FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: YMVK2

Calculation Name: 4J8S-A-Xray549

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J8S

Chain ID: A

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2104494.512576
FMO2-HF: Nuclear repulsion 2028558.659435
FMO2-HF: Total energy -75935.853141
FMO2-MP2: Total energy -76155.59322


3D Structure Molmil
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:815:GLN)


Summations of interaction energy for fragment #1(A:815:GLN)
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.
-50.179-46.30.236-2.044-2.071-0.018
Interaction energy analysis for fragmet #1(A:815:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.910
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].
3A817THR0-0.040-0.0202.744-19.907-16.4390.238-2.003-1.702-0.018
4A818ASP-1-0.823-0.8775.206-25.147-25.046-0.001-0.006-0.0940.000
76A890ARG10.8980.9424.25342.08442.394-0.001-0.035-0.2750.000
5A819LEU0-0.014-0.0178.3080.3320.3320.0000.0000.0000.000
6A820SER0-0.008-0.02911.4902.9572.9570.0000.0000.0000.000
7A821GLN0-0.019-0.02013.0170.8500.8500.0000.0000.0000.000
8A822VAL0-0.070-0.02514.3951.2151.2150.0000.0000.0000.000
9A823TRP0-0.015-0.00513.8271.0501.0500.0000.0000.0000.000
10A824PRO0-0.007-0.00216.663-0.703-0.7030.0000.0000.0000.000
11A825GLU-1-0.798-0.89114.459-20.238-20.2380.0000.0000.0000.000
12A826ALA0-0.0020.01818.1300.8310.8310.0000.0000.0000.000
13A827ASN0-0.037-0.02621.6180.2370.2370.0000.0000.0000.000
14A828GLN00.0510.00721.0570.7020.7020.0000.0000.0000.000
15A829HIS0-0.052-0.02424.2550.1120.1120.0000.0000.0000.000
16A830PHE00.0080.00826.5170.4110.4110.0000.0000.0000.000
17A831SER0-0.035-0.01621.396-0.173-0.1730.0000.0000.0000.000
18A832LYS10.9030.94022.53411.40211.4020.0000.0000.0000.000
19A833GLU-1-0.823-0.91823.548-11.600-11.6000.0000.0000.0000.000
20A834ILE0-0.022-0.01122.1930.1510.1510.0000.0000.0000.000
21A835ASP-1-0.826-0.90719.167-16.553-16.5530.0000.0000.0000.000
22A836ASP-1-0.886-0.93121.577-12.536-12.5360.0000.0000.0000.000
23A837GLU-1-0.882-0.93824.254-10.905-10.9050.0000.0000.0000.000
24A838ALA00.013-0.00521.1000.1820.1820.0000.0000.0000.000
25A839ASN0-0.034-0.01519.8780.4690.4690.0000.0000.0000.000
26A840SER00.0320.02222.3710.3070.3070.0000.0000.0000.000
27A841TYR00.006-0.00724.9350.5110.5110.0000.0000.0000.000
28A842PHE0-0.0020.00519.0140.1910.1910.0000.0000.0000.000
29A843GLN0-0.025-0.01423.2980.5470.5470.0000.0000.0000.000
30A844ARG10.8770.92724.98810.93410.9340.0000.0000.0000.000
31A845ILE0-0.0140.01023.4160.3350.3350.0000.0000.0000.000
32A846TYR0-0.028-0.03719.8950.0460.0460.0000.0000.0000.000
33A847ASN0-0.021-0.00725.5770.0330.0330.0000.0000.0000.000
34A848HIS0-0.068-0.04328.590-0.161-0.1610.0000.0000.0000.000
35A849PRO00.0460.03131.8510.0410.0410.0000.0000.0000.000
36A850PRO0-0.020-0.01435.190-0.046-0.0460.0000.0000.0000.000
37A851HIS00.0080.01231.5350.1910.1910.0000.0000.0000.000
38A852PRO00.0100.00032.547-0.001-0.0010.0000.0000.0000.000
39A853THR0-0.0030.00030.917-0.280-0.2800.0000.0000.0000.000
40A854MET0-0.018-0.01229.4970.1240.1240.0000.0000.0000.000
41A855SER0-0.028-0.03729.752-0.319-0.3190.0000.0000.0000.000
42A856VAL00.038-0.00525.891-0.156-0.1560.0000.0000.0000.000
43A857ASP-1-0.832-0.90528.034-10.367-10.3670.0000.0000.0000.000
44A858GLU-1-0.836-0.87830.663-9.305-9.3050.0000.0000.0000.000
45A859VAL00.0040.00024.877-0.058-0.0580.0000.0000.0000.000
46A860LEU0-0.047-0.01724.778-0.256-0.2560.0000.0000.0000.000
47A861GLU-1-0.861-0.91027.863-9.419-9.4190.0000.0000.0000.000
48A862MET00.0150.01126.8790.1290.1290.0000.0000.0000.000
49A863LEU0-0.018-0.01422.946-0.110-0.1100.0000.0000.0000.000
50A864GLN0-0.037-0.03026.668-0.176-0.1760.0000.0000.0000.000
51A865ARG10.8240.91128.8449.6219.6210.0000.0000.0000.000
52A866PHE0-0.019-0.02726.6740.0700.0700.0000.0000.0000.000
53A867LYS10.8210.91924.05912.08812.0880.0000.0000.0000.000
54A868ASP-1-0.842-0.91326.266-11.783-11.7830.0000.0000.0000.000
55A869SER0-0.015-0.00928.9300.5090.5090.0000.0000.0000.000
56A870THR00.008-0.00430.773-0.262-0.2620.0000.0000.0000.000
57A871ILE0-0.0090.00031.886-0.037-0.0370.0000.0000.0000.000
58A872LYS10.9200.96026.39311.47811.4780.0000.0000.0000.000
59A873ARG10.8910.94227.42710.72610.7260.0000.0000.0000.000
60A874GLU-1-0.831-0.88727.148-10.253-10.2530.0000.0000.0000.000
61A875ARG10.8950.94425.53310.61310.6130.0000.0000.0000.000
62A876GLU-1-0.882-0.96223.121-12.979-12.9790.0000.0000.0000.000
63A877VAL00.0320.02122.233-0.736-0.7360.0000.0000.0000.000
64A878PHE00.0070.00521.666-0.569-0.5690.0000.0000.0000.000
65A879ASN0-0.005-0.01719.463-0.606-0.6060.0000.0000.0000.000
66A880CYS0-0.041-0.01218.073-1.266-1.2660.0000.0000.0000.000
67A881MET0-0.0220.00117.627-0.740-0.7400.0000.0000.0000.000
68A882LEU0-0.004-0.00917.610-0.722-0.7220.0000.0000.0000.000
69A883ARG10.8220.90613.08119.12119.1210.0000.0000.0000.000
70A884ASN00.005-0.00812.828-2.619-2.6190.0000.0000.0000.000
71A885LEU0-0.023-0.00513.114-1.310-1.3100.0000.0000.0000.000
72A886PHE0-0.010-0.02211.796-0.232-0.2320.0000.0000.0000.000
73A887GLU-1-0.865-0.9448.619-31.541-31.5410.0000.0000.0000.000
74A888GLU-1-0.837-0.8998.604-26.832-26.8320.0000.0000.0000.000
75A889TYR0-0.050-0.0179.1930.2600.2600.0000.0000.0000.000
77A891PHE0-0.023-0.0197.068-0.456-0.4560.0000.0000.0000.000
78A892PHE00.0260.03711.0741.7311.7310.0000.0000.0000.000
79A893PRO0-0.010-0.02811.7541.3721.3720.0000.0000.0000.000
80A894GLN0-0.037-0.0289.8061.3481.3480.0000.0000.0000.000
81A895TYR0-0.038-0.02714.4251.2231.2230.0000.0000.0000.000
82A896PRO00.0360.02317.5440.2010.2010.0000.0000.0000.000
83A897ASP-1-0.861-0.94721.107-13.355-13.3550.0000.0000.0000.000
84A898LYS10.8380.93222.83611.33911.3390.0000.0000.0000.000
85A899GLU-1-0.774-0.89821.316-12.326-12.3260.0000.0000.0000.000
86A900LEU0-0.0200.01617.445-0.367-0.3670.0000.0000.0000.000
87A901HIS00.0490.01620.583-0.481-0.4810.0000.0000.0000.000
88A902ILE00.0030.00623.7260.1520.1520.0000.0000.0000.000
89A903THR00.003-0.00817.461-0.072-0.0720.0000.0000.0000.000
90A904ALA0-0.031-0.00420.393-0.332-0.3320.0000.0000.0000.000
91A905CYS0-0.036-0.01921.3180.2470.2470.0000.0000.0000.000
92A906LEU00.0160.00420.8920.2940.2940.0000.0000.0000.000
93A907PHE0-0.022-0.00714.8450.0710.0710.0000.0000.0000.000
94A908GLY00.0350.00520.152-0.026-0.0260.0000.0000.0000.000
95A909GLY0-0.016-0.01222.6560.4230.4230.0000.0000.0000.000
96A910ILE00.0100.00619.6380.3610.3610.0000.0000.0000.000
97A911ILE0-0.046-0.01219.2360.0940.0940.0000.0000.0000.000
98A912GLU-1-0.775-0.87022.924-9.999-9.9990.0000.0000.0000.000
99A913LYS10.8230.89826.23810.53810.5380.0000.0000.0000.000
100A914GLY0-0.0010.01625.1650.1960.1960.0000.0000.0000.000
101A915LEU0-0.026-0.01023.122-0.041-0.0410.0000.0000.0000.000
102A916VAL0-0.0240.00018.139-0.530-0.5300.0000.0000.0000.000
103A917THR00.026-0.00220.9560.3580.3580.0000.0000.0000.000
104A918TYR00.0330.00020.113-0.767-0.7670.0000.0000.0000.000
105A919MET00.0030.01711.7180.1060.1060.0000.0000.0000.000
106A920ALA00.0800.03715.537-0.923-0.9230.0000.0000.0000.000
107A921LEU0-0.0040.01416.622-0.339-0.3390.0000.0000.0000.000
108A922GLY00.0230.00917.4180.0370.0370.0000.0000.0000.000
109A923LEU0-0.044-0.01610.047-0.428-0.4280.0000.0000.0000.000
110A924ALA00.0350.02014.068-0.596-0.5960.0000.0000.0000.000
111A925LEU00.0260.01516.3370.0700.0700.0000.0000.0000.000
112A926ARG10.8790.9338.47327.79127.7910.0000.0000.0000.000
113A927TYR0-0.005-0.0048.647-1.118-1.1180.0000.0000.0000.000
114A928VAL00.0330.03014.0250.1580.1580.0000.0000.0000.000
115A929LEU0-0.0030.00517.1850.3780.3780.0000.0000.0000.000
116A930GLU-1-0.873-0.94011.072-24.982-24.9820.0000.0000.0000.000
117A931ALA0-0.0390.00215.142-0.235-0.2350.0000.0000.0000.000
118A932LEU00.0160.01616.6910.4950.4950.0000.0000.0000.000
119A933ARG10.9560.98316.38717.06817.0680.0000.0000.0000.000
120A934LYS10.8430.93112.84420.62920.6290.0000.0000.0000.000
121A935PRO00.0340.00818.3750.5730.5730.0000.0000.0000.000
122A936PHE00.0620.04421.509-0.144-0.1440.0000.0000.0000.000
123A937GLY00.0190.01524.8640.1050.1050.0000.0000.0000.000
124A938SER0-0.046-0.03519.829-0.276-0.2760.0000.0000.0000.000
125A939LYS10.8870.93417.71515.27815.2780.0000.0000.0000.000
126A940MET00.0050.00714.2900.0110.0110.0000.0000.0000.000
127A941TYR00.0040.02518.5570.0230.0230.0000.0000.0000.000
128A942TYR00.0270.00021.4000.2770.2770.0000.0000.0000.000
129A943PHE0-0.0030.00316.9460.1880.1880.0000.0000.0000.000
130A944GLY00.0340.00120.0140.0330.0330.0000.0000.0000.000
131A945ILE0-0.015-0.01520.7230.2950.2950.0000.0000.0000.000
132A946ALA0-0.014-0.00723.7560.3710.3710.0000.0000.0000.000
133A947ALA00.0030.00320.8280.2290.2290.0000.0000.0000.000
134A948LEU0-0.023-0.02222.8020.2840.2840.0000.0000.0000.000
135A949ASP-1-0.816-0.89724.466-9.723-9.7230.0000.0000.0000.000
136A950ARG10.8210.91325.42411.45711.4570.0000.0000.0000.000
137A951PHE00.0140.01521.9480.1720.1720.0000.0000.0000.000
138A952LYS10.8520.92127.0859.8329.8320.0000.0000.0000.000
139A953ASN0-0.023-0.03529.135-0.099-0.0990.0000.0000.0000.000
140A954ARG10.9030.94626.70811.21611.2160.0000.0000.0000.000
141A955LEU0-0.0280.00025.357-0.222-0.2220.0000.0000.0000.000
142A956LYS10.8580.92128.1498.7668.7660.0000.0000.0000.000
143A957ASP-1-0.906-0.94528.585-9.853-9.8530.0000.0000.0000.000
144A958TYR0-0.066-0.03824.473-0.390-0.3900.0000.0000.0000.000
145A959PRO00.0690.04226.371-0.342-0.3420.0000.0000.0000.000
146A960GLN0-0.019-0.02824.903-0.443-0.4430.0000.0000.0000.000
147A961TYR0-0.011-0.02219.1090.0350.0350.0000.0000.0000.000
148A962CYS0-0.0200.01823.569-0.190-0.1900.0000.0000.0000.000
149A963GLN00.0270.01626.5190.3700.3700.0000.0000.0000.000
150A964HIS0-0.045-0.03021.105-0.228-0.2280.0000.0000.0000.000
151A965LEU0-0.0080.00021.736-0.326-0.3260.0000.0000.0000.000
152A966ALA00.0350.01924.0320.0040.0040.0000.0000.0000.000
153A967SER0-0.111-0.05423.6890.0290.0290.0000.0000.0000.000
154A968ILE0-0.053-0.01521.397-0.397-0.3970.0000.0000.0000.000
155A969SER00.012-0.00424.1070.2820.2820.0000.0000.0000.000
156A970HIS0-0.018-0.00422.0370.6880.6880.0000.0000.0000.000
157A971PHE0-0.0110.00326.8360.0780.0780.0000.0000.0000.000
158A972MET00.0250.00527.8870.2600.2600.0000.0000.0000.000
159A973GLN0-0.041-0.01729.1470.0450.0450.0000.0000.0000.000
160A974PHE0-0.0060.00123.929-0.200-0.2000.0000.0000.0000.000
161A975PRO00.0130.01129.2470.3380.3380.0000.0000.0000.000
162A976HIS00.0030.00432.202-0.213-0.2130.0000.0000.0000.000
163A977HIS00.0360.00831.9630.0800.0800.0000.0000.0000.000
164A978LEU0-0.021-0.01627.699-0.122-0.1220.0000.0000.0000.000
165A979GLN0-0.023-0.01530.399-0.144-0.1440.0000.0000.0000.000
166A980GLU-1-0.846-0.92032.045-8.218-8.2180.0000.0000.0000.000
167A981TYR0-0.083-0.10330.864-0.032-0.0320.0000.0000.0000.000
168A982ILE0-0.0300.00026.532-0.214-0.2140.0000.0000.0000.000
169A983GLU-1-0.891-0.95630.031-9.120-9.1200.0000.0000.0000.000
170A984TYR0-0.050-0.04132.8760.2560.2560.0000.0000.0000.000
171A985GLY00.0860.03830.6890.0870.0870.0000.0000.0000.000
172A986GLN0-0.038-0.03529.399-0.053-0.0530.0000.0000.0000.000
173A987GLN0-0.080-0.03431.3180.2000.2000.0000.0000.0000.000
174A988SER0-0.029-0.00932.9100.1490.1490.0000.0000.0000.000
175A989ARG10.8870.95333.8758.0908.0900.0000.0000.0000.000
176A990ASP-1-0.774-0.87834.895-8.760-8.7600.0000.0000.0000.000
177A991PRO00.0100.00334.8390.1460.1460.0000.0000.0000.000
178A992PRO0-0.032-0.02437.5020.1220.1220.0000.0000.0000.000
179A993VAL0-0.027-0.01039.8170.2280.2280.0000.0000.0000.000
180A994LYS00.0290.05836.348-0.331-0.3310.0000.0000.0000.000