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the question is described below since it can be considered a chemistry or physics question: How to translate from one plane to another? originally posted on mathematics SE

I am trying to get Molecule X (from a xyz file which carries x y and z coordinates of X) to be sandwiched between gold electrodes as shown below:

Sandwiched molecule X

So far I was able, with a python code, to align X using the rotation matrix Rz.
Please not that the images are from VESTA capable of visualization only (otherwise i would not ask the question at all)

I got the following:

Aligned molecule Y

So both X and Y have the same orientation but I am not sure how to properly translate or move X to Y position. In other words I need to sandwich Y around the same gold electrodes X was sandwiched. What I can say is that the yellow balls in X and Y should be the same! However i am not sure what mathematical formulation is needed to move the aligned molecule thus I am here asking for assistance.

So in summary I want to go from starting point to ending point as shown below:

Merged figures

Any assistance would be appreciated.

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