How do I make a ZMAT or XYZ file from scratch?
I know of two three ways to do this, but in either case it's quite a bit of work since I don't know any software that can read molecular structures from pictures. The second and third way use freeware only.


Draw the structure in Chem3D. For whatever stupid reason Chem3D doesn't support xyz files but you can save as *.pdb. If you need *.xyz then:


save as Gaussian input
delete the first 3 lines
Put the total number of atoms in the resulting first line
remove any "atoms" labeled as LP (lone pair, Chem3D uses them for force field optimization)
remove the second column next to the elemental symbol (if you sue Notepad++ you can select that by using ALT)
change file extension

Use openbabel 2.2.0 or higher to convert SMILES into *.xyz or *.pdb using the "gen3d" keyword. Of course for this you need the SMILES so you either have to produce that yourself or you need to draw it in a software that is able to produce SMILES like, again, Chem3D or this free website
It turns out this NIH website is also able to produce 3D structures, also in pdb file format, directly from SMILES or drawing the structure in their editor.