Build the molecule

ADFinput drawing area

Import Coordinates: Select 'Import Coordinates ...' from the 'File' Menu.
Add atom: Select an atom-tool by clicking on the button with the 'C', 'O', 'N', 'H', 'Cl', or '>'.
  Click somewhere in the drawing area to draw the atom.
Add hydrogens: Select 'Add Hydrogen' from the 'Edit' Menu.
Add structure: Select a structure from the Structures' Menu (the button with a benzene molecule).
  Click somewhere in the drawing area to place the structure. Double-click on an atom to replace it with the   structure. Use the atom pop-up menu to replace all atoms in a selection by structures.
  Predefined Structures can be found for:  Alkyl Chains, Aromatic Molecules, Cyclic Hydrocarbons, Ligands,   Polyhedra, Amino Acids, parts of DNA, Metal Complexes, Solvents.
Change atom (bond) type: Press and hold the Right mouse button on the atom (bond).
  Select 'Change atom(s) type' ('Type') from the popup Menu.
Guess bonds: Select 'Guess bonds' from the 'Edit' Menu.
Delete atoms: Select the atoms. Press the backspace key.
Edit commands: Select 'Copy', 'Paste', 'Select ...', etc. from the 'Edit' Menu.
Undo: Select 'Undo' from the 'Edit' Menu to go back in time.

Pre-optimization of the geometry

ADFinput: Click on the MM optimizer button (the smiley button).