FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: JQG89

Calculation Name: 4J8S-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4J8S

Chain ID: A

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102966.139589
FMO2-HF: Nuclear repulsion 2027030.899392
FMO2-HF: Total energy -75935.240197
FMO2-MP2: Total energy -76154.997255


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: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.
-4.857-3.0040.004-0.602-1.2540
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 : 0 / q_Mulliken : -0.020 / 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].
3A817THR0-0.011-0.0073.769-0.6330.716-0.002-0.496-0.8510.001
4A818ASP-1-0.815-0.8755.749-1.020-1.0200.0000.0000.0000.000
5A819LEU0-0.073-0.0508.7900.1830.1830.0000.0000.0000.000
6A820SER0-0.003-0.02911.9530.0920.0920.0000.0000.0000.000
7A821GLN0-0.001-0.00612.761-0.023-0.0230.0000.0000.0000.000
8A822VAL0-0.089-0.03815.0590.0350.0350.0000.0000.0000.000
9A823TRP0-0.030-0.00614.6530.0220.0220.0000.0000.0000.000
10A824PRO00.0090.01017.076-0.032-0.0320.0000.0000.0000.000
11A825GLU-1-0.896-0.95214.382-0.343-0.3430.0000.0000.0000.000
12A826ALA0-0.0100.00718.6550.0140.0140.0000.0000.0000.000
13A827ASN0-0.006-0.01721.664-0.022-0.0220.0000.0000.0000.000
14A828GLN00.0730.00920.9990.0370.0370.0000.0000.0000.000
15A829HIS0-0.094-0.03823.9160.0030.0030.0000.0000.0000.000
16A830PHE00.000-0.00726.2810.0120.0120.0000.0000.0000.000
17A831SER0-0.0190.00821.0680.0130.0130.0000.0000.0000.000
18A832LYS10.9510.98322.5070.0640.0640.0000.0000.0000.000
19A833GLU-1-0.863-0.95123.943-0.056-0.0560.0000.0000.0000.000
20A834ILE0-0.026-0.01522.3910.0240.0240.0000.0000.0000.000
21A835ASP-1-0.869-0.93019.291-0.079-0.0790.0000.0000.0000.000
22A836ASP-1-0.878-0.93721.6130.0340.0340.0000.0000.0000.000
23A837GLU-1-0.917-0.96524.1940.0450.0450.0000.0000.0000.000
24A838ALA0-0.002-0.01121.1100.0290.0290.0000.0000.0000.000
25A839ASN0-0.015-0.00520.3390.0590.0590.0000.0000.0000.000
26A840SER00.0200.01022.0390.0400.0400.0000.0000.0000.000
27A841TYR0-0.003-0.02224.7600.0100.0100.0000.0000.0000.000
28A842PHE00.0050.00319.2810.0250.0250.0000.0000.0000.000
29A843GLN00.0010.00622.9160.0160.0160.0000.0000.0000.000
30A844ARG10.8660.92624.579-0.137-0.1370.0000.0000.0000.000
31A845ILE0-0.0350.00023.4290.0040.0040.0000.0000.0000.000
32A846TYR0-0.043-0.04319.5300.0130.0130.0000.0000.0000.000
33A847ASN0-0.037-0.00125.0550.0180.0180.0000.0000.0000.000
34A848HIS0-0.090-0.04828.0870.0200.0200.0000.0000.0000.000
35A849PRO00.0300.02631.098-0.012-0.0120.0000.0000.0000.000
36A850PRO0-0.036-0.02834.5320.0090.0090.0000.0000.0000.000
37A851HIS00.0030.00131.226-0.021-0.0210.0000.0000.0000.000
38A852PRO00.0200.00332.0390.0070.0070.0000.0000.0000.000
39A853THR00.0160.00630.5270.0080.0080.0000.0000.0000.000
40A854MET0-0.0030.00829.263-0.020-0.0200.0000.0000.0000.000
41A855SER00.0040.01229.5550.0250.0250.0000.0000.0000.000
42A856VAL00.0610.00925.947-0.005-0.0050.0000.0000.0000.000
43A857ASP-1-0.880-0.94228.3850.2380.2380.0000.0000.0000.000
44A858GLU-1-0.871-0.93931.1840.1660.1660.0000.0000.0000.000
45A859VAL00.0160.00525.154-0.014-0.0140.0000.0000.0000.000
46A860LEU0-0.043-0.02025.575-0.010-0.0100.0000.0000.0000.000
47A861GLU-1-0.889-0.92328.4500.1110.1110.0000.0000.0000.000
48A862MET00.0250.01327.416-0.017-0.0170.0000.0000.0000.000
49A863LEU0-0.038-0.02223.914-0.014-0.0140.0000.0000.0000.000
50A864GLN0-0.028-0.02727.603-0.003-0.0030.0000.0000.0000.000
51A865ARG10.8330.92329.964-0.116-0.1160.0000.0000.0000.000
52A866PHE0-0.008-0.01827.528-0.013-0.0130.0000.0000.0000.000
53A867LYS10.8790.96624.805-0.133-0.1330.0000.0000.0000.000
54A868ASP-1-0.913-0.95727.0770.0580.0580.0000.0000.0000.000
55A869SER0-0.002-0.01029.711-0.011-0.0110.0000.0000.0000.000
56A870THR0-0.015-0.01931.250-0.010-0.0100.0000.0000.0000.000
57A871ILE0-0.010-0.00432.663-0.014-0.0140.0000.0000.0000.000
58A872LYS10.9060.95327.0790.1120.1120.0000.0000.0000.000
59A873ARG10.9240.97328.1160.0290.0290.0000.0000.0000.000
60A874GLU-1-0.834-0.89228.0070.0510.0510.0000.0000.0000.000
61A875ARG10.9040.95226.1740.0270.0270.0000.0000.0000.000
62A876GLU-1-0.893-0.96523.957-0.077-0.0770.0000.0000.0000.000
63A877VAL00.0460.02523.0410.0010.0010.0000.0000.0000.000
64A878PHE00.0060.00522.5180.0260.0260.0000.0000.0000.000
65A879ASN00.004-0.01620.1480.0500.0500.0000.0000.0000.000
66A880CYS0-0.0280.00818.8600.0150.0150.0000.0000.0000.000
67A881MET00.0050.00918.1580.0200.0200.0000.0000.0000.000
68A882LEU0-0.002-0.00218.2920.0650.0650.0000.0000.0000.000
69A883ARG10.9030.95713.8360.2530.2530.0000.0000.0000.000
70A884ASN00.0180.00013.6120.0380.0380.0000.0000.0000.000
71A885LEU0-0.0150.00313.6920.1150.1150.0000.0000.0000.000
72A886PHE0-0.034-0.04312.9920.1520.1520.0000.0000.0000.000
73A887GLU-1-0.859-0.9339.6430.0070.0070.0000.0000.0000.000
74A888GLU-1-0.869-0.9239.0211.0421.0420.0000.0000.0000.000
75A889TYR0-0.042-0.0109.5290.3340.3340.0000.0000.0000.000
76A890ARG10.9300.9523.950-2.823-2.3190.006-0.106-0.403-0.001
77A891PHE0-0.010-0.0116.5940.7400.7400.0000.0000.0000.000
78A892PHE00.0280.03710.423-0.199-0.1990.0000.0000.0000.000
79A893PRO0-0.029-0.02911.510-0.217-0.2170.0000.0000.0000.000
80A894GLN0-0.043-0.0309.610-0.380-0.3800.0000.0000.0000.000
81A895TYR0-0.045-0.02313.710-0.166-0.1660.0000.0000.0000.000
82A896PRO00.0250.02017.1850.0320.0320.0000.0000.0000.000
83A897ASP-1-0.868-0.94120.8040.6930.6930.0000.0000.0000.000
84A898LYS10.9270.97422.885-0.363-0.3630.0000.0000.0000.000
85A899GLU-1-0.822-0.93120.7000.4880.4880.0000.0000.0000.000
86A900LEU0-0.0070.01617.1950.0040.0040.0000.0000.0000.000
87A901HIS00.0390.01120.3540.0240.0240.0000.0000.0000.000
88A902ILE0-0.0020.00523.455-0.020-0.0200.0000.0000.0000.000
89A903THR00.0130.00017.258-0.033-0.0330.0000.0000.0000.000
90A904ALA0-0.021-0.00220.416-0.003-0.0030.0000.0000.0000.000
91A905CYS0-0.042-0.01721.307-0.040-0.0400.0000.0000.0000.000
92A906LEU0-0.0050.00120.989-0.033-0.0330.0000.0000.0000.000
93A907PHE0-0.013-0.00515.803-0.017-0.0170.0000.0000.0000.000
94A908GLY00.0340.00720.700-0.021-0.0210.0000.0000.0000.000
95A909GLY0-0.025-0.01523.373-0.034-0.0340.0000.0000.0000.000
96A910ILE00.0450.01320.804-0.035-0.0350.0000.0000.0000.000
97A911ILE0-0.034-0.00420.298-0.031-0.0310.0000.0000.0000.000
98A912GLU-1-0.849-0.91224.0910.2230.2230.0000.0000.0000.000
99A913LYS10.9050.95227.346-0.235-0.2350.0000.0000.0000.000
100A914GLY0-0.0200.01326.549-0.021-0.0210.0000.0000.0000.000
101A915LEU0-0.012-0.01224.470-0.020-0.0200.0000.0000.0000.000
102A916VAL0-0.0010.00019.367-0.011-0.0110.0000.0000.0000.000
103A917THR00.012-0.00122.0770.0090.0090.0000.0000.0000.000
104A918TYR00.0360.00721.280-0.006-0.0060.0000.0000.0000.000
105A919MET00.0120.02012.2830.0340.0340.0000.0000.0000.000
106A920ALA00.0820.03116.4010.0700.0700.0000.0000.0000.000
107A921LEU00.0010.02017.4770.0620.0620.0000.0000.0000.000
108A922GLY00.0100.00218.5370.0440.0440.0000.0000.0000.000
109A923LEU0-0.036-0.01411.2780.0640.0640.0000.0000.0000.000
110A924ALA00.0540.02315.2450.1230.1230.0000.0000.0000.000
111A925LEU00.0080.00817.3730.0630.0630.0000.0000.0000.000
112A926ARG10.9060.9459.754-1.386-1.3860.0000.0000.0000.000
113A927TYR00.0100.0029.7110.2060.2060.0000.0000.0000.000
114A928VAL00.0230.01714.8130.0720.0720.0000.0000.0000.000
115A929LEU0-0.0080.00918.1490.0090.0090.0000.0000.0000.000
116A930GLU-1-0.906-0.96211.8211.7001.7000.0000.0000.0000.000
117A931ALA0-0.028-0.01115.7570.0750.0750.0000.0000.0000.000
118A932LEU00.0180.01216.858-0.024-0.0240.0000.0000.0000.000
119A933ARG10.9390.98016.847-0.860-0.8600.0000.0000.0000.000
120A934LYS10.8660.95812.807-1.689-1.6890.0000.0000.0000.000
121A935PRO00.0410.01318.095-0.084-0.0840.0000.0000.0000.000
122A936PHE00.0680.04821.2790.0180.0180.0000.0000.0000.000
123A937GLY00.0260.01824.585-0.006-0.0060.0000.0000.0000.000
124A938SER0-0.052-0.03419.5550.0410.0410.0000.0000.0000.000
125A939LYS10.9190.94917.161-1.066-1.0660.0000.0000.0000.000
126A940MET00.0280.00714.045-0.032-0.0320.0000.0000.0000.000
127A941TYR0-0.0010.02118.158-0.049-0.0490.0000.0000.0000.000
128A942TYR00.036-0.00220.999-0.055-0.0550.0000.0000.0000.000
129A943PHE00.0090.01517.145-0.034-0.0340.0000.0000.0000.000
130A944GLY00.0300.00020.274-0.047-0.0470.0000.0000.0000.000
131A945ILE0-0.021-0.00620.938-0.060-0.0600.0000.0000.0000.000
132A946ALA0-0.007-0.00723.814-0.047-0.0470.0000.0000.0000.000
133A947ALA00.0030.00121.194-0.043-0.0430.0000.0000.0000.000
134A948LEU0-0.001-0.01123.243-0.044-0.0440.0000.0000.0000.000
135A949ASP-1-0.835-0.92025.0630.2880.2880.0000.0000.0000.000
136A950ARG10.8110.91726.036-0.351-0.3510.0000.0000.0000.000
137A951PHE00.0260.02022.694-0.022-0.0220.0000.0000.0000.000
138A952LYS10.9320.98727.783-0.302-0.3020.0000.0000.0000.000
139A953ASN0-0.110-0.09129.814-0.025-0.0250.0000.0000.0000.000
140A954ARG10.8780.93127.530-0.243-0.2430.0000.0000.0000.000
141A955LEU0-0.0110.01026.3750.0010.0010.0000.0000.0000.000
142A956LYS10.8460.92329.416-0.178-0.1780.0000.0000.0000.000
143A957ASP-1-0.902-0.94129.7330.1830.1830.0000.0000.0000.000
144A958TYR0-0.092-0.05325.7900.0020.0020.0000.0000.0000.000
145A959PRO00.0940.05227.5940.0300.0300.0000.0000.0000.000
146A960GLN00.012-0.01325.8180.0260.0260.0000.0000.0000.000
147A961TYR0-0.043-0.03120.3370.0080.0080.0000.0000.0000.000
148A962CYS0-0.0190.01224.6570.0330.0330.0000.0000.0000.000
149A963GLN00.0090.00927.376-0.010-0.0100.0000.0000.0000.000
150A964HIS0-0.042-0.02222.3290.0340.0340.0000.0000.0000.000
151A965LEU0-0.024-0.01422.6840.0370.0370.0000.0000.0000.000
152A966ALA00.0360.02025.0250.0170.0170.0000.0000.0000.000
153A967SER0-0.090-0.03424.813-0.004-0.0040.0000.0000.0000.000
154A968ILE0-0.051-0.01921.9870.0290.0290.0000.0000.0000.000
155A969SER00.014-0.00424.117-0.018-0.0180.0000.0000.0000.000
156A970HIS0-0.043-0.02822.130-0.062-0.0620.0000.0000.0000.000
157A971PHE00.0040.01627.1170.0020.0020.0000.0000.0000.000
158A972MET00.015-0.00228.204-0.019-0.0190.0000.0000.0000.000
159A973GLN0-0.034-0.01728.8940.0060.0060.0000.0000.0000.000
160A974PHE0-0.032-0.00424.2620.0170.0170.0000.0000.0000.000
161A975PRO00.0160.01729.112-0.027-0.0270.0000.0000.0000.000
162A976HIS00.0820.04532.1830.0100.0100.0000.0000.0000.000
163A977HIS00.002-0.02232.119-0.009-0.0090.0000.0000.0000.000
164A978LEU0-0.004-0.00327.955-0.004-0.0040.0000.0000.0000.000
165A979GLN0-0.022-0.02131.187-0.008-0.0080.0000.0000.0000.000
166A980GLU-1-0.879-0.93832.5550.2090.2090.0000.0000.0000.000
167A981TYR0-0.058-0.07731.806-0.012-0.0120.0000.0000.0000.000
168A982ILE0-0.015-0.00327.348-0.003-0.0030.0000.0000.0000.000
169A983GLU-1-0.895-0.94930.8960.2510.2510.0000.0000.0000.000
170A984TYR0-0.056-0.03533.710-0.021-0.0210.0000.0000.0000.000
171A985GLY00.0610.02731.958-0.013-0.0130.0000.0000.0000.000
172A986GLN0-0.002-0.01930.441-0.001-0.0010.0000.0000.0000.000
173A987GLN0-0.084-0.03332.334-0.021-0.0210.0000.0000.0000.000
174A988SER0-0.039-0.01434.049-0.014-0.0140.0000.0000.0000.000
175A989ARG10.8790.94735.055-0.175-0.1750.0000.0000.0000.000
176A990ASP-1-0.811-0.90635.9710.1910.1910.0000.0000.0000.000
177A991PRO00.0060.00135.846-0.005-0.0050.0000.0000.0000.000
178A992PRO0-0.032-0.02038.395-0.009-0.0090.0000.0000.0000.000
179A993VAL00.0170.01440.824-0.010-0.0100.0000.0000.0000.000
180A994LYS10.9541.01337.251-0.161-0.1610.0000.0000.0000.000