# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:06:25 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-4-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O[C@@H]2OC(=C[C@H](O)[C@H]2O)C(O)=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
 HS2  HS2  2-(acetylamino)-2-deoxy-4-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-alpha-D-glucopyranose  saccharide  46  26  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HS2
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
 HS2  O35   O  OC    -1  -0.582   2.0068  -3.6010  -0.3000
 HS2  C27   C  C      0   0.370   3.1095  -3.0383  -0.3734
 HS2  O34   O  O      0  -0.593   4.2111  -3.5455  -0.6548
 HS2  C19   C  C      0   0.167   3.1237  -1.5411  -0.0747
 HS2  C24   C  C1     0  -0.407   4.2348  -0.8032  -0.0744
 HS2  C17   C  CH1    0   0.003   4.2438   0.6517   0.2821
 HS2  O25   O  OH1    0  -0.673   5.2855   0.9862   1.1800
 HS2  C12   C  CH1    0  -0.022   2.9313   1.0232   0.9583
 HS2  O18   O  OH1    0  -0.661   2.7249   2.4096   0.9985
 HS2  C13   C  CH1    0   0.294   1.8022   0.3854   0.1604
 HS2  O13   O  O2     0  -0.459   1.9025  -1.0231   0.2093
 HS2  O3    O  O2     0  -0.502   0.5950   0.7511   0.7076
 HS2  C1    C  CH1    0   0.011  -0.5535   0.6473  -0.1157
 HS2  C4    C  CH1    0   0.036  -1.6156  -0.1527   0.6265
 HS2  O9    O  OH1    0  -0.639  -1.1585  -1.4670   0.7850
 HS2  C3    C  CH1    0  -0.166  -2.9319  -0.1210  -0.1614
 HS2  N14   N  NH1    0  -0.641  -3.9734  -0.8135   0.5547
 HS2  C7    C  C      0   0.519  -4.6149  -1.9116   0.1053
 HS2  C8    C  CH3    0  -0.781  -5.6749  -2.4511   1.0329
 HS2  O7    O  O      0  -0.498  -4.3627  -2.4482  -0.9635
 HS2  C10   C  CH1    0   0.273  -3.3471   1.3109  -0.4920
 HS2  O15   O  OH1    0  -0.673  -3.7205   1.9378   0.6930
 HS2  O5    O  O2     0  -0.499  -2.2997   1.9659  -1.1486
 HS2  C2    C  CH1    0  -0.001  -1.0843   2.0547  -0.4252
 HS2  C6    C  CH2    0  -0.179  -0.1237   2.8645  -1.2715
 HS2  O11   O  OH1    0  -0.660  -0.6765   4.1430  -1.4799
 HS2  H24   H  H      0   0.252   5.1690  -1.2772  -0.3427
 HS2  H17   H  HCH1   0   0.223   4.3348   1.2578  -0.6314
 HS2  HO25  H  HOH1   0   0.457   6.1136   1.0025   0.6907
 HS2  H12   H  HCH1   0   0.220   2.9250   0.5872   1.9702
 HS2  HO18  H  HOH1   0   0.452   3.5215   2.8175   1.3556
 HS2  H13   H  HCH1   0   0.199   1.8804   0.6980  -0.8961
 HS2  H1    H  HCH1   0   0.238  -0.3154   0.1329  -1.0575
 HS2  H4    H  HCH1   0   0.215  -1.7746   0.3272   1.6045
 HS2  HO9   H  HOH1   0   0.445  -1.7632  -1.9238   1.3783
 HS2  H3    H  HCH1   0   0.278  -2.7772  -0.6434  -1.1076
 HS2  HN14  H  HNH1   0   0.398  -4.2744  -0.4099   1.4281
 HS2  H8    H  HCH3   0   0.248  -5.8503  -1.8282   1.9082
 HS2  H8A   H  HCH3   0   0.267  -6.6126  -2.5585   0.4888
 HS2  H8B   H  HCH3   0   0.269  -5.3813  -3.4445   1.3732
 HS2  H10   H  HCH1   0   0.240  -4.1717   1.2987  -1.2126
 HS2  HO15  H  HOH1   0   0.474  -4.2010   2.7473   0.4889
 HS2  H2    H  HCH1   0   0.239  -1.2390   2.5805   0.5265
 HS2  H6    H  HCH2   0   0.224   0.8328   2.9297  -0.7451
 HS2  H6A   H  HCH2   0   0.188   0.0589   2.3393  -2.2203
 HS2  HO11  H  HOH1   0   0.440   0.0036   4.6963  -1.8737

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
 HS2  C27  O35   deloc   1.240  0.020  1.240
 HS2  O34  C27   deloc   1.245  0.020  1.245
 HS2  C19  C27   single  1.527  0.020  1.527
 HS2  C19  C24   double  1.334  0.020  1.334
 HS2  C17  C24   single  1.498  0.020  1.498
 HS2  O25  C17   single  1.415  0.020  1.415
 HS2  C12  C17   single  1.522  0.020  1.522
 HS2  C12  O18   single  1.402  0.020  1.402
 HS2  C13  C12   single  1.523  0.020  1.523
 HS2  C13  O13   single  1.413  0.020  1.413
 HS2  O13  C19   single  1.357  0.020  1.357
 HS2  O3   C13   single  1.375  0.020  1.375
 HS2  C1   O3    single  1.417  0.020  1.417
 HS2  C4   C1    single  1.523  0.020  1.523
 HS2  C4   O9    single  1.401  0.020  1.401
 HS2  C3   C4    single  1.534  0.020  1.534
 HS2  N14  C3    single  1.441  0.020  1.441
 HS2  N14  C7    single  1.349  0.020  1.349
 HS2  C8   C7    single  1.508  0.020  1.508
 HS2  O7   C7    double  1.222  0.020  1.222
 HS2  C10  C3    single  1.527  0.020  1.527
 HS2  C10  O5    single  1.399  0.020  1.399
 HS2  O15  C10   single  1.392  0.020  1.392
 HS2  O5   C2    single  1.417  0.020  1.417
 HS2  C2   C1    single  1.536  0.020  1.536
 HS2  C2   C6    single  1.515  0.020  1.515
 HS2  O11  C6    single  1.408  0.020  1.408
 HS2  C24  H24   single  0.930  0.020  1.080
 HS2  C17  H17   single  0.970  0.020  1.090
 HS2  O25  HO25  single  0.850  0.020  0.980
 HS2  C12  H12   single  0.970  0.020  1.090
 HS2  O18  HO18  single  0.850  0.020  0.980
 HS2  C13  H13   single  0.970  0.020  1.090
 HS2  C1   H1    single  0.970  0.020  1.090
 HS2  C4   H4    single  0.970  0.020  1.090
 HS2  O9   HO9   single  0.850  0.020  0.980
 HS2  C3   H3    single  0.970  0.020  1.090
 HS2  N14  HN14  single  0.860  0.020  1.020
 HS2  C8   H8    single  0.970  0.020  1.090
 HS2  C8   H8A   single  0.970  0.020  1.090
 HS2  C8   H8B   single  0.970  0.020  1.090
 HS2  C10  H10   single  0.970  0.020  1.090
 HS2  O15  HO15  single  0.850  0.020  0.980
 HS2  C2   H2    single  0.970  0.020  1.090
 HS2  C6   H6    single  0.970  0.020  1.090
 HS2  C6   H6A   single  0.970  0.020  1.090
 HS2  O11  HO11  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
 HS2  C19   C27  O34  115.82  3.000
 HS2  C19   C27  O35  116.21  3.000
 HS2  O34   C27  O35  127.97  3.000
 HS2  O13   C19  C24  122.59  3.000
 HS2  O13   C19  C27  114.02  3.000
 HS2  C24   C19  C27  123.38  3.000
 HS2  H24   C24  C17  118.66  3.000
 HS2  H24   C24  C19  118.50  3.000
 HS2  C17   C24  C19  122.84  3.000
 HS2  H17   C17  C12  107.80  3.000
 HS2  H17   C17  O25  109.61  3.000
 HS2  C12   C17  O25  107.16  3.000
 HS2  H17   C17  C24  109.75  3.000
 HS2  C12   C17  C24  109.73  3.000
 HS2  O25   C17  C24  112.65  3.000
 HS2  HO25  O25  C17  108.35  3.000
 HS2  H12   C12  C13  108.14  3.000
 HS2  H12   C12  O18  111.34  3.000
 HS2  C13   C12  O18  108.66  3.000
 HS2  H12   C12  C17  108.44  3.000
 HS2  C13   C12  C17  107.72  3.000
 HS2  O18   C12  C17  112.39  3.000
 HS2  HO18  O18  C12  107.91  3.000
 HS2  H13   C13  O3   111.57  3.000
 HS2  H13   C13  O13  108.07  3.000
 HS2  O3    C13  O13  108.28  3.000
 HS2  H13   C13  C12  109.28  3.000
 HS2  O3    C13  C12  109.34  3.000
 HS2  O13   C13  C12  110.29  3.000
 HS2  C13   O13  C19  115.93  3.000
 HS2  C1    O3   C13  117.45  3.000
 HS2  H1    C1   C2   109.33  3.000
 HS2  H1    C1   C4   108.84  3.000
 HS2  C2    C1   C4   109.79  3.000
 HS2  H1    C1   O3   110.89  3.000
 HS2  C2    C1   O3   109.28  3.000
 HS2  C4    C1   O3   108.70  3.000
 HS2  H4    C4   C3   108.86  3.000
 HS2  H4    C4   O9   110.84  3.000
 HS2  C3    C4   O9   110.95  3.000
 HS2  H4    C4   C1   107.74  3.000
 HS2  C3    C4   C1   109.70  3.000
 HS2  O9    C4   C1   108.70  3.000
 HS2  HO9   O9   C4   108.06  3.000
 HS2  H3    C3   C10  107.43  3.000
 HS2  H3    C3   N14  107.64  3.000
 HS2  C10   C3   N14  111.20  3.000
 HS2  H3    C3   C4   108.27  3.000
 HS2  C10   C3   C4   111.33  3.000
 HS2  N14   C3   C4   110.78  3.000
 HS2  HN14  N14  C7   118.20  3.000
 HS2  HN14  N14  C3   116.99  3.000
 HS2  C7    N14  C3   124.71  3.000
 HS2  O7    C7   C8   121.72  3.000
 HS2  O7    C7   N14  123.41  3.000
 HS2  C8    C7   N14  114.87  3.000
 HS2  H8B   C8   H8A  107.33  3.000
 HS2  H8B   C8   H8   108.29  3.000
 HS2  H8A   C8   H8   108.62  3.000
 HS2  H8B   C8   C7   109.18  3.000
 HS2  H8A   C8   C7   109.45  3.000
 HS2  H8    C8   C7   113.77  3.000
 HS2  H10   C10  O5   105.07  3.000
 HS2  H10   C10  O15  111.30  3.000
 HS2  O5    C10  O15  112.93  3.000
 HS2  H10   C10  C3   109.68  3.000
 HS2  O15   C10  C3   108.12  3.000
 HS2  O5    C10  C3   109.70  3.000
 HS2  HO15  O15  C10  109.39  3.000
 HS2  C2    O5   C10  115.58  3.000
 HS2  H2    C2   C6   108.51  3.000
 HS2  H2    C2   O5   110.58  3.000
 HS2  C6    C2   O5   106.99  3.000
 HS2  H2    C2   C1   108.23  3.000
 HS2  C6    C2   C1   112.54  3.000
 HS2  O5    C2   C1   109.99  3.000
 HS2  H6A   C6   H6   107.36  3.000
 HS2  H6A   C6   O11  111.78  3.000
 HS2  H6    C6   O11  111.12  3.000
 HS2  H6A   C6   C2   109.39  3.000
 HS2  H6    C6   C2   108.52  3.000
 HS2  O11   C6   C2   108.61  3.000
 HS2  HO11  O11  C6   107.79  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
 HS2  CONST_01  C8    C7   N14  C3   180.00   0.0  0
 HS2  CONST_02  O7    C7   N14  C3     0.00   0.0  0
 HS2  CONST_03  HN14  N14  C7   C8     0.00   0.0  0
 HS2  Var_01    O13   C19  C24  C17    2.06  30.0  1
 HS2  Var_02    C24   C19  C27  O35  178.02  30.0  2
 HS2  Var_03    H8    C8   C7   N14    5.38  30.0  3

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
 HS2  chir_01  C17  C24  O25  C12  positiv
 HS2  chir_02  C12  O18  C17  C13  positiv
 HS2  chir_03  C13  O3   O13  C12  positiv
 HS2  chir_04  C1   O3   C4   C2   negativ
 HS2  chir_05  C4   O9   C3   C1   positiv
 HS2  chir_06  C3   N14  C10  C4   negativ
 HS2  chir_07  C10  O15  O5   C3   negativ
 HS2  chir_08  C2   O5   C6   C1   positiv

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
 HS2  plan-1  C3    0.020
 HS2  plan-1  N14   0.020
 HS2  plan-1  C7    0.020
 HS2  plan-1  C8    0.020
 HS2  plan-1  O7    0.020
 HS2  plan-1  HN14  0.020
 HS2  plan-2  O35   0.020
 HS2  plan-2  C27   0.020
 HS2  plan-2  O34   0.020
 HS2  plan-2  C19   0.020

