Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.

ABSTRACT: In macromolecular structure refinement the low observation-to-parameter ratio and the lack of high-resolution data is countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum Mechanics (QM) can minimise the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints macromolecular refinement. We describe here a library of 37,000 small molecules extracted from the Chemical Components Dictionary in the Protein Data Bank and minimized by density functional QM. The lib

SUBMITTER: Moriarty NW 

PROVIDER: S-EPMC12324484 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature