# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:39:59 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2~{S})-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[NH2+][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
 8LZ  8LZ  (2~{S})-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidin-1-ium  ligand  31  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8LZ
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
 8LZ  C4   C  CR16  0  -0.422  -0.2974   1.0249   0.2822
 8LZ  C5   C  CR6   0   0.139   0.7627   0.2038  -0.0769
 8LZ  C6   C  CR16  0  -0.309   0.4976  -1.0770  -0.5573
 8LZ  C7   C  CR16  0  -0.349  -0.8057  -1.5314  -0.6506
 8LZ  C8   C  CR15  0  -0.185   2.1688   0.7055   0.0587
 8LZ  C9   C  CH2   0  -0.303   4.2013  -0.5973   0.5132
 8LZ  C10  C  CH2   0  -0.476   4.4562   0.3620  -0.6320
 8LZ  C11  C  CH2   0  -0.464   3.0554   0.5944  -1.1826
 8LZ  N    N  N     1  -0.669   2.9358  -0.0789   1.1240
 8LZ  C3   C  CR6   0   0.337  -1.6093   0.5847   0.1708
 8LZ  O    O  O2    0  -0.478  -2.6052   1.4317   0.5144
 8LZ  C2   C  CR6   0   0.316  -1.8674  -0.7113  -0.2879
 8LZ  O1   O  O2    0  -0.475  -3.1236  -1.1961  -0.3879
 8LZ  C1   C  CH2   0  -0.228  -4.1050  -0.4336   0.3017
 8LZ  C    C  CH2   0  -0.229  -3.8898   1.0391   0.0517
 8LZ  H1   H  HCR6  0   0.274  -0.1145   2.0276   0.6508
 8LZ  H2   H  HCR6  0   0.259   1.3031  -1.7379  -0.8551
 8LZ  H3   H  HCR6  0   0.275  -1.0146  -2.5309  -1.0106
 8LZ  H4   H  HCR5  0   0.325   2.1597   1.7342   0.4143
 8LZ  H5   H  HCH2  0   0.292   4.0010  -1.6043   0.1528
 8LZ  H6   H  HCH2  0   0.306   4.9750  -0.6361   1.2743
 8LZ  H8   H  HCH2  0   0.264   4.8969   1.2915  -0.2663
 8LZ  H7   H  HCH2  0   0.281   5.1332  -0.0694  -1.3666
 8LZ  H9   H  HCH2  0   0.262   2.7500  -0.2494  -1.8037
 8LZ  H10  H  HCH2  0   0.288   2.9723   1.4950  -1.7881
 8LZ  H11  H  H     0   0.475   3.1484   0.5361   1.9085
 8LZ  H12  H  H     0   0.472   2.3718  -0.8316   1.5179
 8LZ  H13  H  HCH2  0   0.265  -5.0776  -0.7458  -0.0751
 8LZ  H14  H  HCH2  0   0.247  -4.0620  -0.6508   1.3738
 8LZ  H16  H  HCH2  0   0.264  -4.6234   1.6294   0.5981
 8LZ  H15  H  HCH2  0   0.247  -3.9892   1.2640  -1.0153

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
 8LZ  C10  C11  single    1.523  0.020  1.523
 8LZ  C10  C9   single    1.516  0.020  1.516
 8LZ  C11  C8   single    1.529  0.020  1.529
 8LZ  C8   C5   single    1.499  0.020  1.499
 8LZ  C8   N    single    1.529  0.020  1.529
 8LZ  C9   N    single    1.498  0.020  1.498
 8LZ  C5   C6   aromatic  1.393  0.020  1.393
 8LZ  C5   C4   aromatic  1.388  0.020  1.388
 8LZ  C6   C7   aromatic  1.383  0.020  1.383
 8LZ  C4   C3   aromatic  1.388  0.020  1.388
 8LZ  C7   C2   aromatic  1.390  0.020  1.390
 8LZ  C3   C2   aromatic  1.399  0.020  1.399
 8LZ  C3   O    single    1.352  0.020  1.352
 8LZ  C2   O1   single    1.350  0.020  1.350
 8LZ  O    C    single    1.421  0.020  1.421
 8LZ  C    C1   single    1.509  0.020  1.509
 8LZ  O1   C1   single    1.421  0.020  1.421
 8LZ  C4   H1   single    0.930  0.020  1.080
 8LZ  C6   H2   single    0.930  0.020  1.080
 8LZ  C7   H3   single    0.930  0.020  1.080
 8LZ  C8   H4   single    0.970  0.020  1.090
 8LZ  C9   H5   single    0.970  0.020  1.090
 8LZ  C9   H6   single    0.970  0.020  1.090
 8LZ  C10  H8   single    0.970  0.020  1.090
 8LZ  C10  H7   single    0.970  0.020  1.090
 8LZ  C11  H9   single    0.970  0.020  1.090
 8LZ  C11  H10  single    0.970  0.020  1.090
 8LZ  N    H11  single    0.890  0.020  1.040
 8LZ  N    H12  single    0.890  0.020  1.040
 8LZ  C1   H13  single    0.970  0.020  1.090
 8LZ  C1   H14  single    0.970  0.020  1.090
 8LZ  C    H16  single    0.970  0.020  1.090
 8LZ  C    H15  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
 8LZ  H1   C4   C3   118.70  3.000
 8LZ  H1   C4   C5   120.42  3.000
 8LZ  C3   C4   C5   120.89  3.000
 8LZ  C8   C5   C6   121.15  3.000
 8LZ  C6   C5   C4   119.18  3.000
 8LZ  C8   C5   C4   119.67  3.000
 8LZ  H2   C6   C7   118.78  3.000
 8LZ  H2   C6   C5   120.92  3.000
 8LZ  C7   C6   C5   120.29  3.000
 8LZ  H3   C7   C2   118.96  3.000
 8LZ  H3   C7   C6   120.49  3.000
 8LZ  C2   C7   C6   120.55  3.000
 8LZ  H4   C8   N    105.15  3.000
 8LZ  H4   C8   C11  109.79  3.000
 8LZ  N    C8   C11  103.73  3.000
 8LZ  H4   C8   C5   109.75  3.000
 8LZ  N    C8   C5   111.21  3.000
 8LZ  C11  C8   C5   116.49  3.000
 8LZ  H6   C9   H5   109.28  3.000
 8LZ  H6   C9   N    109.18  3.000
 8LZ  H5   C9   N    107.44  3.000
 8LZ  H6   C9   C10  115.62  3.000
 8LZ  H5   C9   C10  111.50  3.000
 8LZ  N    C9   C10  103.36  3.000
 8LZ  H7   C10  H8   108.21  3.000
 8LZ  H7   C10  C11  112.87  3.000
 8LZ  H8   C10  C11  111.26  3.000
 8LZ  H7   C10  C9   111.33  3.000
 8LZ  H8   C10  C9   110.71  3.000
 8LZ  C11  C10  C9   102.42  3.000
 8LZ  H10  C11  H9   107.57  3.000
 8LZ  H10  C11  C10  113.43  3.000
 8LZ  H9   C11  C10  110.20  3.000
 8LZ  H10  C11  C8   110.31  3.000
 8LZ  H9   C11  C8   110.84  3.000
 8LZ  C10  C11  C8   104.53  3.000
 8LZ  H12  N    H11  105.27  3.000
 8LZ  H12  N    C9   111.68  3.000
 8LZ  H11  N    C9   110.26  3.000
 8LZ  H12  N    C8   111.74  3.000
 8LZ  H11  N    C8   109.35  3.000
 8LZ  C9   N    C8   108.50  3.000
 8LZ  C2   C3   O    121.87  3.000
 8LZ  O    C3   C4   118.50  3.000
 8LZ  C2   C3   C4   119.64  3.000
 8LZ  C    O    C3   114.22  3.000
 8LZ  O1   C2   C3   121.91  3.000
 8LZ  O1   C2   C7   118.66  3.000
 8LZ  C3   C2   C7   119.43  3.000
 8LZ  C1   O1   C2   114.45  3.000
 8LZ  H14  C1   H13  108.49  3.000
 8LZ  H14  C1   C    110.50  3.000
 8LZ  H13  C1   C    110.49  3.000
 8LZ  H14  C1   O1   109.97  3.000
 8LZ  H13  C1   O1   107.16  3.000
 8LZ  C    C1   O1   110.16  3.000
 8LZ  H15  C    H16  108.45  3.000
 8LZ  H15  C    C1   110.42  3.000
 8LZ  H16  C    C1   110.48  3.000
 8LZ  H15  C    O    110.04  3.000
 8LZ  H16  C    O    107.22  3.000
 8LZ  C1   C    O    110.17  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
 8LZ  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 8LZ  CONST_02  C7   C2   C3   C4     0.00   0.0  0
 8LZ  CONST_03  C2   C7   C6   C5     0.00   0.0  0
 8LZ  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 8LZ  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 8LZ  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 8LZ  CONST_07  C8   C5   C6   C7   180.00   0.0  0
 8LZ  CONST_08  C3   C4   C5   C8   180.00   0.0  0
 8LZ  CONST_09  H2   C6   C5   C4   180.00   0.0  0
 8LZ  CONST_10  H3   C7   C6   C5   180.00   0.0  0
 8LZ  CONST_11  H1   C4   C5   C6   180.00   0.0  0
 8LZ  Var_01    C9   C10  C11  C8    40.51  30.0  1
 8LZ  Var_02    C10  C9   N    C8    24.42  30.0  1
 8LZ  Var_03    N    C9   C10  C11  -39.58  30.0  1
 8LZ  Var_04    C1   C    O    C3    44.97  30.0  1
 8LZ  Var_05    O1   C1   C    O    -60.28  30.0  1
 8LZ  Var_06    C    C1   O1   C2    44.12  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
 8LZ  chir_01  C8  C11  C5  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
 8LZ  plan-1  C4  0.020
 8LZ  plan-1  C5  0.020
 8LZ  plan-1  C6  0.020
 8LZ  plan-1  C7  0.020
 8LZ  plan-1  C8  0.020
 8LZ  plan-1  C3  0.020
 8LZ  plan-1  O   0.020
 8LZ  plan-1  C2  0.020
 8LZ  plan-1  O1  0.020
 8LZ  plan-1  H1  0.020
 8LZ  plan-1  H2  0.020
 8LZ  plan-1  H3  0.020

