In Puzzle 2330, the starting ligand has a COO group containing a double-bonded O and a single-bonded O.
Does it matter which of these two O's hydrogen-bonds to the serine 226 sidechain?
If you rotated the COO group so the other O hydrogen-bonded to the serine 226 instead, should you get the same results?
Are the two O's on the COO group chemically equivalent?
If the two O's are really different, which one should hydrogen-bond to serine 226,
and which one should hydrogen-bond to arginine 193?
Thanks!
The oxygens in a charged (deprotonated) COO group (which should be what Foldit uses) are identical. There should be no difference in properties between the two, and it shouldn't matter which one is bonded to which atoms.
The fact that Foldit represents one with a double bond and one with a single bond is mainly due to the difficulty of working with "1.5" bonds in the underlying code.
When I play with the torsions I have a feeling that having the single bond O- forming hbond with serine making it easier to fix the torsional issue for the nearest rotatable bond.
Not sure if its ture that the double bond position of COO- would affect the torsion calculation, or is it by chance?
Even though they're chemically equivalent I am not sure if the bond order info would trigger some rules of torsional filter.
