The XYZ file format is a chemical file format

Chemical file format

This article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...

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

Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids...

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

Ångström

The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....

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

Format

The formatting of the .xyz file format is as follows:




comment line

atom_symbol1 x-coord1 y-coord1 z-coord1

atom_symbol2 x-coord2 y-coord1 z-coord2

...

atom_symboln x-coordn y-coordn z-coordn



Example

The methane

Methane

Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel...

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

5

methane molecule (in Ångström
Ångström
The angstrom or ångström,  is a unit of length equal to 1/10,000,000,000  of a meter . Its symbol is the Swedish letter Å....

s)

C 	 0.000000 	 0.000000 	 0.000000

H 	 0.000000 	 0.000000 	 1.089000

H 	 1.026719 	 0.000000 	-0.363000

H 	-0.513360 	-0.889165 	-0.363000

H 	-0.513360 	 0.889165 	-0.363000

Animation

Some molecule viewers such as VMD

Visual Molecular Dynamics

- External links :* * *...

can show animations using .xyz files. The following is an example formating:




comment line

atom_symbol11 x-coord11 y-coord11 z-coord11

atom_symbol12 x-coord12 y-coord11 z-coord12

...

atom_symbol1n x-coord1n y-coord1n z-coord1n



comment line

atom_symbol21 x-coord21 y-coord1 z-coord21

atom_symbol22 x-coord22 y-coord1 z-coord22

...

atom_symbol2n x-coord2n y-coord2n z-coord2n

.

.

.



comment line

atom_symbolm1 x-coordm1 y-coordm1 z-coordm1

atom_symbolm2 x-coordm2 y-coordm1 z-coordm2

...

atom_symbolmn x-coordmn y-coordmn z-coordmn