# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:24:04 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{R})-2-[(~{S})-(3-methylphenyl)-phenyl-methyl]pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(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
 D4H  D4H  (2~{R})-2-[(~{S})-(3-methylphenyl)-phenyl-methyl]pyrrolidine  ligand  40  19  .  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_D4H
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
 D4H  C14  C  CH2   0  -0.320  -0.7746  -3.8565   0.2145
 D4H  C10  C  CR16  0  -0.240  -2.2759   2.9391  -1.0388
 D4H  C11  C  CR16  0  -0.311  -1.4600   1.8284  -1.2079
 D4H  C12  C  CR15  0  -0.060  -0.8499  -1.5546   0.2201
 D4H  C02  C  CR6   0   0.119   3.4091   0.4923  -0.5213
 D4H  C03  C  CR16  0  -0.386   2.0984   0.1761  -0.8815
 D4H  C04  C  CR6   0   0.256   1.0793   0.0743   0.0567
 D4H  C05  C  CH1   0  -0.481  -0.3288  -0.2570  -0.3942
 D4H  C06  C  CR6   0   0.193  -1.2570   0.9191  -0.1724
 D4H  C07  C  CR16  0  -0.326  -1.8978   1.1507   1.0436
 D4H  C08  C  CR16  0  -0.239  -2.7150   2.2599   1.2179
 D4H  C09  C  CR16  0  -0.273  -2.9061   3.1603   0.1783
 D4H  C15  C  CH2   0  -0.471  -2.2386  -3.5083  -0.1444
 D4H  C16  C  CH2   0  -0.440  -2.2362  -1.9773  -0.2944
 D4H  C17  C  CR16  0  -0.335   1.3850   0.2983   1.3987
 D4H  C18  C  CR16  0  -0.225   2.6811   0.6092   1.7759
 D4H  C19  C  CR16  0  -0.327   3.6893   0.7066   0.8233
 D4H  N13  N  NR15  0  -0.575   0.0363  -2.6764  -0.0637
 D4H  H1   H  HCH2  0   0.221  -0.6989  -4.0934   1.2792
 D4H  H2   H  HCH2  0   0.236  -0.3913  -4.7178  -0.3322
 D4H  H4   H  HCR6  0   0.247  -0.9757   1.6633  -2.1638
 D4H  H5   H  HCR5  0   0.228  -0.8970  -1.4525   1.3113
 D4H  H6   H  HCH3  0   0.247   4.3378   1.4985  -2.1814
 D4H  H7   H  HCH3  0   0.243   5.4704   0.6627  -1.1268
 D4H  H8   H  HCH3  0   0.244   4.4614  -0.2505  -2.2471
 D4H  H9   H  HCR6  0   0.237   1.8677   0.0012  -1.9277
 D4H  H10  H  HCH1  0   0.257  -0.2880  -0.4220  -1.4777
 D4H  H11  H  HCR6  0   0.249  -1.7739   0.4612   1.8695
 D4H  H12  H  HCR6  0   0.254  -3.2066   2.4174   2.1695
 D4H  H13  H  HCR6  0   0.254  -3.5451   4.0233   0.3142
 D4H  H14  H  HCH2  0   0.231  -2.5467  -3.9936  -1.0710
 D4H  H15  H  HCH2  0   0.232  -2.9255  -3.8423   0.6342
 D4H  H16  H  HCH2  0   0.236  -3.0508  -1.4953   0.2461
 D4H  H17  H  HCH2  0   0.225  -2.3378  -1.6898  -1.3450
 D4H  H18  H  HCR6  0   0.240   0.6151   0.2330   2.1575
 D4H  H19  H  HCR6  0   0.250   2.9113   0.7769   2.8205
 D4H  H20  H  HCR6  0   0.244   4.6989   0.9513   1.1315
 D4H  H21  H  HNR5  0   0.335   0.2592  -2.6643  -1.0542
 D4H  H3   H  HCR6  0   0.254  -2.4224   3.6284  -1.8606
 D4H  C01  C  CH3   0  -0.725   4.4773   0.6045  -1.5705

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
 D4H  C19  C18  aromatic  1.391  0.020  1.391
 D4H  C19  C02  aromatic  1.390  0.020  1.390
 D4H  C18  C17  aromatic  1.385  0.020  1.385
 D4H  C01  C02  single    1.502  0.020  1.502
 D4H  C02  C03  aromatic  1.396  0.020  1.396
 D4H  C17  C04  aromatic  1.395  0.020  1.395
 D4H  C03  C04  aromatic  1.389  0.020  1.389
 D4H  C04  C05  single    1.515  0.020  1.515
 D4H  C11  C10  aromatic  1.389  0.020  1.389
 D4H  C11  C06  aromatic  1.393  0.020  1.393
 D4H  C10  C09  aromatic  1.388  0.020  1.388
 D4H  C05  C06  single    1.515  0.020  1.515
 D4H  C05  C12  single    1.527  0.020  1.527
 D4H  C06  C07  aromatic  1.394  0.020  1.394
 D4H  C09  C08  aromatic  1.389  0.020  1.389
 D4H  C07  C08  aromatic  1.389  0.020  1.389
 D4H  C12  N13  single    1.457  0.020  1.457
 D4H  C12  C16  single    1.538  0.020  1.538
 D4H  N13  C14  single    1.459  0.020  1.459
 D4H  C16  C15  single    1.538  0.020  1.538
 D4H  C14  C15  single    1.547  0.020  1.547
 D4H  C14  H1   single    0.970  0.020  1.090
 D4H  C14  H2   single    0.970  0.020  1.090
 D4H  C10  H3   single    0.930  0.020  1.080
 D4H  C11  H4   single    0.930  0.020  1.080
 D4H  C12  H5   single    0.970  0.020  1.090
 D4H  C01  H6   single    0.970  0.020  1.090
 D4H  C01  H7   single    0.970  0.020  1.090
 D4H  C01  H8   single    0.970  0.020  1.090
 D4H  C03  H9   single    0.930  0.020  1.080
 D4H  C05  H10  single    0.970  0.020  1.090
 D4H  C07  H11  single    0.930  0.020  1.080
 D4H  C08  H12  single    0.930  0.020  1.080
 D4H  C09  H13  single    0.930  0.020  1.080
 D4H  C15  H14  single    0.970  0.020  1.090
 D4H  C15  H15  single    0.970  0.020  1.090
 D4H  C16  H16  single    0.970  0.020  1.090
 D4H  C16  H17  single    0.970  0.020  1.090
 D4H  C17  H18  single    0.930  0.020  1.080
 D4H  C18  H19  single    0.930  0.020  1.080
 D4H  C19  H20  single    0.930  0.020  1.080
 D4H  N13  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
 D4H  H2   C14  H1   107.03  3.000
 D4H  H2   C14  N13  110.38  3.000
 D4H  H1   C14  N13  108.81  3.000
 D4H  H2   C14  C15  113.22  3.000
 D4H  H1   C14  C15  109.89  3.000
 D4H  N13  C14  C15  107.44  3.000
 D4H  H3   C10  C09  120.17  3.000
 D4H  H3   C10  C11  119.76  3.000
 D4H  C09  C10  C11  120.07  3.000
 D4H  H4   C11  C06  119.40  3.000
 D4H  H4   C11  C10  119.45  3.000
 D4H  C06  C11  C10  121.15  3.000
 D4H  H5   C12  N13  106.95  3.000
 D4H  H5   C12  C16  108.64  3.000
 D4H  N13  C12  C16  105.75  3.000
 D4H  H5   C12  C05  109.61  3.000
 D4H  C16  C12  C05  113.98  3.000
 D4H  N13  C12  C05  111.60  3.000
 D4H  C19  C02  C03  118.29  3.000
 D4H  C03  C02  C01  120.31  3.000
 D4H  C19  C02  C01  121.40  3.000
 D4H  H9   C03  C04  118.90  3.000
 D4H  H9   C03  C02  119.01  3.000
 D4H  C04  C03  C02  122.10  3.000
 D4H  C17  C04  C05  121.69  3.000
 D4H  C05  C04  C03  119.80  3.000
 D4H  C17  C04  C03  118.51  3.000
 D4H  H10  C05  C06  106.51  3.000
 D4H  H10  C05  C04  107.00  3.000
 D4H  C06  C05  C04  110.87  3.000
 D4H  H10  C05  C12  106.39  3.000
 D4H  C06  C05  C12  113.06  3.000
 D4H  C04  C05  C12  112.53  3.000
 D4H  C07  C06  C05  122.58  3.000
 D4H  C07  C06  C11  118.24  3.000
 D4H  C05  C06  C11  119.16  3.000
 D4H  H11  C07  C08  118.69  3.000
 D4H  H11  C07  C06  120.46  3.000
 D4H  C08  C07  C06  120.84  3.000
 D4H  H12  C08  C09  120.09  3.000
 D4H  H12  C08  C07  119.58  3.000
 D4H  C09  C08  C07  120.33  3.000
 D4H  H13  C09  C08  120.28  3.000
 D4H  H13  C09  C10  120.34  3.000
 D4H  C08  C09  C10  119.38  3.000
 D4H  H15  C15  H14  107.00  3.000
 D4H  H15  C15  C16  112.05  3.000
 D4H  H14  C15  C16  111.13  3.000
 D4H  H15  C15  C14  111.19  3.000
 D4H  H14  C15  C14  111.37  3.000
 D4H  C16  C15  C14  104.19  3.000
 D4H  H17  C16  H16  106.90  3.000
 D4H  H17  C16  C15  110.80  3.000
 D4H  H16  C16  C15  112.99  3.000
 D4H  H17  C16  C12  109.44  3.000
 D4H  H16  C16  C12  112.72  3.000
 D4H  C15  C16  C12  104.02  3.000
 D4H  H18  C17  C18  119.20  3.000
 D4H  H18  C17  C04  120.58  3.000
 D4H  C18  C17  C04  120.22  3.000
 D4H  H19  C18  C19  119.73  3.000
 D4H  H19  C18  C17  119.77  3.000
 D4H  C19  C18  C17  120.51  3.000
 D4H  H20  C19  C18  119.77  3.000
 D4H  H20  C19  C02  119.85  3.000
 D4H  C18  C19  C02  120.38  3.000
 D4H  H21  N13  C12  108.32  3.000
 D4H  H21  N13  C14  108.53  3.000
 D4H  C12  N13  C14  104.33  3.000
 D4H  H8   C01  H7   107.94  3.000
 D4H  H8   C01  H6   107.04  3.000
 D4H  H7   C01  H6   107.50  3.000
 D4H  H8   C01  C02  111.38  3.000
 D4H  H7   C01  C02  111.59  3.000
 D4H  H6   C01  C02  111.18  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
 D4H  CONST_01  C07  C06  C11  C10    0.00   0.0  0
 D4H  CONST_02  C07  C08  C09  C10    0.00   0.0  0
 D4H  CONST_03  C08  C09  C10  C11    0.00   0.0  0
 D4H  CONST_04  C08  C07  C06  C11    0.00   0.0  0
 D4H  CONST_05  C17  C18  C19  C02    0.00   0.0  0
 D4H  CONST_06  C17  C04  C03  C02    0.00   0.0  0
 D4H  CONST_07  C18  C19  C02  C03    0.00   0.0  0
 D4H  CONST_08  C18  C17  C04  C03    0.00   0.0  0
 D4H  CONST_09  C19  C18  C17  C04    0.00   0.0  0
 D4H  CONST_10  C19  C02  C03  C04    0.00   0.0  0
 D4H  CONST_11  C09  C10  C11  C06    0.00   0.0  0
 D4H  CONST_12  C09  C08  C07  C06    0.00   0.0  0
 D4H  CONST_13  C05  C06  C11  C10  180.00   0.0  0
 D4H  CONST_14  C18  C19  C02  C01  180.00   0.0  0
 D4H  CONST_15  C04  C03  C02  C01  180.00   0.0  0
 D4H  CONST_16  C05  C04  C03  C02  180.00   0.0  0
 D4H  CONST_17  C18  C17  C04  C05  180.00   0.0  0
 D4H  CONST_18  C08  C07  C06  C05  180.00   0.0  0
 D4H  CONST_19  H12  C08  C09  C10  180.00   0.0  0
 D4H  CONST_20  H13  C09  C10  C11  180.00   0.0  0
 D4H  CONST_21  H11  C07  C06  C11  180.00   0.0  0
 D4H  CONST_22  H19  C18  C19  C02  180.00   0.0  0
 D4H  CONST_23  H20  C19  C02  C03  180.00   0.0  0
 D4H  CONST_24  H18  C17  C04  C03  180.00   0.0  0
 D4H  CONST_25  H3   C10  C11  C06  180.00   0.0  0
 D4H  CONST_26  H4   C11  C06  C07  180.00   0.0  0
 D4H  CONST_27  H9   C03  C04  C17  180.00   0.0  0
 D4H  Var_01    C12  C16  C15  C14   -9.32  30.0  1
 D4H  Var_02    C15  C14  N13  C12   32.72  30.0  1
 D4H  Var_03    N13  C14  C15  C16  -13.82  30.0  1
 D4H  Var_04    H6   C01  C02  C03   71.06  30.0  2

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
 D4H  chir_01  C12  C05  N13  C16  positiv
 D4H  chir_02  C05  C12  C06  C04  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
 D4H  plan-1  C10  0.020
 D4H  plan-1  C11  0.020
 D4H  plan-1  C05  0.020
 D4H  plan-1  C06  0.020
 D4H  plan-1  C07  0.020
 D4H  plan-1  C08  0.020
 D4H  plan-1  C09  0.020
 D4H  plan-1  H4   0.020
 D4H  plan-1  H11  0.020
 D4H  plan-1  H12  0.020
 D4H  plan-1  H13  0.020
 D4H  plan-1  H3   0.020
 D4H  plan-2  C02  0.020
 D4H  plan-2  C03  0.020
 D4H  plan-2  C04  0.020
 D4H  plan-2  C05  0.020
 D4H  plan-2  C17  0.020
 D4H  plan-2  C18  0.020
 D4H  plan-2  C19  0.020
 D4H  plan-2  H9   0.020
 D4H  plan-2  H18  0.020
 D4H  plan-2  H19  0.020
 D4H  plan-2  H20  0.020
 D4H  plan-2  C01  0.020

