# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:44:52 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-[(1~{R},5~{S})-3-[5-cyano-6-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridin-2-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](O)CN1c2nc(cc(c2C#N)C(F)(F)F)N3C[C@H]4[C@@H](C3)C4CC(O)=O
#
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
 S6S  S6S  '2-[(1~{R},5~{S})-3-[5-cyano-6-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridin-2-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid'  ligand  47  28  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S6S
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
 S6S  N3   N  NT    0  -0.510  -5.4229   0.7480  19.9940
 S6S  C4   C  C     0  -0.300  -2.2193  -1.5859  15.6298
 S6S  N2   N  N     0  -0.517  -4.0327  -0.0749  18.3950
 S6S  C7   C  CR6   0  -0.030  -3.6766  -2.4129  19.8099
 S6S  C6   C  CR6   0  -0.151  -2.9846  -2.2247  18.5970
 S6S  C9   C  CR6   0   0.600  -4.6528  -0.2547  19.5554
 S6S  C13  C  CH2   0  -0.259  -5.6271   1.9636  19.2148
 S6S  C8   C  CR16  0  -0.530  -4.5174  -1.4584  20.3013
 S6S  C18  C  CSP   0  -0.009  -2.0426  -3.1670  18.1320
 S6S  C2   C  C     0  -0.061  -3.0356   0.3860  15.8422
 S6S  C3   C  C     0  -0.006  -2.3686  -0.3901  14.6808
 S6S  N1   N  N     0  -0.499  -2.6528  -0.7193  16.7249
 S6S  C5   C  CR6   0   0.532  -3.2286  -1.0101  17.9044
 S6S  C10  C  CH2   0  -0.272  -6.2940   0.6578  21.1592
 S6S  C11  C  CH1   0  -0.294  -6.7980   2.0658  21.3467
 S6S  C12  C  CH1   0  -0.275  -6.3841   2.8688  20.1501
 S6S  C14  C  CH1   0  -0.208  -5.7564   3.1342  21.4805
 S6S  C15  C  CH2   0  -0.612  -6.1030   4.3940  22.2192
 S6S  O1   O  O     0  -0.439  -4.4822   5.5595  20.8692
 S6S  O2   O  OH1   0  -0.599  -5.5961   6.6761  22.4457
 S6S  F1   F  F     0  -0.312  -2.1879  -3.8011  20.9708
 S6S  F2   F  F     0  -0.292  -4.2186  -3.7596  21.6730
 S6S  F3   F  F     0  -0.310  -3.7438  -4.7597  19.8316
 S6S  N4   N  NS    0  -0.270  -1.2595  -3.9329  17.7632
 S6S  O3   O  OH1   0  -0.659  -3.1379  -0.6712  13.5541
 S6S  H1   H  H     0   0.251  -2.9264  -2.3925  15.4155
 S6S  H2   H  H     0   0.262  -1.2172  -1.9990  15.7296
 S6S  H3   H  HCH2  0   0.258  -4.6681   2.3803  18.9036
 S6S  H4   H  HCH2  0   0.245  -6.2068   1.7582  18.3098
 S6S  H5   H  HCR6  0   0.291  -5.0526  -1.6023  21.2261
 S6S  H6   H  HCH3  0   0.249  -2.9443   2.1409  17.0931
 S6S  H7   H  HCH3  0   0.225  -1.3987   1.6943  16.3584
 S6S  H8   H  HCH3  0   0.234  -2.6638   2.4430  15.3774
 S6S  H9   H  H     0   0.244  -4.1225   0.4369  15.7155
 S6S  H10  H  H     0   0.230  -1.3984   0.0461  14.4173
 S6S  H11  H  HCH2  0   0.255  -7.1250  -0.0319  20.9802
 S6S  H12  H  HCH2  0   0.257  -5.7423   0.2984  22.0310
 S6S  H13  H  HCH1  0   0.271  -7.7660   2.1967  21.8142
 S6S  H14  H  HCH1  0   0.268  -7.0387   3.6127  19.7135
 S6S  H15  H  HCH1  0   0.261  -4.7314   2.7962  21.6152
 S6S  H16  H  HCH2  0   0.285  -7.1658   4.6345  22.1106
 S6S  H17  H  HCH2  0   0.293  -5.9410   4.2696  23.2943
 S6S  H18  H  HOH1  0   0.478  -5.0615   7.4201  22.1306
 S6S  H19  H  HOH1  0   0.457  -3.1609   0.1116  12.9949
 S6S  C17  C  CT    0   1.078  -3.4624  -3.6872  20.5792
 S6S  C16  C  C     0   0.562  -5.3005   5.5796  21.7536
 S6S  C1   C  CH3   0  -0.674  -2.4759   1.7438  16.1939

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
 S6S  O3   C3   single    1.393  0.020  1.393
 S6S  C3   C4   single    1.534  0.020  1.534
 S6S  C3   C2   single    1.548  0.020  1.548
 S6S  C4   N1   single    1.462  0.020  1.462
 S6S  C2   C1   single    1.510  0.020  1.510
 S6S  C2   N1   single    1.465  0.020  1.465
 S6S  N1   C5   single    1.344  0.020  1.344
 S6S  N4   C18  triple    1.156  0.020  1.156
 S6S  C5   N2   aromatic  1.327  0.020  1.327
 S6S  C5   C6   aromatic  1.419  0.020  1.419
 S6S  C18  C6   single    1.411  0.020  1.411
 S6S  N2   C9   aromatic  1.328  0.020  1.328
 S6S  C6   C7   aromatic  1.409  0.020  1.409
 S6S  C13  N3   single    1.458  0.020  1.458
 S6S  C13  C12  single    1.506  0.020  1.506
 S6S  C9   N3   single    1.338  0.020  1.338
 S6S  C9   C8   aromatic  1.422  0.020  1.422
 S6S  C7   C8   aromatic  1.364  0.020  1.364
 S6S  C7   C17  single    1.504  0.020  1.504
 S6S  N3   C10  single    1.458  0.020  1.458
 S6S  C12  C11  single    1.499  0.020  1.499
 S6S  C12  C14  single    1.495  0.020  1.495
 S6S  F3   C17  single    1.337  0.020  1.337
 S6S  C17  F1   single    1.338  0.020  1.338
 S6S  C17  F2   single    1.332  0.020  1.332
 S6S  O1   C16  double    1.205  0.020  1.205
 S6S  C10  C11  single    1.507  0.020  1.507
 S6S  C11  C14  single    1.498  0.020  1.498
 S6S  C14  C15  single    1.501  0.020  1.501
 S6S  C16  C15  single    1.505  0.020  1.505
 S6S  C16  O2   single    1.330  0.020  1.330
 S6S  C4   H1   single    0.970  0.020  1.090
 S6S  C4   H2   single    0.970  0.020  1.090
 S6S  C13  H3   single    0.970  0.020  1.090
 S6S  C13  H4   single    0.970  0.020  1.090
 S6S  C8   H5   single    0.930  0.020  1.080
 S6S  C1   H6   single    0.970  0.020  1.090
 S6S  C1   H7   single    0.970  0.020  1.090
 S6S  C1   H8   single    0.970  0.020  1.090
 S6S  C2   H9   single    0.970  0.020  1.090
 S6S  C3   H10  single    0.970  0.020  1.090
 S6S  C10  H11  single    0.970  0.020  1.090
 S6S  C10  H12  single    0.970  0.020  1.090
 S6S  C11  H13  single    0.970  0.020  1.090
 S6S  C12  H14  single    0.970  0.020  1.090
 S6S  C14  H15  single    0.970  0.020  1.090
 S6S  C15  H16  single    0.970  0.020  1.090
 S6S  C15  H17  single    0.970  0.020  1.090
 S6S  O2   H18  single    0.850  0.020  0.980
 S6S  O3   H19  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
 S6S  C10  N3   C13  113.27  3.000
 S6S  C10  N3   C9   124.02  3.000
 S6S  C13  N3   C9   122.01  3.000
 S6S  H2   C4   H1   109.46  3.000
 S6S  H2   C4   N1   115.41  3.000
 S6S  H1   C4   N1   113.09  3.000
 S6S  H2   C4   C3   116.24  3.000
 S6S  H1   C4   C3   113.01  3.000
 S6S  N1   C4   C3    88.42  3.000
 S6S  C5   N2   C9   120.70  3.000
 S6S  C17  C7   C8   119.78  3.000
 S6S  C17  C7   C6   118.92  3.000
 S6S  C8   C7   C6   121.30  3.000
 S6S  C5   C6   C18  121.69  3.000
 S6S  C18  C6   C7   121.48  3.000
 S6S  C5   C6   C7   116.74  3.000
 S6S  C8   C9   N2   121.89  3.000
 S6S  C8   C9   N3   121.13  3.000
 S6S  N2   C9   N3   116.98  3.000
 S6S  H4   C13  H3   107.54  3.000
 S6S  H4   C13  C12  111.12  3.000
 S6S  H3   C13  C12  112.92  3.000
 S6S  H4   C13  N3   111.08  3.000
 S6S  H3   C13  N3   110.34  3.000
 S6S  C12  C13  N3   103.87  3.000
 S6S  H5   C8   C9   121.03  3.000
 S6S  H5   C8   C7   121.45  3.000
 S6S  C9   C8   C7   117.52  3.000
 S6S  N4   C18  C6   180.00  3.000
 S6S  H9   C2   N1   111.34  3.000
 S6S  H9   C2   C3   111.35  3.000
 S6S  N1   C2   C3    87.77  3.000
 S6S  H9   C2   C1   110.67  3.000
 S6S  N1   C2   C1   116.17  3.000
 S6S  C3   C2   C1   117.76  3.000
 S6S  H10  C3   O3   112.01  3.000
 S6S  H10  C3   C2   111.24  3.000
 S6S  O3   C3   C2   118.04  3.000
 S6S  H10  C3   C4   111.90  3.000
 S6S  C2   C3   C4    88.20  3.000
 S6S  O3   C3   C4   113.38  3.000
 S6S  C5   N1   C2   125.43  3.000
 S6S  C5   N1   C4   130.98  3.000
 S6S  C2   N1   C4    94.21  3.000
 S6S  N1   C5   C6   122.66  3.000
 S6S  C6   C5   N2   121.78  3.000
 S6S  N1   C5   N2   115.55  3.000
 S6S  H12  C10  H11  107.85  3.000
 S6S  H12  C10  C11  112.14  3.000
 S6S  H11  C10  C11  110.80  3.000
 S6S  H12  C10  N3   110.89  3.000
 S6S  H11  C10  N3   111.22  3.000
 S6S  C11  C10  N3   103.97  3.000
 S6S  H13  C11  C14  119.78  3.000
 S6S  H13  C11  C12  121.77  3.000
 S6S  C14  C11  C12   59.83  3.000
 S6S  H13  C11  C10  117.74  3.000
 S6S  C14  C11  C10  116.42  3.000
 S6S  C12  C11  C10  107.98  3.000
 S6S  H14  C12  C14  119.38  3.000
 S6S  H14  C12  C11  121.52  3.000
 S6S  C14  C12  C11   60.04  3.000
 S6S  H14  C12  C13  117.81  3.000
 S6S  C14  C12  C13  116.65  3.000
 S6S  C11  C12  C13  108.21  3.000
 S6S  H15  C14  C15  114.67  3.000
 S6S  H15  C14  C12  116.79  3.000
 S6S  C15  C14  C12  119.35  3.000
 S6S  H15  C14  C11  116.40  3.000
 S6S  C15  C14  C11  118.82  3.000
 S6S  C12  C14  C11   60.13  3.000
 S6S  H17  C15  H16  105.44  3.000
 S6S  H17  C15  C14  110.73  3.000
 S6S  H16  C15  C14  111.07  3.000
 S6S  H17  C15  C16  108.33  3.000
 S6S  H16  C15  C16  108.28  3.000
 S6S  C14  C15  C16  112.69  3.000
 S6S  H18  O2   C16  109.96  3.000
 S6S  H19  O3   C3   108.61  3.000
 S6S  F3   C17  F2   107.22  3.000
 S6S  F2   C17  F1   107.21  3.000
 S6S  F3   C17  F1   107.20  3.000
 S6S  F2   C17  C7   112.67  3.000
 S6S  F1   C17  C7   110.95  3.000
 S6S  F3   C17  C7   111.33  3.000
 S6S  O2   C16  O1   123.13  3.000
 S6S  O2   C16  C15  111.71  3.000
 S6S  O1   C16  C15  125.16  3.000
 S6S  H8   C1   H7   108.18  3.000
 S6S  H8   C1   H6   108.07  3.000
 S6S  H7   C1   H6   108.47  3.000
 S6S  H8   C1   C2   109.75  3.000
 S6S  H7   C1   C2   111.12  3.000
 S6S  H6   C1   C2   111.15  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
 S6S  CONST_01  C7   C6   C5   N2      0.00   0.0  0
 S6S  CONST_02  C7   C8   C9   N2      0.00   0.0  0
 S6S  CONST_03  C9   N2   C5   C6      0.00   0.0  0
 S6S  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 S6S  CONST_05  C5   N2   C9   C8      0.00   0.0  0
 S6S  CONST_06  C5   C6   C7   C8      0.00   0.0  0
 S6S  CONST_07  C5   N2   C9   N3    180.00   0.0  0
 S6S  CONST_08  C7   C8   C9   N3    180.00   0.0  0
 S6S  CONST_09  N1   C5   C6   C7    180.00   0.0  0
 S6S  CONST_10  N1   C5   N2   C9    180.00   0.0  0
 S6S  CONST_11  C18  C6   C5   N2    180.00   0.0  0
 S6S  CONST_12  C17  C7   C8   C9    180.00   0.0  0
 S6S  CONST_13  C18  C6   C7   C8    180.00   0.0  0
 S6S  CONST_14  N1   C5   C6   C18     0.00   0.0  0
 S6S  CONST_15  C17  C7   C6   C5    180.00   0.0  0
 S6S  CONST_16  H5   C8   C9   N3      0.00   0.0  0
 S6S  CONST_17  H18  O2   C16  C15   180.00   0.0  0
 S6S  Var_01    C11  C12  C13  N3     -9.66  30.0  1
 S6S  Var_02    C12  C11  C10  N3      9.38  30.0  1
 S6S  Var_03    N2   C5   N1   C4   -150.21  30.0  2
 S6S  Var_04    C13  N3   C9   N2      2.65  30.0  2
 S6S  Var_05    C12  C13  N3   C9   -172.56  30.0  1
 S6S  Var_06    C11  C10  N3   C9    172.87  30.0  1
 S6S  Var_07    C10  C11  C12  C13     0.19  30.0  1
 S6S  Var_08    C3   C4   N1   C2      9.21  30.0  1
 S6S  Var_09    F3   C17  C7   C6    -56.79  30.0  2
 S6S  Var_10    O1   C16  C15  C14     1.45  30.0  2

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
 S6S  chir_01  C2   C3   C1   N1   positiv
 S6S  chir_02  C3   O3   C4   C2   positiv
 S6S  chir_03  C11  C12  C10  C14  both
 S6S  chir_04  C12  C14  C11  C13  both
 S6S  chir_05  C14  C12  C11  C15  both

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
 S6S  plan-1  N3   0.020
 S6S  plan-1  N2   0.020
 S6S  plan-1  C7   0.020
 S6S  plan-1  C6   0.020
 S6S  plan-1  C9   0.020
 S6S  plan-1  C8   0.020
 S6S  plan-1  C18  0.020
 S6S  plan-1  N1   0.020
 S6S  plan-1  C5   0.020
 S6S  plan-1  N4   0.020
 S6S  plan-1  H5   0.020
 S6S  plan-1  C17  0.020
 S6S  plan-2  C15  0.020
 S6S  plan-2  O1   0.020
 S6S  plan-2  O2   0.020
 S6S  plan-2  H18  0.020
 S6S  plan-2  C16  0.020

