FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8N23Y

Calculation Name: 4A11-B-Xray372

Preferred Name: CRL4(CRBN) E3 ubiquitin ligase

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 4A11

Chain ID: B

ChEMBL ID: CHEMBL3833061

UniProt ID: Q16531

Base Structure: X-ray

Registration Date: 2023-09-26

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 365
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6083806.364897
FMO2-HF: Nuclear repulsion 5938712.854416
FMO2-HF: Total energy -145093.510481
FMO2-MP2: Total energy -145509.505804


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:1:MET)


Summations of interaction energy for fragment #1(B:1: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.
-9.799-1.8352.709-3.413-7.2590.007
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / 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].
3B3GLY00.0250.0133.021-4.240-1.5430.093-1.252-1.5380.007
4B4PHE00.0280.0112.328-2.769-1.0932.145-1.021-2.8000.002
5B5LEU00.009-0.0042.670-1.727-0.1320.274-0.418-1.4510.001
6B6SER00.0010.0055.944-0.152-0.1520.0000.0000.0000.000
7B7ALA00.0430.0277.433-0.103-0.1030.0000.0000.0000.000
8B8ARG10.9680.9676.5000.0280.0280.0000.0000.0000.000
9B9GLN0-0.085-0.0469.251-0.057-0.0570.0000.0000.0000.000
10B10THR0-0.061-0.01111.576-0.056-0.0560.0000.0000.0000.000
11B11GLY00.0100.01112.894-0.020-0.0200.0000.0000.0000.000
12B12LEU0-0.0110.00311.529-0.009-0.0090.0000.0000.0000.000
13B13GLU-1-0.944-0.97810.2800.4320.4320.0000.0000.0000.000
14B14ASP-1-0.826-0.93512.5760.1350.1350.0000.0000.0000.000
15B15PRO00.0300.01811.4390.0480.0480.0000.0000.0000.000
16B16LEU0-0.037-0.03110.9830.0220.0220.0000.0000.0000.000
17B17ARG10.9820.99211.517-0.322-0.3220.0000.0000.0000.000
18B18LEU00.0040.0137.2220.0200.0200.0000.0000.0000.000
19B19ARG10.9811.0127.6930.2590.2590.0000.0000.0000.000
20B20ARG10.9450.9909.420-0.089-0.0890.0000.0000.0000.000
21B21ALA00.044-0.0128.730-0.024-0.0240.0000.0000.0000.000
22B22GLU-1-0.792-0.8584.1091.9152.9420.122-0.369-0.780-0.002
23B23SER0-0.042-0.0327.132-0.180-0.1800.0000.0000.0000.000
24B24THR0-0.089-0.01810.073-0.077-0.0770.0000.0000.0000.000
25B25ARG10.8280.8823.191-1.807-0.8380.075-0.353-0.690-0.001
26B26ARG10.9190.9617.0840.4250.4250.0000.0000.0000.000
27B27VAL0-0.0020.0069.609-0.047-0.0470.0000.0000.0000.000
28B28LEU0-0.038-0.03011.201-0.009-0.0090.0000.0000.0000.000
29B29GLY0-0.0080.01810.5940.0120.0120.0000.0000.0000.000
30B30LEU0-0.073-0.01111.616-0.051-0.0510.0000.0000.0000.000
31B31GLU-1-0.913-0.96814.625-0.195-0.1950.0000.0000.0000.000
32B32LEU0-0.019-0.01416.811-0.020-0.0200.0000.0000.0000.000
33B33ASN00.000-0.00816.061-0.011-0.0110.0000.0000.0000.000
34B34LYS10.9060.94317.9880.1540.1540.0000.0000.0000.000
35B35ASP-1-0.830-0.91617.035-0.305-0.3050.0000.0000.0000.000
36B36ARG10.8090.91414.3820.3520.3520.0000.0000.0000.000
37B37ASP-1-0.885-0.92620.116-0.141-0.1410.0000.0000.0000.000
38B38VAL0-0.035-0.01923.589-0.011-0.0110.0000.0000.0000.000
39B39GLU-1-0.810-0.87225.769-0.115-0.1150.0000.0000.0000.000
40B40ARG10.9010.92229.0980.0980.0980.0000.0000.0000.000
41B41ILE00.0130.01931.9660.0030.0030.0000.0000.0000.000
42B42HIS0-0.076-0.01932.5500.0020.0020.0000.0000.0000.000
43B43GLY00.0320.01835.9840.0000.0000.0000.0000.0000.000
44B44GLY0-0.025-0.01638.5220.0040.0040.0000.0000.0000.000
45B45GLY00.001-0.02335.687-0.004-0.0040.0000.0000.0000.000
46B46ILE00.0020.00730.2600.0020.0020.0000.0000.0000.000
47B47ASN0-0.044-0.02732.9140.0020.0020.0000.0000.0000.000
48B48THR0-0.048-0.04631.1690.0040.0040.0000.0000.0000.000
49B49LEU0-0.007-0.02425.796-0.003-0.0030.0000.0000.0000.000
50B50ASP-1-0.839-0.90626.623-0.084-0.0840.0000.0000.0000.000
51B51ILE0-0.019-0.01520.484-0.006-0.0060.0000.0000.0000.000
52B52GLU-1-0.829-0.90723.372-0.150-0.1500.0000.0000.0000.000
53B53PRO0-0.0080.00022.554-0.010-0.0100.0000.0000.0000.000
54B54VAL0-0.019-0.01721.796-0.003-0.0030.0000.0000.0000.000
55B55GLU-1-0.933-0.97018.800-0.190-0.1900.0000.0000.0000.000
56B56GLY0-0.0160.00718.818-0.026-0.0260.0000.0000.0000.000
57B57ARG10.8660.92619.7160.1960.1960.0000.0000.0000.000
58B58TYR00.017-0.00321.272-0.005-0.0050.0000.0000.0000.000
59B59MET0-0.021-0.00523.9330.0040.0040.0000.0000.0000.000
60B60LEU0-0.0090.01125.8870.0020.0020.0000.0000.0000.000
61B61SER00.0150.00529.167-0.002-0.0020.0000.0000.0000.000
62B62GLY00.0380.00731.1030.0030.0030.0000.0000.0000.000
63B63GLY00.0230.01734.5540.0000.0000.0000.0000.0000.000
64B64SER00.004-0.02436.8380.0050.0050.0000.0000.0000.000
65B65ASP-1-0.823-0.92738.549-0.065-0.0650.0000.0000.0000.000
66B66GLY0-0.0030.01440.2140.0010.0010.0000.0000.0000.000
67B67VAL0-0.0180.00136.6070.0000.0000.0000.0000.0000.000
68B68ILE00.0270.01234.182-0.001-0.0010.0000.0000.0000.000
69B69VAL0-0.053-0.02131.1810.0010.0010.0000.0000.0000.000
70B70LEU00.0570.02928.8220.0000.0000.0000.0000.0000.000
71B71TYR0-0.039-0.02126.1380.0020.0020.0000.0000.0000.000
72B72ASP-1-0.764-0.85322.865-0.217-0.2170.0000.0000.0000.000
73B73LEU0-0.033-0.03920.1190.0010.0010.0000.0000.0000.000
74B74GLU-1-0.877-0.95216.473-0.409-0.4090.0000.0000.0000.000
75B75ASN0-0.065-0.00217.4430.0480.0480.0000.0000.0000.000
76B76SER00.008-0.00318.734-0.025-0.0250.0000.0000.0000.000
77B77SER0-0.087-0.03519.5110.0020.0020.0000.0000.0000.000
78B78ARG10.9420.95618.6000.2400.2400.0000.0000.0000.000
79B79GLN0-0.017-0.00717.479-0.052-0.0520.0000.0000.0000.000
80B80SER00.0410.02314.363-0.013-0.0130.0000.0000.0000.000
81B81TYR0-0.0080.00615.9150.0020.0020.0000.0000.0000.000
82B82TYR0-0.054-0.02717.181-0.004-0.0040.0000.0000.0000.000
83B83THR00.0390.01121.5000.0020.0020.0000.0000.0000.000
84B84CYS0-0.077-0.02722.253-0.011-0.0110.0000.0000.0000.000
85B85LYS10.9000.92224.3370.1410.1410.0000.0000.0000.000
86B86ALA0-0.020-0.02627.660-0.004-0.0040.0000.0000.0000.000
87B87VAL0-0.046-0.02328.4490.0020.0020.0000.0000.0000.000
88B88CYS0-0.0040.00830.9640.0050.0050.0000.0000.0000.000
89B89SER0-0.029-0.03433.651-0.001-0.0010.0000.0000.0000.000
90B90ILE00.0110.03136.2820.0030.0030.0000.0000.0000.000
91B91GLY00.0500.00339.0630.0010.0010.0000.0000.0000.000
92B92ARG10.8670.90838.8770.0700.0700.0000.0000.0000.000
93B93ASP-1-0.894-0.95244.464-0.055-0.0550.0000.0000.0000.000
94B94HIS0-0.0550.00041.6490.0030.0030.0000.0000.0000.000
95B95PRO00.0470.02644.7830.0010.0010.0000.0000.0000.000
96B96ASP-1-0.898-0.95644.375-0.048-0.0480.0000.0000.0000.000
97B97VAL0-0.047-0.01342.4190.0000.0000.0000.0000.0000.000
98B98HIS0-0.084-0.03840.3170.0010.0010.0000.0000.0000.000
99B99ARG10.9440.98443.9090.0360.0360.0000.0000.0000.000
100B100TYR0-0.010-0.02645.2130.0010.0010.0000.0000.0000.000
101B101SER0-0.021-0.00340.059-0.003-0.0030.0000.0000.0000.000
102B102VAL00.0190.02837.3560.0030.0030.0000.0000.0000.000
103B103GLU-1-0.875-0.94437.308-0.048-0.0480.0000.0000.0000.000
104B104THR0-0.018-0.04434.4670.0000.0000.0000.0000.0000.000
105B105VAL00.0120.00331.5070.0020.0020.0000.0000.0000.000
106B106GLN00.0000.01230.6230.0000.0000.0000.0000.0000.000
107B107TRP0-0.021-0.00327.0490.0030.0030.0000.0000.0000.000
108B108TYR00.019-0.00330.6730.0060.0060.0000.0000.0000.000
109B109PRO0-0.0240.00129.601-0.006-0.0060.0000.0000.0000.000
110B110HIS0-0.061-0.05129.1660.0010.0010.0000.0000.0000.000
111B111ASP-1-0.883-0.94130.539-0.077-0.0770.0000.0000.0000.000
112B112THR00.0230.01427.4380.0040.0040.0000.0000.0000.000
113B113GLY0-0.016-0.00230.262-0.002-0.0020.0000.0000.0000.000
114B114MET00.0230.01533.2020.0060.0060.0000.0000.0000.000
115B115PHE00.0030.01132.401-0.003-0.0030.0000.0000.0000.000
116B116THR00.0200.01634.2120.0060.0060.0000.0000.0000.000
117B117SER00.026-0.00335.333-0.004-0.0040.0000.0000.0000.000
118B118SER0-0.0070.02837.8020.0040.0040.0000.0000.0000.000
119B119SER00.0320.01839.640-0.001-0.0010.0000.0000.0000.000
120B120PHE0-0.032-0.04142.2170.0030.0030.0000.0000.0000.000
121B121ASP-1-0.827-0.89744.799-0.041-0.0410.0000.0000.0000.000
122B122LYS10.8810.93646.2510.0280.0280.0000.0000.0000.000
123B123THR0-0.013-0.00144.9670.0000.0000.0000.0000.0000.000
124B124LEU00.012-0.01439.552-0.001-0.0010.0000.0000.0000.000
125B125LYS10.8310.91541.1860.0500.0500.0000.0000.0000.000
126B126VAL00.0230.01139.275-0.003-0.0030.0000.0000.0000.000
127B127TRP0-0.043-0.05536.8960.0010.0010.0000.0000.0000.000
128B128ASP-1-0.832-0.92337.283-0.072-0.0720.0000.0000.0000.000
129B129THR0-0.019-0.01632.4750.0000.0000.0000.0000.0000.000
130B130ASN0-0.041-0.01334.047-0.006-0.0060.0000.0000.0000.000
131B131THR0-0.030-0.03836.0060.0010.0010.0000.0000.0000.000
132B132LEU0-0.0140.02235.8020.0020.0020.0000.0000.0000.000
133B133GLN0-0.030-0.02138.8150.0040.0040.0000.0000.0000.000
134B134THR0-0.026-0.01341.264-0.002-0.0020.0000.0000.0000.000
135B135ALA00.0130.00741.2320.0000.0000.0000.0000.0000.000
136B136ASP-1-0.876-0.93042.974-0.040-0.0400.0000.0000.0000.000
137B137VAL0-0.063-0.03043.678-0.002-0.0020.0000.0000.0000.000
138B138PHE0-0.0030.00243.5480.0030.0030.0000.0000.0000.000
139B139ASN0-0.007-0.02246.690-0.002-0.0020.0000.0000.0000.000
140B140PHE00.007-0.00544.9150.0010.0010.0000.0000.0000.000
141B141GLU-1-0.937-0.96749.799-0.021-0.0210.0000.0000.0000.000
142B142GLU-1-0.944-0.99049.516-0.022-0.0220.0000.0000.0000.000
143B143THR0-0.059-0.01545.737-0.001-0.0010.0000.0000.0000.000
144B144VAL00.0200.01241.1390.0020.0020.0000.0000.0000.000
145B145TYR0-0.091-0.04140.731-0.001-0.0010.0000.0000.0000.000
146B146SER00.0270.00336.390-0.003-0.0030.0000.0000.0000.000
147B147HIS0-0.0110.00136.0420.0060.0060.0000.0000.0000.000
148B148HIS00.0170.02230.6430.0010.0010.0000.0000.0000.000
149B149MET00.0650.04833.8620.0040.0040.0000.0000.0000.000
150B150SER00.010-0.00232.995-0.001-0.0010.0000.0000.0000.000
151B151PRO00.0300.02328.375-0.002-0.0020.0000.0000.0000.000
152B152VAL0-0.0360.00429.515-0.003-0.0030.0000.0000.0000.000
153B153SER0-0.173-0.16931.0220.0000.0000.0000.0000.0000.000
154B154THR00.1210.05633.5090.0000.0000.0000.0000.0000.000
155B155LYS10.8450.93534.8630.0310.0310.0000.0000.0000.000
156B156HIS0-0.050-0.02437.8310.0010.0010.0000.0000.0000.000
157B157CYS00.0470.01438.443-0.002-0.0020.0000.0000.0000.000
158B158LEU0-0.033-0.00240.270-0.001-0.0010.0000.0000.0000.000
159B159VAL00.0320.01438.344-0.002-0.0020.0000.0000.0000.000
160B160ALA0-0.061-0.02838.9120.0030.0030.0000.0000.0000.000
161B161VAL00.027-0.00739.576-0.002-0.0020.0000.0000.0000.000
162B162GLY00.010-0.02141.0950.0030.0030.0000.0000.0000.000
163B163THR00.0220.01142.615-0.001-0.0010.0000.0000.0000.000
164B164ARG10.9210.95645.6650.0260.0260.0000.0000.0000.000
165B165GLY00.0480.03148.1290.0020.0020.0000.0000.0000.000
166B166PRO0-0.002-0.00748.4210.0000.0000.0000.0000.0000.000
167B167LYS10.8910.94849.0630.0160.0160.0000.0000.0000.000
168B168VAL00.0080.00743.229-0.001-0.0010.0000.0000.0000.000
169B169GLN00.0120.01745.0620.0000.0000.0000.0000.0000.000
170B170LEU0-0.0070.00342.278-0.002-0.0020.0000.0000.0000.000
171B171CYS00.003-0.00743.4530.0020.0020.0000.0000.0000.000
172B172ASP-1-0.834-0.93443.017-0.033-0.0330.0000.0000.0000.000
173B173LEU00.0400.03138.5300.0000.0000.0000.0000.0000.000
174B174LYS10.8600.97642.7780.0300.0300.0000.0000.0000.000
175B175SER0-0.065-0.06544.6560.0040.0040.0000.0000.0000.000
176B176GLY00.1050.05946.605-0.001-0.0010.0000.0000.0000.000
177B177SER0-0.036-0.03147.5090.0010.0010.0000.0000.0000.000
178B178CYS00.0260.02547.2380.0000.0000.0000.0000.0000.000
179B179SER0-0.0020.01048.6490.0010.0010.0000.0000.0000.000
180B180HIS0-0.080-0.02746.0990.0010.0010.0000.0000.0000.000
181B181ILE00.0530.01648.076-0.001-0.0010.0000.0000.0000.000
182B182LEU0-0.0020.01643.7470.0010.0010.0000.0000.0000.000
183B183GLN00.003-0.01048.018-0.001-0.0010.0000.0000.0000.000
184B184GLY00.005-0.01750.0270.0010.0010.0000.0000.0000.000
185B185HIS0-0.050-0.02244.3440.0010.0010.0000.0000.0000.000
186B186ARG10.9080.93748.8740.0050.0050.0000.0000.0000.000
187B187GLN0-0.067-0.02748.4760.0010.0010.0000.0000.0000.000
188B188GLU-1-0.822-0.90945.931-0.018-0.0180.0000.0000.0000.000
189B189ILE0-0.0270.03341.9010.0010.0010.0000.0000.0000.000
190B190LEU0-0.061-0.03640.396-0.002-0.0020.0000.0000.0000.000
191B191ALA0-0.007-0.01536.231-0.003-0.0030.0000.0000.0000.000
192B192VAL0-0.037-0.01936.9340.0040.0040.0000.0000.0000.000
193B193SER00.0220.00632.435-0.005-0.0050.0000.0000.0000.000
194B194TRP00.0350.00533.5780.0060.0060.0000.0000.0000.000
195B195SER0-0.026-0.01132.359-0.001-0.0010.0000.0000.0000.000
196B196PRO00.0060.03027.551-0.002-0.0020.0000.0000.0000.000
197B197ARG10.8940.94928.034-0.006-0.0060.0000.0000.0000.000
198B198TYR0-0.018-0.02930.7980.0000.0000.0000.0000.0000.000
199B199ASP-1-0.723-0.82034.516-0.029-0.0290.0000.0000.0000.000
200B200TYR00.016-0.00536.083-0.002-0.0020.0000.0000.0000.000
201B201ILE0-0.0170.00536.5420.0010.0010.0000.0000.0000.000
202B202LEU00.0250.01936.672-0.002-0.0020.0000.0000.0000.000
203B203ALA0-0.034-0.01336.0540.0040.0040.0000.0000.0000.000
204B204THR00.0100.01137.965-0.003-0.0030.0000.0000.0000.000
205B205ALA00.0190.01138.7400.0030.0030.0000.0000.0000.000
206B206SER00.0500.02740.690-0.002-0.0020.0000.0000.0000.000
207B207ALA0-0.011-0.03043.8060.0010.0010.0000.0000.0000.000
208B208ASP-1-0.841-0.91345.536-0.009-0.0090.0000.0000.0000.000
209B209SER0-0.049-0.04744.2370.0020.0020.0000.0000.0000.000
210B210ARG10.8200.91944.2330.0050.0050.0000.0000.0000.000
211B211VAL00.0400.01538.510-0.002-0.0020.0000.0000.0000.000
212B212LYS10.8880.96441.7940.0090.0090.0000.0000.0000.000
213B213LEU00.0510.04236.893-0.002-0.0020.0000.0000.0000.000
214B214TRP00.012-0.01740.8870.0030.0030.0000.0000.0000.000
215B215ASP-1-0.755-0.86641.163-0.012-0.0120.0000.0000.0000.000
216B216VAL00.0350.02541.4940.0010.0010.0000.0000.0000.000
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