[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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