But why should she get nice fit in the electron density? Or is it a negative density?<br>Best, Partha<br><br><div><span class="gmail_quote">On 10/10/07, <b class="gmail_sendername">Claudia Scotti</b> <<a href="mailto:claudiascotti@hotmail.com">
claudiascotti@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Dear William,<br><br>Many thanks for your two messages.
<br><br>I checked the cif file, but the loop you refer to seems in place already (see below).<br><br>Mmhhh... There's something odd, then...<br><br>Thanks a lot,<br><br>Claudia<br><br><br><br>---------------<br># electronic Ligand Builder and Optimisation Workbench (eLBOW)
<br># - a module of PHENIX version 1.3b (Mon Jun 6 22:55:00 2007)<br># - file written: Thu Aug 2 14:49:23 2007<br>#<br># Input file: segid-2.pdb<br># Residue: PHX<br>#<br>data_comp_list<br>loop_<br> _chem_comp.id
<br> _chem_comp.three_letter_code<br> _chem_comp.name<br> _chem_comp.group<br> _chem_comp.number_atoms_all<br> _chem_comp.number_atoms_nh<br> _chem_comp.desc_level<br>PHX PHX 'Unknown ' ligand 22 13 .
<br>#<br>data_comp_PHX<br>#<br>loop_<br> _chem_comp_atom.comp_id<br> _chem_comp_atom.atom_id<br> _chem_comp_atom.type_symbol<br> _chem_comp_atom.type_energy<br> _chem_comp_atom.partial_charge<br> _chem_comp_atom.x
<br> _chem_comp_atom.y<br> _chem_comp_atom.z<br>PHX CAC C CR16 . 13.9538 -10.3993 6.8808<br>PHX CAB C CR16 . 15.0367 -11.4813 7.0721<br>PHX CAM C CR16 . 14.9147
-12.5028 8.2295<br>PHX CAQ C CR16 . 13.7050 -12.4381 9.1959<br>PHX CAR C CR16 . 12.6223 -11.3562 9.0050<br>PHX CAN C CR6 . 12.7430 -10.3358 7.8459<br>PHX CAO C CR5 .
11.6707 -9.2579 7.6598<br>PHX NAD N N . 10.4286 -9.3881 6.8360<br>PHX OAS O O . 11.6809 -7.9102 8.2672<br>PHX CAT C CR5 . 10.4761 -7.2253 7.8562
<br>PHX OAU O OH1 . 10.1162 -5.9143 8.1993<br>PHX CAE C CR5 . 9.6961 -8.1577 6.9389<br>PHX CAF C CH3 . 8.3597 -7.8438 6.2545<br>PHX 1HAC H HCR6 .
14.0395 -9.6867 6.0738<br>PHX 1HAB H HCR6 . 15.8795 -11.5269 6.3982<br>PHX 1HAM H HCR6 . 15.6722 -13.2611 8.3626<br>PHX 1HAQ H HCR6 . 13.6198 -13.1509 10.0028
<br>PHX 1HAR H HCR6 . 11.7797 -11.3111 9.6790<br>PHX 1HAU H HOH1 . 10.7354 -5.5720 9.0154<br>PHX 1HAF H HCH3 . 7.6140 -7.6236 7.0041<br>PHX 2HAF H HCH3 .
8.4797 -6.9898 5.6044<br>PHX 3HAF H HCH3 . 8.0439 -8.6972 5.6728<br>#<br>loop_<br> _chem_comp_bond.comp_id<br> _chem_comp_bond.atom_id_1<br> _chem_comp_bond.atom_id_2<br> _chem_comp_bond.type
<br> _chem_comp_bond.value_dist<br> _chem_comp_bond.value_dist_esd<br>PHX CAC CAB aromatic 1.54271 0.02<br>PHX CAC CAN aromatic 1.54966 0.02<br>PHX CAB CAM aromatic 1.54858 0.02<br>PHX CAM CAQ aromatic
1.54968 0.02<br>PHX CAQ CAR aromatic 1.54248 0.02<br>PHX CAR CAN aromatic 1.54898 0.02<br>PHX CAN CAO aromatic 1.53182 0.02<br>PHX CAO NAD aromatic 1.49616 0.02<br>PHX CAO OAS aromatic
1.47827 0.02<br>PHX NAD CAE aromatic 1.43567 0.02<br>PHX OAS CAT aromatic 1.44556 0.02<br>PHX CAT OAU single 1.40213 0.02<br>PHX CAT CAE aromatic 1.52286 0.02<br>PHX CAE CAF single
1.53391 0.02<br>PHX 1HAC CAC single 1.08000 0.02<br>PHX 1HAB CAB single 1.08000 0.02<br>PHX 1HAM CAM single 1.08000 0.02<br>PHX 1HAQ CAQ single 1.08000 0.02<br>PHX 1HAR CAR single
1.08000 0.02<br>PHX 1HAU OAU single 1.08000 0.02<br>PHX 1HAF CAF single 1.08000 0.02<br>PHX 2HAF CAF single 1.08000 0.02<br>PHX 3HAF CAF single 1.08000 0.02<br>#<br>loop_<br> _chem_comp_angle.comp_id
<br> _chem_comp_angle.atom_id_1<br> _chem_comp_angle.atom_id_2<br> _chem_comp_angle.atom_id_3<br> _chem_comp_angle.value_angle<br> _chem_comp_angle.value_angle_esd<br>PHX CAM CAB CAC 120.00226 3.0
<br>PHX 1HAB CAB CAC 119.99926 3.0<br>PHX CAR CAN CAC 119.99532 3.0<br>PHX CAO CAN CAC 120.01025 3.0<br>PHX CAN CAC CAB 119.99792 3.0<br>PHX 1HAC CAC CAB 119.98327
3.0<br>PHX CAQ CAM CAB 120.00300 3.0<br>PHX 1HAM CAM CAB 119.99851 3.0<br>PHX 1HAB CAB CAM 119.99846 3.0<br>PHX CAR CAQ CAM 120.00313 3.0<br>PHX 1HAQ CAQ CAM 119.99800
3.0<br>PHX 1HAM CAM CAQ 119.99846 3.0<br>PHX CAN CAR CAQ 119.99812 3.0<br>PHX 1HAR CAR CAQ 119.98303 3.0<br>PHX 1HAQ CAQ CAR 119.99886 3.0<br>PHX CAO CAN CAR 119.99302
3.0<br>PHX 1HAC CAC CAN 120.01880 3.0<br>PHX 1HAR CAR CAN 120.01881 3.0<br>PHX NAD CAO CAN 125.92889 3.0<br>PHX OAS CAO CAN 125.92913 3.0<br>PHX CAE NAD CAO 108.02831
3.0<br>PHX CAT OAS CAO 108.01854 3.0<br>PHX OAS CAO NAD 108.14161 3.0<br>PHX CAT CAE NAD 107.85309 3.0<br>PHX CAF CAE NAD 126.00891 3.0<br>PHX OAU CAT OAS 125.96613
3.0<br>PHX CAE CAT OAS 107.94483 3.0<br>PHX 1HAU OAU CAT 109.51845 3.0<br>PHX CAF CAE CAT 126.13638 3.0<br>PHX CAE CAT OAU 126.04431 3.0<br>PHX 1HAF CAF CAE 109.48685
3.0<br>PHX 2HAF CAF CAE 109.48663 3.0<br>PHX 3HAF CAF CAE 109.47785 3.0<br>PHX 2HAF CAF 1HAF 109.46544 3.0<br>PHX 3HAF CAF 1HAF 109.45527 3.0<br>PHX 3HAF CAF 2HAF 109.45527
3.0<br>#<br>loop_<br> _chem_comp_tor.comp_id<br> _chem_comp_tor.id<br> _chem_comp_tor.atom_id_1<br> _chem_comp_tor.atom_id_2<br> _chem_comp_tor.atom_id_3<br> _chem_comp_tor.atom_id_4<br> _chem_comp_tor.value_angle
<br> _chem_comp_tor.value_angle_esd<br> _chem_comp_tor.period<br>PHX CONST_01 CAQ CAM CAB CAC -0.01362 0.0 0<br>PHX CONST_02 CAQ CAR CAN CAC -0.18631 0.0 0<br>PHX CONST_03 CAR CAN CAC CAB
0.17134 0.0 0<br>PHX CONST_04 CAR CAQ CAM CAB -0.00134 0.0 0<br>PHX CONST_05 CAN CAC CAB CAM -0.07140 0.0 0<br>PHX CONST_06 CAN CAR CAQ CAM 0.10130 0.0 0<br>PHX CONST_07 CAT CAE NAD CAO -
0.53152 0.0 0<br>PHX CONST_08 CAE CAT OAS CAO -1.18961 0.0 0<br>PHX CONST_09 CAT OAS CAO NAD 0.87457 0.0 0<br>PHX CONST_10 OAS CAT CAE NAD 1.08244 0.0 0<br>PHX CONST_11 CAE NAD CAO OAS -
0.19123 0.0 0<br>PHX Var_01 NAD CAO CAN CAC 90.70628 30.0 0<br>PHX Var_02 OAS CAO CAN CAC -89.54171 30.0 0<br>PHX Var_03 NAD CAO CAN CAR -89.72740 30.0 0<br>PHX Var_04 OAS CAO CAN CAR
90.02460 30.0 0<br>#<br>loop_<br>_chem_comp_plane_atom.comp_id<br>_chem_comp_plane_atom.plane_id<br>_chem_comp_plane_atom.atom_id<br>_chem_comp_plane_atom.dist_esd<br>PHX plan-1 CAC 0.020<br>PHX plan-1 CAB 0.020<br>PHX plan-1 CAM
0.020<br>PHX plan-1 CAQ 0.020<br>PHX plan-1 CAR 0.020<br>PHX plan-1 CAN 0.020<br>PHX plan-1 1HAC 0.050<br>PHX plan-1 1HAB 0.050<br>PHX plan-1 1HAM 0.050<br>PHX plan-1 1HAQ 0.050<br>PHX plan-1 1HAR 0.050<br>PHX plan-1 CAO
0.050<br>PHX plan-2 CAT 0.020<br>PHX plan-2 CAE 0.020<br>PHX plan-2 NAD 0.020<br>PHX plan-2 CAO 0.020<br>PHX plan-2 OAS 0.020<br>PHX plan-2 OAU 0.050<br>PHX plan-2 CAF 0.050<br>PHX plan-2 CAN 0.050<br><br><br><br>
<br>Claudia Scotti<br>Dipartimento di Medicina Sperimentale<br>Sezione di Patologia Generale<br>Universita' di Pavia<br>Piazza Botta, 10<br>27100 Pavia<br>Italia<br>Tel. 0039 0382 986335/8/1<br>Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 10 Oct 2007 07:03:34 -0700> From:
<a href="mailto:wgscott@chemistry.ucsc.edu">wgscott@chemistry.ucsc.edu</a>> To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>> CC: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org
</a>> 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!
<br> e>> Sezi<br>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 >>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>MRC National Institute for Medical Research<br>Division of Molecular Structure<br>The Ridgeway, NW7 1AA, UK<br>Email: <a href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk
</a><br>Phone: + 44 208 816 2515