# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:25:05 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-[[(3~{R})-oxan-3-yl]methylsulfonyl]-2-azaspiro[4.5]decane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=[S](=O)(C[C@@H]1CCCOC1)N2CCC3(CCCCC3)C2
#
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
 H6E  H6E  2-[[(3~{R})-oxan-3-yl]methylsulfonyl]-2-azaspiro[4.5]decane  ligand  47  20  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H6E
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
 H6E  C4   C  CH2   0  -0.632  -1.5547   0.0593   0.4728
 H6E  C5   C  CH1   0  -0.280  -2.9431   0.4706  -0.0035
 H6E  C6   C  CH2   0  -0.432  -3.5432   1.4369   1.0217
 H6E  C7   C  CH2   0  -0.461  -4.9744   1.7947   0.6432
 H6E  C8   C  CH2   0  -0.181  -5.7825   0.5279   0.4271
 H6E  O9   O  O2    0  -0.485  -5.1853  -0.3082  -0.5422
 H6E  C12  C  CH2   0  -0.289   1.2731  -1.7165   1.0444
 H6E  C15  C  CH2   0  -0.423   3.6903   1.1867   1.0519
 H6E  C16  C  CH2   0  -0.438   4.3845   1.9592  -0.0641
 H6E  C17  C  CH2   0  -0.429   5.3730   1.0729  -0.8129
 H6E  C18  C  CH2   0  -0.439   4.6969  -0.1852  -1.3439
 H6E  C19  C  CH2   0  -0.409   3.9730  -0.9478  -0.2382
 H6E  S2   S  S     0   1.371  -0.6189  -0.9291  -0.6995
 H6E  O3   O  OS    0  -0.672  -0.6258  -0.2280  -1.9773
 H6E  C10  C  CH2   0  -0.148  -3.8854  -0.7187  -0.1894
 H6E  N11  N  N     0  -0.587   0.9197  -0.9378  -0.1560
 H6E  C13  C  CH2   0  -0.448   2.3522  -0.8637   1.7004
 H6E  C14  C  CT    0  -0.125   2.9875  -0.0734   0.5515
 H6E  C20  C  CH2   0  -0.247   1.7488   0.2637  -0.2900
 H6E  H1   H  HCH2  0   0.302  -0.9555   0.9533   0.6630
 H6E  H2   H  HCH2  0   0.294  -1.6010  -0.5112   1.4039
 H6E  H3   H  HCH1  0   0.256  -2.8475   0.9970  -0.9586
 H6E  H4   H  HCH2  0   0.224  -3.5368   0.9629   2.0098
 H6E  H5   H  HCH2  0   0.247  -2.9245   2.3340   1.0973
 H6E  H6   H  HCH2  0   0.240  -5.4409   2.3947   1.4276
 H6E  H7   H  HCH2  0   0.227  -4.9817   2.3982  -0.2691
 H6E  H8   H  HCH2  0   0.196  -5.8848  -0.0083   1.3825
 H6E  H9   H  HCH2  0   0.236  -6.7876   0.7570   0.0694
 H6E  H11  H  HCH2  0   0.257   1.6424  -2.7002   0.7525
 H6E  H12  H  HCH2  0   0.226   4.4350   0.9001   1.8029
 H6E  H13  H  HCH2  0   0.229   2.9662   1.8261   1.5667
 H6E  H14  H  HCH2  0   0.217   3.6408   2.3561  -0.7637
 H6E  H15  H  HCH2  0   0.231   4.8991   2.8272   0.3550
 H6E  H16  H  HCH2  0   0.228   5.8339   1.6276  -1.6338
 H6E  H17  H  HCH2  0   0.209   6.1855   0.7894  -0.1349
 H6E  H18  H  HCH2  0   0.215   3.9916   0.0857  -2.1356
 H6E  H19  H  HCH2  0   0.232   5.4343  -0.8406  -1.8136
 H6E  H20  H  HCH2  0   0.238   3.4567  -1.8147  -0.6609
 H6E  H21  H  HCH2  0   0.223   4.7131  -1.3473   0.4636
 H6E  H22  H  HCH2  0   0.238  -3.5443  -1.3745  -0.9906
 H6E  H23  H  HCH2  0   0.195  -3.9007  -1.3121   0.7387
 H6E  H24  H  HCH2  0   0.246   1.8936  -0.1699   2.4109
 H6E  H25  H  HCH2  0   0.255   3.0759  -1.4678   2.2491
 H6E  H26  H  HCH2  0   0.267   1.9696   0.4600  -1.3383
 H6E  H27  H  HCH2  0   0.239   1.2526   1.1532   0.1210
 H6E  H10  H  HCH2  0   0.256   0.4219  -1.8699   1.7106
 H6E  O1   O  OS    0  -0.667  -1.1009  -2.3040  -0.6434

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
 H6E  C19  C18  single  1.526  0.020  1.526
 H6E  C19  C14  single  1.536  0.020  1.536
 H6E  C18  C17  single  1.524  0.020  1.524
 H6E  C17  C16  single  1.524  0.020  1.524
 H6E  C13  C14  single  1.532  0.020  1.532
 H6E  C13  C12  single  1.524  0.020  1.524
 H6E  C14  C20  single  1.535  0.020  1.535
 H6E  C14  C15  single  1.527  0.020  1.527
 H6E  O3   S2   double  1.458  0.020  1.458
 H6E  C20  N11  single  1.466  0.020  1.466
 H6E  O1   S2   double  1.458  0.020  1.458
 H6E  N11  S2   single  1.632  0.020  1.632
 H6E  N11  C12  single  1.474  0.020  1.474
 H6E  S2   C4   single  1.796  0.020  1.796
 H6E  C15  C16  single  1.525  0.020  1.525
 H6E  C4   C5   single  1.524  0.020  1.524
 H6E  C5   C6   single  1.531  0.020  1.531
 H6E  C5   C10  single  1.529  0.020  1.529
 H6E  C6   C7   single  1.523  0.020  1.523
 H6E  C10  O9   single  1.408  0.020  1.408
 H6E  C7   C8   single  1.518  0.020  1.518
 H6E  O9   C8   single  1.413  0.020  1.413
 H6E  C4   H1   single  0.970  0.020  1.090
 H6E  C4   H2   single  0.970  0.020  1.090
 H6E  C5   H3   single  0.970  0.020  1.090
 H6E  C6   H4   single  0.970  0.020  1.090
 H6E  C6   H5   single  0.970  0.020  1.090
 H6E  C7   H6   single  0.970  0.020  1.090
 H6E  C7   H7   single  0.970  0.020  1.090
 H6E  C8   H8   single  0.970  0.020  1.090
 H6E  C8   H9   single  0.970  0.020  1.090
 H6E  C12  H10  single  0.970  0.020  1.090
 H6E  C12  H11  single  0.970  0.020  1.090
 H6E  C15  H12  single  0.970  0.020  1.090
 H6E  C15  H13  single  0.970  0.020  1.090
 H6E  C16  H14  single  0.970  0.020  1.090
 H6E  C16  H15  single  0.970  0.020  1.090
 H6E  C17  H16  single  0.970  0.020  1.090
 H6E  C17  H17  single  0.970  0.020  1.090
 H6E  C18  H18  single  0.970  0.020  1.090
 H6E  C18  H19  single  0.970  0.020  1.090
 H6E  C19  H20  single  0.970  0.020  1.090
 H6E  C19  H21  single  0.970  0.020  1.090
 H6E  C10  H22  single  0.970  0.020  1.090
 H6E  C10  H23  single  0.970  0.020  1.090
 H6E  C13  H24  single  0.970  0.020  1.090
 H6E  C13  H25  single  0.970  0.020  1.090
 H6E  C20  H26  single  0.970  0.020  1.090
 H6E  C20  H27  single  0.970  0.020  1.090

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
 H6E  H2   C4   H1   107.58  3.000
 H6E  H2   C4   S2   106.91  3.000
 H6E  H1   C4   S2   106.14  3.000
 H6E  H2   C4   C5   111.62  3.000
 H6E  H1   C4   C5   109.45  3.000
 H6E  S2   C4   C5   114.77  3.000
 H6E  H3   C5   C10  108.78  3.000
 H6E  H3   C5   C6   108.35  3.000
 H6E  C10  C5   C6   109.32  3.000
 H6E  H3   C5   C4   108.83  3.000
 H6E  C10  C5   C4   112.93  3.000
 H6E  C6   C5   C4   108.54  3.000
 H6E  H5   C6   H4   106.83  3.000
 H6E  H5   C6   C7   110.89  3.000
 H6E  H4   C6   C7   109.34  3.000
 H6E  H5   C6   C5   110.04  3.000
 H6E  H4   C6   C5   109.17  3.000
 H6E  C7   C6   C5   110.49  3.000
 H6E  H7   C7   H6   107.04  3.000
 H6E  H7   C7   C8   109.77  3.000
 H6E  H6   C7   C8   109.47  3.000
 H6E  H7   C7   C6   110.07  3.000
 H6E  H6   C7   C6   110.60  3.000
 H6E  C8   C7   C6   109.85  3.000
 H6E  H9   C8   H8   107.53  3.000
 H6E  H9   C8   O9   106.78  3.000
 H6E  H8   C8   O9   110.29  3.000
 H6E  H9   C8   C7   111.21  3.000
 H6E  H8   C8   C7   109.43  3.000
 H6E  O9   C8   C7   111.50  3.000
 H6E  C10  O9   C8   113.01  3.000
 H6E  H11  C12  H10  107.50  3.000
 H6E  H11  C12  C13  112.35  3.000
 H6E  H10  C12  C13  111.59  3.000
 H6E  H11  C12  N11  109.86  3.000
 H6E  H10  C12  N11  112.60  3.000
 H6E  C13  C12  N11  102.99  3.000
 H6E  H13  C15  H12  106.26  3.000
 H6E  H13  C15  C14  109.37  3.000
 H6E  H12  C15  C14  108.75  3.000
 H6E  H13  C15  C16  110.46  3.000
 H6E  H12  C15  C16  108.95  3.000
 H6E  C14  C15  C16  112.82  3.000
 H6E  H15  C16  H14  106.07  3.000
 H6E  H15  C16  C17  110.18  3.000
 H6E  H14  C16  C17  109.71  3.000
 H6E  H15  C16  C15  109.65  3.000
 H6E  H14  C16  C15  109.99  3.000
 H6E  C17  C16  C15  111.12  3.000
 H6E  H17  C17  H16  106.47  3.000
 H6E  H17  C17  C18  109.33  3.000
 H6E  H16  C17  C18  110.15  3.000
 H6E  H17  C17  C16  109.11  3.000
 H6E  H16  C17  C16  110.33  3.000
 H6E  C18  C17  C16  111.32  3.000
 H6E  H19  C18  H18  105.81  3.000
 H6E  H19  C18  C19  109.39  3.000
 H6E  H18  C18  C19  110.01  3.000
 H6E  H19  C18  C17  110.22  3.000
 H6E  H18  C18  C17  109.49  3.000
 H6E  C19  C18  C17  111.75  3.000
 H6E  H21  C19  H20  106.11  3.000
 H6E  H21  C19  C14  108.16  3.000
 H6E  H20  C19  C14  110.30  3.000
 H6E  H21  C19  C18  109.03  3.000
 H6E  H20  C19  C18  109.87  3.000
 H6E  C14  C19  C18  113.11  3.000
 H6E  N11  S2   O3   107.40  3.000
 H6E  N11  S2   O1   107.09  3.000
 H6E  O3   S2   O1   119.06  3.000
 H6E  N11  S2   C4   106.07  3.000
 H6E  O1   S2   C4   108.75  3.000
 H6E  O3   S2   C4   107.76  3.000
 H6E  H23  C10  H22  107.42  3.000
 H6E  H23  C10  O9   110.81  3.000
 H6E  H22  C10  O9   106.27  3.000
 H6E  H23  C10  C5   108.97  3.000
 H6E  H22  C10  C5   111.38  3.000
 H6E  O9   C10  C5   111.88  3.000
 H6E  C20  N11  S2   119.90  3.000
 H6E  S2   N11  C12  120.01  3.000
 H6E  C20  N11  C12  111.83  3.000
 H6E  H25  C13  H24  107.62  3.000
 H6E  H25  C13  C14  112.81  3.000
 H6E  H24  C13  C14  109.49  3.000
 H6E  H25  C13  C12  112.12  3.000
 H6E  H24  C13  C12  109.74  3.000
 H6E  C14  C13  C12  105.04  3.000
 H6E  C20  C14  C13  100.93  3.000
 H6E  C20  C14  C19  111.16  3.000
 H6E  C13  C14  C19  110.97  3.000
 H6E  C20  C14  C15  111.71  3.000
 H6E  C13  C14  C15  111.76  3.000
 H6E  C19  C14  C15  110.05  3.000
 H6E  H27  C20  H26  107.80  3.000
 H6E  H27  C20  C14  109.71  3.000
 H6E  H26  C20  C14  113.80  3.000
 H6E  H27  C20  N11  111.96  3.000
 H6E  H26  C20  N11  110.51  3.000
 H6E  C14  C20  N11  103.08  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
 H6E  Var_01  C8   C7   C6   C5     52.84  30.0  1
 H6E  Var_02  O9   C8   C7   C6    -55.93  30.0  1
 H6E  Var_03  C19  C14  C13  C12   -78.59  30.0  3
 H6E  Var_04  C14  C20  N11  C12    21.69  30.0  1
 H6E  Var_05  C18  C19  C14  C15   -52.35  30.0  1
 H6E  Var_06  N11  C20  C14  C15  -155.41  30.0  3
 H6E  Var_07  C18  C17  C16  C15    55.17  30.0  1
 H6E  Var_08  C19  C18  C17  C16   -54.06  30.0  1
 H6E  Var_09  C14  C19  C18  C17    53.35  30.0  1
 H6E  Var_10  C14  C15  C16  C17   -55.90  30.0  1
 H6E  Var_11  C14  C13  C12  N11   -26.52  30.0  1
 H6E  Var_12  C20  N11  C12  C13     2.84  30.0  1
 H6E  Var_13  N11  S2   C4   C5    166.48  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
 H6E  chir_01  C5  C4  C6  C10  positiv

