search

openforcefield / smirnoff99Frosst

A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format
Creative Commons Attribution 4.0 International
28 stars 9 forks source link

Confusing angle in nitro like group #36

Closed bannanc closed 7 years ago

bannanc commented 7 years ago

There is only one angle still being assigned the generic in the filtered drugbank set, it looks like a nitro group, but the nitrogen is bound to three oxygens the third is divalent. Like the molecule below:

ec2a3c43-54ce-4ec7-80fa-93535eb19f91

I've been trying to think through what is "right" for this angle. We draw nitro groups with a neutral and negative oxygen, but really I would think of the #8X1 oxygens as being equivalent, which means the angle to the "other oxygen" should more closely resemble the C-N-O angle in "normal" nitro groups.

I'm going to see how those numbers compare in gaff right now...

bannanc commented 7 years ago

The molecules with these groups didn't make it to our gaff2 mol2 files for some reason.

I suggest we update the nitro angle from:

[#6:1]-[#7X3:2](~[#8X1])~[#8X1:3]  70.000  117.700  Frosst CA-N2-O2 from fit to rhf/6-31G* from T.Halgren 1/26/99

to

[#6,#7,#8:1]-[#7X3:2](~[#8X1])~[#8X1:3]  70.000  117.700  Frosst CA-N2-O2 from fit to rhf/6-31G* from T.Halgren 1/26/99

This is a very specific angle and from what I can tell it doesn't change any of the other nitrogen centered angles.

davidlmobley commented 7 years ago

@bannanc - this seems reasonable to me, though with a prioritization for QM follow-up (e.g. the summer student should pull some molecules and look at whether this angle should be treated separately for [#6], [#7], and [#8], probably.

bannanc commented 7 years ago

Added in pull request #43