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PrevICM User's Guide
7.15 Set Formal Charges

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

To set formal charge:

  • Read in a chemical spreadsheet File/Open SDF
  • Chemistry/Set Formal Charges
  • Enter the name of the chemical spreadsheet (table).
  • Choose the option to either make Charge, Make Neutral, or Charge according to ICM pKa Model
  • Select the groups you want to charge or neutralize.
  • The charges will automatically be added to your table.

The method for pKa prediction is unpublished/proprietary. It is a machine learning (PLS) model based on contributions of various molecular graph fragments to atomic pKa, trained on a carefully curated set of experimental pKa values.

Align/Color by 2D Scaffold
Enumerate Formal Charge States

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