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. 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Joel Tyndall Gesendet: Dienstag, 15. April 2014 07:03 An: CCP4BB@JISCMAIL.AC.UK 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). 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 Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293
