Generate PDB and CIF restrain files for ligands of the LH series

  1. Prepare the 2D chemical structure using Marvin Sketch (ChemAxon)
  2. Add hydrogen atoms to the structure (Structure>Add>Explicit hydrogens)
  3. Convert to 3D (Structure>Clean 3D>Clean in 3D)
  4. Save as Tripos mol2 file (*.mol2)
  5. Go to GRADE server http://grade.globalphasing.org/cgi-bin/grade/server.cgi
  6. Choose the mol2 file import option
  7. Indicate a 3 letter code and the complete ligand name
  8. Indicate the net charge if necessary
  9. Check the resulting 2D structure displayed and save PDB and CIF files