# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 14:13:20 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R)-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN[C@H](C1)c2ccc3OCCOc3c2
#
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
 46O  46O  (2R)-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidine  ligand  30  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_46O
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
 46O  C2   C  CR6   0   0.297  -1.7828   0.7833  -0.1357
 46O  C4   C  CR16  0  -0.447  -0.2605  -1.0518   0.2130
 46O  C5   C  CR6   0   0.132   0.8326  -0.2139   0.0439
 46O  C6   C  CR16  0  -0.314   0.5990   1.1413  -0.1951
 46O  C11  C  CH2   0  -0.469   3.0239  -0.6311  -1.1833
 46O  C10  C  CH2   0  -0.464   4.4453  -0.3149  -0.7307
 46O  C9   C  CH2   0  -0.272   4.1931   0.5747   0.4772
 46O  N    N  NH1   0  -0.619   3.0726  -0.0847   1.1356
 46O  C8   C  CH1   0  -0.131   2.2358  -0.7628   0.1349
 46O  C3   C  CR6   0   0.333  -1.5622  -0.5698   0.1270
 46O  O    O  O2    0  -0.482  -2.5870  -1.4377   0.3126
 46O  C7   C  CR16  0  -0.350  -0.6915   1.6309  -0.2900
 46O  O1   O  O2    0  -0.481  -3.0309   1.3013  -0.2448
 46O  C1   C  CH2   0  -0.226  -4.0513   0.3276  -0.4004
 46O  C    C  CH2   0  -0.227  -3.8354  -0.8120   0.5661
 46O  H1   H  HCR6  0   0.259  -0.1119  -2.1060   0.4195
 46O  H2   H  HCR6  0   0.248   1.4281   1.8268  -0.3255
 46O  H3   H  HCH2  0   0.233   2.6328   0.2029  -1.7704
 46O  H4   H  HCH2  0   0.247   2.9460  -1.5272  -1.7993
 46O  H5   H  HCH2  0   0.228   4.9696  -1.2248  -0.4288
 46O  H6   H  HCH2  0   0.238   5.0405   0.1756  -1.5009
 46O  H7   H  HCH2  0   0.223   5.0576   0.6385   1.1425
 46O  H8   H  HCH2  0   0.197   3.9635   1.5963   0.1429
 46O  H9   H  HNH1  0   0.350   2.5399   0.5420   1.7218
 46O  H11  H  HCH1  0   0.227   2.1525  -1.8246   0.3963
 46O  H12  H  HCR6  0   0.264  -0.8677   2.6816  -0.4862
 46O  H13  H  HCH2  0   0.260  -5.0022   0.8205  -0.2035
 46O  H14  H  HCH2  0   0.242  -4.0620  -0.0461  -1.4301
 46O  H15  H  HCH2  0   0.260  -4.6081  -1.5688   0.4406
 46O  H16  H  HCH2  0   0.242  -3.8721  -0.4481   1.5986

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
 46O  C7   C6   aromatic  1.384  0.020  1.384
 46O  C7   C2   aromatic  1.390  0.020  1.390
 46O  O1   C2   single    1.356  0.020  1.356
 46O  O1   C1   single    1.419  0.020  1.419
 46O  C6   C5   aromatic  1.396  0.020  1.396
 46O  C2   C3   aromatic  1.396  0.020  1.396
 46O  C1   C    single    1.510  0.020  1.510
 46O  C5   C8   single    1.510  0.020  1.510
 46O  C5   C4   aromatic  1.388  0.020  1.388
 46O  C    O    single    1.419  0.020  1.419
 46O  C11  C8   single    1.541  0.020  1.541
 46O  C11  C10  single    1.525  0.020  1.525
 46O  C3   C4   aromatic  1.391  0.020  1.391
 46O  C3   O    single    1.356  0.020  1.356
 46O  C8   N    single    1.470  0.020  1.470
 46O  C10  C9   single    1.521  0.020  1.521
 46O  N    C9   single    1.457  0.020  1.457
 46O  C4   H1   single    0.930  0.020  1.080
 46O  C6   H2   single    0.930  0.020  1.080
 46O  C11  H3   single    0.970  0.020  1.090
 46O  C11  H4   single    0.970  0.020  1.090
 46O  C10  H5   single    0.970  0.020  1.090
 46O  C10  H6   single    0.970  0.020  1.090
 46O  C9   H7   single    0.970  0.020  1.090
 46O  C9   H8   single    0.970  0.020  1.090
 46O  N    H9   single    0.890  0.020  1.040
 46O  C8   H11  single    0.970  0.020  1.090
 46O  C7   H12  single    0.930  0.020  1.080
 46O  C1   H13  single    0.970  0.020  1.090
 46O  C1   H14  single    0.970  0.020  1.090
 46O  C    H15  single    0.970  0.020  1.090
 46O  C    H16  single    0.970  0.020  1.090

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
 46O  O1   C2   C7   118.73  3.000
 46O  O1   C2   C3   122.07  3.000
 46O  C7   C2   C3   119.19  3.000
 46O  H1   C4   C3   118.48  3.000
 46O  H1   C4   C5   120.15  3.000
 46O  C3   C4   C5   121.37  3.000
 46O  C8   C5   C6   121.26  3.000
 46O  C8   C5   C4   120.35  3.000
 46O  C6   C5   C4   118.38  3.000
 46O  H2   C6   C7   118.79  3.000
 46O  H2   C6   C5   120.45  3.000
 46O  C7   C6   C5   120.76  3.000
 46O  H4   C11  H3   107.35  3.000
 46O  H4   C11  C8   112.11  3.000
 46O  H3   C11  C8   109.99  3.000
 46O  H4   C11  C10  113.88  3.000
 46O  H3   C11  C10  109.57  3.000
 46O  C8   C11  C10  103.91  3.000
 46O  H6   C10  H5   107.93  3.000
 46O  H6   C10  C9   112.86  3.000
 46O  H5   C10  C9   110.31  3.000
 46O  H6   C10  C11  113.12  3.000
 46O  H5   C10  C11  110.89  3.000
 46O  C9   C10  C11  101.68  3.000
 46O  H8   C9   H7   107.23  3.000
 46O  H8   C9   N    113.41  3.000
 46O  H7   C9   N    111.08  3.000
 46O  H8   C9   C10  109.67  3.000
 46O  H7   C9   C10  112.73  3.000
 46O  N    C9   C10  102.80  3.000
 46O  H9   N    C8   112.39  3.000
 46O  H9   N    C9   112.77  3.000
 46O  C8   N    C9   109.80  3.000
 46O  H11  C8   N    109.13  3.000
 46O  H11  C8   C11  108.99  3.000
 46O  N    C8   C11  104.58  3.000
 46O  H11  C8   C5   107.21  3.000
 46O  N    C8   C5   113.73  3.000
 46O  C11  C8   C5   113.12  3.000
 46O  O    C3   C4   118.50  3.000
 46O  O    C3   C2   121.80  3.000
 46O  C4   C3   C2   119.70  3.000
 46O  C    O    C3   114.02  3.000
 46O  H12  C7   C6   120.49  3.000
 46O  H12  C7   C2   118.93  3.000
 46O  C6   C7   C2   120.58  3.000
 46O  C1   O1   C2   114.11  3.000
 46O  H14  C1   H13  108.41  3.000
 46O  H14  C1   C    110.22  3.000
 46O  H13  C1   C    110.53  3.000
 46O  H14  C1   O1   110.14  3.000
 46O  H13  C1   O1   107.30  3.000
 46O  C    C1   O1   110.18  3.000
 46O  H16  C    H15  108.41  3.000
 46O  H16  C    C1   110.36  3.000
 46O  H15  C    C1   110.45  3.000
 46O  H16  C    O    110.14  3.000
 46O  H15  C    O    107.29  3.000
 46O  C1   C    O    110.13  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
 46O  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 46O  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 46O  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 46O  CONST_04  C7   C2   C3   C4     0.00   0.0  0
 46O  CONST_05  C3   C2   C7   C6     0.00   0.0  0
 46O  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 46O  CONST_07  C7   C6   C5   C8   180.00   0.0  0
 46O  CONST_08  C3   C4   C5   C8   180.00   0.0  0
 46O  CONST_09  H2   C6   C7   C2   180.00   0.0  0
 46O  CONST_10  H1   C4   C3   C2   180.00   0.0  0
 46O  CONST_11  H12  C7   C6   C5   180.00   0.0  0
 46O  Var_01    C    C1   O1   C2    44.37  30.0  1
 46O  Var_02    N    C9   C10  C11   40.95  30.0  1
 46O  Var_03    C8   N    C9   C10  -30.45  30.0  1
 46O  Var_04    C8   C11  C10  C9   -36.66  30.0  1
 46O  Var_05    C1   C    O    C3    45.33  30.0  1
 46O  Var_06    O1   C1   C    O    -60.87  30.0  1

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
 46O  chir_01  C8  C5  C11  N  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
 46O  plan-1  C2   0.020
 46O  plan-1  C4   0.020
 46O  plan-1  C5   0.020
 46O  plan-1  C6   0.020
 46O  plan-1  C8   0.020
 46O  plan-1  C3   0.020
 46O  plan-1  O    0.020
 46O  plan-1  C7   0.020
 46O  plan-1  O1   0.020
 46O  plan-1  H1   0.020
 46O  plan-1  H2   0.020
 46O  plan-1  H12  0.020

