# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:13:29 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R)-amino(phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C(O)=O)c1ccccc1
#
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
 PGY  PGY  '(2R)-amino(phenyl)ethanoic acid'  L-peptide  19  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PGY
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
 PGY  N    N  NH2    0  -0.776   1.3522   1.2873  -1.4626
 PGY  CA   C  CH1    0  -0.270   0.0187   0.9680  -0.9823
 PGY  CB   C  CR6    0   0.121   0.0452   0.4553   0.4419
 PGY  CG1  C  CR16   0  -0.277  -1.1317   0.4120   1.1917
 PGY  CG2  C  CR16   0  -0.308   1.2169  -0.0142   1.0293
 PGY  CD1  C  CR16   0  -0.229  -1.1367  -0.0855   2.4863
 PGY  CD2  C  CR16   0  -0.224   1.2134  -0.5219   2.3242
 PGY  CE   C  CR16   0  -0.259   0.0379  -0.5600   3.0597
 PGY  C    C  C      0   0.330  -0.7399  -0.0906  -1.8401
 PGY  O    O  O      0  -0.561  -0.0341  -0.9139  -2.4529
 PGY  OXT  O  OC    -1  -0.606  -1.9839  -0.0386  -1.8151
 PGY  H    H  HNH2   0   0.333   1.2589   1.8550  -2.2960
 PGY  H2   H  HNH2   0   0.329   1.7752   0.4247  -1.7891
 PGY  HA   H  HCH1   0   0.239  -0.5720   1.8887  -0.9896
 PGY  HG1  H  HCR6   0   0.237  -2.0539   0.7728   0.7550
 PGY  HG2  H  HCR6   0   0.227   2.1482   0.0279   0.4798
 PGY  HD1  H  HCR6   0   0.231  -2.0605  -0.1050   3.0513
 PGY  HD2  H  HCR6   0   0.231   2.1373  -0.8824   2.7592
 PGY  HE   H  HCR6   0   0.232   0.0346  -0.9518   4.0689

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
 PGY  N    CA   single    1.451  0.016  1.451
 PGY  N    H    single    0.860  0.020  0.860
 PGY  N    H2   single    0.890  0.020  1.040
 PGY  CA   CB   single    1.514  0.020  1.514
 PGY  CA   C    single    1.516  0.018  1.516
 PGY  CA   HA   single    0.970  0.020  1.090
 PGY  CB   CG1  aromatic  1.396  0.020  1.396
 PGY  CB   CG2  aromatic  1.392  0.020  1.392
 PGY  CG1  CD1  aromatic  1.387  0.020  1.387
 PGY  CG1  HG1  single    0.930  0.020  1.080
 PGY  CG2  CD2  aromatic  1.391  0.020  1.391
 PGY  CG2  HG2  single    0.930  0.020  1.080
 PGY  CD1  CE   aromatic  1.391  0.020  1.391
 PGY  CD1  HD1  single    0.930  0.020  1.080
 PGY  CD2  CE   aromatic  1.387  0.020  1.387
 PGY  CD2  HD2  single    0.930  0.020  1.080
 PGY  CE   HE   single    0.930  0.020  1.080
 PGY  C    O    deloc     1.231  0.020  1.231
 PGY  C    OXT  deloc     1.245  0.020  1.245

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
 PGY  H2   N    H    104.49  3.000
 PGY  H2   N    CA   107.59  3.000
 PGY  H    N    CA   114.00  3.000
 PGY  HA   CA   C    107.76  3.000
 PGY  HA   CA   CB   107.51  3.000
 PGY  C    CA   CB   107.22  3.000
 PGY  HA   CA   N    107.97  3.000
 PGY  C    CA   N    113.30  2.900
 PGY  CB   CA   N    111.67  3.000
 PGY  CG2  CB   CG1  118.19  3.000
 PGY  CG2  CB   CA   121.73  3.000
 PGY  CG1  CB   CA   120.06  3.000
 PGY  HG1  CG1  CD1  119.55  3.000
 PGY  HG1  CG1  CB   119.42  3.000
 PGY  CD1  CG1  CB   121.03  3.000
 PGY  HG2  CG2  CD2  119.29  3.000
 PGY  HG2  CG2  CB   119.79  3.000
 PGY  CD2  CG2  CB   120.92  3.000
 PGY  HD1  CD1  CE   119.95  3.000
 PGY  HD1  CD1  CG1  119.77  3.000
 PGY  CE   CD1  CG1  120.28  3.000
 PGY  HD2  CD2  CE   120.05  3.000
 PGY  HD2  CD2  CG2  119.56  3.000
 PGY  CE   CD2  CG2  120.38  3.000
 PGY  HE   CE   CD2  120.45  3.000
 PGY  HE   CE   CD1  120.36  3.000
 PGY  CD2  CE   CD1  119.20  3.000
 PGY  OXT  C    O    127.12  3.000
 PGY  OXT  C    CA   116.52  3.000
 PGY  O    C    CA   120.80  2.100

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
 PGY  CONST_01  CE   CD1  CG1  CB     0.00  0.0  0
 PGY  CONST_02  CE   CD2  CG2  CB     0.00  0.0  0
 PGY  CONST_03  CD2  CG2  CB   CG1    0.00  0.0  0
 PGY  CONST_04  CD2  CE   CD1  CG1    0.00  0.0  0
 PGY  CONST_05  CD1  CG1  CB   CG2    0.00  0.0  0
 PGY  CONST_06  CD1  CE   CD2  CG2    0.00  0.0  0
 PGY  CONST_07  CD1  CG1  CB   CA   180.00  0.0  0
 PGY  CONST_08  CD2  CG2  CB   CA   180.00  0.0  0
 PGY  CONST_09  HD1  CD1  CG1  CB   180.00  0.0  0
 PGY  CONST_10  HD2  CD2  CG2  CB   180.00  0.0  0
 PGY  CONST_11  HG2  CG2  CB   CG1  180.00  0.0  0
 PGY  CONST_12  HE   CE   CD1  CG1  180.00  0.0  0
 PGY  CONST_13  HG1  CG1  CB   CG2  180.00  0.0  0

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
 PGY  chir_01  CA  N  CB  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
 PGY  plan-1  CA   0.020
 PGY  plan-1  CB   0.020
 PGY  plan-1  CG1  0.020
 PGY  plan-1  CG2  0.020
 PGY  plan-1  CD1  0.020
 PGY  plan-1  CD2  0.020
 PGY  plan-1  CE   0.020
 PGY  plan-1  HG1  0.020
 PGY  plan-1  HG2  0.020
 PGY  plan-1  HD1  0.020
 PGY  plan-1  HD2  0.020
 PGY  plan-1  HE   0.020
 PGY  plan-2  CA   0.020
 PGY  plan-2  C    0.020
 PGY  plan-2  O    0.020
 PGY  plan-2  OXT  0.020

