# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:05:26 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (2S)-2-(3-hydroxy-2,4,6-triiodobenzyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](Cc1c(I)cc(I)c(O)c1I)C(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
 IO3  IO3  '(2S)-2-(3-hydroxy-2,4,6-triiodobenzyl)butanoic acid'  ligand  27  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IO3
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
 IO3  I1   I  I      0   0.066   1.1037   3.1378  -0.6189
 IO3  I2   I  I      0   0.092  -4.1589   0.5013   0.2207
 IO3  I3   I  I      0   0.094   0.6417  -3.0043  -0.5852
 IO3  O1   O  OH1    0  -0.594  -2.3608  -1.9987  -0.0728
 IO3  O2   O  O      0  -0.607   3.4759  -1.9687   1.4284
 IO3  O3   O  OC    -1  -0.612   1.8420  -0.8345   2.4315
 IO3  C1   C  CR6    0   0.255   0.6835   0.0730  -0.4908
 IO3  C2   C  CR6    0  -0.316   0.0481   1.3165  -0.4095
 IO3  C3   C  CR16   0  -0.177  -1.3172   1.4422  -0.2071
 IO3  C4   C  CR6    0  -0.358  -2.0944   0.3089  -0.0871
 IO3  C5   C  CR6    0   0.497  -1.5300  -0.9631  -0.1806
 IO3  C6   C  CR6    0  -0.406  -0.1465  -1.0508  -0.3872
 IO3  C8   C  CH1    0  -0.313   2.9725   0.2146   0.6180
 IO3  C9   C  C      0   0.433   2.7497  -0.9675   1.5870
 IO3  C10  C  CH2    0  -0.405   4.4413   0.4397   0.2752
 IO3  C11  C  CH3    0  -0.670   5.2981   0.7717   1.4887
 IO3  H1   H  HOH1   0   0.475  -1.9028  -2.8500  -0.0855
 IO3  H3   H  HCR6   0   0.299  -1.7768   2.4183  -0.1444
 IO3  H4   H  HCH2   0   0.260   2.4575  -0.9797  -1.1005
 IO3  H5   H  HCH2   0   0.259   2.4734   0.7233  -1.4230
 IO3  H6   H  HCH1   0   0.210   2.5923   1.1215   1.0983
 IO3  H7   H  HCH2   0   0.207   4.8367  -0.4488  -0.2234
 IO3  H8   H  HCH2   0   0.206   4.5159   1.2586  -0.4480
 IO3  H9   H  HCH3   0   0.211   4.9326   1.6657   1.9987
 IO3  H10  H  HCH3   0   0.221   5.2993  -0.0462   2.2089
 IO3  H11  H  HCH3   0   0.222   6.3337   0.9600   1.2019
 IO3  C7   C  CH2    0  -0.548   2.1718  -0.0169  -0.6778

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
 IO3  O2   C9   deloc     1.247  0.020  1.247
 IO3  O3   C9   deloc     1.247  0.020  1.247
 IO3  C9   C8   single    1.545  0.020  1.545
 IO3  C11  C10  single    1.522  0.020  1.522
 IO3  C10  C8   single    1.525  0.020  1.525
 IO3  C8   C7   single    1.541  0.020  1.541
 IO3  C7   C1   single    1.503  0.020  1.503
 IO3  I3   C6   single    2.116  0.020  2.116
 IO3  I1   C2   single    2.115  0.020  2.115
 IO3  C1   C6   aromatic  1.401  0.020  1.401
 IO3  C1   C2   aromatic  1.399  0.020  1.399
 IO3  C6   C5   aromatic  1.402  0.020  1.402
 IO3  C2   C3   aromatic  1.386  0.020  1.386
 IO3  C5   O1   single    1.332  0.020  1.332
 IO3  C5   C4   aromatic  1.395  0.020  1.395
 IO3  C3   C4   aromatic  1.379  0.020  1.379
 IO3  C4   I2   single    2.096  0.020  2.096
 IO3  O1   H1   single    0.850  0.020  0.980
 IO3  C3   H3   single    0.930  0.020  1.080
 IO3  C7   H4   single    0.970  0.020  1.090
 IO3  C7   H5   single    0.970  0.020  1.090
 IO3  C8   H6   single    0.970  0.020  1.090
 IO3  C10  H7   single    0.970  0.020  1.090
 IO3  C10  H8   single    0.970  0.020  1.090
 IO3  C11  H9   single    0.970  0.020  1.090
 IO3  C11  H10  single    0.970  0.020  1.090
 IO3  C11  H11  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
 IO3  H1   O1   C5   112.83  3.000
 IO3  C7   C1   C6   123.23  3.000
 IO3  C6   C1   C2   116.08  3.000
 IO3  C7   C1   C2   120.69  3.000
 IO3  C3   C2   C1   122.45  3.000
 IO3  C3   C2   I1   115.34  3.000
 IO3  C1   C2   I1   122.20  3.000
 IO3  H3   C3   C4   119.83  3.000
 IO3  H3   C3   C2   120.62  3.000
 IO3  C4   C3   C2   119.56  3.000
 IO3  C5   C4   C3   121.03  3.000
 IO3  C3   C4   I2   119.49  3.000
 IO3  C5   C4   I2   119.47  3.000
 IO3  C6   C5   C4   117.80  3.000
 IO3  C4   C5   O1   116.82  3.000
 IO3  C6   C5   O1   125.38  3.000
 IO3  C5   C6   C1   123.06  3.000
 IO3  C5   C6   I3   116.06  3.000
 IO3  C1   C6   I3   120.87  3.000
 IO3  H6   C8   C10  108.12  3.000
 IO3  H6   C8   C9   107.98  3.000
 IO3  C10  C8   C9   113.14  3.000
 IO3  H6   C8   C7   108.24  3.000
 IO3  C10  C8   C7   109.49  3.000
 IO3  C9   C8   C7   109.73  3.000
 IO3  C8   C9   O3   116.64  3.000
 IO3  C8   C9   O2   116.78  3.000
 IO3  O3   C9   O2   126.56  3.000
 IO3  H8   C10  H7   106.38  3.000
 IO3  H8   C10  C11  108.97  3.000
 IO3  H7   C10  C11  109.72  3.000
 IO3  H8   C10  C8   108.93  3.000
 IO3  H7   C10  C8   109.33  3.000
 IO3  C11  C10  C8   113.27  3.000
 IO3  H11  C11  H10  107.59  3.000
 IO3  H11  C11  H9   107.40  3.000
 IO3  H10  C11  H9   107.82  3.000
 IO3  H11  C11  C10  111.25  3.000
 IO3  H10  C11  C10  111.33  3.000
 IO3  H9   C11  C10  111.25  3.000
 IO3  H5   C7   H4   105.17  3.000
 IO3  H5   C7   C8   109.17  3.000
 IO3  H4   C7   C8   108.83  3.000
 IO3  H5   C7   C1   108.52  3.000
 IO3  H4   C7   C1   111.15  3.000
 IO3  C8   C7   C1   113.64  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
 IO3  CONST_01  C4  C5   C6   C1    0.00   0.0  0
 IO3  CONST_02  C4  C3   C2   C1    0.00   0.0  0
 IO3  CONST_03  C5  C6   C1   C2    0.00   0.0  0
 IO3  CONST_04  C5  C4   C3   C2    0.00   0.0  0
 IO3  CONST_05  C6  C1   C2   C3    0.00   0.0  0
 IO3  CONST_06  C6  C5   C4   C3    0.00   0.0  0
 IO3  CONST_07  C6  C1   C2   I1  180.00   0.0  0
 IO3  CONST_08  C4  C3   C2   I1  180.00   0.0  0
 IO3  CONST_09  C6  C5   C4   I2  180.00   0.0  0
 IO3  CONST_10  C2  C3   C4   I2  180.00   0.0  0
 IO3  CONST_11  C2  C1   C6   I3  180.00   0.0  0
 IO3  CONST_12  C4  C5   C6   I3  180.00   0.0  0
 IO3  CONST_13  C1  C6   C5   O1  180.00   0.0  0
 IO3  CONST_14  C3  C4   C5   O1  180.00   0.0  0
 IO3  CONST_15  C7  C1   C2   C3  180.00   0.0  0
 IO3  CONST_16  C7  C1   C6   C5  180.00   0.0  0
 IO3  CONST_17  H3  C3   C2   C1  180.00   0.0  0
 IO3  Var_01    C8  C7   C1   C2   78.95  30.0  3
 IO3  Var_02    H9  C11  C10  C8  -58.32  30.0  3

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
 IO3  chir_01  C8  C9  C10  C7  negativ

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
 IO3  plan-1  I1  0.020
 IO3  plan-1  I2  0.020
 IO3  plan-1  I3  0.020
 IO3  plan-1  O1  0.020
 IO3  plan-1  C1  0.020
 IO3  plan-1  C2  0.020
 IO3  plan-1  C3  0.020
 IO3  plan-1  C4  0.020
 IO3  plan-1  C5  0.020
 IO3  plan-1  C6  0.020
 IO3  plan-1  H3  0.020
 IO3  plan-1  C7  0.020
 IO3  plan-2  O2  0.020
 IO3  plan-2  O3  0.020
 IO3  plan-2  C8  0.020
 IO3  plan-2  C9  0.020

