This is the dataset for "The three-dimensional atomic-level structure of an amorphous glucagon-like peptide-1 receptor agonist" Authors: Daria Torodii, Manuel Cordova, Jacob B. Holmes, Pinelopi Moutzouri, Tommaso Casalini, Sten O. Nilsson Lill, Arthur C. Pinon, Christopher S. Knee, Anna Svensk Ankarberg, Okky Dwichandra Putra, Staffan Schantz, Lyndon Emsley The dataset is divided into three main subfolders described below. Within the Data folder the following the sub folders are as described clusters_random coordinate files for a random selection of structure as described in the text clusters_selected_ref coordinate files for the "nmr set" selection of structure as described in the text DFTB_clusters_random DFTB input and output files for structures from clusters_random DFTB_clusters_selected_ref FTB input and output files for structures from clusters_selected_ref geometric_features JSON files containing all extracted geometric features as described in the text interaction_maps_ref 3D atomic density maps as described in https://doi.org/10.1021/jacs.3c04538 MD_snapshots PDB files for MD snapshots used the in the structural analysis ML_shifts Chemical shifts for each atomic environment predicted using ShiftML2 as described in the main text nmr_scoring_ref The score, as described in the main text, for each atomic environment TopSpin_data This directory contains all NMR experiments run on compound 1. Within the Figures folder the following the sub folders are as described cluster_energies_ref Figures showing the relative formation energy as function of the measured geometric figure, also described in the main text nmr_scoring_ref Figures of the distribution of geometric feature observed in the "nmr set" and "md set" This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.