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
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://OpenMOPAC.net/Manual/README_for_JSmol.html.
These files can be used as templates for examining on-site results.
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.