I have a subset of a protein active site containing a metal and its coordinating residues. Is there a tool to automatically measure all bond length, all angles and dihedrals in the subset.
I do not fully understand your question. Do you have a crystal structure of the protein's active site with a metal center? If you do, just open it in a crystallographic data program and measure by hand (there cannot be that many coordinating atoms!), since automation will give you all atoms within a certain radius of which many (most?) will not be truly bonding. Did I interpret your question correctly?