# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 03:54:43 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(I)c(n2cccc2)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
 Y0V  Y0V  '3,5-bis(iodanyl)-2-oxidanyl-4-pyrrol-1-yl-benzoic acid'  ligand  24  17  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y0V
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
 Y0V  C1   C  CR6   0  -0.222  -0.2065  -2.5343   0.0308
 Y0V  I1   I  I     0   0.136  -2.8393   0.9075  -0.2484
 Y0V  N1   N  NR5   0  -0.506   0.2744   1.6313  -0.0109
 Y0V  O1   O  OH1   0  -0.574   0.7130  -4.6841   0.1583
 Y0V  C2   C  CR16  0  -0.256   1.0646  -1.9701   0.1195
 Y0V  I2   I  I     0   0.112   3.1505   0.2151   0.2505
 Y0V  O2   O  OH1   0  -0.596  -2.5706  -2.1787  -0.1594
 Y0V  C3   C  CR6   0  -0.264   1.2267  -0.6014   0.1062
 Y0V  O3   O  O     0  -0.474  -1.4990  -4.5154  -0.0352
 Y0V  C4   C  CR6   0   0.423   0.1125   0.2367   0.0024
 Y0V  C5   C  CR6   0  -0.381  -1.1556  -0.3185  -0.0874
 Y0V  C6   C  CR6   0   0.451  -1.3405  -1.7076  -0.0738
 Y0V  C7   C  CR15  0  -0.066   0.4946   2.3883  -1.1308
 Y0V  C8   C  CR15  0  -0.351   0.6120   3.6923  -0.7352
 Y0V  C9   C  CR15  0  -0.350   0.4571   3.7241   0.6766
 Y0V  C10  C  CR15  0  -0.062   0.2509   2.4384   1.0950
 Y0V  C11  C  C     0   0.618  -0.3990  -3.9965   0.0468
 Y0V  HO1  H  HOH1  0   0.501   0.5292  -5.6363   0.1608
 Y0V  H2   H  HCR6  0   0.304   1.9282  -2.6144   0.1993
 Y0V  HO2  H  HOH1  0   0.491  -2.5280  -3.1622  -0.1362
 Y0V  H7   H  HCR5  0   0.286   0.5483   1.9333  -2.1067
 Y0V  H8   H  HCR5  0   0.247   0.7891   4.5328  -1.3875
 Y0V  H9   H  HCR5  0   0.247   0.4934   4.5936   1.3135
 Y0V  H10  H  HCR5  0   0.286   0.0878   2.0279   2.0782

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
 Y0V  C2   C1   aromatic  1.393  0.020  1.393
 Y0V  C11  C1   single    1.475  0.020  1.475
 Y0V  C1   C6   aromatic  1.407  0.020  1.407
 Y0V  C5   I1   single    2.089  0.020  2.089
 Y0V  C4   N1   single    1.404  0.020  1.404
 Y0V  N1   C7   aromatic  1.369  0.020  1.369
 Y0V  N1   C10  aromatic  1.369  0.020  1.369
 Y0V  C11  O1   single    1.312  0.020  1.312
 Y0V  O1   HO1  single    0.850  0.020  0.980
 Y0V  C2   C3   aromatic  1.378  0.020  1.378
 Y0V  C2   H2   single    0.930  0.020  1.080
 Y0V  I2   C3   single    2.095  0.020  2.095
 Y0V  C6   O2   single    1.320  0.020  1.320
 Y0V  O2   HO2  single    0.850  0.020  0.980
 Y0V  C3   C4   aromatic  1.398  0.020  1.398
 Y0V  O3   C11  double    1.219  0.020  1.219
 Y0V  C4   C5   aromatic  1.387  0.020  1.387
 Y0V  C6   C5   aromatic  1.401  0.020  1.401
 Y0V  C7   C8   aromatic  1.368  0.020  1.368
 Y0V  C7   H7   single    0.930  0.020  1.080
 Y0V  C8   C9   aromatic  1.421  0.020  1.421
 Y0V  C8   H8   single    0.930  0.020  1.080
 Y0V  C10  C9   aromatic  1.368  0.020  1.368
 Y0V  C9   H9   single    0.930  0.020  1.080
 Y0V  C10  H10  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
 Y0V  C11  C1   C6   118.55  3.000
 Y0V  C6   C1   C2   120.13  3.000
 Y0V  C11  C1   C2   121.32  3.000
 Y0V  C10  N1   C7   109.72  3.000
 Y0V  C10  N1   C4   125.15  3.000
 Y0V  C7   N1   C4   125.12  3.000
 Y0V  HO1  O1   C11  110.73  3.000
 Y0V  H2   C2   C3   119.93  3.000
 Y0V  H2   C2   C1   119.49  3.000
 Y0V  C3   C2   C1   120.58  3.000
 Y0V  HO2  O2   C6   108.34  3.000
 Y0V  C4   C3   I2   120.22  3.000
 Y0V  C4   C3   C2   120.15  3.000
 Y0V  I2   C3   C2   119.63  3.000
 Y0V  C5   C4   C3   119.57  3.000
 Y0V  C5   C4   N1   120.15  3.000
 Y0V  C3   C4   N1   120.28  3.000
 Y0V  C6   C5   C4   121.11  3.000
 Y0V  C6   C5   I1   118.43  3.000
 Y0V  C4   C5   I1   120.46  3.000
 Y0V  C5   C6   O2   118.43  3.000
 Y0V  C5   C6   C1   118.47  3.000
 Y0V  O2   C6   C1   123.10  3.000
 Y0V  H7   C7   C8   131.29  3.000
 Y0V  H7   C7   N1   120.99  3.000
 Y0V  C8   C7   N1   107.71  3.000
 Y0V  H8   C8   C9   126.97  3.000
 Y0V  H8   C8   C7   125.60  3.000
 Y0V  C9   C8   C7   107.42  3.000
 Y0V  H9   C9   C10  125.61  3.000
 Y0V  H9   C9   C8   126.96  3.000
 Y0V  C10  C9   C8   107.42  3.000
 Y0V  H10  C10  C9   131.29  3.000
 Y0V  H10  C10  N1   120.99  3.000
 Y0V  C9   C10  N1   107.72  3.000
 Y0V  O3   C11  O1   123.19  3.000
 Y0V  O3   C11  C1   122.62  3.000
 Y0V  O1   C11  C1   114.19  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
 Y0V  CONST_01  C4   C3   C2   C1    0.00   0.0  0
 Y0V  CONST_02  C4   C5   C6   C1    0.00   0.0  0
 Y0V  CONST_03  C2   C3   C4   N1  180.00   0.0  0
 Y0V  CONST_04  C6   C5   C4   N1  180.00   0.0  0
 Y0V  CONST_05  C9   C8   C7   N1    0.00   0.0  0
 Y0V  CONST_06  C8   C9   C10  N1    0.00   0.0  0
 Y0V  CONST_07  C5   C6   C1   C2    0.00   0.0  0
 Y0V  CONST_08  C5   C4   C3   C2    0.00   0.0  0
 Y0V  CONST_09  C6   C1   C2   C3    0.00   0.0  0
 Y0V  CONST_12  C6   C5   C4   C3    0.00   0.0  0
 Y0V  CONST_13  C8   C7   N1   C4  180.00   0.0  0
 Y0V  CONST_14  C9   C10  N1   C4  180.00   0.0  0
 Y0V  CONST_17  C9   C10  N1   C7    0.00   0.0  0
 Y0V  CONST_18  C10  C9   C8   C7    0.00   0.0  0
 Y0V  CONST_19  C10  N1   C7   C8    0.00   0.0  0
 Y0V  CONST_20  I2   C3   C2   C1  180.00   0.0  0
 Y0V  CONST_21  I1   C5   C6   C1  180.00   0.0  0
 Y0V  CONST_22  N1   C4   C5   I1    0.00   0.0  0
 Y0V  CONST_23  C3   C4   C5   I1  180.00   0.0  0
 Y0V  CONST_24  I2   C3   C4   N1    0.00   0.0  0
 Y0V  CONST_25  O2   C6   C1   C2  180.00   0.0  0
 Y0V  CONST_26  C5   C4   C3   I2  180.00   0.0  0
 Y0V  CONST_27  C4   C5   C6   O2  180.00   0.0  0
 Y0V  CONST_28  C11  C1   C2   C3  180.00   0.0  0
 Y0V  CONST_29  C11  C1   C6   C5  180.00   0.0  0
 Y0V  CONST_30  H8   C8   C7   N1  180.00   0.0  0
 Y0V  CONST_31  H9   C9   C10  N1  180.00   0.0  0
 Y0V  CONST_32  H7   C7   N1   C4    0.00   0.0  0
 Y0V  CONST_33  H10  C10  N1   C4    0.00   0.0  0
 Y0V  CONST_34  H2   C2   C3   C4  180.00   0.0  0
 Y0V  CONST_35  HO1  O1   C11  C1  180.00   0.0  0
 Y0V  Var_01    C2   C1   C11  O1    0.41  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
 Y0V  plan-1  N1   0.020
 Y0V  plan-1  C4   0.020
 Y0V  plan-1  C7   0.020
 Y0V  plan-1  C8   0.020
 Y0V  plan-1  C9   0.020
 Y0V  plan-1  C10  0.020
 Y0V  plan-1  H7   0.020
 Y0V  plan-1  H8   0.020
 Y0V  plan-1  H9   0.020
 Y0V  plan-1  H10  0.020
 Y0V  plan-2  C1   0.020
 Y0V  plan-2  I1   0.020
 Y0V  plan-2  N1   0.020
 Y0V  plan-2  C2   0.020
 Y0V  plan-2  I2   0.020
 Y0V  plan-2  O2   0.020
 Y0V  plan-2  C3   0.020
 Y0V  plan-2  C4   0.020
 Y0V  plan-2  C5   0.020
 Y0V  plan-2  C6   0.020
 Y0V  plan-2  C11  0.020
 Y0V  plan-2  H2   0.020
 Y0V  plan-3  C1   0.020
 Y0V  plan-3  O1   0.020
 Y0V  plan-3  O3   0.020
 Y0V  plan-3  C11  0.020
 Y0V  plan-3  HO1  0.020

