You were nearly there (if I've understood your question correctly)
#!/usr/bin/perl
use warnings;
use strict;
use LWP::Simple;
use HTML::TreeBuilder;
print "ELENCO LIGANDI\n";
my $url3 = "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum
+/GetPage.pl?pdbcode=2j6p&template=ligands.html&l=1.1";
my $content =get ($url3);
my $p = HTML::TreeBuilder->new;
$p->parse_content($content);
my @anchors = $p->look_down(_tag => q{a});
for my $anchor (@anchors){
my $txt = $anchor->as_text;
if ($txt=~ /EPE\s/){
print $txt, qq{\n};
my $href = $anchor->attr(q{href});
print $href, qq{\n};
}
}
$p->delete;
__DATA__
output:
ELENCO LIGANDI
EPE 1148(C)
/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2j6p&templat
+e=ligands.html&l=4.1
EPE 1148(D)
/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2j6p&templat
+e=ligands.html&l=4.2
update: changed var names to anchor/s