XYZ file format

The xyz format is used in computational chemistry and bioinformatics and contains Cartesian coordinates in three dimensions to describe the positions of atoms in molecules. The unit of measurement angstroms, rare atomic units are mostly used.

This format is understood by many programs, a formal definition but was never released. Therefore, the format may differ slightly depending on the computer program used, or the particular program may have trouble reading non-conforming xyz files.

Format specification

Like most file formats used in computational chemistry is also the xyz format set up line-oriented:

1st line: number of atoms ( integer) Line 2: Comment ( string) 3rd line and the following: Item Name x -y -z coordinate ( string or integer, 3 -point numbers ) In its most general category the xyz format allowed in the atomic specifications from the third line nor the specification of a ( atomic charge, point number ), three ( Cartesian vibration vector, 3 -point numbers ) or of four ( vibration vector and atomic charge ) additional columns.

Element x y z [x - vector y z vector - vector ] [ q] Unlike other popular file formats (eg pdb format) the xyz format is not set fixed number formats and positions.

Example

The following is a sample file for the water molecule is shown. All coordinate data (from row 3, column 2 to 4) are in angstroms, the charges specified as a multiple of the elementary charge: