# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 16:59:58 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  30  15  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.790   0.0935   1.0641  -1.1767
 PSA  CA   C  CH1   0  -0.100  -0.1443   0.0269  -0.1913
 PSA  CB   C  CH2   0  -0.522   0.8899   0.1412   0.9346
 PSA  CG   C  CR6   0   0.168   2.3009  -0.0256   0.4490
 PSA  CD1  C  CR16  0  -0.312   3.0956   1.0770   0.1457
 PSA  CD2  C  CR16  0  -0.314   2.8416  -1.2977   0.2726
 PSA  CE1  C  CR16  0  -0.244   4.3943   0.9166  -0.3190
 PSA  CE2  C  CR16  0  -0.241   4.1380  -1.4655  -0.1962
 PSA  CZ   C  CR16  0  -0.276   4.9201  -0.3571  -0.4944
 PSA  CH   C  CH1   0   0.033  -1.5660  -0.0157   0.4000
 PSA  OH   O  OH1   0  -0.664  -1.8854   1.1489   1.1304
 PSA  CM   C  CH2   0  -0.619  -2.6126  -0.2873  -0.6738
 PSA  C    C  C     0   0.557  -3.9860  -0.5063  -0.0964
 PSA  O    O  O     0  -0.445  -4.2107  -1.0448   0.9589
 PSA  OXT  O  OH1   0  -0.592  -4.9450  -0.0701  -0.9053
 PSA  H    H  HNH2  0   0.355  -0.5409   0.9921  -1.9613
 PSA  H2   H  HNH2  0   0.337  -0.0152   1.9892  -0.7802
 PSA  HA   H  HCH1  0   0.237   0.0100  -0.9376  -0.6893
 PSA  HB2  H  HCH2  0   0.243   0.7788   1.1097   1.4299
 PSA  HB3  H  HCH2  0   0.247   0.6701  -0.6207   1.6870
 PSA  HD1  H  HCR6  0   0.240   2.6956   2.0746   0.2826
 PSA  HD2  H  HCR6  0   0.242   2.2420  -2.1700   0.5080
 PSA  HE1  H  HCR6  0   0.250   4.9962   1.7881  -0.5441
 PSA  HE2  H  HCR6  0   0.251   4.5388  -2.4630  -0.3254
 PSA  HZ   H  HCR6  0   0.251   5.9325  -0.4853  -0.8555
 PSA  HC   H  HCH1  0   0.237  -1.5954  -0.8357   1.1231
 PSA  HH   H  HOH1  0   0.438  -1.9017   1.8988   0.5257
 PSA  HM1  H  HCH2  0   0.262  -2.6458   0.5182  -1.4114
 PSA  HM2  H  HCH2  0   0.294  -2.3488  -1.1973  -1.2235
 PSA  HXT  H  HOH1  0   0.479  -5.8145  -0.2654  -0.5241

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    1.502  0.020  1.502
 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  1.393  0.020  1.393
 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    1.411  0.020  1.411
 PSA  CH   CM   single    1.524  0.020  1.524
 PSA  CH   HC   single    0.970  0.020  1.090
 PSA  OH   HH   single    0.850  0.020  0.980
 PSA  CM   C    single    1.506  0.020  1.506
 PSA  CM   HM1  single    0.970  0.020  1.090
 PSA  CM   HM2  single    0.970  0.020  1.090
 PSA  C    O    double    1.231  0.020  1.231
 PSA  C    OXT  single    1.328  0.020  1.328
 PSA  OXT  HXT  single    0.850  0.020  0.980

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    107.55  3.000
 PSA  H2   N    CA   111.71  3.000
 PSA  H    N    CA   114.00  3.000
 PSA  HA   CA   CH   106.26  3.000
 PSA  HA   CA   CB   109.00  3.000
 PSA  CH   CA   CB   110.05  3.000
 PSA  HA   CA   N    110.00  3.000
 PSA  CH   CA   N    115.59  3.000
 PSA  CB   CA   N    110.50  1.700
 PSA  HB3  CB   HB2  106.56  3.000
 PSA  HB3  CB   CG   109.52  3.000
 PSA  HB2  CB   CG   109.90  3.000
 PSA  HB3  CB   CA   108.54  3.000
 PSA  HB2  CB   CA   109.28  3.000
 PSA  CG   CB   CA   112.84  3.000
 PSA  CD2  CG   CD1  118.28  3.000
 PSA  CD2  CG   CB   120.46  3.000
 PSA  CD1  CG   CB   121.25  3.000
 PSA  HD1  CD1  CE1  119.60  3.000
 PSA  HD1  CD1  CG   119.39  3.000
 PSA  CE1  CD1  CG   121.01  3.000
 PSA  HD2  CD2  CE2  119.48  3.000
 PSA  HD2  CD2  CG   119.50  3.000
 PSA  CE2  CD2  CG   121.02  3.000
 PSA  HE1  CE1  CZ   120.09  3.000
 PSA  HE1  CE1  CD1  119.77  3.000
 PSA  CZ   CE1  CD1  120.15  3.000
 PSA  HE2  CE2  CZ   120.08  3.000
 PSA  HE2  CE2  CD2  119.82  3.000
 PSA  CZ   CE2  CD2  120.11  3.000
 PSA  HZ   CZ   CE2  120.24  3.000
 PSA  HZ   CZ   CE1  120.32  3.000
 PSA  CE2  CZ   CE1  119.44  3.000
 PSA  HC   CH   CM   108.29  3.000
 PSA  HC   CH   OH   105.69  3.000
 PSA  CM   CH   OH   110.87  3.000
 PSA  HC   CH   CA   107.42  3.000
 PSA  CM   CH   CA   111.61  3.000
 PSA  OH   CH   CA   112.62  3.000
 PSA  HH   OH   CH   108.74  3.000
 PSA  HM2  CM   HM1  106.32  3.000
 PSA  HM2  CM   C    106.93  3.000
 PSA  HM1  CM   C    109.78  3.000
 PSA  HM2  CM   CH   109.65  3.000
 PSA  HM1  CM   CH   111.42  3.000
 PSA  C    CM   CH   112.47  3.000
 PSA  OXT  C    O    123.03  3.000
 PSA  OXT  C    CM   112.16  3.000
 PSA  O    C    CM   124.78  3.000
 PSA  HXT  OXT  C    110.00  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  CONST_14  HXT  OXT  C    CM   180.00   0.0  0
 PSA  Var_01    CD1  CG   CB   CA    96.02  30.0  2
 PSA  Var_02    O    C    CM   CH   -34.29  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
 PSA  plan-2  HXT  0.020

