SETPI

In some instances, the default Lewis structure used in a MOZYME calculation is not correct.  The correct structure can be selected by explicitly supplying one or more p bonds.  To do this, add keyword SETPI.  After the data set, add  the atom-pairs that define one or more p bonds.  For example, a hexagon of carbon atoms with four hydrogen atoms and two oxygen atoms in the 1 and 4 positions, i.e. C6H4O2, can either be the neutral molecule para-benzoquinone or the di-anion of hydroquinone.  The default Lewis structure is the neutral system.  If the di-anion is wanted, then the three aromatic p bonds need to be explicitly defined, thus:
Mozyme setpi charge=-2 
  Di-anion of hydroquinone

  C     0.00000000  0    0.0000000  0    0.0000000  0                      
  C     1.42891759  1    0.0000000  0    0.0000000  0     1     0     0    
  C     1.39123760  1  121.7152363  1    0.0000000  0     2     1     0    
  C     1.42884933  1  121.6862338  1    0.0522686  1     3     2     1    
  C     1.42731168  1  116.6123504  1   -0.0326433  1     4     3     2    
  C     1.39298952  1  121.7002715  1    0.0291866  1     5     4     3    
  O     1.28854675  1  121.6283321  1  179.9905509  1     1     2     3    
  O     1.28863750  1  121.5839611  1  179.9914815  1     4     3     2    
  H     1.07825816  1  117.6731944  1 -179.9642741  1     2     1     3    
  H     1.07822008  1  120.6215632  1 -179.9762574  1     3     2     1    
  H     1.07805743  1  117.7610380  1 -179.9848142  1     5     4     3    
  H     1.07809519  1  120.5409971  1  179.9757231  1     6     5     4   
   
2 3
1 6
4 5

There is no need to supply all the p bonds, only those necessary to resolve any ambiguities.  Other examples of the need for SETPI include:

Distinguishing the anion of p-hydroxy N-methyl pyridine from its quinone type tautomer.
Ensuring that  meso-tetra(para-N-methylpyridinato)-porphyrin has the correct charge.

See also CVB to explicitly make or break bonds, and atom labels to explicitly assign charges.