[phenixbb] "Aromatic" question

Claudia Scotti claudiascotti at hotmail.com
Wed Oct 10 07:21:37 PDT 2007


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 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>> 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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