# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 10:21:46 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  18  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  OH1   0  -0.596   3.1749  -0.1717   0.0589
 Q6T  C10   C  C     0   0.545   2.0626   0.5410  -0.0641
 Q6T  OAB   O  O     0  -0.435   2.0559   1.7439  -0.1716
 Q6T  CAD   C  CR6   0  -0.196   0.8474  -0.2955  -0.0536
 Q6T  CAK   C  CR56  0   0.325  -0.4054   0.2827  -0.1511
 Q6T  CAL   C  CR56  0   0.312  -1.5629  -0.4870  -0.1440
 Q6T  OAH   O  O     0  -0.482  -2.6406   0.3216  -0.2653
 Q6T  CAF   C  CH2   0   0.069  -2.1567   1.6548  -0.2254
 Q6T  OAG   O  O     0  -0.462  -0.7347   1.5796  -0.2723
 Q6T  CAE   C  CR16  0  -0.335  -1.5341  -1.8523  -0.0440
 Q6T  CAJ   C  CR16  0  -0.262  -0.2706  -2.4536   0.0545
 Q6T  CAC   C  CR16  0  -0.286   0.8846  -1.7015   0.0513
 Q6T  HAA   H  HOH1  0   0.488   3.9448   0.4158   0.0400
 Q6T  HAJ   H  HCR6  0   0.269  -0.2055  -3.5297   0.1348
 Q6T  HAE   H  HCR6  0   0.284  -2.4405  -2.4422  -0.0431
 Q6T  HAC   H  HCR6  0   0.270   1.8372  -2.2046   0.1325
 Q6T  HAF1  H  HCH2  0   0.249  -2.5225   2.2111  -1.0891
 Q6T  HAF2  H  HCH2  0   0.242  -2.4668   2.1401   0.7044

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   single    1.327  0.020  1.327
 Q6T  OAB  C10   double    1.208  0.020  1.208
 Q6T  CAJ  CAE   aromatic  1.403  0.020  1.403
 Q6T  CAJ  CAC   aromatic  1.378  0.020  1.378
 Q6T  CAE  CAL   aromatic  1.369  0.020  1.369
 Q6T  CAL  OAH   single    1.353  0.020  1.353
 Q6T  CAL  CAK   aromatic  1.390  0.020  1.390
 Q6T  OAH  CAF   single    1.419  0.020  1.419
 Q6T  CAF  OAG   single    1.425  0.020  1.425
 Q6T  OAG  CAK   single    1.344  0.020  1.344
 Q6T  CAK  CAD   aromatic  1.383  0.020  1.383
 Q6T  CAD  CAC   aromatic  1.410  0.020  1.410
 Q6T  CAD  C10   single    1.475  0.020  1.475
 Q6T  OAA  HAA   single    0.850  0.020  0.980
 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  HAA   OAA  C10   109.80  3.000
 Q6T  CAD   C10  OAB   124.11  3.000
 Q6T  CAD   C10  OAA   112.66  3.000
 Q6T  OAB   C10  OAA   123.23  3.000
 Q6T  CAC   CAD  CAK   116.48  3.000
 Q6T  CAC   CAD  C10   122.96  3.000
 Q6T  CAK   CAD  C10   120.56  3.000
 Q6T  OAG   CAK  CAL   109.32  3.000
 Q6T  OAG   CAK  CAD   129.19  3.000
 Q6T  CAL   CAK  CAD   121.49  3.000
 Q6T  CAE   CAL  OAH   128.27  3.000
 Q6T  OAH   CAL  CAK   109.39  3.000
 Q6T  CAE   CAL  CAK   122.34  3.000
 Q6T  CAF   OAH  CAL   106.71  3.000
 Q6T  HAF2  CAF  HAF1  110.60  3.000
 Q6T  HAF2  CAF  OAG   109.53  3.000
 Q6T  HAF1  CAF  OAG   109.61  3.000
 Q6T  HAF2  CAF  OAH   110.13  3.000
 Q6T  HAF1  CAF  OAH   110.04  3.000
 Q6T  OAG   CAF  OAH   106.85  3.000
 Q6T  CAF   OAG  CAK   107.01  3.000
 Q6T  HAE   CAE  CAJ   121.40  3.000
 Q6T  HAE   CAE  CAL   121.76  3.000
 Q6T  CAJ   CAE  CAL   116.84  3.000
 Q6T  HAJ   CAJ  CAC   119.53  3.000
 Q6T  HAJ   CAJ  CAE   119.09  3.000
 Q6T  CAC   CAJ  CAE   121.38  3.000
 Q6T  HAC   CAC  CAJ   118.99  3.000
 Q6T  HAC   CAC  CAD   119.54  3.000
 Q6T  CAJ   CAC  CAD   121.46  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  CONST_13  HAA  OAA  C10  CAD  180.00   0.0  0
 Q6T  Var_01    OAH  CAF  OAG  CAK   -8.25  30.0  1
 Q6T  Var_02    OAG  CAF  OAH  CAL    8.32  30.0  1
 Q6T  Var_03    CAE  CAL  OAH  CAF  175.48  30.0  1
 Q6T  Var_04    CAK  CAD  C10  OAA  179.00  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
 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-1  HAA  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

