# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:37:43 2021
#   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  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_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  OH1   0  -0.585  36.0724   0.1187  22.7698
 OAJ  C25  C  CH1   0  -0.283  35.6295   2.0067  21.4178
 OAJ  C12  C  CR16  0  -0.282  37.9597   3.3653  15.4230
 OAJ  C13  C  CR16  0  -0.307  37.2172   3.0398  16.5486
 OAJ  C14  C  CR6   0   0.179  37.8340   2.5893  17.7105
 OAJ  C21  C  CH2   0  -0.320  36.2897   4.2729  22.0752
 OAJ  C22  C  CH2   0  -0.197  34.9664   4.3772  22.8056
 OAJ  C02  C  CR6   0   0.154  41.2265   6.2716  12.3086
 OAJ  C03  C  CR16  0  -0.388  40.9217   5.0004  12.7597
 OAJ  C04  C  CR6   0   0.406  40.3287   4.8005  14.0059
 OAJ  C05  C  CR16  0  -0.353  40.0310   5.8820  14.8303
 OAJ  C06  C  CR16  0  -0.222  40.3294   7.1570  14.3893
 OAJ  C07  C  CR6   0  -0.044  40.9188   7.3594  13.1432
 OAJ  C08  C  CSP   0   0.026  41.2102   8.6857  12.7155
 OAJ  C11  C  CR6   0   0.283  39.3385   3.2378  15.4649
 OAJ  C15  C  CR16  0  -0.296  39.2187   2.4615  17.7224
 OAJ  C16  C  CR16  0  -0.294  39.9777   2.7872  16.6084
 OAJ  C17  C  CH2   0  -0.719  37.0219   2.2554  18.9256
 OAJ  C24  C  CH2   0  -0.179  34.3207   2.2607  22.1648
 OAJ  C26  C  C     0   0.571  36.6345   1.1785  22.2148
 OAJ  N09  N  NS    0  -0.259  41.4455   9.7592  12.3655
 OAJ  N20  N  NT    0  -0.466  36.2205   3.2653  21.0234
 OAJ  O10  O  O2    0  -0.503  40.0888   3.5148  14.3434
 OAJ  O19  O  O     0  -0.470  37.6752   4.4073  19.7371
 OAJ  O23  O  O2    0  -0.474  34.5188   3.1164  23.2571
 OAJ  O28  O  O     0  -0.426  37.8064   1.4395  22.2902
 OAJ  H1   H  HOH1  0   0.489  36.7371  -0.4097  23.2383
 OAJ  H2   H  HCH1  0   0.332  35.3611   1.4178  20.5372
 OAJ  H3   H  HCR6  0   0.277  37.4678   3.7097  14.5217
 OAJ  H4   H  HCR6  0   0.258  36.1389   3.1375  16.5137
 OAJ  H5   H  HCH2  0   0.247  37.0936   4.0346  22.7790
 OAJ  H6   H  HCH2  0   0.272  36.5214   5.2390  21.6340
 OAJ  H7   H  HCH2  0   0.253  35.0847   5.0203  23.6776
 OAJ  H8   H  HCH2  0   0.215  34.2138   4.8321  22.1480
 OAJ  H9   H  HCH3  0   0.260  41.2567   7.1313  10.3385
 OAJ  H10  H  HCH3  0   0.261  42.8435   6.9528  11.0709
 OAJ  H11  H  HCH3  0   0.265  42.0000   5.5368  10.4484
 OAJ  H12  H  HCR6  0   0.277  41.1433   4.1418  12.1378
 OAJ  H13  H  HCR6  0   0.292  39.5768   5.7466  15.8021
 OAJ  H14  H  HCR6  0   0.285  40.1031   8.0047  15.0219
 OAJ  H15  H  HCR6  0   0.255  39.7192   2.1030  18.6136
 OAJ  H16  H  HCR6  0   0.274  41.0552   2.6859  16.6261
 OAJ  H17  H  HCH2  0   0.300  35.9990   2.0075  18.6315
 OAJ  H18  H  HCH2  0   0.297  37.4212   1.3599  19.4099
 OAJ  H19  H  HCH2  0   0.237  33.6067   2.6922  21.4505
 OAJ  H20  H  HCH2  0   0.265  33.8995   1.3266  22.5322
 OAJ  C18  C  C     0   0.584  37.0142   3.4027  19.9275
 OAJ  C01  C  CH3   0  -0.745  41.8641   6.4816  10.9703

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    1.497  0.020  1.497
 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    1.351  0.020  1.351
 OAJ  C04  C05  aromatic  1.392  0.020  1.392
 OAJ  C06  C05  aromatic  1.382  0.020  1.382
 OAJ  O10  C11  single    1.377  0.020  1.377
 OAJ  C11  C12  aromatic  1.385  0.020  1.385
 OAJ  C11  C16  aromatic  1.385  0.020  1.385
 OAJ  C12  C13  aromatic  1.387  0.020  1.387
 OAJ  C16  C15  aromatic  1.387  0.020  1.387
 OAJ  C13  C14  aromatic  1.390  0.020  1.390
 OAJ  C15  C14  aromatic  1.391  0.020  1.391
 OAJ  C14  C17  single    1.499  0.020  1.499
 OAJ  C17  C18  single    1.523  0.020  1.523
 OAJ  O19  C18  double    1.218  0.020  1.218
 OAJ  C18  N20  single    1.360  0.020  1.360
 OAJ  N20  C25  single    1.445  0.020  1.445
 OAJ  N20  C21  single    1.458  0.020  1.458
 OAJ  C25  C24  single    1.528  0.020  1.528
 OAJ  C25  C26  single    1.527  0.020  1.527
 OAJ  C24  O23  single    1.402  0.020  1.402
 OAJ  C26  O28  double    1.203  0.020  1.203
 OAJ  C26  O27  single    1.322  0.020  1.322
 OAJ  C21  C22  single    1.515  0.020  1.515
 OAJ  C22  O23  single    1.412  0.020  1.412
 OAJ  O27  H1   single    0.850  0.020  0.980
 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  H1   O27  C26  110.38  3.000
 OAJ  H2   C25  N20  110.48  3.000
 OAJ  H2   C25  C26  106.86  3.000
 OAJ  N20  C25  C26  110.23  3.000
 OAJ  H2   C25  C24  105.85  3.000
 OAJ  C26  C25  C24  113.49  3.000
 OAJ  N20  C25  C24  109.80  3.000
 OAJ  H3   C12  C11  120.43  3.000
 OAJ  H3   C12  C13  120.45  3.000
 OAJ  C11  C12  C13  119.12  3.000
 OAJ  H4   C13  C14  119.85  3.000
 OAJ  H4   C13  C12  119.05  3.000
 OAJ  C14  C13  C12  121.10  3.000
 OAJ  C17  C14  C15  120.79  3.000
 OAJ  C17  C14  C13  120.61  3.000
 OAJ  C15  C14  C13  118.60  3.000
 OAJ  H6   C21  H5   107.33  3.000
 OAJ  H6   C21  N20  109.35  3.000
 OAJ  H5   C21  N20  110.37  3.000
 OAJ  H6   C21  C22  108.70  3.000
 OAJ  H5   C21  C22  110.28  3.000
 OAJ  N20  C21  C22  110.72  3.000
 OAJ  H8   C22  H7   108.00  3.000
 OAJ  H8   C22  O23  110.13  3.000
 OAJ  H7   C22  O23  107.78  3.000
 OAJ  H8   C22  C21  109.78  3.000
 OAJ  H7   C22  C21  109.36  3.000
 OAJ  O23  C22  C21  111.69  3.000
 OAJ  C07  C02  C03  118.01  3.000
 OAJ  C07  C02  C01  121.04  3.000
 OAJ  C03  C02  C01  120.95  3.000
 OAJ  H12  C03  C04  119.11  3.000
 OAJ  H12  C03  C02  119.76  3.000
 OAJ  C04  C03  C02  121.13  3.000
 OAJ  O10  C04  C05  123.61  3.000
 OAJ  C05  C04  C03  120.58  3.000
 OAJ  O10  C04  C03  115.80  3.000
 OAJ  H13  C05  C06  119.54  3.000
 OAJ  H13  C05  C04  121.66  3.000
 OAJ  C06  C05  C04  118.79  3.000
 OAJ  H14  C06  C07  119.85  3.000
 OAJ  H14  C06  C05  119.43  3.000
 OAJ  C07  C06  C05  120.72  3.000
 OAJ  C08  C07  C06  119.39  3.000
 OAJ  C06  C07  C02  120.76  3.000
 OAJ  C08  C07  C02  119.86  3.000
 OAJ  N09  C08  C07  180.00  3.000
 OAJ  O10  C11  C16  119.08  3.000
 OAJ  C16  C11  C12  120.94  3.000
 OAJ  O10  C11  C12  119.94  3.000
 OAJ  H15  C15  C16  119.07  3.000
 OAJ  H15  C15  C14  119.84  3.000
 OAJ  C16  C15  C14  121.09  3.000
 OAJ  H16  C16  C15  120.64  3.000
 OAJ  H16  C16  C11  120.22  3.000
 OAJ  C15  C16  C11  119.14  3.000
 OAJ  H18  C17  H17  105.98  3.000
 OAJ  H18  C17  C18  109.10  3.000
 OAJ  H17  C17  C18  110.07  3.000
 OAJ  H18  C17  C14  110.10  3.000
 OAJ  H17  C17  C14  109.85  3.000
 OAJ  C18  C17  C14  111.60  3.000
 OAJ  H20  C24  H19  107.77  3.000
 OAJ  H20  C24  O23  108.39  3.000
 OAJ  H19  C24  O23  111.03  3.000
 OAJ  H20  C24  C25  110.72  3.000
 OAJ  H19  C24  C25  107.70  3.000
 OAJ  O23  C24  C25  111.18  3.000
 OAJ  O28  C26  C25  123.80  3.000
 OAJ  O28  C26  O27  124.18  3.000
 OAJ  C25  C26  O27  111.98  3.000
 OAJ  C21  N20  C18  118.93  3.000
 OAJ  C21  N20  C25  115.11  3.000
 OAJ  C18  N20  C25  123.12  3.000
 OAJ  C11  O10  C04  119.45  3.000
 OAJ  C24  O23  C22  109.92  3.000
 OAJ  O19  C18  N20  121.75  3.000
 OAJ  N20  C18  C17  117.19  3.000
 OAJ  O19  C18  C17  121.05  3.000
 OAJ  H11  C01  H10  107.88  3.000
 OAJ  H11  C01  H9   107.99  3.000
 OAJ  H10  C01  H9   107.21  3.000
 OAJ  H11  C01  C02  111.12  3.000
 OAJ  H10  C01  C02  111.12  3.000
 OAJ  H9   C01  C02  111.35  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_30  C17  C18  N20  C25     0.00   0.0  0
 OAJ  CONST_31  O19  C18  N20  C25   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  CONST_34  H1   O27  C26  C25   180.00   0.0  0
 OAJ  Var_01    C22  C21  N20  C25   -46.88  30.0  1
 OAJ  Var_02    O23  C22  C21  N20    52.25  30.0  1
 OAJ  Var_03    C16  C11  O10  C04  -104.84  30.0  2
 OAJ  Var_04    H19  C24  O23  C22   -57.23  30.0  1
 OAJ  Var_05    H7   C22  O23  C24   178.60  30.0  1
 OAJ  Var_06    C18  C17  C14  C13   -98.34  30.0  2
 OAJ  Var_07    N20  C18  C17  C14   174.69  30.0  3
 OAJ  Var_08    H9   C01  C02  C03   122.26  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
 OAJ  plan-4  H1   0.020

