russell-taylor
commented
1 year ago If we mark negative ions as acceptors, this should make it possible for hydrogen bonds to form with them.
@todo: This might also help with https://github.com/ReliaSolve/cctbx_project/issues/256 except that the Fe ion in that case should be positive.
In an email on 7/1/2023, Jane writes: As part of studying Hydrogenate's apparently incorrect placement of movable hydrogens on the ligands to ions, I found examples of a few more ion types to test how universal this problem is. I suggest testing Hydrogenate on 1mey Zn 88 and 7bmt Na 215. However, Dave and I learned something else really interesting from 7bmt, which is a 1.47Å HEW lysozyme crystallized with a lot of NaCl. In the NGL graphics at the PDB, Cl atoms are shown in closeups with either just one interaction to, say, a Zn, or no interactions at all. The Cl would not be there if there were really no interactions, but we got no help from either Google search or Wikipedia articles. However, the multi-kin of 7bmt with its many Cl ions shows that they make 2 to 4 excellent H-bonds at good distances (~2.4Å to fixed H like bb NH or Asn NH2, and ~3Å to waters). I've attached an image and also a kin file, so you can explore. Another win for actually looking at things, and for using our own tools ! So Cl-, and probably other negative ions, definitely do not behave as mirrored opposites to positive ions. Hopefully Michael knew this all along and can maybe even explain to us why it is so.