#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @records;
{
    local $/ = '$$$$' . "\n";
    while (my $record = <DATA>) {
        my ($stripped) = split /\nM END\n/, $record, 2;
        push @records, "$stripped\nM END\n$/";
    }
}
print Dumper \@records;

__DATA__
-OECHEM 658567-

1 2 0000 V2000
4 \t 5 8.7 7.655 3
2 \t 55 6 4 5
M END
> <compound id>
665765765
> <source>
db1

$$$$
-OECHEM 35343-

3 6 0000 V2000
1 \t 7 6 4.6 9
2 \t 45 0 3 5
M END
> <compound id>
3546789
> <source>
db1

$$$$