[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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