# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:17:17 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-(4-fluorophenyl)-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(c2ccc(F)cc2)c(n3cccc3)c(I)c1O
#
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
 9GZ  9GZ  '5-(4-fluorophenyl)-3-iodanyl-2-oxidanyl-4-pyrrol-1-yl-benzoic acid'  ligand  34  23  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9GZ
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
 9GZ  N1   N  NR5   0  -0.520   0.4493   1.4358   0.0257
 9GZ  C4   C  CR6   0  -0.410  -1.3126  -0.2322  -0.0402
 9GZ  C5   C  CR6   0   0.420  -1.7412  -1.5643  -0.1172
 9GZ  C6   C  CR6   0  -0.160  -0.7648  -2.5742  -0.1700
 9GZ  C7   C  C     0   0.539  -1.1551  -4.0045  -0.2880
 9GZ  C8   C  CR15  0  -0.055   1.0606   2.0054   1.1104
 9GZ  C10  C  CR15  0  -0.350   0.9328   3.5182  -0.5455
 9GZ  C13  C  CR16  0  -0.272   3.2728  -1.1724   0.8853
 9GZ  C15  C  CR6   0   0.519   5.1762  -0.1010  -0.0538
 9GZ  C17  C  CR16  0  -0.254   3.0401   0.2158  -1.0565
 9GZ  C1   C  CR16  0  -0.328   0.5809  -2.2296  -0.1438
 9GZ  C11  C  CR15  0  -0.078   0.3726   2.3528  -0.9902
 9GZ  C12  C  CR6   0   0.041   2.4586  -0.6063  -0.0931
 9GZ  C14  C  CR16  0  -0.399   4.6373  -0.9251   0.9138
 9GZ  C16  C  CR16  0  -0.398   4.4013   0.4745  -1.0429
 9GZ  C2   C  CR6   0   0.103   1.0112  -0.9121  -0.1040
 9GZ  C3   C  CR6   0   0.333   0.0419   0.0913  -0.0518
 9GZ  C9   C  CR15  0  -0.353   1.3655   3.2990   0.7903
 9GZ  O1   O  O     0  -0.424  -2.1975  -4.4056  -0.7390
 9GZ  O2   O  OH1   0  -0.581  -3.0184  -1.9280  -0.1017
 9GZ  O3   O  OH1   0  -0.592  -0.1981  -4.8131   0.1522
 9GZ  H1   H  HCR5  0   0.282   1.2187   1.4427   2.0159
 9GZ  H2   H  HCR5  0   0.246   1.0233   4.4296  -1.1153
 9GZ  H3   H  HCR6  0   0.268   2.8368  -1.8064   1.6472
 9GZ  H4   H  HCR6  0   0.263   2.4335   0.6543  -1.8375
 9GZ  H5   H  HCR6  0   0.282   1.3284  -3.0090  -0.1923
 9GZ  H6   H  HCR5  0   0.288  -0.0630   2.0930  -1.9414
 9GZ  H7   H  HCR6  0   0.282   5.2645  -1.3628   1.6789
 9GZ  H8   H  HCR6  0   0.281   4.8528   1.1076  -1.7956
 9GZ  H9   H  HCR5  0   0.246   1.8448   4.0127   1.4417
 9GZ  H10  H  HOH1  0   0.474  -3.6156  -1.1719  -0.0225
 9GZ  H11  H  HOH1  0   0.489  -0.4594  -5.7354   0.0109
 9GZ  I1   I  I     0   0.133  -2.7339   1.2979   0.1899
 9GZ  F1   F  F     0  -0.314   6.4954   0.1461  -0.0358

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
 9GZ  F1   C15  single    1.342  0.020  1.342
 9GZ  C15  C14  aromatic  1.380  0.020  1.380
 9GZ  C15  C16  aromatic  1.382  0.020  1.382
 9GZ  C14  C13  aromatic  1.387  0.020  1.387
 9GZ  C16  C17  aromatic  1.386  0.020  1.386
 9GZ  C13  C12  aromatic  1.393  0.020  1.393
 9GZ  O1   C7   double    1.205  0.020  1.205
 9GZ  C17  C12  aromatic  1.394  0.020  1.394
 9GZ  C12  C2   single    1.479  0.020  1.479
 9GZ  C1   C2   aromatic  1.387  0.020  1.387
 9GZ  C1   C6   aromatic  1.389  0.020  1.389
 9GZ  C7   C6   single    1.487  0.020  1.487
 9GZ  C7   O3   single    1.328  0.020  1.328
 9GZ  C2   C3   aromatic  1.396  0.020  1.396
 9GZ  C6   C5   aromatic  1.406  0.020  1.406
 9GZ  C3   N1   single    1.407  0.020  1.407
 9GZ  C3   C4   aromatic  1.393  0.020  1.393
 9GZ  C5   C4   aromatic  1.401  0.020  1.401
 9GZ  C5   O2   single    1.328  0.020  1.328
 9GZ  N1   C11  aromatic  1.371  0.020  1.371
 9GZ  N1   C8   aromatic  1.369  0.020  1.369
 9GZ  C4   I1   single    2.101  0.020  2.101
 9GZ  C11  C10  aromatic  1.367  0.020  1.367
 9GZ  C8   C9   aromatic  1.367  0.020  1.367
 9GZ  C10  C9   aromatic  1.421  0.020  1.421
 9GZ  C8   H1   single    0.930  0.020  1.080
 9GZ  C10  H2   single    0.930  0.020  1.080
 9GZ  C13  H3   single    0.930  0.020  1.080
 9GZ  C17  H4   single    0.930  0.020  1.080
 9GZ  C1   H5   single    0.930  0.020  1.080
 9GZ  C11  H6   single    0.930  0.020  1.080
 9GZ  C14  H7   single    0.930  0.020  1.080
 9GZ  C16  H8   single    0.930  0.020  1.080
 9GZ  C9   H9   single    0.930  0.020  1.080
 9GZ  O2   H10  single    0.850  0.020  0.980
 9GZ  O3   H11  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
 9GZ  C3   N1   C11  125.61  3.000
 9GZ  C11  N1   C8   109.50  3.000
 9GZ  C3   N1   C8   124.78  3.000
 9GZ  I1   C4   C3   119.32  3.000
 9GZ  I1   C4   C5   119.43  3.000
 9GZ  C3   C4   C5   121.19  3.000
 9GZ  O2   C5   C6   118.15  3.000
 9GZ  O2   C5   C4   123.63  3.000
 9GZ  C6   C5   C4   118.19  3.000
 9GZ  C1   C6   C7   119.61  3.000
 9GZ  C7   C6   C5   120.77  3.000
 9GZ  C1   C6   C5   119.60  3.000
 9GZ  O3   C7   O1   123.03  3.000
 9GZ  O3   C7   C6   111.73  3.000
 9GZ  O1   C7   C6   125.24  3.000
 9GZ  H1   C8   C9   131.15  3.000
 9GZ  H1   C8   N1   120.93  3.000
 9GZ  C9   C8   N1   107.93  3.000
 9GZ  H2   C10  C9   126.96  3.000
 9GZ  H2   C10  C11  125.64  3.000
 9GZ  C9   C10  C11  107.40  3.000
 9GZ  H3   C13  C14  119.08  3.000
 9GZ  H3   C13  C12  119.78  3.000
 9GZ  C14  C13  C12  121.13  3.000
 9GZ  F1   C15  C16  118.95  3.000
 9GZ  C16  C15  C14  122.10  3.000
 9GZ  F1   C15  C14  118.95  3.000
 9GZ  H4   C17  C16  118.84  3.000
 9GZ  H4   C17  C12  120.27  3.000
 9GZ  C16  C17  C12  120.89  3.000
 9GZ  H5   C1   C2   118.15  3.000
 9GZ  H5   C1   C6   119.35  3.000
 9GZ  C2   C1   C6   122.46  3.000
 9GZ  H6   C11  C10  131.14  3.000
 9GZ  H6   C11  N1   121.02  3.000
 9GZ  C10  C11  N1   107.83  3.000
 9GZ  C2   C12  C17  121.68  3.000
 9GZ  C2   C12  C13  119.54  3.000
 9GZ  C17  C12  C13  118.77  3.000
 9GZ  H7   C14  C15  120.73  3.000
 9GZ  H7   C14  C13  120.84  3.000
 9GZ  C15  C14  C13  118.43  3.000
 9GZ  H8   C16  C17  120.81  3.000
 9GZ  H8   C16  C15  120.50  3.000
 9GZ  C17  C16  C15  118.69  3.000
 9GZ  C3   C2   C12  122.04  3.000
 9GZ  C3   C2   C1   117.94  3.000
 9GZ  C12  C2   C1   120.02  3.000
 9GZ  C2   C3   C4   120.57  3.000
 9GZ  C4   C3   N1   120.21  3.000
 9GZ  C2   C3   N1   119.20  3.000
 9GZ  H9   C9   C10  126.94  3.000
 9GZ  H9   C9   C8   125.72  3.000
 9GZ  C10  C9   C8   107.34  3.000
 9GZ  H10  O2   C5   112.39  3.000
 9GZ  H11  O3   C7   109.69  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
 9GZ  CONST_01  C12  C2   C3   N1     0.00   0.0  0
 9GZ  CONST_02  C1   C2   C3   N1   180.00   0.0  0
 9GZ  CONST_03  C5   C4   C3   N1   180.00   0.0  0
 9GZ  CONST_04  C9   C10  C11  N1     0.00   0.0  0
 9GZ  CONST_05  C10  C9   C8   N1     0.00   0.0  0
 9GZ  CONST_06  C12  C2   C3   C4   180.00   0.0  0
 9GZ  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 9GZ  CONST_10  C1   C6   C5   C4     0.00   0.0  0
 9GZ  CONST_11  C2   C1   C6   C5     0.00   0.0  0
 9GZ  CONST_12  C2   C3   C4   C5     0.00   0.0  0
 9GZ  CONST_13  C12  C2   C1   C6   180.00   0.0  0
 9GZ  CONST_14  C3   C2   C1   C6     0.00   0.0  0
 9GZ  CONST_15  C3   C4   C5   C6     0.00   0.0  0
 9GZ  CONST_17  C10  C11  N1   C8     0.00   0.0  0
 9GZ  CONST_18  C11  C10  C9   C8     0.00   0.0  0
 9GZ  CONST_19  C3   N1   C11  C10  180.00   0.0  0
 9GZ  CONST_20  C16  C15  C14  C13    0.00   0.0  0
 9GZ  CONST_21  C16  C17  C12  C13    0.00   0.0  0
 9GZ  CONST_24  C12  C13  C14  C15    0.00   0.0  0
 9GZ  CONST_25  C12  C17  C16  C15    0.00   0.0  0
 9GZ  CONST_26  C14  C15  C16  C17    0.00   0.0  0
 9GZ  CONST_27  C14  C13  C12  C17    0.00   0.0  0
 9GZ  CONST_31  C9   C8   N1   C11    0.00   0.0  0
 9GZ  CONST_32  C2   C12  C13  C14  180.00   0.0  0
 9GZ  CONST_33  C2   C12  C17  C16  180.00   0.0  0
 9GZ  CONST_34  C9   C8   N1   C3   180.00   0.0  0
 9GZ  CONST_35  I1   C4   C3   N1     0.00   0.0  0
 9GZ  CONST_36  C7   C6   C5   C4   180.00   0.0  0
 9GZ  CONST_37  I1   C4   C5   C6   180.00   0.0  0
 9GZ  CONST_38  C2   C1   C6   C7   180.00   0.0  0
 9GZ  CONST_39  F1   C15  C14  C13  180.00   0.0  0
 9GZ  CONST_40  F1   C15  C16  C17  180.00   0.0  0
 9GZ  CONST_41  O2   C5   C6   C1   180.00   0.0  0
 9GZ  CONST_42  I1   C4   C3   C2   180.00   0.0  0
 9GZ  CONST_43  O2   C5   C4   C3   180.00   0.0  0
 9GZ  CONST_44  H2   C10  C11  N1   180.00   0.0  0
 9GZ  CONST_45  H9   C9   C8   N1   180.00   0.0  0
 9GZ  CONST_46  H5   C1   C6   C5   180.00   0.0  0
 9GZ  CONST_47  H6   C11  N1   C8   180.00   0.0  0
 9GZ  CONST_48  H1   C8   C9   C10  180.00   0.0  0
 9GZ  CONST_49  H4   C17  C12  C13  180.00   0.0  0
 9GZ  CONST_50  H3   C13  C14  C15  180.00   0.0  0
 9GZ  CONST_51  H7   C14  C13  C12  180.00   0.0  0
 9GZ  CONST_52  H8   C16  C17  C12  180.00   0.0  0
 9GZ  CONST_53  H11  O3   C7   C6   180.00   0.0  0
 9GZ  Var_01    O1   C7   C6   C5    23.60  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
 9GZ  plan-1  N1   0.020
 9GZ  plan-1  C8   0.020
 9GZ  plan-1  C10  0.020
 9GZ  plan-1  C11  0.020
 9GZ  plan-1  C3   0.020
 9GZ  plan-1  C9   0.020
 9GZ  plan-1  H1   0.020
 9GZ  plan-1  H2   0.020
 9GZ  plan-1  H6   0.020
 9GZ  plan-1  H9   0.020
 9GZ  plan-2  C13  0.020
 9GZ  plan-2  C15  0.020
 9GZ  plan-2  C17  0.020
 9GZ  plan-2  C12  0.020
 9GZ  plan-2  C14  0.020
 9GZ  plan-2  C16  0.020
 9GZ  plan-2  C2   0.020
 9GZ  plan-2  H3   0.020
 9GZ  plan-2  H4   0.020
 9GZ  plan-2  H7   0.020
 9GZ  plan-2  H8   0.020
 9GZ  plan-2  F1   0.020
 9GZ  plan-3  N1   0.020
 9GZ  plan-3  C4   0.020
 9GZ  plan-3  C5   0.020
 9GZ  plan-3  C6   0.020
 9GZ  plan-3  C7   0.020
 9GZ  plan-3  C1   0.020
 9GZ  plan-3  C12  0.020
 9GZ  plan-3  C2   0.020
 9GZ  plan-3  C3   0.020
 9GZ  plan-3  O2   0.020
 9GZ  plan-3  H5   0.020
 9GZ  plan-3  I1   0.020
 9GZ  plan-4  C6   0.020
 9GZ  plan-4  C7   0.020
 9GZ  plan-4  O1   0.020
 9GZ  plan-4  O3   0.020
 9GZ  plan-4  H11  0.020

