When information about connectivity is available (i.e. which atom is bonded to what) and about the contents of the ligand (i.e. which element occupies which position), then a minimum description can be used to derive a dictionary entry for the ligand. It is a good idea first to draw the ligand on a piece of paper like:
OH | HO C2 O1-P1(O3) \ /\ / \ / \ / C3 C1 | | | | C4 C6 : \ / : : \/ : O4 C5 OH | | P4(O3) O5 | P5(O3) Figure 1
where dotted lines show that the atom is below the plane of the paper/screen and dashed lines above the plane of the paper/screen.
If this picture is converted to the minimum description, it will have the form as in Text 1.
When making a minimum description, one should be careful with the chiral volumes present in the ligand. For a description of chiral volumes and their relation of them to R- and S-forms, see chiral volume description.
Then LIBCHECK could be run like:
libcheck << eol N _file_l <minimum_description> _mon MON eol
where <minimum_description> is the file containing a minimum description and MON is the name of the ligand.
After LIBCHECK there will be a complete dictionary description and coordinate files in mmCIF and PDB format with all hydrogens present.