# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:04:50 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 3-O-alpha-D-xylopyranosyl-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1O
#
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
 GCX  GCX  3-O-alpha-D-xylopyranosyl-beta-D-glucopyranose  D-saccharide  41  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GCX
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
 GCX  O21  O  OH1   0  -0.657  -0.6537   2.6804   0.4069
 GCX  C21  C  CH1   0  -0.008  -1.4866   1.5832   0.6641
 GCX  C11  C  CH1   0   0.260  -2.8765   1.7877   0.0603
 GCX  O51  O  O2    0  -0.496  -3.6694   0.6481   0.2775
 GCX  C51  C  CH1   0  -0.020  -3.1795  -0.4976  -0.3858
 GCX  C6   C  CH2   0  -0.159  -4.1724  -1.6198  -0.1778
 GCX  O6   O  OH1   0  -0.670  -5.3845  -1.2799  -0.8070
 GCX  C31  C  CH1   0   0.002  -0.8576   0.3450   0.0454
 GCX  C41  C  CH1   0   0.023  -1.7924  -0.8561   0.1634
 GCX  O41  O  OH1   0  -0.665  -1.2250  -1.9267  -0.5538
 GCX  O1   O  O2    0  -0.518   0.3586   0.0580   0.7044
 GCX  C1   C  CH1   0   0.294   1.4558  -0.2132  -0.0908
 GCX  C2   C  CH1   0  -0.016   2.4326  -1.0578   0.7285
 GCX  O2   O  OH1   0  -0.666   2.7341  -0.4658   1.9642
 GCX  C3   C  CH1   0  -0.014   3.7364  -1.2476  -0.0507
 GCX  O3   O  OH1   0  -0.672   3.4332  -2.1497  -1.0924
 GCX  O5   O  O2    0  -0.483   2.0294   1.0101  -0.4710
 GCX  C5   C  CH2   0  -0.224   3.1368   0.8226  -1.3235
 GCX  C4   C  CH1   0  -0.005   4.2644   0.0709  -0.6299
 GCX  O4   O  OH1   0  -0.664   4.8432   0.8061   0.4194
 GCX  O7   O  OH1   0  -0.661  -3.4690   2.8615   0.6932
 GCX  H1   H  HOH1  0   0.451  -1.0189   3.4448   0.8642
 GCX  H2   H  HCH1  0   0.219  -1.6116   1.4134   1.7457
 GCX  H3   H  HCH1  0   0.191  -2.7751   1.9636  -1.0252
 GCX  H4   H  HCH1  0   0.221  -3.0863  -0.3006  -1.4672
 GCX  H5   H  HCH2  0   0.205  -3.7469  -2.5394  -0.5949
 GCX  H6   H  HCH2  0   0.199  -4.3033  -1.7837   0.9009
 GCX  H7   H  HOH1  0   0.457  -6.0019  -2.0047  -0.6748
 GCX  H8   H  HCH1  0   0.236  -0.6794   0.5437  -1.0214
 GCX  H9   H  HCH1  0   0.229  -1.8980  -1.1054   1.2282
 GCX  H10  H  HOH1  0   0.462  -1.3183  -2.7333  -0.0412
 GCX  H11  H  HCH1  0   0.194   1.1665  -0.7782  -0.9909
 GCX  H12  H  HCH1  0   0.223   1.9760  -2.0501   0.8645
 GCX  H13  H  HOH1  0   0.449   1.9083  -0.3445   2.4438
 GCX  H14  H  HCH1  0   0.235   4.4935  -1.6663   0.6272
 GCX  H15  H  HOH1  0   0.456   4.2294  -2.2938  -1.6137
 GCX  H16  H  HCH2  0   0.209   2.8455   0.2753  -2.2305
 GCX  H17  H  HCH2  0   0.249   3.4738   1.8123  -1.6400
 GCX  H18  H  HCH1  0   0.219   5.0180  -0.1704  -1.3964
 GCX  H19  H  HOH1  0   0.451   5.2447   1.5968   0.0459
 GCX  H20  H  HOH1  0   0.468  -4.1604   3.2274   0.1316

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
 GCX  O4   C4   single  1.406  0.020  1.406
 GCX  C4   C5   single  1.522  0.020  1.522
 GCX  C4   C3   single  1.534  0.020  1.534
 GCX  O3   C3   single  1.411  0.020  1.411
 GCX  C5   O5   single  1.410  0.020  1.410
 GCX  C3   C2   single  1.531  0.020  1.531
 GCX  O21  C21  single  1.401  0.020  1.401
 GCX  O5   C1   single  1.404  0.020  1.404
 GCX  C21  C11  single  1.529  0.020  1.529
 GCX  C21  C31  single  1.520  0.020  1.520
 GCX  C2   C1   single  1.529  0.020  1.529
 GCX  C2   O2   single  1.403  0.020  1.403
 GCX  O1   C1   single  1.382  0.020  1.382
 GCX  O1   C31  single  1.413  0.020  1.413
 GCX  C11  O51  single  1.405  0.020  1.405
 GCX  C31  C41  single  1.527  0.020  1.527
 GCX  O51  C51  single  1.412  0.020  1.412
 GCX  C41  C51  single  1.534  0.020  1.534
 GCX  C41  O41  single  1.408  0.020  1.408
 GCX  C51  C6   single  1.513  0.020  1.513
 GCX  O6   C6   single  1.407  0.020  1.407
 GCX  C11  O7   single  1.380  0.020  1.380
 GCX  O21  H1   single  0.850  0.020  0.980
 GCX  C21  H2   single  0.970  0.020  1.090
 GCX  C11  H3   single  0.970  0.020  1.090
 GCX  C51  H4   single  0.970  0.020  1.090
 GCX  C6   H5   single  0.970  0.020  1.090
 GCX  C6   H6   single  0.970  0.020  1.090
 GCX  O6   H7   single  0.850  0.020  0.980
 GCX  C31  H8   single  0.970  0.020  1.090
 GCX  C41  H9   single  0.970  0.020  1.090
 GCX  O41  H10  single  0.850  0.020  0.980
 GCX  C1   H11  single  0.970  0.020  1.090
 GCX  C2   H12  single  0.970  0.020  1.090
 GCX  O2   H13  single  0.850  0.020  0.980
 GCX  C3   H14  single  0.970  0.020  1.090
 GCX  O3   H15  single  0.850  0.020  0.980
 GCX  C5   H16  single  0.970  0.020  1.090
 GCX  C5   H17  single  0.970  0.020  1.090
 GCX  C4   H18  single  0.970  0.020  1.090
 GCX  O4   H19  single  0.850  0.020  0.980
 GCX  O7   H20  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
 GCX  H1   O21  C21  108.01  3.000
 GCX  H2   C21  C31  108.71  3.000
 GCX  H2   C21  C11  107.76  3.000
 GCX  C31  C21  C11  108.92  3.000
 GCX  H2   C21  O21  111.61  3.000
 GCX  C31  C21  O21  108.49  3.000
 GCX  C11  C21  O21  111.29  3.000
 GCX  H3   C11  O7   111.49  3.000
 GCX  H3   C11  O51  109.45  3.000
 GCX  O7   C11  O51  108.53  3.000
 GCX  H3   C11  C21  109.02  3.000
 GCX  O7   C11  C21  108.25  3.000
 GCX  O51  C11  C21  110.08  3.000
 GCX  C51  O51  C11  112.94  3.000
 GCX  H4   C51  C41  108.43  3.000
 GCX  H4   C51  C6   108.83  3.000
 GCX  C41  C51  C6   111.77  3.000
 GCX  H4   C51  O51  110.19  3.000
 GCX  C6   C51  O51  108.04  3.000
 GCX  C41  C51  O51  109.58  3.000
 GCX  H6   C6   H5   107.14  3.000
 GCX  H6   C6   O6   111.86  3.000
 GCX  H5   C6   O6   111.53  3.000
 GCX  H6   C6   C51  108.89  3.000
 GCX  H5   C6   C51  108.38  3.000
 GCX  O6   C6   C51  108.95  3.000
 GCX  H7   O6   C6   108.03  3.000
 GCX  H8   C31  O1   110.47  3.000
 GCX  H8   C31  C41  108.44  3.000
 GCX  O1   C31  C41  109.35  3.000
 GCX  H8   C31  C21  108.34  3.000
 GCX  C41  C31  C21  110.85  3.000
 GCX  O1   C31  C21  109.38  3.000
 GCX  H9   C41  O41  111.09  3.000
 GCX  H9   C41  C31  108.20  3.000
 GCX  O41  C41  C31  108.19  3.000
 GCX  H9   C41  C51  108.24  3.000
 GCX  O41  C41  C51  111.08  3.000
 GCX  C31  C41  C51  110.01  3.000
 GCX  H10  O41  C41  109.13  3.000
 GCX  C1   O1   C31  117.06  3.000
 GCX  H11  C1   O5   109.46  3.000
 GCX  H11  C1   C2   108.80  3.000
 GCX  O5   C1   C2   111.43  3.000
 GCX  H11  C1   O1   111.25  3.000
 GCX  C2   C1   O1   107.89  3.000
 GCX  O5   C1   O1   108.01  3.000
 GCX  H12  C2   C3   107.73  3.000
 GCX  H12  C2   O2   111.14  3.000
 GCX  C3   C2   O2   108.52  3.000
 GCX  H12  C2   C1   107.40  3.000
 GCX  O2   C2   C1   112.10  3.000
 GCX  C3   C2   C1   109.87  3.000
 GCX  H13  O2   C2   107.91  3.000
 GCX  H14  C3   C4   108.86  3.000
 GCX  H14  C3   O3   111.09  3.000
 GCX  C4   C3   O3   110.16  3.000
 GCX  H14  C3   C2   108.66  3.000
 GCX  O3   C3   C2   105.79  3.000
 GCX  C4   C3   C2   112.27  3.000
 GCX  H15  O3   C3   108.53  3.000
 GCX  C5   O5   C1   111.64  3.000
 GCX  H17  C5   H16  107.10  3.000
 GCX  H17  C5   C4   110.54  3.000
 GCX  H16  C5   C4   109.06  3.000
 GCX  H17  C5   O5   107.28  3.000
 GCX  H16  C5   O5   110.92  3.000
 GCX  C4   C5   O5   111.83  3.000
 GCX  H18  C4   O4   110.62  3.000
 GCX  H18  C4   C5   107.33  3.000
 GCX  O4   C4   C5   112.75  3.000
 GCX  H18  C4   C3   108.06  3.000
 GCX  C5   C4   C3   109.97  3.000
 GCX  O4   C4   C3   108.02  3.000
 GCX  H19  O4   C4   108.16  3.000
 GCX  H20  O7   C11  109.67  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
 GCX  Var_01  C4  C5  O5  C1  -63.26  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
 GCX  chir_01  C21  O21  C11  C31  negativ
 GCX  chir_02  C11  O7   O51  C21  positiv
 GCX  chir_03  C51  O51  C6   C41  positiv
 GCX  chir_04  C31  O1   C41  C21  negativ
 GCX  chir_05  C41  O41  C51  C31  positiv
 GCX  chir_06  C1   O1   O5   C2   negativ
 GCX  chir_07  C2   O2   C1   C3   negativ
 GCX  chir_08  C3   O3   C2   C4   positiv
 GCX  chir_09  C4   O4   C3   C5   negativ

