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: 7283K

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1812405.475865
FMO2-HF: Nuclear repulsion 1734134.158349
FMO2-HF: Total energy -78271.317516
FMO2-MP2: Total energy -78498.313831


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.
-4.931-1.4330.154-1.457-2.194-0.007
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 : -0.018 / q_NPA : -0.029
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].
3B352THR0-0.035-0.0153.016-3.347-0.4220.147-1.374-1.697-0.007
4B353ASP-1-0.881-0.9254.808-0.190-0.064-0.001-0.010-0.1140.000
5B354GLN00.020-0.0107.0320.1690.1690.0000.0000.0000.000
6B355PHE0-0.004-0.0169.3230.1550.1550.0000.0000.0000.000
7B356GLY00.0080.0195.9430.3180.3180.0000.0000.0000.000
8B357MET00.036-0.0045.362-0.600-0.476-0.001-0.014-0.1090.000
9B358ILE00.0280.0123.677-0.793-0.4700.009-0.059-0.2740.000
10B359GLY00.0670.0307.456-0.351-0.3510.0000.0000.0000.000
11B360LEU00.0180.0329.796-0.113-0.1130.0000.0000.0000.000
12B361LEU0-0.015-0.0048.313-0.172-0.1720.0000.0000.0000.000
13B362THR0-0.066-0.04911.101-0.161-0.1610.0000.0000.0000.000
14B363PHE00.0440.01913.477-0.082-0.0820.0000.0000.0000.000
15B364ILE0-0.0210.00014.097-0.038-0.0380.0000.0000.0000.000
16B365ARG10.9310.95912.739-0.208-0.2080.0000.0000.0000.000
17B366ALA00.0210.01017.454-0.032-0.0320.0000.0000.0000.000
18B367ALA0-0.022-0.00619.231-0.021-0.0210.0000.0000.0000.000
19B368GLU-1-0.960-0.97020.4180.1530.1530.0000.0000.0000.000
20B369THR0-0.131-0.05221.515-0.028-0.0280.0000.0000.0000.000
21B370ASP-1-0.881-0.95823.4490.0360.0360.0000.0000.0000.000
22B371PRO00.0170.00424.6250.0170.0170.0000.0000.0000.000
23B372GLY0-0.043-0.02627.2430.0080.0080.0000.0000.0000.000
24B373MET0-0.045-0.01820.430-0.006-0.0060.0000.0000.0000.000
25B374VAL00.0400.02822.0730.0250.0250.0000.0000.0000.000
26B375HIS0-0.025-0.01623.1070.0250.0250.0000.0000.0000.000
27B376LEU0-0.040-0.02219.4020.0120.0120.0000.0000.0000.000
28B377ALA0-0.031-0.00618.0430.0440.0440.0000.0000.0000.000
29B378LEU0-0.006-0.00518.4670.0340.0340.0000.0000.0000.000
30B379GLY00.0010.02020.885-0.001-0.0010.0000.0000.0000.000
31B380SER0-0.011-0.01724.124-0.004-0.0040.0000.0000.0000.000
32B381ASP-1-0.803-0.89727.6090.1530.1530.0000.0000.0000.000
33B382LEU00.0100.00029.715-0.012-0.0120.0000.0000.0000.000
34B383THR0-0.085-0.06332.202-0.011-0.0110.0000.0000.0000.000
35B384THR0-0.065-0.02432.983-0.009-0.0090.0000.0000.0000.000
36B385LEU0-0.036-0.00833.666-0.008-0.0080.0000.0000.0000.000
37B386GLY00.0340.01736.985-0.002-0.0020.0000.0000.0000.000
38B387LEU0-0.062-0.02637.250-0.003-0.0030.0000.0000.0000.000
39B388ASN00.0350.00739.6080.0060.0060.0000.0000.0000.000
40B389LEU00.009-0.00134.368-0.001-0.0010.0000.0000.0000.000
41B390ASN0-0.0190.00436.7240.0070.0070.0000.0000.0000.000
42B391SER0-0.010-0.01440.014-0.005-0.0050.0000.0000.0000.000
43B392PRO0-0.035-0.00443.1920.0030.0030.0000.0000.0000.000
44B393GLU-1-0.943-0.96045.3820.0710.0710.0000.0000.0000.000
45B394ASN0-0.026-0.02445.1480.0060.0060.0000.0000.0000.000
46B395LEU00.0820.02340.750-0.003-0.0030.0000.0000.0000.000
47B396TYR0-0.005-0.01244.574-0.001-0.0010.0000.0000.0000.000
48B397PRO0-0.0150.00245.859-0.002-0.0020.0000.0000.0000.000
49B398LYS10.9620.98448.016-0.066-0.0660.0000.0000.0000.000
50B399PHE00.0180.01541.0980.0000.0000.0000.0000.0000.000
51B400ALA00.0320.01346.090-0.002-0.0020.0000.0000.0000.000
52B401SER0-0.015-0.01744.812-0.001-0.0010.0000.0000.0000.000
53B402PRO00.008-0.01239.7590.0020.0020.0000.0000.0000.000
54B403TRP00.0500.01838.4810.0040.0040.0000.0000.0000.000
55B404ALA0-0.063-0.00441.263-0.003-0.0030.0000.0000.0000.000
56B405SER00.0110.00741.3270.0040.0040.0000.0000.0000.000
57B406SER0-0.021-0.02042.3270.0000.0000.0000.0000.0000.000
58B407PRO0-0.0040.00344.8020.0000.0000.0000.0000.0000.000
59B408CYS0-0.0260.00146.814-0.003-0.0030.0000.0000.0000.000
60B409ARG10.8360.89850.285-0.044-0.0440.0000.0000.0000.000
61B410PRO00.009-0.01753.3450.0000.0000.0000.0000.0000.000
62B411GLN0-0.062-0.03056.556-0.001-0.0010.0000.0000.0000.000
63B412ASP-1-0.771-0.85653.1370.0460.0460.0000.0000.0000.000
64B413ILE0-0.057-0.01752.5190.0010.0010.0000.0000.0000.000
65B414ASP-1-0.892-0.93756.2520.0410.0410.0000.0000.0000.000
66B415PHE0-0.059-0.03459.0640.0010.0010.0000.0000.0000.000
67B416HIS0-0.0030.00160.746-0.001-0.0010.0000.0000.0000.000
68B417VAL0-0.044-0.01963.8070.0000.0000.0000.0000.0000.000
69B418PRO00.0280.00966.6230.0000.0000.0000.0000.0000.000
70B419SER00.0140.00070.2920.0000.0000.0000.0000.0000.000
71B420GLU-1-0.904-0.96372.3590.0290.0290.0000.0000.0000.000
72B421TYR0-0.019-0.01368.6090.0000.0000.0000.0000.0000.000
73B422LEU0-0.0510.00069.6120.0000.0000.0000.0000.0000.000
74B423THR00.0700.02771.176-0.001-0.0010.0000.0000.0000.000
75B424ASN00.014-0.00168.588-0.002-0.0020.0000.0000.0000.000
76B425ILE0-0.019-0.01272.210-0.001-0.0010.0000.0000.0000.000
77B426HIS00.0210.01274.021-0.001-0.0010.0000.0000.0000.000
78B427ILE0-0.055-0.02975.668-0.001-0.0010.0000.0000.0000.000
79B428ARG10.9260.96269.968-0.025-0.0250.0000.0000.0000.000
80B429ASP-1-0.874-0.92975.1530.0190.0190.0000.0000.0000.000
81B430LYS10.8830.93078.213-0.019-0.0190.0000.0000.0000.000
82B431LEU00.0000.02271.6640.0000.0000.0000.0000.0000.000
83B432ALA0-0.031-0.01574.7940.0000.0000.0000.0000.0000.000
84B433ALA00.0360.01672.2240.0010.0010.0000.0000.0000.000
85B434ILE00.0520.01766.2350.0000.0000.0000.0000.0000.000
86B435LYS10.9010.95869.291-0.018-0.0180.0000.0000.0000.000
87B436LEU00.0770.02564.2790.0000.0000.0000.0000.0000.000
88B437GLY00.0410.03368.2530.0000.0000.0000.0000.0000.000
89B438ARG10.8420.92371.031-0.021-0.0210.0000.0000.0000.000
90B439TYR00.0320.01867.4460.0000.0000.0000.0000.0000.000
91B440GLY00.0480.01470.170-0.001-0.0010.0000.0000.0000.000
92B441GLU-1-0.850-0.95566.5260.0260.0260.0000.0000.0000.000
93B442ASP-1-0.875-0.91465.0840.0330.0330.0000.0000.0000.000
94B443LEU00.0260.00964.1610.0010.0010.0000.0000.0000.000
95B444LEU0-0.032-0.01463.8100.0010.0010.0000.0000.0000.000
96B445PHE00.0570.02260.4300.0010.0010.0000.0000.0000.000
97B446TYR0-0.016-0.00659.4690.0020.0020.0000.0000.0000.000
98B447LEU0-0.024-0.02759.1070.0010.0010.0000.0000.0000.000
99B448TYR0-0.042-0.00253.8540.0000.0000.0000.0000.0000.000
100B449TYR0-0.013-0.02854.0030.0010.0010.0000.0000.0000.000
101B450MET0-0.0080.00354.0460.0030.0030.0000.0000.0000.000
102B451ASN0-0.040-0.02154.4960.0010.0010.0000.0000.0000.000
103B452GLY00.0610.02951.380-0.001-0.0010.0000.0000.0000.000
104B453GLY0-0.018-0.00649.8060.0010.0010.0000.0000.0000.000
105B454ASP-1-0.867-0.92550.5830.0340.0340.0000.0000.0000.000
106B455VAL00.017-0.00654.015-0.001-0.0010.0000.0000.0000.000
107B456LEU0-0.048-0.02756.863-0.002-0.0020.0000.0000.0000.000
108B457GLN00.0560.04252.182-0.001-0.0010.0000.0000.0000.000
109B458LEU00.014-0.00354.241-0.001-0.0010.0000.0000.0000.000
110B459LEU0-0.024-0.01357.713-0.002-0.0020.0000.0000.0000.000
111B460ALA0-0.0090.00260.053-0.001-0.0010.0000.0000.0000.000
112B461ALA00.0220.00957.987-0.001-0.0010.0000.0000.0000.000
113B462VAL0-0.018-0.00560.119-0.001-0.0010.0000.0000.0000.000
114B463GLU-1-0.893-0.96962.6840.0200.0200.0000.0000.0000.000
115B464LEU0-0.003-0.00160.780-0.001-0.0010.0000.0000.0000.000
116B465PHE0-0.009-0.00361.618-0.001-0.0010.0000.0000.0000.000
117B466ASN0-0.003-0.01264.010-0.001-0.0010.0000.0000.0000.000
118B467ARG10.7640.92166.980-0.023-0.0230.0000.0000.0000.000
119B468ASP-1-0.897-0.94467.0770.0180.0180.0000.0000.0000.000
120B469TRP0-0.054-0.01562.2900.0010.0010.0000.0000.0000.000
121B470ARG10.8630.91560.340-0.021-0.0210.0000.0000.0000.000
122B471TYR00.0450.02052.0840.0010.0010.0000.0000.0000.000
123B472HIS00.0280.03052.4990.0000.0000.0000.0000.0000.000
124B473LYS10.9550.96350.328-0.022-0.0220.0000.0000.0000.000
125B474GLU-1-0.976-0.98147.7750.0360.0360.0000.0000.0000.000
126B475GLU-1-0.945-0.98949.1920.0380.0380.0000.0000.0000.000
127B476ARG10.9250.98046.648-0.047-0.0470.0000.0000.0000.000
128B477VAL0-0.028-0.00951.6080.0010.0010.0000.0000.0000.000
129B478TRP00.0070.00455.214-0.002-0.0020.0000.0000.0000.000
130B479ILE00.013-0.01157.0670.0000.0000.0000.0000.0000.000
131B480THR00.0120.00660.928-0.001-0.0010.0000.0000.0000.000
132B481ARG10.9440.97464.667-0.018-0.0180.0000.0000.0000.000
133B482ALA00.0110.00967.5870.0000.0000.0000.0000.0000.000
134B483PRO00.009-0.00769.282-0.001-0.0010.0000.0000.0000.000
135B484GLY00.003-0.00173.1030.0000.0000.0000.0000.0000.000
136B485MET0-0.069-0.02369.4070.0000.0000.0000.0000.0000.000
137B486GLU-1-0.888-0.94970.5230.0150.0150.0000.0000.0000.000
138B487PRO0-0.098-0.03766.4840.0000.0000.0000.0000.0000.000
139B488THR0-0.015-0.00866.4620.0000.0000.0000.0000.0000.000
140B489MET0-0.039-0.02464.838-0.001-0.0010.0000.0000.0000.000
141B490LYS10.9650.97865.769-0.014-0.0140.0000.0000.0000.000
142B491THR0-0.021-0.00662.868-0.001-0.0010.0000.0000.0000.000
143B492ASN00.005-0.01864.0540.0000.0000.0000.0000.0000.000
144B493THR00.0350.02558.6840.0000.0000.0000.0000.0000.000
145B494TYR00.0160.01358.9250.0010.0010.0000.0000.0000.000
146B495GLU-1-0.838-0.91360.8790.0160.0160.0000.0000.0000.000
147B496ARG10.9700.99060.638-0.020-0.0200.0000.0000.0000.000
148B497GLY00.0210.00362.692-0.001-0.0010.0000.0000.0000.000
149B498THR00.0170.00963.3440.0010.0010.0000.0000.0000.000
150B499TYR0-0.039-0.00962.284-0.001-0.0010.0000.0000.0000.000
151B500TYR0-0.007-0.02564.0760.0010.0010.0000.0000.0000.000
152B501PHE00.0240.02557.4240.0000.0000.0000.0000.0000.000
153B502PHE0-0.002-0.00959.2060.0000.0000.0000.0000.0000.000
154B503ASP-1-0.840-0.90256.8440.0420.0420.0000.0000.0000.000
155B504CYS00.0230.00254.0850.0000.0000.0000.0000.0000.000
156B505LEU0-0.033-0.01251.7330.0010.0010.0000.0000.0000.000
157B506ASN0-0.115-0.07255.6790.0010.0010.0000.0000.0000.000
158B507TRP0-0.073-0.02258.4310.0000.0000.0000.0000.0000.000
159B508ARG10.9690.97460.852-0.036-0.0360.0000.0000.0000.000
160B509LYS10.9300.98062.150-0.025-0.0250.0000.0000.0000.000
161B510VAL0-0.035-0.00761.024-0.001-0.0010.0000.0000.0000.000
162B511ALA00.003-0.00263.031-0.001-0.0010.0000.0000.0000.000
163B512LYS10.9390.97054.767-0.034-0.0340.0000.0000.0000.000
164B513GLU-1-0.958-0.96461.1810.0230.0230.0000.0000.0000.000
165B514PHE00.001-0.00456.2020.0010.0010.0000.0000.0000.000
166B515HIS0-0.008-0.02456.035-0.001-0.0010.0000.0000.0000.000
167B516LEU0-0.0090.00757.0050.0010.0010.0000.0000.0000.000
168B517GLU-1-0.815-0.92154.2310.0190.0190.0000.0000.0000.000
169B518TYR0-0.050-0.04257.1570.0010.0010.0000.0000.0000.000
170B519ASP-1-0.878-0.92553.8110.0160.0160.0000.0000.0000.000
171B520LYS10.8140.90650.210-0.023-0.0230.0000.0000.0000.000
172B521LEU0-0.041-0.01553.9940.0020.0020.0000.0000.0000.000
173B522GLU-1-0.955-0.97254.7590.0260.0260.0000.0000.0000.000
174B523GLU-1-0.947-0.97056.7520.0170.0170.0000.0000.0000.000
175B524ARG10.8730.93959.038-0.016-0.0160.0000.0000.0000.000
176B525PRO00.0400.02357.4260.0000.0000.0000.0000.0000.000
177B526HIS00.0050.00755.635-0.001-0.0010.0000.0000.0000.000
178B527LEU0-0.017-0.01456.3990.0020.0020.0000.0000.0000.000
179B528PRO00.0140.00253.216-0.001-0.0010.0000.0000.0000.000
180B529SER0-0.0010.00055.0100.0000.0000.0000.0000.0000.000
181B530THR0-0.033-0.01750.494-0.001-0.0010.0000.0000.0000.000
182B531PHE00.0220.01551.9110.0010.0010.0000.0000.0000.000
183B532ASN0-0.029-0.03450.681-0.001-0.0010.0000.0000.0000.000
184B533TYR00.0490.04146.0970.0010.0010.0000.0000.0000.000
185B534ASN00.0330.00346.0660.0030.0030.0000.0000.0000.000
186B535PRO00.0660.04345.3120.0000.0000.0000.0000.0000.000
187B536ALA00.010-0.00442.8450.0030.0030.0000.0000.0000.000
188B537GLN0-0.022-0.00541.6410.0020.0020.0000.0000.0000.000
189B538GLN0-0.102-0.06139.895-0.004-0.0040.0000.0000.0000.000
190B539ALA0-0.0140.00938.6760.0020.0020.0000.0000.0000.000
191B540PHE0-0.0060.01133.6700.0080.0080.0000.0000.0000.000