[phenixbb] sugar chain cif file
Daniele de Sanctis
de.sanctisd at gmail.com
Tue Jul 8 08:43:23 PDT 2008
Dear all,
I have a trisaccharide in my structure, and I generate the cif file
with elbow (see below). Unfortunately phenix.refine seems not
recognizing the bonds C5-O1 between different units and is not keeping
the chain together. As far as I could understand I should also use the
keyword "apply_cif_link", but I couldn't find which syntax i should
use.
Thanks for the help
Daniele
# electronic Ligand Builder and Optimisation Workbench (eLBOW)
# - a module of PHENIX version 1.3b (Mon Nov 20 17:20:00 2007)
# - file written: Mon Jul 7 18:19:22 2008
#
# Input file: a3.pdb
#
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
AHR AHR 'Unknown ' ligand 15 9 .
#
data_comp_AHR
#
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
AHR 'C5'' C CH3 . 61.3311 15.7148 36.7946
AHR 'C4'' C CR5 . 60.1817 16.4682 36.1126
AHR 'O4'' O O . 60.3257 17.5507 35.0934
AHR 'C3'' C CR5 . 58.6911 16.2438 36.3556
AHR 'O3'' O OC . 58.1296 15.2877 37.2130
AHR 'C2'' C CR5 . 57.9427 17.1885 35.4852
AHR 'O2'' O OC . 56.5500 17.3383 35.4371
AHR 'C1'' C CR5 . 58.9640 18.0045 34.6971
AHR 'O1'' O OH1 . 58.6701 18.9985 33.7515
AHR 'H5'1' H HCH3 . 61.2131 14.6537 36.6320
AHR 'H5'2' H HCH3 . 61.3175 15.9201 37.8548
AHR 'H5'3' H HCH3 . 62.2726 16.0401 36.3773
AHR 'H3'1' H H . 57.7021 15.7812 38.0734
AHR 'H2'1' H H . 56.1521 16.7529 34.6214
AHR 'H1'1' H HOH1 . 59.4063 19.7861 33.8153
#
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
AHR 'C5'' 'C4'' single 1.53429 0.02
AHR 'C4'' 'O4'' aromatic 1.49380 0.02
AHR 'C4'' 'C3'' aromatic 1.52685 0.02
AHR 'O4'' 'C1'' aromatic 1.48900 0.02
AHR 'C3'' 'O3'' double 1.40168 0.02
AHR 'C3'' 'C2'' aromatic 1.48663 0.02
AHR 'C2'' 'O2'' double 1.40154 0.02
AHR 'C2'' 'C1'' aromatic 1.52635 0.02
AHR 'C1'' 'O1'' single 1.40306 0.02
AHR 'H5'1' 'C5'' single 1.08000 0.02
AHR 'H5'2' 'C5'' single 1.08000 0.02
AHR 'H5'3' 'C5'' single 1.08000 0.02
AHR 'H3'1' 'O3'' single 1.08000 0.02
AHR 'H2'1' 'O2'' single 1.08000 0.02
AHR 'H1'1' 'O1'' 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
AHR 'O4'' 'C4'' 'C5'' 125.93952 3.0
AHR 'C3'' 'C4'' 'C5'' 126.05117 3.0
AHR 'H5'1' 'C5'' 'C4'' 109.48717 3.0
AHR 'H5'2' 'C5'' 'C4'' 109.48699 3.0
AHR 'H5'3' 'C5'' 'C4'' 109.47730 3.0
AHR 'C1'' 'O4'' 'C4'' 108.31507 3.0
AHR 'O3'' 'C3'' 'C4'' 126.06060 3.0
AHR 'C2'' 'C3'' 'C4'' 107.75208 3.0
AHR 'C3'' 'C4'' 'O4'' 108.00930 3.0
AHR 'C2'' 'C1'' 'O4'' 108.15545 3.0
AHR 'O1'' 'C1'' 'O4'' 125.92746 3.0
AHR 'H3'1' 'O3'' 'C3'' 109.52327 3.0
AHR 'O2'' 'C2'' 'C3'' 126.02920 3.0
AHR 'C1'' 'C2'' 'C3'' 107.76809 3.0
AHR 'C2'' 'C3'' 'O3'' 126.15656 3.0
AHR 'H2'1' 'O2'' 'C2'' 109.52075 3.0
AHR 'O1'' 'C1'' 'C2'' 125.91301 3.0
AHR 'C1'' 'C2'' 'O2'' 126.15898 3.0
AHR 'H1'1' 'O1'' 'C1'' 109.51700 3.0
AHR 'H5'2' 'C5'' 'H5'1' 109.46605 3.0
AHR 'H5'3' 'C5'' 'H5'1' 109.45474 3.0
AHR 'H5'3' 'C5'' 'H5'2' 109.45508 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
AHR CONST_01 'C2'' 'C1'' 'O4'' 'C4'' 0.00000 0.0 0
AHR CONST_02 'C1'' 'C2'' 'C3'' 'C4'' -0.00000 0.0 0
AHR CONST_03 'C2'' 'C3'' 'C4'' 'O4'' 0.00000 0.0 0
AHR CONST_04 'C3'' 'C2'' 'C1'' 'O4'' -0.00000 0.0 0
AHR CONST_05 'C1'' 'O4'' 'C4'' 'C3'' -0.00000 0.0 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
AHR plan-1 'C4'' 0.020
AHR plan-1 'O4'' 0.020
AHR plan-1 'C1'' 0.020
AHR plan-1 'C2'' 0.020
AHR plan-1 'C3'' 0.020
AHR plan-1 'C5'' 0.050
AHR plan-1 'O1'' 0.050
AHR plan-1 'O2'' 0.050
AHR plan-1 'O3'' 0.050
AHR plan-2 'C4'' 0.100
AHR plan-2 'O4'' 0.100
AHR plan-2 'C5'' 0.100
AHR plan-2 'C3'' 0.100
AHR plan-3 'C3'' 0.100
AHR plan-3 'O3'' 0.100
AHR plan-3 'C4'' 0.100
AHR plan-3 'C2'' 0.100
AHR plan-4 'C2'' 0.100
AHR plan-4 'O2'' 0.100
AHR plan-4 'C3'' 0.100
AHR plan-4 'C1'' 0.100
--
Daniele de Sanctis, PhD
Homo sum humani nil alienum a me puto
______________________________________________________________
phone ++ 351 21 4469 662 fax ++ 351 21 4433 664
e-mail de.sanctisd at gmail.com, sanctis at itqb.unl.pt
Mailing address:
ITQB, Av. República, Apartado 127
2781-901 Oeiras
Portugal
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