I am using Build Homology Model to complete the 3D structure of a zinc finger protein by copying from a template an experimentally determined protein region (NMR structure from the PDB) that contains the zinc finger.
The resulting model is geometrically correct; however, when I run Prepare Protein (even after performing minimization and protein preparation), the zinc finger is not handled correctly.

In contrast, in the experimental PDB structure, Prepare Protein assigns correct parameters and the Zn–S interactions are defined as dative (N → M) bonds. In the homology-modeled structure, however, these dative bonds are not recognized, and the zinc coordination is effectively ignored.

I have noticed that it is not possible to explicitly assign a dative bond orderduring bond editing. Is this correct?
If so, what is the correct way to represent and prepare a zinc finger motif in a homology-modeled protein so that the Zn–S coordination is treated properly?

Thanks for any advice or help I’m my issue 

Alessandro