# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:15:43 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-(morpholin-4-ylmethyl)-7-oxidanyl-chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2C(=CC(=O)Oc2c1)CN3CCOCC3
#
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
 WY3  WY3  4-(morpholin-4-ylmethyl)-7-oxidanyl-chromen-2-one  ligand  34  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WY3
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
 WY3  C1    C  CR6   0   0.254  -0.0272  -0.1051   0.1571
 WY3  C2    C  CR66  0  -0.049  -1.2772   0.5198   0.5134
 WY3  C3    C  CH2   0  -0.324   1.2516   0.4186   0.7485
 WY3  C4    C  CR16  0  -0.571  -0.0421  -1.1718  -0.6709
 WY3  C5    C  CR66  0   0.394  -2.4510  -0.0020  -0.0338
 WY3  C6    C  CR16  0  -0.325  -1.4060   1.6074   1.3892
 WY3  N7    N  NT    0  -0.434   2.4353  -0.1488   0.1570
 WY3  C8    C  CR6   0   0.559  -1.2653  -1.6870  -1.2308
 WY3  O9    O  O     0  -0.469  -2.4185  -1.0543  -0.8803
 WY3  C10   C  CR16  0  -0.463  -3.7012   0.5211   0.2568
 WY3  C11   C  CR16  0  -0.327  -2.6342   2.1432   1.6963
 WY3  C12   C  CH2   0  -0.306   3.5665  -0.1748   1.0674
 WY3  C13   C  CH2   0  -0.317   2.8087   0.5083  -1.0842
 WY3  O14   O  O     0  -0.441  -1.3652  -2.6250  -1.9844
 WY3  C15   C  CR6   0   0.373  -3.7932   1.5997   1.1256
 WY3  C16   C  CH2   0  -0.188   4.7389  -0.8676   0.4001
 WY3  C17   C  CH2   0  -0.185   4.0033  -0.1936  -1.6998
 WY3  O18   O  OH1   0  -0.617  -4.9632   2.1595   1.4548
 WY3  O19   O  O2    0  -0.485   5.0966  -0.2365  -0.8097
 WY3  H3    H  HCH2  0   0.238   1.2523   1.5188   0.6969
 WY3  H3A   H  HCH2  0   0.282   1.2337   0.1766   1.8166
 WY3  H4    H  HCR6  0   0.279   0.8732  -1.6790  -0.9416
 WY3  H6    H  HCR6  0   0.273  -0.5255   2.0429   1.8415
 WY3  H10   H  HCR6  0   0.297  -4.5862   0.0843  -0.1911
 WY3  H11   H  HCR6  0   0.277  -2.7125   2.9823   2.3745
 WY3  H12   H  HCH2  0   0.203   3.8667   0.8374   1.3854
 WY3  H12A  H  HCH2  0   0.247   3.2948  -0.7301   1.9682
 WY3  H13   H  HCH2  0   0.249   1.9781   0.4703  -1.7919
 WY3  H13A  H  HCH2  0   0.212   3.0452   1.5732  -0.9187
 WY3  H16   H  HCH2  0   0.238   5.6117  -0.8407   1.0541
 WY3  H16A  H  HCH2  0   0.201   4.4804  -1.9210   0.2227
 WY3  H17   H  HCH2  0   0.202   3.7112  -1.2097  -2.0006
 WY3  H17A  H  HCH2  0   0.238   4.3295   0.3403  -2.5934
 WY3  HO18  H  HOH1  0   0.482  -5.6951   1.7205   1.0053

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
 WY3  C1   C2    single    1.442  0.020  1.442
 WY3  C1   C3    single    1.503  0.020  1.503
 WY3  C1   C4    double    1.350  0.020  1.350
 WY3  C2   C5    aromatic  1.396  0.020  1.396
 WY3  C2   C6    aromatic  1.402  0.020  1.402
 WY3  C3   N7    single    1.440  0.020  1.440
 WY3  C4   C8    single    1.441  0.020  1.441
 WY3  C5   O9    single    1.351  0.020  1.351
 WY3  C5   C10   aromatic  1.386  0.020  1.386
 WY3  C6   C11   aromatic  1.375  0.020  1.375
 WY3  N7   C12   single    1.452  0.020  1.452
 WY3  N7   C13   single    1.453  0.020  1.453
 WY3  C8   O9    single    1.361  0.020  1.361
 WY3  C8   O14   double    1.207  0.020  1.207
 WY3  C10  C15   aromatic  1.388  0.020  1.388
 WY3  C11  C15   aromatic  1.402  0.020  1.402
 WY3  C12  C16   single    1.517  0.020  1.517
 WY3  C13  C17   single    1.516  0.020  1.516
 WY3  C15  O18   single    1.338  0.020  1.338
 WY3  C16  O19   single    1.411  0.020  1.411
 WY3  C17  O19   single    1.410  0.020  1.410
 WY3  C3   H3    single    0.970  0.020  1.090
 WY3  C3   H3A   single    0.970  0.020  1.090
 WY3  C4   H4    single    0.930  0.020  1.080
 WY3  C6   H6    single    0.930  0.020  1.080
 WY3  C10  H10   single    0.930  0.020  1.080
 WY3  C11  H11   single    0.930  0.020  1.080
 WY3  C12  H12   single    0.970  0.020  1.090
 WY3  C12  H12A  single    0.970  0.020  1.090
 WY3  C13  H13   single    0.970  0.020  1.090
 WY3  C13  H13A  single    0.970  0.020  1.090
 WY3  C16  H16   single    0.970  0.020  1.090
 WY3  C16  H16A  single    0.970  0.020  1.090
 WY3  C17  H17   single    0.970  0.020  1.090
 WY3  C17  H17A  single    0.970  0.020  1.090
 WY3  O18  HO18  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
 WY3  C4    C1   C3   121.72  3.000
 WY3  C4    C1   C2   118.96  3.000
 WY3  C3    C1   C2   119.29  3.000
 WY3  C6    C2   C5   117.22  3.000
 WY3  C6    C2   C1   124.75  3.000
 WY3  C5    C2   C1   118.03  3.000
 WY3  H3A   C3   H3   105.45  3.000
 WY3  H3A   C3   N7   109.09  3.000
 WY3  H3    C3   N7   111.96  3.000
 WY3  H3A   C3   C1   107.02  3.000
 WY3  H3    C3   C1   109.28  3.000
 WY3  N7    C3   C1   113.61  3.000
 WY3  H4    C4   C8   116.99  3.000
 WY3  H4    C4   C1   120.99  3.000
 WY3  C8    C4   C1   122.01  3.000
 WY3  C10   C5   O9   116.55  3.000
 WY3  C10   C5   C2   122.35  3.000
 WY3  O9    C5   C2   121.10  3.000
 WY3  H6    C6   C11  118.49  3.000
 WY3  H6    C6   C2   119.92  3.000
 WY3  C11   C6   C2   121.59  3.000
 WY3  C13   N7   C12  110.08  3.000
 WY3  C13   N7   C3   112.58  3.000
 WY3  C12   N7   C3   112.95  3.000
 WY3  O14   C8   O9   116.85  3.000
 WY3  O14   C8   C4   126.21  3.000
 WY3  O9    C8   C4   116.94  3.000
 WY3  C8    O9   C5   122.94  3.000
 WY3  H10   C10  C15  121.18  3.000
 WY3  H10   C10  C5   119.85  3.000
 WY3  C15   C10  C5   118.97  3.000
 WY3  H11   C11  C15  119.75  3.000
 WY3  H11   C11  C6   120.47  3.000
 WY3  C15   C11  C6   119.79  3.000
 WY3  H12A  C12  H12  107.25  3.000
 WY3  H12A  C12  C16  108.83  3.000
 WY3  H12   C12  C16  109.62  3.000
 WY3  H12A  C12  N7   109.41  3.000
 WY3  H12   C12  N7   112.11  3.000
 WY3  C16   C12  N7   109.54  3.000
 WY3  H13A  C13  H13  107.09  3.000
 WY3  H13A  C13  C17  109.80  3.000
 WY3  H13   C13  C17  108.67  3.000
 WY3  H13A  C13  N7   111.31  3.000
 WY3  H13   C13  N7   110.03  3.000
 WY3  C17   C13  N7   109.87  3.000
 WY3  O18   C15  C11  117.43  3.000
 WY3  O18   C15  C10  122.48  3.000
 WY3  C11   C15  C10  120.09  3.000
 WY3  H16A  C16  H16  107.97  3.000
 WY3  H16A  C16  O19  110.48  3.000
 WY3  H16   C16  O19  107.47  3.000
 WY3  H16A  C16  C12  109.09  3.000
 WY3  H16   C16  C12  110.09  3.000
 WY3  O19   C16  C12  111.66  3.000
 WY3  H17A  C17  H17  107.92  3.000
 WY3  H17A  C17  O19  107.46  3.000
 WY3  H17   C17  O19  110.53  3.000
 WY3  H17A  C17  C13  109.97  3.000
 WY3  H17   C17  C13  109.25  3.000
 WY3  O19   C17  C13  111.63  3.000
 WY3  HO18  O18  C15  111.00  3.000
 WY3  C17   O19  C16  111.00  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
 WY3  CONST_01  C15  C10  C5   C2      0.00   0.0  0
 WY3  CONST_02  C15  C11  C6   C2      0.00   0.0  0
 WY3  CONST_03  C11  C6   C2   C5      0.00   0.0  0
 WY3  CONST_04  C11  C15  C10  C5      0.00   0.0  0
 WY3  CONST_05  C10  C5   C2   C6      0.00   0.0  0
 WY3  CONST_06  C10  C15  C11  C6      0.00   0.0  0
 WY3  CONST_07  O18  C15  C10  C5    180.00   0.0  0
 WY3  CONST_08  O18  C15  C11  C6    180.00   0.0  0
 WY3  CONST_09  H6   C6   C2   C1      0.00   0.0  0
 WY3  CONST_10  H10  C10  C5   C2    180.00   0.0  0
 WY3  CONST_11  H11  C11  C6   C2    180.00   0.0  0
 WY3  Var_01    O9   C8   C4   C1     -0.46  30.0  1
 WY3  Var_02    C8   C4   C1   C2      1.32  30.0  1
 WY3  Var_03    C5   C2   C1   C4     -0.83  30.0  1
 WY3  Var_04    O19  C16  C12  N7     57.42  30.0  1
 WY3  Var_05    O19  C17  C13  N7    -56.79  30.0  1
 WY3  Var_06    C10  C5   O9   C8   -178.49  30.0  1
 WY3  Var_07    C17  C13  N7   C12    56.76  30.0  1
 WY3  Var_08    C16  C12  N7   C13   -56.94  30.0  1
 WY3  Var_09    C12  N7   C3   C1   -152.28  30.0  3
 WY3  Var_10    N7   C3   C1   C2   -170.81  30.0  3

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
 WY3  plan-1  C4   0.020
 WY3  plan-1  C8   0.020
 WY3  plan-1  O9   0.020
 WY3  plan-1  O14  0.020
 WY3  plan-2  C1   0.020
 WY3  plan-2  C2   0.020
 WY3  plan-2  C5   0.020
 WY3  plan-2  C6   0.020
 WY3  plan-2  O9   0.020
 WY3  plan-2  C10  0.020
 WY3  plan-2  C11  0.020
 WY3  plan-2  C15  0.020
 WY3  plan-2  O18  0.020
 WY3  plan-2  H6   0.020
 WY3  plan-2  H10  0.020
 WY3  plan-2  H11  0.020

