# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:51:32 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R})-2-[(~{R})-(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
 D3Q  D3Q  (2~{R})-2-[(~{R})-(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_D3Q
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
 D3Q  C12  C  CR16  0  -0.274   2.9457  -3.4463  -0.1625
 D3Q  C13  C  CR16  0  -0.244   3.0992  -2.3995  -1.0611
 D3Q  C14  C  CR16  0  -0.318   2.4015  -1.2112  -0.8832
 D3Q  C15  C  CR15  0  -0.066   1.3110   1.4738  -0.1763
 D3Q  C01  C  CH3   0  -0.436  -5.4114  -0.0637   0.7688
 D3Q  C03  C  CR6   0   0.399  -3.0933  -0.0559   0.2636
 D3Q  C04  C  CR16  0  -0.401  -3.3136  -0.3487  -1.0779
 D3Q  C05  C  CR16  0  -0.226  -2.2199  -0.4684  -1.9310
 D3Q  C06  C  CR16  0  -0.326  -0.9266  -0.3043  -1.4705
 D3Q  C07  C  CR6   0   0.217  -0.7019  -0.0067  -0.1247
 D3Q  C08  C  CH1   0  -0.464   0.7029   0.1997   0.4043
 D3Q  C09  C  CR6   0   0.191   1.5326  -1.0499   0.1923
 D3Q  C10  C  CR16  0  -0.300   1.3883  -2.1074   1.0887
 D3Q  C11  C  CR16  0  -0.243   2.0855  -3.2949   0.9175
 D3Q  C17  C  CH2   0  -0.322   2.8854   3.1390   0.0169
 D3Q  C18  C  CH2   0  -0.470   1.5274   3.8744   0.0879
 D3Q  C19  C  CH2   0  -0.435   0.4848   2.7428   0.1007
 D3Q  C20  C  CR16  0  -0.425  -1.7857   0.1129   0.7287
 D3Q  N16  N  NR15  0  -0.573   2.6411   1.7421   0.3556
 D3Q  H1   H  HCR6  0   0.252   3.4932  -4.3699  -0.3003
 D3Q  H2   H  HCR6  0   0.252   3.7704  -2.5032  -1.9042
 D3Q  H3   H  HCR6  0   0.246   2.5497  -0.4079  -1.5935
 D3Q  H4   H  HCR5  0   0.228   1.4106   1.3640  -1.2637
 D3Q  H5   H  HCH3  0   0.259  -6.0276   0.1028   1.6490
 D3Q  H6   H  HCH3  0   0.227  -5.6860   0.6681   0.0047
 D3Q  H7   H  HCH3  0   0.227  -5.6134  -1.0663   0.3824
 D3Q  H8   H  HCR6  0   0.276  -4.3100  -0.4894  -1.4740
 D3Q  H9   H  HCR6  0   0.256  -2.3940  -0.6962  -2.9750
 D3Q  H10  H  HCR6  0   0.245  -0.0960  -0.4115  -2.1567
 D3Q  H11  H  HCH1  0   0.255   0.6191   0.3528   1.4871
 D3Q  H12  H  HCR6  0   0.245   0.7158  -2.0012   1.9329
 D3Q  H13  H  HCR6  0   0.252   1.9572  -4.1012   1.6285
 D3Q  H14  H  HCH2  0   0.221   3.2831   3.1898  -1.0005
 D3Q  H15  H  HCH2  0   0.236   3.6404   3.5652   0.6776
 D3Q  H16  H  HCH2  0   0.231   1.4561   4.4846   0.9887
 D3Q  H17  H  HCH2  0   0.231   1.3970   4.5464  -0.7612
 D3Q  H18  H  HCH2  0   0.236  -0.3104   2.8874  -0.6303
 D3Q  H19  H  HCH2  0   0.224   0.0080   2.6682   1.0821
 D3Q  H20  H  HCR6  0   0.253  -1.6267   0.3418   1.7765
 D3Q  H21  H  HNR5  0   0.336   2.6018   1.6577   1.3670
 D3Q  O02  O  O2    0  -0.474  -4.0684   0.0827   1.1834

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
 D3Q  C12  C11  aromatic  1.389  0.020  1.389
 D3Q  C12  C13  aromatic  1.388  0.020  1.388
 D3Q  C11  C10  aromatic  1.388  0.020  1.388
 D3Q  C13  C14  aromatic  1.389  0.020  1.389
 D3Q  C10  C09  aromatic  1.394  0.020  1.394
 D3Q  C14  C09  aromatic  1.392  0.020  1.392
 D3Q  C09  C08  single    1.515  0.020  1.515
 D3Q  C06  C05  aromatic  1.383  0.020  1.383
 D3Q  C06  C07  aromatic  1.396  0.020  1.396
 D3Q  C05  C04  aromatic  1.392  0.020  1.392
 D3Q  C08  C07  single    1.515  0.020  1.515
 D3Q  C08  C15  single    1.526  0.020  1.526
 D3Q  C07  C20  aromatic  1.385  0.020  1.385
 D3Q  C04  C03  aromatic  1.391  0.020  1.391
 D3Q  C15  N16  single    1.457  0.020  1.457
 D3Q  C15  C19  single    1.539  0.020  1.539
 D3Q  C20  C03  aromatic  1.398  0.020  1.398
 D3Q  N16  C17  single    1.458  0.020  1.458
 D3Q  C03  O02  single    1.348  0.020  1.348
 D3Q  O02  C01  single    1.413  0.020  1.413
 D3Q  C19  C18  single    1.539  0.020  1.539
 D3Q  C17  C18  single    1.546  0.020  1.546
 D3Q  C12  H1   single    0.930  0.020  1.080
 D3Q  C13  H2   single    0.930  0.020  1.080
 D3Q  C14  H3   single    0.930  0.020  1.080
 D3Q  C15  H4   single    0.970  0.020  1.090
 D3Q  C01  H5   single    0.970  0.020  1.090
 D3Q  C01  H6   single    0.970  0.020  1.090
 D3Q  C01  H7   single    0.970  0.020  1.090
 D3Q  C04  H8   single    0.930  0.020  1.080
 D3Q  C05  H9   single    0.930  0.020  1.080
 D3Q  C06  H10  single    0.930  0.020  1.080
 D3Q  C08  H11  single    0.970  0.020  1.090
 D3Q  C10  H12  single    0.930  0.020  1.080
 D3Q  C11  H13  single    0.930  0.020  1.080
 D3Q  C17  H14  single    0.970  0.020  1.090
 D3Q  C17  H15  single    0.970  0.020  1.090
 D3Q  C18  H16  single    0.970  0.020  1.090
 D3Q  C18  H17  single    0.970  0.020  1.090
 D3Q  C19  H18  single    0.970  0.020  1.090
 D3Q  C19  H19  single    0.970  0.020  1.090
 D3Q  C20  H20  single    0.930  0.020  1.080
 D3Q  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
 D3Q  H1   C12  C11  120.35  3.000
 D3Q  H1   C12  C13  120.34  3.000
 D3Q  C11  C12  C13  119.32  3.000
 D3Q  H2   C13  C14  119.53  3.000
 D3Q  H2   C13  C12  120.03  3.000
 D3Q  C14  C13  C12  120.44  3.000
 D3Q  H3   C14  C09  120.43  3.000
 D3Q  H3   C14  C13  118.81  3.000
 D3Q  C09  C14  C13  120.76  3.000
 D3Q  H4   C15  N16  107.29  3.000
 D3Q  H4   C15  C19  108.03  3.000
 D3Q  N16  C15  C19  105.81  3.000
 D3Q  H4   C15  C08  109.24  3.000
 D3Q  C19  C15  C08  113.94  3.000
 D3Q  N16  C15  C08  112.24  3.000
 D3Q  H7   C01  H6   108.69  3.000
 D3Q  H7   C01  H5   108.77  3.000
 D3Q  H6   C01  H5   108.73  3.000
 D3Q  H7   C01  O02  111.98  3.000
 D3Q  H6   C01  O02  111.99  3.000
 D3Q  H5   C01  O02  106.57  3.000
 D3Q  O02  C03  C20  115.93  3.000
 D3Q  O02  C03  C04  124.43  3.000
 D3Q  C20  C03  C04  119.64  3.000
 D3Q  H8   C04  C05  119.22  3.000
 D3Q  H8   C04  C03  121.78  3.000
 D3Q  C05  C04  C03  119.00  3.000
 D3Q  H9   C05  C06  119.77  3.000
 D3Q  H9   C05  C04  118.86  3.000
 D3Q  C06  C05  C04  121.36  3.000
 D3Q  H10  C06  C07  120.56  3.000
 D3Q  H10  C06  C05  119.65  3.000
 D3Q  C07  C06  C05  119.79  3.000
 D3Q  C20  C07  C08  119.92  3.000
 D3Q  C20  C07  C06  119.11  3.000
 D3Q  C08  C07  C06  120.97  3.000
 D3Q  H11  C08  C09  107.16  3.000
 D3Q  H11  C08  C07  107.03  3.000
 D3Q  C09  C08  C07  110.28  3.000
 D3Q  H11  C08  C15  106.83  3.000
 D3Q  C07  C08  C15  110.50  3.000
 D3Q  C09  C08  C15  114.65  3.000
 D3Q  C10  C09  C08  118.63  3.000
 D3Q  C08  C09  C14  123.06  3.000
 D3Q  C10  C09  C14  118.27  3.000
 D3Q  H12  C10  C11  119.43  3.000
 D3Q  H12  C10  C09  119.38  3.000
 D3Q  C11  C10  C09  121.19  3.000
 D3Q  H13  C11  C10  119.79  3.000
 D3Q  H13  C11  C12  120.19  3.000
 D3Q  C10  C11  C12  120.02  3.000
 D3Q  H15  C17  H14  107.09  3.000
 D3Q  H15  C17  N16  110.48  3.000
 D3Q  H14  C17  N16  108.76  3.000
 D3Q  H15  C17  C18  113.24  3.000
 D3Q  H14  C17  C18  109.88  3.000
 D3Q  N16  C17  C18  107.34  3.000
 D3Q  H17  C18  H16  106.89  3.000
 D3Q  H17  C18  C19  112.25  3.000
 D3Q  H16  C18  C19  111.13  3.000
 D3Q  H17  C18  C17  111.24  3.000
 D3Q  H16  C18  C17  111.19  3.000
 D3Q  C19  C18  C17  104.22  3.000
 D3Q  H19  C19  H18  107.03  3.000
 D3Q  H19  C19  C18  110.67  3.000
 D3Q  H18  C19  C18  113.03  3.000
 D3Q  H19  C19  C15  109.83  3.000
 D3Q  H18  C19  C15  112.36  3.000
 D3Q  C18  C19  C15  103.95  3.000
 D3Q  H20  C20  C07  119.94  3.000
 D3Q  H20  C20  C03  118.96  3.000
 D3Q  C07  C20  C03  121.10  3.000
 D3Q  H21  N16  C17  108.51  3.000
 D3Q  H21  N16  C15  108.23  3.000
 D3Q  C17  N16  C15  104.15  3.000
 D3Q  C03  O02  C01  118.48  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
 D3Q  CONST_01  C09  C10  C11  C12     0.00   0.0  0
 D3Q  CONST_02  C09  C14  C13  C12     0.00   0.0  0
 D3Q  CONST_03  C10  C11  C12  C13     0.00   0.0  0
 D3Q  CONST_04  C10  C09  C14  C13     0.00   0.0  0
 D3Q  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 D3Q  CONST_06  C11  C10  C09  C14     0.00   0.0  0
 D3Q  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 D3Q  CONST_08  C06  C07  C20  C03     0.00   0.0  0
 D3Q  CONST_09  C07  C06  C05  C04     0.00   0.0  0
 D3Q  CONST_10  C07  C20  C03  C04     0.00   0.0  0
 D3Q  CONST_11  C20  C07  C06  C05     0.00   0.0  0
 D3Q  CONST_12  C20  C03  C04  C05     0.00   0.0  0
 D3Q  CONST_13  C08  C09  C14  C13   180.00   0.0  0
 D3Q  CONST_14  C08  C07  C20  C03   180.00   0.0  0
 D3Q  CONST_15  C08  C07  C06  C05   180.00   0.0  0
 D3Q  CONST_16  O02  C03  C04  C05   180.00   0.0  0
 D3Q  CONST_17  O02  C03  C20  C07   180.00   0.0  0
 D3Q  CONST_18  C11  C10  C09  C08   180.00   0.0  0
 D3Q  CONST_19  H12  C10  C11  C12   180.00   0.0  0
 D3Q  CONST_20  H3   C14  C13  C12   180.00   0.0  0
 D3Q  CONST_21  H13  C11  C12  C13   180.00   0.0  0
 D3Q  CONST_22  H1   C12  C13  C14   180.00   0.0  0
 D3Q  CONST_23  H9   C05  C04  C03   180.00   0.0  0
 D3Q  CONST_24  H10  C06  C05  C04   180.00   0.0  0
 D3Q  CONST_25  H20  C20  C03  C04   180.00   0.0  0
 D3Q  CONST_26  H8   C04  C05  C06   180.00   0.0  0
 D3Q  CONST_27  H2   C13  C14  C09   180.00   0.0  0
 D3Q  Var_01    C18  C17  N16  C15    33.68  30.0  1
 D3Q  Var_02    C17  C18  C19  C15    -8.21  30.0  1
 D3Q  Var_03    N16  C17  C18  C19   -15.12  30.0  1
 D3Q  Var_04    C04  C03  O02  C01    -0.65  30.0  2
 D3Q  Var_05    H5   C01  O02  C03  -178.98  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
 D3Q  chir_01  C15  C08  N16  C19  positiv
 D3Q  chir_02  C08  C15  C07  C09  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
 D3Q  plan-1  C12  0.020
 D3Q  plan-1  C13  0.020
 D3Q  plan-1  C14  0.020
 D3Q  plan-1  C08  0.020
 D3Q  plan-1  C09  0.020
 D3Q  plan-1  C10  0.020
 D3Q  plan-1  C11  0.020
 D3Q  plan-1  H1   0.020
 D3Q  plan-1  H2   0.020
 D3Q  plan-1  H3   0.020
 D3Q  plan-1  H12  0.020
 D3Q  plan-1  H13  0.020
 D3Q  plan-2  C03  0.020
 D3Q  plan-2  C04  0.020
 D3Q  plan-2  C05  0.020
 D3Q  plan-2  C06  0.020
 D3Q  plan-2  C07  0.020
 D3Q  plan-2  C08  0.020
 D3Q  plan-2  C20  0.020
 D3Q  plan-2  H8   0.020
 D3Q  plan-2  H9   0.020
 D3Q  plan-2  H10  0.020
 D3Q  plan-2  H20  0.020
 D3Q  plan-2  O02  0.020

