# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 18:27:01 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5-{(E)-[(2S)-2-hydroxy-2,3-dihydro-1H-inden-1-ylidene]methyl}-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1Cc2ccccc2\C1=C/c3ccc4OCOc4c3C(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
 ZT4  ZT4  '5-{(E)-[(2S)-2-hydroxy-2,3-dihydro-1H-inden-1-ylidene]methyl}-1,3-benzodioxole-4-carboxylic acid'  ligand  36  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZT4
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
 ZT4  C1    C  CR16   0  -0.258  -2.1687  -2.6597   1.3586
 ZT4  C2    C  CR16   0  -0.260  -3.5463  -2.7990   1.2121
 ZT4  C3    C  CR16   0  -0.318  -1.5202  -1.5172   0.9097
 ZT4  C4    C  CR16   0  -0.302   0.5119  -0.7186  -1.5277
 ZT4  C5    C  CR16   0  -0.316  -4.2975  -1.7887   0.6216
 ZT4  C6    C  CR16   0  -0.342   1.6155  -1.5604  -1.6825
 ZT4  C7    C  CR56   0   0.110  -2.2671  -0.5094   0.3067
 ZT4  C8    C  CR6    0  -0.006   0.5459   0.4209  -0.7283
 ZT4  C9    C  CR6    0  -0.200   1.7251   0.7731  -0.0303
 ZT4  C10   C  CR56   0   0.046  -3.6533  -0.6466   0.1756
 ZT4  C11   C  CR56   0   0.285   2.7489  -1.2095  -0.9941
 ZT4  C12   C  CR56   0   0.293   2.7923  -0.0872  -0.1825
 ZT4  C13   C  CR5    0   0.057  -1.8679   0.8006  -0.2224
 ZT4  C14   C  C1     0  -0.345  -0.6780   1.2406  -0.6361
 ZT4  C15   C  C      0   0.374   1.8368   1.9932   0.8702
 ZT4  C16   C  CH2    0  -0.521  -4.2416   0.5669  -0.4842
 ZT4  C17   C  CH2    0   0.066   4.8300  -0.9615  -0.2870
 ZT4  C18   C  CR15   0   0.009  -3.1494   1.6224  -0.2680
 ZT4  O19   O  O      0  -0.586   2.4577   1.8289   1.9351
 ZT4  O20   O  OC    -1  -0.586   1.3099   3.0419   0.4577
 ZT4  O21   O  O      0  -0.489   3.9454  -1.8496  -0.9539
 ZT4  O22   O  O      0  -0.477   4.0271  -0.0042   0.3812
 ZT4  O23   O  OH1    0  -0.662  -3.1976   2.6216  -1.2475
 ZT4  H1    H  HCR6   0   0.253  -1.5986  -3.4480   1.8334
 ZT4  H2    H  HCR6   0   0.254  -4.0359  -3.6956   1.5701
 ZT4  H3    H  HCR6   0   0.249  -0.4513  -1.4163   1.0402
 ZT4  H5    H  HCR6   0   0.249  -5.3707  -1.8945   0.5187
 ZT4  H14   H  H      0   0.240  -0.5957   2.2695  -0.9639
 ZT4  H161  H  HCH2   0   0.255  -4.3773   0.3903  -1.5569
 ZT4  H162  H  HCH2   0   0.257  -5.2080   0.8603  -0.0730
 ZT4  H171  H  HCH2   0   0.242   5.4303  -1.5118   0.4372
 ZT4  H172  H  HCH2   0   0.225   5.4773  -0.4633  -1.0190
 ZT4  H23   H  HOH1   0   0.457  -2.7250   3.3944  -0.9252
 ZT4  H18   H  HCR5   0   0.231  -3.3002   2.0517   0.7334
 ZT4  H4    H  HCR6   0   0.248  -0.4045  -0.9615  -2.0501
 ZT4  H6    H  HCR6   0   0.267   1.5752  -2.4363  -2.3157

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
 ZT4  C1   C2    aromatic  1.392  0.020  1.392
 ZT4  C1   C3    aromatic  1.388  0.020  1.388
 ZT4  C2   C5    aromatic  1.391  0.020  1.391
 ZT4  C3   C7    aromatic  1.392  0.020  1.392
 ZT4  C4   C6    aromatic  1.397  0.020  1.397
 ZT4  C4   C8    aromatic  1.392  0.020  1.392
 ZT4  C5   C10   aromatic  1.385  0.020  1.385
 ZT4  C6   C11   aromatic  1.372  0.020  1.372
 ZT4  C7   C10   aromatic  1.399  0.020  1.399
 ZT4  C7   C13   single    1.468  0.020  1.468
 ZT4  C8   C9    aromatic  1.415  0.020  1.415
 ZT4  C8   C14   single    1.476  0.020  1.476
 ZT4  C9   C12   aromatic  1.379  0.020  1.379
 ZT4  C9   C15   single    1.521  0.020  1.521
 ZT4  C10  C16   single    1.501  0.020  1.501
 ZT4  C11  C12   aromatic  1.386  0.020  1.386
 ZT4  C11  O21   single    1.358  0.020  1.358
 ZT4  C12  O22   single    1.360  0.020  1.360
 ZT4  C13  C14   double    1.334  0.020  1.334
 ZT4  C13  C18   single    1.523  0.020  1.523
 ZT4  C15  O19   deloc     1.244  0.020  1.244
 ZT4  C15  O20   deloc     1.244  0.020  1.244
 ZT4  C16  C18   single    1.534  0.020  1.534
 ZT4  C17  O21   single    1.420  0.020  1.420
 ZT4  C17  O22   single    1.417  0.020  1.417
 ZT4  C18  O23   single    1.400  0.020  1.400
 ZT4  C1   H1    single    0.930  0.020  1.080
 ZT4  C2   H2    single    0.930  0.020  1.080
 ZT4  C3   H3    single    0.930  0.020  1.080
 ZT4  C5   H5    single    0.930  0.020  1.080
 ZT4  C4   H4    single    0.930  0.020  1.080
 ZT4  C6   H6    single    0.930  0.020  1.080
 ZT4  C14  H14   single    0.930  0.020  1.080
 ZT4  C16  H161  single    0.970  0.020  1.090
 ZT4  C16  H162  single    0.970  0.020  1.090
 ZT4  C17  H171  single    0.970  0.020  1.090
 ZT4  C17  H172  single    0.970  0.020  1.090
 ZT4  O23  H23   single    0.850  0.020  0.980
 ZT4  C18  H18   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
 ZT4  H1    C1   C3    119.68  3.000
 ZT4  H1    C1   C2    119.63  3.000
 ZT4  C3    C1   C2    120.70  3.000
 ZT4  H2    C2   C5    119.86  3.000
 ZT4  H2    C2   C1    119.71  3.000
 ZT4  C5    C2   C1    120.43  3.000
 ZT4  H3    C3   C7    121.00  3.000
 ZT4  H3    C3   C1    119.96  3.000
 ZT4  C7    C3   C1    119.03  3.000
 ZT4  H4    C4   C8    118.77  3.000
 ZT4  H4    C4   C6    118.71  3.000
 ZT4  C8    C4   C6    122.52  3.000
 ZT4  H5    C5   C10   120.71  3.000
 ZT4  H5    C5   C2    120.30  3.000
 ZT4  C10   C5   C2    118.99  3.000
 ZT4  H6    C6   C11   122.12  3.000
 ZT4  H6    C6   C4    121.57  3.000
 ZT4  C11   C6   C4    116.30  3.000
 ZT4  C13   C7   C10   108.85  3.000
 ZT4  C13   C7   C3    131.02  3.000
 ZT4  C10   C7   C3    120.08  3.000
 ZT4  C14   C8   C9    121.47  3.000
 ZT4  C14   C8   C4    118.04  3.000
 ZT4  C9    C8   C4    120.48  3.000
 ZT4  C15   C9   C12   120.60  3.000
 ZT4  C15   C9   C8    123.58  3.000
 ZT4  C12   C9   C8    115.80  3.000
 ZT4  C16   C10  C7    110.49  3.000
 ZT4  C16   C10  C5    128.74  3.000
 ZT4  C7    C10  C5    120.77  3.000
 ZT4  O21   C11  C12   109.69  3.000
 ZT4  O21   C11  C6    128.50  3.000
 ZT4  C12   C11  C6    121.80  3.000
 ZT4  O22   C12  C11   108.70  3.000
 ZT4  O22   C12  C9    128.23  3.000
 ZT4  C11   C12  C9    123.06  3.000
 ZT4  C18   C13  C14   124.27  3.000
 ZT4  C18   C13  C7    105.28  3.000
 ZT4  C14   C13  C7    130.42  3.000
 ZT4  H14   C14  C13   118.35  3.000
 ZT4  H14   C14  C8    116.47  3.000
 ZT4  C13   C14  C8    125.15  3.000
 ZT4  O20   C15  O19   127.36  3.000
 ZT4  O20   C15  C9    116.67  3.000
 ZT4  O19   C15  C9    115.97  3.000
 ZT4  H162  C16  H161  107.63  3.000
 ZT4  H162  C16  C18   113.11  3.000
 ZT4  H161  C16  C18   109.70  3.000
 ZT4  H162  C16  C10   113.52  3.000
 ZT4  H161  C16  C10   110.40  3.000
 ZT4  C18   C16  C10   102.43  3.000
 ZT4  H172  C17  H171  110.35  3.000
 ZT4  H172  C17  O22   110.01  3.000
 ZT4  H171  C17  O22   109.87  3.000
 ZT4  H172  C17  O21   109.77  3.000
 ZT4  H171  C17  O21   109.85  3.000
 ZT4  O22   C17  O21   106.92  3.000
 ZT4  H18   C18  O23   110.72  3.000
 ZT4  H18   C18  C16   107.41  3.000
 ZT4  O23   C18  C16   111.59  3.000
 ZT4  H18   C18  C13   107.38  3.000
 ZT4  O23   C18  C13   115.78  3.000
 ZT4  C16   C18  C13   103.41  3.000
 ZT4  C17   O21  C11   105.55  3.000
 ZT4  C17   O22  C12   106.13  3.000
 ZT4  H23   O23  C18   108.79  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
 ZT4  CONST_01  C10  C5   C2   C1      0.00   0.0  0
 ZT4  CONST_02  C10  C7   C3   C1      0.00   0.0  0
 ZT4  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 ZT4  CONST_04  C7   C10  C5   C2      0.00   0.0  0
 ZT4  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 ZT4  CONST_06  C5   C10  C7   C3      0.00   0.0  0
 ZT4  CONST_07  C12  C11  C6   C4      0.00   0.0  0
 ZT4  CONST_08  C12  C9   C8   C4      0.00   0.0  0
 ZT4  CONST_09  C9   C8   C4   C6      0.00   0.0  0
 ZT4  CONST_10  C9   C12  C11  C6      0.00   0.0  0
 ZT4  CONST_11  C11  C6   C4   C8      0.00   0.0  0
 ZT4  CONST_12  C11  C12  C9   C8      0.00   0.0  0
 ZT4  CONST_13  C15  C9   C8   C4    180.00   0.0  0
 ZT4  CONST_14  C14  C8   C4   C6    180.00   0.0  0
 ZT4  CONST_15  C15  C9   C12  C11   180.00   0.0  0
 ZT4  CONST_16  C14  C8   C9   C12   180.00   0.0  0
 ZT4  CONST_17  O22  C12  C9   C15     0.00   0.0  0
 ZT4  CONST_18  H5   C5   C2   C1    180.00   0.0  0
 ZT4  CONST_19  H3   C3   C1   C2    180.00   0.0  0
 ZT4  CONST_20  H2   C2   C1   C3    180.00   0.0  0
 ZT4  CONST_21  H1   C1   C2   C5    180.00   0.0  0
 ZT4  CONST_22  H6   C6   C4   C8    180.00   0.0  0
 ZT4  CONST_23  H4   C4   C8   C9    180.00   0.0  0
 ZT4  Var_01    C18  C13  C7   C3   -159.62  30.0  1
 ZT4  Var_02    C18  C16  C10  C5    160.58  30.0  1
 ZT4  Var_03    O22  C17  O21  C11    16.85  30.0  1
 ZT4  Var_04    O21  C17  O22  C12   -16.88  30.0  1
 ZT4  Var_05    C13  C14  C8   C4     57.83  30.0  2
 ZT4  Var_06    C8   C14  C13  C7      4.14  30.0  2
 ZT4  Var_07    O19  C15  C9   C8    138.79  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
 ZT4  chir_01  C18  C13  C16  O23  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
 ZT4  plan-1  C1   0.020
 ZT4  plan-1  C2   0.020
 ZT4  plan-1  C3   0.020
 ZT4  plan-1  C5   0.020
 ZT4  plan-1  C7   0.020
 ZT4  plan-1  C10  0.020
 ZT4  plan-1  C13  0.020
 ZT4  plan-1  C16  0.020
 ZT4  plan-1  H1   0.020
 ZT4  plan-1  H2   0.020
 ZT4  plan-1  H3   0.020
 ZT4  plan-1  H5   0.020
 ZT4  plan-2  C4   0.020
 ZT4  plan-2  C6   0.020
 ZT4  plan-2  C8   0.020
 ZT4  plan-2  C9   0.020
 ZT4  plan-2  C11  0.020
 ZT4  plan-2  C12  0.020
 ZT4  plan-2  C14  0.020
 ZT4  plan-2  C15  0.020
 ZT4  plan-2  O21  0.020
 ZT4  plan-2  O22  0.020
 ZT4  plan-2  H4   0.020
 ZT4  plan-2  H6   0.020
 ZT4  plan-3  C9   0.020
 ZT4  plan-3  C15  0.020
 ZT4  plan-3  O19  0.020
 ZT4  plan-3  O20  0.020

