# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:51:02 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
#   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]4C(CO)[C@@H]4C3
#
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
 S6J  S6J  6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile  ligand  45  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S6J
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
 S6J  C4   C  C     0  -0.005  -2.8891  -0.8928  14.7160
 S6J  C6   C  C     0  -0.300  -2.7423  -2.0411  15.7221
 S6J  C9   C  CR6   0  -0.151  -3.4806  -2.5203  18.7274
 S6J  C20  C  CH2   0  -0.260  -6.1414   1.6803  19.1202
 S6J  C21  C  CH1   0  -0.263  -6.2836   3.0019  21.3067
 S6J  C8   C  CR6   0   0.532  -3.7293  -1.3445  17.9728
 S6J  C18  C  CH1   0  -0.282  -6.9098   2.6330  19.9973
 S6J  C16  C  CH1   0  -0.294  -7.3011   1.9051  21.2476
 S6J  C1   C  CH3   0  -0.675  -2.9828   1.3161  16.1177
 S6J  C2   C  C     0  -0.061  -3.5475  -0.0567  15.8403
 S6J  N7   N  N     0  -0.499  -3.1606  -1.1168  16.7756
 S6J  C10  C  CR6   0  -0.031  -4.1620  -2.6422  19.9551
 S6J  C11  C  CR16  0  -0.529  -4.9975  -1.6611  20.4020
 S6J  C12  C  CR6   0   0.599  -5.1411  -0.5010  19.5911
 S6J  N13  N  N     0  -0.516  -4.5310  -0.3851  18.4175
 S6J  N14  N  NT    0  -0.509  -5.9117   0.5227  19.9773
 S6J  C15  C  CH2   0  -0.271  -6.7743   0.4967  21.1518
 S6J  O24  O  OH1   0  -0.672  -5.9305   5.3408  21.3505
 S6J  C25  C  CT    0   1.078  -3.9451  -3.8749  20.7887
 S6J  F26  F  F     0  -0.310  -4.2332  -4.9840  20.0996
 S6J  F27  F  F     0  -0.292  -4.6953  -3.8884  21.8892
 S6J  F28  F  F     0  -0.312  -2.6689  -3.9707  21.1787
 S6J  C29  C  CSP   0  -0.008  -2.5421  -3.4865  18.3060
 S6J  N30  N  NS    0  -0.270  -1.7591  -4.2693  17.9748
 S6J  O31  O  OH1   0  -0.659  -3.6623  -1.2246  13.6058
 S6J  H1   H  H     0   0.230  -1.9170  -0.4756  14.4294
 S6J  H2   H  H     0   0.251  -3.4587  -2.8504  15.5540
 S6J  H3   H  H     0   0.262  -1.7431  -2.4576  15.8357
 S6J  H4   H  HCH2  0   0.246  -6.7223   1.4037  18.2351
 S6J  H5   H  HCH2  0   0.259  -5.1916   2.0893  18.7722
 S6J  H6   H  HCH1  0   0.256  -5.2487   2.7021  21.4627
 S6J  H7   H  HCH1  0   0.269  -7.5835   3.3312  19.5165
 S6J  H8   H  HCH1  0   0.272  -8.2706   2.0494  21.7081
 S6J  H9   H  HCH3  0   0.249  -3.4452   1.7625  16.9970
 S6J  H10  H  HCH3  0   0.225  -1.9050   1.2720  16.2795
 S6J  H11  H  HCH3  0   0.234  -3.1727   1.9716  15.2661
 S6J  H12  H  H     0   0.244  -4.6352  -0.0105  15.7189
 S6J  H13  H  HCR6  0   0.291  -5.5256  -1.7523  21.3375
 S6J  H14  H  HCH2  0   0.255  -7.5962  -0.2151  21.0240
 S6J  H15  H  HCH2  0   0.257  -6.2124   0.2020  22.0413
 S6J  H16  H  HCH2  0   0.191  -7.7470   4.4531  21.8490
 S6J  H17  H  HCH2  0   0.209  -6.4595   4.2378  23.0319
 S6J  H18  H  HOH1  0   0.453  -6.1017   6.1491  21.8421
 S6J  H19  H  HOH1  0   0.457  -3.6805  -0.4705  13.0082
 S6J  C23  C  CH2   0  -0.149  -6.6645   4.2976  21.9560

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
 S6J  O31  C4   single    1.393  0.020  1.393
 S6J  C4   C6   single    1.534  0.020  1.534
 S6J  C4   C2   single    1.548  0.020  1.548
 S6J  C6   N7   single    1.463  0.020  1.463
 S6J  C2   C1   single    1.510  0.020  1.510
 S6J  C2   N7   single    1.466  0.020  1.466
 S6J  N7   C8   single    1.345  0.020  1.345
 S6J  C8   N13  aromatic  1.327  0.020  1.327
 S6J  C8   C9   aromatic  1.419  0.020  1.419
 S6J  N30  C29  triple    1.156  0.020  1.156
 S6J  C29  C9   single    1.411  0.020  1.411
 S6J  N13  C12  aromatic  1.328  0.020  1.328
 S6J  C9   C10  aromatic  1.409  0.020  1.409
 S6J  C20  C18  single    1.506  0.020  1.506
 S6J  C20  N14  single    1.459  0.020  1.459
 S6J  C12  N14  single    1.338  0.020  1.338
 S6J  C12  C11  aromatic  1.423  0.020  1.423
 S6J  C18  C21  single    1.498  0.020  1.498
 S6J  C18  C16  single    1.499  0.020  1.499
 S6J  N14  C15  single    1.457  0.020  1.457
 S6J  C10  C11  aromatic  1.364  0.020  1.364
 S6J  C10  C25  single    1.504  0.020  1.504
 S6J  F26  C25  single    1.337  0.020  1.337
 S6J  C25  F28  single    1.338  0.020  1.338
 S6J  C25  F27  single    1.332  0.020  1.332
 S6J  C15  C16  single    1.507  0.020  1.507
 S6J  C21  C16  single    1.497  0.020  1.497
 S6J  C21  C23  single    1.499  0.020  1.499
 S6J  O24  C23  single    1.412  0.020  1.412
 S6J  C4   H1   single    0.970  0.020  1.090
 S6J  C6   H2   single    0.970  0.020  1.090
 S6J  C6   H3   single    0.970  0.020  1.090
 S6J  C20  H4   single    0.970  0.020  1.090
 S6J  C20  H5   single    0.970  0.020  1.090
 S6J  C21  H6   single    0.970  0.020  1.090
 S6J  C18  H7   single    0.970  0.020  1.090
 S6J  C16  H8   single    0.970  0.020  1.090
 S6J  C1   H9   single    0.970  0.020  1.090
 S6J  C1   H10  single    0.970  0.020  1.090
 S6J  C1   H11  single    0.970  0.020  1.090
 S6J  C2   H12  single    0.970  0.020  1.090
 S6J  C11  H13  single    0.930  0.020  1.080
 S6J  C15  H14  single    0.970  0.020  1.090
 S6J  C15  H15  single    0.970  0.020  1.090
 S6J  C23  H16  single    0.970  0.020  1.090
 S6J  C23  H17  single    0.970  0.020  1.090
 S6J  O24  H18  single    0.850  0.020  0.980
 S6J  O31  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
 S6J  H1   C4   O31  112.00  3.000
 S6J  H1   C4   C2   111.19  3.000
 S6J  O31  C4   C2   118.12  3.000
 S6J  H1   C4   C6   111.82  3.000
 S6J  C2   C4   C6    88.20  3.000
 S6J  O31  C4   C6   113.43  3.000
 S6J  H3   C6   H2   109.52  3.000
 S6J  H3   C6   N7   115.41  3.000
 S6J  H2   C6   N7   113.02  3.000
 S6J  H3   C6   C4   116.28  3.000
 S6J  H2   C6   C4   112.99  3.000
 S6J  N7   C6   C4    88.40  3.000
 S6J  C29  C9   C10  121.49  3.000
 S6J  C10  C9   C8   116.75  3.000
 S6J  C29  C9   C8   121.67  3.000
 S6J  H5   C20  H4   107.39  3.000
 S6J  H5   C20  N14  110.36  3.000
 S6J  H4   C20  N14  111.00  3.000
 S6J  H5   C20  C18  113.13  3.000
 S6J  H4   C20  C18  111.11  3.000
 S6J  N14  C20  C18  103.90  3.000
 S6J  H6   C21  C23  114.69  3.000
 S6J  H6   C21  C16  116.74  3.000
 S6J  C23  C21  C16  118.54  3.000
 S6J  H6   C21  C18  117.06  3.000
 S6J  C23  C21  C18  119.05  3.000
 S6J  C16  C21  C18   60.06  3.000
 S6J  N13  C8   N7   115.56  3.000
 S6J  N13  C8   C9   121.78  3.000
 S6J  N7   C8   C9   122.65  3.000
 S6J  H7   C18  C16  121.41  3.000
 S6J  H7   C18  C21  119.31  3.000
 S6J  C16  C18  C21   59.96  3.000
 S6J  H7   C18  C20  117.82  3.000
 S6J  C16  C18  C20  108.17  3.000
 S6J  C21  C18  C20  116.86  3.000
 S6J  H8   C16  C15  117.69  3.000
 S6J  H8   C16  C18  121.58  3.000
 S6J  C15  C16  C18  108.04  3.000
 S6J  H8   C16  C21  119.60  3.000
 S6J  C15  C16  C21  116.72  3.000
 S6J  C18  C16  C21   59.98  3.000
 S6J  H11  C1   H10  108.18  3.000
 S6J  H11  C1   H9   108.06  3.000
 S6J  H10  C1   H9   108.44  3.000
 S6J  H11  C1   C2   109.73  3.000
 S6J  H10  C1   C2   111.10  3.000
 S6J  H9   C1   C2   111.23  3.000
 S6J  H12  C2   N7   111.31  3.000
 S6J  H12  C2   C1   110.69  3.000
 S6J  N7   C2   C1   116.21  3.000
 S6J  H12  C2   C4   111.38  3.000
 S6J  N7   C2   C4    87.74  3.000
 S6J  C1   C2   C4   117.73  3.000
 S6J  C2   N7   C8   125.37  3.000
 S6J  C8   N7   C6   130.93  3.000
 S6J  C2   N7   C6    94.18  3.000
 S6J  C25  C10  C11  119.76  3.000
 S6J  C25  C10  C9   118.95  3.000
 S6J  C11  C10  C9   121.29  3.000
 S6J  H13  C11  C12  120.94  3.000
 S6J  H13  C11  C10  121.56  3.000
 S6J  C12  C11  C10  117.49  3.000
 S6J  N14  C12  N13  116.93  3.000
 S6J  N14  C12  C11  121.16  3.000
 S6J  N13  C12  C11  121.91  3.000
 S6J  C12  N13  C8   120.71  3.000
 S6J  C15  N14  C12  124.03  3.000
 S6J  C15  N14  C20  113.24  3.000
 S6J  C12  N14  C20  121.88  3.000
 S6J  H15  C15  H14  107.81  3.000
 S6J  H15  C15  N14  110.89  3.000
 S6J  H14  C15  N14  111.21  3.000
 S6J  H15  C15  C16  112.34  3.000
 S6J  H14  C15  C16  110.65  3.000
 S6J  N14  C15  C16  103.97  3.000
 S6J  H18  O24  C23  108.03  3.000
 S6J  F28  C25  F27  107.20  3.000
 S6J  F27  C25  F26  107.22  3.000
 S6J  F28  C25  F26  107.24  3.000
 S6J  F27  C25  C10  112.65  3.000
 S6J  F28  C25  C10  110.97  3.000
 S6J  F26  C25  C10  111.30  3.000
 S6J  N30  C29  C9   180.00  3.000
 S6J  H19  O31  C4   108.59  3.000
 S6J  H17  C23  H16  106.69  3.000
 S6J  H17  C23  O24  111.33  3.000
 S6J  H16  C23  O24  111.46  3.000
 S6J  H17  C23  C21  109.28  3.000
 S6J  H16  C23  C21  109.31  3.000
 S6J  O24  C23  C21  108.72  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
 S6J  CONST_01  C12  N13  C8   C9      0.00   0.0  0
 S6J  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 S6J  CONST_03  C11  C12  N13  C8      0.00   0.0  0
 S6J  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 S6J  CONST_05  N13  C8   C9   C10     0.00   0.0  0
 S6J  CONST_06  N13  C12  C11  C10     0.00   0.0  0
 S6J  CONST_07  N14  C12  N13  C8    180.00   0.0  0
 S6J  CONST_08  C12  N13  C8   N7    180.00   0.0  0
 S6J  CONST_09  C10  C9   C8   N7    180.00   0.0  0
 S6J  CONST_10  N14  C12  C11  C10   180.00   0.0  0
 S6J  CONST_11  C25  C10  C9   C8    180.00   0.0  0
 S6J  CONST_12  C29  C9   C8   N7      0.00   0.0  0
 S6J  CONST_13  C29  C9   C10  C11   180.00   0.0  0
 S6J  CONST_14  C25  C10  C11  C12   180.00   0.0  0
 S6J  CONST_15  C29  C9   C8   N13   180.00   0.0  0
 S6J  CONST_16  H13  C11  C10  C9    180.00   0.0  0
 S6J  Var_01    C2   N7   C6   C4      9.49  30.0  1
 S6J  Var_02    N13  C8   N7   C6   -149.69  30.0  2
 S6J  Var_03    C16  C21  C18  C20   -96.37  30.0  1
 S6J  Var_04    C15  C16  C18  C20     0.10  30.0  1
 S6J  Var_05    N13  C12  N14  C20     3.62  30.0  1
 S6J  Var_06    C16  C15  N14  C20   -16.53  30.0  1
 S6J  Var_07    N14  C20  C18  C21    55.32  30.0  1
 S6J  Var_08    N14  C15  C16  C21   -55.41  30.0  1
 S6J  Var_09    C12  N14  C20  C18  -173.54  30.0  1
 S6J  Var_10    F26  C25  C10  C9    -56.61  30.0  2
 S6J  Var_11    O24  C23  C21  C18   -80.87  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
 S6J  chir_01  C4   O31  C6   C2   positiv
 S6J  chir_05  C2   C4   C1   N7   positiv
 S6J  chir_06  C21  C18  C16  C23  both
 S6J  chir_07  C18  C20  C21  C16  both
 S6J  chir_08  C16  C18  C15  C21  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
 S6J  plan-1  C9   0.020
 S6J  plan-1  C8   0.020
 S6J  plan-1  N7   0.020
 S6J  plan-1  C10  0.020
 S6J  plan-1  C11  0.020
 S6J  plan-1  C12  0.020
 S6J  plan-1  N13  0.020
 S6J  plan-1  N14  0.020
 S6J  plan-1  C25  0.020
 S6J  plan-1  C29  0.020
 S6J  plan-1  N30  0.020
 S6J  plan-1  H13  0.020

