# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:46:14 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc2OCCOc12
#
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
 53E  53E  '2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  21  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_53E
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
 53E  C01  C  CH2   0  -0.229  -2.8680   0.9334   0.2857
 53E  C02  C  CH2   0  -0.229  -1.8691   1.8259  -0.4034
 53E  O03  O  O2    0  -0.458  -0.5505   1.4824   0.0021
 53E  C04  C  CR6   0   0.335  -0.2837   0.1645   0.0218
 53E  C05  C  CR6   0  -0.202   1.0471  -0.2743   0.0639
 53E  C06  C  CR16  0  -0.279   1.3239  -1.6430   0.0361
 53E  C07  C  CR16  0  -0.254   0.2978  -2.5672  -0.0258
 53E  C08  C  CR16  0  -0.353  -1.0197  -2.1368  -0.0551
 53E  C09  C  CR6   0   0.326  -1.3168  -0.7836  -0.0324
 53E  O10  O  O2    0  -0.478  -2.6189  -0.4194  -0.0628
 53E  C11  C  C     0   0.524   2.1561   0.7037   0.1782
 53E  O12  O  OH1   0  -0.595   3.3013   0.2160  -0.2895
 53E  O13  O  O     0  -0.431   2.0631   1.8098   0.6501
 53E  H1   H  HCH2  0   0.247  -2.8117   1.0604   1.3719
 53E  H2   H  HCH2  0   0.266  -3.8806   1.1688  -0.0375
 53E  H3   H  HCH2  0   0.249  -1.9600   1.7377  -1.4908
 53E  H4   H  HCH2  0   0.266  -2.0246   2.8671  -0.1266
 53E  H5   H  HCR6  0   0.269   2.3473  -1.9877   0.0744
 53E  H6   H  HCR6  0   0.264   0.5181  -3.6255  -0.0396
 53E  H7   H  HCR6  0   0.277  -1.8340  -2.8494  -0.0947
 53E  H8   H  HOH1  0   0.485   4.0116   0.8578  -0.1410

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
 53E  C01  O10  single    1.419  0.020  1.419
 53E  C01  C02  single    1.506  0.020  1.506
 53E  C08  C07  aromatic  1.386  0.020  1.386
 53E  C08  C09  aromatic  1.386  0.020  1.386
 53E  O10  C09  single    1.352  0.020  1.352
 53E  C07  C06  aromatic  1.382  0.020  1.382
 53E  C09  C04  aromatic  1.403  0.020  1.403
 53E  C06  C05  aromatic  1.397  0.020  1.397
 53E  C04  C05  aromatic  1.402  0.020  1.402
 53E  C04  O03  single    1.345  0.020  1.345
 53E  O13  C11  double    1.206  0.020  1.206
 53E  C02  O03  single    1.422  0.020  1.422
 53E  C05  C11  single    1.483  0.020  1.483
 53E  C11  O12  single    1.330  0.020  1.330
 53E  C01  H1   single    0.970  0.020  1.090
 53E  C01  H2   single    0.970  0.020  1.090
 53E  C02  H3   single    0.970  0.020  1.090
 53E  C02  H4   single    0.970  0.020  1.090
 53E  C06  H5   single    0.930  0.020  1.080
 53E  C07  H6   single    0.930  0.020  1.080
 53E  C08  H7   single    0.930  0.020  1.080
 53E  O12  H8   single    0.850  0.020  0.980

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
 53E  H2   C01  H1   108.49  3.000
 53E  H2   C01  O10  107.25  3.000
 53E  H1   C01  O10  110.19  3.000
 53E  H2   C01  C02  110.66  3.000
 53E  H1   C01  C02  110.54  3.000
 53E  O10  C01  C02  109.64  3.000
 53E  H4   C02  H3   108.53  3.000
 53E  H4   C02  O03  106.92  3.000
 53E  H3   C02  O03  109.93  3.000
 53E  H4   C02  C01  110.84  3.000
 53E  H3   C02  C01  110.58  3.000
 53E  O03  C02  C01  109.96  3.000
 53E  C04  O03  C02  115.15  3.000
 53E  C09  C04  C05  119.24  3.000
 53E  C05  C04  O03  119.71  3.000
 53E  C09  C04  O03  121.03  3.000
 53E  C11  C05  C06  119.97  3.000
 53E  C11  C05  C04  120.38  3.000
 53E  C06  C05  C04  119.63  3.000
 53E  H5   C06  C07  119.43  3.000
 53E  H5   C06  C05  119.97  3.000
 53E  C07  C06  C05  120.59  3.000
 53E  H6   C07  C08  119.82  3.000
 53E  H6   C07  C06  120.25  3.000
 53E  C08  C07  C06  119.93  3.000
 53E  H7   C08  C09  118.82  3.000
 53E  H7   C08  C07  120.74  3.000
 53E  C09  C08  C07  120.44  3.000
 53E  O10  C09  C08  117.97  3.000
 53E  O10  C09  C04  121.85  3.000
 53E  C08  C09  C04  120.17  3.000
 53E  C09  O10  C01  114.85  3.000
 53E  O13  C11  O12  122.71  3.000
 53E  O12  C11  C05  112.03  3.000
 53E  O13  C11  C05  125.25  3.000
 53E  H8   O12  C11  109.55  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
 53E  CONST_01  C07  C08  C09  C04    0.00   0.0  0
 53E  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 53E  CONST_03  C08  C07  C06  C05    0.00   0.0  0
 53E  CONST_04  C08  C09  C04  C05    0.00   0.0  0
 53E  CONST_05  C09  C08  C07  C06    0.00   0.0  0
 53E  CONST_06  C09  C04  C05  C06    0.00   0.0  0
 53E  CONST_07  C11  C05  C04  O03    0.00   0.0  0
 53E  CONST_08  C11  C05  C06  C07  180.00   0.0  0
 53E  CONST_09  C11  C05  C04  C09  180.00   0.0  0
 53E  CONST_10  H7   C08  C09  C04  180.00   0.0  0
 53E  CONST_11  H5   C06  C05  C04  180.00   0.0  0
 53E  CONST_12  H6   C07  C06  C05  180.00   0.0  0
 53E  CONST_13  H8   O12  C11  C05  180.00   0.0  0
 53E  Var_01    C08  C09  O10  C01  165.43  30.0  1
 53E  Var_02    C09  C04  O03  C02  -14.87  30.0  1
 53E  Var_03    O10  C01  C02  O03  -60.36  30.0  1
 53E  Var_04    H3   C02  O03  C04  -76.90  30.0  1
 53E  Var_05    O13  C11  C05  C04   24.61  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
 53E  plan-1  C05  0.020
 53E  plan-1  C11  0.020
 53E  plan-1  O12  0.020
 53E  plan-1  O13  0.020
 53E  plan-1  H8   0.020
 53E  plan-2  O03  0.020
 53E  plan-2  C04  0.020
 53E  plan-2  C05  0.020
 53E  plan-2  C06  0.020
 53E  plan-2  C07  0.020
 53E  plan-2  C08  0.020
 53E  plan-2  C09  0.020
 53E  plan-2  O10  0.020
 53E  plan-2  C11  0.020
 53E  plan-2  H5   0.020
 53E  plan-2  H6   0.020
 53E  plan-2  H7   0.020

