# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:24:12 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 4-(carboxymethyl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(CC(O)=O)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
 1PA  1PA  4-(carboxymethyl)-L-phenylalanine  L-peptide  27  16  .  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_1PA
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
 1PA  N    N  NH2    0  -0.783  27.0858  -2.7658  -1.5038
 1PA  CA   C  CH1    0  -0.197  26.7684  -1.6225  -0.6639
 1PA  CB   C  CH2    0  -0.519  27.3026  -0.3329  -1.3097
 1PA  CG   C  CR6    0   0.149  28.7952  -0.3049  -1.4748
 1PA  CD1  C  CR16   0  -0.298  29.6236  -0.0012  -0.3970
 1PA  CE1  C  CR16   0  -0.299  31.0043   0.0325  -0.5380
 1PA  CD2  C  CR16   0  -0.313  29.4046  -0.5775  -2.6969
 1PA  CE2  C  CR16   0  -0.299  30.7850  -0.5430  -2.8371
 1PA  CZ   C  CR6    0   0.159  31.6152  -0.2361  -1.7616
 1PA  CH   C  CH2    0  -0.685  33.1039  -0.1913  -1.9067
 1PA  CO   C  C      0   0.413  33.8285  -1.5589  -1.7627
 1PA  O1   O  OC    -1  -0.593  33.1523  -2.5891  -1.9306
 1PA  O2   O  O      0  -0.614  35.0499  -1.4880  -1.5231
 1PA  C    C  C      0   0.378  25.2608  -1.4185  -0.3556
 1PA  O    O  O      0  -0.602  24.4458  -1.9061  -1.1646
 1PA  OXT  O  OC    -1  -0.615  24.9971  -0.7459   0.6625
 1PA  H    H  HNH2   0   0.333  26.8609  -3.6134  -0.9964
 1PA  H2   H  HNH2   0   0.321  26.4407  -2.7604  -2.2868
 1PA  HA   H  HCH1   0   0.210  27.2925  -1.7542   0.2890
 1PA  HB2  H  HCH2   0   0.228  26.8216  -0.2022  -2.2850
 1PA  HB3  H  HCH2   0   0.235  26.9905   0.5142  -0.6944
 1PA  HD1  H  HCR6   0   0.231  29.1816   0.2253   0.5677
 1PA  HE1  H  HCR6   0   0.232  31.6188   0.2843   0.3195
 1PA  HD2  H  HCR6   0   0.230  28.7873  -0.8104  -3.5573
 1PA  HE2  H  HCR6   0   0.230  31.2243  -0.7480  -3.8070
 1PA  HH2  H  HCH2   0   0.240  33.3638   0.1994  -2.8972
 1PA  HH3  H  HCH2   0   0.228  33.5318   0.5127  -1.1889

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
 1PA  N    CA   single    1.458  0.019  1.458
 1PA  N    H    single    0.860  0.020  0.860
 1PA  N    H2   single    0.890  0.020  1.040
 1PA  CA   CB   single    1.530  0.020  1.530
 1PA  CA   C    single    1.525  0.021  1.525
 1PA  CA   HA   single    0.970  0.020  0.970
 1PA  CB   CG   single    1.502  0.020  1.502
 1PA  CB   HB2  single    0.970  0.020  1.090
 1PA  CB   HB3  single    0.970  0.020  1.090
 1PA  CG   CD1  aromatic  1.393  0.020  1.393
 1PA  CG   CD2  aromatic  1.393  0.020  1.393
 1PA  CD1  CE1  aromatic  1.388  0.020  1.388
 1PA  CD1  HD1  single    0.930  0.020  1.080
 1PA  CE1  CZ   aromatic  1.394  0.020  1.394
 1PA  CE1  HE1  single    0.930  0.020  1.080
 1PA  CD2  CE2  aromatic  1.388  0.020  1.388
 1PA  CD2  HD2  single    0.930  0.020  1.080
 1PA  CE2  CZ   aromatic  1.393  0.020  1.393
 1PA  CE2  HE2  single    0.930  0.020  1.080
 1PA  CZ   CH   single    1.496  0.020  1.496
 1PA  CH   CO   single    1.554  0.020  1.554
 1PA  CH   HH2  single    0.970  0.020  1.090
 1PA  CH   HH3  single    0.970  0.020  1.090
 1PA  CO   O1   deloc     1.244  0.020  1.244
 1PA  CO   O2   deloc     1.247  0.020  1.247
 1PA  C    O    deloc     1.231  0.020  1.231
 1PA  C    OXT  deloc     1.248  0.020  1.248

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
 1PA  H2   N    H    104.47  3.000
 1PA  H2   N    CA   107.63  3.000
 1PA  H    N    CA   114.00  3.000
 1PA  HA   CA   C    109.00  3.000
 1PA  HA   CA   CB   109.00  3.000
 1PA  C    CA   CB   110.10  1.900
 1PA  HA   CA   N    110.00  3.000
 1PA  C    CA   N    111.00  2.800
 1PA  CB   CA   N    110.50  1.700
 1PA  HB3  CB   HB2  106.47  3.000
 1PA  HB3  CB   CG   109.35  3.000
 1PA  HB2  CB   CG   109.65  3.000
 1PA  HB3  CB   CA   108.32  3.000
 1PA  HB2  CB   CA   108.75  3.000
 1PA  CG   CB   CA   114.02  3.000
 1PA  CD2  CG   CD1  117.48  3.000
 1PA  CD2  CG   CB   121.85  3.000
 1PA  CD1  CG   CB   120.67  3.000
 1PA  HD1  CD1  CE1  119.37  3.000
 1PA  HD1  CD1  CG   119.41  3.000
 1PA  CE1  CD1  CG   121.21  3.000
 1PA  HE1  CE1  CZ   119.37  3.000
 1PA  HE1  CE1  CD1  119.26  3.000
 1PA  CZ   CE1  CD1  121.36  3.000
 1PA  HD2  CD2  CE2  119.43  3.000
 1PA  HD2  CD2  CG   119.30  3.000
 1PA  CE2  CD2  CG   121.26  3.000
 1PA  HE2  CE2  CZ   119.40  3.000
 1PA  HE2  CE2  CD2  119.25  3.000
 1PA  CZ   CE2  CD2  121.35  3.000
 1PA  CH   CZ   CE2  121.64  3.000
 1PA  CH   CZ   CE1  121.03  3.000
 1PA  CE2  CZ   CE1  117.33  3.000
 1PA  HH3  CH   HH2  105.73  3.000
 1PA  HH3  CH   CO   108.87  3.000
 1PA  HH2  CH   CO   106.67  3.000
 1PA  HH3  CH   CZ   110.19  3.000
 1PA  HH2  CH   CZ   109.52  3.000
 1PA  CO   CH   CZ   115.37  3.000
 1PA  O2   CO   O1   127.28  3.000
 1PA  O2   CO   CH   115.12  3.000
 1PA  O1   CO   CH   117.57  3.000
 1PA  OXT  C    O    126.97  3.000
 1PA  OXT  C    CA   115.98  3.000
 1PA  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
 1PA  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 1PA  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 1PA  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 1PA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 1PA  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 1PA  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 1PA  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 1PA  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 1PA  CONST_09  CH   CZ   CE1  CD1  180.00   0.0  0
 1PA  CONST_10  CH   CZ   CE2  CD2  180.00   0.0  0
 1PA  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 1PA  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 1PA  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 1PA  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 1PA  Var_01    CD1  CG   CB   CA   -79.51  30.0  2
 1PA  Var_02    CO   CH   CZ   CE1   95.31  30.0  2
 1PA  Var_03    O1   CO   CH   CZ    20.36  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
 1PA  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
 1PA  plan-1  CB   0.020
 1PA  plan-1  CG   0.020
 1PA  plan-1  CD1  0.020
 1PA  plan-1  CE1  0.020
 1PA  plan-1  CD2  0.020
 1PA  plan-1  CE2  0.020
 1PA  plan-1  CZ   0.020
 1PA  plan-1  CH   0.020
 1PA  plan-1  HD1  0.020
 1PA  plan-1  HE1  0.020
 1PA  plan-1  HD2  0.020
 1PA  plan-1  HE2  0.020
 1PA  plan-2  CH   0.020
 1PA  plan-2  CO   0.020
 1PA  plan-2  O1   0.020
 1PA  plan-2  O2   0.020
 1PA  plan-3  CA   0.020
 1PA  plan-3  C    0.020
 1PA  plan-3  O    0.020
 1PA  plan-3  OXT  0.020

