Try the Pair-fitting Wizard in PyMOL. In any program, you can't just automatically superimpose an organic molecule onto the DNA, you have to explicitly specify which atoms should be superimposed to which. With the Pair-fit wizard, you can do this to click on the atoms to be superimposed. If you prefer to do this in the command line, use the Pair-fit command: https://pymolwiki.org/index.php/Pair_fit

First of all, create a .pdb file for DNA alone from complex. Then use PyMOL for superimposing of your organic molecule and DNA....

You can use a free/commercial software or you may write a short code using the formula of rotation with a give angle around an axis (see Article Divergence-free description for molecular rotation in Cartes...