Hi everyone, My crystal structure contains a ligand and I generated the cif file of the ligand using phenix.elbow from the smiles file of the ligand. The ligand was drawn and the smiles file was generated from https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that the double bond (shown in the picture) is longer than the single bond in the generated elbow pdb file. Although the bond can be recognized correctly in the Coot (display the correct double bond), the simulation software doesn't recognize them correctly because of the bond length. In my theory, the double bond of the ring should be shorter than the single bond, is there any reason why phenix elbow generate this or any parameters I can set to overcome this? Thank you for your suggestions.
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