# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 19:43:16 2022
#   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  47  28  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.605  19.1532   5.1258   3.0412
 OMJ  C25  C  CH1    0  -0.211  20.8531   4.1398   1.7461
 OMJ  C12  C  C1     0  -0.299  18.6303  -2.1046   0.6086
 OMJ  C13  C  C1     0  -0.297  19.0567  -0.8500   0.1983
 OMJ  C14  C  C      0   0.176  20.4023  -0.5003   0.2307
 OMJ  C21  C  CH2    0  -0.385  21.4276   3.6817  -0.5865
 OMJ  C22  C  CH2    0  -0.137  22.7302   4.4697  -0.4600
 OMJ  C02  C  C      0   0.153  19.0281  -6.6166   4.1473
 OMJ  C03  C  C1     0  -0.389  18.9778  -6.0651   2.8799
 OMJ  C04  C  C      0   0.404  19.2289  -4.7092   2.6713
 OMJ  C05  C  C1     0  -0.353  19.5313  -3.8732   3.7428
 OMJ  C06  C  C1     0  -0.222  19.5908  -4.4145   5.0128
 OMJ  C07  C  C      0  -0.042  19.3466  -5.7701   5.2227
 OMJ  C08  C  CSP    0   0.024  19.4197  -6.2985   6.5427
 OMJ  C11  C  C      0   0.293  19.5661  -3.0275   1.0446
 OMJ  C15  C  C1     0  -0.306  21.3220  -1.4479   0.6687
 OMJ  C16  C  C1     0  -0.284  20.9160  -2.7112   1.0719
 OMJ  C17  C  CH2    0  -0.715  20.8420   0.8705  -0.1860
 OMJ  C24  C  CH2    0  -0.208  21.5667   5.4342   1.3361
 OMJ  C26  C  C      0   0.407  19.3585   4.4482   2.0153
 OMJ  N09  N  NS     0  -0.256  19.4790  -6.7311   7.6103
 OMJ  N20  N  NT     0  -0.447  21.0637   3.1471   0.7050
 OMJ  O10  O  O2     0  -0.500  19.1341  -4.2869   1.3927
 OMJ  O19  O  O      0  -0.493  20.4120   1.5000   2.0843
 OMJ  O23  O  O2     0  -0.483  22.8260   5.1541   0.7729
 OMJ  O28  O  OC    -1  -0.588  18.5276   4.0454   1.1848
 OMJ  H1   H  HCH1   0   0.242  21.3151   3.7800   2.6686
 OMJ  H2   H  H      0   0.269  17.5799  -2.3657   0.5840
 OMJ  H3   H  H      0   0.255  18.3237  -0.1304  -0.1461
 OMJ  H4   H  HCH2   0   0.252  20.6178   4.3130  -0.9638
 OMJ  H5   H  HCH2   0   0.284  21.5719   2.8951  -1.3222
 OMJ  H6   H  HCH2   0   0.222  23.5821   3.7878  -0.5144
 OMJ  H7   H  HCH2   0   0.207  22.8080   5.1661  -1.3046
 OMJ  H8   H  HCH3   0   0.260  19.6199  -8.5761   4.8011
 OMJ  H9   H  HCH3   0   0.259  17.9187  -8.2185   5.0498
 OMJ  H10  H  HCH3   0   0.265  18.5145  -8.5717   3.4287
 OMJ  H11  H  H      0   0.275  18.7398  -6.6931   2.0300
 OMJ  H12  H  H      0   0.294  19.7161  -2.8170   3.6043
 OMJ  H13  H  H      0   0.282  19.8272  -3.7738   5.8520
 OMJ  H14  H  H      0   0.256  22.3767  -1.2014   0.6919
 OMJ  H15  H  H      0   0.277  21.6449  -3.4413   1.4013
 OMJ  H16  H  HCH2   0   0.291  21.8693   0.8399  -0.5599
 OMJ  H17  H  HCH2   0   0.288  20.2263   1.2193  -1.0193
 OMJ  H18  H  HCH2   0   0.252  21.7321   6.0466   2.2215
 OMJ  H19  H  HCH2   0   0.208  20.9498   6.0273   0.6466
 OMJ  C18  C  C      0   0.572  20.7483   1.8657   0.9666
 OMJ  C01  C  CH3    0  -0.744  18.7554  -8.0729   4.3650

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    1.528  0.020  1.528
 OMJ  C22  O23  single    1.413  0.020  1.413
 OMJ  C21  N20  single    1.444  0.020  1.444
 OMJ  O23  C24  single    1.408  0.020  1.408
 OMJ  C17  C14  single    1.499  0.020  1.499
 OMJ  C17  C18  single    1.526  0.020  1.526
 OMJ  C13  C14  aromatic  1.391  0.020  1.391
 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    1.534  0.020  1.534
 OMJ  N20  C18  single    1.345  0.020  1.345
 OMJ  N20  C25  single    1.454  0.020  1.454
 OMJ  C15  C16  aromatic  1.387  0.020  1.387
 OMJ  C11  O10  single    1.376  0.020  1.376
 OMJ  C11  C16  aromatic  1.387  0.020  1.387
 OMJ  O10  C04  single    1.350  0.020  1.350
 OMJ  C18  O19  double    1.223  0.020  1.223
 OMJ  C25  C26  single    1.550  0.020  1.550
 OMJ  O27  C26  deloc     1.246  0.020  1.246
 OMJ  C26  O28  deloc     1.242  0.020  1.242
 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

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  108.57  3.000
 OMJ  H1   C25  C26  109.06  3.000
 OMJ  N20  C25  C26  113.58  3.000
 OMJ  H1   C25  C24  107.87  3.000
 OMJ  C26  C25  C24  109.10  3.000
 OMJ  N20  C25  C24  108.51  3.000
 OMJ  H2   C12  C11  120.14  3.000
 OMJ  H2   C12  C13  120.64  3.000
 OMJ  C11  C12  C13  119.22  3.000
 OMJ  H3   C13  C14  119.67  3.000
 OMJ  H3   C13  C12  119.13  3.000
 OMJ  C14  C13  C12  121.20  3.000
 OMJ  C17  C14  C15  121.10  3.000
 OMJ  C15  C14  C13  118.41  3.000
 OMJ  C17  C14  C13  120.49  3.000
 OMJ  H5   C21  H4   106.41  3.000
 OMJ  H5   C21  N20  111.78  3.000
 OMJ  H4   C21  N20  109.61  3.000
 OMJ  H5   C21  C22  108.43  3.000
 OMJ  H4   C21  C22  111.23  3.000
 OMJ  N20  C21  C22  109.38  3.000
 OMJ  H7   C22  H6   107.61  3.000
 OMJ  H7   C22  O23  111.05  3.000
 OMJ  H6   C22  O23  107.02  3.000
 OMJ  H7   C22  C21  108.91  3.000
 OMJ  H6   C22  C21  109.81  3.000
 OMJ  O23  C22  C21  112.32  3.000
 OMJ  C07  C02  C03  117.99  3.000
 OMJ  C07  C02  C01  121.06  3.000
 OMJ  C03  C02  C01  120.96  3.000
 OMJ  H11  C03  C04  119.07  3.000
 OMJ  H11  C03  C02  119.72  3.000
 OMJ  C04  C03  C02  121.21  3.000
 OMJ  O10  C04  C05  123.81  3.000
 OMJ  C05  C04  C03  120.51  3.000
 OMJ  O10  C04  C03  115.67  3.000
 OMJ  H12  C05  C06  119.54  3.000
 OMJ  H12  C05  C04  121.68  3.000
 OMJ  C06  C05  C04  118.78  3.000
 OMJ  H13  C06  C07  119.84  3.000
 OMJ  H13  C06  C05  119.36  3.000
 OMJ  C07  C06  C05  120.80  3.000
 OMJ  C08  C07  C06  119.46  3.000
 OMJ  C08  C07  C02  119.84  3.000
 OMJ  C06  C07  C02  120.70  3.000
 OMJ  N09  C08  C07  180.00  3.000
 OMJ  O10  C11  C16  120.62  3.000
 OMJ  C16  C11  C12  120.80  3.000
 OMJ  O10  C11  C12  118.51  3.000
 OMJ  H14  C15  C16  119.09  3.000
 OMJ  H14  C15  C14  119.69  3.000
 OMJ  C16  C15  C14  121.22  3.000
 OMJ  H15  C16  C15  120.36  3.000
 OMJ  H15  C16  C11  120.49  3.000
 OMJ  C15  C16  C11  119.15  3.000
 OMJ  H17  C17  H16  106.11  3.000
 OMJ  H17  C17  C18  109.46  3.000
 OMJ  H16  C17  C18  109.53  3.000
 OMJ  H17  C17  C14  109.79  3.000
 OMJ  H16  C17  C14  110.18  3.000
 OMJ  C18  C17  C14  111.62  3.000
 OMJ  H19  C24  H18  106.97  3.000
 OMJ  H19  C24  O23  111.01  3.000
 OMJ  H18  C24  O23  107.54  3.000
 OMJ  H19  C24  C25  111.22  3.000
 OMJ  H18  C24  C25  109.14  3.000
 OMJ  O23  C24  C25  110.80  3.000
 OMJ  O28  C26  C25  117.68  3.000
 OMJ  O28  C26  O27  128.06  3.000
 OMJ  C25  C26  O27  114.21  3.000
 OMJ  C21  N20  C18  125.84  3.000
 OMJ  C18  N20  C25  118.50  3.000
 OMJ  C21  N20  C25  115.09  3.000
 OMJ  C11  O10  C04  120.26  3.000
 OMJ  C24  O23  C22  112.63  3.000
 OMJ  O19  C18  N20  121.80  3.000
 OMJ  O19  C18  C17  120.81  3.000
 OMJ  N20  C18  C17  117.38  3.000
 OMJ  H10  C01  H9   108.00  3.000
 OMJ  H10  C01  H8   107.93  3.000
 OMJ  H9   C01  H8   107.17  3.000
 OMJ  H10  C01  C02  111.17  3.000
 OMJ  H9   C01  C02  111.15  3.000
 OMJ  H8   C01  C02  111.24  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  Var_01    C22  C21  N20  C25    59.89  30.0  1
 OMJ  Var_02    O23  C22  C21  N20   -35.59  30.0  1
 OMJ  Var_03    C16  C11  O10  C04    68.51  30.0  2
 OMJ  Var_04    H18  C24  O23  C22  -174.27  30.0  1
 OMJ  Var_05    H6   C22  O23  C24  -145.69  30.0  1
 OMJ  Var_06    C18  C17  C14  C13    85.36  30.0  2
 OMJ  Var_07    N20  C18  C17  C14  -177.33  30.0  3
 OMJ  Var_08    H8   C01  C02  C03   119.41  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

