How to give an ssl certificate to a third level domain?

Question

Digital certificates

Good day.
I ask you to poke your finger, is it possible to implement such a thing?
There is a physical machine on Windows Server 2012 which is located in the corporate network behind Kerio Control
. There is a third-level domain that I can specify which address to refer to.
Is there any way I can make my third level domain signed with a certificate from Let's Encrypt, so that when I navigate it, I would open the contents of the server's web server behind Kerio?
I can’t find the necessary information, and I’m new to this issue :(
I would be very grateful if you tell me where to start and where to dig?