Included are the Geometry-Complete Diffusion Model (GCDM) checkpoint files and Geometric Latent Diffusion Model (GeoLDM) checkpoint files referenced in our accompanying GCDM manuscript for 3D molecule generation and optimization (https://arxiv.org/abs/2302.04313). Additionally, included with the GCDM checkpoint files are EGNN molecular property prediction checkpoint files trained with three random seeds per property (18 in total). Lastly, GCDM (and EGNN baseline) checkpoint files for structure-based drug design experiments are included (8 in total).