Yikes. I reformatted, made your single A an AoA using array references, and made some little changes. You weren't handling the regex-ed data at all. This is totally untested, but then - so was yours. I suggest showing us some of your input to improve that regular expression (just anchoring it would be nice), and consistently using whitespace metacharacters.

#!/usr/bin/perl 
use strict; 
use warnings; 

open (FILE, 'interpro2go.txt') || die 'cannot open file'; 
my @i2g;
foreach my $line (<FILE>)
{ 
  if ($line =~ /\s*InterPro\:(\S+)\s(.+) > (.+) ; (.+)/)
  {
    push @i2g, [$1, $2, $3, $4];
  }
}

print @i2g; 
close FILE; 
exit 0;
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