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/molecule_idref="([^"]+)/

use strict;
use warnings;
use XML::Simple;
...
molecule_idref="4"/><ComplexComponent5
molecule_idref="5"/>
</xml>

$VAR1 = {
          'ComplexComponent3' => {'molecule_idref' => '3'},
          'ComplexComponent5' => {'molecule_idref' => '5'},
...
          'ComplexComponent4' => {'molecule_idref' => '4'},
          'ComplexComponent2' => {'molecule_idref' => '2'}
        };