Only one severe error has been found in modeling proteins using PM6-D3H4. In the zinc endoprotease 1C7K, one of the sulfur atoms in a cystine formed from Cys-112 and Cys-99 forms a covalent bond with Nε of Arg-79, as can be seen in the Specific Script detail of the unconstrained PM6-D3H4 structure of 1C7K. Because of this, care should be exercised whenever a cysteine group is near to a nitrogen atom of an arginine. If this occurred, and a sulfur-nitrogen bond formed, the MOZYME procedure would detect an unreasonable Lewis structure and report it.
This error could be corrected by re-parameterizing the two S-N diatomic repulsion terms ALPB and XFAC. If this was done, nothing else in PM6-D3H4 would be affected.