use strict;
     use warnings;

     open(IN, "list.txt") or die;
     chomp($line = <IN>);
     ($element, @abc) = split /\s+/, $line;
     while (chomp($line = <IN>)) {
     ($values, @xyz) = split /\s+/, $line;
     for ($i=0; $i<@xyz; $i++) {
     $s{$values}{$abc[$i]} = $xyz[$i];
        }
    }
    close(IN);
[download]

I made the identifiers sensible, but I am not sure what to assign as a explicit package for i, lines 6-10. My understanding is that it should get that information from the file being invoked.

Your code and logic is rather convoluted.

I offer:

use strict;
use warnings;

my %element;
while (<DATA>){
  my ($elem, $value) = split;
  $element{$elem}= $value;
}
print "  ";
print "$_ " for sort keys %element;
print "\n";
for my $k1(sort keys %element){
  print "$k1 ";
  for my $k2(sort keys %element){
     my $val = $element{$k1} eq "X" ? 0
             :  $element{$k2} eq "X" ? 0
             : 2;
     print $val . " ";
  }
  print "\n";
}

__DATA__
  A X
     B Y
     C Z
     D X
     E X
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             I hope life isn't a big joke, because I don't get it.
                   -SNL

Can you please show the output you get when you run this code?

I revised the code some more according to what makes sense. And I get errors regarding uninitialized values @values and @elements in hash element at each line of the file, list.txt.

     use strict; 
     use warnings;

     open(IN, "list.txt") or die;
     chomp($line = <IN>);
     ($element, @abc) = split /\s+/, $line;
     while (chomp($line = <IN>)) {
     ($values, @xyz) = split /\s+/, $line;
     for ($i=0; $i<@xyz; $i++) {
     $s {$elements}{$values[$i]} = $xyz[$i];
        }
    }
    close(IN);
[download]