# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 21:16:08 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (1S,2S,3R,4S,5S)-5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@](O)(CO)[C@@H](O)[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
 W9S  W9S  "(1S,2S,3R,4S,5S)-5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol"
  ligand  28  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W9S
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
 W9S  N1   N  NH2   0  -0.790  14.8696  21.8041  -14.3250
 W9S  C4   C  CH1   0   0.068  15.9057  19.6556  -13.7815
 W9S  C5   C  CH1   0   0.031  14.7531  19.1114  -12.9483
 W9S  C6   C  CH1   0  -0.007  14.9676  19.4480  -11.4767
 W9S  C1   C  CT    0   0.164  15.0666  20.9653  -11.2431
 W9S  C2   C  CH2   0  -0.458  16.1034  21.5668  -12.1916
 W9S  C3   C  CH1   0  -0.119  16.0022  21.1729  -13.6651
 W9S  O1   O  OH1   0  -0.680  13.8748  18.9003  -10.7602
 W9S  O3   O  OH1   0  -0.672  13.8152  21.5761  -11.4792
 W9S  O4   O  OH1   0  -0.681  14.7307  17.7118  -13.1459
 W9S  O5   O  OH1   0  -0.677  15.7750  19.3197  -15.1429
 W9S  H1   H  HNH2  0   0.340  14.8949  22.8005  -14.1500
 W9S  H2   H  HNH2  0   0.339  14.9615  21.6944  -15.3263
 W9S  H4   H  HCH1  0   0.194  16.8400  19.2341  -13.3734
 W9S  H5   H  HCH1  0   0.205  13.8167  19.5680  -13.2947
 W9S  H6   H  HCH1  0   0.221  15.9080  18.9776  -11.1629
 W9S  H9   H  HCH2  0   0.245  17.0925  21.2679  -11.8371
 W9S  H10  H  HCH2  0   0.244  16.0750  22.6578  -12.1040
 W9S  H11  H  HCH1  0   0.218  16.9573  21.4690  -14.1269
 W9S  H12  H  HOH1  0   0.459  14.1647  18.6619   -9.8747
 W9S  H13  H  HOH1  0   0.457  16.8953  20.9109   -8.5536
 W9S  H14  H  HOH1  0   0.436  13.1516  21.0620  -11.0028
 W9S  H15  H  HOH1  0   0.448  13.9689  17.3544  -12.6790
 W9S  H16  H  HOH1  0   0.444  15.6144  18.3721  -15.2013
 W9S  C7   C  CH2   0  -0.171  15.4494  21.2834   -9.7897
 W9S  O2   O  OH1   0  -0.666  16.6676  20.6623   -9.4538
 W9S  H7   H  HCH2  0   0.209  15.5105  22.3756   -9.6920
 W9S  H8   H  HCH2  0   0.200  14.6367  20.9527   -9.1266

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
 W9S  O5  C4   single  1.408  0.020  1.408
 W9S  N1  C3   single  1.455  0.020  1.455
 W9S  C4  C3   single  1.525  0.020  1.525
 W9S  C4  C5   single  1.523  0.020  1.523
 W9S  C3  C2   single  1.529  0.020  1.529
 W9S  O4  C5   single  1.414  0.020  1.414
 W9S  C5  C6   single  1.525  0.020  1.525
 W9S  C2  C1   single  1.529  0.020  1.529
 W9S  O3  C1   single  1.412  0.020  1.412
 W9S  C6  C1   single  1.538  0.020  1.538
 W9S  C6  O1   single  1.417  0.020  1.417
 W9S  C1  C7   single  1.536  0.020  1.536
 W9S  C7  O2   single  1.408  0.020  1.408
 W9S  N1  H1   single  0.890  0.020  1.040
 W9S  N1  H2   single  0.890  0.020  1.040
 W9S  C4  H4   single  0.970  0.020  1.090
 W9S  C5  H5   single  0.970  0.020  1.090
 W9S  C6  H6   single  0.970  0.020  1.090
 W9S  C7  H7   single  0.970  0.020  1.090
 W9S  C7  H8   single  0.970  0.020  1.090
 W9S  C2  H9   single  0.970  0.020  1.090
 W9S  C2  H10  single  0.970  0.020  1.090
 W9S  C3  H11  single  0.970  0.020  1.090
 W9S  O1  H12  single  0.850  0.020  0.980
 W9S  O2  H13  single  0.850  0.020  0.980
 W9S  O3  H14  single  0.850  0.020  0.980
 W9S  O4  H15  single  0.850  0.020  0.980
 W9S  O5  H16  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
 W9S  H2   N1  H1  106.00  3.000
 W9S  H2   N1  C3  109.35  3.000
 W9S  H1   N1  C3  109.23  3.000
 W9S  H4   C4  O5  110.19  3.000
 W9S  H4   C4  C3  107.36  3.000
 W9S  O5   C4  C3  108.48  3.000
 W9S  H4   C4  C5  107.58  3.000
 W9S  C3   C4  C5  111.21  3.000
 W9S  O5   C4  C5  111.93  3.000
 W9S  H5   C5  O4  110.74  3.000
 W9S  H5   C5  C6  109.44  3.000
 W9S  O4   C5  C6  110.84  3.000
 W9S  H5   C5  C4  108.92  3.000
 W9S  C6   C5  C4  110.04  3.000
 W9S  O4   C5  C4  106.82  3.000
 W9S  H6   C6  O1  110.53  3.000
 W9S  H6   C6  C1  108.91  3.000
 W9S  O1   C6  C1  110.74  3.000
 W9S  H6   C6  C5  107.58  3.000
 W9S  O1   C6  C5  107.11  3.000
 W9S  C1   C6  C5  111.92  3.000
 W9S  O3   C1  C2  109.09  3.000
 W9S  O3   C1  C7  106.82  3.000
 W9S  C2   C1  C7  109.67  3.000
 W9S  C7   C1  C6  111.35  3.000
 W9S  O3   C1  C6  110.13  3.000
 W9S  C2   C1  C6  109.73  3.000
 W9S  H10  C2  H9  105.68  3.000
 W9S  H10  C2  C3  109.40  3.000
 W9S  H9   C2  C3  107.59  3.000
 W9S  H10  C2  C1  108.96  3.000
 W9S  H9   C2  C1  107.76  3.000
 W9S  C3   C2  C1  116.86  3.000
 W9S  H11  C3  C2  106.11  3.000
 W9S  H11  C3  C4  106.88  3.000
 W9S  C2   C3  C4  109.53  3.000
 W9S  H11  C3  N1  111.60  3.000
 W9S  C2   C3  N1  112.15  3.000
 W9S  C4   C3  N1  110.35  3.000
 W9S  H12  O1  C6  109.21  3.000
 W9S  H14  O3  C1  107.24  3.000
 W9S  H15  O4  C5  108.21  3.000
 W9S  H16  O5  C4  107.99  3.000
 W9S  H8   C7  H7  106.65  3.000
 W9S  H8   C7  O2  111.27  3.000
 W9S  H7   C7  O2  111.67  3.000
 W9S  H8   C7  C1  108.91  3.000
 W9S  H7   C7  C1  107.69  3.000
 W9S  O2   C7  C1  110.48  3.000
 W9S  H13  O2  C7  108.31  3.000

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
 W9S  chir_01  C4  O5  C3  C5  negativ
 W9S  chir_02  C5  O4  C4  C6  positiv
 W9S  chir_03  C6  O1  C5  C1  negativ
 W9S  chir_04  C1  C7  C6  C2  positiv
 W9S  chir_05  C3  N1  C4  C2  positiv

