JLigand (1.0.37) did not have a problem reading the smiles and displaying the structure although the saved coordinates had the quinolone part mangled.
From: Mailing list for users of COOT Crystallographic Software [mailto:[email protected]] On Behalf Of Ethan A Merritt Sent: Tuesday, March 24, 2015 3:26 PM To: [email protected] Subject: Coot ligand builder bug interpreting SMILES string Seems I am having a bad week with coot. The smiles string NC1=C2C(N(CC6(COC6)CO)N=C2C3=CC=C(N=C(OC5CC5)C=C4)C4=C3)=NC=N1 describes the compound in the attached file 1671.png. However when I feed this string to coot it instead constructs the molecule shown in the file coot-molecule.png. Note that the terminal hydroxyl has jumped two carbons over and a CH2 group has been lost altogether. If I sketch this molecule ab initio in Calculate->Ligand Builder then when I select "Tidy up" it is mangled into the same incorrect isomer as the mis-interpreted SMILES string. Same thing if I ask coot to export a SMILES string and read it back in again. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
