A definition of geometry in Cartesian coordinates consists of the chemical symbol or atomic number, followed by the Cartesian coordinates and optimization flags but no connectivity.
MOPAC uses the lack of connectivity to indicate that Cartesian coordinates are to be used.
Here is an example of a MOPAC data-set for formaldehyde, in which all
coordinates are Cartesian.
PM3
Formaldehyde
All coordinates are Cartesian
O 0.00 0 0.00 0 0.00 0
C 1.21 1 0.00 0 0.00 0
H 1.79 1 0.93 1 0.00 0
H 1.79 1 -0.93 1 0.00 0
the "1" after the "0.93" indicates that the y coordinate of the first hydrogen atom is to be optimized.