[phenixbb] More problems with HEM.cif?

Edward A. Berry BerryE at upstate.edu
Thu Jun 19 13:32:38 PDT 2014

No, those are actually double bonds (hence the name "vinyl"),
unless it it is a c-type heme, in which case you should be using HEC.cif
  HEM      CBC    CAC       double      1.329    0.020
  HEM      CBB    CAB       double      1.330    0.020
  HEC      CBC    CAC       single      1.510    0.020
  HEC      CBB    CAB       single      1.510    0.020  

This is because cysteine Sg's covalently link the vinyl groups,
adding across the double bond as it were.
Unless you have trypanosome or Euglena cytochrome,
in which case one vinyl is native and the other
is substituted by cysteine.

On 06/19/2014 03:11 PM, Yarrow Madrona wrote:
> Hello,
> The HEM.cif in  $Phenix/chem_data/mon_lib
> has ideal angles of 1.337 for single bonds on the vinyl groups.
> HEM   CAC     CBC   coval         1.337 0.02
> HEM   CAB     CBB   coval         1.337 0.02
> As far as I know these are single bonds and the ideal bond angles should be around 1.5.
> -Yarrow
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