# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 24 03:09:11 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: alpha-D-xylopyranosyl-(1->3)-alpha-D-xylopyranosyl-(1->3)-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]3OC[C@@H](O)[C@H](O)[C@H]3O)[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
 GXX  GXX  alpha-D-xylopyranosyl-(1->3)-alpha-D-xylopyranosyl-(1->3)-beta-D-glucopyranose  ligand  58  30  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GXX
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
 GXX  C12  C  CH1   0   0.298  -0.2996  -1.2020  -0.1876
 GXX  C22  C  CH1   0  -0.017   0.6749  -1.4576  -1.3394
 GXX  C32  C  CH1   0  -0.038   2.0708  -1.7355  -0.7757
 GXX  C42  C  CH1   0   0.026   2.0522  -2.7694   0.3570
 GXX  C52  C  CH2   0  -0.227   0.9628  -2.4054   1.3559
 GXX  O22  O  OH1   0  -0.665   0.2879  -2.5502  -2.1275
 GXX  O1   O  O2    0  -0.500   2.5206  -0.5025  -0.2493
 GXX  O42  O  OH1   0  -0.662   1.8740  -4.0415  -0.2139
 GXX  O5   O  O2    0  -0.486  -0.2938  -2.2637   0.7301
 GXX  C21  C  CH1   0  -0.007  -3.8391  -1.2861  -0.0334
 GXX  C31  C  CH1   0   0.003  -2.5588  -0.4693   0.0493
 GXX  C41  C  CH1   0   0.023  -2.7830   0.9519  -0.4623
 GXX  C51  C  CH1   0  -0.020  -3.9984   1.5750   0.2355
 GXX  C6   C  CH2   0  -0.160  -4.3261   2.9444  -0.3180
 GXX  C11  C  CH1   0   0.260  -4.9746  -0.5184   0.6433
 GXX  O21  O  OH1   0  -0.657  -3.6171  -2.5207   0.5916
 GXX  O12  O  O2    0  -0.519  -1.5666  -1.1054  -0.7308
 GXX  O41  O  OH1   0  -0.663  -1.6159   1.6983  -0.2091
 GXX  O51  O  O2    0  -0.496  -5.1249   0.7456   0.0480
 GXX  O6   O  OH1   0  -0.669  -5.3847   3.4968   0.4265
 GXX  C1   C  CH1   0   0.238   3.8957  -0.3089  -0.1934
 GXX  C2   C  CH1   0  -0.001   4.1975   0.6301   0.9833
 GXX  C3   C  CH1   0   0.012   3.6436   2.0190   0.7056
 GXX  C4   C  CH1   0  -0.010   4.1783   2.5012  -0.6377
 GXX  C5   C  CH2   0  -0.225   3.8807   1.4796  -1.7305
 GXX  O2   O  OH1   0  -0.657   3.6512   0.1480   2.1810
 GXX  O3   O  OH1   0  -0.670   4.0364   2.8685   1.7553
 GXX  O4   O  OH1   0  -0.671   3.5626   3.7372  -0.9226
 GXX  O    O  O2    0  -0.489   4.3965   0.2039  -1.3938
 GXX  O7   O  OH1   0  -0.662  -6.1426  -1.2309   0.4606
 GXX  H1   H  HCH1  0   0.199  -0.0092  -0.2716   0.3232
 GXX  H2   H  HCH1  0   0.224   0.7346  -0.5350  -1.9365
 GXX  H3   H  HCH1  0   0.256   2.7210  -2.0827  -1.5898
 GXX  H4   H  HCH1  0   0.216   3.0135  -2.7141   0.8905
 GXX  H5   H  HCH2  0   0.248   0.8610  -3.1858   2.1134
 GXX  H6   H  HCH2  0   0.212   1.2567  -1.4831   1.8746
 GXX  H7   H  HOH1  0   0.449  -0.5990  -2.3769  -2.4594
 GXX  H8   H  HOH1  0   0.451   1.9750  -4.6981   0.4821
 GXX  H9   H  HCH1  0   0.218  -4.1065  -1.4118  -1.0951
 GXX  H10  H  HCH1  0   0.237  -2.2471  -0.4166   1.1023
 GXX  H11  H  HCH1  0   0.227  -2.9920   0.8993  -1.5398
 GXX  H12  H  HCH1  0   0.221  -3.7724   1.6723   1.3109
 GXX  H13  H  HCH2  0   0.206  -3.4252   3.5650  -0.2576
 GXX  H14  H  HCH2  0   0.198  -4.5815   2.8485  -1.3827
 GXX  H15  H  HCH1  0   0.191  -4.7394  -0.3937   1.7153
 GXX  H16  H  HOH1  0   0.451  -4.4066  -3.0592   0.4757
 GXX  H17  H  HOH1  0   0.461  -1.4328   2.2637  -0.9632
 GXX  H18  H  HOH1  0   0.457  -5.5463   4.3859   0.0990
 GXX  H19  H  HCH1  0   0.240   4.4250  -1.2599  -0.0460
 GXX  H20  H  HCH1  0   0.226   5.2923   0.7076   1.0530
 GXX  H21  H  HCH1  0   0.212   2.5457   1.9601   0.6405
 GXX  H22  H  HCH1  0   0.219   5.2675   2.6181  -0.5477
 GXX  H23  H  HCH2  0   0.218   2.8011   1.4407  -1.9150
 GXX  H24  H  HCH2  0   0.244   4.3644   1.7732  -2.6638
 GXX  H25  H  HOH1  0   0.455   4.1634  -0.6143   2.4678
 GXX  H26  H  HOH1  0   0.449   3.7156   3.7533   1.5521
 GXX  H27  H  HOH1  0   0.460   4.0907   4.2024  -1.5783
 GXX  H28  H  HOH1  0   0.467  -6.7899  -0.9662   1.1227

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
 GXX  C4   O4   single  1.410  0.020  1.410
 GXX  C4   C5   single  1.525  0.020  1.525
 GXX  C4   C3   single  1.524  0.020  1.524
 GXX  O3   C3   single  1.406  0.020  1.406
 GXX  O42  C42  single  1.406  0.020  1.406
 GXX  C5   O    single  1.417  0.020  1.417
 GXX  C3   C2   single  1.521  0.020  1.521
 GXX  C2   C1   single  1.535  0.020  1.535
 GXX  C2   O2   single  1.402  0.020  1.402
 GXX  C1   O    single  1.398  0.020  1.398
 GXX  C1   O1   single  1.390  0.020  1.390
 GXX  C42  C52  single  1.522  0.020  1.522
 GXX  C42  C32  single  1.534  0.020  1.534
 GXX  O1   C32  single  1.414  0.020  1.414
 GXX  C52  O5   single  1.411  0.020  1.411
 GXX  C32  C22  single  1.531  0.020  1.531
 GXX  O21  C21  single  1.401  0.020  1.401
 GXX  O5   C12  single  1.403  0.020  1.403
 GXX  C21  C11  single  1.529  0.020  1.529
 GXX  C21  C31  single  1.521  0.020  1.521
 GXX  C22  C12  single  1.530  0.020  1.530
 GXX  C22  O22  single  1.402  0.020  1.402
 GXX  O12  C12  single  1.382  0.020  1.382
 GXX  O12  C31  single  1.413  0.020  1.413
 GXX  C11  O51  single  1.405  0.020  1.405
 GXX  C31  C41  single  1.527  0.020  1.527
 GXX  O51  C51  single  1.411  0.020  1.411
 GXX  C41  C51  single  1.534  0.020  1.534
 GXX  C41  O41  single  1.408  0.020  1.408
 GXX  C51  C6   single  1.513  0.020  1.513
 GXX  O6   C6   single  1.407  0.020  1.407
 GXX  C11  O7   single  1.380  0.020  1.380
 GXX  C12  H1   single  0.970  0.020  1.090
 GXX  C22  H2   single  0.970  0.020  1.090
 GXX  C32  H3   single  0.970  0.020  1.090
 GXX  C42  H4   single  0.970  0.020  1.090
 GXX  C52  H5   single  0.970  0.020  1.090
 GXX  C52  H6   single  0.970  0.020  1.090
 GXX  O22  H7   single  0.850  0.020  0.980
 GXX  O42  H8   single  0.850  0.020  0.980
 GXX  C21  H9   single  0.970  0.020  1.090
 GXX  C31  H10  single  0.970  0.020  1.090
 GXX  C41  H11  single  0.970  0.020  1.090
 GXX  C51  H12  single  0.970  0.020  1.090
 GXX  C6   H13  single  0.970  0.020  1.090
 GXX  C6   H14  single  0.970  0.020  1.090
 GXX  C11  H15  single  0.970  0.020  1.090
 GXX  O21  H16  single  0.850  0.020  0.980
 GXX  O41  H17  single  0.850  0.020  0.980
 GXX  O6   H18  single  0.850  0.020  0.980
 GXX  C1   H19  single  0.970  0.020  1.090
 GXX  C2   H20  single  0.970  0.020  1.090
 GXX  C3   H21  single  0.970  0.020  1.090
 GXX  C4   H22  single  0.970  0.020  1.090
 GXX  C5   H23  single  0.970  0.020  1.090
 GXX  C5   H24  single  0.970  0.020  1.090
 GXX  O2   H25  single  0.850  0.020  0.980
 GXX  O3   H26  single  0.850  0.020  0.980
 GXX  O4   H27  single  0.850  0.020  0.980
 GXX  O7   H28  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
 GXX  H1   C12  O12  111.43  3.000
 GXX  H1   C12  O5   109.57  3.000
 GXX  O12  C12  O5   108.28  3.000
 GXX  H1   C12  C22  108.81  3.000
 GXX  O12  C12  C22  107.44  3.000
 GXX  O5   C12  C22  111.30  3.000
 GXX  H2   C22  O22  111.31  3.000
 GXX  H2   C22  C32  107.61  3.000
 GXX  O22  C22  C32  108.50  3.000
 GXX  H2   C22  C12  107.63  3.000
 GXX  O22  C22  C12  112.18  3.000
 GXX  C32  C22  C12  109.50  3.000
 GXX  H3   C32  O1   111.31  3.000
 GXX  H3   C32  C42  109.97  3.000
 GXX  O1   C32  C42  108.46  3.000
 GXX  H3   C32  C22  108.92  3.000
 GXX  O1   C32  C22  105.60  3.000
 GXX  C42  C32  C22  112.54  3.000
 GXX  H4   C42  O42  110.67  3.000
 GXX  H4   C42  C52  107.15  3.000
 GXX  O42  C42  C52  113.09  3.000
 GXX  H4   C42  C32  108.27  3.000
 GXX  C52  C42  C32  109.40  3.000
 GXX  O42  C42  C32  108.16  3.000
 GXX  H6   C52  H5   107.30  3.000
 GXX  H6   C52  O5   111.31  3.000
 GXX  H5   C52  O5   107.23  3.000
 GXX  H6   C52  C42  108.62  3.000
 GXX  H5   C52  C42  110.55  3.000
 GXX  O5   C52  C42  111.74  3.000
 GXX  H7   O22  C22  107.93  3.000
 GXX  C1   O1   C32  116.82  3.000
 GXX  H8   O42  C42  108.09  3.000
 GXX  C52  O5   C12  111.70  3.000
 GXX  H9   C21  O21  111.56  3.000
 GXX  H9   C21  C11  107.67  3.000
 GXX  O21  C21  C11  111.27  3.000
 GXX  H9   C21  C31  108.53  3.000
 GXX  C11  C21  C31  109.36  3.000
 GXX  O21  C21  C31  108.39  3.000
 GXX  H10  C31  O12  110.56  3.000
 GXX  H10  C31  C41  108.53  3.000
 GXX  O12  C31  C41  109.70  3.000
 GXX  H10  C31  C21  108.45  3.000
 GXX  C41  C31  C21  110.98  3.000
 GXX  O12  C31  C21  108.62  3.000
 GXX  H11  C41  O41  111.05  3.000
 GXX  H11  C41  C51  108.35  3.000
 GXX  O41  C41  C51  111.08  3.000
 GXX  H11  C41  C31  108.17  3.000
 GXX  O41  C41  C31  108.14  3.000
 GXX  C51  C41  C31  110.00  3.000
 GXX  H12  C51  O51  110.17  3.000
 GXX  H12  C51  C6   108.74  3.000
 GXX  O51  C51  C6   108.08  3.000
 GXX  H12  C51  C41  108.48  3.000
 GXX  C6   C51  C41  111.89  3.000
 GXX  O51  C51  C41  109.47  3.000
 GXX  H14  C6   H13  107.10  3.000
 GXX  H14  C6   O6   111.84  3.000
 GXX  H13  C6   O6   111.53  3.000
 GXX  H14  C6   C51  109.01  3.000
 GXX  H13  C6   C51  108.32  3.000
 GXX  O6   C6   C51  108.94  3.000
 GXX  H15  C11  O7   111.53  3.000
 GXX  H15  C11  O51  109.41  3.000
 GXX  O7   C11  O51  108.53  3.000
 GXX  H15  C11  C21  109.15  3.000
 GXX  O7   C11  C21  108.10  3.000
 GXX  O51  C11  C21  110.10  3.000
 GXX  H16  O21  C21  108.01  3.000
 GXX  C31  O12  C12  117.27  3.000
 GXX  H17  O41  C41  109.20  3.000
 GXX  C11  O51  C51  112.77  3.000
 GXX  H18  O6   C6   108.01  3.000
 GXX  H19  C1   O    105.08  3.000
 GXX  H19  C1   C2   109.39  3.000
 GXX  O    C1   C2   111.30  3.000
 GXX  H19  C1   O1   111.20  3.000
 GXX  O    C1   O1   111.78  3.000
 GXX  C2   C1   O1   108.09  3.000
 GXX  H20  C2   O2   110.98  3.000
 GXX  H20  C2   C3   108.05  3.000
 GXX  O2   C2   C3   109.15  3.000
 GXX  H20  C2   C1   106.69  3.000
 GXX  O2   C2   C1   111.58  3.000
 GXX  C3   C2   C1   110.30  3.000
 GXX  H21  C3   O3   110.78  3.000
 GXX  H21  C3   C4   108.33  3.000
 GXX  O3   C3   C4   111.64  3.000
 GXX  H21  C3   C2   108.97  3.000
 GXX  O3   C3   C2   108.28  3.000
 GXX  C4   C3   C2   108.79  3.000
 GXX  H22  C4   O4   110.86  3.000
 GXX  H22  C4   C5   108.85  3.000
 GXX  O4   C4   C5   110.93  3.000
 GXX  H22  C4   C3   108.01  3.000
 GXX  C5   C4   C3   110.56  3.000
 GXX  O4   C4   C3   107.60  3.000
 GXX  H24  C5   H23  107.59  3.000
 GXX  H24  C5   O    106.51  3.000
 GXX  H23  C5   O    111.51  3.000
 GXX  H24  C5   C4   110.25  3.000
 GXX  H23  C5   C4   109.66  3.000
 GXX  O    C5   C4   111.21  3.000
 GXX  H25  O2   C2   108.64  3.000
 GXX  H26  O3   C3   107.73  3.000
 GXX  H27  O4   C4   108.78  3.000
 GXX  C5   O    C1   113.83  3.000
 GXX  H28  O7   C11  109.63  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
 GXX  Var_01  C42  C52  O5  C12  -63.71  30.0  1
 GXX  Var_02  C4   C5   O   C1    58.48  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
 GXX  chir_01  C12  O5   C22  O12  negativ
 GXX  chir_02  C22  O22  C32  C12  positiv
 GXX  chir_03  C32  O1   C42  C22  negativ
 GXX  chir_04  C42  O42  C52  C32  positiv
 GXX  chir_05  C21  O21  C11  C31  negativ
 GXX  chir_06  C31  O12  C41  C21  negativ
 GXX  chir_07  C41  O41  C31  C51  negativ
 GXX  chir_08  C51  O51  C41  C6   negativ
 GXX  chir_09  C11  O7   O51  C21  positiv
 GXX  chir_10  C1   C2   O    O1   positiv
 GXX  chir_11  C2   O2   C1   C3   negativ
 GXX  chir_12  C3   O3   C2   C4   positiv
 GXX  chir_13  C4   O4   C3   C5   negativ

