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: 6NJLZ

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 OptAll
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 -1819332.008997
FMO2-HF: Nuclear repulsion 1741059.296405
FMO2-HF: Total energy -78272.712592
FMO2-MP2: Total energy -78499.792478


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.
-6.578-2.0470.355-1.902-2.984-0.006
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 : 0.016 / q_NPA : 0.006
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].
3B352THR0-0.041-0.0302.935-3.3940.0970.249-1.716-2.024-0.006
4B353ASP-1-0.859-0.9114.684-1.128-0.999-0.001-0.012-0.1160.000
5B354GLN00.012-0.0126.8900.4200.4200.0000.0000.0000.000
6B355PHE00.016-0.0049.0680.1570.1570.0000.0000.0000.000
7B356GLY00.0270.0205.3670.1610.211-0.001-0.008-0.0410.000
8B357MET00.010-0.0124.667-0.804-0.5440.004-0.049-0.2150.000
9B358ILE00.0250.0172.991-1.178-0.5770.104-0.117-0.5880.000
10B359GLY00.0570.0486.873-0.418-0.4180.0000.0000.0000.000
11B360LEU00.0070.0239.192-0.107-0.1070.0000.0000.0000.000
12B361LEU0-0.019-0.0107.964-0.177-0.1770.0000.0000.0000.000
13B362THR0-0.061-0.05510.633-0.150-0.1500.0000.0000.0000.000
14B363PHE00.0270.01012.938-0.073-0.0730.0000.0000.0000.000
15B364ILE00.0110.00713.385-0.031-0.0310.0000.0000.0000.000
16B365ARG10.9410.96812.413-0.172-0.1720.0000.0000.0000.000
17B366ALA00.0020.01117.017-0.028-0.0280.0000.0000.0000.000
18B367ALA0-0.021-0.01018.865-0.016-0.0160.0000.0000.0000.000
19B368GLU-1-0.949-0.97019.9550.1260.1260.0000.0000.0000.000
20B369THR0-0.120-0.05720.784-0.019-0.0190.0000.0000.0000.000
21B370ASP-1-0.882-0.95023.074-0.002-0.0020.0000.0000.0000.000
22B371PRO00.0160.00824.2520.0100.0100.0000.0000.0000.000
23B372GLY0-0.020-0.00526.7050.0050.0050.0000.0000.0000.000
24B373MET0-0.052-0.03919.507-0.009-0.0090.0000.0000.0000.000
25B374VAL00.0540.02921.5800.0180.0180.0000.0000.0000.000
26B375HIS0-0.011-0.00822.0990.0310.0310.0000.0000.0000.000
27B376LEU0-0.049-0.02218.8450.0040.0040.0000.0000.0000.000
28B377ALA0-0.066-0.02816.9240.0320.0320.0000.0000.0000.000
29B378LEU0-0.012-0.00518.0550.0370.0370.0000.0000.0000.000
30B379GLY0-0.0260.00720.650-0.002-0.0020.0000.0000.0000.000
31B380SER00.015-0.00723.858-0.008-0.0080.0000.0000.0000.000
32B381ASP-1-0.817-0.88927.3320.1020.1020.0000.0000.0000.000
33B382LEU00.0160.00529.187-0.010-0.0100.0000.0000.0000.000
34B383THR0-0.086-0.06631.731-0.008-0.0080.0000.0000.0000.000
35B384THR0-0.060-0.03232.455-0.006-0.0060.0000.0000.0000.000
36B385LEU00.0020.01233.181-0.006-0.0060.0000.0000.0000.000
37B386GLY00.0420.02336.5950.0000.0000.0000.0000.0000.000
38B387LEU0-0.059-0.04236.800-0.003-0.0030.0000.0000.0000.000
39B388ASN00.0170.00338.6690.0070.0070.0000.0000.0000.000
40B389LEU00.004-0.00333.555-0.001-0.0010.0000.0000.0000.000
41B390ASN0-0.030-0.00135.9320.0060.0060.0000.0000.0000.000
42B391SER0-0.003-0.01039.201-0.002-0.0020.0000.0000.0000.000
43B392PRO0-0.027-0.00942.2860.0020.0020.0000.0000.0000.000
44B393GLU-1-0.834-0.89744.7170.0390.0390.0000.0000.0000.000
45B394ASN0-0.008-0.00644.5000.0040.0040.0000.0000.0000.000
46B395LEU00.0900.04239.938-0.003-0.0030.0000.0000.0000.000
47B396TYR00.0250.00943.639-0.001-0.0010.0000.0000.0000.000
48B397PRO0-0.055-0.02745.068-0.002-0.0020.0000.0000.0000.000
49B398LYS10.8230.89547.059-0.040-0.0400.0000.0000.0000.000
50B399PHE00.0130.02040.0080.0010.0010.0000.0000.0000.000
51B400ALA00.0680.02545.299-0.002-0.0020.0000.0000.0000.000
52B401SER0-0.022-0.02244.052-0.003-0.0030.0000.0000.0000.000
53B402PRO0-0.004-0.01738.8500.0020.0020.0000.0000.0000.000
54B403TRP00.0240.01437.7240.0020.0020.0000.0000.0000.000
55B404ALA0-0.055-0.00640.747-0.001-0.0010.0000.0000.0000.000
56B405SER00.0320.01540.8170.0020.0020.0000.0000.0000.000
57B406SER0-0.038-0.02041.8770.0010.0010.0000.0000.0000.000
58B407PRO0-0.0130.00044.398-0.001-0.0010.0000.0000.0000.000
59B408CYS0-0.072-0.02446.257-0.001-0.0010.0000.0000.0000.000
60B409ARG10.8120.87149.694-0.020-0.0200.0000.0000.0000.000
61B410PRO0-0.023-0.03252.592-0.001-0.0010.0000.0000.0000.000
62B411GLN0-0.056-0.02455.978-0.001-0.0010.0000.0000.0000.000
63B412ASP-1-0.776-0.85052.1150.0220.0220.0000.0000.0000.000
64B413ILE0-0.015-0.01451.8910.0000.0000.0000.0000.0000.000
65B414ASP-1-0.896-0.93455.7900.0160.0160.0000.0000.0000.000
66B415PHE0-0.060-0.03558.6880.0000.0000.0000.0000.0000.000
67B416HIS00.0000.00260.211-0.001-0.0010.0000.0000.0000.000
68B417VAL0-0.038-0.01963.3020.0000.0000.0000.0000.0000.000
69B418PRO00.0020.00266.0660.0000.0000.0000.0000.0000.000
70B419SER00.007-0.02869.7360.0000.0000.0000.0000.0000.000
71B420GLU-1-0.888-0.92771.8940.0120.0120.0000.0000.0000.000
72B421TYR00.004-0.00867.9110.0000.0000.0000.0000.0000.000
73B422LEU0-0.0210.02368.9200.0000.0000.0000.0000.0000.000
74B423THR00.024-0.01270.387-0.001-0.0010.0000.0000.0000.000
75B424ASN0-0.0090.00269.165-0.001-0.0010.0000.0000.0000.000
76B425ILE00.0030.00171.533-0.001-0.0010.0000.0000.0000.000
77B426HIS00.0460.02173.4310.0000.0000.0000.0000.0000.000
78B427ILE0-0.021-0.01475.2160.0000.0000.0000.0000.0000.000
79B428ARG10.8980.94969.634-0.008-0.0080.0000.0000.0000.000
80B429ASP-1-0.886-0.93674.7550.0060.0060.0000.0000.0000.000
81B430LYS10.8700.91877.129-0.007-0.0070.0000.0000.0000.000
82B431LEU00.0070.02370.7690.0000.0000.0000.0000.0000.000
83B432ALA0-0.030-0.01674.4090.0000.0000.0000.0000.0000.000
84B433ALA00.0270.01571.6800.0000.0000.0000.0000.0000.000
85B434ILE00.0540.03065.4090.0000.0000.0000.0000.0000.000
86B435LYS10.9200.95369.145-0.008-0.0080.0000.0000.0000.000
87B436LEU00.0710.03663.5590.0000.0000.0000.0000.0000.000
88B437GLY00.0260.01967.6000.0000.0000.0000.0000.0000.000
89B438ARG10.8410.92170.483-0.009-0.0090.0000.0000.0000.000
90B439TYR00.0280.02066.7580.0000.0000.0000.0000.0000.000
91B440GLY00.0640.02769.4280.0000.0000.0000.0000.0000.000
92B441GLU-1-0.795-0.89465.5160.0170.0170.0000.0000.0000.000
93B442ASP-1-0.854-0.91164.1450.0200.0200.0000.0000.0000.000
94B443LEU00.0370.02263.1770.0010.0010.0000.0000.0000.000
95B444LEU0-0.019-0.00563.1030.0000.0000.0000.0000.0000.000
96B445PHE00.0500.01459.4700.0000.0000.0000.0000.0000.000
97B446TYR00.0060.00158.6790.0010.0010.0000.0000.0000.000
98B447LEU0-0.010-0.01958.4140.0010.0010.0000.0000.0000.000
99B448TYR00.0020.00753.1700.0000.0000.0000.0000.0000.000
100B449TYR0-0.012-0.01953.1610.0000.0000.0000.0000.0000.000
101B450MET0-0.023-0.00453.4630.0020.0020.0000.0000.0000.000
102B451ASN0-0.055-0.02554.3510.0010.0010.0000.0000.0000.000
103B452GLY00.0270.01150.943-0.001-0.0010.0000.0000.0000.000
104B453GLY0-0.0060.00349.4190.0010.0010.0000.0000.0000.000
105B454ASP-1-0.811-0.90150.3040.0140.0140.0000.0000.0000.000
106B455VAL0-0.002-0.01553.5990.0000.0000.0000.0000.0000.000
107B456LEU0-0.025-0.00756.580-0.001-0.0010.0000.0000.0000.000
108B457GLN00.0390.03552.0310.0000.0000.0000.0000.0000.000
109B458LEU00.0130.00153.4740.0000.0000.0000.0000.0000.000
110B459LEU0-0.028-0.02057.370-0.001-0.0010.0000.0000.0000.000
111B460ALA0-0.020-0.00159.4790.0000.0000.0000.0000.0000.000
112B461ALA00.0280.01557.5100.0000.0000.0000.0000.0000.000
113B462VAL0-0.031-0.01459.6460.0000.0000.0000.0000.0000.000
114B463GLU-1-0.808-0.89962.2190.0110.0110.0000.0000.0000.000
115B464LEU0-0.003-0.00260.2230.0000.0000.0000.0000.0000.000
116B465PHE0-0.019-0.01061.0120.0000.0000.0000.0000.0000.000
117B466ASN0-0.023-0.01863.740-0.001-0.0010.0000.0000.0000.000
118B467ARG10.6910.85466.617-0.013-0.0130.0000.0000.0000.000
119B468ASP-1-0.835-0.90366.3800.0120.0120.0000.0000.0000.000
120B469TRP0-0.0520.00161.5640.0010.0010.0000.0000.0000.000
121B470ARG10.8210.89459.750-0.014-0.0140.0000.0000.0000.000
122B471TYR0-0.020-0.01151.5060.0010.0010.0000.0000.0000.000
123B472HIS00.0380.02352.079-0.001-0.0010.0000.0000.0000.000
124B473LYS10.8320.89750.110-0.015-0.0150.0000.0000.0000.000
125B474GLU-1-0.910-0.95947.5690.0290.0290.0000.0000.0000.000
126B475GLU-1-0.819-0.91948.5490.0300.0300.0000.0000.0000.000
127B476ARG10.9360.98546.167-0.031-0.0310.0000.0000.0000.000
128B477VAL00.0100.01850.9610.0000.0000.0000.0000.0000.000
129B478TRP00.0150.01254.583-0.001-0.0010.0000.0000.0000.000
130B479ILE00.014-0.00956.5370.0010.0010.0000.0000.0000.000
131B480THR00.001-0.01960.462-0.001-0.0010.0000.0000.0000.000
132B481ARG10.8340.91564.223-0.014-0.0140.0000.0000.0000.000
133B482ALA00.0200.01766.8620.0000.0000.0000.0000.0000.000
134B483PRO00.004-0.01068.394-0.001-0.0010.0000.0000.0000.000
135B484GLY00.005-0.00772.2660.0000.0000.0000.0000.0000.000
136B485MET0-0.066-0.01868.5470.0000.0000.0000.0000.0000.000
137B486GLU-1-0.788-0.89368.9960.0130.0130.0000.0000.0000.000
138B487PRO0-0.091-0.02165.8860.0000.0000.0000.0000.0000.000
139B488THR0-0.002-0.01966.0720.0000.0000.0000.0000.0000.000
140B489MET0-0.037-0.01964.3230.0000.0000.0000.0000.0000.000
141B490LYS10.8320.89865.531-0.013-0.0130.0000.0000.0000.000
142B491THR00.0090.00962.4130.0000.0000.0000.0000.0000.000
143B492ASN0-0.010-0.02163.2930.0000.0000.0000.0000.0000.000
144B493THR00.0260.02358.311-0.001-0.0010.0000.0000.0000.000
145B494TYR00.0450.02558.5870.0010.0010.0000.0000.0000.000
146B495GLU-1-0.745-0.81360.6090.0140.0140.0000.0000.0000.000
147B496ARG10.8560.90360.468-0.020-0.0200.0000.0000.0000.000
148B497GLY00.0280.02062.422-0.001-0.0010.0000.0000.0000.000
149B498THR0-0.010-0.00862.9320.0010.0010.0000.0000.0000.000
150B499TYR0-0.054-0.04462.077-0.001-0.0010.0000.0000.0000.000
151B500TYR0-0.008-0.02563.6310.0000.0000.0000.0000.0000.000
152B501PHE00.0310.01156.6940.0000.0000.0000.0000.0000.000
153B502PHE00.0080.00258.3660.0000.0000.0000.0000.0000.000
154B503ASP-1-0.804-0.87956.0610.0310.0310.0000.0000.0000.000
155B504CYS00.002-0.01453.5130.0000.0000.0000.0000.0000.000
156B505LEU0-0.020-0.00551.0210.0000.0000.0000.0000.0000.000
157B506ASN0-0.068-0.05054.9460.0000.0000.0000.0000.0000.000
158B507TRP0-0.079-0.02556.8450.0000.0000.0000.0000.0000.000
159B508ARG10.8750.93759.943-0.026-0.0260.0000.0000.0000.000
160B509LYS10.8530.92161.284-0.017-0.0170.0000.0000.0000.000
161B510VAL0-0.044-0.01860.6450.0000.0000.0000.0000.0000.000
162B511ALA0-0.0010.00062.709-0.001-0.0010.0000.0000.0000.000
163B512LYS10.8250.90454.593-0.027-0.0270.0000.0000.0000.000
164B513GLU-1-0.817-0.87160.7840.0210.0210.0000.0000.0000.000
165B514PHE0-0.025-0.02256.0420.0010.0010.0000.0000.0000.000
166B515HIS0-0.037-0.04255.222-0.001-0.0010.0000.0000.0000.000
167B516LEU0-0.019-0.00256.5700.0010.0010.0000.0000.0000.000
168B517GLU-1-0.798-0.89253.3210.0200.0200.0000.0000.0000.000
169B518TYR0-0.050-0.04656.6330.0010.0010.0000.0000.0000.000
170B519ASP-1-0.904-0.94353.1680.0150.0150.0000.0000.0000.000
171B520LYS10.8210.91049.369-0.023-0.0230.0000.0000.0000.000
172B521LEU0-0.026-0.00353.5110.0010.0010.0000.0000.0000.000
173B522GLU-1-0.941-0.96553.6660.0170.0170.0000.0000.0000.000
174B523GLU-1-0.831-0.91356.3140.0130.0130.0000.0000.0000.000
175B524ARG10.8480.91158.970-0.009-0.0090.0000.0000.0000.000
176B525PRO00.0130.00757.018-0.001-0.0010.0000.0000.0000.000
177B526HIS00.0240.01354.988-0.001-0.0010.0000.0000.0000.000
178B527LEU0-0.012-0.01456.2770.0010.0010.0000.0000.0000.000
179B528PRO00.004-0.00152.625-0.001-0.0010.0000.0000.0000.000
180B529SER00.0010.00654.7030.0000.0000.0000.0000.0000.000
181B530THR0-0.023-0.01150.080-0.001-0.0010.0000.0000.0000.000
182B531PHE00.0180.00251.7330.0010.0010.0000.0000.0000.000
183B532ASN0-0.043-0.03950.550-0.001-0.0010.0000.0000.0000.000
184B533TYR00.0470.04144.9290.0000.0000.0000.0000.0000.000
185B534ASN00.0300.01046.3060.0020.0020.0000.0000.0000.000
186B535PRO00.0580.03344.8430.0000.0000.0000.0000.0000.000
187B536ALA00.0440.01642.2400.0010.0010.0000.0000.0000.000
188B537GLN0-0.060-0.02940.8470.0010.0010.0000.0000.0000.000
189B538GLN0-0.055-0.03739.355-0.004-0.0040.0000.0000.0000.000
190B539ALA0-0.0240.00638.1920.0020.0020.0000.0000.0000.000
191B540PHE0-0.0180.00532.6360.0040.0040.0000.0000.0000.000