# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:26:20 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)cc(\C=C\c2ccc(O)c(O)c2)c1
#
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
 PIT  PIT  4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]benzene-1,2-diol  ligand  30  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PIT
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
 PIT  C1   C  CR6   0   0.282   3.9377  -1.2523  -0.1975
 PIT  C2   C  CR16  0  -0.447   4.8249  -0.1774  -0.1957
 PIT  C3   C  CR6   0   0.427   4.3233   1.1148  -0.1542
 PIT  C4   C  CR16  0  -0.434   2.9502   1.3391  -0.0867
 PIT  C5   C  CR6   0   0.249   2.0648   0.2644  -0.0928
 PIT  C6   C  CR16  0  -0.461   2.5681  -1.0393  -0.1519
 PIT  C7   C  C1    0  -0.277   0.6311   0.5533  -0.0681
 PIT  C8   C  C1    0  -0.299  -0.3530  -0.3293   0.1396
 PIT  C9   C  CR6   0   0.123  -1.7867  -0.0471   0.1613
 PIT  C10  C  CR16  0  -0.412  -2.6807  -1.1168   0.0894
 PIT  C11  C  CR6   0   0.326  -4.0493  -0.9215   0.0665
 PIT  C12  C  CR6   0   0.300  -4.5541   0.3798   0.1368
 PIT  C13  C  CR16  0  -0.422  -3.6796   1.4486   0.2396
 PIT  C14  C  CR16  0  -0.340  -2.3106   1.2415   0.2475
 PIT  O1   O  OH1   0  -0.553  -5.9053   0.4976   0.0853
 PIT  O2   O  OH1   0  -0.685   5.1236   2.1968  -0.1651
 PIT  O3   O  OH1   0  -0.618   4.4781  -2.4843  -0.2580
 PIT  OAD  O  OH1   0  -0.641  -4.8652  -1.9902  -0.0188
 PIT  H3   H  HOH1  0   0.459   3.7846  -3.1494  -0.2521
 PIT  H6   H  HCR6  0   0.238   1.8926  -1.8864  -0.1770
 PIT  H2   H  HCR6  0   0.267   5.8911  -0.3694  -0.2416
 PIT  HA   H  HOH1  0   0.471   6.0456   1.9300  -0.2095
 PIT  H4   H  HCR6  0   0.241   2.5797   2.3564  -0.0664
 PIT  H7   H  H     0   0.250   0.3776   1.5946  -0.2396
 PIT  H8   H  H     0   0.263  -0.0975  -1.3728   0.2969
 PIT  H10  H  HCR6  0   0.254  -2.3095  -2.1336   0.0365
 PIT  H14  H  HCR6  0   0.236  -1.6567   2.0976   0.3426
 PIT  H13  H  HCR6  0   0.227  -4.0649   2.4601   0.3050
 PIT  H1   H  HOH1  0   0.495  -6.1825   1.3790   0.3466
 PIT  HAD  H  HOH1  0   0.482  -5.7834  -1.7031   0.0103

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
 PIT  C1   C6   aromatic  1.387  0.020  1.387
 PIT  C1   C2   aromatic  1.394  0.020  1.394
 PIT  C1   O3   single    1.347  0.020  1.347
 PIT  C2   C3   aromatic  1.387  0.020  1.387
 PIT  C2   H2   single    0.930  0.020  1.080
 PIT  C3   O2   single    1.346  0.020  1.346
 PIT  C3   C4   aromatic  1.393  0.020  1.393
 PIT  C4   C5   aromatic  1.392  0.020  1.392
 PIT  C4   H4   single    0.930  0.020  1.080
 PIT  C5   C7   single    1.463  0.020  1.463
 PIT  C5   C6   aromatic  1.399  0.020  1.399
 PIT  C6   H6   single    0.930  0.020  1.080
 PIT  C7   C8   double    1.338  0.020  1.338
 PIT  C7   H7   single    0.930  0.020  1.080
 PIT  C8   C9   single    1.461  0.020  1.461
 PIT  C8   H8   single    0.930  0.020  1.080
 PIT  C9   C10  aromatic  1.396  0.020  1.396
 PIT  C9   C14  aromatic  1.394  0.020  1.394
 PIT  C10  C11  aromatic  1.383  0.020  1.383
 PIT  C10  H10  single    0.930  0.020  1.080
 PIT  C11  OAD  single    1.347  0.020  1.347
 PIT  C11  C12  aromatic  1.398  0.020  1.398
 PIT  C12  O1   single    1.357  0.020  1.357
 PIT  C12  C13  aromatic  1.385  0.020  1.385
 PIT  C13  H13  single    0.930  0.020  1.080
 PIT  C13  C14  aromatic  1.385  0.020  1.385
 PIT  C14  H14  single    0.930  0.020  1.080
 PIT  O1   H1   single    0.850  0.020  0.980
 PIT  O2   HA   single    0.850  0.020  0.980
 PIT  O3   H3   single    0.850  0.020  0.980
 PIT  OAD  HAD  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
 PIT  O3   C1   C6   122.56  3.000
 PIT  O3   C1   C2   116.76  3.000
 PIT  C6   C1   C2   120.68  3.000
 PIT  H2   C2   C3   121.46  3.000
 PIT  H2   C2   C1   119.30  3.000
 PIT  C3   C2   C1   119.24  3.000
 PIT  O2   C3   C4   117.20  3.000
 PIT  C4   C3   C2   120.54  3.000
 PIT  O2   C3   C2   122.26  3.000
 PIT  H4   C4   C5   120.51  3.000
 PIT  H4   C4   C3   119.31  3.000
 PIT  C5   C4   C3   120.15  3.000
 PIT  C7   C5   C6   122.52  3.000
 PIT  C6   C5   C4   119.39  3.000
 PIT  C7   C5   C4   118.08  3.000
 PIT  H6   C6   C5   120.34  3.000
 PIT  H6   C6   C1   119.66  3.000
 PIT  C5   C6   C1   119.99  3.000
 PIT  H7   C7   C8   119.05  3.000
 PIT  H7   C7   C5   114.57  3.000
 PIT  C8   C7   C5   126.38  3.000
 PIT  H8   C8   C9   114.47  3.000
 PIT  H8   C8   C7   118.91  3.000
 PIT  C9   C8   C7   126.62  3.000
 PIT  C14  C9   C10  118.10  3.000
 PIT  C14  C9   C8   123.24  3.000
 PIT  C10  C9   C8   118.66  3.000
 PIT  H10  C10  C11  118.08  3.000
 PIT  H10  C10  C9   120.14  3.000
 PIT  C11  C10  C9   121.77  3.000
 PIT  OAD  C11  C12  121.53  3.000
 PIT  C12  C11  C10  119.22  3.000
 PIT  OAD  C11  C10  119.24  3.000
 PIT  O1   C12  C13  124.37  3.000
 PIT  C13  C12  C11  119.62  3.000
 PIT  O1   C12  C11  116.01  3.000
 PIT  H13  C13  C14  119.37  3.000
 PIT  C14  C13  C12  120.62  3.000
 PIT  H13  C13  C12  120.00  3.000
 PIT  H14  C14  C13  118.68  3.000
 PIT  H14  C14  C9   120.67  3.000
 PIT  C13  C14  C9   120.64  3.000
 PIT  H1   O1   C12  110.90  3.000
 PIT  HA   O2   C3   110.35  3.000
 PIT  H3   O3   C1   110.08  3.000
 PIT  HAD  OAD  C11  109.83  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
 PIT  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 PIT  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 PIT  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PIT  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PIT  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 PIT  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 PIT  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 PIT  CONST_08  C12  C13  C14  C9      0.00   0.0  0
 PIT  CONST_09  C13  C14  C9   C10     0.00   0.0  0
 PIT  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 PIT  CONST_11  C14  C9   C10  C11     0.00   0.0  0
 PIT  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 PIT  CONST_13  C7   C5   C6   C1    180.00   0.0  0
 PIT  CONST_14  O2   C3   C2   C1    180.00   0.0  0
 PIT  CONST_15  O3   C1   C2   C3    180.00   0.0  0
 PIT  CONST_16  C7   C5   C4   C3    180.00   0.0  0
 PIT  CONST_17  O2   C3   C4   C5    180.00   0.0  0
 PIT  CONST_18  O3   C1   C6   C5    180.00   0.0  0
 PIT  CONST_19  C11  C10  C9   C8    180.00   0.0  0
 PIT  CONST_20  C13  C14  C9   C8    180.00   0.0  0
 PIT  CONST_21  OAD  C11  C10  C9    180.00   0.0  0
 PIT  CONST_22  O1   C12  C11  C10   180.00   0.0  0
 PIT  CONST_23  OAD  C11  C12  C13   180.00   0.0  0
 PIT  CONST_24  O1   C12  C13  C14   180.00   0.0  0
 PIT  CONST_25  H6   C6   C1   C2    180.00   0.0  0
 PIT  CONST_26  H4   C4   C3   C2    180.00   0.0  0
 PIT  CONST_27  H2   C2   C3   C4    180.00   0.0  0
 PIT  CONST_28  H13  C13  C14  C9    180.00   0.0  0
 PIT  CONST_29  H14  C14  C9   C10   180.00   0.0  0
 PIT  CONST_30  H10  C10  C11  C12   180.00   0.0  0
 PIT  Var_01    C9   C8   C7   C5   -179.80   0.0  2
 PIT  Var_02    C8   C7   C5   C4   -168.81  30.0  2
 PIT  Var_03    C10  C9   C8   C7    165.66  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
 PIT  plan-1  C1   0.020
 PIT  plan-1  C2   0.020
 PIT  plan-1  C3   0.020
 PIT  plan-1  C4   0.020
 PIT  plan-1  C5   0.020
 PIT  plan-1  C6   0.020
 PIT  plan-1  C7   0.020
 PIT  plan-1  O2   0.020
 PIT  plan-1  O3   0.020
 PIT  plan-1  H6   0.020
 PIT  plan-1  H2   0.020
 PIT  plan-1  H4   0.020
 PIT  plan-2  C8   0.020
 PIT  plan-2  C9   0.020
 PIT  plan-2  C10  0.020
 PIT  plan-2  C11  0.020
 PIT  plan-2  C12  0.020
 PIT  plan-2  C13  0.020
 PIT  plan-2  C14  0.020
 PIT  plan-2  O1   0.020
 PIT  plan-2  OAD  0.020
 PIT  plan-2  H10  0.020
 PIT  plan-2  H14  0.020
 PIT  plan-2  H13  0.020
 PIT  plan-3  C5   0.020
 PIT  plan-3  C7   0.020
 PIT  plan-3  C8   0.020
 PIT  plan-3  C9   0.020
 PIT  plan-3  H7   0.020
 PIT  plan-3  H8   0.020

