Mogul

[…] such as chirality errors and polymer linkage artifacts., the geometry of all non-standard or modified residues of a polymer, small-molecule ligands, and carbohydrate molecules is analyzed with the mogul software (). for each bond length, bond angle, dihedral angle and ring pucker, mogul searches through high-quality, small-molecule crystal structures in the cambridge structural database (csd) […]

[…] docked into empty density near eef1a and adjusted in coot using real space refinement with chemical restraints generated using phenix.elbow (). the geometry of didemnin b model was analyzed using mogul, a molecular-geometry library derived from the cambridge structural database (csd) (). some of the restraints generated from phenix.elbow were adjusted to match the median angles and distances […]

[…] respectively. the structure was phased by molecular replacement using pdb id 4nie as search model in phaser. ligand restraints were generated using grade (global phasing, version 1.2.8) and ccdc mogul. coot and phenix.refine were used in alternating cycles of model building and refinement. the quality of the final model was evaluated using molprobity. figures were created using pymol (the […]

[…] water molecules removed as a search model. the protein-ligand structures were manually rebuilt in coot and refined with buster in iterative cycles. ligand restraints were generated with grade and mogul . the positioning of the furan ring in compound 13 was guided using isostar maps calculated using data from the cambridge structural database and from the protein databank respectively. […]

[…] preferably derived by analysis of accurate small-molecule crystal structures (). at present, such descriptions are not generally available but could be derived for most ligands using a tool such as mogul (). mogul analyzes geometrical parameters (bond lengths, angles, torsions) by mining structures from the cambridge structure database (csd; ) to produce the distribution of each parameter […]