# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:47:03 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: [(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1COc2cc(Cl)ccc2O1
#
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
 9R5  9R5  '[(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine'  ligand  23  13  .  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_9R5
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
 9R5  C1   C   CR16  0  -0.229   1.9031   1.4521   0.0893
 9R5  C2   C   CR6   0  -0.048   2.4049   0.1668  -0.0387
 9R5  C3   C   CR16  0  -0.325   1.5669  -0.9346  -0.0694
 9R5  C4   C   CR16  0  -0.368   0.5304   1.6301   0.1635
 9R5  C5   C   CR6   0   0.322  -0.3323   0.5439   0.1251
 9R5  C6   C   CR6   0   0.322   0.1934  -0.7477   0.0154
 9R5  C12  C   CH2   0  -0.306  -3.9016  -0.0412   0.1858
 9R5  O7   O   O2    0  -0.479  -0.6016  -1.8382  -0.0125
 9R5  C8   C   CH2   0  -0.194  -1.9449  -1.6084   0.3870
 9R5  C9   C   CH1   0  -0.024  -2.4763  -0.3322  -0.2317
 9R5  O10  O   O2    0  -0.488  -1.6638   0.7628   0.1897
 9R5  CL   CL  CL    0  -0.135   4.1194  -0.0753  -0.1497
 9R5  N13  N   NH2   0  -0.799  -4.4129   1.1407  -0.4856
 9R5  H1   H   HCR6  0   0.279   2.5646   2.3063   0.1175
 9R5  H2   H   HCR6  0   0.288   1.9617  -1.9386  -0.1586
 9R5  H3   H   HCR6  0   0.277   0.1187   2.6275   0.2525
 9R5  H4   H   HCH2  0   0.240  -4.5082  -0.8977  -0.1163
 9R5  H5   H   HCH2  0   0.210  -3.9510   0.0068   1.2827
 9R5  H6   H   HCH2  0   0.262  -2.5230  -2.4671   0.0478
 9R5  H7   H   HCH2  0   0.241  -2.0071  -1.5584   1.4798
 9R5  H8   H   HCH1  0   0.249  -2.4289  -0.4103  -1.3256
 9R5  H9   H   HNH2  0   0.356  -5.4029   1.2248  -0.2966
 9R5  H10  H   HNH2  0   0.346  -3.9875   1.9697  -0.0916

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
 9R5  N13  C12  single    1.452  0.020  1.452
 9R5  C9   C12  single    1.513  0.020  1.513
 9R5  C9   O10  single    1.427  0.020  1.427
 9R5  C9   C8   single    1.515  0.020  1.515
 9R5  O10  C5   single    1.351  0.020  1.351
 9R5  C8   O7   single    1.420  0.020  1.420
 9R5  C5   C4   aromatic  1.388  0.020  1.388
 9R5  C5   C6   aromatic  1.399  0.020  1.399
 9R5  C4   C1   aromatic  1.386  0.020  1.386
 9R5  O7   C6   single    1.350  0.020  1.350
 9R5  C6   C3   aromatic  1.389  0.020  1.389
 9R5  C1   C2   aromatic  1.386  0.020  1.386
 9R5  C3   C2   aromatic  1.384  0.020  1.384
 9R5  C2   CL   single    1.735  0.020  1.735
 9R5  C1   H1   single    0.930  0.020  1.080
 9R5  C3   H2   single    0.930  0.020  1.080
 9R5  C4   H3   single    0.930  0.020  1.080
 9R5  C12  H4   single    0.970  0.020  1.090
 9R5  C12  H5   single    0.970  0.020  1.090
 9R5  C8   H6   single    0.970  0.020  1.090
 9R5  C8   H7   single    0.970  0.020  1.090
 9R5  C9   H8   single    0.970  0.020  1.090
 9R5  N13  H9   single    0.890  0.020  1.040
 9R5  N13  H10  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
 9R5  H1   C1   C4   120.21  3.000
 9R5  H1   C1   C2   120.92  3.000
 9R5  C4   C1   C2   118.86  3.000
 9R5  CL   C2   C3   119.06  3.000
 9R5  CL   C2   C1   119.55  3.000
 9R5  C3   C2   C1   121.39  3.000
 9R5  H2   C3   C6   119.38  3.000
 9R5  H2   C3   C2   121.27  3.000
 9R5  C6   C3   C2   119.36  3.000
 9R5  H3   C4   C5   119.14  3.000
 9R5  H3   C4   C1   119.95  3.000
 9R5  C5   C4   C1   120.91  3.000
 9R5  O10  C5   C6   121.59  3.000
 9R5  C6   C5   C4   119.42  3.000
 9R5  O10  C5   C4   118.99  3.000
 9R5  O7   C6   C5   121.75  3.000
 9R5  O7   C6   C3   118.20  3.000
 9R5  C5   C6   C3   120.05  3.000
 9R5  H5   C12  H4   106.58  3.000
 9R5  H5   C12  N13  114.20  3.000
 9R5  H4   C12  N13  108.35  3.000
 9R5  H5   C12  C9   109.03  3.000
 9R5  H4   C12  C9   107.22  3.000
 9R5  N13  C12  C9   111.13  3.000
 9R5  C8   O7   C6   114.87  3.000
 9R5  H7   C8   H6   108.45  3.000
 9R5  H7   C8   C9   110.43  3.000
 9R5  H6   C8   C9   110.54  3.000
 9R5  H7   C8   O7   109.98  3.000
 9R5  H6   C8   O7   106.67  3.000
 9R5  C9   C8   O7   110.69  3.000
 9R5  H8   C9   O10  108.92  3.000
 9R5  H8   C9   C8   109.39  3.000
 9R5  O10  C9   C8   109.04  3.000
 9R5  H8   C9   C12  109.22  3.000
 9R5  C8   C9   C12  112.32  3.000
 9R5  O10  C9   C12  107.89  3.000
 9R5  C9   O10  C5   115.00  3.000
 9R5  H10  N13  H9   105.70  3.000
 9R5  H10  N13  C12  109.80  3.000
 9R5  H9   N13  C12  109.02  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
 9R5  CONST_01  C6  C5   C4   C1    0.00   0.0  0
 9R5  CONST_02  C6  C3   C2   C1    0.00   0.0  0
 9R5  CONST_03  C5  C4   C1   C2    0.00   0.0  0
 9R5  CONST_04  C5  C6   C3   C2    0.00   0.0  0
 9R5  CONST_05  C4  C5   C6   C3    0.00   0.0  0
 9R5  CONST_06  C4  C1   C2   C3    0.00   0.0  0
 9R5  CONST_07  CL  C2   C1   C4  180.00   0.0  0
 9R5  CONST_08  CL  C2   C3   C6  180.00   0.0  0
 9R5  CONST_09  H2  C3   C2   C1  180.00   0.0  0
 9R5  CONST_10  H3  C4   C1   C2  180.00   0.0  0
 9R5  CONST_11  H1  C1   C2   C3  180.00   0.0  0
 9R5  Var_01    C9  C8   O7   C6   43.63  30.0  1
 9R5  Var_02    H9  N13  C12  C9  171.40  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
 9R5  chir_01  C9  C12  O10  C8  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
 9R5  plan-1  C1   0.020
 9R5  plan-1  C2   0.020
 9R5  plan-1  C3   0.020
 9R5  plan-1  C4   0.020
 9R5  plan-1  C5   0.020
 9R5  plan-1  C6   0.020
 9R5  plan-1  O7   0.020
 9R5  plan-1  O10  0.020
 9R5  plan-1  CL   0.020
 9R5  plan-1  H1   0.020
 9R5  plan-1  H2   0.020
 9R5  plan-1  H3   0.020

