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Simulation report and files

General information

Name: DESRES 100 µs MD of 3CLpro, no water or ions (100 µs)

Included proteins: NSP5

Uniprot ID: P0DTD1

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6Y84

Description: This trajectory is from a 100 µs MD simulation of the apo enzyme started from the apo enzyme structure determined by X-ray crystallography (PDB entry 6Y84) The protein was solvated in a 120 x 120 x 120 Å water box containing 0.15 M NaCl. The simulation was performed on Anton 2 using the DES-Amber force field The interval between frames is 1 ns. The simulation was conducted in the NPT ensemble. This trajectory has been stripped of all waters and ions

Extracted from: BioExcel (ID: MCV1900063)

Author: D. E. Shaw Research

Submission date: October 22, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 9364

Simulation details

Software and version: Anton supercomputer specific tools None

Forcefield and version: DES-Amber

Delta : 10.0 ns

Replicates: 1

Accumulated simulation time: 1.0100 µs

References

D. E. Shaw Research. Molecular Dynamics Simulations Related to SARS-CoV-2. D. E. Shaw Research Technical Data, 2020. http://www.deshawresearch.com/resources_sarscov2.html/

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DESRES 100 µs MD of 3CLpro, no water or ions (100 µs) ( 6Y84)

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RMSD
Trajectory:
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Reference: frame from trajectory
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
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RMSF
Trajectory:
Frames:
All
From to
Stride:
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact

Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:

Display isolate: All isolates
NSP5
AA
Seq. pos.
PDB resID
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Impact score

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Mutation effect 0/16
Substitution scores
0
 BLOSUM90 score
0
 Δ charge
0
 Epstein's coefficient of difference
0
 Experimental exchangeability
0
 Grantham's distance
0
 Miyata's distance
0
 Sneath's index
0
 Δ hydrophobicity
Conservation
0
 Frequency (‰)
0
 SIFT4G Score
0
 SIFT4G Median IC
Structure
0
 Post-translational modification
0
 Surface accessibility
0
 FoldX ΔΔG
Experimental
0
 Mean Experimental Antibody Escape
0
 Max. Experimental Antibody Escape
Others
Annotation
Time-dependent 0/28
Parameter Average Weight average SD Weight SD
RMSD
0
0

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RMSF
0
0

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SASA
0
0

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CHI1
0
0

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All contacts
0
0

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Hydrogen bond contacts
0
0

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Salt bridge contacts
0
0

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Hydrophobic contacts
0
0

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Pi-cation contacts
0
0

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Pi-stacking contacts
0
0

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T-stacking contacts
0
0

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Van der Waals contacts
0
0

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Water bridge contacts
0
0

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Extended water bridge contacts
0
0

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User-provided descriptors 0/0

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