The form you want to post to is found in the <form> tag: prep_job.php

So you want to change your request to something like.

my $response = $browser->post(
  'http://enm.lobos.nih.gov/prep_job.php',
  [
    "upload"=> ["C:\\protean\\1o1l\\1o1l.pdb"],
    "jobname"=> "PRT1",
        "case"  => "2",
    "email" => "email\@gmail.com",
    "optin" => "true",
    "upload2"=> ["C:\\protean\\1o1l\\1o1l.pdb"],

  ],
  'Content_Type' => 'form-data',
);
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