# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 11:47:33 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: 7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2cc(cc(c2c1N=Nc3ccccc3)[S](O)(=O)=O)[S](O)(=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
 ORA  ORA  '7-hydroxy-8-[(E)-phenyldiazenyl]naphthalene-1,3-disulfonic acid'  ligand  37  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ORA
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
 ORA  C1   C  CR16   0  -0.254  -6.3597   1.3726  -0.4132
 ORA  N1   N  N      0  -0.413  -2.9925  -1.0101   0.2530
 ORA  O1   O  OS    -1  -0.755   4.8705   1.0926  -1.7596
 ORA  S1   S  S      0   1.418   4.8932   0.5475  -0.3919
 ORA  C2   C  CR16   0  -0.250  -6.4777   0.0466  -0.0195
 ORA  N2   N  N      0  -0.182  -1.8458  -0.5544   0.0596
 ORA  O2   O  OS    -1  -0.728  -1.0949   1.3268   1.8004
 ORA  S2   S  S      0   1.449  -0.2181   1.8517   0.7444
 ORA  C3   C  CR16   0  -0.257  -5.0971   1.9308  -0.5929
 ORA  O3   O  OS     0  -0.743   5.7673  -0.6279  -0.2431
 ORA  C4   C  CR16   0  -0.293   1.3621  -3.2105   0.1188
 ORA  O4   O  OS     0  -0.749   5.1081   1.5776   0.6385
 ORA  C5   C  CR16   0  -0.293  -5.3389  -0.7154   0.1929
 ORA  O5   O  OS     0  -0.742  -0.8895   2.2834  -0.4936
 ORA  C6   C  CR16   0  -0.310  -3.9532   1.1790  -0.3844
 ORA  O6   O  OS     0  -0.738   0.6944   2.8925   1.2562
 ORA  C7   C  CR16   0  -0.360   0.1099  -3.7044   0.2839
 ORA  O7   O  OH1    0  -0.616  -2.1827  -3.3612   0.4749
 ORA  C8   C  CR16   0  -0.331   2.9421  -1.3826  -0.0943
 ORA  C9   C  CR16   0  -0.241   2.2006   0.8748   0.1041
 ORA  C10  C  CR66   0   0.090   1.6137  -1.8158   0.0691
 ORA  C11  C  CR66   0   0.138   0.5395  -0.8921   0.1935
 ORA  C12  C  CR6    0   0.276  -4.0762  -0.1549   0.0093
 ORA  C13  C  CR6    0   0.037  -0.7917  -1.4289   0.2468
 ORA  C14  C  CR6    0   0.394  -0.9859  -2.8174   0.3574
 ORA  C15  C  CR6    0  -0.202   3.2304  -0.0498  -0.1155
 ORA  C16  C  CR6    0  -0.297   0.8908   0.4902   0.2731
 ORA  H1   H  HCR6   0   0.261  -7.2462   1.9704  -0.5800
 ORA  H2   H  HCR6   0   0.261  -7.4548  -0.3951   0.1242
 ORA  H3   H  HCR6   0   0.259  -5.0050   2.9659  -0.8960
 ORA  H4   H  HCR6   0   0.275   2.2013  -3.8889   0.0312
 ORA  H5   H  HCR6   0   0.267  -5.4225  -1.7504   0.5009
 ORA  H6   H  HCR6   0   0.320  -2.9718   1.6131  -0.5202
 ORA  H7   H  HCR6   0   0.280  -0.0740  -4.7696   0.3372
 ORA  HO7  H  HOH1   0   0.475  -2.8430  -2.6088   0.4879
 ORA  H8   H  HCR6   0   0.273   3.7223  -2.1262  -0.1941
 ORA  H9   H  HCR6   0   0.281   2.4533   1.9227   0.1843

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
 ORA  C1   C2   aromatic  1.388  0.020  1.388
 ORA  C1   C3   aromatic  1.392  0.020  1.392
 ORA  C1   H1   single    0.930  0.020  1.080
 ORA  N1   N2   double    1.249  0.020  1.249
 ORA  N1   C12  single    1.402  0.020  1.402
 ORA  O1   S1   deloc     1.472  0.020  1.472
 ORA  S1   O3   deloc     1.472  0.020  1.472
 ORA  S1   O4   deloc     1.473  0.020  1.473
 ORA  S1   C15  single    1.788  0.020  1.788
 ORA  C2   C5   aromatic  1.387  0.020  1.387
 ORA  C2   H2   single    0.930  0.020  1.080
 ORA  N2   C13  single    1.382  0.020  1.382
 ORA  O2   S2   deloc     1.470  0.020  1.470
 ORA  S2   O5   deloc     1.473  0.020  1.473
 ORA  S2   O6   deloc     1.476  0.020  1.476
 ORA  S2   C16  single    1.818  0.020  1.818
 ORA  C3   C6   aromatic  1.385  0.020  1.385
 ORA  C3   H3   single    0.930  0.020  1.080
 ORA  C4   C7   aromatic  1.356  0.020  1.356
 ORA  C4   C10  aromatic  1.418  0.020  1.418
 ORA  C4   H4   single    0.930  0.020  1.080
 ORA  C5   C12  aromatic  1.394  0.020  1.394
 ORA  C5   H5   single    0.930  0.020  1.080
 ORA  C6   C12  aromatic  1.396  0.020  1.396
 ORA  C6   H6   single    0.930  0.020  1.080
 ORA  C7   C14  aromatic  1.412  0.020  1.412
 ORA  C7   H7   single    0.930  0.020  1.080
 ORA  O7   C14  single    1.320  0.020  1.320
 ORA  O7   HO7  single    0.850  0.020  0.980
 ORA  C8   C10  aromatic  1.407  0.020  1.407
 ORA  C8   C15  aromatic  1.364  0.020  1.364
 ORA  C8   H8   single    0.930  0.020  1.080
 ORA  C9   C15  aromatic  1.401  0.020  1.401
 ORA  C9   C16  aromatic  1.376  0.020  1.376
 ORA  C9   H9   single    0.930  0.020  1.080
 ORA  C10  C11  aromatic  1.422  0.020  1.422
 ORA  C11  C13  aromatic  1.436  0.020  1.436
 ORA  C11  C16  aromatic  1.428  0.020  1.428
 ORA  C13  C14  aromatic  1.406  0.020  1.406

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
 ORA  H1   C1   C3   120.10  3.000
 ORA  H1   C1   C2   120.12  3.000
 ORA  C3   C1   C2   119.78  3.000
 ORA  C12  N1   N2   117.40  3.000
 ORA  C15  S1   O4   105.14  3.000
 ORA  C15  S1   O3   105.65  3.000
 ORA  O4   S1   O3   113.65  3.000
 ORA  C15  S1   O1   104.65  3.000
 ORA  O4   S1   O1   113.15  3.000
 ORA  O3   S1   O1   113.49  3.000
 ORA  H2   C2   C5   119.80  3.000
 ORA  H2   C2   C1   120.29  3.000
 ORA  C5   C2   C1   119.90  3.000
 ORA  C13  N2   N1   116.64  3.000
 ORA  C16  S2   O6   103.94  3.000
 ORA  C16  S2   O5   106.24  3.000
 ORA  O6   S2   O5   111.50  3.000
 ORA  C16  S2   O2   106.42  3.000
 ORA  O6   S2   O2   111.82  3.000
 ORA  O5   S2   O2   115.90  3.000
 ORA  H3   C3   C6   119.42  3.000
 ORA  H3   C3   C1   119.78  3.000
 ORA  C6   C3   C1   120.81  3.000
 ORA  H4   C4   C10  118.41  3.000
 ORA  H4   C4   C7   119.83  3.000
 ORA  C10  C4   C7   121.75  3.000
 ORA  H5   C5   C12  119.45  3.000
 ORA  H5   C5   C2   120.36  3.000
 ORA  C12  C5   C2   120.20  3.000
 ORA  H6   C6   C12  119.91  3.000
 ORA  H6   C6   C3   120.85  3.000
 ORA  C12  C6   C3   119.24  3.000
 ORA  H7   C7   C14  118.94  3.000
 ORA  H7   C7   C4   121.42  3.000
 ORA  C14  C7   C4   119.62  3.000
 ORA  HO7  O7   C14  106.83  3.000
 ORA  H8   C8   C15  121.17  3.000
 ORA  H8   C8   C10  118.67  3.000
 ORA  C15  C8   C10  120.16  3.000
 ORA  H9   C9   C16  118.98  3.000
 ORA  H9   C9   C15  118.66  3.000
 ORA  C16  C9   C15  122.31  3.000
 ORA  C11  C10  C8   121.56  3.000
 ORA  C11  C10  C4   120.11  3.000
 ORA  C8   C10  C4   118.33  3.000
 ORA  C16  C11  C13  125.98  3.000
 ORA  C16  C11  C10  116.59  3.000
 ORA  C13  C11  C10  117.42  3.000
 ORA  C6   C12  C5   120.07  3.000
 ORA  C6   C12  N1   124.32  3.000
 ORA  C5   C12  N1   115.61  3.000
 ORA  C14  C13  C11  119.99  3.000
 ORA  C14  C13  N2   122.00  3.000
 ORA  C11  C13  N2   117.73  3.000
 ORA  C13  C14  O7   122.62  3.000
 ORA  C13  C14  C7   120.60  3.000
 ORA  O7   C14  C7   116.72  3.000
 ORA  C9   C15  C8   119.14  3.000
 ORA  C9   C15  S1   119.15  3.000
 ORA  C8   C15  S1   121.69  3.000
 ORA  C11  C16  C9   119.86  3.000
 ORA  C11  C16  S2   126.09  3.000
 ORA  C9   C16  S2   113.78  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
 ORA  CONST_01  C12  C5   C2   C1      0.00   0.0  0
 ORA  CONST_02  C12  C6   C3   C1      0.00   0.0  0
 ORA  CONST_03  C6   C3   C1   C2      0.00   0.0  0
 ORA  CONST_04  C6   C12  C5   C2      0.00   0.0  0
 ORA  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 ORA  CONST_06  C5   C12  C6   C3      0.00   0.0  0
 ORA  CONST_07  C13  C14  C7   C4      0.00   0.0  0
 ORA  CONST_08  C15  C8   C10  C4    180.00   0.0  0
 ORA  CONST_09  C13  C11  C10  C4      0.00   0.0  0
 ORA  CONST_10  C16  C11  C10  C4    180.00   0.0  0
 ORA  CONST_11  C8   C10  C4   C7    180.00   0.0  0
 ORA  CONST_12  C11  C10  C4   C7      0.00   0.0  0
 ORA  CONST_13  C11  C13  C14  C7      0.00   0.0  0
 ORA  CONST_14  C13  C11  C10  C8    180.00   0.0  0
 ORA  CONST_15  C16  C11  C10  C8      0.00   0.0  0
 ORA  CONST_16  C16  C9   C15  C8      0.00   0.0  0
 ORA  CONST_17  C10  C8   C15  C9      0.00   0.0  0
 ORA  CONST_18  C10  C11  C16  C9      0.00   0.0  0
 ORA  CONST_19  C13  C11  C16  C9    180.00   0.0  0
 ORA  CONST_20  C14  C7   C4   C10     0.00   0.0  0
 ORA  CONST_21  C14  C13  C11  C10     0.00   0.0  0
 ORA  CONST_22  C15  C8   C10  C11     0.00   0.0  0
 ORA  CONST_23  C15  C9   C16  C11     0.00   0.0  0
 ORA  CONST_24  C16  C11  C13  C14   180.00   0.0  0
 ORA  CONST_25  C2   C5   C12  N1    180.00   0.0  0
 ORA  CONST_26  C3   C6   C12  N1    180.00   0.0  0
 ORA  CONST_27  C10  C8   C15  S1    180.00   0.0  0
 ORA  CONST_28  C16  C9   C15  S1    180.00   0.0  0
 ORA  CONST_29  C10  C11  C13  N2    180.00   0.0  0
 ORA  CONST_31  C7   C14  C13  N2    180.00   0.0  0
 ORA  CONST_32  C15  C9   C16  S2    180.00   0.0  0
 ORA  CONST_33  C10  C11  C16  S2    180.00   0.0  0
 ORA  CONST_34  C13  C11  C16  S2      0.00   0.0  0
 ORA  CONST_35  O7   C14  C7   C4    180.00   0.0  0
 ORA  CONST_36  C11  C13  C14  O7    180.00   0.0  0
 ORA  CONST_37  H5   C5   C2   C1    180.00   0.0  0
 ORA  CONST_38  H6   C6   C3   C1    180.00   0.0  0
 ORA  CONST_39  H3   C3   C1   C2    180.00   0.0  0
 ORA  CONST_40  H2   C2   C1   C3    180.00   0.0  0
 ORA  CONST_41  H8   C8   C10  C4      0.00   0.0  0
 ORA  CONST_42  H1   C1   C2   C5    180.00   0.0  0
 ORA  CONST_43  H4   C4   C10  C8      0.00   0.0  0
 ORA  CONST_44  H9   C9   C15  C8    180.00   0.0  0
 ORA  CONST_45  H7   C7   C4   C10   180.00   0.0  0
 ORA  CONST_46  C11  C13  N2   N1    180.00   0.0  0
 ORA  CONST_47  C14  C13  N2   N1      0.00   0.0  0
 ORA  CONST_48  C5   C12  N1   N2    180.00   0.0  0
 ORA  CONST_49  C6   C12  N1   N2      0.00   0.0  0
 ORA  Var_01    C8   C15  S1   O1    106.96  30.0  2
 ORA  Var_02    C9   C16  S2   O2   -137.04  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
 ORA  plan-1  C1   0.020
 ORA  plan-1  N1   0.020
 ORA  plan-1  C2   0.020
 ORA  plan-1  N2   0.020
 ORA  plan-1  C3   0.020
 ORA  plan-1  C5   0.020
 ORA  plan-1  C6   0.020
 ORA  plan-1  C12  0.020
 ORA  plan-1  C13  0.020
 ORA  plan-1  H1   0.020
 ORA  plan-1  H2   0.020
 ORA  plan-1  H3   0.020
 ORA  plan-1  H5   0.020
 ORA  plan-1  H6   0.020
 ORA  plan-2  N1   0.020
 ORA  plan-2  S1   0.020
 ORA  plan-2  N2   0.020
 ORA  plan-2  S2   0.020
 ORA  plan-2  C4   0.020
 ORA  plan-2  C7   0.020
 ORA  plan-2  O7   0.020
 ORA  plan-2  C8   0.020
 ORA  plan-2  C9   0.020
 ORA  plan-2  C10  0.020
 ORA  plan-2  C11  0.020
 ORA  plan-2  C13  0.020
 ORA  plan-2  C14  0.020
 ORA  plan-2  C15  0.020
 ORA  plan-2  C16  0.020
 ORA  plan-2  H4   0.020
 ORA  plan-2  H7   0.020
 ORA  plan-2  H8   0.020
 ORA  plan-2  H9   0.020

