# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 00:01:42 2021
#   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  47  26  .  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_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  OH1   0  -0.580  37.5154  100.5915  9.0629
 HS2  C27   C  C     0   0.503  36.8465   99.5671  8.5698
 HS2  O34   O  O     0  -0.435  35.7126   99.6246  8.1597
 HS2  C19   C  C     0   0.252  37.6370   98.3088  8.5479
 HS2  C24   C  C1    0  -0.319  38.9627   98.2523  8.6540
 HS2  C17   C  CH1   0   0.019  39.7084   96.9595  8.5650
 HS2  O25   O  OH1   0  -0.654  40.5318   97.0125  7.4261
 HS2  C12   C  CH1   0  -0.037  38.7342   95.7753  8.5611
 HS2  O18   O  OH1   0  -0.665  38.3975   95.5327  9.9034
 HS2  C13   C  CH1   0   0.207  37.4714   96.1095  7.7662
 HS2  O13   O  O2    0  -0.488  36.8376   97.2409  8.3350
 HS2  O3    O  O2    0  -0.489  37.8166   96.3558  6.4532
 HS2  C1    C  CH1   0   0.009  36.9213   95.9613  5.4293
 HS2  C4    C  CH1   0   0.033  35.8431   97.0164  5.1547
 HS2  O9    O  OH1   0  -0.672  34.8950   97.0955  6.1869
 HS2  C3    C  CH1   0  -0.152  35.0779   96.6411  3.8817
 HS2  N14   N  NH1   0  -0.625  34.1167   97.6510  3.5284
 HS2  C7    C  C     0   0.523  32.7877   97.5247  3.7023
 HS2  C8    C  CH3   0  -0.782  31.9833   98.7572  3.3720
 HS2  O7    O  O     0  -0.505  32.2542   96.4982  4.0990
 HS2  C10   C  CH1   0   0.265  36.0260   96.3671  2.7178
 HS2  O15   O  OH1   0  -0.668  36.6157   97.5721  2.3473
 HS2  O5    O  O2    0  -0.498  36.9622   95.3932  3.0819
 HS2  C2    C  CH1   0  -0.013  37.7833   95.7215  4.1863
 HS2  C6    C  CH2   0  -0.161  38.7499   94.5706  4.3840
 HS2  O11   O  OH1   0  -0.670  39.5288   94.4327  3.2192
 HS2  HO35  H  HOH1  0   0.494  36.9832  101.3995  9.0058
 HS2  H24   H  H     0   0.283  39.5330   99.1583  8.8037
 HS2  H17   H  HCH1  0   0.247  40.3160   96.8601  9.4761
 HS2  HO25  H  HOH1  0   0.454  41.1513   96.2771  7.4718
 HS2  H12   H  HCH1  0   0.248  39.2157   94.9036  8.0978
 HS2  HO18  H  HOH1  0   0.460  37.8673   94.7309  9.9554
 HS2  H13   H  HCH1  0   0.257  36.7349   95.3025  7.8488
 HS2  H1    H  HCH1  0   0.231  36.4210   95.0215  5.7088
 HS2  H4    H  HCH1  0   0.222  36.3432   97.9835  5.0024
 HS2  HO9   H  HOH1  0   0.452  35.2178   97.6835  6.8786
 HS2  H3    H  HCH1  0   0.276  34.5268   95.7180  4.0747
 HS2  HN14  H  HNH1  0   0.397  34.4766   98.5405  3.2208
 HS2  H8    H  HCH3  0   0.263  31.1295   98.4840  2.7537
 HS2  H8A   H  HCH3  0   0.268  31.5921   99.1855  4.2957
 HS2  H8B   H  HCH3  0   0.248  32.5551   99.5273  2.8577
 HS2  H10   H  HCH1  0   0.246  35.4649   95.9257  1.8872
 HS2  HO15  H  HOH1  0   0.468  37.0256   97.4752  1.4810
 HS2  H2    H  HCH1  0   0.228  38.3617   96.6326  3.9803
 HS2  H6    H  HCH2  0   0.214  39.3715   94.7851  5.2592
 HS2  H6A   H  HCH2  0   0.194  38.1811   93.6558  4.6028
 HS2  HO11  H  HOH1  0   0.457  40.2225   93.7929  3.4006

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   single  1.319  0.020  1.319
 HS2  O34  C27   double  1.207  0.020  1.207
 HS2  C19  C27   single  1.486  0.020  1.486
 HS2  C19  C24   double  1.331  0.020  1.331
 HS2  C17  C24   single  1.495  0.020  1.495
 HS2  O25  C17   single  1.406  0.020  1.406
 HS2  C12  C17   single  1.533  0.020  1.533
 HS2  C12  O18   single  1.405  0.020  1.405
 HS2  C13  C12   single  1.529  0.020  1.529
 HS2  C13  O13   single  1.416  0.020  1.416
 HS2  O13  C19   single  1.351  0.020  1.351
 HS2  O3   C13   single  1.380  0.020  1.380
 HS2  C1   O3    single  1.416  0.020  1.416
 HS2  C4   C1    single  1.533  0.020  1.533
 HS2  C4   O9    single  1.404  0.020  1.404
 HS2  C3   C4    single  1.532  0.020  1.532
 HS2  N14  C3    single  1.438  0.020  1.438
 HS2  N14  C7    single  1.346  0.020  1.346
 HS2  C8   C7    single  1.508  0.020  1.508
 HS2  O7   C7    double  1.223  0.020  1.223
 HS2  C10  C3    single  1.526  0.020  1.526
 HS2  C10  O5    single  1.399  0.020  1.399
 HS2  O15  C10   single  1.392  0.020  1.392
 HS2  O5   C2    single  1.415  0.020  1.415
 HS2  C2   C1    single  1.532  0.020  1.532
 HS2  C2   C6    single  1.516  0.020  1.516
 HS2  O11  C6    single  1.408  0.020  1.408
 HS2  O35  HO35  single  0.850  0.020  0.980
 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  HO35  O35  C27  110.30  3.000
 HS2  C19   C27  O34  122.34  3.000
 HS2  C19   C27  O35  113.16  3.000
 HS2  O34   C27  O35  124.50  3.000
 HS2  O13   C19  C24  124.63  3.000
 HS2  O13   C19  C27  110.91  3.000
 HS2  C24   C19  C27  124.37  3.000
 HS2  H24   C24  C17  118.02  3.000
 HS2  H24   C24  C19  120.06  3.000
 HS2  C17   C24  C19  121.92  3.000
 HS2  H17   C17  C12  106.46  3.000
 HS2  H17   C17  O25  110.54  3.000
 HS2  C12   C17  O25  113.51  3.000
 HS2  H17   C17  C24  107.73  3.000
 HS2  C12   C17  C24  110.55  3.000
 HS2  O25   C17  C24  107.92  3.000
 HS2  HO25  O25  C17  108.04  3.000
 HS2  H12   C12  C13  108.44  3.000
 HS2  H12   C12  O18  111.77  3.000
 HS2  C13   C12  O18  109.66  3.000
 HS2  H12   C12  C17  109.61  3.000
 HS2  C13   C12  C17  110.93  3.000
 HS2  O18   C12  C17  106.45  3.000
 HS2  HO18  O18  C12  109.11  3.000
 HS2  H13   C13  O3   111.80  3.000
 HS2  H13   C13  O13  104.91  3.000
 HS2  O3    C13  O13  110.59  3.000
 HS2  H13   C13  C12  110.79  3.000
 HS2  O3    C13  C12  109.09  3.000
 HS2  O13   C13  C12  109.60  3.000
 HS2  C13   O13  C19  115.47  3.000
 HS2  C1    O3   C13  118.70  3.000
 HS2  H1    C1   C2   109.16  3.000
 HS2  H1    C1   C4   108.27  3.000
 HS2  C2    C1   C4   110.99  3.000
 HS2  H1    C1   O3   109.97  3.000
 HS2  C2    C1   O3   105.94  3.000
 HS2  C4    C1   O3   112.48  3.000
 HS2  H4    C4   C3   109.12  3.000
 HS2  H4    C4   O9   111.07  3.000
 HS2  C3    C4   O9   106.70  3.000
 HS2  H4    C4   C1   108.08  3.000
 HS2  C3    C4   C1   109.36  3.000
 HS2  O9    C4   C1   112.46  3.000
 HS2  HO9   O9   C4   109.63  3.000
 HS2  H3    C3   C10  107.25  3.000
 HS2  H3    C3   N14  107.43  3.000
 HS2  C10   C3   N14  110.72  3.000
 HS2  H3    C3   C4   108.19  3.000
 HS2  C10   C3   C4   111.56  3.000
 HS2  N14   C3   C4   111.46  3.000
 HS2  HN14  N14  C7   118.35  3.000
 HS2  HN14  N14  C3   117.14  3.000
 HS2  C7    N14  C3   124.20  3.000
 HS2  O7    C7   C8   121.62  3.000
 HS2  O7    C7   N14  123.46  3.000
 HS2  C8    C7   N14  114.92  3.000
 HS2  H8B   C8   H8A  108.10  3.000
 HS2  H8B   C8   H8   108.73  3.000
 HS2  H8A   C8   H8   107.34  3.000
 HS2  H8B   C8   C7   113.68  3.000
 HS2  H8A   C8   C7   109.06  3.000
 HS2  H8    C8   C7   109.72  3.000
 HS2  H10   C10  O5   105.05  3.000
 HS2  H10   C10  O15  111.36  3.000
 HS2  O5    C10  O15  112.86  3.000
 HS2  H10   C10  C3   109.42  3.000
 HS2  O15   C10  C3   108.11  3.000
 HS2  O5    C10  C3   110.01  3.000
 HS2  HO15  O15  C10  109.43  3.000
 HS2  C2    O5   C10  115.47  3.000
 HS2  H2    C2   C6   108.57  3.000
 HS2  H2    C2   O5   110.58  3.000
 HS2  C6    C2   O5   107.20  3.000
 HS2  H2    C2   C1   108.58  3.000
 HS2  C6    C2   C1   111.83  3.000
 HS2  O5    C2   C1   110.07  3.000
 HS2  H6A   C6   H6   107.32  3.000
 HS2  H6A   C6   O11  111.68  3.000
 HS2  H6    C6   O11  111.50  3.000
 HS2  H6A   C6   C2   109.14  3.000
 HS2  H6    C6   C2   108.52  3.000
 HS2  O11   C6   C2   108.61  3.000
 HS2  HO11  O11  C6   107.96  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  HO35  O35  C27  C19  180.00   0.0  0
 HS2  CONST_04  HN14  N14  C7   C8     0.00   0.0  0
 HS2  Var_01    O13   C19  C24  C17   -0.97  30.0  1
 HS2  Var_02    C24   C19  C27  O35  -17.48  30.0  2
 HS2  Var_03    H8    C8   C7   N14  132.98  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
 HS2  plan-2  HO35  0.020

