# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:38:26 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3S)-1-cyclohexyl-5-oxo-N-phenylpyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@@H](CN1C2CCCCC2)C(=O)Nc3ccccc3
#
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
 566  566  (3S)-1-cyclohexyl-5-oxo-N-phenylpyrrolidine-3-carboxamide  ligand  43  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_566
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
 566  C1    C  CH2   0  -0.439  -5.5692   0.1918  -0.2740
 566  C2    C  CH2   0  -0.436  -4.3568  -0.6266   0.1625
 566  C3    C  CH1   0  -0.053  -3.0812  -0.0329  -0.4334
 566  C4    C  CH2   0  -0.426  -2.9086   1.4346  -0.0418
 566  C5    C  CH2   0  -0.439  -4.1299   2.2492  -0.4571
 566  C6    C  CH2   0  -0.430  -5.4167   1.6600   0.1123
 566  C15   C  C     0   0.536  -1.4346  -1.1693   1.0578
 566  C16   C  CH2   0  -0.561  -0.1636  -1.9717   0.8636
 566  C17   C  CH1   0  -0.468   0.3070  -1.5772  -0.5428
 566  C18   C  CH2   0  -0.249  -0.9996  -1.1966  -1.2385
 566  N19   N  NT    0  -0.461  -1.8825  -0.8086  -0.1558
 566  C24   C  CR16  0  -0.348   4.9174  -0.6219  -0.0683
 566  C25   C  CR16  0  -0.244   6.0897   0.0775   0.1599
 566  C26   C  CR16  0  -0.273   6.0574   1.4477   0.3862
 566  C27   C  CR16  0  -0.244   4.8334   2.0993   0.3793
 566  C28   C  CR16  0  -0.316   3.6480   1.4115   0.1517
 566  C29   C  CR6   0   0.371   3.6835   0.0345  -0.0751
 566  C33   C  C     0   0.576   1.2530  -0.3932  -0.4290
 566  N35   N  NH1   0  -0.747   2.5535  -0.7587  -0.3021
 566  O37   O  O     0  -0.451   0.8587   0.7580  -0.4071
 566  O38   O  O     0  -0.503  -1.9609  -0.9303   2.1340
 566  H11   H  HCH2  0   0.211  -5.6939   0.1127  -1.3597
 566  H12   H  HCH2  0   0.231  -6.4747  -0.2260   0.1719
 566  H21   H  HCH2  0   0.231  -4.4630  -1.6666  -0.1570
 566  H22   H  HCH2  0   0.228  -4.2952  -0.6278   1.2519
 566  H3    H  HCH1  0   0.237  -3.1976  -0.0721  -1.5222
 566  H41   H  HCH2  0   0.220  -2.7650   1.5044   1.0404
 566  H42   H  HCH2  0   0.236  -2.0031   1.8296  -0.5090
 566  H51   H  HCH2  0   0.212  -4.1951   2.2679  -1.5506
 566  H52   H  HCH2  0   0.231  -4.0108   3.2870  -0.1379
 566  H61   H  HCH2  0   0.228  -6.2797   2.2330  -0.2354
 566  H62   H  HCH2  0   0.211  -5.4042   1.7473   1.2042
 566  H161  H  HCH2  0   0.281   0.5609  -1.7791   1.6548
 566  H162  H  HCH2  0   0.294  -0.4119  -3.0356   0.9056
 566  H17   H  HCH1  0   0.300   0.7967  -2.4070  -1.0531
 566  H181  H  HCH2  0   0.258  -0.8743  -0.3761  -1.9461
 566  H182  H  HCH2  0   0.256  -1.4073  -2.0500  -1.7884
 566  H25   H  HCR6  0   0.260   7.0319  -0.4548   0.1599
 566  H26   H  HCR6  0   0.256   6.9715   1.9971   0.5669
 566  H27   H  HCR6  0   0.258   4.7884   3.1666   0.5541
 566  H28   H  HCR6  0   0.279   2.7157   1.9511   0.1572
 566  HN35  H  HNH1  0   0.418   2.7412  -1.7475  -0.3760
 566  H24   H  HCR6  0   0.270   4.9583  -1.6913  -0.2401

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
 566  C1   C2    single    1.527  0.020  1.527
 566  C1   C6    single    1.526  0.020  1.526
 566  C1   H11   single    0.970  0.020  1.090
 566  C1   H12   single    0.970  0.020  1.090
 566  C2   C3    single    1.528  0.020  1.528
 566  C2   H21   single    0.970  0.020  1.090
 566  C2   H22   single    0.970  0.020  1.090
 566  C3   C4    single    1.529  0.020  1.529
 566  C3   N19   single    1.454  0.020  1.454
 566  C3   H3    single    0.970  0.020  1.090
 566  C4   C5    single    1.526  0.020  1.526
 566  C4   H41   single    0.970  0.020  1.090
 566  C4   H42   single    0.970  0.020  1.090
 566  C5   C6    single    1.525  0.020  1.525
 566  C5   H51   single    0.970  0.020  1.090
 566  C5   H52   single    0.970  0.020  1.090
 566  C6   H61   single    0.970  0.020  1.090
 566  C6   H62   single    0.970  0.020  1.090
 566  C15  C16   single    1.516  0.020  1.516
 566  C15  N19   single    1.343  0.020  1.343
 566  C15  O38   double    1.222  0.020  1.222
 566  C16  C17   single    1.535  0.020  1.535
 566  C16  H161  single    0.970  0.020  1.090
 566  C16  H162  single    0.970  0.020  1.090
 566  C17  C18   single    1.528  0.020  1.528
 566  C17  C33   single    1.520  0.020  1.520
 566  C17  H17   single    0.970  0.020  1.090
 566  C18  N19   single    1.450  0.020  1.450
 566  C18  H181  single    0.970  0.020  1.090
 566  C18  H182  single    0.970  0.020  1.090
 566  C24  C25   aromatic  1.384  0.020  1.384
 566  C24  C29   aromatic  1.398  0.020  1.398
 566  C24  H24   single    0.930  0.020  1.080
 566  C25  C26   aromatic  1.389  0.020  1.389
 566  C25  H25   single    0.930  0.020  1.080
 566  C26  C27   aromatic  1.387  0.020  1.387
 566  C26  H26   single    0.930  0.020  1.080
 566  C27  C28   aromatic  1.389  0.020  1.389
 566  C27  H27   single    0.930  0.020  1.080
 566  C28  C29   aromatic  1.396  0.020  1.396
 566  C28  H28   single    0.930  0.020  1.080
 566  C29  N35   single    1.399  0.020  1.399
 566  C33  N35   single    1.357  0.020  1.357
 566  C33  O37   double    1.217  0.020  1.217
 566  N35  HN35  single    0.860  0.020  1.020

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
 566  H12   C1   H11   106.41  3.000
 566  H12   C1   C6    110.34  3.000
 566  H11   C1   C6    109.37  3.000
 566  H12   C1   C2    109.67  3.000
 566  H11   C1   C2    109.57  3.000
 566  C6    C1   C2    111.35  3.000
 566  H22   C2   H21   107.24  3.000
 566  H22   C2   C3    110.04  3.000
 566  H21   C2   C3    109.68  3.000
 566  H22   C2   C1    109.32  3.000
 566  H21   C2   C1    110.44  3.000
 566  C3    C2   C1    110.07  3.000
 566  H3    C3   N19   104.96  3.000
 566  H3    C3   C4    107.51  3.000
 566  N19   C3   C4    111.72  3.000
 566  H3    C3   C2    106.56  3.000
 566  N19   C3   C2    113.97  3.000
 566  C4    C3   C2    111.55  3.000
 566  H42   C4   H41   106.92  3.000
 566  H42   C4   C5    110.72  3.000
 566  H41   C4   C5    109.90  3.000
 566  H42   C4   C3    109.33  3.000
 566  H41   C4   C3    109.24  3.000
 566  C5    C4   C3    110.64  3.000
 566  H52   C5   H51   106.38  3.000
 566  H52   C5   C6    110.48  3.000
 566  H51   C5   C6    109.20  3.000
 566  H52   C5   C4    109.90  3.000
 566  H51   C5   C4    109.18  3.000
 566  C6    C5   C4    111.56  3.000
 566  H62   C6   H61   106.52  3.000
 566  H62   C6   C5    109.37  3.000
 566  H61   C6   C5    110.18  3.000
 566  H62   C6   C1    109.28  3.000
 566  H61   C6   C1    110.19  3.000
 566  C5    C6   C1    111.19  3.000
 566  O38   C15  N19   126.86  3.000
 566  O38   C15  C16   125.30  3.000
 566  N19   C15  C16   107.82  3.000
 566  H162  C16  H161  107.16  3.000
 566  H162  C16  C17   110.79  3.000
 566  H161  C16  C17   114.58  3.000
 566  H162  C16  C15   108.65  3.000
 566  H161  C16  C15   111.77  3.000
 566  C17   C16  C15   103.80  3.000
 566  H17   C17  C33   110.39  3.000
 566  H17   C17  C18   111.13  3.000
 566  C33   C17  C18   111.85  3.000
 566  H17   C17  C16   111.78  3.000
 566  C33   C17  C16   108.81  3.000
 566  C18   C17  C16   102.65  3.000
 566  H182  C18  H181  107.67  3.000
 566  H182  C18  N19   110.92  3.000
 566  H181  C18  N19   110.67  3.000
 566  H182  C18  C17   110.68  3.000
 566  H181  C18  C17   112.61  3.000
 566  N19   C18  C17   104.32  3.000
 566  C18   N19  C15   113.57  3.000
 566  C18   N19  C3    120.13  3.000
 566  C15   N19  C3    126.20  3.000
 566  H24   C24  C29   119.73  3.000
 566  H24   C24  C25   119.52  3.000
 566  C29   C24  C25   120.75  3.000
 566  H25   C25  C26   120.36  3.000
 566  H25   C25  C24   119.27  3.000
 566  C26   C25  C24   120.37  3.000
 566  H26   C26  C27   120.54  3.000
 566  H26   C26  C25   120.56  3.000
 566  C27   C26  C25   118.90  3.000
 566  H27   C27  C28   118.63  3.000
 566  H27   C27  C26   119.95  3.000
 566  C28   C27  C26   121.42  3.000
 566  H28   C28  C29   121.13  3.000
 566  H28   C28  C27   119.32  3.000
 566  C29   C28  C27   119.55  3.000
 566  N35   C29  C28   124.40  3.000
 566  N35   C29  C24   116.59  3.000
 566  C28   C29  C24   119.00  3.000
 566  O37   C33  N35   124.31  3.000
 566  O37   C33  C17   122.45  3.000
 566  N35   C33  C17   113.19  3.000
 566  HN35  N35  C33   115.81  3.000
 566  HN35  N35  C29   114.65  3.000
 566  C33   N35  C29   129.54  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
 566  CONST_01  C27   C26  C25  C24    0.00   0.0  0
 566  CONST_02  C27   C28  C29  C24    0.00   0.0  0
 566  CONST_03  C28   C29  C24  C25    0.00   0.0  0
 566  CONST_04  C28   C27  C26  C25    0.00   0.0  0
 566  CONST_05  C29   C24  C25  C26    0.00   0.0  0
 566  CONST_06  C29   C28  C27  C26    0.00   0.0  0
 566  CONST_07  C16   C15  N19  C3   180.00   0.0  0
 566  CONST_08  C18   N19  C15  C16    0.00   0.0  0
 566  CONST_09  N35   C29  C24  C25  180.00   0.0  0
 566  CONST_10  N35   C29  C28  C27  180.00   0.0  0
 566  CONST_11  O38   C15  N19  C3     0.00   0.0  0
 566  CONST_12  O38   C15  N19  C18  180.00   0.0  0
 566  CONST_13  H26   C26  C25  C24  180.00   0.0  0
 566  CONST_14  H28   C28  C29  C24  180.00   0.0  0
 566  CONST_15  H27   C27  C26  C25  180.00   0.0  0
 566  CONST_16  H24   C24  C25  C26  180.00   0.0  0
 566  CONST_17  H25   C25  C26  C27  180.00   0.0  0
 566  CONST_18  C29   N35  C33  C17  180.00   0.0  0
 566  CONST_19  C33   N35  C29  C24  180.00   0.0  0
 566  CONST_20  C33   N35  C29  C28    0.00   0.0  0
 566  CONST_21  HN35  N35  C29  C24    0.00   0.0  0
 566  CONST_22  O37   C33  N35  C29    0.00   0.0  0
 566  Var_01    C4    C5   C6   C1   -54.98  30.0  1
 566  Var_02    C5    C6   C1   C2    55.83  30.0  1
 566  Var_03    C6    C1   C2   C3   -56.44  30.0  1
 566  Var_04    C6    C5   C4   C3    54.95  30.0  1
 566  Var_05    C17   C18  N19  C3   162.69  30.0  1
 566  Var_06    N19   C15  C16  C17   20.15  30.0  1

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
 566  chir_01  C3   C2   C4   N19  negativ
 566  chir_02  C17  C16  C18  C33  negativ

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
 566  plan-1  C17   0.020
 566  plan-1  C29   0.020
 566  plan-1  C33   0.020
 566  plan-1  N35   0.020
 566  plan-1  O37   0.020
 566  plan-1  HN35  0.020
 566  plan-2  C24   0.020
 566  plan-2  C25   0.020
 566  plan-2  C26   0.020
 566  plan-2  C27   0.020
 566  plan-2  C28   0.020
 566  plan-2  C29   0.020
 566  plan-2  N35   0.020
 566  plan-2  H25   0.020
 566  plan-2  H26   0.020
 566  plan-2  H27   0.020
 566  plan-2  H28   0.020
 566  plan-2  H24   0.020
 566  plan-3  C3    0.020
 566  plan-3  C15   0.020
 566  plan-3  C16   0.020
 566  plan-3  C18   0.020
 566  plan-3  N19   0.020
 566  plan-3  O38   0.020

