# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 06:48:03 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc2OCOc12
#
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
 Q6T  Q6T  '1,3-benzodioxole-4-carboxylic acid'  ligand  17  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q6T
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
 Q6T  OAA   O  OC    -1  -0.593   3.1651  -0.1305  -0.0745
 Q6T  C10   C  C      0   0.405   2.1084   0.5259  -0.0121
 Q6T  OAB   O  O      0  -0.587   1.9972   1.7637   0.0485
 Q6T  CAD   C  CR6    0  -0.210   0.8166  -0.2756  -0.0081
 Q6T  CAK   C  CR56   0   0.281  -0.4410   0.2976  -0.0112
 Q6T  CAL   C  CR56   0   0.297  -1.6008  -0.4699   0.0027
 Q6T  OAH   O  O      0  -0.489  -2.6869   0.3449   0.0212
 Q6T  CAF   C  CH2    0   0.066  -2.1918   1.6526  -0.2158
 Q6T  OAG   O  O      0  -0.470  -0.7909   1.6093  -0.0061
 Q6T  CAE   C  CR16   0  -0.355  -1.5795  -1.8408   0.0217
 Q6T  CAJ   C  CR16   0  -0.265  -0.3150  -2.4438   0.0234
 Q6T  CAC   C  CR16   0  -0.311   0.8379  -1.6817   0.0061
 Q6T  HAJ   H  HCR6   0   0.251  -0.2454  -3.5233   0.0356
 Q6T  HAE   H  HCR6   0   0.268  -2.4889  -2.4264   0.0366
 Q6T  HAC   H  HCR6   0   0.245   1.8016  -2.1723   0.0031
 Q6T  HAF1  H  HCH2   0   0.225  -2.4054   1.9503  -1.2492
 Q6T  HAF2  H  HCH2   0   0.241  -2.6493   2.3543   0.4819

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
 Q6T  OAA  C10   deloc     1.245  0.020  1.245
 Q6T  OAB  C10   deloc     1.244  0.020  1.244
 Q6T  CAJ  CAE   aromatic  1.401  0.020  1.401
 Q6T  CAJ  CAC   aromatic  1.382  0.020  1.382
 Q6T  CAE  CAL   aromatic  1.371  0.020  1.371
 Q6T  CAL  OAH   single    1.358  0.020  1.358
 Q6T  CAL  CAK   aromatic  1.391  0.020  1.391
 Q6T  OAH  CAF   single    1.418  0.020  1.418
 Q6T  CAF  OAG   single    1.417  0.020  1.417
 Q6T  OAG  CAK   single    1.358  0.020  1.358
 Q6T  CAK  CAD   aromatic  1.382  0.020  1.382
 Q6T  CAD  CAC   aromatic  1.406  0.020  1.406
 Q6T  CAD  C10   single    1.520  0.020  1.520
 Q6T  CAJ  HAJ   single    0.930  0.020  1.080
 Q6T  CAE  HAE   single    0.930  0.020  1.080
 Q6T  CAC  HAC   single    0.930  0.020  1.080
 Q6T  CAF  HAF1  single    0.970  0.020  1.090
 Q6T  CAF  HAF2  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
 Q6T  CAD   C10  OAB   116.65  3.000
 Q6T  CAD   C10  OAA   116.30  3.000
 Q6T  OAB   C10  OAA   127.05  3.000
 Q6T  CAC   CAD  CAK   115.37  3.000
 Q6T  CAC   CAD  C10   120.95  3.000
 Q6T  CAK   CAD  C10   123.68  3.000
 Q6T  OAG   CAK  CAL   108.55  3.000
 Q6T  OAG   CAK  CAD   129.44  3.000
 Q6T  CAL   CAK  CAD   122.00  3.000
 Q6T  CAE   CAL  OAH   127.74  3.000
 Q6T  OAH   CAL  CAK   109.64  3.000
 Q6T  CAE   CAL  CAK   122.61  3.000
 Q6T  CAF   OAH  CAL   105.77  3.000
 Q6T  HAF2  CAF  HAF1  110.28  3.000
 Q6T  HAF2  CAF  OAG   109.87  3.000
 Q6T  HAF1  CAF  OAG   109.90  3.000
 Q6T  HAF2  CAF  OAH   109.88  3.000
 Q6T  HAF1  CAF  OAH   109.87  3.000
 Q6T  OAG   CAF  OAH   106.99  3.000
 Q6T  CAF   OAG  CAK   106.49  3.000
 Q6T  HAE   CAE  CAJ   121.73  3.000
 Q6T  HAE   CAE  CAL   121.89  3.000
 Q6T  CAJ   CAE  CAL   116.38  3.000
 Q6T  HAJ   CAJ  CAC   119.78  3.000
 Q6T  HAJ   CAJ  CAE   119.18  3.000
 Q6T  CAC   CAJ  CAE   121.04  3.000
 Q6T  HAC   CAC  CAJ   119.55  3.000
 Q6T  HAC   CAC  CAD   117.84  3.000
 Q6T  CAJ   CAC  CAD   122.60  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
 Q6T  CONST_01  CAE  CAL  CAK  CAD     0.00   0.0  0
 Q6T  CONST_02  CAE  CAJ  CAC  CAD     0.00   0.0  0
 Q6T  CONST_03  CAJ  CAE  CAL  CAK     0.00   0.0  0
 Q6T  CONST_04  CAJ  CAC  CAD  CAK     0.00   0.0  0
 Q6T  CONST_05  CAC  CAJ  CAE  CAL     0.00   0.0  0
 Q6T  CONST_06  CAC  CAD  CAK  CAL     0.00   0.0  0
 Q6T  CONST_07  CAL  CAK  CAD  C10   180.00   0.0  0
 Q6T  CONST_08  OAG  CAK  CAD  C10     0.00   0.0  0
 Q6T  CONST_09  CAJ  CAC  CAD  C10   180.00   0.0  0
 Q6T  CONST_10  HAJ  CAJ  CAC  CAD   180.00   0.0  0
 Q6T  CONST_11  HAE  CAE  CAL  CAK   180.00   0.0  0
 Q6T  CONST_12  HAC  CAC  CAD  CAK   180.00   0.0  0
 Q6T  Var_01    OAH  CAF  OAG  CAK    15.61  30.0  1
 Q6T  Var_02    OAG  CAF  OAH  CAL   -15.61  30.0  1
 Q6T  Var_03    CAE  CAL  OAH  CAF  -171.39  30.0  1
 Q6T  Var_04    CAK  CAD  C10  OAA  -176.62  30.0  3

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
 Q6T  plan-1  OAA  0.020
 Q6T  plan-1  C10  0.020
 Q6T  plan-1  OAB  0.020
 Q6T  plan-1  CAD  0.020
 Q6T  plan-2  C10  0.020
 Q6T  plan-2  CAD  0.020
 Q6T  plan-2  CAK  0.020
 Q6T  plan-2  CAL  0.020
 Q6T  plan-2  OAH  0.020
 Q6T  plan-2  OAG  0.020
 Q6T  plan-2  CAE  0.020
 Q6T  plan-2  CAJ  0.020
 Q6T  plan-2  CAC  0.020
 Q6T  plan-2  HAJ  0.020
 Q6T  plan-2  HAE  0.020
 Q6T  plan-2  HAC  0.020

