# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:43:54 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1,3-benzodioxole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2OCOc2c1
#
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
 0HN  0HN  '1,3-benzodioxole-5-carboxylic acid'  ligand  18  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0HN
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
 0HN  OAA  O  O     0  -0.445   3.0123  -1.4805   0.0037
 0HN  CAI  C  C     0   0.535   2.6362  -0.3312   0.0207
 0HN  OAB  O  OH1   0  -0.597   3.4712   0.6995   0.0621
 0HN  CAJ  C  CR6   0  -0.103   1.2122   0.0674  -0.0031
 0HN  CAE  C  CR16  0  -0.356   0.2547  -0.9640  -0.0434
 0HN  CAL  C  CR56  0   0.322  -1.0596  -0.5906  -0.0685
 0HN  OAH  O  O     0  -0.484  -2.1604  -1.3766  -0.0946
 0HN  CAF  C  CH2   0   0.071  -3.2813  -0.5100  -0.2023
 0HN  OAG  O  O     0  -0.475  -2.7892   0.8227  -0.0823
 0HN  CAK  C  CR56  0   0.319  -1.4469   0.7431  -0.0575
 0HN  CAD  C  CR16  0  -0.329  -0.5290   1.7646  -0.0163
 0HN  CAC  C  CR16  0  -0.272   0.8194   1.4021   0.0111
 0HN  H1   H  HOH1  0   0.487   4.3857   0.3808   0.0736
 0HN  H2   H  HCR6  0   0.281   0.5479  -2.0047  -0.0524
 0HN  H3   H  HCH2  0   0.243  -3.7605  -0.6376  -1.1767
 0HN  H4   H  HCR6  0   0.283  -0.8305   2.8028  -0.0047
 0HN  H5   H  HCR6  0   0.273   1.5578   2.1900   0.0419
 0HN  H6   H  HCH2  0   0.248  -3.9882  -0.7140   0.6029

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
 0HN  OAA  CAI  double    1.209  0.020  1.209
 0HN  CAI  OAB  single    1.327  0.020  1.327
 0HN  CAI  CAJ  single    1.479  0.020  1.479
 0HN  CAE  CAJ  aromatic  1.408  0.020  1.408
 0HN  CAE  CAL  aromatic  1.367  0.020  1.367
 0HN  CAJ  CAC  aromatic  1.391  0.020  1.391
 0HN  CAL  OAH  single    1.353  0.020  1.353
 0HN  CAL  CAK  aromatic  1.389  0.020  1.389
 0HN  OAH  CAF  single    1.421  0.020  1.421
 0HN  CAC  CAD  aromatic  1.397  0.020  1.397
 0HN  CAK  CAD  aromatic  1.374  0.020  1.374
 0HN  CAK  OAG  single    1.345  0.020  1.345
 0HN  CAF  OAG  single    1.426  0.020  1.426
 0HN  OAB  H1   single    0.850  0.020  0.980
 0HN  CAE  H2   single    0.930  0.020  1.080
 0HN  CAF  H3   single    0.970  0.020  1.090
 0HN  CAD  H4   single    0.930  0.020  1.080
 0HN  CAC  H5   single    0.930  0.020  1.080
 0HN  CAF  H6   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
 0HN  CAJ  CAI  OAB  113.39  3.000
 0HN  CAJ  CAI  OAA  123.73  3.000
 0HN  OAB  CAI  OAA  122.88  3.000
 0HN  H1   OAB  CAI  109.81  3.000
 0HN  CAC  CAJ  CAE  120.73  3.000
 0HN  CAC  CAJ  CAI  122.02  3.000
 0HN  CAE  CAJ  CAI  117.25  3.000
 0HN  H2   CAE  CAL  121.58  3.000
 0HN  H2   CAE  CAJ  121.40  3.000
 0HN  CAL  CAE  CAJ  117.03  3.000
 0HN  CAK  CAL  OAH  109.34  3.000
 0HN  CAK  CAL  CAE  122.04  3.000
 0HN  OAH  CAL  CAE  128.62  3.000
 0HN  CAF  OAH  CAL  106.80  3.000
 0HN  H6   CAF  H3   110.61  3.000
 0HN  H6   CAF  OAG  109.66  3.000
 0HN  H3   CAF  OAG  109.60  3.000
 0HN  H6   CAF  OAH  109.95  3.000
 0HN  H3   CAF  OAH  110.00  3.000
 0HN  OAG  CAF  OAH  106.94  3.000
 0HN  CAK  OAG  CAF  106.90  3.000
 0HN  CAD  CAK  OAG  128.56  3.000
 0HN  OAG  CAK  CAL  109.57  3.000
 0HN  CAD  CAK  CAL  121.87  3.000
 0HN  H4   CAD  CAC  121.22  3.000
 0HN  H4   CAD  CAK  121.87  3.000
 0HN  CAC  CAD  CAK  116.91  3.000
 0HN  H5   CAC  CAD  118.11  3.000
 0HN  H5   CAC  CAJ  120.46  3.000
 0HN  CAD  CAC  CAJ  121.43  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
 0HN  CONST_01  CAK  CAL  CAE  CAJ    0.00   0.0  0
 0HN  CONST_02  CAK  CAD  CAC  CAJ    0.00   0.0  0
 0HN  CONST_03  CAD  CAC  CAJ  CAE    0.00   0.0  0
 0HN  CONST_04  CAD  CAK  CAL  CAE    0.00   0.0  0
 0HN  CONST_05  CAC  CAJ  CAE  CAL    0.00   0.0  0
 0HN  CONST_06  CAC  CAD  CAK  CAL    0.00   0.0  0
 0HN  CONST_07  CAL  CAE  CAJ  CAI  180.00   0.0  0
 0HN  CONST_08  CAD  CAC  CAJ  CAI  180.00   0.0  0
 0HN  CONST_09  H4   CAD  CAC  CAJ  180.00   0.0  0
 0HN  CONST_10  H5   CAC  CAJ  CAE  180.00   0.0  0
 0HN  CONST_11  H2   CAE  CAL  OAH    0.00   0.0  0
 0HN  CONST_12  H1   OAB  CAI  CAJ  180.00   0.0  0
 0HN  Var_01    OAG  CAF  OAH  CAL   -6.56  30.0  1
 0HN  Var_02    CAK  CAL  OAH  CAF    4.30  30.0  1
 0HN  Var_03    CAD  CAK  OAG  CAF  176.63  30.0  1
 0HN  Var_04    CAE  CAJ  CAI  OAA    0.21  30.0  2

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
 0HN  plan-1  OAA  0.020
 0HN  plan-1  CAI  0.020
 0HN  plan-1  OAB  0.020
 0HN  plan-1  CAJ  0.020
 0HN  plan-1  H1   0.020
 0HN  plan-2  CAI  0.020
 0HN  plan-2  CAJ  0.020
 0HN  plan-2  CAE  0.020
 0HN  plan-2  CAL  0.020
 0HN  plan-2  OAH  0.020
 0HN  plan-2  OAG  0.020
 0HN  plan-2  CAK  0.020
 0HN  plan-2  CAD  0.020
 0HN  plan-2  CAC  0.020
 0HN  plan-2  H2   0.020
 0HN  plan-2  H4   0.020
 0HN  plan-2  H5   0.020

