# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:18:50 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2~{R})-2-[(~{R})-[2-(2-methoxyethoxy)phenyl]-phenyl-methyl]pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1ccccc1[C@H]([C@H]2CCCN2)c3ccccc3
#
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
 D3K  D3K  (2~{R})-2-[(~{R})-[2-(2-methoxyethoxy)phenyl]-phenyl-methyl]pyrrolidine  ligand  48  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D3K
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
 D3K  C14  C  CR16  0  -0.309  -0.5321   0.5123  -2.0050
 D3K  C10  C  CR16  0  -0.306  -0.7047  -1.2326   2.3571
 D3K  C13  C  CR6   0   0.239  -1.0791   0.1246  -0.7871
 D3K  C11  C  CR6   0   0.061   0.0081  -0.7101   1.2886
 D3K  C12  C  CH1   0  -0.437  -0.4215   0.5211   0.5196
 D3K  C01  C  CH3   0  -0.369   3.9205   1.2084  -2.9752
 D3K  C03  C  CH2   0  -0.141   3.2372  -0.8250  -2.0596
 D3K  C04  C  CH2   0  -0.201   2.9038  -1.5140  -0.7625
 D3K  C06  C  CR6   0   0.388   1.1655  -1.3895   0.8704
 D3K  C07  C  CR16  0  -0.364   1.5968  -2.5304   1.5385
 D3K  C08  C  CR16  0  -0.235   0.8646  -3.0215   2.6130
 D3K  C09  C  CR16  0  -0.248  -0.2907  -2.3819   3.0221
 D3K  C15  C  CR16  0  -0.222  -1.1333   0.1501  -3.2034
 D3K  C16  C  CR16  0  -0.255  -2.2940  -0.6094  -3.1990
 D3K  C17  C  CR16  0  -0.219  -2.8459  -1.0069  -1.9878
 D3K  C18  C  CR16  0  -0.305  -2.2395  -0.6454  -0.7941
 D3K  C19  C  CH1   0  -0.070  -1.2967   1.4809   1.3229
 D3K  C21  C  CH2   0  -0.307  -2.0851   3.6536   1.5017
 D3K  C22  C  CH2   0  -0.463  -1.3556   3.3671   2.8359
 D3K  C23  C  CH2   0  -0.426  -0.6362   2.0325   2.5949
 D3K  N20  N  NH1   0  -0.579  -1.6389   2.6590   0.5289
 D3K  O02  O  O2    0  -0.473   3.6188   0.4975  -1.8052
 D3K  O05  O  O2    0  -0.457   1.7916  -0.8595  -0.1937
 D3K  H1   H  HCR6  0   0.226   0.3810   1.0959  -2.0188
 D3K  H2   H  HCR6  0   0.229  -1.6090  -0.7409   2.6911
 D3K  H3   H  HCH1  0   0.246   0.4866   1.0816   0.2679
 D3K  H4   H  HCH3  0   0.226   4.1904   2.2246  -2.6928
 D3K  H5   H  HCH3  0   0.196   4.7624   0.7686  -3.5238
 D3K  H6   H  HCH3  0   0.191   3.0664   1.2574  -3.6617
 D3K  H7   H  HCH2  0   0.201   4.0440  -1.3936  -2.5434
 D3K  H8   H  HCH2  0   0.204   2.3673  -0.8691  -2.7311
 D3K  H9   H  HCH2  0   0.218   2.6779  -2.5632  -0.9813
 D3K  H10  H  HCH2  0   0.220   3.7630  -1.4900  -0.0823
 D3K  H11  H  HCR6  0   0.254   2.4970  -3.0489   1.2385
 D3K  H12  H  HCR6  0   0.237   1.2086  -3.9108   3.1240
 D3K  H13  H  HCR6  0   0.232  -0.8680  -2.7644   3.8523
 D3K  H14  H  HCR6  0   0.231  -0.6928   0.4575  -4.1427
 D3K  H15  H  HCR6  0   0.235  -2.7634  -0.8932  -4.1314
 D3K  H16  H  HCR6  0   0.234  -3.7475  -1.6052  -1.9736
 D3K  H17  H  HCR6  0   0.227  -2.6742  -0.9750   0.1428
 D3K  H18  H  HCH1  0   0.216  -2.2427   0.9923   1.5917
 D3K  H19  H  HCH2  0   0.218  -3.1653   3.5602   1.6399
 D3K  H20  H  HCH2  0   0.228  -1.9008   4.6588   1.1235
 D3K  H21  H  HCH2  0   0.229  -0.6519   4.1589   3.0911
 D3K  H22  H  HCH2  0   0.227  -2.0662   3.2956   3.6597
 D3K  H23  H  HCH2  0   0.235  -0.7055   1.3527   3.4433
 D3K  H24  H  HCH2  0   0.218   0.4290   2.1934   2.4042
 D3K  H25  H  HNH1  0   0.321  -0.7895   2.9973   0.0874

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
 D3K  C16  C17  aromatic  1.389  0.020  1.389
 D3K  C16  C15  aromatic  1.387  0.020  1.387
 D3K  C17  C18  aromatic  1.387  0.020  1.387
 D3K  C15  C14  aromatic  1.389  0.020  1.389
 D3K  C18  C13  aromatic  1.393  0.020  1.393
 D3K  C14  C13  aromatic  1.390  0.020  1.390
 D3K  C13  C12  single    1.516  0.020  1.516
 D3K  C10  C09  aromatic  1.391  0.020  1.391
 D3K  C10  C11  aromatic  1.387  0.020  1.387
 D3K  C12  C11  single    1.514  0.020  1.514
 D3K  C12  C19  single    1.527  0.020  1.527
 D3K  C09  C08  aromatic  1.382  0.020  1.382
 D3K  C11  C06  aromatic  1.406  0.020  1.406
 D3K  C08  C07  aromatic  1.390  0.020  1.390
 D3K  C06  C07  aromatic  1.391  0.020  1.391
 D3K  C06  O05  single    1.344  0.020  1.344
 D3K  C19  N20  single    1.461  0.020  1.461
 D3K  C19  C23  single    1.536  0.020  1.536
 D3K  O05  C04  single    1.410  0.020  1.410
 D3K  N20  C21  single    1.461  0.020  1.461
 D3K  C01  O02  single    1.402  0.020  1.402
 D3K  C03  C04  single    1.506  0.020  1.506
 D3K  C03  O02  single    1.400  0.020  1.400
 D3K  C23  C22  single    1.535  0.020  1.535
 D3K  C21  C22  single    1.547  0.020  1.547
 D3K  C14  H1   single    0.930  0.020  1.080
 D3K  C10  H2   single    0.930  0.020  1.080
 D3K  C12  H3   single    0.970  0.020  1.090
 D3K  C01  H4   single    0.970  0.020  1.090
 D3K  C01  H5   single    0.970  0.020  1.090
 D3K  C01  H6   single    0.970  0.020  1.090
 D3K  C03  H7   single    0.970  0.020  1.090
 D3K  C03  H8   single    0.970  0.020  1.090
 D3K  C04  H9   single    0.970  0.020  1.090
 D3K  C04  H10  single    0.970  0.020  1.090
 D3K  C07  H11  single    0.930  0.020  1.080
 D3K  C08  H12  single    0.930  0.020  1.080
 D3K  C09  H13  single    0.930  0.020  1.080
 D3K  C15  H14  single    0.930  0.020  1.080
 D3K  C16  H15  single    0.930  0.020  1.080
 D3K  C17  H16  single    0.930  0.020  1.080
 D3K  C18  H17  single    0.930  0.020  1.080
 D3K  C19  H18  single    0.970  0.020  1.090
 D3K  C21  H19  single    0.970  0.020  1.090
 D3K  C21  H20  single    0.970  0.020  1.090
 D3K  C22  H21  single    0.970  0.020  1.090
 D3K  C22  H22  single    0.970  0.020  1.090
 D3K  C23  H23  single    0.970  0.020  1.090
 D3K  C23  H24  single    0.970  0.020  1.090
 D3K  N20  H25  single    0.890  0.020  1.040

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
 D3K  H1   C14  C15  119.62  3.000
 D3K  H1   C14  C13  119.53  3.000
 D3K  C15  C14  C13  120.85  3.000
 D3K  H2   C10  C09  118.46  3.000
 D3K  H2   C10  C11  119.75  3.000
 D3K  C09  C10  C11  121.79  3.000
 D3K  C18  C13  C12  120.70  3.000
 D3K  C12  C13  C14  120.77  3.000
 D3K  C18  C13  C14  118.53  3.000
 D3K  C06  C11  C12  118.39  3.000
 D3K  C06  C11  C10  118.06  3.000
 D3K  C12  C11  C10  123.51  3.000
 D3K  H3   C12  C19  105.91  3.000
 D3K  H3   C12  C11  107.30  3.000
 D3K  C19  C12  C11  113.99  3.000
 D3K  H3   C12  C13  107.17  3.000
 D3K  C19  C12  C13  111.67  3.000
 D3K  C11  C12  C13  110.38  3.000
 D3K  H6   C01  H5   107.61  3.000
 D3K  H6   C01  H4   108.27  3.000
 D3K  H5   C01  H4   108.28  3.000
 D3K  H6   C01  O02  112.17  3.000
 D3K  H5   C01  O02  112.29  3.000
 D3K  H4   C01  O02  108.07  3.000
 D3K  H8   C03  H7   106.92  3.000
 D3K  H8   C03  O02  111.38  3.000
 D3K  H7   C03  O02  111.63  3.000
 D3K  H8   C03  C04  109.41  3.000
 D3K  H7   C03  C04  107.75  3.000
 D3K  O02  C03  C04  109.63  3.000
 D3K  H10  C04  H9   107.85  3.000
 D3K  H10  C04  O05  110.97  3.000
 D3K  H9   C04  O05  111.25  3.000
 D3K  H10  C04  C03  110.54  3.000
 D3K  H9   C04  C03  108.17  3.000
 D3K  O05  C04  C03  108.04  3.000
 D3K  O05  C06  C07  124.03  3.000
 D3K  O05  C06  C11  115.39  3.000
 D3K  C07  C06  C11  120.59  3.000
 D3K  H11  C07  C08  118.92  3.000
 D3K  H11  C07  C06  121.22  3.000
 D3K  C08  C07  C06  119.86  3.000
 D3K  H12  C08  C09  120.41  3.000
 D3K  H12  C08  C07  119.22  3.000
 D3K  C09  C08  C07  120.37  3.000
 D3K  H13  C09  C08  120.65  3.000
 D3K  H13  C09  C10  120.04  3.000
 D3K  C08  C09  C10  119.31  3.000
 D3K  H14  C15  C16  119.93  3.000
 D3K  H14  C15  C14  119.91  3.000
 D3K  C16  C15  C14  120.16  3.000
 D3K  H15  C16  C17  120.27  3.000
 D3K  H15  C16  C15  120.27  3.000
 D3K  C17  C16  C15  119.46  3.000
 D3K  H16  C17  C18  119.81  3.000
 D3K  H16  C17  C16  120.04  3.000
 D3K  C18  C17  C16  120.14  3.000
 D3K  H17  C18  C17  119.29  3.000
 D3K  H17  C18  C13  119.86  3.000
 D3K  C17  C18  C13  120.85  3.000
 D3K  H18  C19  N20  106.86  3.000
 D3K  H18  C19  C23  109.12  3.000
 D3K  N20  C19  C23  105.14  3.000
 D3K  H18  C19  C12  110.05  3.000
 D3K  C23  C19  C12  114.51  3.000
 D3K  N20  C19  C12  110.80  3.000
 D3K  H20  C21  H19  106.85  3.000
 D3K  H20  C21  N20  110.19  3.000
 D3K  H19  C21  N20  109.14  3.000
 D3K  H20  C21  C22  112.97  3.000
 D3K  H19  C21  C22  109.94  3.000
 D3K  N20  C21  C22  107.70  3.000
 D3K  H22  C22  H21  106.95  3.000
 D3K  H22  C22  C23  111.53  3.000
 D3K  H21  C22  C23  111.46  3.000
 D3K  H22  C22  C21  110.88  3.000
 D3K  H21  C22  C21  111.83  3.000
 D3K  C23  C22  C21  104.27  3.000
 D3K  H24  C23  H23  106.82  3.000
 D3K  H24  C23  C22  110.84  3.000
 D3K  H23  C23  C22  112.98  3.000
 D3K  H24  C23  C19  109.10  3.000
 D3K  H23  C23  C19  113.17  3.000
 D3K  C22  C23  C19  103.93  3.000
 D3K  H25  N20  C21  108.56  3.000
 D3K  H25  N20  C19  108.00  3.000
 D3K  C21  N20  C19  104.98  3.000
 D3K  C03  O02  C01  112.71  3.000
 D3K  C06  O05  C04  120.26  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
 D3K  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 D3K  CONST_02  C17  C18  C13  C14     0.00   0.0  0
 D3K  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 D3K  CONST_04  C07  C06  C11  C10     0.00   0.0  0
 D3K  CONST_05  C16  C17  C18  C13     0.00   0.0  0
 D3K  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 D3K  CONST_07  C08  C09  C10  C11     0.00   0.0  0
 D3K  CONST_08  C08  C07  C06  C11     0.00   0.0  0
 D3K  CONST_09  C09  C10  C11  C06     0.00   0.0  0
 D3K  CONST_10  C09  C08  C07  C06     0.00   0.0  0
 D3K  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 D3K  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 D3K  CONST_13  O05  C06  C11  C10   180.00   0.0  0
 D3K  CONST_14  C17  C18  C13  C12   180.00   0.0  0
 D3K  CONST_15  C15  C14  C13  C12   180.00   0.0  0
 D3K  CONST_16  C09  C10  C11  C12   180.00   0.0  0
 D3K  CONST_17  C07  C06  C11  C12   180.00   0.0  0
 D3K  CONST_18  O05  C06  C07  C08   180.00   0.0  0
 D3K  CONST_19  H15  C16  C15  C14   180.00   0.0  0
 D3K  CONST_20  H17  C18  C13  C14   180.00   0.0  0
 D3K  CONST_21  H12  C08  C09  C10   180.00   0.0  0
 D3K  CONST_22  H16  C17  C18  C13   180.00   0.0  0
 D3K  CONST_23  H14  C15  C14  C13   180.00   0.0  0
 D3K  CONST_24  H13  C09  C10  C11   180.00   0.0  0
 D3K  CONST_25  H11  C07  C06  C11   180.00   0.0  0
 D3K  CONST_26  H2   C10  C11  C06   180.00   0.0  0
 D3K  CONST_27  H1   C14  C15  C16   180.00   0.0  0
 D3K  Var_01    C22  C21  N20  C19    28.76  30.0  1
 D3K  Var_02    C21  C22  C23  C19   -14.72  30.0  1
 D3K  Var_03    N20  C21  C22  C23    -7.94  30.0  1
 D3K  Var_04    C07  C06  O05  C04     4.68  30.0  1
 D3K  Var_05    H9   C04  O05  C06    51.75  30.0  3
 D3K  Var_06    C04  C03  O02  C01  -178.89  30.0  1
 D3K  Var_07    O05  C04  C03  O02    63.42  30.0  3
 D3K  Var_08    H4   C01  O02  C03   179.10  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
 D3K  chir_01  C12  C13  C11  C19  positiv
 D3K  chir_02  C19  N20  C23  C12  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
 D3K  plan-1  C10  0.020
 D3K  plan-1  C11  0.020
 D3K  plan-1  C12  0.020
 D3K  plan-1  C06  0.020
 D3K  plan-1  C07  0.020
 D3K  plan-1  C08  0.020
 D3K  plan-1  C09  0.020
 D3K  plan-1  O05  0.020
 D3K  plan-1  H2   0.020
 D3K  plan-1  H11  0.020
 D3K  plan-1  H12  0.020
 D3K  plan-1  H13  0.020
 D3K  plan-2  C14  0.020
 D3K  plan-2  C13  0.020
 D3K  plan-2  C12  0.020
 D3K  plan-2  C15  0.020
 D3K  plan-2  C16  0.020
 D3K  plan-2  C17  0.020
 D3K  plan-2  C18  0.020
 D3K  plan-2  H1   0.020
 D3K  plan-2  H14  0.020
 D3K  plan-2  H15  0.020
 D3K  plan-2  H16  0.020
 D3K  plan-2  H17  0.020

