# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:13:12 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN(C1)Cc2ccc(Cl)cc2
#
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
 WKJ  WKJ  (3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-ol  ligand  28  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WKJ
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
 WKJ  C10  C   CR6   0  -0.057  -27.5978  -8.0817  -19.9348
 WKJ  C13  C   CR16  0  -0.289  -29.7658  -7.4251  -19.1691
 WKJ  C02  C   CR15  0   0.047  -34.4920  -6.0958  -19.7935
 WKJ  C03  C   CH2   0  -0.506  -33.6930  -5.6275  -21.0140
 WKJ  C04  C   CH2   0  -0.268  -32.4777  -6.5666  -21.0728
 WKJ  C06  C   CH2   0  -0.315  -31.8512  -8.6246  -19.9278
 WKJ  C07  C   CR6   0   0.097  -30.3590  -8.4140  -19.9500
 WKJ  C08  C   CR16  0  -0.319  -29.5400  -9.2258  -20.7265
 WKJ  C09  C   CR16  0  -0.197  -28.1600  -9.0715  -20.7232
 WKJ  C12  C   CR16  0  -0.199  -28.3907  -7.2513  -19.1564
 WKJ  C14  C   CH2   0  -0.300  -33.9946  -7.5255  -19.6008
 WKJ  N05  N   NR5   0  -0.437  -32.5809  -7.3860  -19.8697
 WKJ  CL1  CL  CL    0  -0.137  -25.8747  -7.8713  -19.9247
 WKJ  H1   H   HCR6  0   0.256  -30.3910  -6.7750  -18.5702
 WKJ  H2   H   HCR5  0   0.209  -34.1924  -5.5093  -18.9155
 WKJ  H3   H   HCH2  0   0.248  -33.4080  -4.5783  -20.9408
 WKJ  H4   H   HCH2  0   0.239  -34.3057  -5.7377  -21.9103
 WKJ  H5   H   HCH2  0   0.204  -32.5151  -7.1863  -21.9820
 WKJ  H6   H   HCH2  0   0.234  -31.5283  -6.0283  -21.0942
 WKJ  H7   H   HCH2  0   0.212  -32.1430  -9.2353  -20.7992
 WKJ  H8   H   HCH2  0   0.256  -32.1073  -9.2146  -19.0419
 WKJ  H9   H   HCR6  0   0.258  -29.9801  -9.9954  -21.3497
 WKJ  H10  H   HCR6  0   0.277  -27.5365  -9.7113  -21.3331
 WKJ  H11  H   HCR6  0   0.276  -27.9427  -6.4769  -18.5482
 WKJ  H12  H   HCH2  0   0.238  -34.1683  -7.9134  -18.5937
 WKJ  H13  H   HCH2  0   0.192  -34.5067  -8.1942  -20.3150
 WKJ  O01  O   OH1   0  -0.672  -35.8733  -5.9734  -20.0272
 WKJ  H15  H   HOH1  0   0.450  -36.3374  -6.2016  -19.2163

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
 WKJ  C09  C08  aromatic  1.389  0.020  1.389
 WKJ  C09  C10  aromatic  1.385  0.020  1.385
 WKJ  C04  C03  single    1.537  0.020  1.537
 WKJ  C04  N05  single    1.459  0.020  1.459
 WKJ  C03  C02  single    1.532  0.020  1.532
 WKJ  C08  C07  aromatic  1.390  0.020  1.390
 WKJ  O01  C02  single    1.406  0.020  1.406
 WKJ  CL1  C10  single    1.736  0.020  1.736
 WKJ  C02  C14  single    1.526  0.020  1.526
 WKJ  C10  C12  aromatic  1.387  0.020  1.387
 WKJ  C07  C06  single    1.507  0.020  1.507
 WKJ  C07  C13  aromatic  1.393  0.020  1.393
 WKJ  N05  C06  single    1.439  0.020  1.439
 WKJ  N05  C14  single    1.446  0.020  1.446
 WKJ  C12  C13  aromatic  1.386  0.020  1.386
 WKJ  C13  H1   single    0.930  0.020  1.080
 WKJ  C02  H2   single    0.970  0.020  1.090
 WKJ  C03  H3   single    0.970  0.020  1.090
 WKJ  C03  H4   single    0.970  0.020  1.090
 WKJ  C04  H5   single    0.970  0.020  1.090
 WKJ  C04  H6   single    0.970  0.020  1.090
 WKJ  C06  H7   single    0.970  0.020  1.090
 WKJ  C06  H8   single    0.970  0.020  1.090
 WKJ  C08  H9   single    0.930  0.020  1.080
 WKJ  C09  H10  single    0.930  0.020  1.080
 WKJ  C12  H11  single    0.930  0.020  1.080
 WKJ  C14  H12  single    0.970  0.020  1.090
 WKJ  C14  H13  single    0.970  0.020  1.090
 WKJ  O01  H15  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
 WKJ  CL1  C10  C12  119.44  3.000
 WKJ  C12  C10  C09  121.02  3.000
 WKJ  CL1  C10  C09  119.54  3.000
 WKJ  H1   C13  C12  119.50  3.000
 WKJ  H1   C13  C07  119.38  3.000
 WKJ  C12  C13  C07  121.11  3.000
 WKJ  H2   C02  O01  110.77  3.000
 WKJ  H2   C02  C14  108.10  3.000
 WKJ  O01  C02  C14  115.01  3.000
 WKJ  H2   C02  C03  109.37  3.000
 WKJ  C14  C02  C03  102.53  3.000
 WKJ  O01  C02  C03  110.69  3.000
 WKJ  H4   C03  H3   107.41  3.000
 WKJ  H4   C03  C04  110.54  3.000
 WKJ  H3   C03  C04  112.59  3.000
 WKJ  H4   C03  C02  109.31  3.000
 WKJ  H3   C03  C02  112.16  3.000
 WKJ  C04  C03  C02  104.84  3.000
 WKJ  H6   C04  H5   106.91  3.000
 WKJ  H6   C04  N05  110.76  3.000
 WKJ  H5   C04  N05  111.26  3.000
 WKJ  H6   C04  C03  112.78  3.000
 WKJ  H5   C04  C03  110.41  3.000
 WKJ  N05  C04  C03  104.81  3.000
 WKJ  H8   C06  H7   106.20  3.000
 WKJ  H8   C06  N05  108.22  3.000
 WKJ  H7   C06  N05  111.98  3.000
 WKJ  H8   C06  C07  108.59  3.000
 WKJ  H7   C06  C07  109.12  3.000
 WKJ  N05  C06  C07  112.48  3.000
 WKJ  C08  C07  C06  120.65  3.000
 WKJ  C06  C07  C13  120.85  3.000
 WKJ  C08  C07  C13  118.48  3.000
 WKJ  H9   C08  C09  118.94  3.000
 WKJ  H9   C08  C07  119.78  3.000
 WKJ  C09  C08  C07  121.28  3.000
 WKJ  H10  C09  C08  120.38  3.000
 WKJ  H10  C09  C10  120.65  3.000
 WKJ  C08  C09  C10  118.97  3.000
 WKJ  H11  C12  C13  120.38  3.000
 WKJ  H11  C12  C10  120.48  3.000
 WKJ  C13  C12  C10  119.14  3.000
 WKJ  H13  C14  H12  107.89  3.000
 WKJ  H13  C14  N05  113.06  3.000
 WKJ  H12  C14  N05  111.16  3.000
 WKJ  H13  C14  C02  109.55  3.000
 WKJ  H12  C14  C02  113.39  3.000
 WKJ  N05  C14  C02  101.82  3.000
 WKJ  C14  N05  C06  114.86  3.000
 WKJ  C14  N05  C04  106.06  3.000
 WKJ  C06  N05  C04  114.47  3.000
 WKJ  H15  O01  C02  108.25  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
 WKJ  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 WKJ  CONST_02  C07  C13  C12  C10    0.00   0.0  0
 WKJ  CONST_03  C09  C08  C07  C13    0.00   0.0  0
 WKJ  CONST_04  C09  C10  C12  C13    0.00   0.0  0
 WKJ  CONST_05  C12  C10  C09  C08    0.00   0.0  0
 WKJ  CONST_06  C12  C13  C07  C08    0.00   0.0  0
 WKJ  CONST_07  CL1  C10  C12  C13  180.00   0.0  0
 WKJ  CONST_08  C09  C08  C07  C06  180.00   0.0  0
 WKJ  CONST_09  C12  C13  C07  C06  180.00   0.0  0
 WKJ  CONST_10  CL1  C10  C09  C08  180.00   0.0  0
 WKJ  CONST_11  H9   C08  C09  C10  180.00   0.0  0
 WKJ  CONST_12  H1   C13  C12  C10  180.00   0.0  0
 WKJ  CONST_13  H10  C09  C08  C07  180.00   0.0  0
 WKJ  CONST_14  H11  C12  C13  C07  180.00   0.0  0
 WKJ  Var_01    N05  C04  C03  C02   -5.17  30.0  1
 WKJ  Var_02    C04  N05  C14  C02  -45.12  30.0  1
 WKJ  Var_03    C14  N05  C04  C03   31.52  30.0  1
 WKJ  Var_04    N05  C06  C07  C13   39.29  30.0  2
 WKJ  Var_05    C07  C06  N05  C04   67.71  30.0  3

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
 WKJ  chir_01  C02  C03  O01  C14  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
 WKJ  plan-1  C10  0.020
 WKJ  plan-1  C13  0.020
 WKJ  plan-1  C06  0.020
 WKJ  plan-1  C07  0.020
 WKJ  plan-1  C08  0.020
 WKJ  plan-1  C09  0.020
 WKJ  plan-1  C12  0.020
 WKJ  plan-1  CL1  0.020
 WKJ  plan-1  H1   0.020
 WKJ  plan-1  H9   0.020
 WKJ  plan-1  H10  0.020
 WKJ  plan-1  H11  0.020

