# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:40:06 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-amino-2,4,5-trideoxy-5-phenyl-L-threo-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)CC(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
 PSA  PSA  '4-amino-2,4,5-trideoxy-5-phenyl-L-threo-pentonic acid'  peptide  29  15  .  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_PSA
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
 PSA  N    N  NH2    0  -0.791   0.0598   1.0938  -1.1580
 PSA  CA   C  CH1    0  -0.086  -0.1898   0.0303  -0.1999
 PSA  CB   C  CH2    0  -0.521   0.8382   0.1156   0.9342
 PSA  CG   C  CR6    0   0.169   2.2539  -0.0333   0.4575
 PSA  CD1  C  CR16   0  -0.312   3.0418   1.0789   0.1701
 PSA  CD2  C  CR16   0  -0.315   2.8079  -1.2985   0.2718
 PSA  CE1  C  CR16   0  -0.245   4.3446   0.9346  -0.2879
 PSA  CE2  C  CR16   0  -0.241   4.1088  -1.4505  -0.1900
 PSA  CZ   C  CR16   0  -0.277   4.8831  -0.3326  -0.4726
 PSA  CH   C  CH1    0   0.034  -1.6185  -0.0215   0.3719
 PSA  OH   O  OH1    0  -0.674  -1.9250   1.1463   1.1154
 PSA  CM   C  CH2    0  -0.610  -2.6693  -0.2816  -0.6952
 PSA  C    C  C      0   0.414  -4.0816  -0.5095  -0.1225
 PSA  O    O  O      0  -0.615  -4.1695  -1.2728   0.8604
 PSA  OXT  O  OC    -1  -0.619  -5.0278   0.0587  -0.7043
 PSA  H    H  HNH2   0   0.350  -0.5983   1.0530  -1.9262
 PSA  H2   H  HNH2   0   0.331  -0.0526   2.0011  -0.7219
 PSA  HA   H  HCH1   0   0.223  -0.0315  -0.9221  -0.7210
 PSA  HB2  H  HCH2   0   0.238   0.7191   1.0690   1.4566
 PSA  HB3  H  HCH2   0   0.241   0.6153  -0.6678   1.6635
 PSA  HD1  H  HCR6   0   0.238   2.6329   2.0717   0.3148
 PSA  HD2  H  HCR6   0   0.241   2.2148  -2.1784   0.4951
 PSA  HE1  H  HCR6   0   0.249   4.9403   1.8136  -0.5004
 PSA  HE2  H  HCR6   0   0.250   4.5192  -2.4432  -0.3256
 PSA  HZ   H  HCR6   0   0.250   5.8990  -0.4483  -0.8282
 PSA  HC   H  HCH1   0   0.211  -1.6579  -0.8472   1.0888
 PSA  HH   H  HOH1   0   0.435  -2.0884   1.8627   0.4931
 PSA  HM1  H  HCH2   0   0.201  -2.6903   0.5375  -1.4219
 PSA  HM2  H  HCH2   0   0.231  -2.3829  -1.1804  -1.2539

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
 PSA  N    CA   single    1.458  0.019  1.458
 PSA  N    H    single    0.860  0.020  0.860
 PSA  N    H2   single    0.890  0.020  1.040
 PSA  CA   CB   single    1.530  0.020  1.530
 PSA  CA   CH   single    1.540  0.020  1.540
 PSA  CA   HA   single    0.970  0.020  0.970
 PSA  CB   CG   single    1.501  0.020  1.501
 PSA  CB   HB2  single    0.970  0.020  1.090
 PSA  CB   HB3  single    0.970  0.020  1.090
 PSA  CG   CD1  aromatic  1.393  0.020  1.393
 PSA  CG   CD2  aromatic  1.394  0.020  1.394
 PSA  CD1  CE1  aromatic  1.389  0.020  1.389
 PSA  CD1  HD1  single    0.930  0.020  1.080
 PSA  CD2  CE2  aromatic  1.389  0.020  1.389
 PSA  CD2  HD2  single    0.930  0.020  1.080
 PSA  CE1  CZ   aromatic  1.389  0.020  1.389
 PSA  CE1  HE1  single    0.930  0.020  1.080
 PSA  CE2  CZ   aromatic  1.389  0.020  1.389
 PSA  CE2  HE2  single    0.930  0.020  1.080
 PSA  CZ   HZ   single    0.930  0.020  1.080
 PSA  CH   OH   single    1.418  0.020  1.418
 PSA  CH   CM   single    1.520  0.020  1.520
 PSA  CH   HC   single    0.970  0.020  1.090
 PSA  OH   HH   single    0.850  0.020  0.980
 PSA  CM   C    single    1.541  0.020  1.541
 PSA  CM   HM1  single    0.970  0.020  1.090
 PSA  CM   HM2  single    0.970  0.020  1.090
 PSA  C    O    deloc     1.231  0.020  1.231
 PSA  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
 PSA  H2   N    H    106.89  3.000
 PSA  H2   N    CA   110.65  3.000
 PSA  H    N    CA   114.00  3.000
 PSA  HA   CA   CH   106.32  3.000
 PSA  HA   CA   CB   109.00  3.000
 PSA  CH   CA   CB   110.45  3.000
 PSA  HA   CA   N    110.00  3.000
 PSA  CH   CA   N    115.40  3.000
 PSA  CB   CA   N    110.50  1.700
 PSA  HB3  CB   HB2  106.48  3.000
 PSA  HB3  CB   CG   109.45  3.000
 PSA  HB2  CB   CG   109.93  3.000
 PSA  HB3  CB   CA   108.48  3.000
 PSA  HB2  CB   CA   109.20  3.000
 PSA  CG   CB   CA   113.08  3.000
 PSA  CD2  CG   CD1  118.20  3.000
 PSA  CD2  CG   CB   120.48  3.000
 PSA  CD1  CG   CB   121.31  3.000
 PSA  HD1  CD1  CE1  119.57  3.000
 PSA  HD1  CD1  CG   119.38  3.000
 PSA  CE1  CD1  CG   121.05  3.000
 PSA  HD2  CD2  CE2  119.47  3.000
 PSA  HD2  CD2  CG   119.46  3.000
 PSA  CE2  CD2  CG   121.07  3.000
 PSA  HE1  CE1  CZ   120.07  3.000
 PSA  HE1  CE1  CD1  119.77  3.000
 PSA  CZ   CE1  CD1  120.16  3.000
 PSA  HE2  CE2  CZ   120.08  3.000
 PSA  HE2  CE2  CD2  119.81  3.000
 PSA  CZ   CE2  CD2  120.11  3.000
 PSA  HZ   CZ   CE2  120.26  3.000
 PSA  HZ   CZ   CE1  120.33  3.000
 PSA  CE2  CZ   CE1  119.41  3.000
 PSA  HC   CH   CM   107.82  3.000
 PSA  HC   CH   OH   105.67  3.000
 PSA  CM   CH   OH   111.08  3.000
 PSA  HC   CH   CA   107.58  3.000
 PSA  CM   CH   CA   112.74  3.000
 PSA  OH   CH   CA   111.57  3.000
 PSA  HH   OH   CH   108.09  3.000
 PSA  HM2  CM   HM1  106.26  3.000
 PSA  HM2  CM   C    107.91  3.000
 PSA  HM1  CM   C    109.85  3.000
 PSA  HM2  CM   CH   108.51  3.000
 PSA  HM1  CM   CH   110.55  3.000
 PSA  C    CM   CH   113.45  3.000
 PSA  OXT  C    O    126.34  3.000
 PSA  OXT  C    CM   117.03  3.000
 PSA  O    C    CM   116.61  3.000

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
 PSA  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PSA  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PSA  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PSA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PSA  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PSA  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PSA  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PSA  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PSA  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 PSA  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 PSA  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 PSA  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 PSA  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 PSA  Var_01    CD1  CG   CB   CA    94.92  30.0  2
 PSA  Var_02    O    C    CM   CH   -45.20  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
 PSA  chir_01  CA  N   CB  CH  negativ
 PSA  chir_02  CH  OH  CA  CM  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
 PSA  plan-1  CB   0.020
 PSA  plan-1  CG   0.020
 PSA  plan-1  CD1  0.020
 PSA  plan-1  CD2  0.020
 PSA  plan-1  CE1  0.020
 PSA  plan-1  CE2  0.020
 PSA  plan-1  CZ   0.020
 PSA  plan-1  HD1  0.020
 PSA  plan-1  HD2  0.020
 PSA  plan-1  HE1  0.020
 PSA  plan-1  HE2  0.020
 PSA  plan-1  HZ   0.020
 PSA  plan-2  CM   0.020
 PSA  plan-2  C    0.020
 PSA  plan-2  O    0.020
 PSA  plan-2  OXT  0.020

