# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:31:21 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 3-iodo-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccc(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
 33S  33S  '3-iodo-L-phenylalanine   '  L-peptide  22  13  .  2016-04-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_33S
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
 33S  CZ   C  CR16   0  -0.247   6.5738  47.1329  30.3819
 33S  CE2  C  CR16   0  -0.236   5.7425  46.0636  30.6864
 33S  CD2  C  CR16   0  -0.297   6.2745  44.8239  31.0111
 33S  N    N  NH2    0  -0.791   7.0199  43.2139  33.5610
 33S  CA   C  CH1    0  -0.205   8.2984  42.9389  32.9017
 33S  CB   C  CH2    0  -0.490   8.2151  43.2696  31.4043
 33S  CG   C  CR6    0   0.126   7.6534  44.6215  31.0569
 33S  CD1  C  CR16   0  -0.264   8.4897  45.6946  30.7480
 33S  CE1  C  CR6    0  -0.204   7.9445  46.9231  30.4104
 33S  I1   I  I      0   0.026   9.2385  48.5178  29.9271
 33S  C    C  C      0   0.397   9.4926  43.5772  33.6523
 33S  OXT  O  OC    -1  -0.620   9.7227  43.0895  34.7795
 33S  O    O  O      0  -0.589  10.1019  44.5222  33.1128
 33S  HZ   H  HCR6   0   0.272   6.1536  48.0962  30.1259
 33S  HE2  H  HCR6   0   0.258   4.6692  46.2028  30.6625
 33S  HD2  H  HCR6   0   0.248   5.6096  43.9988  31.2321
 33S  H7   H  HCH1   0   0.214   8.4322  41.8531  32.9632
 33S  HB2  H  HCH2   0   0.232   7.5799  42.5130  30.9355
 33S  HB3  H  HCH2   0   0.236   9.2058  43.1550  30.9627
 33S  HD1  H  HCR6   0   0.260   9.5598  45.5518  30.7789
 33S  H    H  HNH2   0   0.338   7.0716  42.8570  34.5074
 33S  H2   H  HNH2   0   0.335   6.8968  44.2156  33.6585

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
 33S  I1   CE1  single    2.110  0.020  2.110
 33S  CZ   CE1  aromatic  1.387  0.020  1.387
 33S  CZ   CE2  aromatic  1.388  0.020  1.388
 33S  CE1  CD1  aromatic  1.386  0.020  1.386
 33S  CE2  CD2  aromatic  1.388  0.020  1.388
 33S  CD1  CG   aromatic  1.395  0.020  1.395
 33S  CD2  CG   aromatic  1.394  0.020  1.394
 33S  CG   CB   single    1.505  0.020  1.505
 33S  CB   CA   single    1.530  0.020  1.530
 33S  CA   N    single    1.458  0.019  1.458
 33S  CA   C    single    1.525  0.021  1.525
 33S  O    C    deloc     1.231  0.020  1.231
 33S  C    OXT  deloc     1.250  0.020  1.250
 33S  CZ   HZ   single    0.930  0.020  1.080
 33S  CE2  HE2  single    0.930  0.020  1.080
 33S  CD2  HD2  single    0.930  0.020  1.080
 33S  N    H    single    0.860  0.020  0.860
 33S  N    H2   single    0.890  0.020  1.040
 33S  CA   H7   single    0.970  0.020  1.090
 33S  CB   HB2  single    0.970  0.020  1.090
 33S  CB   HB3  single    0.970  0.020  1.090
 33S  CD1  HD1  single    0.930  0.020  1.080

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
 33S  HZ   CZ   CE1  121.57  3.000
 33S  HZ   CZ   CE2  120.35  3.000
 33S  CE1  CZ   CE2  118.08  3.000
 33S  HE2  CE2  CD2  120.01  3.000
 33S  HE2  CE2  CZ   119.33  3.000
 33S  CD2  CE2  CZ   120.66  3.000
 33S  HD2  CD2  CG   119.35  3.000
 33S  HD2  CD2  CE2  119.55  3.000
 33S  CG   CD2  CE2  121.10  3.000
 33S  H2   N    H    105.34  3.000
 33S  H2   N    CA   109.56  3.000
 33S  H    N    CA   114.00  3.000
 33S  H7   CA   C    106.68  3.000
 33S  H7   CA   CB   105.95  3.000
 33S  C    CA   CB   110.10  1.900
 33S  H7   CA   N    105.51  3.000
 33S  C    CA   N    111.00  2.800
 33S  CB   CA   N    110.50  1.700
 33S  HB3  CB   HB2  106.34  3.000
 33S  HB3  CB   CG   109.88  3.000
 33S  HB2  CB   CG   107.81  3.000
 33S  HB3  CB   CA   108.84  3.000
 33S  HB2  CB   CA   107.49  3.000
 33S  CG   CB   CA   116.03  3.000
 33S  CD1  CG   CB   121.23  3.000
 33S  CB   CG   CD2  120.47  3.000
 33S  CD1  CG   CD2  118.29  3.000
 33S  HD1  CD1  CE1  120.93  3.000
 33S  HD1  CD1  CG   119.07  3.000
 33S  CE1  CD1  CG   120.00  3.000
 33S  I1   CE1  CD1  118.99  3.000
 33S  CD1  CE1  CZ   121.87  3.000
 33S  I1   CE1  CZ   119.15  3.000
 33S  O    C    OXT  126.59  3.000
 33S  OXT  C    CA   114.74  3.000
 33S  O    C    CA   120.80  1.700

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
 33S  CONST_01  CG   CD1  CE1  CZ     0.00   0.0  0
 33S  CONST_02  CG   CD2  CE2  CZ     0.00   0.0  0
 33S  CONST_03  CD1  CE1  CZ   CE2    0.00   0.0  0
 33S  CONST_04  CD1  CG   CD2  CE2    0.00   0.0  0
 33S  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 33S  CONST_06  CE1  CD1  CG   CD2    0.00   0.0  0
 33S  CONST_07  I1   CE1  CZ   CE2  180.00   0.0  0
 33S  CONST_08  CB   CG   CD2  CE2  180.00   0.0  0
 33S  CONST_09  CE1  CD1  CG   CB   180.00   0.0  0
 33S  CONST_10  I1   CE1  CD1  CG   180.00   0.0  0
 33S  CONST_11  HD1  CD1  CE1  CZ   180.00   0.0  0
 33S  CONST_12  HD2  CD2  CE2  CZ   180.00   0.0  0
 33S  CONST_13  HZ   CZ   CE2  CD2  180.00   0.0  0
 33S  CONST_14  HE2  CE2  CD2  CG   180.00   0.0  0
 33S  Var_01    CA   CB   CG   CD2  -82.16  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
 33S  chir_01  CA  CB  N  C  positiv

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
 33S  plan-1  CZ   0.020
 33S  plan-1  CE2  0.020
 33S  plan-1  CD2  0.020
 33S  plan-1  CB   0.020
 33S  plan-1  CG   0.020
 33S  plan-1  CD1  0.020
 33S  plan-1  CE1  0.020
 33S  plan-1  I1   0.020
 33S  plan-1  HZ   0.020
 33S  plan-1  HE2  0.020
 33S  plan-1  HD2  0.020
 33S  plan-1  HD1  0.020
 33S  plan-2  CA   0.020
 33S  plan-2  C    0.020
 33S  plan-2  OXT  0.020
 33S  plan-2  O    0.020

