# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 01:11:52 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-acetyl-3,5-diiodo-L-tyrosyl-D-allothreonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](NC(=O)[C@H](Cc1cc(I)c(O)c(I)c1)NC(C)=O)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
 IYT  IYT  N-acetyl-3,5-diiodo-L-tyrosyl-D-allothreonine  D-peptide  42  25  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IYT
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
 IYT  CAN   C  CH3    0  -0.773   0.7339  -4.0239  -0.9140
 IYT  CN    C  C      0   0.533   1.4839  -2.8129  -0.4209
 IYT  ON    O  O      0  -0.501   2.0760  -2.8073   0.6502
 IYT  N     N  NH1    0  -0.619   1.4347  -1.7356  -1.2201
 IYT  CA    C  CH1    0  -0.184   2.0828  -0.4936  -0.8948
 IYT  CB    C  CH2    0  -0.577   1.4318   0.2242   0.3041
 IYT  CG    C  CR6    0   0.152  -0.0638   0.2591   0.1778
 IYT  CD1   C  CR16   0  -0.281  -0.8573  -0.6719   0.8331
 IYT  CE1   C  CR6    0  -0.335  -2.2351  -0.6690   0.6754
 IYT  CD2   C  CR16   0  -0.267  -0.6879   1.1980  -0.6370
 IYT  CE2   C  CR6    0  -0.323  -2.0620   1.1963  -0.7924
 IYT  CZ    C  CR6    0   0.464  -2.8764   0.2629  -0.1441
 IYT  OH    O  OH1    0  -0.595  -4.1930   0.3341  -0.3482
 IYT  I1    I  I      0   0.088  -3.3625  -2.1194   1.7051
 IYT  I2    I  I      0   0.081  -2.9614   2.6318  -2.0326
 IYT  C     C  C      0   0.573   3.6028  -0.7046  -0.7868
 IYT  O     O  O      0  -0.509   4.1519  -1.5753  -1.4475
 IYT  NT    N  NH1    0  -0.650   4.2608   0.1562  -0.0103
 IYT  CAT   C  CH1    0  -0.211   5.7008   0.2109   0.1029
 IYT  CBT   C  CH1    0   0.046   6.2159  -0.8689   1.0640
 IYT  OGT   O  OH1    0  -0.675   5.8531  -0.4696   2.3717
 IYT  CGT   C  CH3    0  -0.693   7.7077  -1.1341   0.9400
 IYT  CT    C  C      0   0.425   6.1027   1.6355   0.5663
 IYT  OX1   O  OC    -1  -0.594   7.3075   1.9233   0.4748
 IYT  OX2   O  O      0  -0.597   5.1849   2.3674   0.9878
 IYT  HAN1  H  HCH3   0   0.250   0.3137  -3.9028  -1.9107
 IYT  HAN2  H  HCH3   0   0.265   1.3979  -4.8876  -0.9192
 IYT  HAN3  H  HCH3   0   0.263  -0.0809  -4.2469  -0.2242
 IYT  H     H  HNH1   0   0.403   0.9518  -1.7988  -2.0995
 IYT  HA    H  HCH1   0   0.302   1.9455   0.1498  -1.7693
 IYT  HB2   H  HCH2   0   0.275   1.7170  -0.2601   1.2373
 IYT  HB3   H  HCH2   0   0.265   1.8021   1.2510   0.3452
 IYT  HD1   H  HCR6   0   0.278  -0.3908  -1.4077   1.4757
 IYT  HD2   H  HCR6   0   0.279  -0.0883   1.9371  -1.1536
 IYT  HH    H  HOH1   0   0.477  -4.6739  -0.3787   0.0921
 IYT  HNT   H  HNH1   0   0.392   3.7901   0.9085   0.4711
 IYT  HAT   H  HCH1   0   0.243   6.1420   0.0186  -0.8792
 IYT  HBT   H  HCH1   0   0.210   5.6945  -1.7982   0.7967
 IYT  HGT   H  HOH1   0   0.447   6.1201  -1.1649   2.9805
 IYT  HGT1  H  HCH3   0   0.221   8.0036  -1.9512   1.6021
 IYT  HGT2  H  HCH3   0   0.218   7.9598  -1.4352  -0.0780
 IYT  HGT3  H  HCH3   0   0.234   8.2956  -0.2538   1.1898

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
 IYT  CAN  CN    single    1.507  0.020  1.507
 IYT  CAN  HAN1  single    0.970  0.020  1.090
 IYT  CAN  HAN2  single    0.970  0.020  1.090
 IYT  CAN  HAN3  single    0.970  0.020  1.090
 IYT  CN   ON    double    1.224  0.020  1.224
 IYT  CN   N     single    1.342  0.020  1.342
 IYT  N    CA    single    1.458  0.019  1.458
 IYT  N    H     single    0.860  0.020  0.860
 IYT  CA   CB    single    1.521  0.033  1.521
 IYT  CA   C     single    1.525  0.021  1.525
 IYT  CA   HA    single    0.970  0.020  0.970
 IYT  CB   CG    single    1.501  0.020  1.501
 IYT  CB   HB2   single    0.970  0.020  1.090
 IYT  CB   HB3   single    0.970  0.020  1.090
 IYT  CG   CD1   aromatic  1.388  0.020  1.388
 IYT  CG   CD2   aromatic  1.391  0.020  1.391
 IYT  CD1  CE1   aromatic  1.387  0.020  1.387
 IYT  CD1  HD1   single    0.930  0.020  1.080
 IYT  CE1  CZ    aromatic  1.397  0.020  1.397
 IYT  CE1  I1    single    2.106  0.020  2.106
 IYT  CD2  CE2   aromatic  1.383  0.020  1.383
 IYT  CD2  HD2   single    0.930  0.020  1.080
 IYT  CE2  CZ    aromatic  1.398  0.020  1.398
 IYT  CE2  I2    single    2.099  0.020  2.099
 IYT  CZ   OH    single    1.334  0.020  1.334
 IYT  OH   HH    single    0.850  0.020  0.980
 IYT  C    O     double    1.231  0.020  1.231
 IYT  C    NT    single    1.333  0.020  1.333
 IYT  NT   CAT   single    1.445  0.020  1.445
 IYT  NT   HNT   single    0.860  0.020  1.020
 IYT  CAT  CBT   single    1.535  0.020  1.535
 IYT  CAT  CT    single    1.551  0.020  1.551
 IYT  CAT  HAT   single    0.970  0.020  1.090
 IYT  CBT  OGT   single    1.415  0.020  1.415
 IYT  CBT  CGT   single    1.520  0.020  1.520
 IYT  CBT  HBT   single    0.970  0.020  1.090
 IYT  OGT  HGT   single    0.850  0.020  0.980
 IYT  CGT  HGT1  single    0.970  0.020  1.090
 IYT  CGT  HGT2  single    0.970  0.020  1.090
 IYT  CGT  HGT3  single    0.970  0.020  1.090
 IYT  CT   OX1   deloc     1.242  0.020  1.242
 IYT  CT   OX2   deloc     1.247  0.020  1.247

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
 IYT  HAN3  CAN  HAN2  107.23  3.000
 IYT  HAN3  CAN  HAN1  108.27  3.000
 IYT  HAN2  CAN  HAN1  108.61  3.000
 IYT  HAN3  CAN  CN    109.21  3.000
 IYT  HAN2  CAN  CN    109.59  3.000
 IYT  HAN1  CAN  CN    113.72  3.000
 IYT  N     CN   ON    122.35  3.000
 IYT  N     CN   CAN   115.58  3.000
 IYT  ON    CN   CAN   122.05  3.000
 IYT  H     N    CA    114.00  3.000
 IYT  H     N    CN    119.21  3.000
 IYT  CA    N    CN    122.82  3.000
 IYT  HA    CA   C     110.00  3.000
 IYT  HA    CA   CB    109.00  3.000
 IYT  C     CA   CB    110.50  1.500
 IYT  HA    CA   N     110.00  3.000
 IYT  C     CA   N     111.00  2.800
 IYT  CB    CA   N     110.40  1.500
 IYT  HB3   CB   HB2   107.26  3.000
 IYT  HB3   CB   CG    108.61  3.000
 IYT  HB2   CB   CG    110.07  3.000
 IYT  HB3   CB   CA    108.89  3.000
 IYT  HB2   CB   CA    110.41  3.000
 IYT  CG    CB   CA    111.48  3.000
 IYT  CD2   CG   CD1   118.22  3.000
 IYT  CD2   CG   CB    120.79  3.000
 IYT  CD1   CG   CB    120.95  3.000
 IYT  HD1   CD1  CE1   119.80  3.000
 IYT  HD1   CD1  CG    119.33  3.000
 IYT  CE1   CD1  CG    120.86  3.000
 IYT  I1    CE1  CZ    120.04  3.000
 IYT  I1    CE1  CD1   118.35  3.000
 IYT  CZ    CE1  CD1   121.61  3.000
 IYT  HD2   CD2  CE2   119.83  3.000
 IYT  HD2   CD2  CG    119.46  3.000
 IYT  CE2   CD2  CG    120.71  3.000
 IYT  I2    CE2  CZ    118.74  3.000
 IYT  I2    CE2  CD2   119.42  3.000
 IYT  CZ    CE2  CD2   121.84  3.000
 IYT  OH    CZ   CE2   117.92  3.000
 IYT  OH    CZ   CE1   125.33  3.000
 IYT  CE2   CZ   CE1   116.74  3.000
 IYT  HH    OH   CZ    112.47  3.000
 IYT  NT    C    O     123.55  3.000
 IYT  NT    C    CA    116.11  3.000
 IYT  O     C    CA    120.80  1.700
 IYT  HNT   NT   CAT   113.51  3.000
 IYT  HNT   NT   C     121.93  3.000
 IYT  CAT   NT   C     124.18  3.000
 IYT  HAT   CAT  CT    108.98  3.000
 IYT  HAT   CAT  CBT   107.65  3.000
 IYT  CT    CAT  CBT   111.85  3.000
 IYT  HAT   CAT  NT    108.96  3.000
 IYT  CT    CAT  NT    108.44  3.000
 IYT  CBT   CAT  NT    110.91  3.000
 IYT  HBT   CBT  CGT   107.36  3.000
 IYT  HBT   CBT  OGT   110.00  3.000
 IYT  CGT   CBT  OGT   112.10  3.000
 IYT  HBT   CBT  CAT   106.47  3.000
 IYT  CGT   CBT  CAT   113.64  3.000
 IYT  OGT   CBT  CAT   107.11  3.000
 IYT  HGT   OGT  CBT   108.05  3.000
 IYT  HGT3  CGT  HGT2  108.23  3.000
 IYT  HGT3  CGT  HGT1  108.64  3.000
 IYT  HGT2  CGT  HGT1  107.24  3.000
 IYT  HGT3  CGT  CBT   111.75  3.000
 IYT  HGT2  CGT  CBT   110.54  3.000
 IYT  HGT1  CGT  CBT   110.29  3.000
 IYT  OX2   CT   OX1   127.06  3.000
 IYT  OX2   CT   CAT   116.70  3.000
 IYT  OX1   CT   CAT   116.24  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
 IYT  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 IYT  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 IYT  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 IYT  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 IYT  CONST_05  CD2   CG   CD1  CE1     0.00   0.0  0
 IYT  CONST_06  CD2   CE2  CZ   CE1     0.00   0.0  0
 IYT  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 IYT  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 IYT  CONST_09  I1    CE1  CD1  CG    180.00   0.0  0
 IYT  CONST_10  I2    CE2  CD2  CG    180.00   0.0  0
 IYT  CONST_11  OH    CZ   CE1  CD1   180.00   0.0  0
 IYT  CONST_12  I2    CE2  CZ   CE1   180.00   0.0  0
 IYT  CONST_13  OH    CZ   CE2  CD2   180.00   0.0  0
 IYT  CONST_14  I1    CE1  CZ   CE2   180.00   0.0  0
 IYT  CONST_15  HD2   CD2  CG   CD1   180.00   0.0  0
 IYT  CONST_16  HD1   CD1  CG   CD2   180.00   0.0  0
 IYT  CONST_17  CA    N    CN   CAN   180.00   0.0  0
 IYT  CONST_18  CA    N    CN   ON      0.00   0.0  0
 IYT  CONST_19  CAT   NT   C    CA    180.00   0.0  0
 IYT  CONST_20  CAT   NT   C    O       0.00   0.0  0
 IYT  CONST_21  H     N    CN   CAN     0.00   0.0  0
 IYT  CONST_22  HNT   NT   C    CA      0.00   0.0  0
 IYT  Var_01    CD1   CG   CB   CA     97.78  30.0  2
 IYT  Var_02    HAN1  CAN  CN   ON   -176.14  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
 IYT  chir_01  CA   N    CB   C    negativ
 IYT  chir_02  CAT  NT   CBT  CT   positiv
 IYT  chir_03  CBT  OGT  CAT  CGT  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
 IYT  plan-1  CB   0.020
 IYT  plan-1  CG   0.020
 IYT  plan-1  CD1  0.020
 IYT  plan-1  CE1  0.020
 IYT  plan-1  CD2  0.020
 IYT  plan-1  CE2  0.020
 IYT  plan-1  CZ   0.020
 IYT  plan-1  OH   0.020
 IYT  plan-1  I1   0.020
 IYT  plan-1  I2   0.020
 IYT  plan-1  HD1  0.020
 IYT  plan-1  HD2  0.020
 IYT  plan-2  CAN  0.020
 IYT  plan-2  CN   0.020
 IYT  plan-2  ON   0.020
 IYT  plan-2  N    0.020
 IYT  plan-2  CA   0.020
 IYT  plan-2  H    0.020
 IYT  plan-3  CA   0.020
 IYT  plan-3  C    0.020
 IYT  plan-3  O    0.020
 IYT  plan-3  NT   0.020
 IYT  plan-3  CAT  0.020
 IYT  plan-3  HNT  0.020
 IYT  plan-4  CAT  0.020
 IYT  plan-4  CT   0.020
 IYT  plan-4  OX1  0.020
 IYT  plan-4  OX2  0.020

