I think that this answer may also apply to your system. The allyl molecule in your second fragment interacts with the Ru atom in your first fragment through coordination bonds that have strong covalent character, so SAPT’s noncovalent perturbation theory doesn’t describe this interaction well. You might be able to use I-SAPT to understand the noncovalent interaction between two different ligands in the context of the metal, but you cannot use SAPT to understand the interaction between a ligand and any fragment containing the metal.