# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 09:39:25 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}-[3-[(9~{S})-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#C[C@@]1(N=C(N)OCC12CC(F)(F)C2)c3cc(NC(=O)c4ccc(cn4)C#N)ccc3F
#
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
 GX6  GX6  ~{N}-[3-[(9~{S})-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide  ligand  51  33  .  2022-03-18  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GX6
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
 GX6  C1   C  CR6   0   0.523  20.0111  38.3796   -9.1876
 GX6  C2   C  CR16  0  -0.394  21.3160  38.7552   -8.9465
 GX6  C3   C  CR16  0  -0.310  21.6449  39.4703   -7.8064
 GX6  C4   C  CR6   0   0.421  20.6373  39.7927   -6.9016
 GX6  C5   C  C     0   0.542  21.9825  40.9688   -5.1845
 GX6  C6   C  CR6   0   0.143  21.7737  41.7218   -3.8969
 GX6  N1   N  NH1   0  -0.765  20.8358  40.5082   -5.7183
 GX6  N2   N  N     0  -0.436  20.5265  41.8467   -3.4562
 GX6  N3   N  NS    0  -0.228  20.8086  44.4080    0.5437
 GX6  O1   O  O     0  -0.443  23.0990  40.8289   -5.6492
 GX6  C7   C  CR16  0  -0.016  20.3029  42.5143   -2.3435
 GX6  C8   C  CR6   0  -0.080  21.3385  43.0964   -1.6101
 GX6  C9   C  CSP   0   0.058  21.0473  43.8214   -0.4178
 GX6  C10  C  CR16  0  -0.114  22.6466  42.9609   -2.0641
 GX6  C11  C  CR16  0  -0.281  22.8683  42.2569   -3.2333
 GX6  C12  C  CR16  0  -0.434  19.3284  39.3900   -7.1693
 GX6  C13  C  CR6   0  -0.021  18.9728  38.6954   -8.3177
 GX6  C14  C  CT    0  -0.123  17.4984  38.3233   -8.5718
 GX6  C15  C  CSP   0   0.325  17.4271  36.9355   -9.0523
 GX6  O2   O  O2    0  -0.455  16.0259  40.5732   -7.7134
 GX6  F1   F  F     0  -0.308  19.7733  37.6767  -10.3067
 GX6  C16  C  CSP   0  -0.169  17.3512  35.7948   -9.4239
 GX6  C17  C  CH3   0  -0.833  17.2785  34.4129   -9.8718
 GX6  C18  C  C     0  -0.183  16.8474  39.2971   -9.5877
 GX6  C19  C  C     0  -0.567  17.3629  39.3881  -11.0415
 GX6  C20  C  C     0   0.749  15.9139  39.3733  -11.4964
 GX6  F2   F  F     0  -0.337  15.6165  38.6032  -12.5734
 GX6  F3   F  F     0  -0.340  15.4329  40.6150  -11.7953
 GX6  C21  C  C     0  -0.544  15.4586  38.8705  -10.1381
 GX6  C22  C  CH2   0  -0.150  16.7794  40.6529   -8.9191
 GX6  C23  C  C     0   0.635  16.0959  39.4253   -7.0289
 GX6  N4   N  NH2   0  -0.828  15.4023  39.5094   -5.8676
 GX6  N5   N  N     0  -0.473  16.7443  38.3683   -7.3364
 GX6  H1   H  HCR6  0   0.281  22.0867  38.4857   -9.6571
 GX6  H2   H  HCR6  0   0.290  22.6701  39.7575   -7.6420
 GX6  H3   H  HNH1  0   0.427  20.0056  40.7227   -5.1779
 GX6  H4   H  HCR6  0   0.301  19.2750  42.6004   -2.0117
 GX6  H5   H  HCR6  0   0.304  23.4700  43.3978   -1.5158
 GX6  H6   H  HCR6  0   0.295  23.8684  42.1303   -3.6208
 GX6  H7   H  HCR6  0   0.292  18.5665  39.6202   -6.4375
 GX6  H8   H  HCH3  0   0.265  16.7526  34.3359  -10.8238
 GX6  H9   H  HCH3  0   0.265  18.2752  33.9922  -10.0069
 GX6  H10  H  HCH3  0   0.265  16.7497  33.7921   -9.1484
 GX6  H11  H  H     0   0.287  17.8633  38.4748  -11.3548
 GX6  H12  H  H     0   0.280  17.9728  40.2495  -11.3162
 GX6  H13  H  H     0   0.279  14.5711  39.3353   -9.7086
 GX6  H14  H  H     0   0.285  15.3333  37.7874  -10.1418
 GX6  H15  H  HCH2  0   0.262  17.7795  41.0405   -8.7036
 GX6  H16  H  HCH2  0   0.268  16.2716  41.3896   -9.5397
 GX6  H17  H  HNH2  0   0.396  14.6779  40.2051   -5.7951
 GX6  H18  H  HNH2  0   0.394  15.2022  38.6361   -5.4095

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
 GX6  F2   C20  single    1.357  0.020  1.357
 GX6  F3   C20  single    1.365  0.020  1.365
 GX6  C20  C19  single    1.519  0.020  1.519
 GX6  C20  C21  single    1.518  0.020  1.518
 GX6  C19  C18  single    1.545  0.020  1.545
 GX6  F1   C1   single    1.343  0.020  1.343
 GX6  C21  C18  single    1.554  0.020  1.554
 GX6  C17  C16  single    1.454  0.020  1.454
 GX6  C18  C22  single    1.513  0.020  1.513
 GX6  C18  C14  single    1.551  0.020  1.551
 GX6  C16  C15  triple    1.202  0.020  1.202
 GX6  C1   C2   aromatic  1.379  0.020  1.379
 GX6  C1   C13  aromatic  1.391  0.020  1.391
 GX6  C22  O2   single    1.424  0.020  1.424
 GX6  C15  C14  single    1.470  0.020  1.470
 GX6  C2   C3   aromatic  1.385  0.020  1.385
 GX6  C14  C13  single    1.542  0.020  1.542
 GX6  C14  N5   single    1.448  0.020  1.448
 GX6  C13  C12  aromatic  1.388  0.020  1.388
 GX6  O2   C23  single    1.338  0.020  1.338
 GX6  C3   C4   aromatic  1.392  0.020  1.392
 GX6  N5   C23  double    1.278  0.020  1.278
 GX6  C12  C4   aromatic  1.395  0.020  1.395
 GX6  C23  N4   single    1.355  0.020  1.355
 GX6  C4   N1   single    1.397  0.020  1.397
 GX6  N1   C5   single    1.346  0.020  1.346
 GX6  O1   C5   double    1.217  0.020  1.217
 GX6  C5   C6   single    1.506  0.020  1.506
 GX6  C6   C11  aromatic  1.387  0.020  1.387
 GX6  C6   N2   aromatic  1.329  0.020  1.329
 GX6  C11  C10  aromatic  1.383  0.020  1.383
 GX6  N2   C7   aromatic  1.317  0.020  1.317
 GX6  C10  C8   aromatic  1.391  0.020  1.391
 GX6  C7   C8   aromatic  1.396  0.020  1.396
 GX6  C8   C9   single    1.426  0.020  1.426
 GX6  C9   N3   triple    1.151  0.020  1.151
 GX6  C2   H1   single    0.930  0.020  1.080
 GX6  C3   H2   single    0.930  0.020  1.080
 GX6  N1   H3   single    0.860  0.020  1.020
 GX6  C7   H4   single    0.930  0.020  1.080
 GX6  C10  H5   single    0.930  0.020  1.080
 GX6  C11  H6   single    0.930  0.020  1.080
 GX6  C12  H7   single    0.930  0.020  1.080
 GX6  C17  H8   single    0.970  0.020  1.090
 GX6  C17  H9   single    0.970  0.020  1.090
 GX6  C17  H10  single    0.970  0.020  1.090
 GX6  C19  H11  single    0.970  0.020  1.090
 GX6  C19  H12  single    0.970  0.020  1.090
 GX6  C21  H13  single    0.970  0.020  1.090
 GX6  C21  H14  single    0.970  0.020  1.090
 GX6  C22  H15  single    0.970  0.020  1.090
 GX6  C22  H16  single    0.970  0.020  1.090
 GX6  N4   H17  single    0.890  0.020  1.040
 GX6  N4   H18  single    0.890  0.020  1.040

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
 GX6  F1   C1   C13  120.53  3.000
 GX6  C13  C1   C2   122.35  3.000
 GX6  F1   C1   C2   117.12  3.000
 GX6  H1   C2   C3   119.98  3.000
 GX6  H1   C2   C1   119.42  3.000
 GX6  C3   C2   C1   120.60  3.000
 GX6  H2   C3   C4   121.86  3.000
 GX6  H2   C3   C2   119.28  3.000
 GX6  C4   C3   C2   118.86  3.000
 GX6  C12  C4   N1   116.33  3.000
 GX6  N1   C4   C3   124.50  3.000
 GX6  C12  C4   C3   119.17  3.000
 GX6  O1   C5   N1   126.19  3.000
 GX6  O1   C5   C6   120.72  3.000
 GX6  N1   C5   C6   113.08  3.000
 GX6  C11  C6   N2   123.07  3.000
 GX6  N2   C6   C5   117.43  3.000
 GX6  C11  C6   C5   119.50  3.000
 GX6  H3   N1   C5   114.45  3.000
 GX6  H3   N1   C4   116.34  3.000
 GX6  C5   N1   C4   129.21  3.000
 GX6  C7   N2   C6   119.17  3.000
 GX6  H4   C7   C8   120.65  3.000
 GX6  H4   C7   N2   117.40  3.000
 GX6  C8   C7   N2   121.95  3.000
 GX6  C10  C8   C9   120.97  3.000
 GX6  C9   C8   C7   119.99  3.000
 GX6  C10  C8   C7   119.04  3.000
 GX6  C8   C9   N3   180.00  3.000
 GX6  H5   C10  C11  120.82  3.000
 GX6  H5   C10  C8   120.73  3.000
 GX6  C11  C10  C8   118.44  3.000
 GX6  H6   C11  C10  120.77  3.000
 GX6  H6   C11  C6   120.92  3.000
 GX6  C10  C11  C6   118.32  3.000
 GX6  H7   C12  C13  119.07  3.000
 GX6  H7   C12  C4   118.02  3.000
 GX6  C13  C12  C4   122.91  3.000
 GX6  C14  C13  C12  120.13  3.000
 GX6  C12  C13  C1   116.09  3.000
 GX6  C14  C13  C1   123.78  3.000
 GX6  N5   C14  C18  108.71  3.000
 GX6  N5   C14  C15  106.43  3.000
 GX6  C18  C14  C15  110.99  3.000
 GX6  N5   C14  C13  110.48  3.000
 GX6  C15  C14  C13  109.15  3.000
 GX6  C18  C14  C13  110.98  3.000
 GX6  C16  C15  C14  180.00  3.000
 GX6  C23  O2   C22  116.96  3.000
 GX6  C17  C16  C15  180.00  3.000
 GX6  H10  C17  H9   107.82  3.000
 GX6  H10  C17  H8   107.77  3.000
 GX6  H9   C17  H8   107.79  3.000
 GX6  H10  C17  C16  111.16  3.000
 GX6  H9   C17  C16  111.05  3.000
 GX6  H8   C17  C16  111.10  3.000
 GX6  C22  C18  C21  111.25  3.000
 GX6  C22  C18  C19  112.20  3.000
 GX6  C21  C18  C19   88.92  3.000
 GX6  C22  C18  C14  106.98  3.000
 GX6  C21  C18  C14  115.79  3.000
 GX6  C19  C18  C14  120.89  3.000
 GX6  H12  C19  H11  109.48  3.000
 GX6  H12  C19  C20  117.76  3.000
 GX6  H11  C19  C20  110.15  3.000
 GX6  H12  C19  C18  118.04  3.000
 GX6  H11  C19  C18  112.03  3.000
 GX6  C20  C19  C18   87.87  3.000
 GX6  C21  C20  F3   113.05  3.000
 GX6  C21  C20  F2   117.15  3.000
 GX6  F3   C20  F2   105.38  3.000
 GX6  C21  C20  C19   91.23  3.000
 GX6  F3   C20  C19  113.14  3.000
 GX6  F2   C20  C19  116.89  3.000
 GX6  H14  C21  H13  109.35  3.000
 GX6  H14  C21  C20  111.13  3.000
 GX6  H13  C21  C20  117.09  3.000
 GX6  H14  C21  C18  112.13  3.000
 GX6  H13  C21  C18  118.11  3.000
 GX6  C20  C21  C18   87.59  3.000
 GX6  H16  C22  H15  107.39  3.000
 GX6  H16  C22  C18  112.04  3.000
 GX6  H15  C22  C18  111.31  3.000
 GX6  H16  C22  O2   105.89  3.000
 GX6  H15  C22  O2   109.68  3.000
 GX6  C18  C22  O2   110.35  3.000
 GX6  N5   C23  N4   121.15  3.000
 GX6  N4   C23  O2   111.00  3.000
 GX6  N5   C23  O2   127.81  3.000
 GX6  H18  N4   H17  115.07  3.000
 GX6  H18  N4   C23  115.98  3.000
 GX6  H17  N4   C23  118.21  3.000
 GX6  C23  N5   C14  119.69  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
 GX6  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 GX6  CONST_02  C4   C12  C13  C1      0.00   0.0  0
 GX6  CONST_03  C12  C13  C1   C2      0.00   0.0  0
 GX6  CONST_04  C12  C4   C3   C2      0.00   0.0  0
 GX6  CONST_05  C13  C1   C2   C3      0.00   0.0  0
 GX6  CONST_06  C13  C12  C4   C3      0.00   0.0  0
 GX6  CONST_07  C8   C10  C11  C6      0.00   0.0  0
 GX6  CONST_08  C8   C7   N2   C6      0.00   0.0  0
 GX6  CONST_09  C10  C11  C6   N2      0.00   0.0  0
 GX6  CONST_10  C10  C8   C7   N2      0.00   0.0  0
 GX6  CONST_11  C11  C6   N2   C7      0.00   0.0  0
 GX6  CONST_12  C11  C10  C8   C7      0.00   0.0  0
 GX6  CONST_13  C14  C13  C1   C2    180.00   0.0  0
 GX6  CONST_14  C14  C13  C12  C4    180.00   0.0  0
 GX6  CONST_15  O2   C23  N5   C14     0.00   0.0  0
 GX6  CONST_16  N1   C4   C3   C2    180.00   0.0  0
 GX6  CONST_17  F1   C1   C2   C3    180.00   0.0  0
 GX6  CONST_18  C10  C11  C6   C5    180.00   0.0  0
 GX6  CONST_19  C7   N2   C6   C5    180.00   0.0  0
 GX6  CONST_20  C13  C12  C4   N1    180.00   0.0  0
 GX6  CONST_21  C9   C8   C7   N2    180.00   0.0  0
 GX6  CONST_22  C11  C10  C8   C9    180.00   0.0  0
 GX6  CONST_23  F1   C1   C13  C12   180.00   0.0  0
 GX6  CONST_24  F1   C1   C13  C14     0.00   0.0  0
 GX6  CONST_25  N4   C23  N5   C14   180.00   0.0  0
 GX6  CONST_26  H2   C3   C2   C1    180.00   0.0  0
 GX6  CONST_27  H7   C12  C13  C1    180.00   0.0  0
 GX6  CONST_28  H1   C2   C3   C4    180.00   0.0  0
 GX6  CONST_29  H5   C10  C11  C6    180.00   0.0  0
 GX6  CONST_30  H4   C7   N2   C6    180.00   0.0  0
 GX6  CONST_31  H6   C11  C6   N2    180.00   0.0  0
 GX6  CONST_32  C6   C5   N1   C4    180.00   0.0  0
 GX6  CONST_33  C5   N1   C4   C3      0.00   0.0  0
 GX6  CONST_34  C12  C4   N1   C5    180.00   0.0  0
 GX6  CONST_35  H3   N1   C4   C3    180.00   0.0  0
 GX6  CONST_38  O1   C5   N1   C4      0.00   0.0  0
 GX6  Var_01    C20  C19  C18  C14   135.32  30.0  3
 GX6  Var_02    C20  C21  C18  C14  -139.74  30.0  3
 GX6  Var_03    O2   C22  C18  C14   -58.44  30.0  1
 GX6  Var_04    C21  C20  C19  C18   -15.98  30.0  1
 GX6  Var_05    N5   C23  O2   C22    -1.34  30.0  1
 GX6  Var_06    C11  C6   C5   N1   -179.91  30.0  2
 GX6  Var_07    H8   C17  C16  C15  -126.32  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
 GX6  chir_01  C14  C18  C13  N5  negativ

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
 GX6  plan-1  C1   0.020
 GX6  plan-1  C2   0.020
 GX6  plan-1  C3   0.020
 GX6  plan-1  C4   0.020
 GX6  plan-1  N1   0.020
 GX6  plan-1  C12  0.020
 GX6  plan-1  C13  0.020
 GX6  plan-1  C14  0.020
 GX6  plan-1  F1   0.020
 GX6  plan-1  H1   0.020
 GX6  plan-1  H2   0.020
 GX6  plan-1  H7   0.020
 GX6  plan-2  C5   0.020
 GX6  plan-2  C6   0.020
 GX6  plan-2  N2   0.020
 GX6  plan-2  N3   0.020
 GX6  plan-2  C7   0.020
 GX6  plan-2  C8   0.020
 GX6  plan-2  C9   0.020
 GX6  plan-2  C10  0.020
 GX6  plan-2  C11  0.020
 GX6  plan-2  H4   0.020
 GX6  plan-2  H5   0.020
 GX6  plan-2  H6   0.020
 GX6  plan-3  C4   0.020
 GX6  plan-3  C5   0.020
 GX6  plan-3  C6   0.020
 GX6  plan-3  N1   0.020
 GX6  plan-3  O1   0.020
 GX6  plan-3  H3   0.020
 GX6  plan-4  C14  0.020
 GX6  plan-4  O2   0.020
 GX6  plan-4  C23  0.020
 GX6  plan-4  N4   0.020
 GX6  plan-4  N5   0.020
 GX6  plan-4  H17  0.020
 GX6  plan-4  H18  0.020

