REFMAC (CCP4: Supported Program)
User's manual for the program refmac version 5.0.36
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.