# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:45:49 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2S)-2-amino-3-phenylpropanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)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
 PHA  PHA  (2S)-2-amino-3-phenylpropanal  L-peptide  22  11  .  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_PHA
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
 PHA  N    N  NH2   0  -0.790  -14.8478  21.6596  23.8005
 PHA  CA   C  CH1   0  -0.207  -15.1465  21.0725  25.0910
 PHA  C    C  C1    0   0.185  -13.8317  20.7296  25.7526
 PHA  O    O  O     0  -0.371  -13.6125  19.7361  26.3960
 PHA  CB   C  CH2   0  -0.525  -16.1353  19.9002  25.0972
 PHA  CG   C  CR6   0   0.132  -17.4754  20.3021  24.5512
 PHA  CD1  C  CR16  0  -0.301  -18.4191  20.9187  25.3714
 PHA  CD2  C  CR16  0  -0.316  -17.7920  20.1074  23.2083
 PHA  CE1  C  CR16  0  -0.238  -19.6455  21.3273  24.8662
 PHA  CE2  C  CR16  0  -0.238  -19.0182  20.5141  22.6976
 PHA  CZ   C  CR16  0  -0.271  -19.9493  21.1264  23.5253
 PHA  H    H  HNH2  0   0.362  -15.6578  22.1443  23.4383
 PHA  H2   H  HNH2  0   0.350  -14.6202  20.9365  23.1285
 PHA  HA   H  HCH1  0   0.278  -15.5568  21.8786  25.7164
 PHA  HC   H  H     0   0.202  -13.0530  21.4998  25.5989
 PHA  HB2  H  HCH2  0   0.251  -15.7207  19.0808  24.5036
 PHA  HB3  H  HCH2  0   0.251  -16.2484  19.5277  26.1177
 PHA  HD1  H  HCR6  0   0.245  -18.1925  21.0765  26.4199
 PHA  HD2  H  HCR6  0   0.246  -17.0743  19.6228  22.5566
 PHA  HE1  H  HCR6  0   0.251  -20.3666  21.7997  25.5211
 PHA  HE2  H  HCR6  0   0.251  -19.2461  20.3500  21.6520
 PHA  HZ   H  HCR6  0   0.251  -20.9062  21.4422  23.1299

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
 PHA  N    CA   single    1.458  0.019  1.458
 PHA  N    H    single    0.860  0.020  0.860
 PHA  N    H2   single    0.890  0.020  1.040
 PHA  CA   C    single    1.525  0.021  1.525
 PHA  CA   CB   single    1.530  0.020  1.530
 PHA  CA   HA   single    0.970  0.020  0.970
 PHA  C    O    double    1.231  0.020  1.231
 PHA  C    HC   single    0.930  0.020  1.080
 PHA  CB   CG   single    1.502  0.020  1.502
 PHA  CB   HB2  single    0.970  0.020  1.090
 PHA  CB   HB3  single    0.970  0.020  1.090
 PHA  CG   CD1  aromatic  1.394  0.020  1.394
 PHA  CG   CD2  aromatic  1.393  0.020  1.393
 PHA  CD1  CE1  aromatic  1.388  0.020  1.388
 PHA  CD1  HD1  single    0.930  0.020  1.080
 PHA  CD2  CE2  aromatic  1.389  0.020  1.389
 PHA  CD2  HD2  single    0.930  0.020  1.080
 PHA  CE1  CZ   aromatic  1.389  0.020  1.389
 PHA  CE1  HE1  single    0.930  0.020  1.080
 PHA  CE2  CZ   aromatic  1.388  0.020  1.388
 PHA  CE2  HE2  single    0.930  0.020  1.080
 PHA  CZ   HZ   single    0.930  0.020  1.080

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
 PHA  H2   N    H    106.53  3.000
 PHA  H2   N    CA   110.36  3.000
 PHA  H    N    CA   114.00  3.000
 PHA  HA   CA   CB   109.00  3.000
 PHA  HA   CA   C    109.00  3.000
 PHA  CB   CA   C    110.10  1.900
 PHA  HA   CA   N    110.00  3.000
 PHA  CB   CA   N    110.50  1.700
 PHA  C    CA   N    111.00  2.800
 PHA  HC   C    O    121.38  3.000
 PHA  HC   C    CA   113.19  3.000
 PHA  O    C    CA   120.80  1.700
 PHA  HB3  CB   HB2  106.91  3.000
 PHA  HB3  CB   CG   109.79  3.000
 PHA  HB2  CB   CG   109.97  3.000
 PHA  HB3  CB   CA   109.34  3.000
 PHA  HB2  CB   CA   109.03  3.000
 PHA  CG   CB   CA   111.67  3.000
 PHA  CD2  CG   CD1  118.36  3.000
 PHA  CD2  CG   CB   121.05  3.000
 PHA  CD1  CG   CB   120.56  3.000
 PHA  HD1  CD1  CE1  119.59  3.000
 PHA  HD1  CD1  CG   119.47  3.000
 PHA  CE1  CD1  CG   120.95  3.000
 PHA  HD2  CD2  CE2  119.63  3.000
 PHA  HD2  CD2  CG   119.44  3.000
 PHA  CE2  CD2  CG   120.93  3.000
 PHA  HE1  CE1  CZ   120.08  3.000
 PHA  HE1  CE1  CD1  119.80  3.000
 PHA  CZ   CE1  CD1  120.12  3.000
 PHA  HE2  CE2  CZ   120.11  3.000
 PHA  HE2  CE2  CD2  119.76  3.000
 PHA  CZ   CE2  CD2  120.13  3.000
 PHA  HZ   CZ   CE2  120.25  3.000
 PHA  HZ   CZ   CE1  120.24  3.000
 PHA  CE2  CZ   CE1  119.51  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
 PHA  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PHA  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PHA  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PHA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PHA  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PHA  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PHA  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PHA  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PHA  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 PHA  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 PHA  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 PHA  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 PHA  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 PHA  Var_01    CD1  CG   CB   CA   -83.75  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
 PHA  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
 PHA  plan-1  CB   0.020
 PHA  plan-1  CG   0.020
 PHA  plan-1  CD1  0.020
 PHA  plan-1  CD2  0.020
 PHA  plan-1  CE1  0.020
 PHA  plan-1  CE2  0.020
 PHA  plan-1  CZ   0.020
 PHA  plan-1  HD1  0.020
 PHA  plan-1  HD2  0.020
 PHA  plan-1  HE1  0.020
 PHA  plan-1  HE2  0.020
 PHA  plan-1  HZ   0.020
 PHA  plan-2  CA   0.020
 PHA  plan-2  C    0.020
 PHA  plan-2  O    0.020
 PHA  plan-2  HC   0.020

