# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:19:54 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cc(I)c(Oc2cc(I)c(O)c(I)c2)c(I)c1
#
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
 T4A  T4A  '[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]acetic acid'  ligand  29  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4A
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
 T4A  C1    C  CR6    0   0.178   0.0794  -0.5239   4.1797
 T4A  C2    C  CR16   0  -0.297   1.2496  -0.1644   3.5199
 T4A  C3    C  CR6    0  -0.276   1.2011   0.4553   2.2800
 T4A  C4    C  CR6    0   0.390  -0.0146   0.7328   1.6696
 T4A  C5    C  CR6    0  -0.285  -1.1842   0.3706   2.3317
 T4A  C6    C  CR16   0  -0.280  -1.1421  -0.2412   3.5718
 T4A  C7    C  CH2    0  -0.690   0.1285  -1.1714   5.5248
 T4A  C8    C  C      0   0.428  -0.2356  -0.2246   6.7013
 T4A  C1'   C  CR6    0   0.372  -0.0203   0.6306  -0.6776
 T4A  C6'   C  CR16   0  -0.289   0.0105   1.3484  -1.8653
 T4A  C5'   C  CR6    0  -0.331   0.0515   0.6691  -3.0666
 T4A  C4'   C  CR6    0   0.465   0.0639  -0.7284  -3.1331
 T4A  C3'   C  CR6    0  -0.343   0.0299  -1.4129  -1.9189
 T4A  C2'   C  CR16   0  -0.295  -0.0113  -0.7524  -0.6969
 T4A  I3    I  I      0   0.096   2.9823   1.0010   1.3170
 T4A  I5    I  I      0   0.093  -3.0344   0.7857   1.4346
 T4A  I5'   I  I      0   0.098   0.0988   1.7645  -4.8537
 T4A  I3'   I  I      0   0.105   0.0350  -3.5168  -1.8997
 T4A  O8    O  O      0  -0.592  -0.8770   0.8045   6.4306
 T4A  O9    O  OC    -1  -0.614   0.1314  -0.6143   7.8250
 T4A  O4    O  O2     0  -0.489  -0.0643   1.3726   0.4706
 T4A  O4'   O  OH1    0  -0.597   0.1071  -1.2939  -4.3427
 T4A  H21   H  HCR6   0   0.280   2.2052  -0.3731   3.9831
 T4A  H61   H  HCR6   0   0.277  -2.0610  -0.5200   4.0691
 T4A  H71   H  HCH2   0   0.248   1.1151  -1.6046   5.6994
 T4A  H72   H  HCH2   0   0.261  -0.5800  -2.0062   5.5549
 T4A  H6'1  H  HCR6   0   0.302   0.0044   2.4298  -1.8359
 T4A  H2'1  H  HCR6   0   0.310  -0.0369  -1.3252   0.2203
 T4A  H4'O  H  HOH1   0   0.478   0.1124  -2.2587  -4.2986

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
 T4A  C1   C2    aromatic  1.391  0.020  1.391
 T4A  C1   C6    aromatic  1.393  0.020  1.393
 T4A  C1   C7    single    1.494  0.020  1.494
 T4A  C2   C3    aromatic  1.387  0.020  1.387
 T4A  C2   H21   single    0.930  0.020  1.080
 T4A  C3   C4    aromatic  1.388  0.020  1.388
 T4A  C3   I3    single    2.097  0.020  2.097
 T4A  C4   C5    aromatic  1.392  0.020  1.392
 T4A  C4   O4    single    1.360  0.020  1.360
 T4A  C5   C6    aromatic  1.383  0.020  1.383
 T4A  C5   I5    single    2.098  0.020  2.098
 T4A  C6   H61   single    0.930  0.020  1.080
 T4A  C7   C8    single    1.553  0.020  1.553
 T4A  C7   H71   single    0.970  0.020  1.090
 T4A  C7   H72   single    0.970  0.020  1.090
 T4A  C8   O8    deloc     1.242  0.020  1.242
 T4A  C8   O9    deloc     1.245  0.020  1.245
 T4A  C1'  C6'   aromatic  1.388  0.020  1.388
 T4A  C1'  C2'   aromatic  1.383  0.020  1.383
 T4A  C1'  O4    single    1.368  0.020  1.368
 T4A  C6'  C5'   aromatic  1.381  0.020  1.381
 T4A  C6'  H6'1  single    0.930  0.020  1.080
 T4A  C5'  C4'   aromatic  1.399  0.020  1.399
 T4A  C5'  I5'   single    2.097  0.020  2.097
 T4A  C4'  C3'   aromatic  1.394  0.020  1.394
 T4A  C4'  O4'   single    1.336  0.020  1.336
 T4A  C3'  C2'   aromatic  1.390  0.020  1.390
 T4A  C3'  I3'   single    2.104  0.020  2.104
 T4A  C2'  H2'1  single    0.930  0.020  1.080
 T4A  O4'  H4'O  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
 T4A  C7    C1   C6   120.64  3.000
 T4A  C7    C1   C2   120.78  3.000
 T4A  C6    C1   C2   118.57  3.000
 T4A  H21   C2   C3   119.98  3.000
 T4A  H21   C2   C1   119.35  3.000
 T4A  C3    C2   C1   120.68  3.000
 T4A  I3    C3   C4   119.33  3.000
 T4A  I3    C3   C2   119.81  3.000
 T4A  C4    C3   C2   120.86  3.000
 T4A  O4    C4   C5   120.74  3.000
 T4A  O4    C4   C3   120.91  3.000
 T4A  C5    C4   C3   118.33  3.000
 T4A  I5    C5   C6   119.85  3.000
 T4A  I5    C5   C4   119.09  3.000
 T4A  C6    C5   C4   121.06  3.000
 T4A  H61   C6   C5   120.03  3.000
 T4A  H61   C6   C1   119.47  3.000
 T4A  C5    C6   C1   120.50  3.000
 T4A  H72   C7   H71  106.13  3.000
 T4A  H72   C7   C8   106.99  3.000
 T4A  H71   C7   C8   109.42  3.000
 T4A  H72   C7   C1   109.51  3.000
 T4A  H71   C7   C1   110.23  3.000
 T4A  C8    C7   C1   114.21  3.000
 T4A  O9    C8   O8   127.46  3.000
 T4A  O9    C8   C7   115.08  3.000
 T4A  O8    C8   C7   117.44  3.000
 T4A  O4    C1'  C2'  123.67  3.000
 T4A  O4    C1'  C6'  116.00  3.000
 T4A  C2'   C1'  C6'  120.33  3.000
 T4A  H6'1  C6'  C5'  121.04  3.000
 T4A  H6'1  C6'  C1'  119.58  3.000
 T4A  C5'   C6'  C1'  119.39  3.000
 T4A  I5'   C5'  C4'  118.76  3.000
 T4A  I5'   C5'  C6'  119.03  3.000
 T4A  C4'   C5'  C6'  122.21  3.000
 T4A  O4'   C4'  C3'  125.56  3.000
 T4A  O4'   C4'  C5'  117.78  3.000
 T4A  C3'   C4'  C5'  116.66  3.000
 T4A  I3'   C3'  C2'  117.86  3.000
 T4A  I3'   C3'  C4'  119.92  3.000
 T4A  C2'   C3'  C4'  122.22  3.000
 T4A  H2'1  C2'  C3'  119.64  3.000
 T4A  H2'1  C2'  C1'  121.17  3.000
 T4A  C3'   C2'  C1'  119.19  3.000
 T4A  C1'   O4   C4   118.93  3.000
 T4A  H4'O  O4'  C4'  112.44  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
 T4A  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 T4A  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 T4A  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 T4A  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 T4A  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 T4A  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 T4A  CONST_07  C4'   C5'  C6'  C1'     0.00   0.0  0
 T4A  CONST_08  C4'   C3'  C2'  C1'     0.00   0.0  0
 T4A  CONST_09  C3'   C2'  C1'  C6'     0.00   0.0  0
 T4A  CONST_10  C3'   C4'  C5'  C6'     0.00   0.0  0
 T4A  CONST_11  C2'   C1'  C6'  C5'     0.00   0.0  0
 T4A  CONST_12  C2'   C3'  C4'  C5'     0.00   0.0  0
 T4A  CONST_13  I3    C3   C2   C1    180.00   0.0  0
 T4A  CONST_14  I5    C5   C6   C1    180.00   0.0  0
 T4A  CONST_15  O4    C4   C3   C2    180.00   0.0  0
 T4A  CONST_16  C7    C1   C2   C3    180.00   0.0  0
 T4A  CONST_17  I5    C5   C4   C3    180.00   0.0  0
 T4A  CONST_18  I3    C3   C4   C5    180.00   0.0  0
 T4A  CONST_19  C7    C1   C6   C5    180.00   0.0  0
 T4A  CONST_20  O4    C4   C5   C6    180.00   0.0  0
 T4A  CONST_21  I5'   C5'  C6'  C1'   180.00   0.0  0
 T4A  CONST_22  I3'   C3'  C2'  C1'   180.00   0.0  0
 T4A  CONST_23  O4'   C4'  C5'  C6'   180.00   0.0  0
 T4A  CONST_24  O4    C1'  C6'  C5'   180.00   0.0  0
 T4A  CONST_25  I3'   C3'  C4'  C5'   180.00   0.0  0
 T4A  CONST_26  I5'   C5'  C4'  C3'   180.00   0.0  0
 T4A  CONST_27  O4    C1'  C2'  C3'   180.00   0.0  0
 T4A  CONST_28  O4'   C4'  C3'  C2'   180.00   0.0  0
 T4A  CONST_29  H61   C6   C1   C2    180.00   0.0  0
 T4A  CONST_30  H21   C2   C3   C4    180.00   0.0  0
 T4A  CONST_31  H2'1  C2'  C1'  C6'   180.00   0.0  0
 T4A  CONST_32  H6'1  C6'  C5'  C4'   180.00   0.0  0
 T4A  Var_01    C6'   C1'  O4   C4   -176.07  30.0  3
 T4A  Var_02    C8    C7   C1   C2    103.97  30.0  2
 T4A  Var_03    O8    C8   C7   C1     19.88  30.0  3

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
 T4A  plan-1  C1    0.020
 T4A  plan-1  C2    0.020
 T4A  plan-1  C3    0.020
 T4A  plan-1  C4    0.020
 T4A  plan-1  C5    0.020
 T4A  plan-1  C6    0.020
 T4A  plan-1  C7    0.020
 T4A  plan-1  I3    0.020
 T4A  plan-1  I5    0.020
 T4A  plan-1  O4    0.020
 T4A  plan-1  H21   0.020
 T4A  plan-1  H61   0.020
 T4A  plan-2  C1'   0.020
 T4A  plan-2  C6'   0.020
 T4A  plan-2  C5'   0.020
 T4A  plan-2  C4'   0.020
 T4A  plan-2  C3'   0.020
 T4A  plan-2  C2'   0.020
 T4A  plan-2  I5'   0.020
 T4A  plan-2  I3'   0.020
 T4A  plan-2  O4    0.020
 T4A  plan-2  O4'   0.020
 T4A  plan-2  H6'1  0.020
 T4A  plan-2  H2'1  0.020
 T4A  plan-3  C7    0.020
 T4A  plan-3  C8    0.020
 T4A  plan-3  O8    0.020
 T4A  plan-3  O9    0.020

