Dear Rafal, Apologies my email client rather scrambled the text from my previous message, so I will send again here
Please find attached (in the previous message!) a restraint CIF file and a corresponding PDB file for your FESAN ligand. Details: Your ligand FESAN is a difficult test case for all restraint generation and refinement programs. It combines two carborane groups with a charged iron atom. Carborane groups have unusual chemistry that does not conform to normal valence models (they have carbon atoms bonded to six other atoms). Combining these groups with an iron atom that is bonded to 12 other atoms makes things even more complicated. Starting from a SMILES string is not wise for such a molecule. Fortunately, such chemistry can be handled by the Grade2 restraint generator, that is supplied with BUSTER: https://gphl.gitlab.io/grade2_docs/ <https://gphl.gitlab.io/grade2_docs/> Starting from the PDB file you supplied I converted to MOL2 format using CSD Mercury. Grade2 can read the MOL2 file and produce restraints (despite RDKit not being able to handle carboranes). All bond restraints are based on Mogul searches of CSD small molecule structures. I manually edited the restraint CIF because there were too many bond angles to be useful. In the carborane cluster, each non-hydrogen atom is bonded to 5 others to form an icosahedral shell, so that the bond length restraints alone are sufficient to fully define the geometry since all angles are implied. Additional bond angle restraints both within the cluster and for the 12-coordinated FE atom are unnecessary and likely to be counter-productive. It appears from CSD entries that FESAN is a cation carrying an overall charge of +1. But I did not correct this. Please note that the atom names are slightly different from your PDB file as the FE atom has an uppercase atom name. Unfortunately, the current CCP4 distribution of Coot 0.8.9.2-pre EL (revision count 7766) cannot cope this molecule as 'Send in the bond angels! Ahem I mean "Regularize Zone (Click two atoms)' produces a lock-up using all the CPU that has to be terminated by a kill. But you should be able to do a manual fit in Coot. BUSTER has no difficulty refining a structure with such restraints, as shown in this test using PDB entry 3I8W with FESAN replacing the CB5 ligand: (Picture attached to previous message) I hope that the restraint dictionary works for you. All the best, Oliver Smart, Andrew Sharff for BUSTER Developers. > On 7 Jun 2022, at 08:35, Rafal Dolot <rdo...@cbmm.lodz.pl> wrote: > > Dear all, > > Thank you very much for all your messages. Unfortunately, I'm still on the > same place, as yesterday... > > First of all, I prepared a pdb/cif file of the ligand based on CCDC entry > 1176355 containing FESAN molecule. Also, I prepared SMILES file based on > SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co > into Fe atom. > > -> When I tried use acedrg with SMILES, I received an error info: > > Input file: FSM.smi > Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif > Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb > workMode : 12 > Can not generate a molecule from the input SMILES string! > Check your SMILES or report the bug > Can not get the element symbols of atoms. Check input file format > Error : The job stops because of errors > > -> When I tried use acedrg with *pdb/*cif files I received no output files: > > Input file: fsm.cif > Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif > Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb > workMode : 11 > Number of atoms in the cif file 0 > > -> When I tried use acedrg with *.mol file I received no output files: > > Input file: fsm.mol > Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif > Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb > workMode : 13 > The system contains atoms of the following elements > C B Fe H > The input ligands/molecules contains metal or other heavier atoms > Acedrg currently deals with ligands/molecules with following elements only > C, N, O, S, P, B, F, Cl, Br, I, H > The job finishes succesfully > > > -> When I tried use prodrg, the program has been crashed: > > The program run with command: cprodrg XYZIN > "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT > "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT > "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT > "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol" > has failed with error message > forrtl: severe (157): Program Exception - access violation > Image PC Routine Line Source > cprodrg.exe 00007FF623CB058F Unknown Unknown Unknown > cprodrg.exe 00007FF623CB05E0 Unknown Unknown Unknown > cprodrg.exe 00007FF623CAFB4F Unknown Unknown Unknown > cprodrg.exe 00007FF623CB008E Unknown Unknown Unknown > cprodrg.exe 00007FF623C5BDA8 Unknown Unknown Unknown > cprodrg.exe 00007FF623C3204E Unknown Unknown Unknown > cprodrg.exe 00007FF623CAA81E Unknown Unknown Unknown > cprodrg.exe 00007FF623CB3144 Unknown Unknown Unknown > KERNEL32.DLL 00007FFEB3447034 Unknown Unknown Unknown > ntdll.dll 00007FFEB4A22651 Unknown Unknown Unknown > *************************************************************************** > > -> I am still waiting for tokens from the prodrg web page ;) To be sure, I > used two emails, but with no response... > > -> Ok, then I back to way I used years ago... JLigand was a good solution, > but... actually it is not working at all. I'm working under Windows 10 / > CCP4i, and I remember, there was the same issue in previous version of CCP4. > > -> Ok, then I back to the oldest solution -> using Sketcher. The program is > reading my PDB/CIF, but gave a warning when preparing a library, and of > course, no output _mon_lib.cif: > > WARNING : monomer:FSM - has a minimal description. > WARNING: there is no metal chirality for:Fe1 > WARNING: coords are not good enough to create Chirality > WARNING : /subroutine CALC_VOBSN/ > > I attached the PDB file containing the ligand of interest. From my knowledge, > it looks correct, but maybe I'm wrong. Have you any idea, where is a problem? > > Best, > > Rafal > > --- > |----------------------------------------------| > |Rafal Dolot, Ph.D. | > | | > |Polish Academy of Sciences | > |Centre of Molecular and Macromolecular Studies| > |Division of Bioorganic Chemistry | > |Macromolecular Crystallography Laboratory | > |Sienkiewicza 112 | > |90-363 Lodz, Poland | > |Phone: +48(42)6803325 | > |Cell: +48 502897781 | > |----------------------------------------------| > > > > W dniu 2022-06-06 14:52, Paul Emsley napisał(a): >> Although it may not be apparent, there has been a lot of work going on >> in Acedrg development regarding Boron. >> One cannot say the same for Coot though and I can reproduce the >> behaviour reported by Rafa Dolot. If/when I can fix it, it will be >> available in 0.9.8.4. >> Paul. >> On 06/06/2022 13:24, Boaz Shaanan wrote: >>> Hi, >>> In case you don't have a cif file for the ligand, I would load the >>> SMILES expression into acedrg (or use any other input option) to >>> create a cif file which you can then read into Coot. >>> Cheers, >>> Boaz >>> On Jun 6, 2022 15:06, Rafal Dolot <rdo...@cbmm.lodz.pl> wrote: >>> Dear CCP4 Users, >>> I am working with data containing a possible complex of protein with >>> FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, >>> this >>> ligand is not available in PDB. The closest molecule is COSAN >>> (cobalt >>> bis(1,2-dicarbollide)), which is labelled as CB5 and is available in >>> two >>> PDB entries. I can load this molecule into Coot, but attempts at >>> ligand >>> search or refinement of the manually matched molecule result in >>> freezing >>> of the Coot window. FESAN is not present in CCDC as a single >>> molecule, >>> but only in some complexes. Could you give me some advice on how to >>> prepare a new ligand like this one, for incorporation into the >>> protein >>> and further refinement? >> ------------------------- >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/<fsm.pdb> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
