Evaluating the script in Coot will provide a new menu item "Acedrg"

Clicking on "Make Link with Link Dictionary from Acedrg" will create a new small dialog

The bond order can be selected

The name of the atom that gets deleted (if any) can be added to the entry (note that you need not
concern yourself with Hydrogen atoms)

Click on "Start (Pick 2 atoms)" and then pick the two atoms that are linked. Click on the atom of
the ligand that has a deleted atom (if any) first - this is usually a ligand atom

After the second atoms has been clicked, Coot will then run Acedrg in link-generation mode and the
interface will freeze for several seconds

A link will be generated and displayed in dotted lines

If you haven't already done so, you should now delete the atom from the model that gets removed in 
the formation of this link (if any). Do this with Delete -> Atom -> [click on Atom]

You can now go ahead and refine with this link

If you are using CCP4i2, the dictionary will be a "Result" of this Coot job and can be used when you
run Refmac