How would you add saccharide residue information to PDB files?
Short answer: your workflow doesn't include residue perception, so you would need to do this manually.

I don't use CORINA, but I suspect the answer is the same as if you generated coordinates using Open Babel.

You're using ChemDraw, which as far as I know, doesn't include any sort of residue information in the file, then creating SMILES and/or SD files, which definitely don't include residue information.

Then you create 3D coordinates with CORINA.

But nowhere along that chain is there a step to create / perceive / retain residue information. So I'm not surprised that you get one large unknown residue.

Open Babel does have code that does amino acid and nucleic acid residue perception when translating to PDB or Mol2 or other format that allows storing residue information. It does not have support for perceiving saccharides. Indeed, I'm not even sure what algorithms exist for automatically perceiving sugars.

My suggestion would be to either:


Number / label the saccharides by hand (yuck)
Write some sort of script in Python to label the residues - since presumably the atoms come in a particular order
Use a software builder that creates the residue information with the 3D coordinates.


For the latter case, a quick search suggested a few possibilities, although I haven't tried any of them:


Glycam
Yasara