Use https://github.com/charnley/rmsd.

Docked and co-crystallized structure should be saved in two XYZ file

Import both docked and crystallized ligand in pymol and use align obj1, obj2, cycles=0, transform=0. RMSD ll appear in the GUI

As suggested by R C Dash, the command

align object1, object2, cycles=0, transform=0

works in PyMol for docked conformer ligand and co-crystallized pose of same ligand. See that the atom numbers and atom sequence is same for object1 and object2.

Hope, it helps

We have recently developed a web server with a tool for RMSD calculation. Have a look:

https://pegasus.lbic.unibo.it/pacdock/index.php