It is not reasonable to have a sort that excludes members of the list entirely. Sort rearranges lists; grep filters them.

What you might want to do is a Schwartzian Transform so that the regex doesn't need to be applied to $a and $b repeatedly.

print map {"$_->[0]\n"}
      sort {$a->[1] <=> $b->[1]}
      map  { [$_, (/C(\d*)/)[0]] }
      grep { /P/} 
      @compounds;
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Hoping for partial credit, I eliminated the join.