# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 13:37:11 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1COc2ccccc2O1
#
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
 0JD  0JD  '(2S)-2,3-dihydro-1,4-benzodioxine-2-carboxylic acid'  ligand  20  13  .  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_0JD
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
 0JD  OAA  O  OC    -1  -0.608  -3.5972  -0.5496  -0.3405
 0JD  CAJ  C  C      0   0.387  -2.7495   0.3294  -0.0950
 0JD  OAB  O  O      0  -0.582  -2.9333   1.4766   0.3316
 0JD  CAM  C  CH1    0  -0.145  -1.2985  -0.1102  -0.3799
 0JD  OAI  O  O2     0  -0.478  -0.3929   0.9281  -0.0324
 0JD  CAL  C  CR6    0   0.302   0.9074   0.5593  -0.0078
 0JD  CAF  C  CR16   0  -0.365   1.8834   1.5486  -0.0447
 0JD  CAD  C  CR16   0  -0.270   3.2292   1.2129  -0.0272
 0JD  CAC  C  CR16   0  -0.268   3.6101  -0.1223   0.0158
 0JD  CAE  C  CR16   0  -0.365   2.6429  -1.1154   0.0604
 0JD  CAK  C  CR6    0   0.316   1.2933  -0.7847   0.0517
 0JD  OAH  O  O2     0  -0.484   0.3820  -1.7835   0.0979
 0JD  CAG  C  CH2    0  -0.200  -0.9440  -1.3649   0.3929
 0JD  H2   H  HCH1   0   0.247  -1.2026  -0.3219  -1.4547
 0JD  H3   H  HCR6   0   0.261   1.5741   2.5858  -0.0896
 0JD  H4   H  HCR6   0   0.253   3.9761   1.9946  -0.0583
 0JD  H5   H  HCR6   0   0.252   4.6576  -0.3929   0.0238
 0JD  H6   H  HCR6   0   0.262   2.9247  -2.1606   0.1040
 0JD  H7   H  HCH2   0   0.234  -1.0469  -1.1890   1.4706
 0JD  H8   H  HCH2   0   0.252  -1.6029  -2.1823   0.1114

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
 0JD  OAB  CAJ  deloc     1.238  0.020  1.238
 0JD  CAJ  OAA  deloc     1.246  0.020  1.246
 0JD  CAJ  CAM  single    1.543  0.020  1.543
 0JD  CAG  CAM  single    1.516  0.020  1.516
 0JD  CAG  OAH  single    1.421  0.020  1.421
 0JD  CAM  OAI  single    1.421  0.020  1.421
 0JD  OAH  CAK  single    1.353  0.020  1.353
 0JD  OAI  CAL  single    1.352  0.020  1.352
 0JD  CAK  CAL  aromatic  1.400  0.020  1.400
 0JD  CAK  CAE  aromatic  1.390  0.020  1.390
 0JD  CAL  CAF  aromatic  1.390  0.020  1.390
 0JD  CAE  CAC  aromatic  1.387  0.020  1.387
 0JD  CAF  CAD  aromatic  1.387  0.020  1.387
 0JD  CAC  CAD  aromatic  1.389  0.020  1.389
 0JD  CAM  H2   single    0.970  0.020  1.090
 0JD  CAF  H3   single    0.930  0.020  1.080
 0JD  CAD  H4   single    0.930  0.020  1.080
 0JD  CAC  H5   single    0.930  0.020  1.080
 0JD  CAE  H6   single    0.930  0.020  1.080
 0JD  CAG  H7   single    0.970  0.020  1.090
 0JD  CAG  H8   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
 0JD  CAM  CAJ  OAB  117.87  3.000
 0JD  CAM  CAJ  OAA  113.74  3.000
 0JD  OAB  CAJ  OAA  128.39  3.000
 0JD  H2   CAM  CAG  108.58  3.000
 0JD  H2   CAM  OAI  108.91  3.000
 0JD  CAG  CAM  OAI  109.34  3.000
 0JD  H2   CAM  CAJ  108.50  3.000
 0JD  OAI  CAM  CAJ  110.25  3.000
 0JD  CAG  CAM  CAJ  111.21  3.000
 0JD  CAL  OAI  CAM  114.72  3.000
 0JD  CAK  CAL  CAF  119.40  3.000
 0JD  CAF  CAL  OAI  118.73  3.000
 0JD  CAK  CAL  OAI  121.87  3.000
 0JD  H3   CAF  CAD  120.61  3.000
 0JD  H3   CAF  CAL  118.82  3.000
 0JD  CAD  CAF  CAL  120.57  3.000
 0JD  H4   CAD  CAC  120.41  3.000
 0JD  H4   CAD  CAF  119.65  3.000
 0JD  CAC  CAD  CAF  119.94  3.000
 0JD  H5   CAC  CAE  119.72  3.000
 0JD  H5   CAC  CAD  120.41  3.000
 0JD  CAE  CAC  CAD  119.87  3.000
 0JD  H6   CAE  CAK  118.85  3.000
 0JD  H6   CAE  CAC  120.71  3.000
 0JD  CAK  CAE  CAC  120.44  3.000
 0JD  OAH  CAK  CAE  118.57  3.000
 0JD  CAE  CAK  CAL  119.78  3.000
 0JD  OAH  CAK  CAL  121.65  3.000
 0JD  CAG  OAH  CAK  114.71  3.000
 0JD  H8   CAG  H7   108.55  3.000
 0JD  H8   CAG  OAH  106.87  3.000
 0JD  H7   CAG  OAH  109.80  3.000
 0JD  H8   CAG  CAM  110.41  3.000
 0JD  H7   CAG  CAM  110.26  3.000
 0JD  OAH  CAG  CAM  110.87  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
 0JD  CONST_01  CAC  CAE  CAK  CAL    0.00   0.0  0
 0JD  CONST_02  CAC  CAD  CAF  CAL    0.00   0.0  0
 0JD  CONST_03  CAE  CAK  CAL  CAF    0.00   0.0  0
 0JD  CONST_04  CAE  CAC  CAD  CAF    0.00   0.0  0
 0JD  CONST_05  CAK  CAL  CAF  CAD    0.00   0.0  0
 0JD  CONST_06  CAK  CAE  CAC  CAD    0.00   0.0  0
 0JD  CONST_07  H3   CAF  CAL  OAI    0.00   0.0  0
 0JD  CONST_08  H6   CAE  CAK  CAL  180.00   0.0  0
 0JD  CONST_09  H4   CAD  CAF  CAL  180.00   0.0  0
 0JD  CONST_10  H5   CAC  CAD  CAF  180.00   0.0  0
 0JD  Var_01    CAK  CAL  OAI  CAM  -17.34  30.0  1
 0JD  Var_02    H7   CAG  OAH  CAK  -79.00  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0JD  chir_01  CAM  CAJ  CAG  OAI  positiv

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
 0JD  plan-1  OAA  0.020
 0JD  plan-1  CAJ  0.020
 0JD  plan-1  OAB  0.020
 0JD  plan-1  CAM  0.020
 0JD  plan-2  OAI  0.020
 0JD  plan-2  CAL  0.020
 0JD  plan-2  CAF  0.020
 0JD  plan-2  CAD  0.020
 0JD  plan-2  CAC  0.020
 0JD  plan-2  CAE  0.020
 0JD  plan-2  CAK  0.020
 0JD  plan-2  OAH  0.020
 0JD  plan-2  H3   0.020
 0JD  plan-2  H4   0.020
 0JD  plan-2  H5   0.020
 0JD  plan-2  H6   0.020

