# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:45:19 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-[2,4,5,7-tetrakis(iodanyl)-3-oxidanyl-6-oxidanylidene-xanthen-9-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1C2=C3C=C(I)C(=O)C(=C3Oc4c(I)c(O)c(I)cc24)I
#
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
 9ZZ  9ZZ  '2-[2,4,5,7-tetrakis(iodanyl)-3-oxidanyl-6-oxidanylidene-xanthen-9-yl]benzoic acid'  ligand  36  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9ZZ
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
 9ZZ  O3   O  OC    -1  -0.565  -0.2094  -4.0265   3.2063
 9ZZ  C4   C  CR66   0   0.499   1.1506   0.5550  -0.0068
 9ZZ  C5   C  CR6    0  -0.522   2.3407   1.2647   0.0724
 9ZZ  O4   O  O      0  -0.555  -0.1271  -2.0028   2.2651
 9ZZ  C6   C  CR6    0   0.497   3.5574   0.5848   0.1405
 9ZZ  C7   C  CR6    0  -0.372   3.5414  -0.8247   0.1218
 9ZZ  C8   C  CR16   0  -0.297   2.3569  -1.5156   0.0518
 9ZZ  C9   C  CR66   0   0.035   1.1350  -0.8410  -0.0137
 9ZZ  C10  C  CR6    0  -0.611  -2.2886   1.4567  -0.3334
 9ZZ  C11  C  CR6    0   0.492  -3.6187   0.9079  -0.4822
 9ZZ  C12  C  CR6    0   0.298  -0.1278  -1.5176  -0.0701
 9ZZ  C13  C  CR6    0  -0.054  -0.1630  -2.9881  -0.2473
 9ZZ  C14  C  CR16   0  -0.275  -0.1731  -3.4952  -1.5435
 9ZZ  C15  C  CR16   0  -0.246  -0.1936  -4.8669  -1.7490
 9ZZ  C    C  CR6    0  -0.410  -3.6634  -0.5561  -0.4786
 9ZZ  O    O  O      0  -0.460   0.0144   1.2603  -0.0796
 9ZZ  C1   C  CR16   0  -0.252  -2.5679  -1.3334  -0.3578
 9ZZ  C16  C  CR16   0  -0.244  -0.2069  -5.7306  -0.6611
 9ZZ  C17  C  CR16   0  -0.289  -0.2002  -5.2202   0.6282
 9ZZ  C18  C  CR6    0  -0.097  -0.1761  -3.8482   0.8474
 9ZZ  C19  C  C      0   0.425  -0.1720  -3.2530   2.2393
 9ZZ  C2   C  CR66   0  -0.056  -1.2704  -0.7569  -0.2265
 9ZZ  C3   C  CR66   0   0.547  -1.1830   0.6660  -0.2122
 9ZZ  I    I  I      0   0.062  -5.5655  -1.4105  -0.6761
 9ZZ  I3   I  I      0   0.080  -2.1319   3.5375  -0.3258
 9ZZ  O1   O  OH1    0  -0.573   4.6562   1.3175   0.2150
 9ZZ  O2   O  O      0  -0.446  -4.6242   1.5980  -0.6037
 9ZZ  H1   H  HCR6   0   0.297   2.3571  -2.5968   0.0457
 9ZZ  H2   H  HCR6   0   0.263  -0.1636  -2.8192  -2.3896
 9ZZ  H3   H  HCR6   0   0.265  -0.2009  -5.2586  -2.7577
 9ZZ  H    H  HCR6   0   0.292  -2.6478  -2.4118  -0.3544
 9ZZ  H4   H  HCR6   0   0.261  -0.2253  -6.8009  -0.8198
 9ZZ  H5   H  HCR6   0   0.257  -0.2160  -5.8894   1.4781
 9ZZ  HO1  H  HOH1   0   0.483   5.4619   0.7834   0.2529
 9ZZ  I1   I  I      0   0.146   2.3236   3.3503   0.0860
 9ZZ  I2   I  I      0   0.125   5.3432  -1.9010   0.2051

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
 9ZZ  O2   C11  double    1.226  0.020  1.226
 9ZZ  I3   C10  single    2.087  0.020  2.087
 9ZZ  I    C    single    2.095  0.020  2.095
 9ZZ  C11  C10  single    1.447  0.020  1.447
 9ZZ  C11  C    single    1.465  0.020  1.465
 9ZZ  C10  C3   double    1.365  0.020  1.365
 9ZZ  C    C1   double    1.349  0.020  1.349
 9ZZ  C3   O    single    1.343  0.020  1.343
 9ZZ  C3   C2   single    1.426  0.020  1.426
 9ZZ  O    C4   single    1.339  0.020  1.339
 9ZZ  C1   C2   single    1.426  0.020  1.426
 9ZZ  I1   C5   single    2.086  0.020  2.086
 9ZZ  C2   C12  double    1.381  0.020  1.381
 9ZZ  C4   C5   aromatic  1.388  0.020  1.388
 9ZZ  C4   C9   aromatic  1.396  0.020  1.396
 9ZZ  C5   C6   aromatic  1.395  0.020  1.395
 9ZZ  C12  C9   single    1.434  0.020  1.434
 9ZZ  C12  C13  single    1.482  0.020  1.482
 9ZZ  C9   C8   aromatic  1.397  0.020  1.397
 9ZZ  C14  C13  aromatic  1.392  0.020  1.392
 9ZZ  C14  C15  aromatic  1.387  0.020  1.387
 9ZZ  C13  C18  aromatic  1.392  0.020  1.392
 9ZZ  C6   O1   single    1.323  0.020  1.323
 9ZZ  C6   C7   aromatic  1.410  0.020  1.410
 9ZZ  C15  C16  aromatic  1.389  0.020  1.389
 9ZZ  C8   C7   aromatic  1.373  0.020  1.373
 9ZZ  C7   I2   single    2.100  0.020  2.100
 9ZZ  O3   C19  deloc     1.239  0.020  1.239
 9ZZ  C18  C19  single    1.514  0.020  1.514
 9ZZ  C18  C17  aromatic  1.390  0.020  1.390
 9ZZ  C16  C17  aromatic  1.387  0.020  1.387
 9ZZ  C19  O4   deloc     1.251  0.020  1.251
 9ZZ  C8   H1   single    0.930  0.020  1.080
 9ZZ  C14  H2   single    0.930  0.020  1.080
 9ZZ  C15  H3   single    0.930  0.020  1.080
 9ZZ  C1   H    single    0.930  0.020  1.080
 9ZZ  C16  H4   single    0.930  0.020  1.080
 9ZZ  C17  H5   single    0.930  0.020  1.080
 9ZZ  O1   HO1  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
 9ZZ  O    C4   C9   121.12  3.000
 9ZZ  C9   C4   C5   121.41  3.000
 9ZZ  O    C4   C5   117.47  3.000
 9ZZ  I1   C5   C6   119.61  3.000
 9ZZ  C6   C5   C4   120.08  3.000
 9ZZ  I1   C5   C4   120.31  3.000
 9ZZ  O1   C6   C7   124.34  3.000
 9ZZ  C7   C6   C5   118.46  3.000
 9ZZ  O1   C6   C5   117.20  3.000
 9ZZ  I2   C7   C8   118.96  3.000
 9ZZ  I2   C7   C6   120.13  3.000
 9ZZ  C8   C7   C6   120.90  3.000
 9ZZ  H1   C8   C9   118.87  3.000
 9ZZ  H1   C8   C7   120.21  3.000
 9ZZ  C9   C8   C7   120.92  3.000
 9ZZ  C12  C9   C8   122.97  3.000
 9ZZ  C8   C9   C4   118.21  3.000
 9ZZ  C12  C9   C4   118.81  3.000
 9ZZ  I3   C10  C3   121.11  3.000
 9ZZ  C3   C10  C11  122.29  3.000
 9ZZ  I3   C10  C11  116.60  3.000
 9ZZ  O2   C11  C    122.55  3.000
 9ZZ  C    C11  C10  114.02  3.000
 9ZZ  O2   C11  C10  123.43  3.000
 9ZZ  C2   C12  C13  120.89  3.000
 9ZZ  C13  C12  C9   119.60  3.000
 9ZZ  C2   C12  C9   118.23  3.000
 9ZZ  C18  C13  C14  120.47  3.000
 9ZZ  C18  C13  C12  121.29  3.000
 9ZZ  C14  C13  C12  118.24  3.000
 9ZZ  H2   C14  C15  120.11  3.000
 9ZZ  H2   C14  C13  120.00  3.000
 9ZZ  C15  C14  C13  119.89  3.000
 9ZZ  H3   C15  C16  120.32  3.000
 9ZZ  H3   C15  C14  119.75  3.000
 9ZZ  C16  C15  C14  119.93  3.000
 9ZZ  I    C    C1   120.73  3.000
 9ZZ  C1   C    C11  123.47  3.000
 9ZZ  I    C    C11  115.80  3.000
 9ZZ  C3   O    C4   121.91  3.000
 9ZZ  H    C1   C2   118.04  3.000
 9ZZ  H    C1   C    121.00  3.000
 9ZZ  C2   C1   C    120.96  3.000
 9ZZ  H4   C16  C17  120.03  3.000
 9ZZ  H4   C16  C15  120.02  3.000
 9ZZ  C17  C16  C15  119.95  3.000
 9ZZ  H5   C17  C18  119.15  3.000
 9ZZ  H5   C17  C16  120.18  3.000
 9ZZ  C18  C17  C16  120.67  3.000
 9ZZ  C19  C18  C17  122.23  3.000
 9ZZ  C17  C18  C13  119.08  3.000
 9ZZ  C19  C18  C13  118.68  3.000
 9ZZ  C18  C19  O4   114.33  3.000
 9ZZ  O4   C19  O3   127.50  3.000
 9ZZ  C18  C19  O3   118.17  3.000
 9ZZ  C3   C2   C1   117.40  3.000
 9ZZ  C1   C2   C12  122.71  3.000
 9ZZ  C3   C2   C12  119.85  3.000
 9ZZ  C2   C3   O    119.81  3.000
 9ZZ  C2   C3   C10  121.86  3.000
 9ZZ  O    C3   C10  118.33  3.000
 9ZZ  HO1  O1   C6   112.84  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
 9ZZ  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 9ZZ  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 9ZZ  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 9ZZ  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 9ZZ  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 9ZZ  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 9ZZ  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 9ZZ  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 9ZZ  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 9ZZ  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 9ZZ  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 9ZZ  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 9ZZ  CONST_13  C15  C14  C13  C12   180.00   0.0  0
 9ZZ  CONST_14  C17  C18  C13  C12   180.00   0.0  0
 9ZZ  CONST_15  O1   C6   C5   C4    180.00   0.0  0
 9ZZ  CONST_16  I2   C7   C6   C5    180.00   0.0  0
 9ZZ  CONST_17  I1   C5   C6   C7    180.00   0.0  0
 9ZZ  CONST_18  O1   C6   C7   C8    180.00   0.0  0
 9ZZ  CONST_19  I1   C5   C4   C9    180.00   0.0  0
 9ZZ  CONST_20  I2   C7   C8   C9    180.00   0.0  0
 9ZZ  CONST_21  C19  C18  C13  C12     0.00   0.0  0
 9ZZ  CONST_22  C19  C18  C13  C14   180.00   0.0  0
 9ZZ  CONST_23  I1   C5   C4   O       0.00   0.0  0
 9ZZ  CONST_24  C19  C18  C17  C16   180.00   0.0  0
 9ZZ  CONST_25  H1   C8   C9   C4    180.00   0.0  0
 9ZZ  CONST_26  H2   C14  C13  C12     0.00   0.0  0
 9ZZ  CONST_27  H3   C15  C14  C13   180.00   0.0  0
 9ZZ  CONST_28  H5   C17  C18  C13   180.00   0.0  0
 9ZZ  CONST_29  H4   C16  C15  C14   180.00   0.0  0
 9ZZ  Var_01    C10  C3   O    C4   -177.40  30.0  1
 9ZZ  Var_02    C2   C12  C9   C4      5.25  30.0  1
 9ZZ  Var_03    C3   C2   C12  C9     -5.35  30.0  1
 9ZZ  Var_04    C14  C13  C12  C9    -88.59  30.0  2
 9ZZ  Var_05    C13  C18  C19  O3    178.65  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
 9ZZ  plan-1  C12  0.020
 9ZZ  plan-1  C13  0.020
 9ZZ  plan-1  C14  0.020
 9ZZ  plan-1  C15  0.020
 9ZZ  plan-1  C16  0.020
 9ZZ  plan-1  C17  0.020
 9ZZ  plan-1  C18  0.020
 9ZZ  plan-1  C19  0.020
 9ZZ  plan-1  H2   0.020
 9ZZ  plan-1  H3   0.020
 9ZZ  plan-1  H4   0.020
 9ZZ  plan-1  H5   0.020
 9ZZ  plan-2  C4   0.020
 9ZZ  plan-2  C5   0.020
 9ZZ  plan-2  C6   0.020
 9ZZ  plan-2  C7   0.020
 9ZZ  plan-2  C8   0.020
 9ZZ  plan-2  C9   0.020
 9ZZ  plan-2  C12  0.020
 9ZZ  plan-2  O    0.020
 9ZZ  plan-2  O1   0.020
 9ZZ  plan-2  H1   0.020
 9ZZ  plan-2  I1   0.020
 9ZZ  plan-2  I2   0.020
 9ZZ  plan-3  C10  0.020
 9ZZ  plan-3  C11  0.020
 9ZZ  plan-3  C12  0.020
 9ZZ  plan-3  C    0.020
 9ZZ  plan-3  O    0.020
 9ZZ  plan-3  C1   0.020
 9ZZ  plan-3  C2   0.020
 9ZZ  plan-3  C3   0.020
 9ZZ  plan-3  I    0.020
 9ZZ  plan-3  I3   0.020
 9ZZ  plan-3  O2   0.020
 9ZZ  plan-3  H    0.020
 9ZZ  plan-4  O3   0.020
 9ZZ  plan-4  O4   0.020
 9ZZ  plan-4  C18  0.020
 9ZZ  plan-4  C19  0.020

