use Modern::Perl;

my $sequence;

while (<DATA>) {
    if (/ENERGY/) {
        $sequence++;
        next;
    }
    my ( $first, @fields ) = grep { $_ } split;
    say "$first $_ $sequence" for @fields;
}

__DATA__
536 ENERGY = -176.2 gag
1 0 2 0
2 1 3 533
3 2 4 532
536 ENERGY = -175.9 gag
1 0 2 0
2 1 3 533
3 2 4 532