# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:47:36 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-iodo-L-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
 PHI  PHI  '4-iodo-L-phenylalanine   '  L-peptide  22  13  .  2012-08-28  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_PHI
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
 PHI  N    N  NH2    0  -0.809  89.2158  12.9131  33.6306
 PHI  CA   C  CH1    0  -0.211  88.7326  14.2825  33.6665
 PHI  CB   C  CH2    0  -0.488  88.5917  14.7554  35.1192
 PHI  CG   C  C      0   0.137  87.6100  13.9244  35.8932
 PHI  CD1  C  C1     0  -0.306  88.0226  12.8923  36.7315
 PHI  CD2  C  C1     0  -0.297  86.2402  14.1475  35.7593
 PHI  CE1  C  C1     0  -0.209  87.1073  12.1058  37.4202
 PHI  CE2  C  C1     0  -0.208  85.3074  13.3725  36.4329
 PHI  CZ   C  C      0  -0.240  85.7523  12.3532  37.2628
 PHI  I    I  I      0   0.035  84.3506  11.1734  38.3009
 PHI  C    C  C      0   0.414  89.6522  15.2264  32.8428
 PHI  O    O  O      0  -0.596  90.4314  14.6877  32.0319
 PHI  OXT  O  OC    -1  -0.603  89.4991  16.4483  33.0319
 PHI  H    H  HNH2   0   0.335  89.6285  12.7518  32.7214
 PHI  H2   H  HNH2   0   0.332  88.4461  12.2649  33.7294
 PHI  HA   H  HCH1   0   0.202  87.7352  14.3806  33.2026
 PHI  HB2  H  HCH2   0   0.227  89.5717  14.7187  35.6021
 PHI  HB3  H  HCH2   0   0.234  88.2655  15.7954  35.1215
 PHI  HD1  H  H      0   0.252  89.0803  12.6962  36.8578
 PHI  HD2  H  H      0   0.254  85.8883  14.9477  35.1183
 PHI  HE1  H  H      0   0.273  87.4604  11.3140  38.0672
 PHI  HE2  H  H      0   0.273  84.2517  13.5738  36.3095

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
 PHI  N    CA   single    1.458  0.019  1.458
 PHI  N    H    single    0.860  0.020  0.860
 PHI  N    H2   single    0.890  0.020  1.040
 PHI  CA   CB   single    1.530  0.020  1.530
 PHI  CA   C    single    1.525  0.021  1.525
 PHI  CA   HA   single    0.970  0.020  0.970
 PHI  CB   CG   single    1.501  0.020  1.501
 PHI  CB   HB2  single    0.970  0.020  1.090
 PHI  CB   HB3  single    0.970  0.020  1.090
 PHI  CG   CD1  aromatic  1.392  0.020  1.392
 PHI  CG   CD2  aromatic  1.394  0.020  1.394
 PHI  CD1  CE1  aromatic  1.389  0.020  1.389
 PHI  CD1  HD1  single    0.930  0.020  1.080
 PHI  CD2  CE2  aromatic  1.387  0.020  1.387
 PHI  CD2  HD2  single    0.930  0.020  1.080
 PHI  CE1  CZ   aromatic  1.386  0.020  1.386
 PHI  CE1  HE1  single    0.930  0.020  1.080
 PHI  CE2  CZ   aromatic  1.388  0.020  1.388
 PHI  CE2  HE2  single    0.930  0.020  1.080
 PHI  CZ   I    single    2.106  0.020  2.106
 PHI  C    O    deloc     1.231  0.020  1.231
 PHI  C    OXT  deloc     1.246  0.020  1.246

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
 PHI  H2   N    H    107.23  3.000
 PHI  H2   N    CA   110.41  3.000
 PHI  H    N    CA   114.00  3.000
 PHI  HA   CA   C    109.00  3.000
 PHI  HA   CA   CB   109.00  3.000
 PHI  C    CA   CB   110.10  1.900
 PHI  HA   CA   N    110.00  3.000
 PHI  C    CA   N    111.00  2.800
 PHI  CB   CA   N    110.50  1.700
 PHI  HB3  CB   HB2  107.42  3.000
 PHI  HB3  CB   CG   109.36  3.000
 PHI  HB2  CB   CG   109.87  3.000
 PHI  HB3  CB   CA   108.88  3.000
 PHI  HB2  CB   CA   109.00  3.000
 PHI  CG   CB   CA   112.19  3.000
 PHI  CD2  CG   CD1  117.88  3.000
 PHI  CD2  CG   CB   120.29  3.000
 PHI  CD1  CG   CB   121.81  3.000
 PHI  HD1  CD1  CE1  118.88  3.000
 PHI  HD1  CD1  CG   119.59  3.000
 PHI  CE1  CD1  CG   121.52  3.000
 PHI  HD2  CD2  CE2  118.77  3.000
 PHI  HD2  CD2  CG   119.59  3.000
 PHI  CE2  CD2  CG   121.64  3.000
 PHI  HE1  CE1  CZ   121.17  3.000
 PHI  HE1  CE1  CD1  119.71  3.000
 PHI  CZ   CE1  CD1  119.12  3.000
 PHI  HE2  CE2  CZ   121.18  3.000
 PHI  HE2  CE2  CD2  119.80  3.000
 PHI  CZ   CE2  CD2  119.02  3.000
 PHI  I    CZ   CE2  119.53  3.000
 PHI  I    CZ   CE1  119.65  3.000
 PHI  CE2  CZ   CE1  120.82  3.000
 PHI  OXT  C    O    126.81  3.000
 PHI  OXT  C    CA   116.27  3.000
 PHI  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
 PHI  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PHI  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PHI  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PHI  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PHI  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PHI  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PHI  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PHI  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PHI  CONST_09  I    CZ   CE1  CD1  180.00   0.0  0
 PHI  CONST_10  I    CZ   CE2  CD2  180.00   0.0  0
 PHI  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 PHI  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 PHI  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 PHI  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 PHI  Var_01    CD1  CG   CB   CA    98.43  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
 PHI  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
 PHI  plan-1  CB   0.020
 PHI  plan-1  CG   0.020
 PHI  plan-1  CD1  0.020
 PHI  plan-1  CD2  0.020
 PHI  plan-1  CE1  0.020
 PHI  plan-1  CE2  0.020
 PHI  plan-1  CZ   0.020
 PHI  plan-1  I    0.020
 PHI  plan-1  HD1  0.020
 PHI  plan-1  HD2  0.020
 PHI  plan-1  HE1  0.020
 PHI  plan-1  HE2  0.020
 PHI  plan-2  CA   0.020
 PHI  plan-2  C    0.020
 PHI  plan-2  O    0.020
 PHI  plan-2  OXT  0.020

