# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 23:05:38 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-2-amino-3-(4-hydroxyphenyl)propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C=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
 TYB  TYB  (2S)-2-amino-3-(4-hydroxyphenyl)propanal  L-peptide  23  12  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TYB
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
 TYB  N    N  NH2   0  -0.790  26.4478  14.0419  11.8499
 TYB  CA   C  CH1   0  -0.207  26.9150  13.1953  12.9302
 TYB  C    C  C1    0   0.184  26.6837  13.9433  14.2220
 TYB  O    O  O     0  -0.371  27.4559  13.9960  15.1441
 TYB  CB   C  CH2   0  -0.522  28.3442  12.6539  12.8005
 TYB  CG   C  CR6   0   0.108  28.5057  11.8103  11.5686
 TYB  CD1  C  CR16  0  -0.303  28.9570  12.3499  10.3662
 TYB  CD2  C  CR16  0  -0.286  28.1567  10.4625  11.5779
 TYB  CE1  C  CR16  0  -0.323  29.0611  11.5817   9.2164
 TYB  CE2  C  CR16  0  -0.367  28.2524   9.6784  10.4382
 TYB  CZ   C  CR6   0   0.337  28.7051  10.2359   9.2449
 TYB  OH   O  OH1   0  -0.632  28.8229   9.5260   8.1030
 TYB  H    H  HNH2  0   0.362  26.3517  13.5016  11.0004
 TYB  H2   H  HNH2  0   0.350  27.1306  14.7642  11.6534
 TYB  HA   H  HCH1  0   0.276  26.2238  12.3417  12.9834
 TYB  HC   H  H     0   0.202  25.7065  14.4602  14.2590
 TYB  HB2  H  HCH2  0   0.247  29.0413  13.4965  12.7761
 TYB  HB3  H  HCH2  0   0.247  28.5905  12.0659  13.6874
 TYB  HD1  H  HCR6  0   0.247  29.2434  13.3945  10.3244
 TYB  HD2  H  HCR6  0   0.248  27.8031  10.0075  12.4963
 TYB  HE1  H  HCR6  0   0.257  29.4196  12.0238   8.2949
 TYB  HE2  H  HCR6  0   0.265  27.9764   8.6302  10.4811
 TYB  HH   H  HOH1  0   0.470  28.5481   8.6127   8.2431

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
 TYB  N    CA   single    1.458  0.019  1.458
 TYB  N    H    single    0.860  0.020  0.860
 TYB  N    H2   single    0.890  0.020  1.040
 TYB  CA   C    single    1.525  0.021  1.525
 TYB  CA   CB   single    1.530  0.020  1.530
 TYB  CA   HA   single    0.970  0.020  0.970
 TYB  C    O    double    1.231  0.020  1.231
 TYB  C    HC   single    0.930  0.020  1.080
 TYB  CB   CG   single    1.502  0.020  1.502
 TYB  CB   HB2  single    0.970  0.020  1.090
 TYB  CB   HB3  single    0.970  0.020  1.090
 TYB  CG   CD1  aromatic  1.393  0.020  1.393
 TYB  CG   CD2  aromatic  1.392  0.020  1.392
 TYB  CD1  CE1  aromatic  1.387  0.020  1.387
 TYB  CD1  HD1  single    0.930  0.020  1.080
 TYB  CD2  CE2  aromatic  1.387  0.020  1.387
 TYB  CD2  HD2  single    0.930  0.020  1.080
 TYB  CE1  CZ   aromatic  1.392  0.020  1.392
 TYB  CE1  HE1  single    0.930  0.020  1.080
 TYB  CE2  CZ   aromatic  1.393  0.020  1.393
 TYB  CE2  HE2  single    0.930  0.020  1.080
 TYB  CZ   OH   single    1.350  0.020  1.350
 TYB  OH   HH   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
 TYB  H2   N    H    106.38  3.000
 TYB  H2   N    CA   110.10  3.000
 TYB  H    N    CA   114.00  3.000
 TYB  HA   CA   CB   109.00  3.000
 TYB  HA   CA   C    109.00  3.000
 TYB  CB   CA   C    110.10  1.900
 TYB  HA   CA   N    110.00  3.000
 TYB  CB   CA   N    110.50  1.700
 TYB  C    CA   N    111.00  2.800
 TYB  HC   C    O    121.37  3.000
 TYB  HC   C    CA   113.29  3.000
 TYB  O    C    CA   120.80  1.700
 TYB  HB3  CB   HB2  106.81  3.000
 TYB  HB3  CB   CG   109.84  3.000
 TYB  HB2  CB   CG   110.23  3.000
 TYB  HB3  CB   CA   109.36  3.000
 TYB  HB2  CB   CA   108.90  3.000
 TYB  CG   CB   CA   111.58  3.000
 TYB  CD2  CG   CD1  117.51  3.000
 TYB  CD2  CG   CB   120.75  3.000
 TYB  CD1  CG   CB   121.69  3.000
 TYB  HD1  CD1  CE1  118.82  3.000
 TYB  HD1  CD1  CG   119.48  3.000
 TYB  CE1  CD1  CG   121.70  3.000
 TYB  HD2  CD2  CE2  118.77  3.000
 TYB  HD2  CD2  CG   119.59  3.000
 TYB  CE2  CD2  CG   121.64  3.000
 TYB  HE1  CE1  CZ   119.77  3.000
 TYB  HE1  CE1  CD1  120.28  3.000
 TYB  CZ   CE1  CD1  119.95  3.000
 TYB  HE2  CE2  CZ   120.22  3.000
 TYB  HE2  CE2  CD2  119.76  3.000
 TYB  CZ   CE2  CD2  120.02  3.000
 TYB  OH   CZ   CE2  122.87  3.000
 TYB  OH   CZ   CE1  117.95  3.000
 TYB  CE2  CZ   CE1  119.18  3.000
 TYB  HH   OH   CZ   110.52  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
 TYB  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 TYB  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 TYB  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TYB  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 TYB  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 TYB  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 TYB  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 TYB  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 TYB  CONST_09  OH   CZ   CE1  CD1  180.00   0.0  0
 TYB  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 TYB  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 TYB  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 TYB  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 TYB  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 TYB  Var_01    CD1  CG   CB   CA    93.26  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
 TYB  chir_01  CA  N  C  CB  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
 TYB  plan-1  CB   0.020
 TYB  plan-1  CG   0.020
 TYB  plan-1  CD1  0.020
 TYB  plan-1  CD2  0.020
 TYB  plan-1  CE1  0.020
 TYB  plan-1  CE2  0.020
 TYB  plan-1  CZ   0.020
 TYB  plan-1  OH   0.020
 TYB  plan-1  HD1  0.020
 TYB  plan-1  HD2  0.020
 TYB  plan-1  HE1  0.020
 TYB  plan-1  HE2  0.020
 TYB  plan-2  CA   0.020
 TYB  plan-2  C    0.020
 TYB  plan-2  O    0.020
 TYB  plan-2  HC   0.020

