340.0230.0230.0000.0000.0000.000
146A1987GLN00.0660.02321.401-0.014-0.0140.0000.0000.0000.000
147A1988LEU0-0.054-0.02623.823-0.002-0.0020.0000.0000.0000.000
148A1989PRO00.0570.02220.8380.0030.0030.0000.0000.0000.000
149A1990TYR00.0670.01316.587-0.001-0.0010.0000.0000.0000.000
150A1991HIS0-0.034-0.01122.715-0.007-0.0070.0000.0000.0000.000
151A1992ARG10.8440.91326.3490.0080.0080.0000.0000.0000.000
152A1993ILE00.0300.00521.6890.0050.0050.0000.0000.0000.000
153A1994PHE00.0200.00321.7410.0030.0030.0000.0000.0000.000
154A1995ILE00.003-0.00126.8300.0030.0030.0000.0000.0000.000
155A1996MET0-0.006-0.00129.4420.0050.0050.0000.0000.0000.000
156A1997LEU00.0280.01725.6020.0050.0050.0000.0000.0000.000
157A1998LEU0-0.032-0.01229.4180.0010.0010.0000.0000.0000.000
158A1999LEU0-0.065-0.05131.6980.0030.0030.0000.0000.0000.000
159A2000GLU-1-0.894-0.94831.623-0.009-0.0090.0000.0000.0000.000
160A2001LEU0-0.029-0.02429.3170.0020.0020.0000.0000.0000.000
161A2002ASN0-0.048-0.01433.706-0.004-0.0040.0000.0000.0000.000
162A2003ALA00.0080.00336.8990.0030.0030.0000.0000.0000.000
163A2004PRO0-0.0030.00238.874-0.003-0.0030.0000.0000.0000.000
164A2005GLU-1-0.871-0.94837.600-0.017-0.0170.0000.0000.0000.000
165A2006HIS00.0620.01640.721-0.004-0.0040.0000.0000.0000.000
166A2007VAL00.0230.00736.052-0.004-0.0040.0000.0000.0000.000
167A2008LEU0-0.022-0.00634.587-0.006-0.0060.0000.0000.0000.000
168A2009GLU-1-0.957-0.96437.256-0.053-0.0530.0000.0000.0000.000
169A2010THR0-0.099-0.05238.653-0.005-0.0050.0000.0000.0000.000
170A2011ILE00.0170.00932.689-0.005-0.0050.0000.0000.0000.000
171A2012ASN00.0470.03934.737-0.010-0.0100.0000.0000.0000.000
172A2013PHE00.0440.01335.485-0.005-0.0050.0000.0000.0000.000
173A2014GLN00.0460.01831.919-0.003-0.0030.0000.0000.0000.000
174A2015THR0-0.0040.00230.939-0.012-0.0120.0000.0000.0000.000
175A2016LEU00.004-0.00330.845-0.009-0.0090.0000.0000.0000.000
176A2017THR0-0.013-0.02030.299-0.007-0.0070.0000.0000.0000.000
177A2018ALA00.0020.01426.854-0.013-0.0130.0000.0000.0000.000
178A2019PHE0-0.009-0.01226.921-0.017-0.0170.0000.0000.0000.000
179A2020CYS0-0.013-0.00128.343-0.004-0.0040.0000.0000.0000.000
180A2021ASN00.007-0.00626.021-0.003-0.0030.0000.0000.0000.000
181A2022THR0-0.004-0.00223.273-0.025-0.0250.0000.0000.0000.000
182A2023PHE00.020-0.00324.423-0.013-0.0130.0000.0000.0000.000
183A2024HIS0-0.052-0.00526.663-0.011-0.0110.0000.0000.0000.000
184A2025ILE0-0.023-0.02420.291-0.008-0.0080.0000.0000.0000.000
185A2026LEU0-0.046-0.00520.483-0.020-0.0200.0000.0000.0000.000
186A2027ARG10.9330.98923.5490.2570.2570.0000.0000.0000.000
187A2028PRO00.0770.05124.635-0.016-0.0160.0000.0000.0000.000
188A2029THR0-0.003-0.02325.9570.0020.0020.0000.0000.0000.000
189A2030LYS10.8290.92021.4470.3100.3100.0000.0000.0000.000
190A2031ALA00.0420.02420.835-0.028-0.0280.0000.0000.0000.000
191A2032PRO00.0200.01821.9980.0230.0230.0000.0000.0000.000
192A2033GLY00.0180.01422.9690.0190.0190.0000.0000.0000.000
193A2034PHE00.0020.00222.6750.0170.0170.0000.0000.0000.000
194A2035VAL0-0.0060.00124.6870.0080.0080.0000.0000.0000.000
195A2036TYR00.005-0.01028.0520.0070.0070.0000.0000.0000.000
196A2037ALA00.0640.02527.1270.0040.0040.0000.0000.0000.000
197A2038TRP0-0.006-0.01626.7810.0110.0110.0000.0000.0000.000
198A2039LEU00.0220.00528.9360.0030.0030.0000.0000.0000.000
199A2040GLU-1-0.963-0.97132.022-0.052-0.0520.0000.0000.0000.000
200A2041LEU0-0.067-0.02727.2150.0050.0050.0000.0000.0000.000
201A2042ILE0-0.0120.01531.7710.0020.0020.0000.0000.0000.000
202A2043SER0-0.082-0.07234.0790.0070.0070.0000.0000.0000.000
203A2044HIS00.0580.03335.0090.0050.0050.0000.0000.0000.000
204A2045ARG11.0110.98837.0680.0320.0320.0000.0000.0000.000
205A2046ILE0-0.023-0.00536.7570.0000.0000.0000.0000.0000.000
206A2047PHE00.0420.01832.983-0.001-0.0010.0000.0000.0000.000
207A2048ILE00.0300.02136.969-0.003-0.0030.0000.0000.0000.000
208A2049ALA0-0.0070.00739.8090.0000.0000.0000.0000.0000.000
209A2050ARG10.9090.96238.0300.0510.0510.0000.0000.0000.000
210A2051MET0-0.0100.04235.979-0.002-0.0020.0000.0000.0000.000
211A2052LEU0-0.055-0.02839.291-0.002-0.0020.0000.0000.0000.000
212A2053ALA0-0.0080.00542.6770.0030.0030.0000.0000.0000.000
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