# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:29:38 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (4-oxo-5-phenyl-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)methyl 3-(3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCN1C(=O)COc2ccccc12)OCC3=Nc4scc(c5ccccc5)c4C(=O)N3
#
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
 O6S  O6S  '(4-oxo-5-phenyl-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)methyl 3-(3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl)propanoate'  ligand  52  33  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O6S
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
 O6S  C02  C  C     0   0.626  -2.0146   1.9134   0.3241
 O6S  C03  C  CH2   0  -0.596  -3.1141   0.9664  -0.0622
 O6S  C04  C  CH2   0  -0.334  -4.4693   1.6596  -0.0996
 O6S  C06  C  CR6   0   0.505  -6.0497   0.8130  -1.7447
 O6S  C08  C  C     0  -0.305  -7.1506  -0.1830  -2.0325
 O6S  C10  C  CR66  0   0.329  -6.6746  -1.3438  -0.0894
 O6S  C11  C  CR16  0  -0.355  -7.1039  -2.3571   0.7495
 O6S  C12  C  CR16  0  -0.261  -6.8313  -2.2906   2.1089
 O6S  C13  C  CR16  0  -0.265  -6.1473  -1.1988   2.6201
 O6S  C14  C  CR16  0  -0.326  -5.7221  -0.1796   1.7784
 O6S  C15  C  CR66  0   0.314  -5.9760  -0.2420   0.4123
 O6S  C17  C  CH2   0  -0.243   0.3042   2.1271   0.5427
 O6S  C18  C  CR6   0   0.454   1.5340   1.2872   0.3699
 O6S  C20  C  CR56  0  -0.036   2.6617  -0.5813  -0.0658
 O6S  C22  C  CR15  0  -0.554   4.4831  -2.1999  -0.3682
 O6S  C23  C  CR5   0   0.203   4.9769  -0.9648  -0.0782
 O6S  C24  C  CR6   0   0.065   6.4245  -0.7003   0.0000
 O6S  C25  C  CR16  0  -0.302   7.2380  -1.5173   0.7837
 O6S  C26  C  CR16  0  -0.243   8.6114  -1.3168   0.8256
 O6S  C27  C  CR16  0  -0.264   9.1884  -0.2975   0.0818
 O6S  C28  C  CR16  0  -0.248   8.3846   0.5189  -0.7058
 O6S  C29  C  CR16  0  -0.279   7.0132   0.3211  -0.7455
 O6S  C30  C  CR56  0  -0.084   3.9144  -0.0192   0.1050
 O6S  C31  C  CR6   0   0.520   3.9715   1.3675   0.5035
 O6S  N05  N  NR6   0  -0.570  -5.5210   0.7352  -0.4932
 O6S  N19  N  N     0  -0.437   1.4674   0.0407   0.0521
 O6S  N33  N  NR16  0  -0.698   2.7029   1.9360   0.5856
 O6S  O01  O  O     0  -0.440  -2.1703   3.0538   0.6754
 O6S  O09  O  O     0  -0.471  -6.9150  -1.4320  -1.4192
 O6S  O16  O  O2    0  -0.449  -0.8197   1.3334   0.2299
 O6S  O32  O  O     0  -0.443   4.9595   2.0271   0.7624
 O6S  S21  S  S2    0   0.261   2.7648  -2.2560  -0.4395
 O6S  H1   H  HCH2  0   0.299  -2.8806   0.5360  -1.0393
 O6S  H2   H  HCH2  0   0.298  -3.1132   0.1311   0.6455
 O6S  H3   H  HCH2  0   0.276  -4.7177   2.0990   0.8654
 O6S  H4   H  HCH2  0   0.293  -4.4589   2.4750  -0.8171
 O6S  H5   H  H     0   0.268  -8.1076   0.2438  -1.7043
 O6S  H6   H  H     0   0.285  -7.2029  -0.3518  -3.1055
 O6S  H7   H  HCR6  0   0.273  -7.6385  -3.1996   0.3299
 O6S  H8   H  HCR6  0   0.262  -7.1636  -3.0853   2.7630
 O6S  H9   H  HCR6  0   0.263  -5.9342  -1.1326   3.6784
 O6S  H10  H  HCR6  0   0.279  -5.1892   0.6582   2.2054
 O6S  H11  H  HCH2  0   0.289   0.2616   2.4939   1.5732
 O6S  H12  H  HCH2  0   0.287   0.3666   3.0000  -0.1142
 O6S  H13  H  HCR5  0   0.304   5.0546  -3.0923  -0.5747
 O6S  H14  H  HCR6  0   0.253   6.7921  -2.3082   1.3739
 O6S  H15  H  HCR6  0   0.257   9.2282  -1.9557   1.4441
 O6S  H16  H  HCR6  0   0.257  10.2585  -0.1381   0.1137
 O6S  H17  H  HCR6  0   0.257   8.8290   1.3119  -1.2933
 O6S  H18  H  HCR6  0   0.248   6.3992   0.9523  -1.3738
 O6S  H19  H  HNR6  0   0.437   2.6758   2.9147   0.8471
 O6S  O07  O  O     0  -0.461  -5.7071   1.6352  -2.5720

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
 O6S  C27  C26  aromatic  1.388  0.020  1.388
 O6S  C27  C28  aromatic  1.390  0.020  1.390
 O6S  C26  C25  aromatic  1.389  0.020  1.389
 O6S  C28  C29  aromatic  1.386  0.020  1.386
 O6S  C25  C24  aromatic  1.394  0.020  1.394
 O6S  C29  C24  aromatic  1.395  0.020  1.395
 O6S  C24  C23  single    1.474  0.020  1.474
 O6S  C23  C22  aromatic  1.361  0.020  1.361
 O6S  C23  C30  aromatic  1.434  0.020  1.434
 O6S  C22  S21  aromatic  1.721  0.020  1.721
 O6S  O32  C31  double    1.216  0.020  1.216
 O6S  C30  C31  single    1.444  0.020  1.444
 O6S  C30  C20  aromatic  1.384  0.020  1.384
 O6S  C31  N33  single    1.393  0.020  1.393
 O6S  S21  C20  aromatic  1.719  0.020  1.719
 O6S  C20  N19  single    1.352  0.020  1.352
 O6S  N33  C18  single    1.354  0.020  1.354
 O6S  N19  C18  double    1.288  0.020  1.288
 O6S  C18  C17  single    1.499  0.020  1.499
 O6S  C17  O16  single    1.411  0.020  1.411
 O6S  O16  C02  single    1.332  0.020  1.332
 O6S  O01  C02  double    1.203  0.020  1.203
 O6S  C02  C03  single    1.502  0.020  1.502
 O6S  C03  C04  single    1.523  0.020  1.523
 O6S  C04  N05  single    1.454  0.020  1.454
 O6S  C14  C13  aromatic  1.389  0.020  1.389
 O6S  C14  C15  aromatic  1.391  0.020  1.391
 O6S  N05  C15  single    1.408  0.020  1.408
 O6S  N05  C06  single    1.361  0.020  1.361
 O6S  C13  C12  aromatic  1.386  0.020  1.386
 O6S  C15  C10  aromatic  1.398  0.020  1.398
 O6S  O07  C06  double    1.216  0.020  1.216
 O6S  C06  C08  single    1.512  0.020  1.512
 O6S  C10  C11  aromatic  1.384  0.020  1.384
 O6S  C10  O09  single    1.354  0.020  1.354
 O6S  C12  C11  aromatic  1.388  0.020  1.388
 O6S  O09  C08  single    1.411  0.020  1.411
 O6S  C03  H1   single    0.970  0.020  1.090
 O6S  C03  H2   single    0.970  0.020  1.090
 O6S  C04  H3   single    0.970  0.020  1.090
 O6S  C04  H4   single    0.970  0.020  1.090
 O6S  C08  H5   single    0.970  0.020  1.090
 O6S  C08  H6   single    0.970  0.020  1.090
 O6S  C11  H7   single    0.930  0.020  1.080
 O6S  C12  H8   single    0.930  0.020  1.080
 O6S  C13  H9   single    0.930  0.020  1.080
 O6S  C14  H10  single    0.930  0.020  1.080
 O6S  C17  H11  single    0.970  0.020  1.090
 O6S  C17  H12  single    0.970  0.020  1.090
 O6S  C22  H13  single    0.930  0.020  1.080
 O6S  C25  H14  single    0.930  0.020  1.080
 O6S  C26  H15  single    0.930  0.020  1.080
 O6S  C27  H16  single    0.930  0.020  1.080
 O6S  C28  H17  single    0.930  0.020  1.080
 O6S  C29  H18  single    0.930  0.020  1.080
 O6S  N33  H19  single    0.860  0.020  1.020

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
 O6S  O16  C02  O01  123.34  3.000
 O6S  O01  C02  C03  125.31  3.000
 O6S  O16  C02  C03  111.36  3.000
 O6S  H2   C03  H1   106.09  3.000
 O6S  H2   C03  C04  111.34  3.000
 O6S  H1   C03  C04  110.33  3.000
 O6S  H2   C03  C02  108.32  3.000
 O6S  H1   C03  C02  108.78  3.000
 O6S  C04  C03  C02  111.77  3.000
 O6S  H4   C04  H3   106.54  3.000
 O6S  H4   C04  N05  107.78  3.000
 O6S  H3   C04  N05  109.35  3.000
 O6S  H4   C04  C03  110.46  3.000
 O6S  H3   C04  C03  111.40  3.000
 O6S  N05  C04  C03  111.15  3.000
 O6S  O07  C06  N05  123.72  3.000
 O6S  O07  C06  C08  121.40  3.000
 O6S  N05  C06  C08  114.85  3.000
 O6S  H6   C08  H5   108.26  3.000
 O6S  H6   C08  O09  107.42  3.000
 O6S  H5   C08  O09  111.08  3.000
 O6S  H6   C08  C06  108.97  3.000
 O6S  H5   C08  C06  108.75  3.000
 O6S  O09  C08  C06  112.25  3.000
 O6S  O09  C10  C15  119.51  3.000
 O6S  O09  C10  C11  119.51  3.000
 O6S  C15  C10  C11  120.98  3.000
 O6S  H7   C11  C12  120.92  3.000
 O6S  H7   C11  C10  119.22  3.000
 O6S  C12  C11  C10  119.85  3.000
 O6S  H8   C12  C13  120.49  3.000
 O6S  H8   C12  C11  119.78  3.000
 O6S  C13  C12  C11  119.73  3.000
 O6S  H9   C13  C14  119.20  3.000
 O6S  H9   C13  C12  120.42  3.000
 O6S  C14  C13  C12  120.38  3.000
 O6S  H10  C14  C15  120.85  3.000
 O6S  H10  C14  C13  118.71  3.000
 O6S  C15  C14  C13  120.44  3.000
 O6S  N05  C15  C14  122.79  3.000
 O6S  N05  C15  C10  118.54  3.000
 O6S  C14  C15  C10  118.63  3.000
 O6S  H12  C17  H11  107.46  3.000
 O6S  H12  C17  O16  111.17  3.000
 O6S  H11  C17  O16  111.48  3.000
 O6S  H12  C17  C18  109.33  3.000
 O6S  H11  C17  C18  109.15  3.000
 O6S  O16  C17  C18  108.22  3.000
 O6S  N33  C18  N19  123.20  3.000
 O6S  N19  C18  C17  121.88  3.000
 O6S  N33  C18  C17  114.91  3.000
 O6S  S21  C20  N19  121.35  3.000
 O6S  N19  C20  C30  127.03  3.000
 O6S  S21  C20  C30  111.61  3.000
 O6S  H13  C22  S21  119.58  3.000
 O6S  H13  C22  C23  126.77  3.000
 O6S  S21  C22  C23  113.62  3.000
 O6S  C30  C23  C24  127.06  3.000
 O6S  C30  C23  C22  110.90  3.000
 O6S  C24  C23  C22  122.04  3.000
 O6S  C29  C24  C25  118.90  3.000
 O6S  C29  C24  C23  121.18  3.000
 O6S  C25  C24  C23  119.86  3.000
 O6S  H14  C25  C26  119.76  3.000
 O6S  H14  C25  C24  119.61  3.000
 O6S  C26  C25  C24  120.63  3.000
 O6S  H15  C26  C27  120.21  3.000
 O6S  H15  C26  C25  119.71  3.000
 O6S  C27  C26  C25  120.08  3.000
 O6S  H16  C27  C28  120.13  3.000
 O6S  H16  C27  C26  120.23  3.000
 O6S  C28  C27  C26  119.64  3.000
 O6S  H17  C28  C29  119.68  3.000
 O6S  H17  C28  C27  120.02  3.000
 O6S  C29  C28  C27  120.30  3.000
 O6S  H18  C29  C28  119.67  3.000
 O6S  H18  C29  C24  119.88  3.000
 O6S  C28  C29  C24  120.44  3.000
 O6S  C31  C30  C23  129.73  3.000
 O6S  C31  C30  C20  117.39  3.000
 O6S  C23  C30  C20  112.78  3.000
 O6S  O32  C31  N33  120.41  3.000
 O6S  N33  C31  C30  111.85  3.000
 O6S  O32  C31  C30  127.73  3.000
 O6S  C15  N05  C06  120.37  3.000
 O6S  C06  N05  C04  119.57  3.000
 O6S  C15  N05  C04  120.06  3.000
 O6S  C20  N19  C18  114.91  3.000
 O6S  H19  N33  C31  115.71  3.000
 O6S  H19  N33  C18  118.74  3.000
 O6S  C31  N33  C18  125.54  3.000
 O6S  C10  O09  C08  113.50  3.000
 O6S  C17  O16  C02  117.00  3.000
 O6S  C22  S21  C20   91.09  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
 O6S  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 O6S  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 O6S  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 O6S  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 O6S  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 O6S  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 O6S  CONST_07  C24  C23  C30  C20   180.00   0.0  0
 O6S  CONST_08  C22  C23  C30  C20     0.00   0.0  0
 O6S  CONST_09  C23  C22  S21  C20     0.00   0.0  0
 O6S  CONST_12  C30  C20  S21  C22     0.00   0.0  0
 O6S  CONST_13  C26  C25  C24  C23   180.00   0.0  0
 O6S  CONST_14  C28  C29  C24  C23   180.00   0.0  0
 O6S  CONST_15  S21  C20  C30  C23     0.00   0.0  0
 O6S  CONST_16  C27  C26  C25  C24     0.00   0.0  0
 O6S  CONST_17  C27  C28  C29  C24     0.00   0.0  0
 O6S  CONST_18  S21  C22  C23  C24   180.00   0.0  0
 O6S  CONST_19  C28  C27  C26  C25     0.00   0.0  0
 O6S  CONST_20  C28  C29  C24  C25     0.00   0.0  0
 O6S  CONST_22  C29  C28  C27  C26     0.00   0.0  0
 O6S  CONST_23  C29  C24  C25  C26     0.00   0.0  0
 O6S  CONST_25  S21  C22  C23  C30     0.00   0.0  0
 O6S  CONST_26  C31  C30  C23  C24     0.00   0.0  0
 O6S  CONST_27  C15  N05  C06  C08     0.00   0.0  0
 O6S  CONST_28  C30  C31  N33  C18     0.00   0.0  0
 O6S  CONST_29  N33  C18  N19  C20     0.00   0.0  0
 O6S  CONST_30  N19  C18  N33  C31     0.00   0.0  0
 O6S  CONST_31  C08  C06  N05  C04   180.00   0.0  0
 O6S  CONST_32  O07  C06  N05  C15   180.00   0.0  0
 O6S  CONST_33  C31  N33  C18  C17   180.00   0.0  0
 O6S  CONST_34  C20  N19  C18  C17   180.00   0.0  0
 O6S  CONST_35  O32  C31  N33  C18   180.00   0.0  0
 O6S  CONST_36  H10  C14  C15  C10   180.00   0.0  0
 O6S  CONST_37  H8   C12  C11  C10   180.00   0.0  0
 O6S  CONST_38  H9   C13  C12  C11   180.00   0.0  0
 O6S  CONST_39  H7   C11  C12  C13   180.00   0.0  0
 O6S  CONST_40  H13  C22  S21  C20   180.00   0.0  0
 O6S  CONST_41  H14  C25  C24  C23     0.00   0.0  0
 O6S  CONST_42  H18  C29  C24  C23     0.00   0.0  0
 O6S  CONST_43  H15  C26  C25  C24   180.00   0.0  0
 O6S  CONST_44  H17  C28  C29  C24   180.00   0.0  0
 O6S  CONST_45  H16  C27  C26  C25   180.00   0.0  0
 O6S  CONST_46  H19  N33  C31  C30   180.00   0.0  0
 O6S  CONST_47  O07  C06  N05  C04     0.00   0.0  0
 O6S  Var_01    C14  C15  N05  C06  -164.17  30.0  1
 O6S  Var_02    C15  C10  O09  C08   -34.90  30.0  1
 O6S  Var_03    O09  C08  C06  N05   -36.60  30.0  1
 O6S  Var_04    H5   C08  O09  C10   -68.93  30.0  1
 O6S  Var_05    C15  N05  C04  C03    73.83  30.0  3
 O6S  Var_06    O16  C17  C18  N19    -3.12  30.0  3
 O6S  Var_07    C18  C17  O16  C02  -179.89  30.0  2
 O6S  Var_08    N05  C04  C03  C02   179.20  30.0  3
 O6S  Var_09    O16  C02  C03  C04  -174.00  30.0  1

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
 O6S  plan-1  C23  0.020
 O6S  plan-1  C24  0.020
 O6S  plan-1  C25  0.020
 O6S  plan-1  C26  0.020
 O6S  plan-1  C27  0.020
 O6S  plan-1  C28  0.020
 O6S  plan-1  C29  0.020
 O6S  plan-1  H14  0.020
 O6S  plan-1  H15  0.020
 O6S  plan-1  H16  0.020
 O6S  plan-1  H17  0.020
 O6S  plan-1  H18  0.020
 O6S  plan-2  C17  0.020
 O6S  plan-2  C18  0.020
 O6S  plan-2  C20  0.020
 O6S  plan-2  C22  0.020
 O6S  plan-2  C23  0.020
 O6S  plan-2  C24  0.020
 O6S  plan-2  C30  0.020
 O6S  plan-2  C31  0.020
 O6S  plan-2  N19  0.020
 O6S  plan-2  N33  0.020
 O6S  plan-2  O32  0.020
 O6S  plan-2  S21  0.020
 O6S  plan-2  H13  0.020
 O6S  plan-2  H19  0.020
 O6S  plan-3  C10  0.020
 O6S  plan-3  C11  0.020
 O6S  plan-3  C12  0.020
 O6S  plan-3  C13  0.020
 O6S  plan-3  C14  0.020
 O6S  plan-3  C15  0.020
 O6S  plan-3  N05  0.020
 O6S  plan-3  O09  0.020
 O6S  plan-3  H7   0.020
 O6S  plan-3  H8   0.020
 O6S  plan-3  H9   0.020
 O6S  plan-3  H10  0.020
 O6S  plan-4  C04  0.020
 O6S  plan-4  C06  0.020
 O6S  plan-4  C08  0.020
 O6S  plan-4  C15  0.020
 O6S  plan-4  N05  0.020
 O6S  plan-4  O07  0.020
 O6S  plan-5  C02  0.020
 O6S  plan-5  C03  0.020
 O6S  plan-5  O01  0.020
 O6S  plan-5  O16  0.020

