# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:10:19 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: (3S)-4-{[4-(4-cyano-3-methylphenoxy)phenyl]acetyl}morpholine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Oc2ccc(CC(=O)N3CCOC[C@H]3C(O)=O)cc2)ccc1C#N
#
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
 OMJ  OMJ  '(3S)-4-{[4-(4-cyano-3-methylphenoxy)phenyl]acetyl}morpholine-3-carboxylic acid'  ligand  48  28  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OMJ
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
 OMJ  O27  O  O     0  -0.439  20.0544   4.3227   3.9239
 OMJ  C25  C  CH1   0  -0.203  21.2289   3.9662   1.8692
 OMJ  C12  C  CR16  0  -0.283  18.9795  -2.3721   0.7140
 OMJ  C13  C  CR16  0  -0.305  19.1742  -1.0644   0.2948
 OMJ  C14  C  CR6   0   0.178  20.4533  -0.5354   0.1634
 OMJ  C21  C  CH2   0  -0.388  21.0264   3.7728  -0.5772
 OMJ  C22  C  CH2   0  -0.140  22.2754   4.6296  -0.7465
 OMJ  C02  C  CR6   0   0.154  18.9579  -6.5008   4.2190
 OMJ  C03  C  CR16  0  -0.389  19.3061  -6.0892   2.9456
 OMJ  C04  C  CR6   0   0.407  19.5734  -4.7485   2.6689
 OMJ  C05  C  CR16  0  -0.354  19.4989  -3.7894   3.6752
 OMJ  C06  C  CR16  0  -0.222  19.1491  -4.1891   4.9510
 OMJ  C07  C  CR6   0  -0.043  18.8779  -5.5267   5.2289
 OMJ  C08  C  CSP   0   0.026  18.5172  -5.9063   6.5528
 OMJ  C11  C  CR6   0   0.282  20.0825  -3.1572   1.0074
 OMJ  C15  C  CR16  0  -0.296  21.5435  -1.3494   0.4510
 OMJ  C16  C  CR16  0  -0.292  21.3677  -2.6575   0.8771
 OMJ  C17  C  CH2   0  -0.721  20.6528   0.8894  -0.2570
 OMJ  C24  C  CH2   0  -0.206  21.6138   5.3757   1.3933
 OMJ  C26  C  C     0   0.540  19.9982   4.0531   2.7509
 OMJ  N09  N  NS    0  -0.259  18.2255  -6.2183   7.6242
 OMJ  N20  N  NT    0  -0.474  21.0549   3.1122   0.7121
 OMJ  O10  O  O2    0  -0.503  19.9093  -4.4690   1.3912
 OMJ  O19  O  O     0  -0.480  20.7836   1.3755   2.0899
 OMJ  O23  O  O2    0  -0.483  22.6476   5.2878   0.4536
 OMJ  O28  O  OH1   0  -0.581  18.8717   3.8825   2.0799
 OMJ  H1   H  HCH1  0   0.299  22.0419   3.5833   2.4902
 OMJ  H2   H  HCR6  0   0.277  17.9789  -2.7744   0.8106
 OMJ  H3   H  HCR6  0   0.258  18.3109  -0.4512   0.0663
 OMJ  H4   H  HCH2  0   0.267  20.1192   4.3765  -0.6642
 OMJ  H5   H  HCH2  0   0.299  20.9971   3.0463  -1.3841
 OMJ  H6   H  HCH2  0   0.232  23.1189   4.0026  -1.0430
 OMJ  H7   H  HCH2  0   0.224  22.1001   5.3563  -1.5468
 OMJ  H8   H  HCH3  0   0.260  19.3172  -8.3227   5.3007
 OMJ  H9   H  HCH3  0   0.261  17.6391  -8.0756   4.8462
 OMJ  H10  H  HCH3  0   0.265  18.8164  -8.5582   3.6282
 OMJ  H11  H  HCR6  0   0.278  19.3727  -6.8157   2.1453
 OMJ  H12  H  HCR6  0   0.292  19.7091  -2.7467   3.4835
 OMJ  H13  H  HCR6  0   0.286  19.0877  -3.4518   5.7399
 OMJ  H14  H  HCR6  0   0.259  22.5490  -0.9611   0.3438
 OMJ  H15  H  HCR6  0   0.273  22.2222  -3.2839   1.0998
 OMJ  H16  H  HCH2  0   0.301  21.5235   0.9792  -0.9124
 OMJ  H17  H  HCH2  0   0.301  19.7960   1.2336  -0.8419
 OMJ  H18  H  HCH2  0   0.277  21.9855   5.9471   2.2433
 OMJ  H19  H  HCH2  0   0.231  20.7412   5.9108   0.9974
 OMJ  H20  H  HOH1  0   0.486  18.1118   3.9909   2.6721
 OMJ  C18  C  C     0   0.595  20.8324   1.8003   0.9458
 OMJ  C01  C  CH3   0  -0.746  18.6687  -7.9404   4.5112

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
 OMJ  C22  C21  single    1.524  0.020  1.524
 OMJ  C22  O23  single    1.418  0.020  1.418
 OMJ  C21  N20  single    1.449  0.020  1.449
 OMJ  O23  C24  single    1.400  0.020  1.400
 OMJ  C17  C14  single    1.499  0.020  1.499
 OMJ  C17  C18  single    1.519  0.020  1.519
 OMJ  C13  C14  aromatic  1.390  0.020  1.390
 OMJ  C13  C12  aromatic  1.387  0.020  1.387
 OMJ  C14  C15  aromatic  1.391  0.020  1.391
 OMJ  C12  C11  aromatic  1.385  0.020  1.385
 OMJ  C24  C25  single    1.537  0.020  1.537
 OMJ  N20  C18  single    1.351  0.020  1.351
 OMJ  N20  C25  single    1.449  0.020  1.449
 OMJ  C15  C16  aromatic  1.387  0.020  1.387
 OMJ  C11  O10  single    1.378  0.020  1.378
 OMJ  C11  C16  aromatic  1.385  0.020  1.385
 OMJ  O10  C04  single    1.350  0.020  1.350
 OMJ  C18  O19  double    1.221  0.020  1.221
 OMJ  C25  C26  single    1.516  0.020  1.516
 OMJ  O27  C26  double    1.205  0.020  1.205
 OMJ  C26  O28  single    1.322  0.020  1.322
 OMJ  C04  C03  aromatic  1.395  0.020  1.395
 OMJ  C04  C05  aromatic  1.392  0.020  1.392
 OMJ  C03  C02  aromatic  1.383  0.020  1.383
 OMJ  C05  C06  aromatic  1.382  0.020  1.382
 OMJ  C02  C01  single    1.497  0.020  1.497
 OMJ  C02  C07  aromatic  1.405  0.020  1.405
 OMJ  C06  C07  aromatic  1.393  0.020  1.393
 OMJ  C07  C08  single    1.424  0.020  1.424
 OMJ  C08  N09  triple    1.153  0.020  1.153
 OMJ  C25  H1   single    0.970  0.020  1.090
 OMJ  C12  H2   single    0.930  0.020  1.080
 OMJ  C13  H3   single    0.930  0.020  1.080
 OMJ  C21  H4   single    0.970  0.020  1.090
 OMJ  C21  H5   single    0.970  0.020  1.090
 OMJ  C22  H6   single    0.970  0.020  1.090
 OMJ  C22  H7   single    0.970  0.020  1.090
 OMJ  C01  H8   single    0.970  0.020  1.090
 OMJ  C01  H9   single    0.970  0.020  1.090
 OMJ  C01  H10  single    0.970  0.020  1.090
 OMJ  C03  H11  single    0.930  0.020  1.080
 OMJ  C05  H12  single    0.930  0.020  1.080
 OMJ  C06  H13  single    0.930  0.020  1.080
 OMJ  C15  H14  single    0.930  0.020  1.080
 OMJ  C16  H15  single    0.930  0.020  1.080
 OMJ  C17  H16  single    0.970  0.020  1.090
 OMJ  C17  H17  single    0.970  0.020  1.090
 OMJ  C24  H18  single    0.970  0.020  1.090
 OMJ  C24  H19  single    0.970  0.020  1.090
 OMJ  O28  H20  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
 OMJ  H1   C25  N20  109.69  3.000
 OMJ  H1   C25  C26  107.07  3.000
 OMJ  N20  C25  C26  113.62  3.000
 OMJ  H1   C25  C24  108.13  3.000
 OMJ  C26  C25  C24  109.32  3.000
 OMJ  N20  C25  C24  108.87  3.000
 OMJ  H2   C12  C11  120.42  3.000
 OMJ  H2   C12  C13  120.46  3.000
 OMJ  C11  C12  C13  119.12  3.000
 OMJ  H3   C13  C14  119.86  3.000
 OMJ  H3   C13  C12  119.05  3.000
 OMJ  C14  C13  C12  121.09  3.000
 OMJ  C17  C14  C15  120.67  3.000
 OMJ  C15  C14  C13  118.62  3.000
 OMJ  C17  C14  C13  120.70  3.000
 OMJ  H5   C21  H4   106.73  3.000
 OMJ  H5   C21  N20  110.88  3.000
 OMJ  H4   C21  N20  109.80  3.000
 OMJ  H5   C21  C22  108.40  3.000
 OMJ  H4   C21  C22  111.16  3.000
 OMJ  N20  C21  C22  109.82  3.000
 OMJ  H7   C22  H6   107.83  3.000
 OMJ  H7   C22  O23  110.63  3.000
 OMJ  H6   C22  O23  107.07  3.000
 OMJ  H7   C22  C21  108.84  3.000
 OMJ  H6   C22  C21  109.90  3.000
 OMJ  O23  C22  C21  112.46  3.000
 OMJ  C07  C02  C03  118.02  3.000
 OMJ  C07  C02  C01  121.01  3.000
 OMJ  C03  C02  C01  120.97  3.000
 OMJ  H11  C03  C04  119.11  3.000
 OMJ  H11  C03  C02  119.75  3.000
 OMJ  C04  C03  C02  121.14  3.000
 OMJ  O10  C04  C05  123.69  3.000
 OMJ  C05  C04  C03  120.56  3.000
 OMJ  O10  C04  C03  115.74  3.000
 OMJ  H12  C05  C06  119.47  3.000
 OMJ  H12  C05  C04  121.74  3.000
 OMJ  C06  C05  C04  118.80  3.000
 OMJ  H13  C06  C07  119.87  3.000
 OMJ  H13  C06  C05  119.39  3.000
 OMJ  C07  C06  C05  120.74  3.000
 OMJ  C08  C07  C06  119.40  3.000
 OMJ  C08  C07  C02  119.86  3.000
 OMJ  C06  C07  C02  120.74  3.000
 OMJ  N09  C08  C07  180.00  3.000
 OMJ  O10  C11  C16  119.10  3.000
 OMJ  C16  C11  C12  120.96  3.000
 OMJ  O10  C11  C12  119.90  3.000
 OMJ  H14  C15  C16  119.09  3.000
 OMJ  H14  C15  C14  119.83  3.000
 OMJ  C16  C15  C14  121.08  3.000
 OMJ  H15  C16  C15  120.59  3.000
 OMJ  H15  C16  C11  120.28  3.000
 OMJ  C15  C16  C11  119.13  3.000
 OMJ  H17  C17  H16  106.12  3.000
 OMJ  H17  C17  C18  109.11  3.000
 OMJ  H16  C17  C18  109.34  3.000
 OMJ  H17  C17  C14  110.19  3.000
 OMJ  H16  C17  C14  110.62  3.000
 OMJ  C18  C17  C14  111.32  3.000
 OMJ  H19  C24  H18  107.27  3.000
 OMJ  H19  C24  O23  112.07  3.000
 OMJ  H18  C24  O23  107.74  3.000
 OMJ  H19  C24  C25  111.09  3.000
 OMJ  H18  C24  C25  108.95  3.000
 OMJ  O23  C24  C25  109.59  3.000
 OMJ  O28  C26  C25  112.89  3.000
 OMJ  O28  C26  O27  124.24  3.000
 OMJ  C25  C26  O27  122.75  3.000
 OMJ  C21  N20  C18  126.40  3.000
 OMJ  C18  N20  C25  117.01  3.000
 OMJ  C21  N20  C25  116.38  3.000
 OMJ  C11  O10  C04  119.46  3.000
 OMJ  C24  O23  C22  113.78  3.000
 OMJ  H20  O28  C26  110.09  3.000
 OMJ  O19  C18  N20  120.42  3.000
 OMJ  O19  C18  C17  121.89  3.000
 OMJ  N20  C18  C17  117.69  3.000
 OMJ  H10  C01  H9   107.88  3.000
 OMJ  H10  C01  H8   107.93  3.000
 OMJ  H9   C01  H8   107.18  3.000
 OMJ  H10  C01  C02  111.19  3.000
 OMJ  H9   C01  C02  111.18  3.000
 OMJ  H8   C01  C02  111.31  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
 OMJ  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 OMJ  CONST_02  C15  C16  C11  C12     0.00   0.0  0
 OMJ  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 OMJ  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 OMJ  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 OMJ  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 OMJ  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 OMJ  CONST_08  C05  C06  C07  C02     0.00   0.0  0
 OMJ  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 OMJ  CONST_10  C06  C07  C02  C03     0.00   0.0  0
 OMJ  CONST_11  C07  C02  C03  C04     0.00   0.0  0
 OMJ  CONST_12  C07  C06  C05  C04     0.00   0.0  0
 OMJ  CONST_13  C17  C14  C13  C12   180.00   0.0  0
 OMJ  CONST_14  O10  C11  C12  C13   180.00   0.0  0
 OMJ  CONST_15  C04  C03  C02  C01   180.00   0.0  0
 OMJ  CONST_16  C06  C07  C02  C01   180.00   0.0  0
 OMJ  CONST_17  O10  C04  C03  C02   180.00   0.0  0
 OMJ  CONST_18  C08  C07  C02  C03   180.00   0.0  0
 OMJ  CONST_19  C08  C07  C06  C05   180.00   0.0  0
 OMJ  CONST_20  O10  C04  C05  C06   180.00   0.0  0
 OMJ  CONST_21  O10  C11  C16  C15   180.00   0.0  0
 OMJ  CONST_22  C17  C14  C15  C16   180.00   0.0  0
 OMJ  CONST_23  H15  C16  C11  C12   180.00   0.0  0
 OMJ  CONST_24  H14  C15  C14  C13   180.00   0.0  0
 OMJ  CONST_25  H2   C12  C13  C14   180.00   0.0  0
 OMJ  CONST_26  H13  C06  C07  C02   180.00   0.0  0
 OMJ  CONST_27  H12  C05  C04  C03   180.00   0.0  0
 OMJ  CONST_28  H11  C03  C04  C05   180.00   0.0  0
 OMJ  CONST_29  H3   C13  C12  C11   180.00   0.0  0
 OMJ  CONST_30  C17  C18  N20  C25   180.00   0.0  0
 OMJ  CONST_31  O19  C18  N20  C25     0.00   0.0  0
 OMJ  CONST_32  C17  C18  N20  C21     0.00   0.0  0
 OMJ  CONST_33  O19  C18  N20  C21   180.00   0.0  0
 OMJ  CONST_34  H20  O28  C26  C25   180.00   0.0  0
 OMJ  Var_01    C22  C21  N20  C25    54.30  30.0  1
 OMJ  Var_02    O23  C22  C21  N20   -38.98  30.0  1
 OMJ  Var_03    C16  C11  O10  C04   101.78  30.0  2
 OMJ  Var_04    H18  C24  O23  C22  -176.60  30.0  1
 OMJ  Var_05    H6   C22  O23  C24  -140.04  30.0  1
 OMJ  Var_06    C18  C17  C14  C13    95.47  30.0  2
 OMJ  Var_07    N20  C18  C17  C14   178.42  30.0  3
 OMJ  Var_08    H8   C01  C02  C03   122.92  30.0  2

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
 OMJ  chir_01  C25  C24  N20  C26  positiv

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
 OMJ  plan-1  C12  0.020
 OMJ  plan-1  C13  0.020
 OMJ  plan-1  C14  0.020
 OMJ  plan-1  C11  0.020
 OMJ  plan-1  C15  0.020
 OMJ  plan-1  C16  0.020
 OMJ  plan-1  C17  0.020
 OMJ  plan-1  O10  0.020
 OMJ  plan-1  H2   0.020
 OMJ  plan-1  H3   0.020
 OMJ  plan-1  H14  0.020
 OMJ  plan-1  H15  0.020
 OMJ  plan-2  C02  0.020
 OMJ  plan-2  C03  0.020
 OMJ  plan-2  C04  0.020
 OMJ  plan-2  C05  0.020
 OMJ  plan-2  C06  0.020
 OMJ  plan-2  C07  0.020
 OMJ  plan-2  C08  0.020
 OMJ  plan-2  N09  0.020
 OMJ  plan-2  O10  0.020
 OMJ  plan-2  H11  0.020
 OMJ  plan-2  H12  0.020
 OMJ  plan-2  H13  0.020
 OMJ  plan-2  C01  0.020
 OMJ  plan-3  C25  0.020
 OMJ  plan-3  C21  0.020
 OMJ  plan-3  C17  0.020
 OMJ  plan-3  N20  0.020
 OMJ  plan-3  O19  0.020
 OMJ  plan-3  C18  0.020
 OMJ  plan-4  O27  0.020
 OMJ  plan-4  C25  0.020
 OMJ  plan-4  C26  0.020
 OMJ  plan-4  O28  0.020
 OMJ  plan-4  H20  0.020

