# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 00:09:05 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R})-2-[(~{S})-(3-methoxyphenyl)-phenyl-methyl]pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)[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
 D4K  D4K  (2~{R})-2-[(~{S})-(3-methoxyphenyl)-phenyl-methyl]pyrrolidine  ligand  41  20  .  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_D4K
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
 D4K  C14  C  CR16  0  -0.306  -1.6112  -1.5277  -0.9359
 D4K  C10  C  CR16  0  -0.329  -1.7538  -1.5785   1.4522
 D4K  C13  C  CR16  0  -0.239  -2.3043  -2.7276  -1.0030
 D4K  C11  C  CR16  0  -0.240  -2.4421  -2.7841   1.3905
 D4K  C12  C  CR16  0  -0.273  -2.7211  -3.3629   0.1608
 D4K  C01  C  CH3   0  -0.436   5.3596  -0.9666   0.6655
 D4K  C03  C  CR6   0   0.398   3.1202  -0.3486   0.1784
 D4K  C04  C  CR16  0  -0.399   3.4012  -0.1223  -1.1661
 D4K  C05  C  CR16  0  -0.229   2.3751   0.2960  -2.0064
 D4K  C06  C  CR16  0  -0.342   1.0882   0.4888  -1.5342
 D4K  C07  C  CR6   0   0.207   0.8005   0.2590  -0.1879
 D4K  C08  C  CH1   0  -0.481  -0.5984   0.3876   0.3805
 D4K  C09  C  CR6   0   0.209  -1.3318  -0.9338   0.2938
 D4K  C15  C  CR15  0  -0.036  -1.4250   1.5152  -0.2375
 D4K  C17  C  CH2   0  -0.275  -1.7844   3.8491  -0.0065
 D4K  C18  C  CH2   0  -0.490  -3.1424   3.1271  -0.0210
 D4K  C19  C  CH2   0  -0.428  -2.7962   1.7089   0.4133
 D4K  C20  C  CR16  0  -0.401   1.8227  -0.1520   0.6547
 D4K  N16  N  NR15  0  -0.605  -0.7530   2.8080  -0.1202
 D4K  H1   H  HCR6  0   0.249  -1.2834  -1.0573  -1.8552
 D4K  H2   H  HCR6  0   0.248  -1.5404  -1.1344   2.4175
 D4K  H3   H  HCR6  0   0.254  -2.5157  -3.1710  -1.9679
 D4K  H4   H  HCR6  0   0.254  -2.7540  -3.2709   2.3057
 D4K  H5   H  HCR6  0   0.253  -3.2571  -4.3017   0.1073
 D4K  H6   H  HCH3  0   0.227   5.4292  -1.7463  -0.0976
 D4K  H7   H  HCH3  0   0.227   5.8174  -0.0528   0.2777
 D4K  H8   H  HCH3  0   0.258   5.9147  -1.2890   1.5432
 D4K  H9   H  HCR6  0   0.275   4.3940  -0.2631  -1.5712
 D4K  H10  H  HCR6  0   0.256   2.5946   0.4763  -3.0510
 D4K  H11  H  HCR6  0   0.243   0.3146   0.8176  -2.2158
 D4K  H12  H  HCH1  0   0.256  -0.4939   0.6279   1.4455
 D4K  H13  H  HCR5  0   0.217  -1.5887   1.2982  -1.3020
 D4K  H14  H  HCH2  0   0.214  -1.7154   4.5689  -0.8257
 D4K  H15  H  HCH2  0   0.220  -1.6553   4.4107   0.9212
 D4K  H16  H  HCH2  0   0.240  -3.8775   3.6124   0.6215
 D4K  H17  H  HCH2  0   0.228  -3.5563   3.1127  -1.0318
 D4K  H18  H  HCH2  0   0.236  -3.5322   0.9677   0.1009
 D4K  H19  H  HCH2  0   0.217  -2.6960   1.6452   1.5018
 D4K  H20  H  HCR6  0   0.251   1.6205  -0.3340   1.7047
 D4K  H21  H  HNR5  0   0.345  -0.1793   2.8132   0.7130
 D4K  O02  O  O2    0  -0.474   4.0279  -0.7547   1.0881

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
 D4K  C01  O02  single    1.413  0.020  1.413
 D4K  C04  C05  aromatic  1.391  0.020  1.391
 D4K  C04  C03  aromatic  1.392  0.020  1.392
 D4K  C05  C06  aromatic  1.384  0.020  1.384
 D4K  O02  C03  single    1.348  0.020  1.348
 D4K  C03  C20  aromatic  1.396  0.020  1.396
 D4K  C06  C07  aromatic  1.396  0.020  1.396
 D4K  C20  C07  aromatic  1.387  0.020  1.387
 D4K  C07  C08  single    1.515  0.020  1.515
 D4K  C14  C13  aromatic  1.387  0.020  1.387
 D4K  C14  C09  aromatic  1.394  0.020  1.394
 D4K  C13  C12  aromatic  1.390  0.020  1.390
 D4K  C08  C09  single    1.514  0.020  1.514
 D4K  C08  C15  single    1.529  0.020  1.529
 D4K  C09  C10  aromatic  1.391  0.020  1.391
 D4K  C12  C11  aromatic  1.387  0.020  1.387
 D4K  C15  N16  single    1.462  0.020  1.462
 D4K  C15  C19  single    1.530  0.020  1.530
 D4K  N16  C17  single    1.470  0.020  1.470
 D4K  C10  C11  aromatic  1.390  0.020  1.390
 D4K  C19  C18  single    1.523  0.020  1.523
 D4K  C17  C18  single    1.538  0.020  1.538
 D4K  C14  H1   single    0.930  0.020  1.080
 D4K  C10  H2   single    0.930  0.020  1.080
 D4K  C13  H3   single    0.930  0.020  1.080
 D4K  C11  H4   single    0.930  0.020  1.080
 D4K  C12  H5   single    0.930  0.020  1.080
 D4K  C01  H6   single    0.970  0.020  1.090
 D4K  C01  H7   single    0.970  0.020  1.090
 D4K  C01  H8   single    0.970  0.020  1.090
 D4K  C04  H9   single    0.930  0.020  1.080
 D4K  C05  H10  single    0.930  0.020  1.080
 D4K  C06  H11  single    0.930  0.020  1.080
 D4K  C08  H12  single    0.970  0.020  1.090
 D4K  C15  H13  single    0.970  0.020  1.090
 D4K  C17  H14  single    0.970  0.020  1.090
 D4K  C17  H15  single    0.970  0.020  1.090
 D4K  C18  H16  single    0.970  0.020  1.090
 D4K  C18  H17  single    0.970  0.020  1.090
 D4K  C19  H18  single    0.970  0.020  1.090
 D4K  C19  H19  single    0.970  0.020  1.090
 D4K  C20  H20  single    0.930  0.020  1.080
 D4K  N16  H21  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
 D4K  H1   C14  C09  120.20  3.000
 D4K  H1   C14  C13  119.05  3.000
 D4K  C09  C14  C13  120.75  3.000
 D4K  H2   C10  C09  119.47  3.000
 D4K  H2   C10  C11  119.51  3.000
 D4K  C09  C10  C11  121.02  3.000
 D4K  H3   C13  C12  120.03  3.000
 D4K  H3   C13  C14  119.66  3.000
 D4K  C12  C13  C14  120.31  3.000
 D4K  H4   C11  C12  120.25  3.000
 D4K  H4   C11  C10  119.69  3.000
 D4K  C12  C11  C10  120.06  3.000
 D4K  H5   C12  C11  120.35  3.000
 D4K  H5   C12  C13  120.24  3.000
 D4K  C11  C12  C13  119.41  3.000
 D4K  H8   C01  H7   108.69  3.000
 D4K  H8   C01  H6   108.63  3.000
 D4K  H7   C01  H6   108.78  3.000
 D4K  H8   C01  O02  106.51  3.000
 D4K  H7   C01  O02  112.05  3.000
 D4K  H6   C01  O02  112.07  3.000
 D4K  O02  C03  C20  115.99  3.000
 D4K  C20  C03  C04  119.62  3.000
 D4K  O02  C03  C04  124.40  3.000
 D4K  H9   C04  C05  119.35  3.000
 D4K  H9   C04  C03  121.73  3.000
 D4K  C05  C04  C03  118.92  3.000
 D4K  H10  C05  C06  119.64  3.000
 D4K  H10  C05  C04  118.92  3.000
 D4K  C06  C05  C04  121.45  3.000
 D4K  H11  C06  C07  120.68  3.000
 D4K  H11  C06  C05  119.47  3.000
 D4K  C07  C06  C05  119.85  3.000
 D4K  C20  C07  C08  118.53  3.000
 D4K  C08  C07  C06  122.55  3.000
 D4K  C20  C07  C06  118.87  3.000
 D4K  H12  C08  C15  106.41  3.000
 D4K  H12  C08  C09  107.04  3.000
 D4K  C15  C08  C09  111.03  3.000
 D4K  H12  C08  C07  107.15  3.000
 D4K  C15  C08  C07  114.21  3.000
 D4K  C09  C08  C07  110.59  3.000
 D4K  C08  C09  C10  120.25  3.000
 D4K  C10  C09  C14  118.44  3.000
 D4K  C08  C09  C14  121.30  3.000
 D4K  H13  C15  N16  108.72  3.000
 D4K  H13  C15  C19  107.67  3.000
 D4K  N16  C15  C19  105.42  3.000
 D4K  H13  C15  C08  109.07  3.000
 D4K  C19  C15  C08  113.95  3.000
 D4K  N16  C15  C08  111.80  3.000
 D4K  H15  C17  H14  106.90  3.000
 D4K  H15  C17  N16  110.30  3.000
 D4K  H14  C17  N16  111.36  3.000
 D4K  H15  C17  C18  110.72  3.000
 D4K  H14  C17  C18  110.97  3.000
 D4K  N16  C17  C18  106.64  3.000
 D4K  H17  C18  H16  107.20  3.000
 D4K  H17  C18  C19  109.74  3.000
 D4K  H16  C18  C19  113.55  3.000
 D4K  H17  C18  C17  110.46  3.000
 D4K  H16  C18  C17  112.38  3.000
 D4K  C19  C18  C17  103.52  3.000
 D4K  H19  C19  H18  107.89  3.000
 D4K  H19  C19  C18  111.00  3.000
 D4K  H18  C19  C18  113.45  3.000
 D4K  H19  C19  C15  109.47  3.000
 D4K  H18  C19  C15  113.39  3.000
 D4K  C18  C19  C15  101.55  3.000
 D4K  H20  C20  C07  120.03  3.000
 D4K  H20  C20  C03  118.68  3.000
 D4K  C07  C20  C03  121.30  3.000
 D4K  H21  N16  C17  109.30  3.000
 D4K  H21  N16  C15  109.35  3.000
 D4K  C17  N16  C15  108.06  3.000
 D4K  C03  O02  C01  118.56  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
 D4K  CONST_01  C11  C12  C13  C14    0.00   0.0  0
 D4K  CONST_02  C11  C10  C09  C14    0.00   0.0  0
 D4K  CONST_03  C13  C14  C09  C10    0.00   0.0  0
 D4K  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 D4K  CONST_05  C09  C14  C13  C12    0.00   0.0  0
 D4K  CONST_06  C09  C10  C11  C12    0.00   0.0  0
 D4K  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 D4K  CONST_08  C06  C07  C20  C03    0.00   0.0  0
 D4K  CONST_09  C07  C06  C05  C04    0.00   0.0  0
 D4K  CONST_10  C07  C20  C03  C04    0.00   0.0  0
 D4K  CONST_11  C20  C03  C04  C05    0.00   0.0  0
 D4K  CONST_12  C20  C07  C06  C05    0.00   0.0  0
 D4K  CONST_13  C08  C09  C14  C13  180.00   0.0  0
 D4K  CONST_14  C08  C09  C10  C11  180.00   0.0  0
 D4K  CONST_15  C08  C07  C20  C03  180.00   0.0  0
 D4K  CONST_16  O02  C03  C04  C05  180.00   0.0  0
 D4K  CONST_17  C08  C07  C06  C05  180.00   0.0  0
 D4K  CONST_18  O02  C03  C20  C07  180.00   0.0  0
 D4K  CONST_19  H5   C12  C13  C14  180.00   0.0  0
 D4K  CONST_20  H2   C10  C09  C14  180.00   0.0  0
 D4K  CONST_21  H1   C14  C09  C10  180.00   0.0  0
 D4K  CONST_22  H4   C11  C12  C13  180.00   0.0  0
 D4K  CONST_23  H3   C13  C12  C11  180.00   0.0  0
 D4K  CONST_24  H10  C05  C04  C03  180.00   0.0  0
 D4K  CONST_25  H11  C06  C05  C04  180.00   0.0  0
 D4K  CONST_26  H20  C20  C03  C04  180.00   0.0  0
 D4K  CONST_27  H9   C04  C05  C06  180.00   0.0  0
 D4K  Var_01    C18  C17  N16  C15    1.51  30.0  1
 D4K  Var_02    C17  C18  C19  C15  -35.60  30.0  1
 D4K  Var_03    N16  C17  C18  C19   21.98  30.0  1
 D4K  Var_04    C04  C03  O02  C01    0.15  30.0  2
 D4K  Var_05    H6   C01  O02  C03  -61.13  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
 D4K  chir_01  C08  C07  C09  C15  positiv
 D4K  chir_02  C15  N16  C19  C08  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
 D4K  plan-1  C14  0.020
 D4K  plan-1  C10  0.020
 D4K  plan-1  C13  0.020
 D4K  plan-1  C11  0.020
 D4K  plan-1  C12  0.020
 D4K  plan-1  C08  0.020
 D4K  plan-1  C09  0.020
 D4K  plan-1  H1   0.020
 D4K  plan-1  H2   0.020
 D4K  plan-1  H3   0.020
 D4K  plan-1  H4   0.020
 D4K  plan-1  H5   0.020
 D4K  plan-2  C03  0.020
 D4K  plan-2  C04  0.020
 D4K  plan-2  C05  0.020
 D4K  plan-2  C06  0.020
 D4K  plan-2  C07  0.020
 D4K  plan-2  C08  0.020
 D4K  plan-2  C20  0.020
 D4K  plan-2  H9   0.020
 D4K  plan-2  H10  0.020
 D4K  plan-2  H11  0.020
 D4K  plan-2  H20  0.020
 D4K  plan-2  O02  0.020

