Open cbayly13 opened 5 years ago
Here is an example molecule. DrugBank_2592: c1nc(c2c(n1)n(cn2)[C@H]3C@@HOP(=O)(O)O)O)N
Just to support this, I scanned the "group1" torsiondrive for "O(C)C" and it shows that 1.37 is for esters rather than ethers.
@cbayly13 in a draft refit by Yudong, he's ending up with this as output:
<Bond smirks="[#6X4:1]-[#8X2H0:2]" length="1.430632479559e+00 * angstrom" k="6.441291139148e+02 * angstrom**-2 * mole**-1 * kilocalorie" id="b15" parameterize="k,length"/>
Your estimate of 1.43 looks like it was right on the money.
(This paid no attention to this particular parameter/particular molecule -- it's a refit of all parameters based on the Roche dataset (torsion drives and geometry optimizations). Not our full dataset yet, but a good chunk of it.)
b15 with smarts
[#6X4:1]-[#8X2H0:2]
has an egregiously shortlength="1.370"
; could we please change this to an improvedlength="1.430"
as a starting point?