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);
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You did not run the code you show us or you would have gotten messages that look like:

lobal symbol "$line" requires explicit package name at noname.pl line 
+5.
Global symbol "$element" requires explicit package name at noname.pl l
+ine 6.
...
[download]

Prefix your code with:

use strict;
use warnings;

my $fname = 'list.txt';

open my $fOut, '>', $fname or die "Can't create $fname: $!\n";
print $fOut <<TESTDATA;
some test data goes here
TESTDATA
close $fOut;

...
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providing some sensible test data where indicated then show us the result of actually running the code.

True laziness is hard work