Atomic coordinate file

From Proteopedia

Atomic coordinate files are the data files that specify three-dimensional (3D) molecular structures. At a minimum, they must specify the positions of each atom in space, typically with X, Y and Z Cartesian coordinates.

Atomic coordinate files use many possible data formats. The XYZ format (file type .xyz) is specifies only the coordinates for each atom, and is useful for small molecules.

Bonds: Connectivity

Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The PDB format requires that covalent bonds be specified between atoms that are not members of Standard Residues in protein or nucleic acid chains. These are specified in CONECT records.