Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2JZ7R

Calculation Name: 4C0D-B-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0D

Chain ID: B

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1813681.015554
FMO2-HF: Nuclear repulsion 1735408.778357
FMO2-HF: Total energy -78272.237197
FMO2-MP2: Total energy -78499.265552


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(B:350:MET)


Summations of interaction energy for fragment #1(B:350:MET)
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.
-5.852-1.4270.142-1.968-2.599-0.002
Interaction energy analysis for fragmet #1(B:350:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.004
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].
3B352THR0-0.019-0.0063.073-3.2840.4560.123-1.853-2.010-0.002
4B353ASP-1-0.883-0.9374.818-0.895-0.791-0.001-0.010-0.0930.000
5B354GLN0-0.005-0.0147.0880.2970.2970.0000.0000.0000.000
6B355PHE00.012-0.0109.3790.1760.1760.0000.0000.0000.000
7B356GLY00.0200.0235.6610.1460.182-0.001-0.005-0.0290.000
8B357MET00.034-0.0025.176-0.591-0.451-0.001-0.018-0.1210.000
9B358ILE00.0200.0113.541-0.905-0.5000.022-0.082-0.3460.000
10B359GLY00.0650.0377.320-0.371-0.3710.0000.0000.0000.000
11B360LEU00.0190.0309.593-0.112-0.1120.0000.0000.0000.000
12B361LEU0-0.010-0.0078.386-0.152-0.1520.0000.0000.0000.000
13B362THR0-0.065-0.05511.262-0.151-0.1510.0000.0000.0000.000
14B363PHE00.0260.01313.379-0.081-0.0810.0000.0000.0000.000
15B364ILE0-0.0060.00313.607-0.033-0.0330.0000.0000.0000.000
16B365ARG10.9450.96712.838-0.236-0.2360.0000.0000.0000.000
17B366ALA00.0180.01317.343-0.028-0.0280.0000.0000.0000.000
18B367ALA0-0.028-0.00919.101-0.020-0.0200.0000.0000.0000.000
19B368GLU-1-0.948-0.96820.3180.1410.1410.0000.0000.0000.000
20B369THR0-0.134-0.05521.360-0.020-0.0200.0000.0000.0000.000
21B370ASP-1-0.902-0.96123.3300.0120.0120.0000.0000.0000.000
22B371PRO00.0160.00524.4850.0120.0120.0000.0000.0000.000
23B372GLY0-0.033-0.01927.1000.0040.0040.0000.0000.0000.000
24B373MET0-0.038-0.02920.410-0.011-0.0110.0000.0000.0000.000
25B374VAL00.0380.02421.8880.0180.0180.0000.0000.0000.000
26B375HIS0-0.020-0.01022.9200.0250.0250.0000.0000.0000.000
27B376LEU0-0.041-0.02019.2200.0020.0020.0000.0000.0000.000
28B377ALA0-0.035-0.01317.8620.0310.0310.0000.0000.0000.000
29B378LEU0-0.0030.00418.4600.0260.0260.0000.0000.0000.000
30B379GLY0-0.0020.01820.733-0.001-0.0010.0000.0000.0000.000
31B380SER00.002-0.00623.950-0.003-0.0030.0000.0000.0000.000
32B381ASP-1-0.824-0.90427.4490.1100.1100.0000.0000.0000.000
33B382LEU00.014-0.00629.407-0.010-0.0100.0000.0000.0000.000
34B383THR0-0.090-0.06831.859-0.008-0.0080.0000.0000.0000.000
35B384THR0-0.063-0.02132.720-0.006-0.0060.0000.0000.0000.000
36B385LEU0-0.033-0.00533.402-0.006-0.0060.0000.0000.0000.000
37B386GLY00.0380.01936.7500.0000.0000.0000.0000.0000.000
38B387LEU0-0.069-0.02736.994-0.001-0.0010.0000.0000.0000.000
39B388ASN00.0390.00639.1670.0060.0060.0000.0000.0000.000
40B389LEU00.0150.00033.813-0.001-0.0010.0000.0000.0000.000
41B390ASN0-0.029-0.00236.1120.0040.0040.0000.0000.0000.000
42B391SER0-0.001-0.00839.506-0.003-0.0030.0000.0000.0000.000
43B392PRO0-0.034-0.00742.6650.0010.0010.0000.0000.0000.000
44B393GLU-1-0.894-0.93244.8630.0430.0430.0000.0000.0000.000
45B394ASN0-0.018-0.02444.6320.0040.0040.0000.0000.0000.000
46B395LEU00.0790.02440.230-0.002-0.0020.0000.0000.0000.000
47B396TYR00.0200.00044.306-0.001-0.0010.0000.0000.0000.000
48B397PRO0-0.023-0.00345.630-0.002-0.0020.0000.0000.0000.000
49B398LYS10.8740.94247.559-0.042-0.0420.0000.0000.0000.000
50B399PHE00.0240.01640.5800.0010.0010.0000.0000.0000.000
51B400ALA00.0500.02145.886-0.002-0.0020.0000.0000.0000.000
52B401SER0-0.022-0.02144.590-0.002-0.0020.0000.0000.0000.000
53B402PRO00.012-0.00939.5020.0020.0020.0000.0000.0000.000
54B403TRP00.0420.01638.1370.0030.0030.0000.0000.0000.000
55B404ALA0-0.074-0.01241.060-0.001-0.0010.0000.0000.0000.000
56B405SER00.0430.02241.1450.0020.0020.0000.0000.0000.000
57B406SER0-0.016-0.01942.1570.0020.0020.0000.0000.0000.000
58B407PRO0-0.032-0.00744.542-0.001-0.0010.0000.0000.0000.000
59B408CYS0-0.051-0.01046.597-0.001-0.0010.0000.0000.0000.000
60B409ARG10.8220.88650.100-0.024-0.0240.0000.0000.0000.000
61B410PRO00.017-0.01253.134-0.001-0.0010.0000.0000.0000.000
62B411GLN0-0.065-0.02656.303-0.001-0.0010.0000.0000.0000.000
63B412ASP-1-0.762-0.85852.7010.0250.0250.0000.0000.0000.000
64B413ILE0-0.056-0.01952.2080.0000.0000.0000.0000.0000.000
65B414ASP-1-0.897-0.93756.0510.0190.0190.0000.0000.0000.000
66B415PHE0-0.058-0.03458.8530.0000.0000.0000.0000.0000.000
67B416HIS0-0.0020.00260.540-0.001-0.0010.0000.0000.0000.000
68B417VAL0-0.043-0.02063.5940.0000.0000.0000.0000.0000.000
69B418PRO00.0220.00766.418-0.001-0.0010.0000.0000.0000.000
70B419SER0-0.001-0.02070.0850.0000.0000.0000.0000.0000.000
71B420GLU-1-0.892-0.94472.1450.0140.0140.0000.0000.0000.000
72B421TYR0-0.020-0.01668.2160.0000.0000.0000.0000.0000.000
73B422LEU0-0.0440.00269.3610.0000.0000.0000.0000.0000.000
74B423THR00.0820.02970.971-0.001-0.0010.0000.0000.0000.000
75B424ASN0-0.013-0.00369.411-0.001-0.0010.0000.0000.0000.000
76B425ILE00.010-0.00372.0090.0000.0000.0000.0000.0000.000
77B426HIS00.0330.02273.8110.0000.0000.0000.0000.0000.000
78B427ILE0-0.058-0.03075.5430.0000.0000.0000.0000.0000.000
79B428ARG10.9210.95770.026-0.009-0.0090.0000.0000.0000.000
80B429ASP-1-0.891-0.93874.9540.0070.0070.0000.0000.0000.000
81B430LYS10.8900.93378.019-0.009-0.0090.0000.0000.0000.000
82B431LEU0-0.0040.01971.5340.0000.0000.0000.0000.0000.000
83B432ALA0-0.031-0.01274.7980.0000.0000.0000.0000.0000.000
84B433ALA00.0400.01672.1300.0000.0000.0000.0000.0000.000
85B434ILE00.0550.02466.0210.0000.0000.0000.0000.0000.000
86B435LYS10.9140.95669.134-0.010-0.0100.0000.0000.0000.000
87B436LEU00.0800.03064.0330.0000.0000.0000.0000.0000.000
88B437GLY00.0250.02268.1160.0000.0000.0000.0000.0000.000
89B438ARG10.8430.92470.902-0.011-0.0110.0000.0000.0000.000
90B439TYR00.0310.01667.2720.0000.0000.0000.0000.0000.000
91B440GLY00.0520.02069.8360.0000.0000.0000.0000.0000.000
92B441GLU-1-0.778-0.89566.0910.0190.0190.0000.0000.0000.000
93B442ASP-1-0.868-0.91564.6940.0220.0220.0000.0000.0000.000
94B443LEU00.0270.01163.7660.0010.0010.0000.0000.0000.000
95B444LEU0-0.029-0.01163.5400.0000.0000.0000.0000.0000.000
96B445PHE00.0550.01859.8350.0000.0000.0000.0000.0000.000
97B446TYR0-0.003-0.00159.1180.0010.0010.0000.0000.0000.000
98B447LEU0-0.017-0.02658.8250.0010.0010.0000.0000.0000.000
99B448TYR0-0.0170.00753.6660.0000.0000.0000.0000.0000.000
100B449TYR0-0.008-0.01853.4870.0000.0000.0000.0000.0000.000
101B450MET0-0.0100.00853.7550.0020.0020.0000.0000.0000.000
102B451ASN0-0.061-0.02254.3140.0010.0010.0000.0000.0000.000
103B452GLY00.0530.02651.230-0.001-0.0010.0000.0000.0000.000
104B453GLY0-0.015-0.00349.6540.0000.0000.0000.0000.0000.000
105B454ASP-1-0.823-0.91550.4340.0170.0170.0000.0000.0000.000
106B455VAL0-0.006-0.01953.8600.0000.0000.0000.0000.0000.000
107B456LEU0-0.032-0.01156.713-0.001-0.0010.0000.0000.0000.000
108B457GLN00.0270.02052.3660.0000.0000.0000.0000.0000.000
109B458LEU00.0250.00453.7690.0000.0000.0000.0000.0000.000
110B459LEU0-0.019-0.01257.586-0.001-0.0010.0000.0000.0000.000
111B460ALA0-0.023-0.00559.908-0.001-0.0010.0000.0000.0000.000
112B461ALA00.0270.01157.8350.0000.0000.0000.0000.0000.000
113B462VAL0-0.015-0.00559.9740.0000.0000.0000.0000.0000.000
114B463GLU-1-0.810-0.90362.5740.0130.0130.0000.0000.0000.000
115B464LEU00.0010.00260.7110.0000.0000.0000.0000.0000.000
116B465PHE0-0.008-0.00161.0610.0000.0000.0000.0000.0000.000
117B466ASN0-0.025-0.01263.814-0.001-0.0010.0000.0000.0000.000
118B467ARG10.7150.87866.748-0.015-0.0150.0000.0000.0000.000
119B468ASP-1-0.849-0.91566.6330.0150.0150.0000.0000.0000.000
120B469TRP0-0.051-0.00761.8580.0010.0010.0000.0000.0000.000
121B470ARG10.8320.89660.061-0.017-0.0170.0000.0000.0000.000
122B471TYR00.0190.01051.8450.0010.0010.0000.0000.0000.000
123B472HIS00.0290.01652.3310.0000.0000.0000.0000.0000.000
124B473LYS10.8970.95050.036-0.019-0.0190.0000.0000.0000.000
125B474GLU-1-0.936-0.97047.5660.0340.0340.0000.0000.0000.000
126B475GLU-1-0.837-0.93148.8360.0340.0340.0000.0000.0000.000
127B476ARG10.9450.99146.404-0.036-0.0360.0000.0000.0000.000
128B477VAL0-0.012-0.00351.2180.0000.0000.0000.0000.0000.000
129B478TRP00.0040.00954.820-0.001-0.0010.0000.0000.0000.000
130B479ILE00.016-0.01256.6480.0000.0000.0000.0000.0000.000
131B480THR0-0.002-0.01460.554-0.001-0.0010.0000.0000.0000.000
132B481ARG10.8860.94464.295-0.016-0.0160.0000.0000.0000.000
133B482ALA00.0140.00767.2310.0000.0000.0000.0000.0000.000
134B483PRO00.0200.00068.925-0.001-0.0010.0000.0000.0000.000
135B484GLY0-0.005-0.00672.7430.0000.0000.0000.0000.0000.000
136B485MET0-0.070-0.02369.0650.0000.0000.0000.0000.0000.000
137B486GLU-1-0.846-0.94270.1960.0150.0150.0000.0000.0000.000
138B487PRO0-0.122-0.03766.0780.0010.0010.0000.0000.0000.000
139B488THR0-0.011-0.01166.3140.0000.0000.0000.0000.0000.000
140B489MET0-0.035-0.01864.4560.0000.0000.0000.0000.0000.000
141B490LYS10.8980.93965.507-0.015-0.0150.0000.0000.0000.000
142B491THR0-0.027-0.00762.595-0.001-0.0010.0000.0000.0000.000
143B492ASN00.017-0.01363.7330.0000.0000.0000.0000.0000.000
144B493THR00.0340.02758.5210.0000.0000.0000.0000.0000.000
145B494TYR00.0120.00358.6180.0010.0010.0000.0000.0000.000
146B495GLU-1-0.742-0.83160.6170.0160.0160.0000.0000.0000.000
147B496ARG10.8820.93960.327-0.023-0.0230.0000.0000.0000.000
148B497GLY00.0250.00862.394-0.001-0.0010.0000.0000.0000.000
149B498THR00.005-0.00263.0350.0010.0010.0000.0000.0000.000
150B499TYR0-0.055-0.04262.160-0.001-0.0010.0000.0000.0000.000
151B500TYR0-0.011-0.02763.7240.0000.0000.0000.0000.0000.000
152B501PHE00.0290.02556.6710.0000.0000.0000.0000.0000.000
153B502PHE00.001-0.00858.7750.0000.0000.0000.0000.0000.000
154B503ASP-1-0.828-0.89156.5470.0330.0330.0000.0000.0000.000
155B504CYS00.027-0.00253.639-0.001-0.0010.0000.0000.0000.000
156B505LEU0-0.028-0.01251.3160.0000.0000.0000.0000.0000.000
157B506ASN0-0.077-0.05155.2400.0000.0000.0000.0000.0000.000
158B507TRP0-0.084-0.02957.4220.0000.0000.0000.0000.0000.000
159B508ARG10.9120.95460.406-0.029-0.0290.0000.0000.0000.000
160B509LYS10.8360.90861.733-0.019-0.0190.0000.0000.0000.000
161B510VAL0-0.028-0.00560.7310.0000.0000.0000.0000.0000.000
162B511ALA0-0.0020.00162.6540.0000.0000.0000.0000.0000.000
163B512LYS10.8400.91754.555-0.030-0.0300.0000.0000.0000.000
164B513GLU-1-0.866-0.91061.1240.0230.0230.0000.0000.0000.000
165B514PHE0-0.031-0.01755.9650.0010.0010.0000.0000.0000.000
166B515HIS0-0.031-0.03655.303-0.001-0.0010.0000.0000.0000.000
167B516LEU0-0.0150.00756.7180.0010.0010.0000.0000.0000.000
168B517GLU-1-0.787-0.89453.6540.0230.0230.0000.0000.0000.000
169B518TYR0-0.032-0.03256.8550.0000.0000.0000.0000.0000.000
170B519ASP-1-0.882-0.92553.6010.0180.0180.0000.0000.0000.000
171B520LYS10.8210.90449.638-0.026-0.0260.0000.0000.0000.000
172B521LEU0-0.032-0.00753.6800.0010.0010.0000.0000.0000.000
173B522GLU-1-0.959-0.97954.1530.0200.0200.0000.0000.0000.000
174B523GLU-1-0.910-0.95956.5550.0150.0150.0000.0000.0000.000
175B524ARG10.8390.90958.942-0.012-0.0120.0000.0000.0000.000
176B525PRO00.0330.01657.3330.0000.0000.0000.0000.0000.000
177B526HIS00.0100.01155.233-0.001-0.0010.0000.0000.0000.000
178B527LEU0-0.017-0.01356.2810.0010.0010.0000.0000.0000.000
179B528PRO00.0120.00153.062-0.001-0.0010.0000.0000.0000.000
180B529SER00.000-0.00154.8720.0000.0000.0000.0000.0000.000
181B530THR0-0.037-0.01350.283-0.001-0.0010.0000.0000.0000.000
182B531PHE00.0220.01151.9300.0010.0010.0000.0000.0000.000
183B532ASN0-0.039-0.03850.820-0.001-0.0010.0000.0000.0000.000
184B533TYR00.0550.03945.6430.0000.0000.0000.0000.0000.000
185B534ASN00.0340.00346.3230.0020.0020.0000.0000.0000.000
186B535PRO00.0750.04345.0940.0000.0000.0000.0000.0000.000
187B536ALA00.0130.00842.6560.0020.0020.0000.0000.0000.000
188B537GLN0-0.050-0.02241.4430.0000.0000.0000.0000.0000.000
189B538GLN0-0.082-0.05139.717-0.003-0.0030.0000.0000.0000.000
190B539ALA0-0.0170.00738.4940.0020.0020.0000.0000.0000.000
191B540PHE0-0.0030.01333.4930.0050.0050.0000.0000.0000.000