# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:29:34 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (3R)-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
 OAJ  OAJ  '(3R)-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_OAJ
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
 OAJ  O27  O  OC    -1  -0.591  37.0704  0.3608  22.7520
 OAJ  C25  C  CH1    0  -0.292  35.8392  1.9499  21.4873
 OAJ  C12  C  CR16   0  -0.284  37.6242  3.3818  15.2499
 OAJ  C13  C  CR16   0  -0.315  36.8661  3.0766  16.3727
 OAJ  C14  C  CR6    0   0.172  37.4711  2.7244  17.5732
 OAJ  C21  C  CH2    0  -0.310  36.0321  4.3387  21.9711
 OAJ  C22  C  CH2    0  -0.193  34.9012  4.1688  22.9664
 OAJ  C02  C  C      0   0.152  41.4461  6.2008  12.4014
 OAJ  C03  C  C1     0  -0.387  40.9563  4.9666  12.7865
 OAJ  C04  C  C      0   0.409  40.1861  4.8231  13.9408
 OAJ  C05  C  C1     0  -0.356  39.8938  5.9263  14.7378
 OAJ  C06  C  C1     0  -0.222  40.3790  7.1649  14.3625
 OAJ  C07  C  C      0  -0.043  41.1466  7.3112  13.2092
 OAJ  C08  C  CSP    0   0.024  41.6299  8.6008  12.8489
 OAJ  C11  C  CR6    0   0.280  39.0049  3.3313  15.3340
 OAJ  C15  C  CR16   0  -0.295  38.8620  2.6866  17.6308
 OAJ  C16  C  CR16   0  -0.285  39.6345  2.9896  16.5208
 OAJ  C17  C  CH2    0  -0.700  36.6640  2.3759  18.7866
 OAJ  C24  C  CH2    0  -0.170  34.7009  1.9222  22.4948
 OAJ  C26  C  C      0   0.433  37.1794  1.3871  22.0582
 OAJ  N09  N  NS     0  -0.257  42.0257  9.6420  12.5496
 OAJ  N20  N  NT     0  -0.452  35.9858  3.2967  20.9577
 OAJ  O10  O  O2     0  -0.502  39.7633  3.5705  14.2088
 OAJ  O19  O  O      0  -0.490  36.9601  4.6550  19.4405
 OAJ  O23  O  O2     0  -0.477  34.8778  2.8736  23.5172
 OAJ  O28  O  O      0  -0.585  38.2223  1.9815  21.7325
 OAJ  H2   H  HCH1   0   0.277  35.5279  1.2811  20.6804
 OAJ  H3   H  HCR6   0   0.272  37.1428  3.6465  14.3168
 OAJ  H4   H  HCR6   0   0.256  35.7854  3.1078  16.3041
 OAJ  H5   H  HCH2   0   0.229  36.9965  4.3139  22.4901
 OAJ  H6   H  HCH2   0   0.255  35.9404  5.3149  21.4994
 OAJ  H7   H  HCH2   0   0.239  35.0313  4.8777  23.7858
 OAJ  H8   H  HCH2   0   0.201  33.9422  4.3936  22.4773
 OAJ  H9   H  HCH3   0   0.259  41.8212  7.0589  10.4677
 OAJ  H10  H  HCH3   0   0.260  43.2723  6.7175  11.3958
 OAJ  H11  H  HCH3   0   0.265  42.3788  5.3961  10.6458
 OAJ  H12  H  H      0   0.275  41.1707  4.0925  12.1839
 OAJ  H13  H  H      0   0.292  39.2997  5.8362  15.6367
 OAJ  H14  H  H      0   0.282  40.1571  8.0288  14.9750
 OAJ  H15  H  HCR6   0   0.253  39.3501  2.4087  18.5577
 OAJ  H16  H  HCR6   0   0.272  40.7153  2.9496  16.5737
 OAJ  H17  H  HCH2   0   0.292  35.6522  2.0736  18.5008
 OAJ  H18  H  HCH2   0   0.285  37.1137  1.5130  19.2777
 OAJ  H19  H  HCH2   0   0.204  33.7483  2.0992  21.9744
 OAJ  H20  H  HCH2   0   0.237  34.6559  0.9378  22.9565
 OAJ  C18  C  C      0   0.572  36.5703  3.5421  19.7623
 OAJ  C01  C  CH3    0  -0.744  42.2726  6.3481  11.1614

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
 OAJ  C01  C02  single    1.498  0.020  1.498
 OAJ  N09  C08  triple    1.153  0.020  1.153
 OAJ  C02  C03  aromatic  1.383  0.020  1.383
 OAJ  C02  C07  aromatic  1.405  0.020  1.405
 OAJ  C08  C07  single    1.424  0.020  1.424
 OAJ  C03  C04  aromatic  1.395  0.020  1.395
 OAJ  C07  C06  aromatic  1.393  0.020  1.393
 OAJ  C04  O10  single    1.349  0.020  1.349
 OAJ  C04  C05  aromatic  1.392  0.020  1.392
 OAJ  C06  C05  aromatic  1.382  0.020  1.382
 OAJ  O10  C11  single    1.378  0.020  1.378
 OAJ  C11  C12  aromatic  1.384  0.020  1.384
 OAJ  C11  C16  aromatic  1.386  0.020  1.386
 OAJ  C12  C13  aromatic  1.389  0.020  1.389
 OAJ  C16  C15  aromatic  1.386  0.020  1.386
 OAJ  C13  C14  aromatic  1.390  0.020  1.390
 OAJ  C15  C14  aromatic  1.393  0.020  1.393
 OAJ  C14  C17  single    1.498  0.020  1.498
 OAJ  C17  C18  single    1.523  0.020  1.523
 OAJ  O19  C18  double    1.222  0.020  1.222
 OAJ  C18  N20  single    1.353  0.020  1.353
 OAJ  N20  C25  single    1.455  0.020  1.455
 OAJ  N20  C21  single    1.454  0.020  1.454
 OAJ  C25  C24  single    1.520  0.020  1.520
 OAJ  C25  C26  single    1.562  0.020  1.562
 OAJ  C24  O23  single    1.408  0.020  1.408
 OAJ  C26  O28  deloc     1.244  0.020  1.244
 OAJ  C26  O27  deloc     1.244  0.020  1.244
 OAJ  C21  C22  single    1.516  0.020  1.516
 OAJ  C22  O23  single    1.408  0.020  1.408
 OAJ  C25  H2   single    0.970  0.020  1.090
 OAJ  C12  H3   single    0.930  0.020  1.080
 OAJ  C13  H4   single    0.930  0.020  1.080
 OAJ  C21  H5   single    0.970  0.020  1.090
 OAJ  C21  H6   single    0.970  0.020  1.090
 OAJ  C22  H7   single    0.970  0.020  1.090
 OAJ  C22  H8   single    0.970  0.020  1.090
 OAJ  C01  H9   single    0.970  0.020  1.090
 OAJ  C01  H10  single    0.970  0.020  1.090
 OAJ  C01  H11  single    0.970  0.020  1.090
 OAJ  C03  H12  single    0.930  0.020  1.080
 OAJ  C05  H13  single    0.930  0.020  1.080
 OAJ  C06  H14  single    0.930  0.020  1.080
 OAJ  C15  H15  single    0.930  0.020  1.080
 OAJ  C16  H16  single    0.930  0.020  1.080
 OAJ  C17  H17  single    0.970  0.020  1.090
 OAJ  C17  H18  single    0.970  0.020  1.090
 OAJ  C24  H19  single    0.970  0.020  1.090
 OAJ  C24  H20  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
 OAJ  H2   C25  N20  109.05  3.000
 OAJ  H2   C25  C26  107.08  3.000
 OAJ  N20  C25  C26  112.35  3.000
 OAJ  H2   C25  C24  105.35  3.000
 OAJ  C26  C25  C24  113.18  3.000
 OAJ  N20  C25  C24  109.49  3.000
 OAJ  H3   C12  C11  120.31  3.000
 OAJ  H3   C12  C13  120.51  3.000
 OAJ  C11  C12  C13  119.17  3.000
 OAJ  H4   C13  C14  119.76  3.000
 OAJ  H4   C13  C12  119.14  3.000
 OAJ  C14  C13  C12  121.10  3.000
 OAJ  C17  C14  C15  119.88  3.000
 OAJ  C17  C14  C13  121.60  3.000
 OAJ  C15  C14  C13  118.52  3.000
 OAJ  H6   C21  H5   107.45  3.000
 OAJ  H6   C21  N20  109.76  3.000
 OAJ  H5   C21  N20  109.99  3.000
 OAJ  H6   C21  C22  108.81  3.000
 OAJ  H5   C21  C22  110.07  3.000
 OAJ  N20  C21  C22  110.70  3.000
 OAJ  H8   C22  H7   107.76  3.000
 OAJ  H8   C22  O23  110.34  3.000
 OAJ  H7   C22  O23  107.81  3.000
 OAJ  H8   C22  C21  109.61  3.000
 OAJ  H7   C22  C21  109.34  3.000
 OAJ  O23  C22  C21  111.86  3.000
 OAJ  C07  C02  C03  118.01  3.000
 OAJ  C07  C02  C01  121.05  3.000
 OAJ  C03  C02  C01  120.93  3.000
 OAJ  H12  C03  C04  119.12  3.000
 OAJ  H12  C03  C02  119.69  3.000
 OAJ  C04  C03  C02  121.19  3.000
 OAJ  O10  C04  C05  123.81  3.000
 OAJ  C05  C04  C03  120.54  3.000
 OAJ  O10  C04  C03  115.65  3.000
 OAJ  H13  C05  C06  119.56  3.000
 OAJ  H13  C05  C04  121.69  3.000
 OAJ  C06  C05  C04  118.75  3.000
 OAJ  H14  C06  C07  119.86  3.000
 OAJ  H14  C06  C05  119.33  3.000
 OAJ  C07  C06  C05  120.82  3.000
 OAJ  C08  C07  C06  119.45  3.000
 OAJ  C06  C07  C02  120.68  3.000
 OAJ  C08  C07  C02  119.86  3.000
 OAJ  N09  C08  C07  180.00  3.000
 OAJ  O10  C11  C16  119.47  3.000
 OAJ  C16  C11  C12  120.93  3.000
 OAJ  O10  C11  C12  119.54  3.000
 OAJ  H15  C15  C16  119.34  3.000
 OAJ  H15  C15  C14  119.48  3.000
 OAJ  C16  C15  C14  121.18  3.000
 OAJ  H16  C16  C15  120.61  3.000
 OAJ  H16  C16  C11  120.28  3.000
 OAJ  C15  C16  C11  119.11  3.000
 OAJ  H18  C17  H17  106.29  3.000
 OAJ  H18  C17  C18  110.05  3.000
 OAJ  H17  C17  C18  108.79  3.000
 OAJ  H18  C17  C14  109.07  3.000
 OAJ  H17  C17  C14  110.54  3.000
 OAJ  C18  C17  C14  111.95  3.000
 OAJ  H20  C24  H19  108.09  3.000
 OAJ  H20  C24  O23  107.96  3.000
 OAJ  H19  C24  O23  110.10  3.000
 OAJ  H20  C24  C25  109.19  3.000
 OAJ  H19  C24  C25  109.39  3.000
 OAJ  O23  C24  C25  112.02  3.000
 OAJ  O28  C26  C25  116.85  3.000
 OAJ  O28  C26  O27  127.88  3.000
 OAJ  C25  C26  O27  115.22  3.000
 OAJ  C21  N20  C18  118.16  3.000
 OAJ  C21  N20  C25  114.39  3.000
 OAJ  C18  N20  C25  122.22  3.000
 OAJ  C11  O10  C04  119.73  3.000
 OAJ  C24  O23  C22  109.86  3.000
 OAJ  O19  C18  N20  122.38  3.000
 OAJ  N20  C18  C17  116.97  3.000
 OAJ  O19  C18  C17  120.58  3.000
 OAJ  H11  C01  H10  107.98  3.000
 OAJ  H11  C01  H9   108.01  3.000
 OAJ  H10  C01  H9   107.17  3.000
 OAJ  H11  C01  C02  111.11  3.000
 OAJ  H10  C01  C02  111.16  3.000
 OAJ  H9   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
 OAJ  CONST_01  C15  C16  C11  C12     0.00   0.0  0
 OAJ  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 OAJ  CONST_03  C16  C11  C12  C13     0.00   0.0  0
 OAJ  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 OAJ  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 OAJ  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 OAJ  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 OAJ  CONST_08  C05  C06  C07  C02     0.00   0.0  0
 OAJ  CONST_09  C06  C07  C02  C03     0.00   0.0  0
 OAJ  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 OAJ  CONST_11  C07  C02  C03  C04     0.00   0.0  0
 OAJ  CONST_12  C07  C06  C05  C04     0.00   0.0  0
 OAJ  CONST_13  C17  C14  C13  C12   180.00   0.0  0
 OAJ  CONST_14  O10  C11  C12  C13   180.00   0.0  0
 OAJ  CONST_15  C04  C03  C02  C01   180.00   0.0  0
 OAJ  CONST_16  C06  C07  C02  C01   180.00   0.0  0
 OAJ  CONST_17  O10  C04  C03  C02   180.00   0.0  0
 OAJ  CONST_18  C08  C07  C02  C03   180.00   0.0  0
 OAJ  CONST_19  C08  C07  C06  C05   180.00   0.0  0
 OAJ  CONST_20  O10  C04  C05  C06   180.00   0.0  0
 OAJ  CONST_21  O10  C11  C16  C15   180.00   0.0  0
 OAJ  CONST_22  C17  C14  C15  C16   180.00   0.0  0
 OAJ  CONST_23  H16  C16  C11  C12   180.00   0.0  0
 OAJ  CONST_24  H15  C15  C14  C13   180.00   0.0  0
 OAJ  CONST_25  H3   C12  C13  C14   180.00   0.0  0
 OAJ  CONST_26  H14  C06  C07  C02   180.00   0.0  0
 OAJ  CONST_27  H13  C05  C04  C03   180.00   0.0  0
 OAJ  CONST_28  H12  C03  C04  C05   180.00   0.0  0
 OAJ  CONST_29  H4   C13  C12  C11   180.00   0.0  0
 OAJ  CONST_32  C17  C18  N20  C21   180.00   0.0  0
 OAJ  CONST_33  O19  C18  N20  C21     0.00   0.0  0
 OAJ  Var_01    C22  C21  N20  C25   -48.56  30.0  1
 OAJ  Var_02    O23  C22  C21  N20    53.30  30.0  1
 OAJ  Var_03    C16  C11  O10  C04   -90.96  30.0  2
 OAJ  Var_04    H19  C24  O23  C22   -60.45  30.0  1
 OAJ  Var_05    H7   C22  O23  C24   179.56  30.0  1
 OAJ  Var_06    C18  C17  C14  C13   -99.96  30.0  2
 OAJ  Var_07    N20  C18  C17  C14  -173.17  30.0  3
 OAJ  Var_08    H9   C01  C02  C03   122.19  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
 OAJ  chir_01  C25  N20  C24  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
 OAJ  plan-1  C02  0.020
 OAJ  plan-1  C03  0.020
 OAJ  plan-1  C04  0.020
 OAJ  plan-1  C05  0.020
 OAJ  plan-1  C06  0.020
 OAJ  plan-1  C07  0.020
 OAJ  plan-1  C08  0.020
 OAJ  plan-1  N09  0.020
 OAJ  plan-1  O10  0.020
 OAJ  plan-1  H12  0.020
 OAJ  plan-1  H13  0.020
 OAJ  plan-1  H14  0.020
 OAJ  plan-1  C01  0.020
 OAJ  plan-2  C12  0.020
 OAJ  plan-2  C13  0.020
 OAJ  plan-2  C14  0.020
 OAJ  plan-2  C11  0.020
 OAJ  plan-2  C15  0.020
 OAJ  plan-2  C16  0.020
 OAJ  plan-2  C17  0.020
 OAJ  plan-2  O10  0.020
 OAJ  plan-2  H3   0.020
 OAJ  plan-2  H4   0.020
 OAJ  plan-2  H15  0.020
 OAJ  plan-2  H16  0.020
 OAJ  plan-3  C25  0.020
 OAJ  plan-3  C21  0.020
 OAJ  plan-3  C17  0.020
 OAJ  plan-3  N20  0.020
 OAJ  plan-3  O19  0.020
 OAJ  plan-3  C18  0.020
 OAJ  plan-4  O27  0.020
 OAJ  plan-4  C25  0.020
 OAJ  plan-4  C26  0.020
 OAJ  plan-4  O28  0.020

