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    use Chemistry::Mol;

...
    $c = $mol->new_atom(symbol => "C", coords => [0,0,0]); 
    $o = $mol->new_atom(symbol => "O", coords => [0,0,1.23]); 
    $mol->new_bond(atoms => [$c, $o], order => 3);

    print $mol->print;