[phenixbb] "Aromatic" question

Partha Chakrabarti ppchak at gmail.com
Wed Oct 10 07:58:09 PDT 2007


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 <claudiascotti at hotmail.com> 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: wgscott at chemistry.ucsc.edu> To:
> phenixbb at phenix-online.org> CC: phenixbb at phenix-online.org> 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>>>>
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-- 
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pchakra at nimr.mrc.ac.uk
Phone: + 44 208 816 2515
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