# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 03:31:21 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (2r,3aR,7aS)-3a,4,7,7a-tetrahydro-1,3-benzodioxol-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H]2CC=CC[C@H]2O1
#
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
 BD1  BD1  (2r,3aR,7aS)-3a,4,7,7a-tetrahydro-1,3-benzodioxol-2-ol  ligand  20  10  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BD1
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
 BD1  C1    C  C1    0  -0.238  -0.6916   0.4804  -2.3531
 BD1  C2    C  CH2   0  -0.498  -1.4555   0.2180  -1.0936
 BD1  C3    C  CH1   0   0.010  -0.7405  -0.7212  -0.1188
 BD1  O3    O  O2    0  -0.521  -1.0608  -0.3832   1.2257
 BD1  C4    C  CH1   0  -0.017   0.7728  -0.5711  -0.1026
 BD1  O4    O  O2    0  -0.518   0.8918   0.5929   0.7111
 BD1  C5    C  CH2   0  -0.516   1.4562  -0.3970  -1.4437
 BD1  C6    C  C1    0  -0.223   0.6060   0.2380  -2.4961
 BD1  C7    C  CH1   0   0.487  -0.0800   0.4835   1.7069
 BD1  O1    O  OH1   0  -0.657   0.3974  -0.0855   2.8700
 BD1  H1    H  H     0   0.243  -1.2438   0.9255  -3.1734
 BD1  H2C1  H  HCH2  0   0.253  -2.4381  -0.1936  -1.3361
 BD1  H2C2  H  HCH2  0   0.254  -1.6589   1.1773  -0.6058
 BD1  H3    H  HCH1  0   0.266  -1.0381  -1.7567  -0.2938
 BD1  H4    H  HCH1  0   0.246   1.2197  -1.4308   0.4134
 BD1  H5C1  H  HCH2  0   0.255   1.7703  -1.3841  -1.7966
 BD1  H5C2  H  HCH2  0   0.259   2.3871   0.1615  -1.3068
 BD1  H6    H  H     0   0.243   1.0935   0.4755  -3.4352
 BD1  H7    H  HCH1  0   0.210  -0.4753   1.4898   1.8952
 BD1  HA    H  HOH1  0   0.464   0.8071   0.5982   3.4116

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
 BD1  C1  C2    single  1.496  0.020  1.496
 BD1  C1  C6    double  1.328  0.020  1.328
 BD1  C1  H1    single  0.930  0.020  1.080
 BD1  C2  C3    single  1.531  0.020  1.531
 BD1  C2  H2C1  single  0.970  0.020  1.090
 BD1  C2  H2C2  single  0.970  0.020  1.090
 BD1  C3  O3    single  1.423  0.020  1.423
 BD1  C3  C4    single  1.521  0.020  1.521
 BD1  C3  H3    single  0.970  0.020  1.090
 BD1  O3  C7    single  1.395  0.020  1.395
 BD1  C4  O4    single  1.425  0.020  1.425
 BD1  C4  C5    single  1.515  0.020  1.515
 BD1  C4  H4    single  0.970  0.020  1.090
 BD1  O4  C7    single  1.396  0.020  1.396
 BD1  C5  C6    single  1.495  0.020  1.495
 BD1  C5  H5C1  single  0.970  0.020  1.090
 BD1  C5  H5C2  single  0.970  0.020  1.090
 BD1  C6  H6    single  0.930  0.020  1.080
 BD1  C7  O1    single  1.380  0.020  1.380
 BD1  C7  H7    single  0.970  0.020  1.090
 BD1  O1  HA    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
 BD1  H1    C1  C6    119.41  3.000
 BD1  H1    C1  C2    116.67  3.000
 BD1  C6    C1  C2    123.89  3.000
 BD1  H2C2  C2  H2C1  105.17  3.000
 BD1  H2C2  C2  C3    109.91  3.000
 BD1  H2C1  C2  C3    109.28  3.000
 BD1  H2C2  C2  C1    108.43  3.000
 BD1  H2C1  C2  C1    109.78  3.000
 BD1  C3    C2  C1    113.90  3.000
 BD1  H3    C3  C4    111.51  3.000
 BD1  H3    C3  O3    108.39  3.000
 BD1  C4    C3  O3    100.98  3.000
 BD1  H3    C3  C2    110.65  3.000
 BD1  C4    C3  C2    114.26  3.000
 BD1  O3    C3  C2    110.54  3.000
 BD1  C7    O3  C3    108.38  3.000
 BD1  H4    C4  C5    108.81  3.000
 BD1  H4    C4  O4    109.71  3.000
 BD1  C5    C4  O4    111.95  3.000
 BD1  H4    C4  C3    109.44  3.000
 BD1  C5    C4  C3    116.79  3.000
 BD1  O4    C4  C3     99.77  3.000
 BD1  C7    O4  C4    106.57  3.000
 BD1  H5C2  C5  H5C1  104.87  3.000
 BD1  H5C2  C5  C6    110.81  3.000
 BD1  H5C1  C5  C6    108.63  3.000
 BD1  H5C2  C5  C4    109.37  3.000
 BD1  H5C1  C5  C4    108.13  3.000
 BD1  C6    C5  C4    114.55  3.000
 BD1  H6    C6  C5    116.55  3.000
 BD1  H6    C6  C1    119.52  3.000
 BD1  C5    C6  C1    123.89  3.000
 BD1  H7    C7  O1    110.98  3.000
 BD1  H7    C7  O4    107.54  3.000
 BD1  O1    C7  O4    113.13  3.000
 BD1  H7    C7  O3    112.07  3.000
 BD1  O1    C7  O3    106.13  3.000
 BD1  O4    C7  O3    106.99  3.000
 BD1  HA    O1  C7    109.16  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
 BD1  Var_01  C4  C5  C6  C1   -8.44  30.0  1
 BD1  Var_02  C5  C6  C1  C2    3.47  30.0  1
 BD1  Var_03  C6  C1  C2  C3  -17.00  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
 BD1  chir_01  C3  C2  O3  C4  positiv
 BD1  chir_02  C4  O4  C5  C3  positiv
 BD1  chir_03  C7  O3  O4  O1  positiv

