Supplementary Material for the article (back)
"An investigation into the Application of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme Chymotrypsin "
James J. P. Stewart, J. Mol. Model., (2017)  23: 154. doi:10.1007/s00894-017-3326-8

Step 1 Transition state 1→2  
Step 2 Transition state 2→3  
Step 3 Transition state 1→3  
Step 4 Transition state 4→5  
Step 5 Transition state 5→6  
Step 6 ZIP file (1 Mb)  
Figures 3 to 13 in the paper are snapshots of individual ground state and transition state geometries.  More detailed information can be obtained by clicking on the "Step n" and "Transition state n→m" in the table "Figures". 

A copy of the files used in making the figures can be extracted from the ZIP file.  For instructions on modifying Firefox to run JSmol locally, see:
HTTP://  These files can be used as templates for examining on-site results.



  MOPAC files

 Catalytic cycle only ZIP file 2.0Mb     This ZIP file contains MOPAC data-sets and archive files for various systems described in the article.  If these files are run using MOPAC, they will generate the PDB and HTML files used in constructing the figures.  The commonest use of these files is as the starting-point for other calculations, such as FORCE, IRC, etc.

 Mutations only Zip file 2.6Mb  This ZIP file contains all the mutations used in evaluating changes in hydrogen bond energies and electrostatic interactions.

Compare Transition states 1-2 and 2-3  An example JSmol comparison of transition states 1-2 and 2-3.  The imidazolium ring on His 57 rotates on going from one transition state to the other.  The output file shows that H2O 647 moves significantly as hydrogen bonds make and break, although the heats of formation are only different by 0.35 kcal/mol.