Finds atoms on a protein that can act as a hydrogen-bond donors and creates constraints to find potential locations for acceptor atoms on the ligand. This feature type is represented by a single point at the designated location.
Limitations:
UNITY attempts to model what would happen to a molecule at physiological pH. As a result, some structures might yield slightly different site points than expected.
Use the donor on protein feature when you are defining a query using the receptor or protein. However, if a molecule area contains a ligand rather than a receptor or protein, use methods for defining a Donor Atom or Donor Site.
Define Protein Donor Atom Feature in SYBYL
UNITY > Define Query > From Protein > Donor
Entire molecule is searched, identifying possible feature locations. (For multiple monomer molecules, select desired monomer(s). Chosen monomer(s), plus any monomers within 3 Å, are searched. Note: Results depend on the order in which monomers are selected. To reproduce results, the same selection order must be maintained.)
Click the identified features to include in the query, press End Select when finished.
Specify molecular area containing the query.
Specify if spatial constraints should be created. If Yes, enter a tolerance and a color for each constraint.
The labels are "RD_#" and "LA_#" for receptor donor atom and ligand acceptor atom, respectively. The number indicates the atom associated with that feature, e.g., RD_3 indicates that atom 3 is a receptor hydrogen donor atom.
