# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:53:33 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (3R)-4-(4-chlorophenyl)-1-[(3S,4R)-3-(4-chlorophenyl)-4-(hydroxymethyl)pyrrolidin-1-yl]-3-hydroxybutan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN(C[C@@H]1c2ccc(Cl)cc2)C(=O)C[C@H](O)Cc3ccc(Cl)cc3
#
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
 A62  A62  (3R)-4-(4-chlorophenyl)-1-[(3S,4R)-3-(4-chlorophenyl)-4-(hydroxymethyl)pyrrolidin-1-yl]-3-hydroxybutan-1-one  ligand  50  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A62
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
 A62  C     C   CH2   0  -0.130   3.4608  -2.9006   0.3266
 A62  N     N   NT    0  -0.486   0.9548  -0.2428  -0.1712
 A62  O     O   OH1   0  -0.671   3.0524  -4.0010  -0.4539
 A62  C1    C   CH1   0  -0.295   2.8316  -1.6482  -0.2396
 A62  C2    C   CH2   0  -0.256   1.3058  -1.6584  -0.2237
 A62  O2    O   OH1   0  -0.656  -2.8426   0.0015   1.1638
 A62  C3    C   CH2   0  -0.219   2.1052   0.6040   0.1023
 A62  C4    C   CH1   0  -0.409   3.1730  -0.3878   0.5643
 A62  C5    C   CR6   0   0.211   4.5830   0.1039   0.4016
 A62  C6    C   CR16  0  -0.337   5.4233   0.2239   1.5034
 A62  C7    C   CR16  0  -0.193   6.7330   0.6651   1.3708
 A62  C8    C   CR6   0  -0.060   7.2077   0.9888   0.1113
 A62  C9    C   CR16  0  -0.193   6.3940   0.8823  -1.0070
 A62  C10   C   CR16  0  -0.328   5.0892   0.4426  -0.8526
 A62  C11   C   C     0   0.578  -0.2702   0.2768  -0.3475
 A62  C12   C   CH2   0  -0.630  -1.3879  -0.7057  -0.6345
 A62  C13   C   CH1   0   0.055  -2.7571  -0.1766  -0.2311
 A62  C14   C   CH2   0  -0.563  -3.8637  -1.0941  -0.7638
 A62  C15   C   CR6   0   0.173  -5.2305  -0.6067  -0.3836
 A62  C16   C   CR16  0  -0.313  -5.8851   0.3468  -1.1596
 A62  C17   C   CR16  0  -0.197  -7.1317   0.8387  -0.8012
 A62  C18   C   CR6   0  -0.059  -7.7329   0.3670   0.3549
 A62  C19   C   CR16  0  -0.198  -7.1091  -0.5833   1.1473
 A62  C20   C   CR16  0  -0.324  -5.8611  -1.0592   0.7717
 A62  H     H   HCH2  0   0.193   3.1515  -3.0114   1.3756
 A62  HA    H   HCH2  0   0.210   4.5529  -2.7881   0.3252
 A62  HO    H   HOH1  0   0.456   3.4529  -4.7951  -0.0885
 A62  H1    H   HCH1  0   0.257   3.1737  -1.5111  -1.2722
 A62  H2    H   HCH2  0   0.242   0.9301  -2.1877   0.6594
 A62  H2A   H   HCH2  0   0.263   0.8921  -2.1433  -1.1077
 A62  H3    H   HCH2  0   0.239   2.4224   1.1329  -0.8020
 A62  H3A   H   HCH2  0   0.259   1.8837   1.3520   0.8633
 A62  H4    H   HCH1  0   0.270   3.0022  -0.6028   1.6251
 A62  H6    H   HCR6  0   0.264   5.0538  -0.0294   2.4897
 A62  H7    H   HCR6  0   0.279   7.3700   0.7532   2.2404
 A62  H9    H   HCR6  0   0.279   6.7707   1.1375  -1.9882
 A62  H10   H   HCR6  0   0.262   4.4632   0.3661  -1.7337
 A62  H12   H   HCH2  0   0.283  -1.3695  -0.9240  -1.7080
 A62  H12A  H   HCH2  0   0.266  -1.2119  -1.6635  -0.1365
 A62  H13   H   HCH1  0   0.241  -2.9017   0.8169  -0.6621
 A62  H14   H   HCH2  0   0.257  -3.7741  -1.1440  -1.8516
 A62  H14A  H   HCH2  0   0.252  -3.7093  -2.1121  -0.3915
 A62  H16   H   HCR6  0   0.257  -5.4181   0.7140  -2.0660
 A62  H17   H   HCR6  0   0.277  -7.6274   1.5761  -1.4180
 A62  H19   H   HCR6  0   0.276  -7.5866  -0.9494   2.0463
 A62  H20   H   HCR6  0   0.254  -5.3804  -1.8068   1.3913
 A62  HO2   H   HOH1  0   0.440  -2.7313  -0.8557   1.5888
 A62  CL    CL  CL    0  -0.132   8.8433   1.5361  -0.0724
 A62  O1    O   O     0  -0.509  -0.4654   1.4863  -0.3091
 A62  CL1   CL  CL    0  -0.137  -9.2949   0.9708   0.8125

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
 A62  C    O     single    1.409  0.020  1.409
 A62  C    C1    single    1.512  0.020  1.512
 A62  N    C2    single    1.459  0.020  1.459
 A62  N    C3    single    1.454  0.020  1.454
 A62  N    C11   single    1.342  0.020  1.342
 A62  CL   C8    single    1.735  0.020  1.735
 A62  C1   C2    single    1.526  0.020  1.526
 A62  C1   C4    single    1.533  0.020  1.533
 A62  O1   C11   double    1.226  0.020  1.226
 A62  CL1  C18   single    1.736  0.020  1.736
 A62  O2   C13   single    1.409  0.020  1.409
 A62  C3   C4    single    1.529  0.020  1.529
 A62  C4   C5    single    1.502  0.020  1.502
 A62  C5   C6    aromatic  1.391  0.020  1.391
 A62  C5   C10   aromatic  1.394  0.020  1.394
 A62  C6   C7    aromatic  1.388  0.020  1.388
 A62  C7   C8    aromatic  1.384  0.020  1.384
 A62  C8   C9    aromatic  1.387  0.020  1.387
 A62  C9   C10   aromatic  1.386  0.020  1.386
 A62  C11  C12   single    1.516  0.020  1.516
 A62  C12  C13   single    1.522  0.020  1.522
 A62  C13  C14   single    1.533  0.020  1.533
 A62  C14  C15   single    1.500  0.020  1.500
 A62  C15  C16   aromatic  1.393  0.020  1.393
 A62  C15  C20   aromatic  1.392  0.020  1.392
 A62  C16  C17   aromatic  1.387  0.020  1.387
 A62  C17  C18   aromatic  1.386  0.020  1.386
 A62  C18  C19   aromatic  1.386  0.020  1.386
 A62  C19  C20   aromatic  1.387  0.020  1.387
 A62  C    H     single    0.970  0.020  1.090
 A62  C    HA    single    0.970  0.020  1.090
 A62  O    HO    single    0.850  0.020  0.980
 A62  C1   H1    single    0.970  0.020  1.090
 A62  C2   H2    single    0.970  0.020  1.090
 A62  C2   H2A   single    0.970  0.020  1.090
 A62  O2   HO2   single    0.850  0.020  0.980
 A62  C3   H3    single    0.970  0.020  1.090
 A62  C3   H3A   single    0.970  0.020  1.090
 A62  C4   H4    single    0.970  0.020  1.090
 A62  C6   H6    single    0.930  0.020  1.080
 A62  C7   H7    single    0.930  0.020  1.080
 A62  C9   H9    single    0.930  0.020  1.080
 A62  C10  H10   single    0.930  0.020  1.080
 A62  C12  H12   single    0.970  0.020  1.090
 A62  C12  H12A  single    0.970  0.020  1.090
 A62  C13  H13   single    0.970  0.020  1.090
 A62  C14  H14   single    0.970  0.020  1.090
 A62  C14  H14A  single    0.970  0.020  1.090
 A62  C16  H16   single    0.930  0.020  1.080
 A62  C17  H17   single    0.930  0.020  1.080
 A62  C19  H19   single    0.930  0.020  1.080
 A62  C20  H20   single    0.930  0.020  1.080

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
 A62  HA    C    H    106.94  3.000
 A62  HA    C    C1   109.18  3.000
 A62  H     C    C1   108.89  3.000
 A62  HA    C    O    111.56  3.000
 A62  H     C    O    111.61  3.000
 A62  C1    C    O    108.60  3.000
 A62  C11   N    C3   121.41  3.000
 A62  C11   N    C2   126.17  3.000
 A62  C3    N    C2   112.42  3.000
 A62  HO    O    C    108.28  3.000
 A62  H1    C1   C4   108.75  3.000
 A62  H1    C1   C2   108.82  3.000
 A62  C4    C1   C2   102.86  3.000
 A62  H1    C1   C    109.06  3.000
 A62  C4    C1   C    113.08  3.000
 A62  C2    C1   C    114.00  3.000
 A62  H2A   C2   H2   107.97  3.000
 A62  H2A   C2   C1   111.97  3.000
 A62  H2    C2   C1   110.75  3.000
 A62  H2A   C2   N    111.68  3.000
 A62  H2    C2   N    110.92  3.000
 A62  C1    C2   N    103.56  3.000
 A62  HO2   O2   C13  108.50  3.000
 A62  H3A   C3   H3   107.71  3.000
 A62  H3A   C3   C4   112.09  3.000
 A62  H3    C3   C4   111.14  3.000
 A62  H3A   C3   N    111.73  3.000
 A62  H3    C3   N    110.81  3.000
 A62  C4    C3   N    103.39  3.000
 A62  H4    C4   C5   108.39  3.000
 A62  H4    C4   C3   108.12  3.000
 A62  C5    C4   C3   114.24  3.000
 A62  H4    C4   C1   108.15  3.000
 A62  C5    C4   C1   114.91  3.000
 A62  C3    C4   C1   102.67  3.000
 A62  C10   C5   C6   118.18  3.000
 A62  C10   C5   C4   121.18  3.000
 A62  C6    C5   C4   120.63  3.000
 A62  H6    C6   C7   118.89  3.000
 A62  H6    C6   C5   119.67  3.000
 A62  C7    C6   C5   121.44  3.000
 A62  H7    C7   C8   120.70  3.000
 A62  H7    C7   C6   120.31  3.000
 A62  C8    C7   C6   118.99  3.000
 A62  C9    C8   C7   120.96  3.000
 A62  C9    C8   CL   119.47  3.000
 A62  C7    C8   CL   119.57  3.000
 A62  H9    C9   C10  120.27  3.000
 A62  H9    C9   C8   120.60  3.000
 A62  C10   C9   C8   119.14  3.000
 A62  H10   C10  C9   118.41  3.000
 A62  H10   C10  C5   120.30  3.000
 A62  C9    C10  C5   121.29  3.000
 A62  C12   C11  O1   121.89  3.000
 A62  C12   C11  N    116.55  3.000
 A62  O1    C11  N    121.54  3.000
 A62  H12A  C12  H12  105.61  3.000
 A62  H12A  C12  C13  109.17  3.000
 A62  H12   C12  C13  110.12  3.000
 A62  H12A  C12  C11  111.27  3.000
 A62  H12   C12  C11  107.60  3.000
 A62  C13   C12  C11  112.81  3.000
 A62  H13   C13  C14  108.16  3.000
 A62  H13   C13  C12  109.30  3.000
 A62  C14   C13  C12  110.43  3.000
 A62  H13   C13  O2   105.52  3.000
 A62  C14   C13  O2   112.08  3.000
 A62  C12   C13  O2   111.16  3.000
 A62  H14A  C14  H14  106.53  3.000
 A62  H14A  C14  C15  110.15  3.000
 A62  H14   C14  C15  110.00  3.000
 A62  H14A  C14  C13  109.66  3.000
 A62  H14   C14  C13  108.30  3.000
 A62  C15   C14  C13  112.03  3.000
 A62  C20   C15  C16  118.18  3.000
 A62  C20   C15  C14  121.17  3.000
 A62  C16   C15  C14  120.63  3.000
 A62  H16   C16  C17  118.89  3.000
 A62  H16   C16  C15  119.70  3.000
 A62  C17   C16  C15  121.41  3.000
 A62  H17   C17  C18  120.59  3.000
 A62  H17   C17  C16  120.42  3.000
 A62  C18   C17  C16  118.99  3.000
 A62  C19   C18  C17  121.01  3.000
 A62  C19   C18  CL1  119.52  3.000
 A62  C17   C18  CL1  119.46  3.000
 A62  H19   C19  C20  120.39  3.000
 A62  H19   C19  C18  120.58  3.000
 A62  C20   C19  C18  119.03  3.000
 A62  H20   C20  C19  118.75  3.000
 A62  H20   C20  C15  119.87  3.000
 A62  C19   C20  C15  121.38  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
 A62  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 A62  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 A62  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 A62  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 A62  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 A62  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 A62  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 A62  CONST_08  C18  C19  C20  C15    0.00   0.0  0
 A62  CONST_09  C19  C20  C15  C16    0.00   0.0  0
 A62  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 A62  CONST_11  C20  C15  C16  C17    0.00   0.0  0
 A62  CONST_12  C20  C19  C18  C17    0.00   0.0  0
 A62  CONST_13  C7   C6   C5   C4   180.00   0.0  0
 A62  CONST_14  C9   C10  C5   C4   180.00   0.0  0
 A62  CONST_15  C6   C7   C8   CL   180.00   0.0  0
 A62  CONST_16  C10  C9   C8   CL   180.00   0.0  0
 A62  CONST_17  C16  C17  C18  CL1  180.00   0.0  0
 A62  CONST_18  C20  C19  C18  CL1  180.00   0.0  0
 A62  CONST_19  C17  C16  C15  C14  180.00   0.0  0
 A62  CONST_20  C19  C20  C15  C14  180.00   0.0  0
 A62  CONST_21  H6   C6   C5   C4     0.00   0.0  0
 A62  CONST_22  H10  C10  C5   C4     0.00   0.0  0
 A62  CONST_23  H7   C7   C6   C5   180.00   0.0  0
 A62  CONST_24  H9   C9   C10  C5   180.00   0.0  0
 A62  CONST_25  H17  C17  C16  C15  180.00   0.0  0
 A62  CONST_26  H19  C19  C20  C15  180.00   0.0  0
 A62  CONST_27  H20  C20  C15  C16  180.00   0.0  0
 A62  CONST_28  H16  C16  C17  C18  180.00   0.0  0
 A62  CONST_29  C2   N    C11  O1   180.00   0.0  0
 A62  CONST_30  C3   N    C11  O1     0.00   0.0  0
 A62  CONST_31  C12  C11  N    C2     0.00   0.0  0
 A62  CONST_32  C12  C11  N    C3   180.00   0.0  0
 A62  Var_01    C3   N    C2   C1   -10.99  30.0  1
 A62  Var_02    C4   C3   N    C2   -13.46  30.0  1
 A62  Var_03    C16  C15  C14  C13   85.11  30.0  2
 A62  Var_04    C13  C12  C11  N    154.99  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
 A62  chir_01  C1   C   C2   C4   negativ
 A62  chir_02  C4   C1  C3   C5   positiv
 A62  chir_03  C13  O2  C12  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
 A62  plan-1  C4   0.020
 A62  plan-1  C5   0.020
 A62  plan-1  C6   0.020
 A62  plan-1  C7   0.020
 A62  plan-1  C8   0.020
 A62  plan-1  C9   0.020
 A62  plan-1  C10  0.020
 A62  plan-1  H6   0.020
 A62  plan-1  H7   0.020
 A62  plan-1  H9   0.020
 A62  plan-1  H10  0.020
 A62  plan-1  CL   0.020
 A62  plan-2  C14  0.020
 A62  plan-2  C15  0.020
 A62  plan-2  C16  0.020
 A62  plan-2  C17  0.020
 A62  plan-2  C18  0.020
 A62  plan-2  C19  0.020
 A62  plan-2  C20  0.020
 A62  plan-2  H16  0.020
 A62  plan-2  H17  0.020
 A62  plan-2  H19  0.020
 A62  plan-2  H20  0.020
 A62  plan-2  CL1  0.020
 A62  plan-3  N    0.020
 A62  plan-3  C2   0.020
 A62  plan-3  C3   0.020
 A62  plan-3  C11  0.020
 A62  plan-3  C12  0.020
 A62  plan-3  O1   0.020

