Dear Joel, I suspect that you will have a mixture of different puckers. Relaxing the restraints would not be the way to go, since it might lead to a distorted average structure. If your cif file is correct (tetrahedral nitrogens), it should not impose a specific pucker. However, you will have to construct manually the approximate pucker and then real-space refine it, since the energy barrier is such that the molecule will not flip on its own from one pucker to the other. To check your restraints, you could first regularize to be sure that the results are not influenced by the electron density map.
If your ring always flips back to the original pucker, you should check the cif file to see that the nitrogens are truly sp3, e.g. no planarity restraints are imposed and that the torsion restraints have a periodicity of 3 etc. By specifying for chirality "both", if the fit is approximately correct, the structure will refine to the nearest chiral value and you won't have to worry about it. Good luck! Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Joel Tyndall Gesendet: Dienstag, 15. April 2014 11:45 An: [email protected] Betreff: Re: [ccp4bb] AW: appropriate torsion angles Dear Herman and Paul, Thanks for your input. I have already looked at the CSD and it conclusively tells me that both nitrogens are tetrahedral and both have a phenyl ring. I have added appropriate chiral restraints for the nitrogens. That part I am comfortable with. What I am looking to do is make the two (four) carbon atoms flexible enough (not adopt chair or boat alone) such that they could be a twisted boat conformation or the like. I need to adopt the opposite chirality at one of the nitrogens, probably the other, ensure that both adjacent phenyl rings remain relative stable (positionally) and optimise a H-bond to a water molecule Herman, the molecule in question are known drug (itraconazole & posaconazole) so we don't have the option to not use it. It is hard to know what conformation (mess) is correct but I believe I had enough evidence to put my argument forward the way I believe it should go, I just need the parameters. Regularizing in Coot doesn't help Thanks both. Joel ________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of [email protected]<mailto:[email protected]> [[email protected]] Sent: Tuesday, April 15, 2014 8:52 PM To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] AW: [ccp4bb] AW: appropriate torsion angles Dear Paul, I find it difficult to predict when a pipirazine nitrogen will be sp2 and when sp3, so I usually search the csd with the exact substituent at hand and supposed that Joel will have done the same. In general, I find that auto generate programs are overly optimistic how far delocalization of binding electrons will extend, and also about the effect of steric hindrance by other substituents at staggered positions. So in general, compounds tend to be in reality less flat than cif generating programs think. It is also important to carefully look at the electron density maps and the fit of the compound. With large substituents like phenyl groups, choosing the wrong conformation should produce significant distortions. Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Paul Emsley Gesendet: Dienstag, 15. April 2014 10:28 An: [email protected]<mailto:[email protected]> Betreff: Re: [ccp4bb] AW: appropriate torsion angles Dear Joel and Herman, On 15/04/14 04:39, [email protected]<mailto:[email protected]> wrote: Dear Joel, I always tell our chemists not to include piperazine rings etc. in their compounds because of this conformational mess, but somehow they do not seem to listen. ;-) Unfortunately, do did not tell us how and with software you auto generated your cif file, so I can only give some general remarks: I would try grade from global phasing to generate your cif file. Grade uses Mogul, which consults the CSD to find the appropriate conformational parameters. Is you nitrogen flat, or has it the wrong chirality? If the chirality is wrong, you should change all _chem_comp_chir.volume_sign's from positive/negative to both. However, real-space refinement will usually not get through the energy barrier to change the chirality, so you will have to move the atoms manually. In the "Rotate Translate Zone" mode, you can move individual atoms by pressing <cntrl> and picking the atom with the left mouse button. FWIW, for this sort of thing I usually fix atoms before refinement and ctrl-move fixed atoms during refinement. If one of the R groups is merely a hydrogen, coot's refinement pathology detection should jump the hydrogen to the other side of incorrect chiral centres. You may need to try this in "regularization mode" sometimes. In my experience, without a formal charge prodrg likes to make piperazine nitrogens sp2 if connected to at least one aromatic carbon (as in Joel's case - at least in my reading). This may well be The Right Thing to do, so the whole boat/chair thing is a bit moot. If the nitrogen is flat and you auto generate from a pdb file, you should make sure the nitrogen on the input file has a tetrahedral conformation. You may force the program to make a tetrahedral nitrogen by adding a proton (and positive charge) or remove the phenyl and copy the nitrogen parameters generated to the cif file for the complete molecule, but better would be to use grade. Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Joel Tyndall Gesendet: Dienstag, 15. April 2014 07:03 An: [email protected]<mailto:[email protected]> Betreff: [ccp4bb] appropriate torsion angles Hi folks, We are trying to model multiple instances of a small molecule that contains a piperazine ring. I am looking for the appropriate torsion angles that are needed for a cif file in order for the piperazine ring to be able to adopt either a chair or a boat or any combination between the two (i.e. relaxed torsion restraints but remaining tetrahedral). Have you ever seen convincing density for a boat piperazine in PDB data? (given sp3 hybrization, of course) Any help would be much appreciated before I launch into writing a new cif file from scratch. As a little background, the piperazine contains a phenyl substituent on the nitrogen which is tetrahedral according to the CSD for small molecules. This has meant that the auto generated cif files gave the wrong geometry for the nitrogen in the first place. Many thanks
