Dear list, I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring. As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now? Any help would be very appreciated. Many many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
It is probably an error in the cif file due to the wrong number of hydrogens. If you can define a SMILES string, (c1ccccc1 is benzene, C1CCCCC1 is cyclohexane), you should be able to get the right thing. Aromatic rings should be planar to within 1 degree or so. Visually, they should appear flat. You can generate a proper SMILES string with a java molecular editor. http://www.molinspiration.com/jme/ Claudia Scotti wrote:
Dear list,
I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring.
As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now?
Any help would be very appreciated.
Many many thanks,
Claudia
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
_________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that elbow.builder failed to put in planar restraints at the bottom of the cif file. I had to do this manually, or the ring looked puckered. Fortunately it was fairly easy to do: loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 5BU plan N1 0.020 5BU plan C2 0.020 5BU plan O2 0.020 5BU plan N3 0.020 5BU plan C4 0.020 5BU plan O4 0.020 5BU plan C5 0.020 5BU plan C6 0.020 5BU plan C1* 0.020 5BU plan H3 0.020 5BU plan BR 0.020 5BU plan H6 0.020 This keeps the six membered ring and the exocyclic functional groups (two keto oxygens and one Br atom) constrained to a plane. Claudia Scotti wrote:
Dear list,
I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring.
As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now?
Any help would be very appreciated.
Many many thanks,
Claudia
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
_________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Dear William, Many thanks for your two messages. I checked the cif file, but the loop you refer to seems in place already (see below). Mmhhh... There's something odd, then... Thanks a lot, Claudia --------------- # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Jun 6 22:55:00 2007) # - file written: Thu Aug 2 14:49:23 2007 # # Input file: segid-2.pdb # Residue: PHX # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level PHX PHX 'Unknown ' ligand 22 13 . # data_comp_PHX # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z PHX CAC C CR16 . 13.9538 -10.3993 6.8808 PHX CAB C CR16 . 15.0367 -11.4813 7.0721 PHX CAM C CR16 . 14.9147 -12.5028 8.2295 PHX CAQ C CR16 . 13.7050 -12.4381 9.1959 PHX CAR C CR16 . 12.6223 -11.3562 9.0050 PHX CAN C CR6 . 12.7430 -10.3358 7.8459 PHX CAO C CR5 . 11.6707 -9.2579 7.6598 PHX NAD N N . 10.4286 -9.3881 6.8360 PHX OAS O O . 11.6809 -7.9102 8.2672 PHX CAT C CR5 . 10.4761 -7.2253 7.8562 PHX OAU O OH1 . 10.1162 -5.9143 8.1993 PHX CAE C CR5 . 9.6961 -8.1577 6.9389 PHX CAF C CH3 . 8.3597 -7.8438 6.2545 PHX 1HAC H HCR6 . 14.0395 -9.6867 6.0738 PHX 1HAB H HCR6 . 15.8795 -11.5269 6.3982 PHX 1HAM H HCR6 . 15.6722 -13.2611 8.3626 PHX 1HAQ H HCR6 . 13.6198 -13.1509 10.0028 PHX 1HAR H HCR6 . 11.7797 -11.3111 9.6790 PHX 1HAU H HOH1 . 10.7354 -5.5720 9.0154 PHX 1HAF H HCH3 . 7.6140 -7.6236 7.0041 PHX 2HAF H HCH3 . 8.4797 -6.9898 5.6044 PHX 3HAF H HCH3 . 8.0439 -8.6972 5.6728 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd PHX CAC CAB aromatic 1.54271 0.02 PHX CAC CAN aromatic 1.54966 0.02 PHX CAB CAM aromatic 1.54858 0.02 PHX CAM CAQ aromatic 1.54968 0.02 PHX CAQ CAR aromatic 1.54248 0.02 PHX CAR CAN aromatic 1.54898 0.02 PHX CAN CAO aromatic 1.53182 0.02 PHX CAO NAD aromatic 1.49616 0.02 PHX CAO OAS aromatic 1.47827 0.02 PHX NAD CAE aromatic 1.43567 0.02 PHX OAS CAT aromatic 1.44556 0.02 PHX CAT OAU single 1.40213 0.02 PHX CAT CAE aromatic 1.52286 0.02 PHX CAE CAF single 1.53391 0.02 PHX 1HAC CAC single 1.08000 0.02 PHX 1HAB CAB single 1.08000 0.02 PHX 1HAM CAM single 1.08000 0.02 PHX 1HAQ CAQ single 1.08000 0.02 PHX 1HAR CAR single 1.08000 0.02 PHX 1HAU OAU single 1.08000 0.02 PHX 1HAF CAF single 1.08000 0.02 PHX 2HAF CAF single 1.08000 0.02 PHX 3HAF CAF single 1.08000 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd PHX CAM CAB CAC 120.00226 3.0 PHX 1HAB CAB CAC 119.99926 3.0 PHX CAR CAN CAC 119.99532 3.0 PHX CAO CAN CAC 120.01025 3.0 PHX CAN CAC CAB 119.99792 3.0 PHX 1HAC CAC CAB 119.98327 3.0 PHX CAQ CAM CAB 120.00300 3.0 PHX 1HAM CAM CAB 119.99851 3.0 PHX 1HAB CAB CAM 119.99846 3.0 PHX CAR CAQ CAM 120.00313 3.0 PHX 1HAQ CAQ CAM 119.99800 3.0 PHX 1HAM CAM CAQ 119.99846 3.0 PHX CAN CAR CAQ 119.99812 3.0 PHX 1HAR CAR CAQ 119.98303 3.0 PHX 1HAQ CAQ CAR 119.99886 3.0 PHX CAO CAN CAR 119.99302 3.0 PHX 1HAC CAC CAN 120.01880 3.0 PHX 1HAR CAR CAN 120.01881 3.0 PHX NAD CAO CAN 125.92889 3.0 PHX OAS CAO CAN 125.92913 3.0 PHX CAE NAD CAO 108.02831 3.0 PHX CAT OAS CAO 108.01854 3.0 PHX OAS CAO NAD 108.14161 3.0 PHX CAT CAE NAD 107.85309 3.0 PHX CAF CAE NAD 126.00891 3.0 PHX OAU CAT OAS 125.96613 3.0 PHX CAE CAT OAS 107.94483 3.0 PHX 1HAU OAU CAT 109.51845 3.0 PHX CAF CAE CAT 126.13638 3.0 PHX CAE CAT OAU 126.04431 3.0 PHX 1HAF CAF CAE 109.48685 3.0 PHX 2HAF CAF CAE 109.48663 3.0 PHX 3HAF CAF CAE 109.47785 3.0 PHX 2HAF CAF 1HAF 109.46544 3.0 PHX 3HAF CAF 1HAF 109.45527 3.0 PHX 3HAF CAF 2HAF 109.45527 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period PHX CONST_01 CAQ CAM CAB CAC -0.01362 0.0 0 PHX CONST_02 CAQ CAR CAN CAC -0.18631 0.0 0 PHX CONST_03 CAR CAN CAC CAB 0.17134 0.0 0 PHX CONST_04 CAR CAQ CAM CAB -0.00134 0.0 0 PHX CONST_05 CAN CAC CAB CAM -0.07140 0.0 0 PHX CONST_06 CAN CAR CAQ CAM 0.10130 0.0 0 PHX CONST_07 CAT CAE NAD CAO -0.53152 0.0 0 PHX CONST_08 CAE CAT OAS CAO -1.18961 0.0 0 PHX CONST_09 CAT OAS CAO NAD 0.87457 0.0 0 PHX CONST_10 OAS CAT CAE NAD 1.08244 0.0 0 PHX CONST_11 CAE NAD CAO OAS -0.19123 0.0 0 PHX Var_01 NAD CAO CAN CAC 90.70628 30.0 0 PHX Var_02 OAS CAO CAN CAC -89.54171 30.0 0 PHX Var_03 NAD CAO CAN CAR -89.72740 30.0 0 PHX Var_04 OAS CAO CAN CAR 90.02460 30.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd PHX plan-1 CAC 0.020 PHX plan-1 CAB 0.020 PHX plan-1 CAM 0.020 PHX plan-1 CAQ 0.020 PHX plan-1 CAR 0.020 PHX plan-1 CAN 0.020 PHX plan-1 1HAC 0.050 PHX plan-1 1HAB 0.050 PHX plan-1 1HAM 0.050 PHX plan-1 1HAQ 0.050 PHX plan-1 1HAR 0.050 PHX plan-1 CAO 0.050 PHX plan-2 CAT 0.020 PHX plan-2 CAE 0.020 PHX plan-2 NAD 0.020 PHX plan-2 CAO 0.020 PHX plan-2 OAS 0.020 PHX plan-2 OAU 0.050 PHX plan-2 CAF 0.050 PHX plan-2 CAN 0.050 Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 10 Oct 2007 07:03:34 -0700> From: [email protected]> To: [email protected]> CC: [email protected]> Subject: Re: [phenixbb] "Aromatic" question>> Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that> elbow.builder failed to put in planar restraints at the bottom of the cif> file. I had to do this manually, or the ring looked puckered. Fortunately> it was fairly easy to do:>> loop_> _chem_comp_plane_atom.comp_id> _chem_comp_plane_atom.plane_id> _chem_comp_plane_atom.atom_id> _chem_comp_plane_atom.dist_esd> 5BU plan N1 0.020> 5BU plan C2 0.020> 5BU plan O2 0.020> 5BU plan N3 0.020> 5BU plan C4 0.020> 5BU plan O4 0.020> 5BU plan C5 0.020> 5BU plan C6 0.020> 5BU plan C1* 0.020> 5BU plan H3 0.020> 5BU plan BR 0.020> 5BU plan H6 0.020>> This keeps the six membered ring and the exocyclic functional groups (two> keto oxygens and one Br atom) constrained to a plane.>> Claudia Scotti wrote:>>>> Dear list,>>>> I've refined a protein at 2.0 A resolution with its ligand, a small>> molecule which includes a phenyl group. For this, I used elbow to generate>> the cif file, and in this file the atoms of the phenyl ring are correctly>> defined as "aromatic". However, the pdb output of the refinement shows a>> boat configuration for the 6 carbon atoms ring, with a very nice fit to>> the electron density. This would suggest a flexible cyclohexyl->> substituent instead of the expected, typically planar phenyl ring.>>>> As my chemistry is poor, I'd really need some suggestions on where I'm>> wrong: did I give the wrong cif file or does phenix recognise a better>> fitting in a boat structure, indicating that my ligand phenyl moiety has>> been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the>> phenyl group not so planar as I've supposed it to be until now?>>>> Any help would be very appreciated.>>>> Many many thanks,>>>> Claudia>>>>>>>> Claudia Scotti>> Dipartimento di Medicina Sperimentale>> Sezione di Patologia Generale>> Universita' di Pavia>> Piazza Botta, 10>> 27100 Pavia>> Italia>> Tel. 0039 0382 986335/8/1>> Facs 0039 0382 303673>>>> _________________________________________________________________>> Connect to the next generation of MSN Messenger >> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline>> _______________________________________________>> phenixbb mailing list>> [email protected]>> http://www.phenix-online.org/mailman/listinfo/phenixbb>>> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx
But why should she get nice fit in the electron density? Or is it a negative
density?
Best, Partha
On 10/10/07, Claudia Scotti
Dear William,
Many thanks for your two messages.
I checked the cif file, but the loop you refer to seems in place already (see below).
Mmhhh... There's something odd, then...
Thanks a lot,
Claudia
--------------- # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Jun 6 22:55:00 2007) # - file written: Thu Aug 2 14:49:23 2007 # # Input file: segid-2.pdb # Residue: PHX # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level PHX PHX 'Unknown ' ligand 22 13 . # data_comp_PHX # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z PHX CAC C CR16 . 13.9538 -10.3993 6.8808 PHX CAB C CR16 . 15.0367 -11.4813 7.0721 PHX CAM C CR16 . 14.9147 -12.5028 8.2295 PHX CAQ C CR16 . 13.7050 -12.4381 9.1959 PHX CAR C CR16 . 12.6223 -11.3562 9.0050 PHX CAN C CR6 . 12.7430 -10.3358 7.8459 PHX CAO C CR5 . 11.6707 -9.2579 7.6598 PHX NAD N N . 10.4286 -9.3881 6.8360 PHX OAS O O . 11.6809 -7.9102 8.2672 PHX CAT C CR5 . 10.4761 -7.2253 7.8562 PHX OAU O OH1 . 10.1162 -5.9143 8.1993 PHX CAE C CR5 . 9.6961 -8.1577 6.9389 PHX CAF C CH3 . 8.3597 -7.8438 6.2545 PHX 1HAC H HCR6 . 14.0395 -9.6867 6.0738 PHX 1HAB H HCR6 . 15.8795 -11.5269 6.3982 PHX 1HAM H HCR6 . 15.6722 -13.2611 8.3626 PHX 1HAQ H HCR6 . 13.6198 -13.1509 10.0028 PHX 1HAR H HCR6 . 11.7797 -11.3111 9.6790 PHX 1HAU H HOH1 . 10.7354 -5.5720 9.0154 PHX 1HAF H HCH3 . 7.6140 -7.6236 7.0041 PHX 2HAF H HCH3 . 8.4797 -6.9898 5.6044 PHX 3HAF H HCH3 . 8.0439 -8.6972 5.6728 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd PHX CAC CAB aromatic 1.54271 0.02 PHX CAC CAN aromatic 1.54966 0.02 PHX CAB CAM aromatic 1.54858 0.02 PHX CAM CAQ aromatic 1.54968 0.02 PHX CAQ CAR aromatic 1.54248 0.02 PHX CAR CAN aromatic 1.54898 0.02 PHX CAN CAO aromatic 1.53182 0.02 PHX CAO NAD aromatic 1.49616 0.02 PHX CAO OAS aromatic 1.47827 0.02 PHX NAD CAE aromatic 1.43567 0.02 PHX OAS CAT aromatic 1.44556 0.02 PHX CAT OAU single 1.40213 0.02 PHX CAT CAE aromatic 1.52286 0.02 PHX CAE CAF single 1.53391 0.02 PHX 1HAC CAC single 1.08000 0.02 PHX 1HAB CAB single 1.08000 0.02 PHX 1HAM CAM single 1.08000 0.02 PHX 1HAQ CAQ single 1.08000 0.02 PHX 1HAR CAR single 1.08000 0.02 PHX 1HAU OAU single 1.08000 0.02 PHX 1HAF CAF single 1.08000 0.02 PHX 2HAF CAF single 1.08000 0.02 PHX 3HAF CAF single 1.08000 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd PHX CAM CAB CAC 120.00226 3.0 PHX 1HAB CAB CAC 119.99926 3.0 PHX CAR CAN CAC 119.99532 3.0 PHX CAO CAN CAC 120.01025 3.0 PHX CAN CAC CAB 119.99792 3.0 PHX 1HAC CAC CAB 119.98327 3.0 PHX CAQ CAM CAB 120.00300 3.0 PHX 1HAM CAM CAB 119.99851 3.0 PHX 1HAB CAB CAM 119.99846 3.0 PHX CAR CAQ CAM 120.00313 3.0 PHX 1HAQ CAQ CAM 119.99800 3.0 PHX 1HAM CAM CAQ 119.99846 3.0 PHX CAN CAR CAQ 119.99812 3.0 PHX 1HAR CAR CAQ 119.98303 3.0 PHX 1HAQ CAQ CAR 119.99886 3.0 PHX CAO CAN CAR 119.99302 3.0 PHX 1HAC CAC CAN 120.01880 3.0 PHX 1HAR CAR CAN 120.01881 3.0 PHX NAD CAO CAN 125.92889 3.0 PHX OAS CAO CAN 125.92913 3.0 PHX CAE NAD CAO 108.02831 3.0 PHX CAT OAS CAO 108.01854 3.0 PHX OAS CAO NAD 108.14161 3.0 PHX CAT CAE NAD 107.85309 3.0 PHX CAF CAE NAD 126.00891 3.0 PHX OAU CAT OAS 125.96613 3.0 PHX CAE CAT OAS 107.94483 3.0 PHX 1HAU OAU CAT 109.51845 3.0 PHX CAF CAE CAT 126.13638 3.0 PHX CAE CAT OAU 126.04431 3.0 PHX 1HAF CAF CAE 109.48685 3.0 PHX 2HAF CAF CAE 109.48663 3.0 PHX 3HAF CAF CAE 109.47785 3.0 PHX 2HAF CAF 1HAF 109.46544 3.0 PHX 3HAF CAF 1HAF 109.45527 3.0 PHX 3HAF CAF 2HAF 109.45527 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period PHX CONST_01 CAQ CAM CAB CAC -0.01362 0.0 0 PHX CONST_02 CAQ CAR CAN CAC -0.18631 0.0 0 PHX CONST_03 CAR CAN CAC CAB 0.17134 0.0 0 PHX CONST_04 CAR CAQ CAM CAB -0.00134 0.0 0 PHX CONST_05 CAN CAC CAB CAM -0.07140 0.0 0 PHX CONST_06 CAN CAR CAQ CAM 0.10130 0.0 0 PHX CONST_07 CAT CAE NAD CAO -0.53152 0.0 0 PHX CONST_08 CAE CAT OAS CAO -1.18961 0.0 0 PHX CONST_09 CAT OAS CAO NAD 0.87457 0.0 0 PHX CONST_10 OAS CAT CAE NAD 1.08244 0.0 0 PHX CONST_11 CAE NAD CAO OAS -0.19123 0.0 0 PHX Var_01 NAD CAO CAN CAC 90.70628 30.0 0 PHX Var_02 OAS CAO CAN CAC -89.54171 30.0 0 PHX Var_03 NAD CAO CAN CAR -89.72740 30.0 0 PHX Var_04 OAS CAO CAN CAR 90.02460 30.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd PHX plan-1 CAC 0.020 PHX plan-1 CAB 0.020 PHX plan-1 CAM 0.020 PHX plan-1 CAQ 0.020 PHX plan-1 CAR 0.020 PHX plan-1 CAN 0.020 PHX plan-1 1HAC 0.050 PHX plan-1 1HAB 0.050 PHX plan-1 1HAM 0.050 PHX plan-1 1HAQ 0.050 PHX plan-1 1HAR 0.050 PHX plan-1 CAO 0.050 PHX plan-2 CAT 0.020 PHX plan-2 CAE 0.020 PHX plan-2 NAD 0.020 PHX plan-2 CAO 0.020 PHX plan-2 OAS 0.020 PHX plan-2 OAU 0.050 PHX plan-2 CAF 0.050 PHX plan-2 CAN 0.050
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 10 Oct 2007 07:03:34 -0700> From: [email protected]> To: [email protected]> CC: [email protected]> Subject: Re: [phenixbb] "Aromatic" question>> Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that> elbow.builder failed to put in planar restraints at the bottom of the cif> file. I had to do this manually, or the ring looked puckered. Fortunately> it was fairly easy to do:>> loop_> _chem_comp_plane_atom.comp_id> _chem_comp_plane_atom.plane_id> _chem_comp_plane_atom.atom_id> _chem_comp_plane_atom.dist_esd> 5BU plan N1 0.020> 5BU plan C2 0.020> 5BU plan O2 0.020> 5BU plan N3 0.020> 5BU plan C4 0.020> 5BU plan O4 0.020> 5BU plan C5 0.020> 5BU plan C6 0.020> 5BU plan C1* 0.020> 5BU plan H3 0.020> 5BU plan BR 0.020> 5BU plan H6 0.020>> This keeps the six membered ring and the exocyclic functional groups (two> keto oxygens and one Br atom) constrained to a plane.>> Claudia Scotti wrote:>>>> Dear list,>>>> I've refined a protein at 2.0 A resolution with its ligand, a small>> molecule which includes a phenyl group. For this, I used elbow to generate>> the cif file, and in this file the atoms of the phenyl ring are correctly>> defined as "aromatic". However, the pdb output of the refinement shows a>> boat configuration for the 6 carbon atoms ring, with a very nice fit to>> the electron density. This would suggest a flexible cyclohexyl->> substituent instead of the expected, typically planar phenyl ring.>>>> As my chemistry is poor, I'd really need some suggestions on where I'm>> wrong: did I give the wrong cif file or does phenix recognise a better>> fitting in a boat structure, indicating that my ligand phenyl moiety has>> been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the>> phenyl group not so planar as I've supposed it to be until now?>>>> Any help would be very appreciated.>>>> Many many thanks,>>>> Claudia>>>>>>>> Claudia Scotti>> Dipartimento di Medicina Sperimental! e>> Sezi one di Patologia Generale>> Universita' di Pavia>> Piazza Botta, 10>> 27100 Pavia>> Italia>> Tel. 0039 0382 986335/8/1>> Facs 0039 0382 303673>>>> _________________________________________________________________>> Connect to the next generation of MSN Messenger >> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline>> _______________________________________________>> phenixbb mailing list>> [email protected]>> http://www.phenix-online.org/mailman/listinfo/phenixbb>>> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb
_________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [email protected] Phone: + 44 208 816 2515
check the geo file generated by phenix.refine to find all geometry
restraints used. You can check there if the planarity restraints have
been used or not.
HTH
Peter
2007/10/10, Claudia Scotti
Dear William,
Many thanks for your two messages.
I checked the cif file, but the loop you refer to seems in place already (see below).
Mmhhh... There's something odd, then...
Thanks a lot,
Claudia
--------------- # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Jun 6 22:55:00 2007) # - file written: Thu Aug 2 14:49:23 2007 # # Input file: segid-2.pdb # Residue: PHX # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level PHX PHX 'Unknown ' ligand 22 13 . # data_comp_PHX # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z PHX CAC C CR16 . 13.9538 -10.3993 6.8808 PHX CAB C CR16 . 15.0367 -11.4813 7.0721 PHX CAM C CR16 . 14.9147 -12.5028 8.2295 PHX CAQ C CR16 . 13.7050 -12.4381 9.1959 PHX CAR C CR16 . 12.6223 -11.3562 9.0050 PHX CAN C CR6 . 12.7430 -10.3358 7.8459 PHX CAO C CR5 . 11.6707 -9.2579 7.6598 PHX NAD N N . 10.4286 -9.3881 6.8360 PHX OAS O O . 11.6809 -7.9102 8.2672 PHX CAT C CR5 . 10.4761 -7.2253 7.8562 PHX OAU O OH1 . 10.1162 -5.9143 8.1993 PHX CAE C CR5 . 9.6961 -8.1577 6.9389 PHX CAF C CH3 . 8.3597 -7.8438 6.2545 PHX 1HAC H HCR6 . 14.0395 -9.6867 6.0738 PHX 1HAB H HCR6 . 15.8795 -11.5269 6.3982 PHX 1HAM H HCR6 . 15.6722 -13.2611 8.3626 PHX 1HAQ H HCR6 . 13.6198 -13.1509 10.0028 PHX 1HAR H HCR6 . 11.7797 -11.3111 9.6790 PHX 1HAU H HOH1 . 10.7354 -5.5720 9.0154 PHX 1HAF H HCH3 . 7.6140 -7.6236 7.0041 PHX 2HAF H HCH3 . 8.4797 -6.9898 5.6044 PHX 3HAF H HCH3 . 8.0439 -8.6972 5.6728 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd PHX CAC CAB aromatic 1.54271 0.02 PHX CAC CAN aromatic 1.54966 0.02 PHX CAB CAM aromatic 1.54858 0.02 PHX CAM CAQ aromatic 1.54968 0.02 PHX CAQ CAR aromatic 1.54248 0.02 PHX CAR CAN aromatic 1.54898 0.02 PHX CAN CAO aromatic 1.53182 0.02 PHX CAO NAD aromatic 1.49616 0.02 PHX CAO OAS aromatic 1.47827 0.02 PHX NAD CAE aromatic 1.43567 0.02 PHX OAS CAT aromatic 1.44556 0.02 PHX CAT OAU single 1.40213 0.02 PHX CAT CAE aromatic 1.52286 0.02 PHX CAE CAF single 1.53391 0.02 PHX 1HAC CAC single 1.08000 0.02 PHX 1HAB CAB single 1.08000 0.02 PHX 1HAM CAM single 1.08000 0.02 PHX 1HAQ CAQ single 1.08000 0.02 PHX 1HAR CAR single 1.08000 0.02 PHX 1HAU OAU single 1.08000 0.02 PHX 1HAF CAF single 1.08000 0.02 PHX 2HAF CAF single 1.08000 0.02 PHX 3HAF CAF single 1.08000 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd PHX CAM CAB CAC 120.00226 3.0 PHX 1HAB CAB CAC 119.99926 3.0 PHX CAR CAN CAC 119.99532 3.0 PHX CAO CAN CAC 120.01025 3.0 PHX CAN CAC CAB 119.99792 3.0 PHX 1HAC CAC CAB 119.98327 3.0 PHX CAQ CAM CAB 120.00300 3.0 PHX 1HAM CAM CAB 119.99851 3.0 PHX 1HAB CAB CAM 119.99846 3.0 PHX CAR CAQ CAM 120.00313 3.0 PHX 1HAQ CAQ CAM 119.99800 3.0 PHX 1HAM CAM CAQ 119.99846 3.0 PHX CAN CAR CAQ 119.99812 3.0 PHX 1HAR CAR CAQ 119.98303 3.0 PHX 1HAQ CAQ CAR 119.99886 3.0 PHX CAO CAN CAR 119.99302 3.0 PHX 1HAC CAC CAN 120.01880 3.0 PHX 1HAR CAR CAN 120.01881 3.0 PHX NAD CAO CAN 125.92889 3.0 PHX OAS CAO CAN 125.92913 3.0 PHX CAE NAD CAO 108.02831 3.0 PHX CAT OAS CAO 108.01854 3.0 PHX OAS CAO NAD 108.14161 3.0 PHX CAT CAE NAD 107.85309 3.0 PHX CAF CAE NAD 126.00891 3.0 PHX OAU CAT OAS 125.96613 3.0 PHX CAE CAT OAS 107.94483 3.0 PHX 1HAU OAU CAT 109.51845 3.0 PHX CAF CAE CAT 126.13638 3.0 PHX CAE CAT OAU 126.04431 3.0 PHX 1HAF CAF CAE 109.48685 3.0 PHX 2HAF CAF CAE 109.48663 3.0 PHX 3HAF CAF CAE 109.47785 3.0 PHX 2HAF CAF 1HAF 109.46544 3.0 PHX 3HAF CAF 1HAF 109.45527 3.0 PHX 3HAF CAF 2HAF 109.45527 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period PHX CONST_01 CAQ CAM CAB CAC -0.01362 0.0 0 PHX CONST_02 CAQ CAR CAN CAC -0.18631 0.0 0 PHX CONST_03 CAR CAN CAC CAB 0.17134 0.0 0 PHX CONST_04 CAR CAQ CAM CAB -0.00134 0.0 0 PHX CONST_05 CAN CAC CAB CAM -0.07140 0.0 0 PHX CONST_06 CAN CAR CAQ CAM 0.10130 0.0 0 PHX CONST_07 CAT CAE NAD CAO -0.53152 0.0 0 PHX CONST_08 CAE CAT OAS CAO -1.18961 0.0 0 PHX CONST_09 CAT OAS CAO NAD 0.87457 0.0 0 PHX CONST_10 OAS CAT CAE NAD 1.08244 0.0 0 PHX CONST_11 CAE NAD CAO OAS -0.19123 0.0 0 PHX Var_01 NAD CAO CAN CAC 90.70628 30.0 0 PHX Var_02 OAS CAO CAN CAC -89.54171 30.0 0 PHX Var_03 NAD CAO CAN CAR -89.72740 30.0 0 PHX Var_04 OAS CAO CAN CAR 90.02460 30.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd PHX plan-1 CAC 0.020 PHX plan-1 CAB 0.020 PHX plan-1 CAM 0.020 PHX plan-1 CAQ 0.020 PHX plan-1 CAR 0.020 PHX plan-1 CAN 0.020 PHX plan-1 1HAC 0.050 PHX plan-1 1HAB 0.050 PHX plan-1 1HAM 0.050 PHX plan-1 1HAQ 0.050 PHX plan-1 1HAR 0.050 PHX plan-1 CAO 0.050 PHX plan-2 CAT 0.020 PHX plan-2 CAE 0.020 PHX plan-2 NAD 0.020 PHX plan-2 CAO 0.020 PHX plan-2 OAS 0.020 PHX plan-2 OAU 0.050 PHX plan-2 CAF 0.050 PHX plan-2 CAN 0.050
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 10 Oct 2007 07:03:34 -0700> From: [email protected]> To: [email protected]> CC: [email protected]> Subject: Re: [phenixbb] "Aromatic" question>> Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that> elbow.builder failed to put in planar restraints at the bottom of the cif> file. I had to do this manually, or the ring looked puckered. Fortunately> it was fairly easy to do:>> loop_> _chem_comp_plane_atom.comp_id> _chem_comp_plane_atom.plane_id> _chem_comp_plane_atom.atom_id> _chem_comp_plane_atom.dist_esd> 5BU plan N1 0.020> 5BU plan C2 0.020> 5BU plan O2 0.020> 5BU plan N3 0.020> 5BU plan C4 0.020> 5BU plan O4 0.020> 5BU plan C5 0.020> 5BU plan C6 0.020> 5BU plan C1* 0.020> 5BU plan H3 0.020> 5BU plan BR 0.020> 5BU plan H6 0.020>> This keeps the six membered ring and the exocyclic functional groups (two> keto oxygens and one Br atom) constrained to a pl!
an!
e.>> Claudia Scotti wrote:>>>> Dear list,>>>> I've refined a protein at 2.0 A resolution with its ligand, a small>> molecule which includes a phenyl group. For this, I used elbow to generate>> the cif file, and in this file the atoms of the phenyl ring are correctly>> defined as "aromatic". However, the pdb output of the refinement shows a>> boat configuration for the 6 carbon atoms ring, with a very nice fit to>> the electron density. This would suggest a flexible cyclohexyl->> substituent instead of the expected, typically planar phenyl ring.>>>> As my chemistry is poor, I'd really need some suggestions on where I'm>> wrong: did I give the wrong cif file or does phenix recognise a better>> fitting in a boat structure, indicating that my ligand phenyl moiety has>> been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the>> phenyl group not so planar as I've supposed it to be until now?>>>> Any help would be very appreciated.>>>> Many many thanks,>>>> Claud! ia!
>>> Claudia Scotti>> Dipartimento di Medicina Sperimental! e>> Sezi one di Patologia Generale>> Universita' di Pavia>> Piazza Botta, 10>> 27100 Pavia>> Italia>> Tel. 0039 0382 986335/8/1>> Facs 0039 0382 303673>>>> _________________________________________________________________>> Connect to the next generation of MSN Messenger >> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline>> _______________________________________________>> phenixbb mailing list>> [email protected]>> http://www.phenix-online.org/mailman/listinfo/phenixbb>>> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb
_________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Claudia As you noticed, if eLBOW gives a ring aromatic bonds it also puts it into a planar group. We would all like to know what was the cause of the ring not being planar in the refinement. Could we have access to the data? If so email me directly. Nigel On 10/10/2007 7:21 AM, Claudia Scotti wrote:
Dear William,
Many thanks for your two messages.
I checked the cif file, but the loop you refer to seems in place already (see below).
Mmhhh... There's something odd, then...
Thanks a lot,
Claudia
--------------- # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Jun 6 22:55:00 2007) # - file written: Thu Aug 2 14:49:23 2007 # # Input file: segid-2.pdb # Residue: PHX # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level PHX PHX 'Unknown ' ligand 22 13 . # data_comp_PHX # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z PHX CAC C CR16 . 13.9538 -10.3993 6.8808 PHX CAB C CR16 . 15.0367 -11.4813 7.0721 PHX CAM C CR16 . 14.9147 -12.5028 8.2295 PHX CAQ C CR16 . 13.7050 -12.4381 9.1959 PHX CAR C CR16 . 12.6223 -11.3562 9.0050 PHX CAN C CR6 . 12.7430 -10.3358 7.8459 PHX CAO C CR5 . 11.6707 -9.2579 7.6598 PHX NAD N N . 10.4286 -9.3881 6.8360 PHX OAS O O . 11.6809 -7.9102 8.2672 PHX CAT C CR5 . 10.4761 -7.2253 7.8562 PHX OAU O OH1 . 10.1162 -5.9143 8.1993 PHX CAE C CR5 . 9.6961 -8.1577 6.9389 PHX CAF C CH3 . 8.3597 -7.8438 6.2545 PHX 1HAC H HCR6 . 14.0395 -9.6867 6.0738 PHX 1HAB H HCR6 . 15.8795 -11.5269 6.3982 PHX 1HAM H HCR6 . 15.6722 -13.2611 8.3626 PHX 1HAQ H HCR6 . 13.6198 -13.1509 10.0028 PHX 1HAR H HCR6 . 11.7797 -11.3111 9.6790 PHX 1HAU H HOH1 . 10.7354 -5.5720 9.0154 PHX 1HAF H HCH3 . 7.6140 -7.6236 7.0041 PHX 2HAF H HCH3 . 8.4797 -6.9898 5.6044 PHX 3HAF H HCH3 . 8.0439 -8.6972 5.6728 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd PHX CAC CAB aromatic 1.54271 0.02 PHX CAC CAN aromatic 1.54966 0.02 PHX CAB CAM aromatic 1.54858 0.02 PHX CAM CAQ aromatic 1.54968 0.02 PHX CAQ CAR aromatic 1.54248 0.02 PHX CAR CAN aromatic 1.54898 0.02 PHX CAN CAO aromatic 1.53182 0.02 PHX CAO NAD aromatic 1.49616 0.02 PHX CAO OAS aromatic 1.47827 0.02 PHX NAD CAE aromatic 1.43567 0.02 PHX OAS CAT aromatic 1.44556 0.02 PHX CAT OAU single 1.40213 0.02 PHX CAT CAE aromatic 1.52286 0.02 PHX CAE CAF single 1.53391 0.02 PHX 1HAC CAC single 1.08000 0.02 PHX 1HAB CAB single 1.08000 0.02 PHX 1HAM CAM single 1.08000 0.02 PHX 1HAQ CAQ single 1.08000 0.02 PHX 1HAR CAR single 1.08000 0.02 PHX 1HAU OAU single 1.08000 0.02 PHX 1HAF CAF single 1.08000 0.02 PHX 2HAF CAF single 1.08000 0.02 PHX 3HAF CAF single 1.08000 0.02 #
loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd PHX CAM CAB CAC 120.00226 3.0 PHX 1HAB CAB CAC 119.99926 3.0 PHX CAR CAN CAC 119.99532 3.0 PHX CAO CAN CAC 120.01025 3.0 PHX CAN CAC CAB 119.99792 3.0 PHX 1HAC CAC CAB 119.98327 3.0 PHX CAQ CAM CAB 120.00300 3.0 PHX 1HAM CAM CAB 119.99851 3.0 PHX 1HAB CAB CAM 119.99846 3.0 PHX CAR CAQ CAM 120.00313 3.0 PHX 1HAQ CAQ CAM 119.99800 3.0 PHX 1HAM CAM CAQ 119.99846 3.0 PHX CAN CAR CAQ 119.99812 3.0 PHX 1HAR CAR CAQ 119.98303 3.0 PHX 1HAQ CAQ CAR 119.99886 3.0 PHX CAO CAN CAR 119.99302 3.0 PHX 1HAC CAC CAN 120.01880 3.0 PHX 1HAR CAR CAN 120.01881 3.0 PHX NAD CAO CAN 125.92889 3.0 PHX OAS CAO CAN 125.92913 3.0 PHX CAE NAD CAO 108.02831 3.0 PHX CAT OAS CAO 108.01854 3.0 PHX OAS CAO NAD 108.14161 3.0 PHX CAT CAE NAD 107.85309 3.0 PHX CAF CAE NAD 126.00891 3.0 PHX OAU CAT OAS 125.96613 3.0 PHX CAE CAT OAS 107.94483 3.0 PHX 1HAU OAU CAT 109.51845 3.0 PHX CAF CAE CAT 126.13638 3.0 PHX CAE CAT OAU 126.04431 3.0 PHX 1HAF CAF CAE 109.48685 3.0 PHX 2HAF CAF CAE 109.48663 3.0 PHX 3HAF CAF CAE 109.47785 3.0 PHX 2HAF CAF 1HAF 109.46544 3.0 PHX 3HAF CAF 1HAF 109.45527 3.0 PHX 3HAF CAF 2HAF 109.45527 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period PHX CONST_01 CAQ CAM CAB CAC -0.01362 0.0 0 PHX CONST_02 CAQ CAR CAN CAC -0.18631 0.0 0 PHX CONST_03 CAR CAN CAC CAB 0.17134 0.0 0 PHX CONST_04 CAR CAQ CAM CAB -0.00134 0.0 0 PHX CONST_05 CAN CAC CAB CAM -0.07140 0.0 0 PHX CONST_06 CAN CAR CAQ CAM 0.10130 0.0 0 PHX CONST_07 CAT CAE NAD CAO -0.53152 0.0 0 PHX CONST_08 CAE CAT OAS CAO -1.18961 0.0 0 PHX CONST_09 CAT OAS CAO NAD 0.87457 0.0 0 PHX CONST_10 OAS CAT CAE NAD 1.08244 0.0 0 PHX CONST_11 CAE NAD CAO OAS -0.19123 0.0 0 PHX Var_01 NAD CAO CAN CAC 90.70628 30.0 0 PHX Var_02 OAS CAO CAN CAC -89.54171 30.0 0 PHX Var_03 NAD CAO CAN CAR -89.72740 30.0 0 PHX Var_04 OAS CAO CAN CAR 90.02460 30.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd PHX plan-1 CAC 0.020 PHX plan-1 CAB 0.020 PHX plan-1 CAM 0.020 PHX plan-1 CAQ 0.020 PHX plan-1 CAR 0.020 PHX plan-1 CAN 0.020 PHX plan-1 1HAC 0.050 PHX plan-1 1HAB 0.050 PHX plan-1 1HAM 0.050 PHX plan-1 1HAQ 0.050 PHX plan-1 1HAR 0.050 PHX plan-1 CAO 0.050 PHX plan-2 CAT 0.020 PHX plan-2 CAE 0.020 PHX plan-2 NAD 0.020 PHX plan-2 CAO 0.020 PHX plan-2 OAS 0.020 PHX plan-2 OAU 0.050 PHX plan-2 CAF 0.050 PHX plan-2 CAN 0.050
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 10 Oct 2007 07:03:34 -0700> From: [email protected]> To: [email protected]> CC: [email protected]> Subject: Re: [phenixbb] "Aromatic" question>> Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that> elbow.builder failed to put in planar restraints at the bottom of the cif> file. I had to do this manually, or the ring looked puckered. Fortunately> it was fairly easy to do:>> loop_> _chem_comp_plane_atom.comp_id> _chem_comp_plane_atom.plane_id> _chem_comp_plane_atom.atom_id> _chem_comp_plane_atom.dist_esd> 5BU plan N1 0.020> 5BU plan C2 0.020> 5BU plan O2 0.020> 5BU plan N3 0.020> 5BU plan C4 0.020> 5BU plan O4 0.020> 5BU plan C5 0.020> 5BU plan C6 0.020> 5BU plan C1* 0.020> 5BU plan H3 0.020> 5BU plan BR 0.020> 5BU plan H6 0.020>> This keeps the six membered ring and the exocyclic functional groups (two> keto oxygens and one Br atom) constrained to a plan! e.>> Claudia Scotti wrote:>>>> Dear list,>>>> I've refined a protein at 2.0 A resolution with its ligand, a small>> molecule which includes a phenyl group. For this, I used elbow to generate>> the cif file, and in this file the atoms of the phenyl ring are correctly>> defined as "aromatic". However, the pdb output of the refinement shows a>> boat configuration for the 6 carbon atoms ring, with a very nice fit to>> the electron density. This would suggest a flexible cyclohexyl->> substituent instead of the expected, typically planar phenyl ring.>>>> As my chemistry is poor, I'd really need some suggestions on where I'm>> wrong: did I give the wrong cif file or does phenix recognise a better>> fitting in a boat structure, indicating that my ligand phenyl moiety has>> been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the>> phenyl group not so planar as I've supposed it to be until now?>>>> Any help would be very appreciated.>>>> Many many thanks,>>>> Claudia!
>>> Claudia Scotti>> Dipartimento di Medicina Sperimental! e>> Sezi one di Patologia Generale>> Universita' di Pavia>> Piazza Botta, 10>> 27100 Pavia>> Italia>> Tel. 0039 0382 986335/8/1>> Facs 0039 0382 303673>>>> _________________________________________________________________>> Connect to the next generation of MSN Messenger >> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline>> _______________________________________________>> phenixbb mailing list>> [email protected]>> http://www.phenix-online.org/mailman/listinfo/phenixbb>>> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb
_________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
participants (5)
-
Claudia Scotti -
Nigel W. Moriarty -
Partha Chakrabarti -
Peter Zwart -
William Scott