The 2D Screen license includes the usage of the Chemical Hashed Fingerprint but not the others (ECFP, MACCS, BCUT and the Pharmacophore Fingerprint). The license also covers the usage of the generatemd, screenmd, hitstatistics and optimizer command line tools.
The 3D Screen license includes the 3D (shape) descriptor for shape-based virtual screening using flexible alignment. Flexible Alignment is also available as a separate calculator plugin. The 3D screen license also covers the usage of a hit validation tool.