# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:40:16 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[(3aR,7aR)-2-amino-7a-(2,4-difluorophenyl)-3a,6,7,7a-tetrahydro[1,3]oxazolo[5,4-c]pyridin-5(4H)-yl]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=N[C@]2(CCN(C[C@H]2O1)c3ncccc3C#N)c4ccc(F)cc4F
#
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
 1W1  1W1  2-[(3aR,7aR)-2-amino-7a-(2,4-difluorophenyl)-3a,6,7,7a-tetrahydro[1,3]oxazolo[5,4-c]pyridin-5(4H)-yl]pyridine-3-carbonitrile  ligand  41  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1W1
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
 1W1  C4   C  CR6   0   0.544   2.8534  -0.9987  -0.1936
 1W1  C6   C  CR16  0  -0.034   4.2888  -2.6017  -0.9941
 1W1  C8   C  C     0  -0.312   0.5867  -0.9479  -1.1011
 1W1  C10  C  CR6   0  -0.039  -1.0612   0.7909  -0.1887
 1W1  C17  C  CR6   0  -0.055  -2.3112  -0.0205   0.0878
 1W1  C20  C  CR6   0   0.532  -4.6391  -1.5113   0.5093
 1W1  C21  C  CR16  0  -0.557  -4.5755  -0.6611  -0.5768
 1W1  C22  C  CR6   0   0.556  -3.4114   0.0581  -0.7629
 1W1  C1   C  CR16  0  -0.352   5.3858  -2.0921  -0.3173
 1W1  C2   C  CR16  0  -0.124   5.1977  -0.9322   0.4096
 1W1  C3   C  CR6   0  -0.129   3.9332  -0.3527   0.4590
 1W1  N5   N  N     0  -0.453   3.0710  -2.0861  -0.9255
 1W1  N7   N  NR6   0  -0.497   1.5785  -0.5033  -0.1365
 1W1  C9   C  C     0  -0.428  -0.3218   0.2244  -1.4251
 1W1  C11  C  CR16  0   0.051  -0.1012   0.8734   1.0247
 1W1  C12  C  C     0  -0.359   0.9681  -0.1878   1.1400
 1W1  O13  O  O2    0  -0.472   0.4713   2.1718   0.8576
 1W1  C14  C  C     0   0.647  -0.4389   2.8574   0.1391
 1W1  N15  N  N     0  -0.480  -1.3815   2.1992  -0.4128
 1W1  N16  N  NH2   0  -0.843  -0.2033   4.1805   0.0377
 1W1  C18  C  CR16  0  -0.299  -2.4385  -0.8994   1.1594
 1W1  C19  C  CR16  0  -0.408  -3.5854  -1.6492   1.3857
 1W1  F23  F  F     0  -0.301  -3.3625   0.8543  -1.8372
 1W1  F24  F  F     0  -0.309  -5.7593  -2.2179   0.7064
 1W1  C25  C  CSP   0   0.040   3.7999   0.9259   1.0650
 1W1  N26  N  NS    0  -0.246   3.7394   1.9731   1.5441
 1W1  H1   H  HCR6  0   0.277   4.3955  -3.4822  -1.6176
 1W1  H2   H  H     0   0.273   1.0827  -1.2808  -2.0088
 1W1  H3   H  H     0   0.230   0.0195  -1.8049  -0.7129
 1W1  H4   H  HCR6  0   0.301  -5.4051  -0.5584  -1.2641
 1W1  H5   H  HCR6  0   0.280   6.3529  -2.5674  -0.3848
 1W1  H6   H  HCR6  0   0.294   6.0258  -0.4525   0.9140
 1W1  H7   H  H     0   0.246   0.2937   1.0140  -1.8627
 1W1  H8   H  H     0   0.256  -1.0366  -0.0704  -2.1932
 1W1  H9   H  HCR6  0   0.263  -0.6690   0.8827   1.9625
 1W1  H10  H  H     0   0.262   0.5002  -1.0942   1.5474
 1W1  H11  H  H     0   0.289   1.7034   0.1207   1.8794
 1W1  H12  H  HNH2  0   0.400   0.2820   4.6306   0.7969
 1W1  H13  H  HNH2  0   0.400  -0.9415   4.7298  -0.3704
 1W1  H14  H  HCR6  0   0.268  -1.6316  -1.0208   1.8671
 1W1  H15  H  HCR6  0   0.286  -3.6487  -2.3206   2.2308

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
 1W1  N16  C14  single    1.348  0.020  1.348
 1W1  N15  C14  double    1.275  0.020  1.275
 1W1  N15  C10  single    1.462  0.020  1.462
 1W1  C19  C18  aromatic  1.389  0.020  1.389
 1W1  C19  C20  aromatic  1.377  0.020  1.377
 1W1  C18  C17  aromatic  1.392  0.020  1.392
 1W1  C14  O13  single    1.347  0.020  1.347
 1W1  F24  C20  single    1.339  0.020  1.339
 1W1  N26  C25  triple    1.153  0.020  1.153
 1W1  C20  C21  aromatic  1.381  0.020  1.381
 1W1  C10  C17  single    1.516  0.020  1.516
 1W1  C10  C9   single    1.548  0.020  1.548
 1W1  C10  C11  single    1.549  0.020  1.549
 1W1  C17  C22  aromatic  1.393  0.020  1.393
 1W1  O13  C11  single    1.429  0.020  1.429
 1W1  C9   C8   single    1.518  0.020  1.518
 1W1  C8   N7   single    1.453  0.020  1.453
 1W1  C25  C3   single    1.421  0.020  1.421
 1W1  C11  C12  single    1.511  0.020  1.511
 1W1  C21  C22  aromatic  1.381  0.020  1.381
 1W1  C22  F23  single    1.338  0.020  1.338
 1W1  N7   C12  single    1.450  0.020  1.450
 1W1  N7   C4   single    1.369  0.020  1.369
 1W1  C3   C4   aromatic  1.418  0.020  1.418
 1W1  C3   C2   aromatic  1.392  0.020  1.392
 1W1  C4   N5   aromatic  1.329  0.020  1.329
 1W1  C2   C1   aromatic  1.382  0.020  1.382
 1W1  N5   C6   aromatic  1.324  0.020  1.324
 1W1  C1   C6   aromatic  1.386  0.020  1.386
 1W1  C6   H1   single    0.930  0.020  1.080
 1W1  C8   H2   single    0.970  0.020  1.090
 1W1  C8   H3   single    0.970  0.020  1.090
 1W1  C21  H4   single    0.930  0.020  1.080
 1W1  C1   H5   single    0.930  0.020  1.080
 1W1  C2   H6   single    0.930  0.020  1.080
 1W1  C9   H7   single    0.970  0.020  1.090
 1W1  C9   H8   single    0.970  0.020  1.090
 1W1  C11  H9   single    0.970  0.020  1.090
 1W1  C12  H10  single    0.970  0.020  1.090
 1W1  C12  H11  single    0.970  0.020  1.090
 1W1  N16  H12  single    0.890  0.020  1.040
 1W1  N16  H13  single    0.890  0.020  1.040
 1W1  C18  H14  single    0.930  0.020  1.080
 1W1  C19  H15  single    0.930  0.020  1.080

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
 1W1  N7   C4   N5   118.15  3.000
 1W1  N5   C4   C3   120.12  3.000
 1W1  N7   C4   C3   121.69  3.000
 1W1  H1   C6   N5   115.88  3.000
 1W1  H1   C6   C1   120.10  3.000
 1W1  N5   C6   C1   124.01  3.000
 1W1  H3   C8   H2   106.97  3.000
 1W1  H3   C8   C9   111.64  3.000
 1W1  H2   C8   C9   109.36  3.000
 1W1  H3   C8   N7   110.88  3.000
 1W1  H2   C8   N7   109.67  3.000
 1W1  C9   C8   N7   108.29  3.000
 1W1  N15  C10  C11  101.80  3.000
 1W1  C11  C10  C9   110.43  3.000
 1W1  N15  C10  C9   109.56  3.000
 1W1  C11  C10  C17  113.37  3.000
 1W1  C9   C10  C17  110.11  3.000
 1W1  N15  C10  C17  111.29  3.000
 1W1  C18  C17  C22  115.70  3.000
 1W1  C22  C17  C10  120.64  3.000
 1W1  C18  C17  C10  123.64  3.000
 1W1  F24  C20  C19  119.57  3.000
 1W1  F24  C20  C21  118.64  3.000
 1W1  C19  C20  C21  121.79  3.000
 1W1  H4   C21  C22  120.74  3.000
 1W1  H4   C21  C20  121.51  3.000
 1W1  C22  C21  C20  117.75  3.000
 1W1  F23  C22  C21  116.67  3.000
 1W1  F23  C22  C17  119.68  3.000
 1W1  C21  C22  C17  123.65  3.000
 1W1  H5   C1   C2   121.63  3.000
 1W1  H5   C1   C6   121.10  3.000
 1W1  C2   C1   C6   117.25  3.000
 1W1  H6   C2   C3   119.62  3.000
 1W1  H6   C2   C1   120.89  3.000
 1W1  C3   C2   C1   119.46  3.000
 1W1  C25  C3   C2   118.36  3.000
 1W1  C2   C3   C4   119.08  3.000
 1W1  C25  C3   C4   122.33  3.000
 1W1  C6   N5   C4   119.85  3.000
 1W1  C12  N7   C8   111.33  3.000
 1W1  C12  N7   C4   120.51  3.000
 1W1  C8   N7   C4   119.81  3.000
 1W1  H8   C9   H7   106.42  3.000
 1W1  H8   C9   C10  110.40  3.000
 1W1  H7   C9   C10  108.93  3.000
 1W1  H8   C9   C8   109.51  3.000
 1W1  H7   C9   C8   107.84  3.000
 1W1  C10  C9   C8   113.45  3.000
 1W1  H9   C11  O13  107.44  3.000
 1W1  H9   C11  C12  107.89  3.000
 1W1  O13  C11  C12  111.33  3.000
 1W1  H9   C11  C10  110.45  3.000
 1W1  C12  C11  C10  117.45  3.000
 1W1  O13  C11  C10  101.83  3.000
 1W1  H11  C12  H10  105.67  3.000
 1W1  H11  C12  C11  109.34  3.000
 1W1  H10  C12  C11  107.84  3.000
 1W1  H11  C12  N7   112.07  3.000
 1W1  H10  C12  N7   109.05  3.000
 1W1  C11  C12  N7   112.56  3.000
 1W1  C14  O13  C11  104.72  3.000
 1W1  N16  C14  N15  127.11  3.000
 1W1  N15  C14  O13  117.88  3.000
 1W1  N16  C14  O13  114.93  3.000
 1W1  C14  N15  C10  105.60  3.000
 1W1  H13  N16  H12  114.52  3.000
 1W1  H13  N16  C14  115.97  3.000
 1W1  H12  N16  C14  117.79  3.000
 1W1  H14  C18  C19  116.71  3.000
 1W1  H14  C18  C17  120.47  3.000
 1W1  C19  C18  C17  122.82  3.000
 1W1  H15  C19  C18  120.73  3.000
 1W1  H15  C19  C20  120.98  3.000
 1W1  C18  C19  C20  118.29  3.000
 1W1  N26  C25  C3   180.00  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
 1W1  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 1W1  CONST_02  C1   C6   N5   C4      0.00   0.0  0
 1W1  CONST_03  C3   C4   N5   C6      0.00   0.0  0
 1W1  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 1W1  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 1W1  CONST_06  C20  C21  C22  C17     0.00   0.0  0
 1W1  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 1W1  CONST_08  C18  C17  C22  C21     0.00   0.0  0
 1W1  CONST_09  C19  C18  C17  C22     0.00   0.0  0
 1W1  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 1W1  CONST_11  N5   C4   C3   C2      0.00   0.0  0
 1W1  CONST_12  N5   C6   C1   C2      0.00   0.0  0
 1W1  CONST_13  N7   C4   N5   C6    180.00   0.0  0
 1W1  CONST_14  C19  C18  C17  C10   180.00   0.0  0
 1W1  CONST_15  C21  C22  C17  C10   180.00   0.0  0
 1W1  CONST_16  N7   C4   C3   C2    180.00   0.0  0
 1W1  CONST_17  O13  C14  N15  C10     0.00   0.0  0
 1W1  CONST_18  F23  C22  C17  C10     0.00   0.0  0
 1W1  CONST_19  F23  C22  C21  C20   180.00   0.0  0
 1W1  CONST_20  F24  C20  C21  C22   180.00   0.0  0
 1W1  CONST_21  C25  C3   C2   C1    180.00   0.0  0
 1W1  CONST_22  C25  C3   C4   N5    180.00   0.0  0
 1W1  CONST_23  C25  C3   C4   N7      0.00   0.0  0
 1W1  CONST_24  F24  C20  C19  C18   180.00   0.0  0
 1W1  CONST_25  F23  C22  C17  C18   180.00   0.0  0
 1W1  CONST_26  N16  C14  N15  C10   180.00   0.0  0
 1W1  CONST_27  H6   C2   C3   C4    180.00   0.0  0
 1W1  CONST_28  H1   C6   N5   C4    180.00   0.0  0
 1W1  CONST_29  H14  C18  C17  C10     0.00   0.0  0
 1W1  CONST_30  H15  C19  C18  C17   180.00   0.0  0
 1W1  CONST_31  H4   C21  C22  C17   180.00   0.0  0
 1W1  CONST_32  H5   C1   C2   C3    180.00   0.0  0
 1W1  CONST_34  H13  N16  C14  O13   180.00   0.0  0
 1W1  Var_01    C9   C8   N7   C4   -144.64  30.0  1
 1W1  Var_02    C11  C12  N7   C4    154.03  30.0  1
 1W1  Var_03    C3   C4   N7   C8    162.41  30.0  2
 1W1  Var_04    N7   C8   C9   C10   -59.58  30.0  1
 1W1  Var_05    N15  C14  O13  C11   -12.89  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
 1W1  chir_01  C10  C17  C9   C11  positiv
 1W1  chir_02  C11  O13  C10  C12  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
 1W1  plan-1  C4   0.020
 1W1  plan-1  C6   0.020
 1W1  plan-1  C1   0.020
 1W1  plan-1  C2   0.020
 1W1  plan-1  C3   0.020
 1W1  plan-1  N5   0.020
 1W1  plan-1  N7   0.020
 1W1  plan-1  C25  0.020
 1W1  plan-1  N26  0.020
 1W1  plan-1  H1   0.020
 1W1  plan-1  H5   0.020
 1W1  plan-1  H6   0.020
 1W1  plan-2  C10  0.020
 1W1  plan-2  C17  0.020
 1W1  plan-2  C20  0.020
 1W1  plan-2  C21  0.020
 1W1  plan-2  C22  0.020
 1W1  plan-2  C18  0.020
 1W1  plan-2  C19  0.020
 1W1  plan-2  F23  0.020
 1W1  plan-2  F24  0.020
 1W1  plan-2  H4   0.020
 1W1  plan-2  H14  0.020
 1W1  plan-2  H15  0.020
 1W1  plan-3  C10  0.020
 1W1  plan-3  O13  0.020
 1W1  plan-3  C14  0.020
 1W1  plan-3  N15  0.020
 1W1  plan-3  N16  0.020
 1W1  plan-3  H12  0.020
 1W1  plan-3  H13  0.020

