# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:09:32 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2S,3S)-2,3-bis(1,3-benzodioxol-5-ylmethyl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccc2OCOc2c1)[C@H](Cc3ccc4OCOc4c3)C(O)=O
#
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
 BDS  BDS  '(2S,3S)-2,3-bis(1,3-benzodioxol-5-ylmethyl)butanedioic acid'  ligand  44  28  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BDS
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
 BDS  C1    C  CH1    0  -0.315   0.6652  -0.0140   0.7864
 BDS  C2    C  C      0   0.430   1.9837   0.5926   1.3099
 BDS  O3    O  O      0  -0.618   2.1300   1.8231   1.1476
 BDS  O4    O  OC    -1  -0.620   2.8068  -0.1796   1.8403
 BDS  C5    C  CH2    0  -0.505  -0.5287   0.7546   1.3694
 BDS  C6    C  CR6    0   0.126  -0.5945   0.6758   2.8699
 BDS  C7    C  CR16   0  -0.318  -0.1041   1.7028   3.6670
 BDS  C8    C  CR16   0  -0.333  -0.1288   1.6415   5.0667
 BDS  C9    C  CR6    0   0.275  -0.6597   0.5085   5.6289
 BDS  O10   O  O2     0  -0.490  -0.8366   0.2021   6.9423
 BDS  C11   C  CH2    0   0.068  -1.2311  -1.1614   6.9692
 BDS  O12   O  O2     0  -0.490  -1.6436  -1.5008   5.6529
 BDS  C13   C  CR6    0   0.310  -1.1507  -0.5240   4.8469
 BDS  C14   C  CR16   0  -0.403  -1.1355  -0.4717   3.4761
 BDS  C15   C  CH1    0  -0.315   0.6690  -0.0032  -0.7540
 BDS  C16   C  C      0   0.430   1.9627  -0.6611  -1.2762
 BDS  O17   O  O      0  -0.618   2.0659  -1.8940  -1.1010
 BDS  O18   O  OC    -1  -0.620   2.8080   0.0750  -1.8229
 BDS  C19   C  CH2    0  -0.505  -0.5503  -0.7237  -1.3468
 BDS  C20   C  CR6    0   0.125  -0.5979  -0.6427  -2.8481
 BDS  C21   C  CR16   0  -0.318  -0.1354  -1.6867  -3.6398
 BDS  C22   C  CR16   0  -0.333  -0.1413  -1.6247  -5.0396
 BDS  C23   C  CR6    0   0.275  -0.6247  -0.4735  -5.6077
 BDS  O24   O  O2     0  -0.490  -0.7735  -0.1612  -6.9230
 BDS  C25   C  CH2    0   0.069  -1.1328   1.2121  -6.9566
 BDS  O26   O  O2     0  -0.491  -1.5371   1.5691  -5.6422
 BDS  C27   C  CR6    0   0.310  -1.0884   0.5755  -4.8313
 BDS  C28   C  CR16   0  -0.403  -1.0911   0.5229  -3.4603
 BDS  HC11  H  HCH1   0   0.190   0.6005  -1.0573   1.1139
 BDS  HC51  H  HCH2   0   0.226  -0.4601   1.7985   1.0563
 BDS  HC52  H  HCH2   0   0.233  -1.4637   0.3650   0.9602
 BDS  HC71  H  HCR6   0   0.243   0.3230   2.5748   3.1910
 BDS  HC81  H  HCR6   0   0.265   0.2509   2.4554   5.6698
 BDS  H111  H  HCH2   0   0.227  -0.3826  -1.7896   7.2656
 BDS  H112  H  HCH2   0   0.243  -2.0616  -1.2930   7.6622
 BDS  H141  H  HCR6   0   0.258  -1.5333  -1.2835   2.8792
 BDS  H151  H  HCH1   0   0.190   0.6463   1.0421  -1.0803
 BDS  H191  H  HCH2   0   0.226  -0.5262  -1.7696  -1.0343
 BDS  H192  H  HCH2   0   0.233  -1.4728  -0.2971  -0.9464
 BDS  H211  H  HCR6   0   0.243   0.2558  -2.5732  -3.1595
 BDS  H221  H  HCR6   0   0.265   0.2173  -2.4511  -5.6387
 BDS  H251  H  HCH2   0   0.228  -0.2688   1.8166  -7.2565
 BDS  H252  H  HCH2   0   0.242  -1.9598   1.3613  -7.6506
 BDS  H281  H  HCR6   0   0.257  -1.4676   1.3484  -2.8683

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
 BDS  C1   C2    single    1.543  0.020  1.543
 BDS  C1   C5    single    1.535  0.020  1.535
 BDS  C1   C15   single    1.540  0.020  1.540
 BDS  C1   HC11  single    0.970  0.020  1.090
 BDS  C2   O3    deloc     1.250  0.020  1.250
 BDS  C2   O4    deloc     1.247  0.020  1.247
 BDS  C5   C6    single    1.504  0.020  1.504
 BDS  C5   HC51  single    0.970  0.020  1.090
 BDS  C5   HC52  single    0.970  0.020  1.090
 BDS  C6   C7    aromatic  1.389  0.020  1.389
 BDS  C6   C14   aromatic  1.406  0.020  1.406
 BDS  C7   C8    aromatic  1.401  0.020  1.401
 BDS  C7   HC71  single    0.930  0.020  1.080
 BDS  C8   C9    aromatic  1.372  0.020  1.372
 BDS  C8   HC81  single    0.930  0.020  1.080
 BDS  C9   O10   single    1.360  0.020  1.360
 BDS  C9   C13   aromatic  1.385  0.020  1.385
 BDS  O10  C11   single    1.420  0.020  1.420
 BDS  C11  O12   single    1.421  0.020  1.421
 BDS  C11  H111  single    0.970  0.020  1.090
 BDS  C11  H112  single    0.970  0.020  1.090
 BDS  O12  C13   single    1.359  0.020  1.359
 BDS  C13  C14   aromatic  1.372  0.020  1.372
 BDS  C14  H141  single    0.930  0.020  1.080
 BDS  C15  C16   single    1.542  0.020  1.542
 BDS  C15  C19   single    1.535  0.020  1.535
 BDS  C15  H151  single    0.970  0.020  1.090
 BDS  C16  O17   deloc     1.250  0.020  1.250
 BDS  C16  O18   deloc     1.247  0.020  1.247
 BDS  C19  C20   single    1.504  0.020  1.504
 BDS  C19  H191  single    0.970  0.020  1.090
 BDS  C19  H192  single    0.970  0.020  1.090
 BDS  C20  C21   aromatic  1.389  0.020  1.389
 BDS  C20  C28   aromatic  1.406  0.020  1.406
 BDS  C21  C22   aromatic  1.401  0.020  1.401
 BDS  C21  H211  single    0.930  0.020  1.080
 BDS  C22  C23   aromatic  1.372  0.020  1.372
 BDS  C22  H221  single    0.930  0.020  1.080
 BDS  C23  O24   single    1.360  0.020  1.360
 BDS  C23  C27   aromatic  1.385  0.020  1.385
 BDS  O24  C25   single    1.420  0.020  1.420
 BDS  C25  O26   single    1.421  0.020  1.421
 BDS  C25  H251  single    0.970  0.020  1.090
 BDS  C25  H252  single    0.970  0.020  1.090
 BDS  O26  C27   single    1.359  0.020  1.359
 BDS  C27  C28   aromatic  1.372  0.020  1.372
 BDS  C28  H281  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
 BDS  HC11  C1   C15   107.80  3.000
 BDS  HC11  C1   C5    108.50  3.000
 BDS  C15   C1   C5    112.22  3.000
 BDS  HC11  C1   C2    108.88  3.000
 BDS  C15   C1   C2    109.54  3.000
 BDS  C5    C1   C2    109.82  3.000
 BDS  O4    C2   O3    125.99  3.000
 BDS  O4    C2   C1    117.70  3.000
 BDS  O3    C2   C1    116.30  3.000
 BDS  HC52  C5   HC51  106.70  3.000
 BDS  HC52  C5   C6    108.52  3.000
 BDS  HC51  C5   C6    109.81  3.000
 BDS  HC52  C5   C1    110.17  3.000
 BDS  HC51  C5   C1    108.72  3.000
 BDS  C6    C5   C1    112.75  3.000
 BDS  C14   C6   C7    119.45  3.000
 BDS  C14   C6   C5    119.33  3.000
 BDS  C7    C6   C5    121.21  3.000
 BDS  HC71  C7   C8    118.81  3.000
 BDS  HC71  C7   C6    118.87  3.000
 BDS  C8    C7   C6    122.31  3.000
 BDS  HC81  C8   C9    121.92  3.000
 BDS  HC81  C8   C7    121.18  3.000
 BDS  C9    C8   C7    116.89  3.000
 BDS  C13   C9   O10   109.33  3.000
 BDS  C13   C9   C8    121.43  3.000
 BDS  O10   C9   C8    129.21  3.000
 BDS  C11   O10  C9    105.71  3.000
 BDS  H112  C11  H111  110.41  3.000
 BDS  H112  C11  O12   109.82  3.000
 BDS  H111  C11  O12   109.77  3.000
 BDS  H112  C11  O10   109.87  3.000
 BDS  H111  C11  O10   109.90  3.000
 BDS  O12   C11  O10   107.01  3.000
 BDS  C13   O12  C11   105.81  3.000
 BDS  C14   C13  O12   128.61  3.000
 BDS  C14   C13  C9    122.12  3.000
 BDS  O12   C13  C9    109.24  3.000
 BDS  H141  C14  C13   121.19  3.000
 BDS  H141  C14  C6    121.02  3.000
 BDS  C13   C14  C6    117.79  3.000
 BDS  H151  C15  C19   108.44  3.000
 BDS  H151  C15  C16   108.88  3.000
 BDS  C19   C15  C16   109.59  3.000
 BDS  H151  C15  C1    107.73  3.000
 BDS  C19   C15  C1    112.39  3.000
 BDS  C16   C15  C1    109.73  3.000
 BDS  O18   C16  O17   126.01  3.000
 BDS  O18   C16  C15   117.72  3.000
 BDS  O17   C16  C15   116.27  3.000
 BDS  H192  C19  H191  106.72  3.000
 BDS  H192  C19  C20   108.55  3.000
 BDS  H191  C19  C20   109.75  3.000
 BDS  H192  C19  C15   110.24  3.000
 BDS  H191  C19  C15   108.75  3.000
 BDS  C20   C19  C15   112.66  3.000
 BDS  C28   C20  C21   119.44  3.000
 BDS  C28   C20  C19   119.36  3.000
 BDS  C21   C20  C19   121.18  3.000
 BDS  H211  C21  C22   118.78  3.000
 BDS  H211  C21  C20   118.90  3.000
 BDS  C22   C21  C20   122.32  3.000
 BDS  H221  C22  C23   121.90  3.000
 BDS  H221  C22  C21   121.20  3.000
 BDS  C23   C22  C21   116.90  3.000
 BDS  C27   C23  O24   109.37  3.000
 BDS  C27   C23  C22   121.43  3.000
 BDS  O24   C23  C22   129.18  3.000
 BDS  C25   O24  C23   105.82  3.000
 BDS  H252  C25  H251  110.39  3.000
 BDS  H252  C25  O26   109.80  3.000
 BDS  H251  C25  O26   109.80  3.000
 BDS  H252  C25  O24   109.85  3.000
 BDS  H251  C25  O24   109.90  3.000
 BDS  O26   C25  O24   107.05  3.000
 BDS  C27   O26  C25   105.93  3.000
 BDS  C28   C27  O26   128.59  3.000
 BDS  C28   C27  C23   122.13  3.000
 BDS  O26   C27  C23   109.26  3.000
 BDS  H281  C28  C27   121.17  3.000
 BDS  H281  C28  C20   121.04  3.000
 BDS  C27   C28  C20   117.79  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
 BDS  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 BDS  CONST_02  C9    C13  C14  C6     0.00   0.0  0
 BDS  CONST_03  C13   C14  C6   C7     0.00   0.0  0
 BDS  CONST_04  C13   C9   C8   C7     0.00   0.0  0
 BDS  CONST_05  C14   C6   C7   C8     0.00   0.0  0
 BDS  CONST_06  C14   C13  C9   C8     0.00   0.0  0
 BDS  CONST_07  C23   C22  C21  C20    0.00   0.0  0
 BDS  CONST_08  C23   C27  C28  C20    0.00   0.0  0
 BDS  CONST_09  C27   C28  C20  C21    0.00   0.0  0
 BDS  CONST_10  C27   C23  C22  C21    0.00   0.0  0
 BDS  CONST_11  C28   C20  C21  C22    0.00   0.0  0
 BDS  CONST_12  C28   C27  C23  C22    0.00   0.0  0
 BDS  CONST_13  C8    C7   C6   C5   180.00   0.0  0
 BDS  CONST_14  C13   C14  C6   C5   180.00   0.0  0
 BDS  CONST_15  C22   C21  C20  C19  180.00   0.0  0
 BDS  CONST_16  C27   C28  C20  C19  180.00   0.0  0
 BDS  CONST_17  HC81  C8   C7   C6   180.00   0.0  0
 BDS  CONST_18  H141  C14  C6   C7   180.00   0.0  0
 BDS  CONST_19  HC71  C7   C8   C9   180.00   0.0  0
 BDS  CONST_20  H221  C22  C21  C20  180.00   0.0  0
 BDS  CONST_21  H281  C28  C20  C21  180.00   0.0  0
 BDS  CONST_22  H211  C21  C22  C23  180.00   0.0  0
 BDS  Var_01    O12   C11  O10  C9   -16.55  30.0  1
 BDS  Var_02    C13   C9   O10  C11   10.42  30.0  1
 BDS  Var_03    C14   C13  O12  C11  171.46  30.0  1
 BDS  Var_04    O26   C25  O24  C23  -15.63  30.0  1
 BDS  Var_05    C27   C23  O24  C25    9.81  30.0  1
 BDS  Var_06    C28   C27  O26  C25  171.96  30.0  1
 BDS  Var_07    C7    C6   C5   C1    98.25  30.0  2
 BDS  Var_08    C21   C20  C19  C15   97.92  30.0  2

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
 BDS  chir_01  C1   C2  C5   C15  negativ
 BDS  chir_02  C15  C1  C16  C19  negativ

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
 BDS  plan-1  C5    0.020
 BDS  plan-1  C6    0.020
 BDS  plan-1  C7    0.020
 BDS  plan-1  C8    0.020
 BDS  plan-1  C9    0.020
 BDS  plan-1  O10   0.020
 BDS  plan-1  O12   0.020
 BDS  plan-1  C13   0.020
 BDS  plan-1  C14   0.020
 BDS  plan-1  HC71  0.020
 BDS  plan-1  HC81  0.020
 BDS  plan-1  H141  0.020
 BDS  plan-2  C19   0.020
 BDS  plan-2  C20   0.020
 BDS  plan-2  C21   0.020
 BDS  plan-2  C22   0.020
 BDS  plan-2  C23   0.020
 BDS  plan-2  O24   0.020
 BDS  plan-2  O26   0.020
 BDS  plan-2  C27   0.020
 BDS  plan-2  C28   0.020
 BDS  plan-2  H211  0.020
 BDS  plan-2  H221  0.020
 BDS  plan-2  H281  0.020
 BDS  plan-3  C1    0.020
 BDS  plan-3  C2    0.020
 BDS  plan-3  O3    0.020
 BDS  plan-3  O4    0.020
 BDS  plan-4  C15   0.020
 BDS  plan-4  C16   0.020
 BDS  plan-4  O17   0.020
 BDS  plan-4  O18   0.020

