[phenixbb] Restraints file for a modified peptide

I have a peptide that has a fluorescent tag attached to its N-terminus along with a unnatural amino acid incorporated into the sequence. I know how to generate .cif files for the individual ligands using elbow, but I'm at a loss as to get Phenix to recognize these modifications to the peptide so that it refines the structure as one molecule with covalent linkages between the fluorescent tag, peptide and modified amino acid. Any help would be much appreciated. Thanks, Michael