# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:21:00 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  20  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.222  -2.8353   0.9507   0.3006
 53E  C02  C  CH2    0  -0.228  -1.8371   1.8019  -0.4424
 53E  O03  O  O2     0  -0.464  -0.5206   1.4743  -0.0355
 53E  C04  C  CR6    0   0.290  -0.2582   0.1438   0.0039
 53E  C05  C  CR6    0  -0.185   1.0704  -0.2905  -0.0045
 53E  C06  C  CR16   0  -0.312   1.3259  -1.6592  -0.0217
 53E  C07  C  CR16   0  -0.258   0.2936  -2.5854  -0.0066
 53E  C08  C  CR16   0  -0.373  -1.0216  -2.1512   0.0116
 53E  C09  C  CR6    0   0.312  -1.3021  -0.7914   0.0094
 53E  O10  O  O2     0  -0.484  -2.6073  -0.4184   0.0129
 53E  C11  C  C      0   0.378   2.2470   0.6786   0.0365
 53E  O12  O  OC    -1  -0.601   3.2314   0.3664  -0.6600
 53E  O13  O  O      0  -0.592   2.1371   1.6678   0.7812
 53E  H1   H  HCH2   0   0.238  -2.7599   1.1295   1.3789
 53E  H2   H  HCH2   0   0.257  -3.8513   1.1833  -0.0156
 53E  H3   H  HCH2   0   0.237  -1.9478   1.6609  -1.5240
 53E  H4   H  HCH2   0   0.257  -1.9902   2.8567  -0.2180
 53E  H5   H  HCR6   0   0.243   2.3529  -1.9992  -0.0456
 53E  H6   H  HCR6   0   0.247   0.5085  -3.6460  -0.0074
 53E  H7   H  HCR6   0   0.260  -1.8426  -2.8574   0.0213

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    1.417  0.020  1.417
 53E  C01  C02  single    1.508  0.020  1.508
 53E  C08  C07  aromatic  1.385  0.020  1.385
 53E  C08  C09  aromatic  1.388  0.020  1.388
 53E  O10  C09  single    1.357  0.020  1.357
 53E  C07  C06  aromatic  1.387  0.020  1.387
 53E  C09  C04  aromatic  1.402  0.020  1.402
 53E  C06  C05  aromatic  1.392  0.020  1.392
 53E  C04  C05  aromatic  1.398  0.020  1.398
 53E  C04  O03  single    1.357  0.020  1.357
 53E  O13  C11  deloc     1.243  0.020  1.243
 53E  C02  O03  single    1.416  0.020  1.416
 53E  C05  C11  single    1.525  0.020  1.525
 53E  C11  O12  deloc     1.246  0.020  1.246
 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

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   108.36  3.000
 53E  H2   C01  O10  107.30  3.000
 53E  H1   C01  O10  110.26  3.000
 53E  H2   C01  C02  110.73  3.000
 53E  H1   C01  C02  110.33  3.000
 53E  O10  C01  C02  109.80  3.000
 53E  H4   C02  H3   108.28  3.000
 53E  H4   C02  O03  107.18  3.000
 53E  H3   C02  O03  110.34  3.000
 53E  H4   C02  C01  110.62  3.000
 53E  H3   C02  C01  110.29  3.000
 53E  O03  C02  C01  110.07  3.000
 53E  C04  O03  C02  114.51  3.000
 53E  C09  C04  C05  120.04  3.000
 53E  C05  C04  O03  119.23  3.000
 53E  C09  C04  O03  120.70  3.000
 53E  C11  C05  C06  118.91  3.000
 53E  C11  C05  C04  122.39  3.000
 53E  C06  C05  C04  118.68  3.000
 53E  H5   C06  C07  119.79  3.000
 53E  H5   C06  C05  118.89  3.000
 53E  C07  C06  C05  121.31  3.000
 53E  H6   C07  C08  119.72  3.000
 53E  H6   C07  C06  120.44  3.000
 53E  C08  C07  C06  119.84  3.000
 53E  H7   C08  C09  119.05  3.000
 53E  H7   C08  C07  121.03  3.000
 53E  C09  C08  C07  119.92  3.000
 53E  O10  C09  C08  117.60  3.000
 53E  O10  C09  C04  122.19  3.000
 53E  C08  C09  C04  120.20  3.000
 53E  C09  O10  C01  114.87  3.000
 53E  O13  C11  O12  127.18  3.000
 53E  O12  C11  C05  115.81  3.000
 53E  O13  C11  C05  116.98  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  Var_01    C08  C09  O10  C01  166.96  30.0  1
 53E  Var_02    C09  C04  O03  C02  -16.89  30.0  1
 53E  Var_03    O10  C01  C02  O03  -60.82  30.0  1
 53E  Var_04    H3   C02  O03  C04  -74.91  30.0  1
 53E  Var_05    O13  C11  C05  C04   39.83  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-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

