# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:15:22 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-O-beta-D-xylopyranosyl-beta-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[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
 XYB  XYB  4-O-beta-D-xylopyranosyl-beta-D-xylopyranose  saccharide  37  19  .  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_XYB
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
 XYB  O4'  O  O2    0  -0.510  -0.0429   0.1758  -0.6209
 XYB  C1   C  CH1   0   0.289  -1.2075   0.0219   0.1045
 XYB  C2   C  CH1   0  -0.017  -2.3111   0.8263  -0.5867
 XYB  C3   C  CH1   0   0.012  -3.6208   0.6056   0.1530
 XYB  C4   C  CH1   0  -0.005  -3.8939  -0.8896   0.2781
 XYB  C5   C  CH2   0  -0.229  -2.6882  -1.5897   0.8988
 XYB  O2   O  OH1   0  -0.662  -2.0152   2.1976  -0.5695
 XYB  O3   O  OH1   0  -0.667  -4.6440   1.2704  -0.5417
 XYB  O4   O  OH1   0  -0.671  -5.0425  -1.0421   1.0799
 XYB  O5   O  O2    0  -0.482  -1.5263  -1.3427   0.1371
 XYB  C4'  C  CH1   0   0.002   1.1597   0.0003   0.1056
 XYB  C5'  C  CH2   0  -0.212   1.6378   1.3538   0.6300
 XYB  O5'  O  O2    0  -0.488   2.8744   1.2275   1.2897
 XYB  C1'  C  CH1   0   0.268   3.8953   0.8065   0.4134
 XYB  O1'  O  OH1   0  -0.661   5.0777   0.7303   1.1179
 XYB  C2'  C  CH1   0  -0.035   3.5662  -0.5842  -0.1254
 XYB  O2'  O  OH1   0  -0.670   4.5186  -1.0096  -1.0681
 XYB  C3'  C  CH1   0   0.006   2.2091  -0.5819  -0.8251
 XYB  O3'  O  OH1   0  -0.663   1.8164  -1.8760  -1.1985
 XYB  H1   H  HCH1  0   0.195  -1.0877   0.3985   1.1379
 XYB  H2   H  HCH1  0   0.222  -2.4162   0.4475  -1.6154
 XYB  H3   H  HCH1  0   0.209  -3.5075   1.0122   1.1726
 XYB  H4   H  HCH1  0   0.221  -4.0590  -1.2959  -0.7300
 XYB  H5   H  HCH2  0   0.216  -2.5605  -1.2525   1.9378
 XYB  H6   H  HCH2  0   0.252  -2.8378  -2.6704   0.9169
 XYB  H7   H  HOH1  0   0.451  -1.2414   2.3431  -1.1230
 XYB  H8   H  HOH1  0   0.450  -5.4700   1.1106  -0.0735
 XYB  H9   H  HOH1  0   0.461  -5.3884  -1.9313   0.9585
 XYB  H10  H  HCH1  0   0.243   1.0106  -0.6901   0.9458
 XYB  H11  H  HCH2  0   0.217   1.7089   2.0609  -0.2095
 XYB  H12  H  HCH2  0   0.254   0.9273   1.7649   1.3488
 XYB  H13  H  HCH1  0   0.193   3.9671   1.5195  -0.4267
 XYB  H14  H  HOH1  0   0.468   5.4705   1.6068   1.1876
 XYB  H15  H  HCH1  0   0.223   3.5148  -1.2733   0.7323
 XYB  H16  H  HOH1  0   0.458   5.3388  -1.2092  -0.6065
 XYB  H17  H  HCH1  0   0.213   2.2816   0.0777  -1.7066
 XYB  H18  H  HOH1  0   0.451   2.4850  -2.2290  -1.7946

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
 XYB  O3   C3   single  1.404  0.020  1.404
 XYB  C3   C4   single  1.525  0.020  1.525
 XYB  C3   C2   single  1.520  0.020  1.520
 XYB  C4   O4   single  1.409  0.020  1.409
 XYB  C4   C5   single  1.526  0.020  1.526
 XYB  O5'  C5'  single  1.407  0.020  1.407
 XYB  O5'  C1'  single  1.410  0.020  1.410
 XYB  C2   O2   single  1.403  0.020  1.403
 XYB  C2   C1   single  1.531  0.020  1.531
 XYB  O1'  C1'  single  1.378  0.020  1.378
 XYB  C5   O5   single  1.411  0.020  1.411
 XYB  C5'  C4'  single  1.528  0.020  1.528
 XYB  C1'  C2'  single  1.527  0.020  1.527
 XYB  O4'  C1   single  1.381  0.020  1.381
 XYB  O4'  C4'  single  1.416  0.020  1.416
 XYB  C1   O5   single  1.402  0.020  1.402
 XYB  C4'  C3'  single  1.519  0.020  1.519
 XYB  C2'  C3'  single  1.527  0.020  1.527
 XYB  C2'  O2'  single  1.406  0.020  1.406
 XYB  C3'  O3'  single  1.403  0.020  1.403
 XYB  C1   H1   single  0.970  0.020  1.090
 XYB  C2   H2   single  0.970  0.020  1.090
 XYB  C3   H3   single  0.970  0.020  1.090
 XYB  C4   H4   single  0.970  0.020  1.090
 XYB  C5   H5   single  0.970  0.020  1.090
 XYB  C5   H6   single  0.970  0.020  1.090
 XYB  O2   H7   single  0.850  0.020  0.980
 XYB  O3   H8   single  0.850  0.020  0.980
 XYB  O4   H9   single  0.850  0.020  0.980
 XYB  C4'  H10  single  0.970  0.020  1.090
 XYB  C5'  H11  single  0.970  0.020  1.090
 XYB  C5'  H12  single  0.970  0.020  1.090
 XYB  C1'  H13  single  0.970  0.020  1.090
 XYB  O1'  H14  single  0.850  0.020  0.980
 XYB  C2'  H15  single  0.970  0.020  1.090
 XYB  O2'  H16  single  0.850  0.020  0.980
 XYB  C3'  H17  single  0.970  0.020  1.090
 XYB  O3'  H18  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
 XYB  C4'  O4'  C1   115.66  3.000
 XYB  H1   C1   O5   109.53  3.000
 XYB  H1   C1   C2   108.72  3.000
 XYB  O5   C1   C2   110.98  3.000
 XYB  H1   C1   O4'  111.19  3.000
 XYB  O5   C1   O4'  108.22  3.000
 XYB  C2   C1   O4'  108.20  3.000
 XYB  H2   C2   O2   111.58  3.000
 XYB  H2   C2   C3   108.80  3.000
 XYB  O2   C2   C3   108.52  3.000
 XYB  H2   C2   C1   108.06  3.000
 XYB  O2   C2   C1   110.86  3.000
 XYB  C3   C2   C1   108.97  3.000
 XYB  H3   C3   O3   110.95  3.000
 XYB  H3   C3   C4   107.69  3.000
 XYB  O3   C3   C4   111.98  3.000
 XYB  H3   C3   C2   107.91  3.000
 XYB  C4   C3   C2   109.67  3.000
 XYB  O3   C3   C2   108.56  3.000
 XYB  H4   C4   O4   111.07  3.000
 XYB  H4   C4   C5   108.79  3.000
 XYB  O4   C4   C5   111.28  3.000
 XYB  H4   C4   C3   108.30  3.000
 XYB  C5   C4   C3   109.97  3.000
 XYB  O4   C4   C3   107.38  3.000
 XYB  H6   C5   H5   107.69  3.000
 XYB  H6   C5   O5   107.17  3.000
 XYB  H5   C5   O5   111.14  3.000
 XYB  H6   C5   C4   110.65  3.000
 XYB  H5   C5   C4   109.59  3.000
 XYB  O5   C5   C4   110.53  3.000
 XYB  H7   O2   C2   108.08  3.000
 XYB  H8   O3   C3   107.81  3.000
 XYB  H9   O4   C4   108.74  3.000
 XYB  C5   O5   C1   111.73  3.000
 XYB  H10  C4'  C3'  108.78  3.000
 XYB  H10  C4'  C5'  109.69  3.000
 XYB  C3'  C4'  C5'  109.49  3.000
 XYB  H10  C4'  O4'  110.82  3.000
 XYB  C3'  C4'  O4'  108.66  3.000
 XYB  C5'  C4'  O4'  109.39  3.000
 XYB  H12  C5'  H11  107.62  3.000
 XYB  H12  C5'  O5'  107.29  3.000
 XYB  H11  C5'  O5'  111.03  3.000
 XYB  H12  C5'  C4'  110.85  3.000
 XYB  H11  C5'  C4'  109.13  3.000
 XYB  O5'  C5'  C4'  110.87  3.000
 XYB  C1'  O5'  C5'  111.82  3.000
 XYB  H13  C1'  C2'  109.48  3.000
 XYB  H13  C1'  O1'  111.64  3.000
 XYB  C2'  C1'  O1'  108.35  3.000
 XYB  H13  C1'  O5'  109.10  3.000
 XYB  C2'  C1'  O5'  109.59  3.000
 XYB  O1'  C1'  O5'  108.66  3.000
 XYB  H14  O1'  C1'  109.67  3.000
 XYB  H15  C2'  C3'  108.44  3.000
 XYB  H15  C2'  O2'  111.37  3.000
 XYB  C3'  C2'  O2'  107.17  3.000
 XYB  H15  C2'  C1'  107.75  3.000
 XYB  O2'  C2'  C1'  111.48  3.000
 XYB  C3'  C2'  C1'  110.60  3.000
 XYB  H16  O2'  C2'  108.58  3.000
 XYB  H17  C3'  O3'  110.93  3.000
 XYB  H17  C3'  C2'  107.97  3.000
 XYB  O3'  C3'  C2'  111.68  3.000
 XYB  H17  C3'  C4'  107.81  3.000
 XYB  O3'  C3'  C4'  108.86  3.000
 XYB  C2'  C3'  C4'  109.50  3.000
 XYB  H18  O3'  C3'  107.98  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
 XYB  Var_01  C4  C5  O5  C1  62.17  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
 XYB  chir_01  C1   C2   O4'  O5   positiv
 XYB  chir_02  C2   O2   C1   C3   negativ
 XYB  chir_03  C3   O3   C2   C4   positiv
 XYB  chir_04  C4   O4   C3   C5   negativ
 XYB  chir_05  C4'  O4'  C5'  C3'  positiv
 XYB  chir_06  C1'  O5'  O1'  C2'  negativ
 XYB  chir_07  C2'  O2'  C1'  C3'  negativ
 XYB  chir_08  C3'  O3'  C2'  C4'  positiv

