# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:42:27 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 4-{[(5R,7S)-1-(3-fluorophenyl)-3,7-dimethyl-2,2-dioxido-2-thia-1,3,8-triazaspiro[4.5]dec-8-yl]methyl}-2-(propan-2-yloxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1cc(CN2CC[C@@]3(C[C@@H]2C)CN(C)[S](=O)(=O)N3c4cccc(F)c4)ccc1O
#
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
 0UP  0UP  4-{[(5R,7S)-1-(3-fluorophenyl)-3,7-dimethyl-2,2-dioxido-2-thia-1,3,8-triazaspiro[4.5]dec-8-yl]methyl}-2-(propan-2-yloxy)phenol  ligand  65  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0UP
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
 0UP  C1   C  CR16  0  -0.243   3.1222   3.1915   0.6062
 0UP  C2   C  CR16  0  -0.336  -3.7126   2.3592   0.9782
 0UP  C3   C  CR16  0  -0.261   3.0159   1.8417   0.9087
 0UP  C4   C  CR16  0  -0.333  -4.9367   2.4131   0.3172
 0UP  C5   C  CR16  0  -0.399   3.0341   3.6310  -0.7066
 0UP  C6   C  CR16  0  -0.398  -3.6216  -0.0065   0.6176
 0UP  C7   C  CR16  0  -0.407   2.7540   1.3399  -1.4367
 0UP  C8   C  CR6   0   0.061  -3.0485   1.1547   1.1392
 0UP  C9   C  CR6   0   0.298   2.8091   0.9202  -0.1111
 0UP  C10  C  CR6   0   0.250  -5.5004   1.2644  -0.2074
 0UP  C11  C  CR6   0   0.327  -4.8281   0.0390  -0.0601
 0UP  C12  C  CR6   0   0.530   2.8540   2.6903  -1.7030
 0UP  C13  C  CH2   0  -0.455   0.3292  -0.7218  -0.6144
 0UP  C14  C  CH2   0  -0.361   0.9693  -1.5048   1.6503
 0UP  C15  C  CH2   0  -0.279   1.9758  -2.6057  -0.3811
 0UP  C16  C  CH2   0  -0.292  -0.3834   0.4359   0.0617
 0UP  C17  C  CH1   0  -0.054   0.2515  -0.2998   2.2555
 0UP  C18  C  CT    0   0.091   1.4661  -1.2953   0.2180
 0UP  C19  C  CH3   0  -0.698  -0.1994  -0.6709   3.6634
 0UP  C20  C  CH3   0  -0.676  -4.8271  -3.1877   0.2558
 0UP  C21  C  CH3   0  -0.659  -5.3324  -2.8025  -2.1782
 0UP  C24  C  CH1   0   0.008  -4.7353  -2.2206  -0.9120
 0UP  N25  N  N     0  -0.766   2.6934  -0.4564   0.2018
 0UP  N26  N  N     0  -0.591   3.2972  -2.7904   0.1986
 0UP  N27  N  NT    0  -0.425  -0.8606   0.0648   1.3820
 0UP  O30  O  OH1   0  -0.636  -6.6773   1.3393  -0.8664
 0UP  O31  O  O2    0  -0.506  -5.4548  -1.0150  -0.6302
 0UP  F32  F  F     0  -0.312   2.7883   3.1012  -2.9780
 0UP  S33  S  S     0   1.534   4.0895  -1.3335   0.1838
 0UP  H1   H  HCR6  0   0.277   3.2719   3.9113   1.3992
 0UP  H2   H  HCR6  0   0.243  -3.2791   3.2741   1.3638
 0UP  H3   H  HCR6  0   0.270   3.0768   1.5017   1.9332
 0UP  H4   H  HCR6  0   0.259  -5.4476   3.3594   0.1871
 0UP  H5   H  HCR6  0   0.288   3.1097   4.6822  -0.9512
 0UP  H6   H  HCR6  0   0.261  -3.0839  -0.9382   0.7400
 0UP  H7   H  HCR6  0   0.288   2.6340   0.6285  -2.2422
 0UP  H8   H  HCH2  0   0.256  -0.3942  -1.5314  -0.7513
 0UP  H9   H  HCH2  0   0.256   0.6680  -0.4348  -1.6106
 0UP  H10  H  HCH2  0   0.241   1.8048  -1.7946   2.2906
 0UP  H11  H  HCH2  0   0.228   0.2628  -2.3413   1.6457
 0UP  H12  H  HCH2  0   0.282   1.3411  -3.4457  -0.1007
 0UP  H13  H  HCH2  0   0.258   2.0097  -2.5477  -1.4777
 0UP  H14  H  HCH2  0   0.212   0.2661   1.3247   0.1076
 0UP  H15  H  HCH2  0   0.255  -1.2369   0.7153  -0.5581
 0UP  H16  H  HCH1  0   0.200   0.9685   0.5358   2.3415
 0UP  H17  H  HCH3  0   0.240   0.6330  -1.1170   4.2084
 0UP  H18  H  HCH3  0   0.240  -0.5343   0.1862   4.2459
 0UP  H19  H  HCH3  0   0.227  -1.0103  -1.4010   3.6290
 0UP  H20  H  HCH3  0   0.239  -4.3923  -2.7829   1.1697
 0UP  H21  H  HCH3  0   0.233  -5.8658  -3.4507   0.4614
 0UP  H22  H  HCH3  0   0.236  -4.2905  -4.1055   0.0137
 0UP  H23  H  HCH3  0   0.230  -6.3841  -3.0584  -2.0396
 0UP  H24  H  HCH3  0   0.241  -5.2514  -2.1044  -3.0115
 0UP  H25  H  HCH3  0   0.234  -4.7995  -3.7133  -2.4507
 0UP  H26  H  HCH3  0   0.241   4.2338  -3.9326  -1.3387
 0UP  H27  H  HCH3  0   0.262   5.0443  -3.9472   0.2432
 0UP  H28  H  HCH3  0   0.270   3.5463  -4.8365   0.0241
 0UP  H29  H  HCH2  0   0.208  -1.2851   2.0789   1.9323
 0UP  H30  H  HCH2  0   0.260  -1.9913   0.8341   2.9428
 0UP  H31  H  HCH1  0   0.225  -3.6856  -1.9703  -1.1033
 0UP  H33  H  HOH1  0   0.467  -6.9153   0.4657  -1.2011
 0UP  O28  O  OS    0  -0.653   4.8328  -1.0931  -1.0469
 0UP  C22  C  CH3   0  -0.528   4.0774  -3.9298  -0.2570
 0UP  C23  C  CH2   0  -0.310  -1.7513   1.0787   1.9075
 0UP  O29  O  OS    0  -0.648   4.8586  -1.1791   1.4065

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
 0UP  C20  C24  single    1.519  0.020  1.519
 0UP  C23  C8   single    1.510  0.020  1.510
 0UP  C23  N27  single    1.448  0.020  1.448
 0UP  C24  C21  single    1.516  0.020  1.516
 0UP  C24  O31  single    1.432  0.020  1.432
 0UP  C8   C6   aromatic  1.396  0.020  1.396
 0UP  C8   C2   aromatic  1.385  0.020  1.385
 0UP  C6   C11  aromatic  1.385  0.020  1.385
 0UP  C2   C4   aromatic  1.392  0.020  1.392
 0UP  C11  O31  single    1.352  0.020  1.352
 0UP  C11  C10  aromatic  1.405  0.020  1.405
 0UP  N27  C16  single    1.452  0.020  1.452
 0UP  N27  C17  single    1.460  0.020  1.460
 0UP  C19  C17  single    1.524  0.020  1.524
 0UP  C4   C10  aromatic  1.383  0.020  1.383
 0UP  C10  O30  single    1.351  0.020  1.351
 0UP  C16  C13  single    1.518  0.020  1.518
 0UP  C17  C14  single    1.528  0.020  1.528
 0UP  C13  C18  single    1.521  0.020  1.521
 0UP  C14  C18  single    1.530  0.020  1.530
 0UP  C18  C15  single    1.528  0.020  1.528
 0UP  C18  N25  single    1.487  0.020  1.487
 0UP  C15  N26  single    1.455  0.020  1.455
 0UP  C3   C1   aromatic  1.387  0.020  1.387
 0UP  C3   C9   aromatic  1.390  0.020  1.390
 0UP  C1   C5   aromatic  1.387  0.020  1.387
 0UP  C9   N25  single    1.416  0.020  1.416
 0UP  C9   C7   aromatic  1.392  0.020  1.392
 0UP  N25  S33  single    1.649  0.020  1.649
 0UP  C5   C12  aromatic  1.382  0.020  1.382
 0UP  C7   C12  aromatic  1.380  0.020  1.380
 0UP  C12  F32  single    1.341  0.020  1.341
 0UP  N26  S33  single    1.658  0.020  1.658
 0UP  N26  C22  single    1.454  0.020  1.454
 0UP  S33  O28  double    1.458  0.020  1.458
 0UP  S33  O29  double    1.453  0.020  1.453
 0UP  C1   H1   single    0.930  0.020  1.080
 0UP  C2   H2   single    0.930  0.020  1.080
 0UP  C3   H3   single    0.930  0.020  1.080
 0UP  C4   H4   single    0.930  0.020  1.080
 0UP  C5   H5   single    0.930  0.020  1.080
 0UP  C6   H6   single    0.930  0.020  1.080
 0UP  C7   H7   single    0.930  0.020  1.080
 0UP  C13  H8   single    0.970  0.020  1.090
 0UP  C13  H9   single    0.970  0.020  1.090
 0UP  C14  H10  single    0.970  0.020  1.090
 0UP  C14  H11  single    0.970  0.020  1.090
 0UP  C15  H12  single    0.970  0.020  1.090
 0UP  C15  H13  single    0.970  0.020  1.090
 0UP  C16  H14  single    0.970  0.020  1.090
 0UP  C16  H15  single    0.970  0.020  1.090
 0UP  C17  H16  single    0.970  0.020  1.090
 0UP  C19  H17  single    0.970  0.020  1.090
 0UP  C19  H18  single    0.970  0.020  1.090
 0UP  C19  H19  single    0.970  0.020  1.090
 0UP  C20  H20  single    0.970  0.020  1.090
 0UP  C20  H21  single    0.970  0.020  1.090
 0UP  C20  H22  single    0.970  0.020  1.090
 0UP  C21  H23  single    0.970  0.020  1.090
 0UP  C21  H24  single    0.970  0.020  1.090
 0UP  C21  H25  single    0.970  0.020  1.090
 0UP  C22  H26  single    0.970  0.020  1.090
 0UP  C22  H27  single    0.970  0.020  1.090
 0UP  C22  H28  single    0.970  0.020  1.090
 0UP  C23  H29  single    0.970  0.020  1.090
 0UP  C23  H30  single    0.970  0.020  1.090
 0UP  C24  H31  single    0.970  0.020  1.090
 0UP  O30  H33  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
 0UP  H1   C1   C5   119.47  3.000
 0UP  H1   C1   C3   119.89  3.000
 0UP  C5   C1   C3   120.64  3.000
 0UP  H2   C2   C8   120.08  3.000
 0UP  H2   C2   C4   119.21  3.000
 0UP  C8   C2   C4   120.70  3.000
 0UP  H3   C3   C9   119.68  3.000
 0UP  H3   C3   C1   120.54  3.000
 0UP  C9   C3   C1   119.77  3.000
 0UP  H4   C4   C10  119.20  3.000
 0UP  H4   C4   C2   120.37  3.000
 0UP  C10  C4   C2   120.42  3.000
 0UP  H5   C5   C12  120.49  3.000
 0UP  H5   C5   C1   121.15  3.000
 0UP  C12  C5   C1   118.36  3.000
 0UP  H6   C6   C11  121.09  3.000
 0UP  H6   C6   C8   118.01  3.000
 0UP  C11  C6   C8   120.88  3.000
 0UP  H7   C7   C12  120.54  3.000
 0UP  H7   C7   C9   121.03  3.000
 0UP  C12  C7   C9   118.43  3.000
 0UP  C23  C8   C6   120.07  3.000
 0UP  C6   C8   C2   118.89  3.000
 0UP  C23  C8   C2   121.00  3.000
 0UP  N25  C9   C7   120.02  3.000
 0UP  C7   C9   C3   120.32  3.000
 0UP  N25  C9   C3   119.64  3.000
 0UP  O30  C10  C11  121.07  3.000
 0UP  O30  C10  C4   119.61  3.000
 0UP  C11  C10  C4   119.31  3.000
 0UP  O31  C11  C10  114.44  3.000
 0UP  C10  C11  C6   119.79  3.000
 0UP  O31  C11  C6   125.78  3.000
 0UP  F32  C12  C7   118.66  3.000
 0UP  F32  C12  C5   118.90  3.000
 0UP  C7   C12  C5   122.44  3.000
 0UP  H9   C13  H8   106.61  3.000
 0UP  H9   C13  C18  111.52  3.000
 0UP  H8   C13  C18  106.47  3.000
 0UP  H9   C13  C16  110.60  3.000
 0UP  H8   C13  C16  108.04  3.000
 0UP  C18  C13  C16  113.24  3.000
 0UP  H11  C14  H10  107.07  3.000
 0UP  H11  C14  C18  108.06  3.000
 0UP  H10  C14  C18  109.68  3.000
 0UP  H11  C14  C17  107.53  3.000
 0UP  H10  C14  C17  109.67  3.000
 0UP  C18  C14  C17  114.54  3.000
 0UP  H13  C15  H12  108.39  3.000
 0UP  H13  C15  N26  112.11  3.000
 0UP  H12  C15  N26  109.19  3.000
 0UP  H13  C15  C18  110.87  3.000
 0UP  H12  C15  C18  111.46  3.000
 0UP  N26  C15  C18  104.81  3.000
 0UP  H15  C16  H14  106.15  3.000
 0UP  H15  C16  N27  108.96  3.000
 0UP  H14  C16  N27  111.23  3.000
 0UP  H15  C16  C13  108.02  3.000
 0UP  H14  C16  C13  110.92  3.000
 0UP  N27  C16  C13  111.36  3.000
 0UP  H16  C17  N27  110.62  3.000
 0UP  H16  C17  C19  107.72  3.000
 0UP  N27  C17  C19  112.83  3.000
 0UP  H16  C17  C14  108.82  3.000
 0UP  C19  C17  C14  108.23  3.000
 0UP  N27  C17  C14  108.53  3.000
 0UP  N25  C18  C15  101.78  3.000
 0UP  N25  C18  C14  110.82  3.000
 0UP  C15  C18  C14  110.96  3.000
 0UP  N25  C18  C13  113.47  3.000
 0UP  C15  C18  C13  110.98  3.000
 0UP  C14  C18  C13  108.73  3.000
 0UP  H19  C19  H18  108.34  3.000
 0UP  H19  C19  H17  108.01  3.000
 0UP  H18  C19  H17  106.82  3.000
 0UP  H19  C19  C17  110.70  3.000
 0UP  H18  C19  C17  113.16  3.000
 0UP  H17  C19  C17  109.61  3.000
 0UP  H22  C20  H21  107.90  3.000
 0UP  H22  C20  H20  107.61  3.000
 0UP  H21  C20  H20  108.13  3.000
 0UP  H22  C20  C24  109.60  3.000
 0UP  H21  C20  C24  110.85  3.000
 0UP  H20  C20  C24  112.58  3.000
 0UP  H25  C21  H24  107.92  3.000
 0UP  H25  C21  H23  107.89  3.000
 0UP  H24  C21  H23  108.60  3.000
 0UP  H25  C21  C24  109.69  3.000
 0UP  H24  C21  C24  111.30  3.000
 0UP  H23  C21  C24  111.31  3.000
 0UP  H31  C24  O31  108.86  3.000
 0UP  H31  C24  C21  108.61  3.000
 0UP  O31  C24  C21  106.84  3.000
 0UP  H31  C24  C20  109.72  3.000
 0UP  O31  C24  C20  110.76  3.000
 0UP  C21  C24  C20  111.96  3.000
 0UP  S33  N25  C18  113.51  3.000
 0UP  S33  N25  C9   116.45  3.000
 0UP  C18  N25  C9   128.19  3.000
 0UP  S33  N26  C22  115.42  3.000
 0UP  C22  N26  C15  117.52  3.000
 0UP  S33  N26  C15  108.59  3.000
 0UP  C23  N27  C17  115.22  3.000
 0UP  C17  N27  C16  110.94  3.000
 0UP  C23  N27  C16  110.68  3.000
 0UP  H33  O30  C10  109.50  3.000
 0UP  C24  O31  C11  120.42  3.000
 0UP  O29  S33  O28  115.03  3.000
 0UP  O29  S33  N26  109.80  3.000
 0UP  O28  S33  N26  113.33  3.000
 0UP  O29  S33  N25  112.49  3.000
 0UP  O28  S33  N25  110.69  3.000
 0UP  N26  S33  N25   93.60  3.000
 0UP  H28  C22  H27  107.56  3.000
 0UP  H28  C22  H26  108.87  3.000
 0UP  H27  C22  H26  109.13  3.000
 0UP  H28  C22  N26  108.07  3.000
 0UP  H27  C22  N26  110.19  3.000
 0UP  H26  C22  N26  112.88  3.000
 0UP  H30  C23  H29  105.96  3.000
 0UP  H30  C23  N27  108.83  3.000
 0UP  H29  C23  N27  112.50  3.000
 0UP  H30  C23  C8   107.78  3.000
 0UP  H29  C23  C8   109.20  3.000
 0UP  N27  C23  C8   112.28  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
 0UP  CONST_01  C7   C9   C3   C1      0.00   0.0  0
 0UP  CONST_02  C7   C12  C5   C1      0.00   0.0  0
 0UP  CONST_03  C11  C6   C8   C2      0.00   0.0  0
 0UP  CONST_04  C11  C10  C4   C2      0.00   0.0  0
 0UP  CONST_05  C12  C5   C1   C3      0.00   0.0  0
 0UP  CONST_06  C12  C7   C9   C3      0.00   0.0  0
 0UP  CONST_07  C6   C8   C2   C4      0.00   0.0  0
 0UP  CONST_08  C6   C11  C10  C4      0.00   0.0  0
 0UP  CONST_09  C9   C3   C1   C5      0.00   0.0  0
 0UP  CONST_10  C9   C7   C12  C5      0.00   0.0  0
 0UP  CONST_11  C10  C11  C6   C8      0.00   0.0  0
 0UP  CONST_12  C10  C4   C2   C8      0.00   0.0  0
 0UP  CONST_13  N25  C9   C3   C1    180.00   0.0  0
 0UP  CONST_14  N25  C9   C7   C12   180.00   0.0  0
 0UP  CONST_15  F32  C12  C5   C1    180.00   0.0  0
 0UP  CONST_16  O30  C10  C4   C2    180.00   0.0  0
 0UP  CONST_17  C23  C8   C2   C4    180.00   0.0  0
 0UP  CONST_18  O31  C11  C10  C4    180.00   0.0  0
 0UP  CONST_19  O30  C10  C11  C6    180.00   0.0  0
 0UP  CONST_20  O31  C11  C6   C8    180.00   0.0  0
 0UP  CONST_21  F32  C12  C7   C9    180.00   0.0  0
 0UP  CONST_22  C23  C8   C6   C11   180.00   0.0  0
 0UP  CONST_23  H6   C6   C8   C2    180.00   0.0  0
 0UP  CONST_24  H5   C5   C1   C3    180.00   0.0  0
 0UP  CONST_25  H7   C7   C9   C3    180.00   0.0  0
 0UP  CONST_26  H3   C3   C1   C5    180.00   0.0  0
 0UP  CONST_27  H2   C2   C8   C6    180.00   0.0  0
 0UP  CONST_28  H4   C4   C2   C8    180.00   0.0  0
 0UP  CONST_29  H1   C1   C3   C9    180.00   0.0  0
 0UP  Var_01    C18  N25  C9   C3    105.56  30.0  2
 0UP  Var_02    N26  S33  N25  C9   -165.95  30.0  1
 0UP  Var_03    C17  N27  C16  C13    61.76  30.0  1
 0UP  Var_04    N25  S33  N26  C15    25.71  30.0  1
 0UP  Var_05    N27  C16  C13  C18   -54.91  30.0  1
 0UP  Var_06    S33  N26  C15  C18   -42.85  30.0  1
 0UP  Var_07    N27  C23  C8   C2   -147.16  30.0  1
 0UP  Var_08    C16  N27  C23  C8     67.80  30.0  3
 0UP  Var_09    H26  C22  N26  C15    57.10  30.0  3
 0UP  Var_10    C20  C24  O31  C11    91.47  30.0  2
 0UP  Var_11    H23  C21  C24  C20    59.30  30.0  3
 0UP  Var_12    H20  C20  C24  C21   179.48  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
 0UP  chir_01  C17  N27  C19  C14  negativ
 0UP  chir_02  C18  C15  C14  C13  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
 0UP  plan-1  C1   0.020
 0UP  plan-1  C3   0.020
 0UP  plan-1  C5   0.020
 0UP  plan-1  C7   0.020
 0UP  plan-1  C9   0.020
 0UP  plan-1  C12  0.020
 0UP  plan-1  N25  0.020
 0UP  plan-1  F32  0.020
 0UP  plan-1  H1   0.020
 0UP  plan-1  H3   0.020
 0UP  plan-1  H5   0.020
 0UP  plan-1  H7   0.020
 0UP  plan-2  C9   0.020
 0UP  plan-2  C18  0.020
 0UP  plan-2  N25  0.020
 0UP  plan-2  S33  0.020
 0UP  plan-3  C2   0.020
 0UP  plan-3  C4   0.020
 0UP  plan-3  C6   0.020
 0UP  plan-3  C8   0.020
 0UP  plan-3  C10  0.020
 0UP  plan-3  C11  0.020
 0UP  plan-3  O30  0.020
 0UP  plan-3  O31  0.020
 0UP  plan-3  H2   0.020
 0UP  plan-3  H4   0.020
 0UP  plan-3  H6   0.020
 0UP  plan-3  C23  0.020
 0UP  plan-4  C15  0.020
 0UP  plan-4  N26  0.020
 0UP  plan-4  S33  0.020
 0UP  plan-4  C22  0.020

