The XYZ file format is a

chemical file format A chemical file format is a type of data file which is used specifically to depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files ...

. There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of

atoms Every atom is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Only the most common variety of hydrogen has no neutrons. Every solid, liquid, gas ...

with

Cartesian coordinates A Cartesian coordinate system (, ) in a plane is a coordinate system that specifies each point uniquely by a pair of numerical coordinates, which are the signed distances to the point from two fixed perpendicular oriented lines, measured i ...

that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines. The file format is used in

computational chemistry Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of mo ...

programs for importing and exporting geometries. The units are generally in

ångström The angstromEntry "angstrom" in the Oxford online dictionary. Retrieved on 2019-03-02 from https://en.oxforddictionaries.com/definition/angstrom.Entry "angstrom" in the Merriam-Webster online dictionary. Retrieved on 2019-03-02 from https://www.m ...

s. Some variations include using atomic numbers instead of atomic symbols, or skipping the comment line. Files using the XYZ format conventionally have the extension.

Format

The formatting of the .xyz file format is as follows: comment line ... Connectivity information in the XYZ file format is implied rather than explicit. According to the main page for XYZ (part of XMol),

Note that the XYZ format doesn't contain connectivity information. This intentional omission allows for greater flexibility: to create an XYZ file, you don't need to know where a molecule's bonds are; you just need to know where its atoms are. Connectivity information is generated automatically for XYZ files as they are read into XMol-related applications. Briefly, if the distance between two atoms is less than the sum of their covalent radii, they are considered bonded.{{Cite web, url = http://www.ccl.net/chemistry/resources/messages/1996/10/21.005-dir/index.html, title = XYZ man page (part of XMol), access-date = 22 September 2015

Example

The

pyridine Pyridine is a basic (chemistry), basic heterocyclic compound, heterocyclic organic compound with the chemical formula . It is structurally related to benzene, with one methine group replaced by a nitrogen atom. It is a highly flammable, weakl ...

molecule can be described in the XYZ format by the following:

11

C       -0.180226841      0.360945118     -1.120304970
C       -0.180226841      1.559292118     -0.407860970
C       -0.180226841      1.503191118      0.986935030
N       -0.180226841      0.360945118      1.29018350
C       -0.180226841     -0.781300882      0.986935030
C       -0.180226841     -0.837401882     -0.407860970
H       -0.180226841      0.360945118     -2.206546970
H       -0.180226841      2.517950118     -0.917077970
H       -0.180226841      2.421289118      1.572099030
H       -0.180226841     -1.699398882      1.572099030
H       -0.180226841     -1.796059882     -0.917077970

Animation

Most molecule viewers such as

Jmol Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in th ...

and VMD can show animations using .xyz files. The following is an example xyz format for m successive snapshot which can be rendered as an animation: comment line atom_symbol₁₁ x-coord₁₁ y-coord₁₁ z-coord₁₁ atom_symbol₁₂ x-coord₁₂ y-coord₁₂ z-coord₁₂ ... atom_symbol_1n x-coord_1n y-coord_1n z-coord_1n comment line atom_symbol₂₁ x-coord₂₁ y-coord₂₁ z-coord₂₁ atom_symbol₂₂ x-coord₂₂ y-coord₂₂ z-coord₂₂ ... atom_symbol_2n x-coord_2n y-coord_2n z-coord_2n . . . comment line atom_symbol_m1 x-coord_m1 y-coord_m1 z-coord_m1 atom_symbol_m2 x-coord_m2 y-coord_m2 z-coord_m2 ...
atom_symbol_mn x-coord_mn y-coord_mn z-coord_mn Note that the xyz standard does not require that the number or chemical nature of atoms should be the same at subsequent snapshots, which allows for atoms disappearing from or coming into the field of view during the animation.

References

Chemical file formats

Format

Example

Animation

See also

References