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Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)

These two links go through the specifications required for the PDB format: Link1: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look ...