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
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 $CCP4/lib/data/monomers/h/HEM.cif: HEM CBC CAC double 1.329 0.020 HEM CBB CAB double 1.330 0.020 $CCP4/lib/data/monomers/h/HEC.cif 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. eab 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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Yea,
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
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 $CCP4/lib/data/monomers/h/HEM.cif: HEM CBC CAC double 1.329 0.020 HEM CBB CAB double 1.330 0.020 $CCP4/lib/data/monomers/h/HEC.cif 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. eab
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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Dear Yarrow, 1.337 refers to a double bond. If you are sure your heme has a single bond here, you may need to manually edit this cif-file to adjust it to your ligand. Best, Tim On 06/19/2014 09:11 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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-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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Yarrow Madrona