Re: [ccp4bb]: CO2-conformation

[Phoebe Rice <price@midway.uchicago.edu>]

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Is this a bug in the library or trouble specifying CO2 vs HCO2- (formate, 
which is what is in 1mkm)?
         Phoebe

At 04:21 PM 10/22/2002 +0200, jjm wrote:
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>
>Dear all,
>refining a high resolution structure with refmac5 we found a CO2 molecule.
>Refmac5 dictionary knows CO2 but the molecule has an dihedral angle of 109 
>degr. and C-O distances of 1.41 A. The HIC-Up server comes up with a linear
>molecule and C-O distances of 1.18A. Textbooks contain only a linear 
>CO2-molecule.
>PDB-entries contain CO2 in both conformations (1kek,1e5h - 
>linear);1mkm,1krb with 109 degr.)).
>Is there really a kinked CO2 or is it a bug in the library
>$CCP4/lib/data/monomers/mon_lib_met.cif?
>Greetings,
>Juergen
>
>data_comp_CO2
>#
>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
>CO2      O1   O    O         0.000
>CO2      C    C    C         0.000
>CO2      O2   O    O         0.000
>loop_
>_chem_comp_tree.comp_id
>_chem_comp_tree.atom_id
>_chem_comp_tree.atom_back
>_chem_comp_tree.back_type
>_chem_comp_tree.atom_forward
>_chem_comp_tree.connect_type
>CO2      O1   .    .        C    START
>CO2      C    O1   .        .    END
>CO2      O2   C    .        .    .
>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
>CO2        C    O1      coval       1.410    0.020
>CO2        O2   C       coval       1.410    0.020
>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
>CO2        O1   C    O2    109.470    3.000
>#
>

Phoebe A. Rice
Asst. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://molbiol.bsd.uchicago.edu/faculty/pRice/index.html
http://bmb.bsd.uchicago.edu/