Dear users, I am working on a structure of a protein-ligand complex, and the ligand contains an azetidine group. Whenever I display this structure in pymol, an unwanted bond forms between 2 carbon atoms in the azetidine ring.
The pdb file of this ligand was generated by Chem3D and the restraint cif file was generated by eLBOW in Phenix. I tried to edit both pdb and cif files of the ligand but it did not work very well. I was able to remove certain atoms but not the bond. I am kindly asking if there is a way to remove this unnecessary bond? Thank you. Regards, Hao
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