Abstract
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 CCP4. 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 REFMAC5 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.
Highlights
Macromolecular crystallography (MX) is the most widely used experimental technique in structural biology that allows the study of three-dimensional structures of macromolecules in atomic, and sometimes electronic, detail, which is an essential step in understanding biological processes
In x2, we briefly introduce the program AceDRG
The corresponding AceDRG-derived bond length is around 1.32 A, which seems to reflect the fact that this ring is aromatic and the bond length is longer than a double bond but shorter than a single bond
Summary
Macromolecular crystallography (MX) is the most widely used experimental technique in structural biology that allows the study of three-dimensional structures of macromolecules in atomic, and sometimes electronic, detail, which is an essential step in understanding biological processes. AceDRG is a multifunctional software tool that analyses molecules in small-molecule databases (currently only the COD), extracts all atom types, bond lengths and angles from those databases, and organizes them in a hierarchical manner. It reads an input file containing basic chemical information about a ligand, such as a bonding graph and stereochemistry. The atom typing used in AceDRG encapsulates the local topological and chemical environments of atoms This includes the atom’s number of bonds and those of its neighbours (up to the third neighbours) and, if they belong to ring(s), information regarding ring size and aromaticity. (iii) We set the selected atom to the current atom. (iv) We check all neighbours of the current atom. (v) If the neighbour is not the ‘original atom’ and it is not the atom that preceded the current atom, and it is in the list of atoms that we have already seen, we call this neighbour Nachbarpunkt (this terminology is taken from Downs et al, 1989) and we stop walking further. (vi) If no Nachbarpunkt is found we check the current atom’s neighbours one by one to see if one of them closes the
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