I get a lot more warnings. For example

Name "main::ZNx" used only once: possible typo at ....
Name "main::Znz" used only once: possible typo at ....
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$ZNx is a different variable from $Znx because Perl is case-sensitive. You really want to start using strict (Tip #1 from the Basic debugging checklist).

Also, you probably want to change:

if ($pdbline =~ /OD2 ASP/ or /NE2 HIS/)
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to:

if ($pdbline =~ /OD2 ASP/ or $pdbline =~ /NE2 HIS/)
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