Most efficient level of theory for sulfur-containing proline analogues (one that will work)
You seem to be running Gaussian through another program or script. Consequently, I have no idea where the various arguments should go. Conventionally, you make a Gaussian input file with keywords, such as:


  %n B3LYP/6-311G** EmpiricalDispersion=GD3BJ Opt
  
  [... molecule goes here ..]



For dispersion-correction (i.e., GD3BJ) you would need an appropriately recent version of Gaussian and use the separate term as indicated. It is not part of the functional designation. (Although some functionals implicitly have dispersion correction, B3LYP does not.)
I don't know a priori that PBEPBE would give more accurate results than B3LYP or any other functional. Your best bet is to either consider results from papers in the field (e.g., molecular crystal prediction or runs with DMACRYS) or testing a few functionals and finding out for yourself. Consider reading this question and answers.
Intermolecular interactions are not likely to be handled well by B3LYP. This is the whole reason for range-separated functionals and dispersion corrections. As to a specific functional suggestion, I highly recommend trying a few and looking at how to choose a functional.