# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:42:00 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-iodo-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(I)cc1)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
 IOY  IOY  '4-iodo-D-phenylalanine   '  D-peptide  22  13  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_IOY
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
 IOY  CG   C  CR6    0   0.128  18.2504  -15.6953  -58.3635
 IOY  CD1  C  CR16   0  -0.293  17.7820  -16.3680  -59.4887
 IOY  CE1  C  CR16   0  -0.209  17.7942  -17.7553  -59.5602
 IOY  CZ   C  CR6    0  -0.239  18.2748  -18.4833  -58.4827
 IOY  I1   I  I      0   0.034  18.2985  -20.5872  -58.5758
 IOY  CE2  C  CR16   0  -0.210  18.7436  -17.8438  -57.3445
 IOY  CD2  C  CR16   0  -0.301  18.7273  -16.4568  -57.2982
 IOY  CB   C  CH2    0  -0.492  18.2281  -14.1967  -58.2704
 IOY  N    N  NH2    0  -0.793  17.2095  -12.2355  -57.2538
 IOY  C    C  C      0   0.400  15.6760  -14.0099  -58.0952
 IOY  OXT  O  OC    -1  -0.610  14.7445  -14.2793  -57.3100
 IOY  O    O  O      0  -0.606  15.5999  -13.9147  -59.3390
 IOY  CA   C  CH1    0  -0.192  17.0452  -13.6794  -57.4530
 IOY  HD1  H  HCR6   0   0.251  17.3979  -15.8024  -60.3274
 IOY  HE1  H  HCR6   0   0.272  17.4274  -18.2494  -60.4498
 IOY  HE2  H  HCR6   0   0.273  19.1234  -18.4049  -56.5012
 IOY  HD2  H  HCR6   0   0.254  19.1023  -15.9592  -56.4112
 IOY  HB3  H  HCH2   0   0.232  19.1505  -13.8501  -57.7972
 IOY  HB2  H  HCH2   0   0.229  18.1940  -13.7610  -59.2704
 IOY  H    H  HNH2   0   0.339  16.4609  -11.8971  -56.6602
 IOY  H2   H  HNH2   0   0.330  17.0734  -11.7690  -58.1446
 IOY  HA   H  HCH1   0   0.202  17.0880  -14.1440  -56.4626

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
 IOY  CG   CD1  aromatic  1.392  0.020  1.392
 IOY  CG   CD2  aromatic  1.394  0.020  1.394
 IOY  CG   CB   single    1.502  0.020  1.502
 IOY  CD1  CE1  aromatic  1.389  0.020  1.389
 IOY  CD1  HD1  single    0.930  0.020  1.080
 IOY  CE1  CZ   aromatic  1.386  0.020  1.386
 IOY  CE1  HE1  single    0.930  0.020  1.080
 IOY  CZ   I1   single    2.106  0.020  2.106
 IOY  CZ   CE2  aromatic  1.387  0.020  1.387
 IOY  CE2  CD2  aromatic  1.388  0.020  1.388
 IOY  CE2  HE2  single    0.930  0.020  1.080
 IOY  CD2  HD2  single    0.930  0.020  1.080
 IOY  CB   CA   single    1.521  0.033  1.521
 IOY  CB   HB3  single    0.970  0.020  1.090
 IOY  CB   HB2  single    0.970  0.020  1.090
 IOY  N    CA   single    1.458  0.019  1.458
 IOY  N    H    single    0.860  0.020  0.860
 IOY  N    H2   single    0.890  0.020  1.040
 IOY  C    OXT  deloc     1.248  0.020  1.248
 IOY  C    O    deloc     1.231  0.020  1.231
 IOY  C    CA   single    1.525  0.021  1.525
 IOY  CA   HA   single    0.970  0.020  0.970

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
 IOY  CB   CG   CD2  120.20  3.000
 IOY  CB   CG   CD1  121.83  3.000
 IOY  CD2  CG   CD1  117.96  3.000
 IOY  HD1  CD1  CE1  119.03  3.000
 IOY  HD1  CD1  CG   119.56  3.000
 IOY  CE1  CD1  CG   121.42  3.000
 IOY  HE1  CE1  CZ   121.12  3.000
 IOY  HE1  CE1  CD1  119.71  3.000
 IOY  CZ   CE1  CD1  119.18  3.000
 IOY  CE2  CZ   I1   119.54  3.000
 IOY  CE2  CZ   CE1  120.85  3.000
 IOY  I1   CZ   CE1  119.61  3.000
 IOY  HE2  CE2  CD2  119.77  3.000
 IOY  HE2  CE2  CZ   121.28  3.000
 IOY  CD2  CE2  CZ   118.95  3.000
 IOY  HD2  CD2  CE2  118.81  3.000
 IOY  HD2  CD2  CG   119.54  3.000
 IOY  CE2  CD2  CG   121.64  3.000
 IOY  HB2  CB   HB3  107.24  3.000
 IOY  HB2  CB   CA   109.32  3.000
 IOY  HB3  CB   CA   108.31  3.000
 IOY  HB2  CB   CG   110.00  3.000
 IOY  HB3  CB   CG   109.32  3.000
 IOY  CA   CB   CG   112.49  3.000
 IOY  H2   N    H    105.16  3.000
 IOY  H2   N    CA   108.56  3.000
 IOY  H    N    CA   114.00  3.000
 IOY  CA   C    O    120.80  1.700
 IOY  CA   C    OXT  120.80  1.700
 IOY  O    C    OXT  126.68  3.000
 IOY  HA   CA   C    110.00  3.000
 IOY  HA   CA   N    110.00  3.000
 IOY  C    CA   N    111.00  2.800
 IOY  HA   CA   CB   109.00  3.000
 IOY  C    CA   CB   110.50  1.500
 IOY  N    CA   CB   110.40  1.500

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
 IOY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 IOY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 IOY  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 IOY  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 IOY  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 IOY  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 IOY  CONST_07  I1   CZ   CE1  CD1  180.00   0.0  0
 IOY  CONST_08  CB   CG   CD1  CE1  180.00   0.0  0
 IOY  CONST_09  CD2  CE2  CZ   I1   180.00   0.0  0
 IOY  CONST_10  CB   CG   CD2  CE2  180.00   0.0  0
 IOY  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 IOY  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 IOY  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 IOY  CONST_14  HD1  CD1  CE1  CZ   180.00   0.0  0
 IOY  Var_01    CA   CB   CG   CD1   99.81  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
 IOY  chir_01  CA  CB  N  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
 IOY  plan-1  CG   0.020
 IOY  plan-1  CD1  0.020
 IOY  plan-1  CE1  0.020
 IOY  plan-1  CZ   0.020
 IOY  plan-1  I1   0.020
 IOY  plan-1  CE2  0.020
 IOY  plan-1  CD2  0.020
 IOY  plan-1  CB   0.020
 IOY  plan-1  HD1  0.020
 IOY  plan-1  HE1  0.020
 IOY  plan-1  HE2  0.020
 IOY  plan-1  HD2  0.020
 IOY  plan-2  C    0.020
 IOY  plan-2  OXT  0.020
 IOY  plan-2  O    0.020
 IOY  plan-2  CA   0.020

