PDB entries for structures of P-loop NTPases were extracted from InterPro database entry IPR027417 ‘P-loop containing nucleoside triphosphate hydrolase’ and filtered to contain only those X-ray structures that contain Mg2+ ions, resulting in a list of 1,333 PDB IDs. Selected structures were analyzed with custom MATLAB scripts to select only those structures which contain either an NTP molecule, or its non-hydrolyzable analog, or a transition state analog. Additionally, we only considered NTP-like molecules bound in the proximity of at least one Lys residue (with less than 4.5 Å distance from NZ atom of Lys to any of the phosphate chain P atoms or the corresponding atoms in mimicking groups). In total, 1,357 NTP-like molecules from 670 PDB entries were used in the measurements. Isotherms for the heat map of the structure shape distribution are shown to indicate the most and least populated areas. Bold lines indicate isotherms chosen to represent crystallographic data in comparison with the MD results. (A) Shapes of ATP and GTP molecules. Native ATP and GTP molecules are most likely to be crystallized with inactive proteins, so the majority of them represent non-productive conformations of the phosphate chain. (B) Shapes of non-hydrolyzable analogs (PDB IDs: ANP, GNP, ACP, GCP, AGS, GSP). Non-hydrolyzable analogs cover lower values of the angle that is analogous to the PB-O3B-PG angle, since in such molecules, the ester oxygen between PB and PG is replaced with another atom (N in ANP, GNP; C in ACP, GCP); or one of free oxygens of γ-phosphate is replaced with S (GSP, AGS).