Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3JR2L

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:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2104450.765139
FMO2-HF: Nuclear repulsion 2028514.646573
FMO2-HF: Total energy -75936.118566
FMO2-MP2: Total energy -76155.933081


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.
-13.447-9.4370.503-1.885-2.6270.014
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 : 0.017 / q_NPA : 0.003
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].
3A817THR0-0.019-0.0093.833-2.679-0.672-0.005-0.959-1.0430.005
4A818ASP-1-0.826-0.8855.698-0.368-0.3680.0000.0000.0000.000
5A819LEU0-0.066-0.0518.7840.0360.0360.0000.0000.0000.000
6A820SER0-0.004-0.03211.9500.1450.1450.0000.0000.0000.000
7A821GLN0-0.011-0.00612.2310.0520.0520.0000.0000.0000.000
8A822VAL0-0.076-0.03015.0510.0450.0450.0000.0000.0000.000
9A823TRP0-0.032-0.01114.0260.0420.0420.0000.0000.0000.000
10A824PRO00.0030.00617.069-0.010-0.0100.0000.0000.0000.000
11A825GLU-1-0.819-0.89714.935-0.110-0.1100.0000.0000.0000.000
12A826ALA0-0.0220.00318.6460.0020.0020.0000.0000.0000.000
13A827ASN0-0.005-0.01721.797-0.009-0.0090.0000.0000.0000.000
14A828GLN00.0680.00921.0590.0200.0200.0000.0000.0000.000
15A829HIS0-0.084-0.03023.9490.0120.0120.0000.0000.0000.000
16A830PHE0-0.017-0.01826.1130.0080.0080.0000.0000.0000.000
17A831SER00.0330.02720.7690.0080.0080.0000.0000.0000.000
18A832LYS10.8580.92521.972-0.059-0.0590.0000.0000.0000.000
19A833GLU-1-0.823-0.91823.2920.0590.0590.0000.0000.0000.000
20A834ILE0-0.035-0.02221.8820.0130.0130.0000.0000.0000.000
21A835ASP-1-0.823-0.90518.6980.0990.0990.0000.0000.0000.000
22A836ASP-1-0.876-0.92321.0310.1610.1610.0000.0000.0000.000
23A837GLU-1-0.888-0.94523.6830.0840.0840.0000.0000.0000.000
24A838ALA00.002-0.00820.7630.0130.0130.0000.0000.0000.000
25A839ASN0-0.011-0.00420.3730.0610.0610.0000.0000.0000.000
26A840SER00.0100.01821.7400.0180.0180.0000.0000.0000.000
27A841TYR00.001-0.01824.6040.0010.0010.0000.0000.0000.000
28A842PHE00.0130.00819.1650.0090.0090.0000.0000.0000.000
29A843GLN0-0.010-0.00222.7940.0100.0100.0000.0000.0000.000
30A844ARG10.8630.92024.381-0.157-0.1570.0000.0000.0000.000
31A845ILE0-0.0260.00223.140-0.006-0.0060.0000.0000.0000.000
32A846TYR0-0.029-0.04119.1840.0000.0000.0000.0000.0000.000
33A847ASN0-0.036-0.00824.5970.0210.0210.0000.0000.0000.000
34A848HIS0-0.078-0.04027.6400.0080.0080.0000.0000.0000.000
35A849PRO00.0390.02930.547-0.005-0.0050.0000.0000.0000.000
36A850PRO0-0.032-0.02033.9610.0070.0070.0000.0000.0000.000
37A851HIS00.0100.00630.509-0.017-0.0170.0000.0000.0000.000
38A852PRO00.0190.00131.8550.0010.0010.0000.0000.0000.000
39A853THR00.0420.02030.2190.0130.0130.0000.0000.0000.000
40A854MET0-0.064-0.02329.125-0.015-0.0150.0000.0000.0000.000
41A855SER0-0.010-0.03329.2310.0180.0180.0000.0000.0000.000
42A856VAL00.0590.00826.023-0.002-0.0020.0000.0000.0000.000
43A857ASP-1-0.819-0.89428.3420.1470.1470.0000.0000.0000.000
44A858GLU-1-0.804-0.86131.1570.1290.1290.0000.0000.0000.000
45A859VAL00.0100.00225.192-0.010-0.0100.0000.0000.0000.000
46A860LEU0-0.035-0.01625.195-0.010-0.0100.0000.0000.0000.000
47A861GLU-1-0.873-0.91528.1900.0710.0710.0000.0000.0000.000
48A862MET00.0180.01126.988-0.011-0.0110.0000.0000.0000.000
49A863LEU0-0.026-0.01723.543-0.012-0.0120.0000.0000.0000.000
50A864GLN0-0.023-0.02227.288-0.011-0.0110.0000.0000.0000.000
51A865ARG10.8270.91429.435-0.088-0.0880.0000.0000.0000.000
52A866PHE0-0.021-0.02527.210-0.008-0.0080.0000.0000.0000.000
53A867LYS10.8180.91824.584-0.026-0.0260.0000.0000.0000.000
54A868ASP-1-0.856-0.91726.903-0.005-0.0050.0000.0000.0000.000
55A869SER00.010-0.00529.522-0.005-0.0050.0000.0000.0000.000
56A870THR0-0.006-0.00531.245-0.008-0.0080.0000.0000.0000.000
57A871ILE0-0.016-0.00932.680-0.007-0.0070.0000.0000.0000.000
58A872LYS10.8050.88426.7410.0420.0420.0000.0000.0000.000
59A873ARG10.9010.94327.707-0.039-0.0390.0000.0000.0000.000
60A874GLU-1-0.822-0.88427.7960.0500.0500.0000.0000.0000.000
61A875ARG10.8920.94026.1830.0260.0260.0000.0000.0000.000
62A876GLU-1-0.796-0.89423.936-0.033-0.0330.0000.0000.0000.000
63A877VAL00.0360.02222.9470.0040.0040.0000.0000.0000.000
64A878PHE00.0170.00822.2110.0220.0220.0000.0000.0000.000
65A879ASN0-0.003-0.01620.2250.0200.0200.0000.0000.0000.000
66A880CYS0-0.038-0.00618.6780.0080.0080.0000.0000.0000.000
67A881MET0-0.0040.00817.9850.0290.0290.0000.0000.0000.000
68A882LEU00.000-0.00118.1610.0540.0540.0000.0000.0000.000
69A883ARG10.8310.91213.6110.1450.1450.0000.0000.0000.000
70A884ASN00.003-0.00913.5320.0650.0650.0000.0000.0000.000
71A885LEU0-0.017-0.00113.6360.1260.1260.0000.0000.0000.000
72A886PHE0-0.021-0.03612.4010.1040.1040.0000.0000.0000.000
73A887GLU-1-0.852-0.9259.404-0.176-0.1760.0000.0000.0000.000
74A888GLU-1-0.844-0.8949.0271.7371.7370.0000.0000.0000.000
75A889TYR0-0.063-0.0269.3960.3350.3350.0000.0000.0000.000
76A890ARG10.9170.9492.663-12.281-10.2780.508-0.926-1.5840.009
77A891PHE0-0.010-0.0126.1630.9650.9650.0000.0000.0000.000
78A892PHE00.0390.0399.617-0.325-0.3250.0000.0000.0000.000
79A893PRO0-0.018-0.02410.653-0.196-0.1960.0000.0000.0000.000
80A894GLN0-0.046-0.0278.331-0.336-0.3360.0000.0000.0000.000
81A895TYR0-0.061-0.04813.106-0.178-0.1780.0000.0000.0000.000
82A896PRO00.0260.02016.283-0.025-0.0250.0000.0000.0000.000
83A897ASP-1-0.840-0.93519.8430.5000.5000.0000.0000.0000.000
84A898LYS10.8410.92821.924-0.333-0.3330.0000.0000.0000.000
85A899GLU-1-0.783-0.90419.9870.3870.3870.0000.0000.0000.000
86A900LEU0-0.0080.02116.491-0.003-0.0030.0000.0000.0000.000
87A901HIS00.0430.01419.629-0.003-0.0030.0000.0000.0000.000
88A902ILE00.0030.00722.969-0.025-0.0250.0000.0000.0000.000
89A903THR00.0130.00017.000-0.022-0.0220.0000.0000.0000.000
90A904ALA0-0.025-0.00220.415-0.019-0.0190.0000.0000.0000.000
91A905CYS0-0.035-0.01321.309-0.044-0.0440.0000.0000.0000.000
92A906LEU00.0040.00021.119-0.030-0.0300.0000.0000.0000.000
93A907PHE0-0.024-0.00915.196-0.024-0.0240.0000.0000.0000.000
94A908GLY00.0310.00720.464-0.031-0.0310.0000.0000.0000.000
95A909GLY0-0.022-0.01822.983-0.027-0.0270.0000.0000.0000.000
96A910ILE00.0370.01520.187-0.024-0.0240.0000.0000.0000.000
97A911ILE0-0.037-0.00319.478-0.026-0.0260.0000.0000.0000.000
98A912GLU-1-0.770-0.86623.2380.0870.0870.0000.0000.0000.000
99A913LYS10.8200.90226.623-0.121-0.1210.0000.0000.0000.000
100A914GLY0-0.0210.01425.723-0.010-0.0100.0000.0000.0000.000
101A915LEU0-0.015-0.01223.719-0.013-0.0130.0000.0000.0000.000
102A916VAL00.0000.00218.719-0.011-0.0110.0000.0000.0000.000
103A917THR00.012-0.00421.5180.0040.0040.0000.0000.0000.000
104A918TYR00.0340.00520.744-0.016-0.0160.0000.0000.0000.000
105A919MET00.0150.02211.9370.0330.0330.0000.0000.0000.000
106A920ALA00.0810.03215.7380.0070.0070.0000.0000.0000.000
107A921LEU00.0040.02016.8260.0360.0360.0000.0000.0000.000
108A922GLY00.0100.00417.6280.0290.0290.0000.0000.0000.000
109A923LEU0-0.035-0.01410.2660.0230.0230.0000.0000.0000.000
110A924ALA00.0520.02014.2660.0630.0630.0000.0000.0000.000
111A925LEU00.0060.00816.4280.0510.0510.0000.0000.0000.000
112A926ARG10.8940.9418.512-0.080-0.0800.0000.0000.0000.000
113A927TYR0-0.0050.0009.0120.0080.0080.0000.0000.0000.000
114A928VAL00.0310.02714.1120.0790.0790.0000.0000.0000.000
115A929LEU00.0060.01417.1980.0180.0180.0000.0000.0000.000
116A930GLU-1-0.872-0.94111.1730.4380.4380.0000.0000.0000.000
117A931ALA0-0.0350.00215.2870.0540.0540.0000.0000.0000.000
118A932LEU00.0250.01416.841-0.001-0.0010.0000.0000.0000.000
119A933ARG10.9370.97116.498-0.267-0.2670.0000.0000.0000.000
120A934LYS10.8450.93413.021-0.727-0.7270.0000.0000.0000.000
121A935PRO00.0420.01618.145-0.039-0.0390.0000.0000.0000.000
122A936PHE00.0620.04421.3280.0230.0230.0000.0000.0000.000
123A937GLY00.0170.01324.539-0.003-0.0030.0000.0000.0000.000
124A938SER0-0.055-0.04019.3530.0350.0350.0000.0000.0000.000
125A939LYS10.8870.93216.457-0.767-0.7670.0000.0000.0000.000
126A940MET00.0290.01314.0380.0020.0020.0000.0000.0000.000
127A941TYR0-0.0020.01917.921-0.037-0.0370.0000.0000.0000.000
128A942TYR00.028-0.00220.996-0.036-0.0360.0000.0000.0000.000
129A943PHE00.0140.01617.116-0.019-0.0190.0000.0000.0000.000
130A944GLY00.0270.00120.264-0.034-0.0340.0000.0000.0000.000
131A945ILE0-0.015-0.01020.913-0.039-0.0390.0000.0000.0000.000
132A946ALA0-0.016-0.00623.776-0.028-0.0280.0000.0000.0000.000
133A947ALA00.002-0.00121.091-0.025-0.0250.0000.0000.0000.000
134A948LEU0-0.001-0.00923.056-0.029-0.0290.0000.0000.0000.000
135A949ASP-1-0.822-0.90424.6410.1400.1400.0000.0000.0000.000
136A950ARG10.7800.88225.776-0.194-0.1940.0000.0000.0000.000
137A951PHE00.0220.01721.983-0.015-0.0150.0000.0000.0000.000
138A952LYS10.8620.93127.098-0.157-0.1570.0000.0000.0000.000
139A953ASN0-0.066-0.06029.105-0.005-0.0050.0000.0000.0000.000
140A954ARG10.8430.91226.573-0.088-0.0880.0000.0000.0000.000
141A955LEU0-0.0110.01025.531-0.005-0.0050.0000.0000.0000.000
142A956LYS10.8490.92028.412-0.065-0.0650.0000.0000.0000.000
143A957ASP-1-0.897-0.94428.6560.0520.0520.0000.0000.0000.000
144A958TYR0-0.067-0.04524.778-0.005-0.0050.0000.0000.0000.000
145A959PRO00.0980.05926.5850.0110.0110.0000.0000.0000.000
146A960GLN00.008-0.01324.8330.0060.0060.0000.0000.0000.000
147A961TYR0-0.049-0.04219.2440.0060.0060.0000.0000.0000.000
148A962CYS0-0.0140.00623.6490.0180.0180.0000.0000.0000.000
149A963GLN00.0140.00826.5540.0040.0040.0000.0000.0000.000
150A964HIS0-0.037-0.01921.3410.0180.0180.0000.0000.0000.000
151A965LEU0-0.030-0.01321.9890.0180.0180.0000.0000.0000.000
152A966ALA00.0340.02024.1840.0110.0110.0000.0000.0000.000
153A967SER0-0.085-0.03923.940-0.001-0.0010.0000.0000.0000.000
154A968ILE0-0.060-0.02221.5610.0090.0090.0000.0000.0000.000
155A969SER00.0240.00423.716-0.004-0.0040.0000.0000.0000.000
156A970HIS0-0.044-0.02321.916-0.030-0.0300.0000.0000.0000.000
157A971PHE00.0020.01826.8690.0070.0070.0000.0000.0000.000
158A972MET00.0210.00327.868-0.005-0.0050.0000.0000.0000.000
159A973GLN0-0.040-0.02028.7080.0040.0040.0000.0000.0000.000
160A974PHE0-0.0130.00523.8220.0120.0120.0000.0000.0000.000
161A975PRO00.0020.00629.149-0.013-0.0130.0000.0000.0000.000
162A976HIS00.0370.01532.1170.0010.0010.0000.0000.0000.000
163A977HIS00.014-0.01331.921-0.008-0.0080.0000.0000.0000.000
164A978LEU0-0.013-0.01027.654-0.005-0.0050.0000.0000.0000.000
165A979GLN0-0.011-0.01230.606-0.009-0.0090.0000.0000.0000.000
166A980GLU-1-0.831-0.90932.0370.0840.0840.0000.0000.0000.000
167A981TYR0-0.058-0.06831.038-0.008-0.0080.0000.0000.0000.000
168A982ILE0-0.017-0.00226.602-0.005-0.0050.0000.0000.0000.000
169A983GLU-1-0.889-0.94730.0480.0880.0880.0000.0000.0000.000
170A984TYR0-0.045-0.03232.786-0.011-0.0110.0000.0000.0000.000
171A985GLY00.0560.03030.941-0.007-0.0070.0000.0000.0000.000
172A986GLN0-0.007-0.01629.396-0.002-0.0020.0000.0000.0000.000
173A987GLN0-0.094-0.03831.326-0.012-0.0120.0000.0000.0000.000
174A988SER0-0.043-0.01733.037-0.006-0.0060.0000.0000.0000.000
175A989ARG10.8840.95034.048-0.058-0.0580.0000.0000.0000.000
176A990ASP-1-0.779-0.87934.9590.0720.0720.0000.0000.0000.000
177A991PRO00.0360.01634.887-0.003-0.0030.0000.0000.0000.000
178A992PRO0-0.034-0.01537.549-0.003-0.0030.0000.0000.0000.000
179A993VAL00.0030.00440.155-0.004-0.0040.0000.0000.0000.000
180A994LYS10.8800.95936.989-0.062-0.0620.0000.0000.0000.000