Hi,

The script below could do want you want like so:

use warnings;
use strict;

my ( $file1, $file2 ) = @ARGV;

my $matched_word = {};

open my $fh, '<', $file1 or die "can't open file: $!";
while (<$fh>) {
    s/^\s+?|\s+?$//;
    if (m{(.+?)\s+?.+?=(.+?)\s+?.*?$}) {
        push @{ $matched_word->{$1} }, $2;  
    }
}
close $fh or die "can't close file: $!";

open $fh, '<', $file2 or die "can't open file: $!";
while (<$fh>) {
    s/^\s+?|\s+?$//;
    my ( $value1, $value2 ) = split /\s+?\|\s+?/, $_;
    print $value1, " ", @{ $matched_word->{$value1} }, " ", $value2, $
+/
      if exists $matched_word->{$value1};
}
close $fh or die "can't close file: $!";
[download]

OUTPUT
Q197F8 IIV3-002R PF04947.9
Q91G88 IIV6-006L PF01486.12 PF00319.13
[download]

Please, I need also point out some other things I think might be good you look out for
1. Please, use 3 - arugment open function,
2. Please, don't use "DATA" as your filehandles, it is used by perl, see SelfLoader,
3. use lexical variable instead of BAREWORDs,
4. You might not need Modern::Perl, since you have used use warnings;use strict; or vise versa