Marvin imports and exports XYZ molecule files that have the following format:
[ # optional comment line ] not written but allowed at import
[ N ] always written, but can be omitted in imported files
[ name\tE ] always written, but can be omitted in imported files
atom1 x y z
atom2 x y z
atomN x y z
where N is the number of atoms and E is the energy (optional). If energy is set for the molecule, then it is separated from the molecule name with a TAB ("\t") character.
Restrictions of the XYZ format:
Bonds are not stored.
As a consequence, all the hydrogens must be explicit, otherwise the bond types can not be guessed reliably by the importing program. In Marvin, implicit hydrogens are automatically converted to explicit H atoms at XYZ export.
Charges are not stored.
Query properties and other extra features are not stored.
Do not export 2D structures in XYZ!
XYZ export in Marvin is only meaningful for 3D molecules with realistic atomic distances.