# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:04:56 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(I)c(Oc2ccc(O)c(I)c2)c(I)c1)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
 T3  T3  O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine  ligand  34  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T3
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
 T3  C1    C  CR6    0   0.141  -0.0570  -0.8896   2.7466
 T3  C2    C  CR6    0   0.362   0.0868   1.2137  -1.7922
 T3  C3    C  CR16   0  -0.307   1.1614  -0.4968   2.1998
 T3  C4    C  CR16   0  -0.290   0.0347  -0.1373  -2.0936
 T3  C5    C  CR6    0  -0.281   1.1992   0.3523   1.1039
 T3  C6    C  CR6    0  -0.329   0.0609  -0.5354  -3.4243
 T3  C7    C  CR6    0   0.399   0.0282   0.8325   0.5300
 T3  C8    C  CR6    0   0.410   0.1375   0.3890  -4.4607
 T3  C9    C  CR6    0  -0.279  -1.1879   0.4366   1.0799
 T3  C10   C  CR16   0  -0.369   0.1859   1.7424  -4.1272
 T3  C11   C  CR16   0  -0.286  -1.2329  -0.4077   2.1756
 T3  C12   C  CR16   0  -0.310   0.1616   2.1550  -2.8087
 T3  C13   C  CH2    0  -0.535  -0.1127  -1.7517   3.9707
 T3  C15   C  CH1    0  -0.191  -0.2189  -0.9138   5.2676
 T3  C17   C  C      0   0.407  -0.3786  -1.8930   6.4510
 T3  I1    I  I      0   0.101   3.0464   0.9410   0.3062
 T3  I2    I  I      0   0.073  -0.0166  -2.5806  -3.8833
 T3  I3    I  I      0   0.099  -2.9699   1.1480   0.2349
 T3  N1    N  NH2    0  -0.794   0.9127  -0.0379   5.5092
 T3  O1    O  OH1    0  -0.615   0.1599  -0.0521  -5.7285
 T3  O2    O  O2     0  -0.491   0.0675   1.7027  -0.5101
 T3  O3    O  OC    -1  -0.610  -1.5278  -2.0648   6.8996
 T3  O4    O  O      0  -0.613   0.6665  -2.4576   6.8325
 T3  HC3   H  HCR6   0   0.285   2.0823  -0.8700   2.6281
 T3  HC4   H  HCR6   0   0.301  -0.0214  -0.8821  -1.3108
 T3  HC10  H  HCR6   0   0.288   0.2433   2.4855  -4.9139
 T3  HC11  H  HCR6   0   0.281  -2.1858  -0.7041   2.5952
 T3  HC12  H  HCR6   0   0.284   0.2016   3.2103  -2.5723
 T3  H131  H  HCH2   0   0.248   0.7796  -2.3799   4.0289
 T3  H132  H  HCH2   0   0.251  -0.9757  -2.4197   3.9049
 T3  HC15  H  HCH1   0   0.215  -1.1189  -0.2951   5.1933
 T3  HN11  H  HNH2   0   0.331   1.7451  -0.6039   5.6215
 T3  HN12  H  HNH2   0   0.340   1.0759   0.5687   4.7142
 T3  HO1   H  HOH1   0   0.482   0.2365   0.6877  -6.3420

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
 T3  C1   C3    aromatic  1.392  0.020  1.392
 T3  C1   C11   aromatic  1.393  0.020  1.393
 T3  C1   C13   single    1.498  0.020  1.498
 T3  C2   C4    aromatic  1.385  0.020  1.385
 T3  C2   C12   aromatic  1.387  0.020  1.387
 T3  C2   O2    single    1.372  0.020  1.372
 T3  C3   C5    aromatic  1.387  0.020  1.387
 T3  C3   HC3   single    0.930  0.020  1.080
 T3  C4   C6    aromatic  1.389  0.020  1.389
 T3  C4   HC4   single    0.930  0.020  1.080
 T3  C5   C7    aromatic  1.390  0.020  1.390
 T3  C5   I1    single    2.096  0.020  2.096
 T3  C6   C8    aromatic  1.391  0.020  1.391
 T3  C6   I2    single    2.098  0.020  2.098
 T3  C7   C9    aromatic  1.392  0.020  1.392
 T3  C7   O2    single    1.357  0.020  1.357
 T3  C8   C10   aromatic  1.395  0.020  1.395
 T3  C8   O1    single    1.343  0.020  1.343
 T3  C9   C11   aromatic  1.384  0.020  1.384
 T3  C9   I3    single    2.097  0.020  2.097
 T3  C10  C12   aromatic  1.382  0.020  1.382
 T3  C10  HC10  single    0.930  0.020  1.080
 T3  C11  HC11  single    0.930  0.020  1.080
 T3  C12  HC12  single    0.930  0.020  1.080
 T3  C13  C15   single    1.548  0.020  1.548
 T3  C13  H131  single    0.970  0.020  1.090
 T3  C13  H132  single    0.970  0.020  1.090
 T3  C15  C17   single    1.544  0.020  1.544
 T3  C15  N1    single    1.451  0.020  1.451
 T3  C15  HC15  single    0.970  0.020  1.090
 T3  C17  O3    deloc     1.246  0.020  1.246
 T3  C17  O4    deloc     1.248  0.020  1.248
 T3  N1   HN11  single    0.890  0.020  1.040
 T3  N1   HN12  single    0.890  0.020  1.040
 T3  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
 T3  C13   C1   C11   120.16  3.000
 T3  C13   C1   C3    121.06  3.000
 T3  C11   C1   C3    118.69  3.000
 T3  O2    C2   C12   116.33  3.000
 T3  O2    C2   C4    123.39  3.000
 T3  C12   C2   C4    120.28  3.000
 T3  HC3   C3   C5    120.05  3.000
 T3  HC3   C3   C1    119.48  3.000
 T3  C5    C3   C1    120.47  3.000
 T3  HC4   C4   C6    119.78  3.000
 T3  HC4   C4   C2    121.06  3.000
 T3  C6    C4   C2    119.16  3.000
 T3  I1    C5   C7    119.23  3.000
 T3  I1    C5   C3    119.78  3.000
 T3  C7    C5   C3    120.99  3.000
 T3  I2    C6   C8    119.15  3.000
 T3  I2    C6   C4    119.23  3.000
 T3  C8    C6   C4    121.63  3.000
 T3  O2    C7   C9    120.70  3.000
 T3  O2    C7   C5    120.92  3.000
 T3  C9    C7   C5    118.34  3.000
 T3  O1    C8   C10   122.96  3.000
 T3  O1    C8   C6    119.09  3.000
 T3  C10   C8   C6    117.95  3.000
 T3  I3    C9   C11   119.90  3.000
 T3  I3    C9   C7    119.13  3.000
 T3  C11   C9   C7    120.97  3.000
 T3  HC10  C10  C12   119.27  3.000
 T3  HC10  C10  C8    119.58  3.000
 T3  C12   C10  C8    121.15  3.000
 T3  HC11  C11  C9    120.17  3.000
 T3  HC11  C11  C1    119.30  3.000
 T3  C9    C11  C1    120.53  3.000
 T3  HC12  C12  C10   119.93  3.000
 T3  HC12  C12  C2    120.23  3.000
 T3  C10   C12  C2    119.84  3.000
 T3  H132  C13  H131  107.24  3.000
 T3  H132  C13  C15   109.09  3.000
 T3  H131  C13  C15   108.82  3.000
 T3  H132  C13  C1    109.38  3.000
 T3  H131  C13  C1    110.12  3.000
 T3  C15   C13  C1    112.07  3.000
 T3  HC15  C15  N1    108.13  3.000
 T3  HC15  C15  C17   108.99  3.000
 T3  N1    C15  C17   109.62  3.000
 T3  HC15  C15  C13   107.79  3.000
 T3  N1    C15  C13   114.38  3.000
 T3  C17   C15  C13   107.82  3.000
 T3  O4    C17  O3    126.90  3.000
 T3  O4    C17  C15   115.76  3.000
 T3  O3    C17  C15   117.31  3.000
 T3  HN12  N1   HN11  106.81  3.000
 T3  HN12  N1   C15   110.87  3.000
 T3  HN11  N1   C15   108.78  3.000
 T3  HO1   O1   C8    110.49  3.000
 T3  C7    O2   C2    119.21  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
 T3  CONST_01  C7    C5   C3   C1      0.00   0.0  0
 T3  CONST_02  C7    C9   C11  C1      0.00   0.0  0
 T3  CONST_03  C8    C6   C4   C2      0.00   0.0  0
 T3  CONST_04  C8    C10  C12  C2      0.00   0.0  0
 T3  CONST_05  C9    C11  C1   C3      0.00   0.0  0
 T3  CONST_06  C9    C7   C5   C3      0.00   0.0  0
 T3  CONST_07  C10   C12  C2   C4      0.00   0.0  0
 T3  CONST_08  C10   C8   C6   C4      0.00   0.0  0
 T3  CONST_09  C11   C1   C3   C5      0.00   0.0  0
 T3  CONST_10  C11   C9   C7   C5      0.00   0.0  0
 T3  CONST_11  C12   C2   C4   C6      0.00   0.0  0
 T3  CONST_12  C12   C10  C8   C6      0.00   0.0  0
 T3  CONST_13  I1    C5   C3   C1    180.00   0.0  0
 T3  CONST_14  I3    C9   C11  C1    180.00   0.0  0
 T3  CONST_15  I2    C6   C4   C2    180.00   0.0  0
 T3  CONST_16  O2    C7   C5   C3    180.00   0.0  0
 T3  CONST_17  O1    C8   C6   C4    180.00   0.0  0
 T3  CONST_18  C13   C1   C3   C5    180.00   0.0  0
 T3  CONST_19  I3    C9   C7   C5    180.00   0.0  0
 T3  CONST_20  O2    C2   C4   C6    180.00   0.0  0
 T3  CONST_21  I1    C5   C7   C9    180.00   0.0  0
 T3  CONST_22  C13   C1   C11  C9    180.00   0.0  0
 T3  CONST_23  I2    C6   C8   C10   180.00   0.0  0
 T3  CONST_24  O2    C2   C12  C10   180.00   0.0  0
 T3  CONST_25  O2    C7   C9   C11   180.00   0.0  0
 T3  CONST_26  O1    C8   C10  C12   180.00   0.0  0
 T3  CONST_27  HC10  C10  C12  C2    180.00   0.0  0
 T3  CONST_28  HC11  C11  C1   C3    180.00   0.0  0
 T3  CONST_29  HC12  C12  C2   C4    180.00   0.0  0
 T3  CONST_30  HC3   C3   C5   C7    180.00   0.0  0
 T3  CONST_31  HC4   C4   C6   C8    180.00   0.0  0
 T3  Var_01    C5    C7   O2   C2     90.01  30.0  2
 T3  Var_02    C12   C2   O2   C7   -178.40  30.0  1
 T3  Var_03    C15   C13  C1   C3     93.08  30.0  2

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
 T3  chir_01  C15  C13  C17  N1  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
 T3  plan-1  C1    0.020
 T3  plan-1  C3    0.020
 T3  plan-1  C5    0.020
 T3  plan-1  C7    0.020
 T3  plan-1  C9    0.020
 T3  plan-1  C11   0.020
 T3  plan-1  C13   0.020
 T3  plan-1  I1    0.020
 T3  plan-1  I3    0.020
 T3  plan-1  O2    0.020
 T3  plan-1  HC3   0.020
 T3  plan-1  HC11  0.020
 T3  plan-2  C2    0.020
 T3  plan-2  C4    0.020
 T3  plan-2  C6    0.020
 T3  plan-2  C8    0.020
 T3  plan-2  C10   0.020
 T3  plan-2  C12   0.020
 T3  plan-2  I2    0.020
 T3  plan-2  O1    0.020
 T3  plan-2  O2    0.020
 T3  plan-2  HC4   0.020
 T3  plan-2  HC10  0.020
 T3  plan-2  HC12  0.020
 T3  plan-3  C15   0.020
 T3  plan-3  C17   0.020
 T3  plan-3  O3    0.020
 T3  plan-3  O4    0.020

