Dear Henry,
First of all, directly asking for help about eLBOW on the ccp4bb is a little
bit impolite. It is a bit like asking a
Nottingham Forest* fan about how Derby City* played on the weekend. Anyway this
is my suggestion
(as kind of a Leicester City* supporter).
Directly asking any restraint generator to produce good restraints for a
complicated iridium complex is
Unlikely to produce optimal results. The way I would approach your problem is
to:
(a) produce restraints for phenanthroline. This is likely to be PDB component
PHN https://www.rcsb.org/ligand/PHN "1,10-phenanthroline”
There should be no problems in CCP4 Acedrg or eLBOW doing this and
producing planar rings
Of course you could use
Global Phasing Grade2 on the Grade Web Server:
https://grade.globalphasing.org/
(b) produce restraints for a cyclopentadienide anion from the SMILES string
[cH-]1cccc1
(c) work out sensible restraint for the iridium to ligand contact distances by
using CCDC conquest
https://www.ccdc.cam.ac.uk/solutions/software/conquest/
to datamine the CSD (Nottingham School of Pharmacy must have a licence for
this).
I had a quick at this and found for instance CSD entry ODUPUS that looks
relevant
https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ODUPOS
but you should do a search based on the input geometry of your ligand.
(d) manually edit the results of (a) (b) (c) to produce a restraint file for
the complex.
An alternative to (d) is use the restraints (a) and (b) to refine the complex
without explicitly
Restraint the iridium to ligand complex distances. This may well be appropriate
if your diffraction
data goes to high resolution.
Hope this helps,
Oliver
p.s. I you get stuck I would be happy to help contact me off ccp4bb.
* for CCP4bb readers who are not familiar these are 3 English soccer teams
close to Nottingham that
are traditional rivals.
> On 12 Jun 2023, at 10:56, Henry Padley
> <0000a46e12e1d431-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi all,
>
>
> I'm trying to generate a CIF file of an iridium piano stool complex ligand
> (Cp*Ir-Phenanthroline).
>
> Can Phenix eLBOW generate correctly restrained aromatic ring systems which
> stay flat in refinement?
>
> The phenanthroline bonds in the output CIF are listed as "aromatic" in the
> REEL text table but they are not recognised as such in refinement. I've tried
> manually editing the CIF via this text table to produce the alternating
> "double/single bond" structure but it still puckers slightly in refinement.
>
> My eLBOW input is a PDB file of the ligand (I have also tried SDF input). I
> have tried Automatic and eLBOW AM1 QM settings. Might a different Geometry
> optimisation software selectable within eLBOW generate the restrained
> phenanthroline?
>
> Any advice greatly appreciated.
>
>
> Henry Padley, MSci
> School of Pharmacy
> University of Nottingham
>
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