[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:
> 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.
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