# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:38:05 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R})-2-[(~{R})-(2-methoxyphenyl)-phenyl-methyl]pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1[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
 D3W  D3W  (2~{R})-2-[(~{R})-(2-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_D3W
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
 D3W  C14  C  CR16  0  -0.244   2.3717   2.1896  -1.7657
 D3W  C10  C  CR6   0   0.233   1.0924   0.6723  -0.3813
 D3W  C13  C  CR16  0  -0.276   2.8681   2.8247  -0.6362
 D3W  C11  C  CR16  0  -0.311   1.5929   1.3206   0.7460
 D3W  C12  C  CR16  0  -0.242   2.4749   2.3843   0.6223
 D3W  C01  C  CH3   0  -0.434  -2.7781   1.5285  -2.4148
 D3W  C03  C  CR6   0   0.367  -2.1188   0.6520  -0.3057
 D3W  C04  C  CR16  0  -0.384  -3.2782   1.1173   0.3090
 D3W  C05  C  CR16  0  -0.256  -3.4731   0.9145   1.6702
 D3W  C06  C  CR16  0  -0.270  -2.5193   0.2509   2.4204
 D3W  C07  C  CR16  0  -0.321  -1.3665  -0.2142   1.7964
 D3W  C08  C  CR6   0   0.062  -1.1421  -0.0340   0.4384
 D3W  C09  C  CH1   0  -0.444   0.1290  -0.4903  -0.2486
 D3W  C15  C  CR16  0  -0.327   1.4902   1.1231  -1.6353
 D3W  C16  C  CH1   0  -0.066   0.7858  -1.7023   0.4113
 D3W  C18  C  CH2   0  -0.321   2.2637  -3.4500   0.1485
 D3W  C19  C  CH2   0  -0.470   0.8981  -4.1307   0.3901
 D3W  C20  C  CH2   0  -0.440  -0.1015  -2.9616   0.4419
 D3W  N17  N  NH1   0  -0.575   1.9967  -2.0904  -0.3027
 D3W  O02  O  O2    0  -0.463  -1.8530   0.8233  -1.6148
 D3W  H1   H  HCR6  0   0.251   2.6658   2.5259  -2.7518
 D3W  H2   H  HCR6  0   0.251   3.5527   3.6574  -0.7328
 D3W  H3   H  HCR6  0   0.245   1.2927   0.9969   1.7359
 D3W  H4   H  HCR6  0   0.251   2.8532   2.8741   1.5107
 D3W  H5   H  HCH3  0   0.258  -2.3564   1.5625  -3.4163
 D3W  H6   H  HCH3  0   0.227  -3.7486   1.0269  -2.4585
 D3W  H7   H  HCH3  0   0.227  -2.9271   2.5520  -2.0613
 D3W  H8   H  HCR6  0   0.277  -4.0367   1.6433  -0.2549
 D3W  H9   H  HCR6  0   0.256  -4.3778   1.2845   2.1350
 D3W  H10  H  HCR6  0   0.249  -2.6634   0.0912   3.4806
 D3W  H11  H  HCR6  0   0.252  -0.6265  -0.7285   2.3961
 D3W  H12  H  HCH1  0   0.255  -0.1340  -0.8134  -1.2618
 D3W  H13  H  HCR6  0   0.241   1.1028   0.6372  -2.5228
 D3W  H14  H  HCH1  0   0.228   1.0890  -1.4570   1.4367
 D3W  H15  H  HCH2  0   0.221   2.8301  -3.4072   1.0830
 D3W  H16  H  HCH2  0   0.236   2.8843  -3.9764  -0.5766
 D3W  H17  H  HCH2  0   0.231   0.6533  -4.8210  -0.4183
 D3W  H18  H  HCH2  0   0.231   0.9011  -4.7119   1.3129
 D3W  H19  H  HCH2  0   0.234  -0.7487  -2.9999   1.3179
 D3W  H20  H  HCH2  0   0.226  -0.7520  -2.9689  -0.4366
 D3W  H21  H  HNH1  0   0.334   1.7888  -2.1163  -1.2964

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
 D3W  C12  C13  aromatic  1.390  0.020  1.390
 D3W  C12  C11  aromatic  1.387  0.020  1.387
 D3W  C13  C14  aromatic  1.388  0.020  1.388
 D3W  C11  C10  aromatic  1.393  0.020  1.393
 D3W  C14  C15  aromatic  1.390  0.020  1.390
 D3W  C10  C15  aromatic  1.391  0.020  1.391
 D3W  C10  C09  single    1.516  0.020  1.516
 D3W  C07  C06  aromatic  1.391  0.020  1.391
 D3W  C07  C08  aromatic  1.388  0.020  1.388
 D3W  C06  C05  aromatic  1.383  0.020  1.383
 D3W  C09  C08  single    1.515  0.020  1.515
 D3W  C09  C16  single    1.528  0.020  1.528
 D3W  C08  C03  aromatic  1.406  0.020  1.406
 D3W  C05  C04  aromatic  1.390  0.020  1.390
 D3W  C16  N17  single    1.458  0.020  1.458
 D3W  C16  C20  single    1.541  0.020  1.541
 D3W  N17  C18  single    1.457  0.020  1.457
 D3W  C03  C04  aromatic  1.392  0.020  1.392
 D3W  C03  O02  single    1.347  0.020  1.347
 D3W  O02  C01  single    1.412  0.020  1.412
 D3W  C20  C19  single    1.539  0.020  1.539
 D3W  C18  C19  single    1.545  0.020  1.545
 D3W  C14  H1   single    0.930  0.020  1.080
 D3W  C13  H2   single    0.930  0.020  1.080
 D3W  C11  H3   single    0.930  0.020  1.080
 D3W  C12  H4   single    0.930  0.020  1.080
 D3W  C01  H5   single    0.970  0.020  1.090
 D3W  C01  H6   single    0.970  0.020  1.090
 D3W  C01  H7   single    0.970  0.020  1.090
 D3W  C04  H8   single    0.930  0.020  1.080
 D3W  C05  H9   single    0.930  0.020  1.080
 D3W  C06  H10  single    0.930  0.020  1.080
 D3W  C07  H11  single    0.930  0.020  1.080
 D3W  C09  H12  single    0.970  0.020  1.090
 D3W  C15  H13  single    0.930  0.020  1.080
 D3W  C16  H14  single    0.970  0.020  1.090
 D3W  C18  H15  single    0.970  0.020  1.090
 D3W  C18  H16  single    0.970  0.020  1.090
 D3W  C19  H17  single    0.970  0.020  1.090
 D3W  C19  H18  single    0.970  0.020  1.090
 D3W  C20  H19  single    0.970  0.020  1.090
 D3W  C20  H20  single    0.970  0.020  1.090
 D3W  N17  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
 D3W  H1   C14  C15  119.74  3.000
 D3W  H1   C14  C13  120.14  3.000
 D3W  C15  C14  C13  120.12  3.000
 D3W  C15  C10  C09  120.62  3.000
 D3W  C09  C10  C11  120.95  3.000
 D3W  C15  C10  C11  118.42  3.000
 D3W  H2   C13  C12  120.23  3.000
 D3W  H2   C13  C14  120.38  3.000
 D3W  C12  C13  C14  119.39  3.000
 D3W  H3   C11  C12  119.11  3.000
 D3W  H3   C11  C10  120.03  3.000
 D3W  C12  C11  C10  120.86  3.000
 D3W  H4   C12  C11  119.72  3.000
 D3W  H4   C12  C13  120.05  3.000
 D3W  C11  C12  C13  120.23  3.000
 D3W  H7   C01  H6   108.76  3.000
 D3W  H7   C01  H5   108.75  3.000
 D3W  H6   C01  H5   108.78  3.000
 D3W  H7   C01  O02  111.94  3.000
 D3W  H6   C01  O02  112.03  3.000
 D3W  H5   C01  O02  106.47  3.000
 D3W  O02  C03  C08  116.06  3.000
 D3W  O02  C03  C04  123.43  3.000
 D3W  C08  C03  C04  120.51  3.000
 D3W  H8   C04  C05  118.89  3.000
 D3W  H8   C04  C03  121.09  3.000
 D3W  C05  C04  C03  120.02  3.000
 D3W  H9   C05  C06  120.50  3.000
 D3W  H9   C05  C04  119.20  3.000
 D3W  C06  C05  C04  120.30  3.000
 D3W  H10  C06  C07  120.04  3.000
 D3W  H10  C06  C05  120.70  3.000
 D3W  C07  C06  C05  119.25  3.000
 D3W  H11  C07  C08  119.54  3.000
 D3W  H11  C07  C06  118.49  3.000
 D3W  C08  C07  C06  121.97  3.000
 D3W  C09  C08  C07  122.69  3.000
 D3W  C09  C08  C03  119.31  3.000
 D3W  C07  C08  C03  117.94  3.000
 D3W  H12  C09  C16  105.58  3.000
 D3W  H12  C09  C08  107.87  3.000
 D3W  C16  C09  C08  113.80  3.000
 D3W  H12  C09  C10  107.33  3.000
 D3W  C16  C09  C10  111.89  3.000
 D3W  C08  C09  C10  110.00  3.000
 D3W  H13  C15  C10  119.41  3.000
 D3W  H13  C15  C14  119.61  3.000
 D3W  C10  C15  C14  120.98  3.000
 D3W  H14  C16  N17  106.72  3.000
 D3W  H14  C16  C20  108.86  3.000
 D3W  N17  C16  C20  105.69  3.000
 D3W  H14  C16  C09  110.18  3.000
 D3W  C20  C16  C09  114.16  3.000
 D3W  N17  C16  C09  110.88  3.000
 D3W  H16  C18  H15  107.01  3.000
 D3W  H16  C18  N17  110.43  3.000
 D3W  H15  C18  N17  108.84  3.000
 D3W  H16  C18  C19  113.24  3.000
 D3W  H15  C18  C19  109.96  3.000
 D3W  N17  C18  C19  107.31  3.000
 D3W  H18  C19  H17  106.88  3.000
 D3W  H18  C19  C20  112.22  3.000
 D3W  H17  C19  C20  111.09  3.000
 D3W  H18  C19  C18  111.39  3.000
 D3W  H17  C19  C18  111.18  3.000
 D3W  C20  C19  C18  104.16  3.000
 D3W  H20  C20  H19  107.00  3.000
 D3W  H20  C20  C19  110.75  3.000
 D3W  H19  C20  C19  112.71  3.000
 D3W  H20  C20  C16  109.40  3.000
 D3W  H19  C20  C16  112.74  3.000
 D3W  C19  C20  C16  104.25  3.000
 D3W  H21  N17  C18  108.46  3.000
 D3W  H21  N17  C16  108.42  3.000
 D3W  C18  N17  C16  104.41  3.000
 D3W  C03  O02  C01  119.01  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
 D3W  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 D3W  CONST_02  C11  C10  C15  C14     0.00   0.0  0
 D3W  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 D3W  CONST_04  C13  C14  C15  C10     0.00   0.0  0
 D3W  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 D3W  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 D3W  CONST_07  C06  C07  C08  C03     0.00   0.0  0
 D3W  CONST_08  C06  C05  C04  C03     0.00   0.0  0
 D3W  CONST_09  C07  C06  C05  C04     0.00   0.0  0
 D3W  CONST_10  C07  C08  C03  C04     0.00   0.0  0
 D3W  CONST_11  C08  C07  C06  C05     0.00   0.0  0
 D3W  CONST_12  C08  C03  C04  C05     0.00   0.0  0
 D3W  CONST_13  C09  C10  C15  C14   180.00   0.0  0
 D3W  CONST_14  C09  C10  C11  C12   180.00   0.0  0
 D3W  CONST_15  C09  C08  C03  C04   180.00   0.0  0
 D3W  CONST_16  O02  C03  C04  C05   180.00   0.0  0
 D3W  CONST_17  C09  C08  C07  C06   180.00   0.0  0
 D3W  CONST_18  O02  C03  C08  C07   180.00   0.0  0
 D3W  CONST_19  H4   C12  C13  C14   180.00   0.0  0
 D3W  CONST_20  H1   C14  C15  C10   180.00   0.0  0
 D3W  CONST_21  H3   C11  C12  C13   180.00   0.0  0
 D3W  CONST_22  H13  C15  C14  C13   180.00   0.0  0
 D3W  CONST_23  H2   C13  C12  C11   180.00   0.0  0
 D3W  CONST_24  H11  C07  C08  C03   180.00   0.0  0
 D3W  CONST_25  H9   C05  C04  C03   180.00   0.0  0
 D3W  CONST_26  H10  C06  C05  C04   180.00   0.0  0
 D3W  CONST_27  H8   C04  C05  C06   180.00   0.0  0
 D3W  Var_01    C19  C18  N17  C16    33.92  30.0  1
 D3W  Var_02    C18  C19  C20  C16    -7.13  30.0  1
 D3W  Var_03    N17  C18  C19  C20   -15.92  30.0  1
 D3W  Var_04    C08  C03  O02  C01  -178.68  30.0  1
 D3W  Var_05    H5   C01  O02  C03   178.89  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
 D3W  chir_01  C09  C10  C08  C16  positiv
 D3W  chir_02  C16  N17  C20  C09  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
 D3W  plan-1  C14  0.020
 D3W  plan-1  C10  0.020
 D3W  plan-1  C13  0.020
 D3W  plan-1  C11  0.020
 D3W  plan-1  C12  0.020
 D3W  plan-1  C09  0.020
 D3W  plan-1  C15  0.020
 D3W  plan-1  H1   0.020
 D3W  plan-1  H2   0.020
 D3W  plan-1  H3   0.020
 D3W  plan-1  H4   0.020
 D3W  plan-1  H13  0.020
 D3W  plan-2  C03  0.020
 D3W  plan-2  C04  0.020
 D3W  plan-2  C05  0.020
 D3W  plan-2  C06  0.020
 D3W  plan-2  C07  0.020
 D3W  plan-2  C08  0.020
 D3W  plan-2  C09  0.020
 D3W  plan-2  O02  0.020
 D3W  plan-2  H8   0.020
 D3W  plan-2  H9   0.020
 D3W  plan-2  H10  0.020
 D3W  plan-2  H11  0.020

