Visualizing a lot of FMO PIEDA numbers. Part II

In the last post on the subject of FMO PIEDA numbers, there were some issues with the fragmentation that did not match between two different snapshots in the same reaction trajectory.

I fixed that fragmentation problem, ran the numbers again and it looks like some neat stuff can be extracted.

Remember that the structures are generated using PM6 with MOZYME enabled and that energy-refinement of the barrier is done at the FMO2/6-31G(d)/PCM level of theory. The CON structures have some part of the structure constrained (far away from the active site) and the UCO structures are allowed to fully relax. The problem still looks like this

To tease you with some data, here is a table from a short write-up I did. Column two and three represents the difference in energy (by the method in the first column) between the TS and the reactant. The last column is the energy difference between column two and three. The first row is thus the difference in sum of one-body energies, second row is difference in the sum of fragment interaction energies (FIEs) and the last row is the difference in total FMO2 energy.

	dE(1,5)_con	dE(1,5)_uco	ddE(uco-con)
FMO1-MP2/6-31G(d)/PCM	25.4	29.4	4.0
$\sum_{IJ} \Delta E^{MP2}_{IJ}$	-3.7	18.6	22.4
FMO2-MP2/6-31G(d)/PCM	25.9	55.0	29.1

The one-body case is a solved case because inspection reveals that the internal energies of the substrate contributes +3.5 kcal/mol, ASP119 contributes +5.3 kcal/mol and ASN35 contributes -4.3 kcal/mol which when summed up is roughly the 4 kcal/mol we need. The rest is just internal re-arrangement that eventually cancels out.

The problem with the barrier height, however, is that at the two-body level (second row), the CON structures provide almost 4 kcal/mol worth of stabilization whereas the UCO structures are destabilized by 18.6 kcal/mol. It would be natural to investigate what happens if we look at the FIEs between the substrate and the entire enzyme. This looks like the following

what is curious is that we see distinct peaks - the largest (positive) peak can be attributed to an interaction with ARG112, but if we sum all IEFs up they amount to +0.5 kcal/mol which is very far from the +18.6 we are trying to account for. The conclusion is (currently) that because the protein is allowed to fully relax, many small contributions amount to the 18.6.

credits to this sites table-generator because I lost all my HTML skills whilst fighting FORTRAN

DALTON mol File Input Generator for Open Babel

Because of my new engagement with DALTON, I felt there was a serious lack of availability in the open source tool chain that I am used to: There is no input file generator in Open Babel for DALTON, until now.

Through a series of commits in my own fork of the official Open Babel repository, I've added a basic mol file input generator (and reader too!). The commits have been marked with a pull request to be merged into the official repository, but it looks like it is only updated every now and then. If you want to get all crazy right away, clone my repository and get cracking.

Experienced users with DALTON knows that there are two input files. the molecule file and the DALTON input file (dal file). The mol file contains the coordinates of the atoms, their charge and the basis set for the computation. The dal file tells DALTON what to actually do with the content of the mol file. Thus, the dal file is about the quantum chemistry which is traditionally left out in Open Babel and I've only focused on getting the mol-file ready - most users of DALTON use a single dal file anyways and use different mol files. I guess my own scripts to make easy conversions to and from DALTON are now void (at least partially).

Hooray for Open Source!

Addendum: I should mention that coordinates can also be extracted from DALTON log files. As I myself do not (usually) have a need beyond coordinate extractions I will leave it as is for now.