# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:28:08 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: (2S,3S,4S,5R)-2-{[(4-methylpentyl)sulfonyl]methyl}piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[S](=O)(=O)C[C@H]1NC[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
 P8Y  P8Y  (2S,3S,4S,5R)-2-{[(4-methylpentyl)sulfonyl]methyl}piperidine-3,4,5-triol  ligand  44  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P8Y
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
 P8Y  C1   C  CH2   0  -0.450  -47.4764  38.0463   -6.0520
 P8Y  C11  C  CH3   0  -0.651  -47.3891  36.5148   -8.7462
 P8Y  C16  C  CH2   0  -0.647  -44.1238  39.3804   -6.2735
 P8Y  C18  C  CH2   0  -0.621  -46.1863  37.6166   -5.3671
 P8Y  C2   C  CH2   0  -0.436  -47.3463  38.6774   -7.4347
 P8Y  C3   C  CH1   0  -0.166  -43.5675  40.7971   -6.1610
 P8Y  C4   C  CH1   0   0.038  -42.7400  41.1709   -7.4100
 P8Y  C5   C  CH1   0   0.023  -41.4034  40.4445   -7.4235
 P8Y  C6   C  CH1   0   0.012  -40.6676  40.7084   -6.1144
 P8Y  C7   C  CH2   0  -0.357  -41.5368  40.3213   -4.9197
 P8Y  C8   C  CH1   0  -0.253  -46.6476  37.8236   -8.4961
 P8Y  C9   C  CH3   0  -0.646  -46.4911  38.6235   -9.7850
 P8Y  N2   N  NH1   0  -0.577  -42.8314  40.9745   -4.9268
 P8Y  O10  O  OH1   0  -0.676  -39.4632  39.9714   -6.1577
 P8Y  O12  O  OH1   0  -0.663  -43.4184  40.8866   -8.6091
 P8Y  O13  O  OS    0  -0.683  -45.9434  40.1045   -4.4685
 P8Y  O14  O  OS    0  -0.681  -44.2219  38.3936   -3.8038
 P8Y  O8   O  OH1   0  -0.673  -40.6672  40.9020   -8.5318
 P8Y  S17  S  S     0   1.229  -45.1064  38.9553   -4.8269
 P8Y  H1   H  HCH2  0   0.258  -48.0149  38.7289   -5.3930
 P8Y  H2   H  HCH2  0   0.256  -48.0997  37.1511   -6.1138
 P8Y  H3   H  HCH3  0   0.228  -47.4115  35.8825   -7.8574
 P8Y  H4   H  HCH3  0   0.216  -48.4226  36.7011   -9.0491
 P8Y  H5   H  HCH3  0   0.230  -46.9089  35.9395   -9.5395
 P8Y  H6   H  HCH2  0   0.308  -44.7658  39.3051   -7.1486
 P8Y  H7   H  HCH2  0   0.306  -43.3637  38.6029   -6.3593
 P8Y  H8   H  HCH2  0   0.318  -46.4161  37.0920   -4.4367
 P8Y  H9   H  HCH2  0   0.295  -45.5773  36.9408   -5.9720
 P8Y  H10  H  HCH2  0   0.218  -46.8461  39.6484   -7.3507
 P8Y  H11  H  HCH2  0   0.241  -48.3547  38.9105   -7.7913
 P8Y  H12  H  HCH1  0   0.278  -44.4233  41.4765   -6.1242
 P8Y  H13  H  HCH1  0   0.232  -42.5307  42.2490   -7.3310
 P8Y  H14  H  HCH1  0   0.204  -41.5810  39.3586   -7.5045
 P8Y  H15  H  HCH1  0   0.210  -40.4599  41.7877   -6.0566
 P8Y  H16  H  HCH2  0   0.230  -41.6750  39.2361   -4.9009
 P8Y  H17  H  HCH2  0   0.251  -41.0272  40.5824   -3.9899
 P8Y  H18  H  HCH1  0   0.213  -45.6397  37.5662   -8.1474
 P8Y  H19  H  HCH3  0   0.219  -45.9101  39.5328   -9.6168
 P8Y  H20  H  HCH3  0   0.228  -45.9790  38.0430  -10.5536
 P8Y  H21  H  HCH3  0   0.216  -47.4642  38.9215  -10.1825
 P8Y  H22  H  HNH1  0   0.361  -42.7259  41.9624   -4.7346
 P8Y  H24  H  HOH1  0   0.458  -38.8498  40.3499   -5.5213
 P8Y  H25  H  HOH1  0   0.456  -44.1443  41.5113   -8.7017
 P8Y  H26  H  HOH1  0   0.447  -39.7829  40.5254   -8.4676

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
 P8Y  C9   C8   single  1.525  0.020  1.525
 P8Y  C8   C11  single  1.525  0.020  1.525
 P8Y  C8   C2   single  1.531  0.020  1.531
 P8Y  O8   C5   single  1.407  0.020  1.407
 P8Y  C2   C1   single  1.525  0.020  1.525
 P8Y  O12  C4   single  1.407  0.020  1.407
 P8Y  C5   C4   single  1.521  0.020  1.521
 P8Y  C5   C6   single  1.525  0.020  1.525
 P8Y  O10  C6   single  1.413  0.020  1.413
 P8Y  C4   C3   single  1.544  0.020  1.544
 P8Y  C1   C18  single  1.523  0.020  1.523
 P8Y  C16  C3   single  1.526  0.020  1.526
 P8Y  C16  S17  single  1.800  0.020  1.800
 P8Y  C6   C7   single  1.527  0.020  1.527
 P8Y  C3   N2   single  1.448  0.020  1.448
 P8Y  C18  S17  single  1.803  0.020  1.803
 P8Y  C7   N2   single  1.450  0.020  1.450
 P8Y  S17  O13  double  1.466  0.020  1.466
 P8Y  S17  O14  double  1.464  0.020  1.464
 P8Y  C1   H1   single  0.970  0.020  1.090
 P8Y  C1   H2   single  0.970  0.020  1.090
 P8Y  C11  H3   single  0.970  0.020  1.090
 P8Y  C11  H4   single  0.970  0.020  1.090
 P8Y  C11  H5   single  0.970  0.020  1.090
 P8Y  C16  H6   single  0.970  0.020  1.090
 P8Y  C16  H7   single  0.970  0.020  1.090
 P8Y  C18  H8   single  0.970  0.020  1.090
 P8Y  C18  H9   single  0.970  0.020  1.090
 P8Y  C2   H10  single  0.970  0.020  1.090
 P8Y  C2   H11  single  0.970  0.020  1.090
 P8Y  C3   H12  single  0.970  0.020  1.090
 P8Y  C4   H13  single  0.970  0.020  1.090
 P8Y  C5   H14  single  0.970  0.020  1.090
 P8Y  C6   H15  single  0.970  0.020  1.090
 P8Y  C7   H16  single  0.970  0.020  1.090
 P8Y  C7   H17  single  0.970  0.020  1.090
 P8Y  C8   H18  single  0.970  0.020  1.090
 P8Y  C9   H19  single  0.970  0.020  1.090
 P8Y  C9   H20  single  0.970  0.020  1.090
 P8Y  C9   H21  single  0.970  0.020  1.090
 P8Y  N2   H22  single  0.890  0.020  1.040
 P8Y  O10  H24  single  0.850  0.020  0.980
 P8Y  O12  H25  single  0.850  0.020  0.980
 P8Y  O8   H26  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
 P8Y  H2   C1   H1   105.39  3.000
 P8Y  H2   C1   C2   109.66  3.000
 P8Y  H1   C1   C2   109.32  3.000
 P8Y  H2   C1   C18  106.11  3.000
 P8Y  H1   C1   C18  108.85  3.000
 P8Y  C2   C1   C18  116.89  3.000
 P8Y  H5   C11  H4   107.73  3.000
 P8Y  H5   C11  H3   107.20  3.000
 P8Y  H4   C11  H3   107.77  3.000
 P8Y  H5   C11  C8   110.96  3.000
 P8Y  H4   C11  C8   111.04  3.000
 P8Y  H3   C11  C8   111.95  3.000
 P8Y  H7   C16  H6   107.38  3.000
 P8Y  H7   C16  S17  105.98  3.000
 P8Y  H6   C16  S17  107.94  3.000
 P8Y  H7   C16  C3   114.43  3.000
 P8Y  H6   C16  C3   109.80  3.000
 P8Y  S17  C16  C3   111.04  3.000
 P8Y  H9   C18  H8   106.96  3.000
 P8Y  H9   C18  S17  106.94  3.000
 P8Y  H8   C18  S17  103.14  3.000
 P8Y  H9   C18  C1   113.44  3.000
 P8Y  H8   C18  C1   109.90  3.000
 P8Y  S17  C18  C1   115.64  3.000
 P8Y  H11  C2   H10  104.89  3.000
 P8Y  H11  C2   C8   108.26  3.000
 P8Y  H10  C2   C8   109.82  3.000
 P8Y  H11  C2   C1   107.75  3.000
 P8Y  H10  C2   C1   109.64  3.000
 P8Y  C8   C2   C1   115.89  3.000
 P8Y  H12  C3   N2   107.04  3.000
 P8Y  H12  C3   C4   107.23  3.000
 P8Y  N2   C3   C4   112.79  3.000
 P8Y  H12  C3   C16  107.10  3.000
 P8Y  N2   C3   C16  111.21  3.000
 P8Y  C4   C3   C16  111.13  3.000
 P8Y  H13  C4   O12  110.53  3.000
 P8Y  H13  C4   C5   107.53  3.000
 P8Y  O12  C4   C5   108.64  3.000
 P8Y  H13  C4   C3   106.31  3.000
 P8Y  C5   C4   C3   111.25  3.000
 P8Y  O12  C4   C3   112.46  3.000
 P8Y  H14  C5   O8   110.27  3.000
 P8Y  H14  C5   C6   108.12  3.000
 P8Y  O8   C5   C6   111.56  3.000
 P8Y  H14  C5   C4   109.22  3.000
 P8Y  C6   C5   C4   109.49  3.000
 P8Y  O8   C5   C4   108.15  3.000
 P8Y  H15  C6   O10  110.63  3.000
 P8Y  H15  C6   C7   108.35  3.000
 P8Y  O10  C6   C7   112.14  3.000
 P8Y  H15  C6   C5   107.81  3.000
 P8Y  C7   C6   C5   110.68  3.000
 P8Y  O10  C6   C5   107.15  3.000
 P8Y  H17  C7   H16  106.35  3.000
 P8Y  H17  C7   N2   108.25  3.000
 P8Y  H16  C7   N2   109.52  3.000
 P8Y  H17  C7   C6   109.87  3.000
 P8Y  H16  C7   C6   109.67  3.000
 P8Y  N2   C7   C6   112.96  3.000
 P8Y  H18  C8   C9   107.30  3.000
 P8Y  H18  C8   C2   109.26  3.000
 P8Y  C9   C8   C2   109.89  3.000
 P8Y  H18  C8   C11  107.31  3.000
 P8Y  C2   C8   C11  111.74  3.000
 P8Y  C9   C8   C11  111.19  3.000
 P8Y  H21  C9   H20  107.88  3.000
 P8Y  H21  C9   H19  107.63  3.000
 P8Y  H20  C9   H19  107.57  3.000
 P8Y  H21  C9   C8   111.05  3.000
 P8Y  H20  C9   C8   111.38  3.000
 P8Y  H19  C9   C8   111.17  3.000
 P8Y  H22  N2   C7   110.23  3.000
 P8Y  H22  N2   C3   109.54  3.000
 P8Y  C7   N2   C3   113.76  3.000
 P8Y  H24  O10  C6   108.55  3.000
 P8Y  H25  O12  C4   108.34  3.000
 P8Y  H26  O8   C5   107.50  3.000
 P8Y  O14  S17  O13  118.33  3.000
 P8Y  O14  S17  C18  106.64  3.000
 P8Y  O13  S17  C18  108.26  3.000
 P8Y  O14  S17  C16  108.81  3.000
 P8Y  O13  S17  C16  108.85  3.000
 P8Y  C18  S17  C16  105.17  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
 P8Y  Var_01  C6   C7   N2   C3     53.31  30.0  1
 P8Y  Var_02  C3   C16  S17  C18   158.10  30.0  1
 P8Y  Var_03  C9   C8   C2   C1   -175.42  30.0  2
 P8Y  Var_04  C16  S17  C18  C1    -84.80  30.0  3
 P8Y  Var_05  C8   C2   C1   C18    57.62  30.0  2
 P8Y  Var_06  S17  C18  C1   C2     69.43  30.0  3
 P8Y  Var_07  H19  C9   C8   C11  -176.72  30.0  3
 P8Y  Var_08  H3   C11  C8   C2    -63.13  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
 P8Y  chir_01  C3  C4   C16  N2  negativ
 P8Y  chir_02  C4  O12  C3   C5  negativ
 P8Y  chir_03  C5  O8   C4   C6  positiv
 P8Y  chir_04  C6  O10  C5   C7  negativ

