[phenixbb] More problems with HEM.cif?
amadrona at uci.edu
Thu Jun 19 17:02:28 PDT 2014
That was dumb. Sorry. Vinyl is a double bond. Sleepy time for me.
On Thu, Jun 19, 2014 at 1:32 PM, Edward A. Berry <BerryE at upstate.edu> wrote:
> 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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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