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use strict;
use warnings;
...
close $array2FH or die qq{close: < HEREDOC 2: $!\n};

print Data::Dumper->Dumpxs( [ \ @array2 ], [ qw{ *array2 } ] );

%array1Lookup = (
                  'C:MET:L:52' => 1,
...
            'ATOM   2215  CE  MET L  52      17.198  97.429  87.820  1
+.00  0.00',
            'ATOM   2216  N   ARG L  53      19.331  91.671  87.132  1
+.00  0.00'
          );