Jmol is open-source Java software for interactive 3D viewing of molecular structures. It can easily be embedded into a webpage... including a Moodle page.
The Moodle Jmol resource module extension is easy to install. It requires no additional capability on your web server, but requires both Java and a JavaScript-enabled browser for the user.
For ultimate flexibility you may also wish to install the Jmol filter.
How to use
Just use it like any other resource in Moodle. Choose to "Add > A 3D molecule viewer" from Moodle's pull-down menu, then choose or upload the data file. You are provided with extra options on the config screen, such as whether to display certain controls, or whether to run any additional Jmol script upon initialisation.