# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:10:48 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-acetyl-3,5-diiodo-L-tyrosylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1cc(I)c(O)c(I)c1)C(=O)NCC(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
 IYG  IYG  N-acetyl-3,5-diiodo-L-tyrosylglycine  ligand  36  22  .  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_IYG
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
 IYG  CAN   C  CH3   0  -0.773   4.0558   1.1043   1.2913
 IYG  CN    C  C     0   0.531   2.8869   0.6162   2.1052
 IYG  ON    O  O     0  -0.500   2.9849  -0.3070   2.9029
 IYG  N     N  NH1   0  -0.622   1.7248   1.2614   1.9081
 IYG  CA    C  CH1   0  -0.183   0.5115   0.8726   2.5784
 IYG  CB    C  CH2   0  -0.588  -0.0572  -0.4526   2.0397
 IYG  CG    C  CR6   0   0.148  -0.1996  -0.4107   0.5457
 IYG  CD1   C  CR16  0  -0.282   0.7827  -0.9373  -0.2808
 IYG  CE1   C  CR6   0  -0.335   0.6737  -0.8479  -1.6605
 IYG  CD2   C  CR16  0  -0.263  -1.2975   0.2063  -0.0450
 IYG  CE2   C  CR6   0  -0.324  -1.4013   0.2950  -1.4208
 IYG  CZ    C  CR6   0   0.466  -0.4194  -0.2255  -2.2691
 IYG  OH    O  OH1   0  -0.594  -0.5987  -0.0961  -3.5842
 IYG  I1    I  I     0   0.091   2.2082  -1.6736  -2.8426
 IYG  I2    I  I     0   0.083  -3.0756   1.2338  -2.2700
 IYG  C     C  C     0   0.583   0.7173   0.9479   4.0969
 IYG  O     O  O     0  -0.493   1.3592   1.8595   4.5918
 IYG  NT    N  NH1   0  -0.663   0.0926   0.0240   4.8377
 IYG  CAT   C  CH2   0  -0.370   0.1689   0.0384   6.2719
 IYG  CT    C  C     0   0.522  -0.7261  -1.0280   6.8483
 IYG  OT1   O  O     0  -0.434  -1.3849  -1.7936   6.1915
 IYG  OT2   O  OH1   0  -0.584  -0.6886  -1.0176   8.1687
 IYG  HAN1  H  HCH3  0   0.271   4.7982   1.5479   1.9554
 IYG  HAN2  H  HCH3  0   0.265   4.5294   0.2588   0.7938
 IYG  HAN3  H  HCH3  0   0.252   3.7850   1.8427   0.5392
 IYG  H     H  HNH1  0   0.407   1.6779   2.0075   1.2358
 IYG  HA    H  HCH1  0   0.311  -0.2199   1.6567   2.3583
 IYG  HB1   H  HCH2  0   0.280   0.5831  -1.2871   2.3290
 IYG  HB2   H  HCH2  0   0.271  -1.0418  -0.6266   2.4804
 IYG  HD1   H  HCR6  0   0.279   1.6389  -1.4298   0.1619
 IYG  HD2   H  HCR6  0   0.280  -2.0776   0.6211   0.5812
 IYG  H1O   H  HOH1  0   0.478   0.1382  -0.4563  -4.0944
 IYG  HT1   H  HNH1  0   0.415  -0.3775  -0.7551   4.4069
 IYG  HAT1  H  HCH2  0   0.291   1.1902  -0.1351   6.6264
 IYG  HAT2  H  HCH2  0   0.293  -0.1376   1.0089   6.6712
 IYG  HXT   H  HOH1  0   0.490  -1.2575  -1.7155   8.5277

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
 IYG  CAN  CN    single    1.506  0.020  1.506
 IYG  CAN  HAN1  single    0.970  0.020  1.090
 IYG  CAN  HAN2  single    0.970  0.020  1.090
 IYG  CAN  HAN3  single    0.970  0.020  1.090
 IYG  CN   ON    double    1.224  0.020  1.224
 IYG  CN   N     single    1.344  0.020  1.344
 IYG  N    CA    single    1.440  0.020  1.440
 IYG  N    H     single    0.860  0.020  1.020
 IYG  CA   CB    single    1.539  0.020  1.539
 IYG  CA   C     single    1.534  0.020  1.534
 IYG  CA   HA    single    0.970  0.020  1.090
 IYG  CB   CG    single    1.501  0.020  1.501
 IYG  CB   HB1   single    0.970  0.020  1.090
 IYG  CB   HB2   single    0.970  0.020  1.090
 IYG  CG   CD1   aromatic  1.388  0.020  1.388
 IYG  CG   CD2   aromatic  1.391  0.020  1.391
 IYG  CD1  CE1   aromatic  1.387  0.020  1.387
 IYG  CD1  HD1   single    0.930  0.020  1.080
 IYG  CE1  CZ    aromatic  1.397  0.020  1.397
 IYG  CE1  I1    single    2.106  0.020  2.106
 IYG  CD2  CE2   aromatic  1.383  0.020  1.383
 IYG  CD2  HD2   single    0.930  0.020  1.080
 IYG  CE2  CZ    aromatic  1.398  0.020  1.398
 IYG  CE2  I2    single    2.099  0.020  2.099
 IYG  CZ   OH    single    1.334  0.020  1.334
 IYG  OH   H1O   single    0.850  0.020  0.980
 IYG  C    O     double    1.220  0.020  1.220
 IYG  C    NT    single    1.339  0.020  1.339
 IYG  NT   CAT   single    1.436  0.020  1.436
 IYG  NT   HT1   single    0.860  0.020  1.020
 IYG  CAT  CT    single    1.507  0.020  1.507
 IYG  CAT  HAT1  single    0.970  0.020  1.090
 IYG  CAT  HAT2  single    0.970  0.020  1.090
 IYG  CT   OT1   double    1.205  0.020  1.205
 IYG  CT   OT2   single    1.321  0.020  1.321
 IYG  OT2  HXT   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
 IYG  HAN3  CAN  HAN2  108.62  3.000
 IYG  HAN3  CAN  HAN1  108.32  3.000
 IYG  HAN2  CAN  HAN1  107.33  3.000
 IYG  HAN3  CAN  CN    113.60  3.000
 IYG  HAN2  CAN  CN    109.44  3.000
 IYG  HAN1  CAN  CN    109.34  3.000
 IYG  N     CN   ON    121.80  3.000
 IYG  N     CN   CAN   115.88  3.000
 IYG  ON    CN   CAN   122.32  3.000
 IYG  H     N    CA    118.19  3.000
 IYG  H     N    CN    119.65  3.000
 IYG  CA    N    CN    122.07  3.000
 IYG  HA    CA   C     104.69  3.000
 IYG  HA    CA   CB    107.42  3.000
 IYG  C     CA   CB    115.99  3.000
 IYG  HA    CA   N     106.02  3.000
 IYG  C     CA   N     109.54  3.000
 IYG  CB    CA   N     112.39  3.000
 IYG  HB2   CB   HB1   107.46  3.000
 IYG  HB2   CB   CG    108.68  3.000
 IYG  HB1   CB   CG    109.93  3.000
 IYG  HB2   CB   CA    109.20  3.000
 IYG  HB1   CB   CA    110.42  3.000
 IYG  CG    CB   CA    111.06  3.000
 IYG  CD2   CG   CD1   118.30  3.000
 IYG  CD2   CG   CB    120.65  3.000
 IYG  CD1   CG   CB    121.00  3.000
 IYG  HD1   CD1  CE1   119.89  3.000
 IYG  HD1   CD1  CG    119.28  3.000
 IYG  CE1   CD1  CG    120.83  3.000
 IYG  I1    CE1  CZ    120.02  3.000
 IYG  I1    CE1  CD1   118.42  3.000
 IYG  CZ    CE1  CD1   121.56  3.000
 IYG  HD2   CD2  CE2   119.78  3.000
 IYG  HD2   CD2  CG    119.54  3.000
 IYG  CE2   CD2  CG    120.68  3.000
 IYG  I2    CE2  CZ    118.77  3.000
 IYG  I2    CE2  CD2   119.42  3.000
 IYG  CZ    CE2  CD2   121.81  3.000
 IYG  OH    CZ   CE2   117.89  3.000
 IYG  OH    CZ   CE1   125.30  3.000
 IYG  CE2   CZ   CE1   116.81  3.000
 IYG  H1O   OH   CZ    112.46  3.000
 IYG  NT    C    O     122.46  3.000
 IYG  NT    C    CA    116.82  3.000
 IYG  O     C    CA    120.58  3.000
 IYG  HT1   NT   CAT   117.38  3.000
 IYG  HT1   NT   C     121.00  3.000
 IYG  CAT   NT   C     121.39  3.000
 IYG  HAT2  CAT  HAT1  106.49  3.000
 IYG  HAT2  CAT  CT    108.79  3.000
 IYG  HAT1  CAT  CT    108.54  3.000
 IYG  HAT2  CAT  NT    111.02  3.000
 IYG  HAT1  CAT  NT    111.79  3.000
 IYG  CT    CAT  NT    110.08  3.000
 IYG  OT2   CT   OT1   124.44  3.000
 IYG  OT2   CT   CAT   111.09  3.000
 IYG  OT1   CT   CAT   124.47  3.000
 IYG  HXT   OT2  CT    110.35  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
 IYG  CONST_01  CZ    CE1  CD1  CG     0.00   0.0  0
 IYG  CONST_02  CZ    CE2  CD2  CG     0.00   0.0  0
 IYG  CONST_03  CE2   CD2  CG   CD1    0.00   0.0  0
 IYG  CONST_04  CE2   CZ   CE1  CD1    0.00   0.0  0
 IYG  CONST_05  CD2   CG   CD1  CE1    0.00   0.0  0
 IYG  CONST_06  CD2   CE2  CZ   CE1    0.00   0.0  0
 IYG  CONST_07  CE1   CD1  CG   CB   180.00   0.0  0
 IYG  CONST_08  CE2   CD2  CG   CB   180.00   0.0  0
 IYG  CONST_09  I1    CE1  CD1  CG   180.00   0.0  0
 IYG  CONST_10  I2    CE2  CD2  CG   180.00   0.0  0
 IYG  CONST_11  OH    CZ   CE1  CD1  180.00   0.0  0
 IYG  CONST_12  I2    CE2  CZ   CE1  180.00   0.0  0
 IYG  CONST_13  OH    CZ   CE2  CD2  180.00   0.0  0
 IYG  CONST_14  I1    CE1  CZ   CE2  180.00   0.0  0
 IYG  CONST_15  HD2   CD2  CG   CD1  180.00   0.0  0
 IYG  CONST_16  HD1   CD1  CG   CD2  180.00   0.0  0
 IYG  CONST_17  CA    N    CN   CAN  180.00   0.0  0
 IYG  CONST_18  CA    N    CN   ON     0.00   0.0  0
 IYG  CONST_19  CAT   NT   C    CA   180.00   0.0  0
 IYG  CONST_20  CAT   NT   C    O      0.00   0.0  0
 IYG  CONST_21  H     N    CN   CAN    0.00   0.0  0
 IYG  CONST_22  HT1   NT   C    CA     0.00   0.0  0
 IYG  CONST_23  HXT   OT2  CT   CAT  180.00   0.0  0
 IYG  Var_01    CD1   CG   CB   CA    96.36  30.0  2
 IYG  Var_02    CT    CAT  NT   C    174.69  30.0  3
 IYG  Var_03    OT1   CT   CAT  NT     1.37  30.0  3
 IYG  Var_04    HAN1  CAN  CN   ON   -66.20  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
 IYG  chir_01  CA  N  CB  C  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
 IYG  plan-1  CB   0.020
 IYG  plan-1  CG   0.020
 IYG  plan-1  CD1  0.020
 IYG  plan-1  CE1  0.020
 IYG  plan-1  CD2  0.020
 IYG  plan-1  CE2  0.020
 IYG  plan-1  CZ   0.020
 IYG  plan-1  OH   0.020
 IYG  plan-1  I1   0.020
 IYG  plan-1  I2   0.020
 IYG  plan-1  HD1  0.020
 IYG  plan-1  HD2  0.020
 IYG  plan-2  CAN  0.020
 IYG  plan-2  CN   0.020
 IYG  plan-2  ON   0.020
 IYG  plan-2  N    0.020
 IYG  plan-2  CA   0.020
 IYG  plan-2  H    0.020
 IYG  plan-3  CA   0.020
 IYG  plan-3  C    0.020
 IYG  plan-3  O    0.020
 IYG  plan-3  NT   0.020
 IYG  plan-3  CAT  0.020
 IYG  plan-3  HT1  0.020
 IYG  plan-4  CAT  0.020
 IYG  plan-4  CT   0.020
 IYG  plan-4  OT1  0.020
 IYG  plan-4  OT2  0.020
 IYG  plan-4  HXT  0.020

