microstates

pK_a Microstates of SAMPL7 Molecules

22 small molecules are assigned moleculed IDs in the form of SMXX from SM25 to SM46. This directory includes their enumerated microstates.

Also provided are the microstates in Tripos MOL2 (.mol2) and SDF (.sdf) file format.

Please note, the microstate lists provided here may not be comprehensive.

Manifest

• SMXX_microstates.csv - Files include updated microstate IDs and canonical SMILES of each microstate. The first microstate in each CSV file indicated by SMXX_micro000 is our selected neutral reference state.
• get_states.ipynb - Notebook used to generate tautomers and protomers of the molecules. Note, additional microstates were enumerated outside of this notebook by Chemicilaize (Chemaxon) and Epik (Schrodinger), and added to the SMXX_microstates.csv files here.
• make_mol2_sdf_files.ipynb - The jupyter notebook used to generate the MOL2 and SDF files for each microstate using OpenEye toolkits and the SMILES strings and codenames found in the SMXX_microstates.csv files. A random stereoisomer was chosen for microstates SM25_micro000, SM25_micro002, SM25_micro003, SM28_micro003, SM42_micro000, and SM43_micro000 when generating MOL2 and SDF files.
• SAMPL7_molecule_ID_and_SMILES.csv - A .CSV file that indicates SAMPL7 pK_a challenge molecule IDs and canonical isomeric SMILES.