# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:06:06 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,6-anhydro-3-deoxy-L-xylo-hexonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[C@@H](C[C@@H]1O)C(O)=O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 GCT  GCT  '2,6-anhydro-3-deoxy-L-xylo-hexonic acid'  D-saccharide  21  11  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GCT
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 GCT  C1    C  CH2   0  -0.224   1.5694  -0.3324   0.9127
 GCT  C2    C  CH1   0   0.003   0.4958   0.2341   1.8404
 GCT  O2    O  OH1   0  -0.672   0.6765  -0.2260   3.1602
 GCT  C3    C  CH1   0   0.043  -0.8729  -0.2280   1.3649
 GCT  O3    O  OH1   0  -0.669  -1.9225   0.3604   2.0930
 GCT  C4    C  CH2   0  -0.502  -1.0512   0.1354  -0.1019
 GCT  C5    C  CH1   0  -0.050   0.1266  -0.4083  -0.9146
 GCT  C6    C  C     0   0.512   0.0365   0.0123  -2.3655
 GCT  O6A   O  O     0  -0.425   0.8239   0.7303  -2.9209
 GCT  O6B   O  OH1   0  -0.593  -1.0325  -0.5133  -2.9465
 GCT  O5    O  O2    0  -0.481   1.3524   0.0581  -0.4246
 GCT  HC11  H  HCH2  0   0.249   2.5549   0.0408   1.1964
 GCT  HC12  H  HCH2  0   0.211   1.5879  -1.4285   1.0044
 GCT  HC2   H  HCH1  0   0.217   0.5277   1.3321   1.7932
 GCT  HO2   H  HOH1  0   0.459   1.4029   0.2599   3.5623
 GCT  HC3   H  HCH1  0   0.204  -0.9036  -1.3271   1.4546
 GCT  HO3   H  HOH1  0   0.450  -1.8001   0.1422   3.0229
 GCT  HC41  H  HCH2  0   0.251  -1.1049   1.2233  -0.2099
 GCT  HC42  H  HCH2  0   0.269  -1.9871  -0.2831  -0.4750
 GCT  HC5   H  HCH1  0   0.259   0.0921  -1.5096  -0.8807
 GCT  HO6   H  HOH1  0   0.488  -1.0904  -0.2223  -3.8692

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
_chem_comp_bond.value_dist_neutron
 GCT  C1   C2    single  1.528  0.020  1.528
 GCT  C1   O5    single  1.410  0.020  1.410
 GCT  C1   HC11  single  0.970  0.020  1.090
 GCT  C1   HC12  single  0.970  0.020  1.090
 GCT  C2   O2    single  1.409  0.020  1.409
 GCT  C2   C3    single  1.521  0.020  1.521
 GCT  C2   HC2   single  0.970  0.020  1.090
 GCT  O2   HO2   single  0.850  0.020  0.980
 GCT  C3   O3    single  1.406  0.020  1.406
 GCT  C3   C4    single  1.522  0.020  1.522
 GCT  C3   HC3   single  0.970  0.020  1.090
 GCT  O3   HO3   single  0.850  0.020  0.980
 GCT  C4   C5    single  1.531  0.020  1.531
 GCT  C4   HC41  single  0.970  0.020  1.090
 GCT  C4   HC42  single  0.970  0.020  1.090
 GCT  C5   C6    single  1.513  0.020  1.513
 GCT  C5   O5    single  1.400  0.020  1.400
 GCT  C5   HC5   single  0.970  0.020  1.090
 GCT  C6   O6A   double  1.202  0.020  1.202
 GCT  C6   O6B   single  1.325  0.020  1.325
 GCT  O6B  HO6   single  0.850  0.020  0.980

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
 GCT  HC12  C1   HC11  107.69  3.000
 GCT  HC12  C1   O5    110.95  3.000
 GCT  HC11  C1   O5    106.91  3.000
 GCT  HC12  C1   C2    109.31  3.000
 GCT  HC11  C1   C2    110.48  3.000
 GCT  O5    C1   C2    111.41  3.000
 GCT  HC2   C2   C3    108.43  3.000
 GCT  HC2   C2   O2    111.25  3.000
 GCT  C3    C2   O2    108.00  3.000
 GCT  HC2   C2   C1    108.89  3.000
 GCT  C3    C2   C1    109.26  3.000
 GCT  O2    C2   C1    110.95  3.000
 GCT  HO2   O2   C2    108.86  3.000
 GCT  HC3   C3   C4    108.24  3.000
 GCT  HC3   C3   O3    110.73  3.000
 GCT  C4    C3   O3    108.16  3.000
 GCT  HC3   C3   C2    107.60  3.000
 GCT  C4    C3   C2    109.53  3.000
 GCT  O3    C3   C2    112.50  3.000
 GCT  HO3   O3   C3    108.08  3.000
 GCT  HC42  C4   HC41  107.79  3.000
 GCT  HC42  C4   C5    110.01  3.000
 GCT  HC41  C4   C5    109.78  3.000
 GCT  HC42  C4   C3    109.79  3.000
 GCT  HC41  C4   C3    109.77  3.000
 GCT  C5    C4   C3    109.68  3.000
 GCT  HC5   C5   O5    110.45  3.000
 GCT  HC5   C5   C6    107.78  3.000
 GCT  O5    C5   C6    107.16  3.000
 GCT  HC5   C5   C4    108.33  3.000
 GCT  O5    C5   C4    111.68  3.000
 GCT  C6    C5   C4    111.37  3.000
 GCT  O6B   C6   O6A   124.25  3.000
 GCT  O6B   C6   C5    110.98  3.000
 GCT  O6A   C6   C5    124.76  3.000
 GCT  HO6   O6B  C6    110.27  3.000
 GCT  C5    O5   C1    111.99  3.000

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
 GCT  CONST_01  HO6   O6B  C6  C5  180.00   0.0  0
 GCT  Var_01    HC11  C1   O5  C5  178.00  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GCT  chir_01  C2  C1  O2  C3  positiv
 GCT  chir_02  C3  O3  C2  C4  positiv
 GCT  chir_03  C5  O5  C4  C6  negativ

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
 GCT  plan-1  C5   0.020
 GCT  plan-1  C6   0.020
 GCT  plan-1  O6A  0.020
 GCT  plan-1  O6B  0.020
 GCT  plan-1  HO6  0.020

