Cyclic amide regognized as amines

Computer-Aided Drug Design at the Durrant Lab Forums Dimorphite-DL Cyclic amide regognized as amines

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      Andrey Frolov
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      Hi all,

      Dimorphite-DL seems to confuse the cyclic amides with amines. E.g. see the test molecule below. These substructures used in cross-linking peptides known as TATA or TATB cores (https://pubs.acs.org/doi/10.1021/acs.accounts.7b00184), so they are not very exotic. Would be great if you could you propose a workaround. Thanks!

      …/dimorphite_dl-1.2.4/dimorphite_dl.py –smiles ‘CC(=O)N1CN(CN(C1)C(C)=O)C(C)=O’

      For help, use: python dimorphite_dl.py –help
      t
      If you use Dimorphite-DL in your research, please cite:
      Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An
      open-source program for enumerating the ionization states of drug-like small
      molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.

      PARAMETERS:

      label_states: False
      max_ph: 8.4
      max_variants: 128
      min_ph: 6.4
      output_file: None
      pka_precision: 1.0
      silent: False
      smiles: CC(=O)N1CN(CN(C1)C(C)=O)C(C)=O
      smiles_file: None
      test: False

      CC(=O)N1CN(C(C)=O)CN(C(C)=O)C1
      CC(=O)N1CNH+CNH+C1
      CC(=O)N1CN(C(C)=O)CNH+C1
      CC(=O)[NH+]1CNH+CNH+C1

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