Ligand Formatting

[VGPReys]

• To know if your file is properly formatted, you can refer to this online resource : https://cupnet.net/pdb-format/.
• Also, make sure the file extension is the appropriate one: .pdb.
• I just tried an example using OpenBabel online version 3.1.1, with a Chlorine atom, (SMILES to PDB, 3D coordinates, add hydrogen) and it was functional.

See one not-functional and functional example (from SMILES ClCCCCOc1ccccc1):

• File with wrong file extension:
  obabel_with_chlorine.pdb.txt (3.8 KB)
• File with .pdb file extension:
  obabel_with_chlorine.pdb (4.3 KB)