[phenixbb] "Aromatic" question

Nigel W. Moriarty nwmoriarty at lbl.gov
Wed Oct 10 09:16:41 PDT 2007


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: 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 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>> phenixbb at phenix-online.org>> http://www.phenix-online.org/mailman/listinfo/phenixbb>>> _______________________________________________> phenixbb mailing list> phenixbb at phenix-online.org> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
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-- 
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 : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov





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