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AceDRG : a stereochemical description generator for ligands
Author(s) -
Long Fei,
Nicholls Robert A.,
Emsley Paul,
Gražulis Saulius,
Merkys Andrius,
Vaitkus Antanas,
Murshudov Garib N.
Publication year - 2017
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798317000067
Subject(s) - atom (system on chip) , ring (chemistry) , ligand (biochemistry) , crystallography , aromaticity , bond length , chemistry , chirality (physics) , molecule , single bond , generator (circuit theory) , computer science , group (periodic table) , physics , crystal structure , quantum mechanics , biochemistry , nambu–jona lasinio model , receptor , chiral symmetry breaking , organic chemistry , embedded system , quark , power (physics)
The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment‐based atom typing to derive and organize bond lengths and angles from a small‐molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven‐membered rings), ring aromaticity and nearest‐neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine‐readable form that is freely available from CCP 4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the `ideal' bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC 5 and the model‐building program Coot . Other refinement and model‐building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files.