# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:06:31 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2S)-2-amino-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCc1ccccc1)C(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
 HPE  HPE  '(2S)-2-amino-4-phenylbutanoic acid'  L-peptide  25  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HPE
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
 HPE  N    N  NH2    0  -0.800  5.1201  20.0280  15.4011
 HPE  CA   C  CH1    0  -0.201  4.0824  20.6517  16.2074
 HPE  C    C  C      0   0.400  2.7785  20.8194  15.3903
 HPE  O    O  O      0  -0.603  2.8956  20.9224  14.1529
 HPE  CB   C  CH2    0  -0.421  4.4584  22.0222  16.7948
 HPE  CG   C  CH2    0  -0.513  5.6537  21.9793  17.7497
 HPE  CD   C  CR6    0   0.144  5.9466  23.3312  18.3360
 HPE  CE1  C  CR16   0  -0.311  6.7615  24.2400  17.6634
 HPE  CE2  C  CR16   0  -0.314  5.3709  23.7277  19.5417
 HPE  CZ1  C  CR16   0  -0.238  6.9945  25.5083  18.1785
 HPE  CZ2  C  CR16   0  -0.238  5.6013  24.9943  20.0625
 HPE  CH   C  CR16   0  -0.274  6.4149  25.8906  19.3818
 HPE  OXT  O  OC    -1  -0.613  1.7219  20.8860  16.0504
 HPE  H    H  HNH2   0   0.334  6.0125  20.0599  15.8781
 HPE  H2   H  HNH2   0   0.324  5.2250  20.5595  14.5458
 HPE  HA   H  HCH1   0   0.197  3.8652  19.9843  17.0502
 HPE  HB2  H  HCH2   0   0.214  4.6728  22.7208  15.9779
 HPE  HB3  H  HCH2   0   0.218  3.5971  22.4265  17.3337
 HPE  HG2  H  HCH2   0   0.235  5.4448  21.2639  18.5501
 HPE  HG3  H  HCH2   0   0.230  6.5402  21.6154  17.2234
 HPE  HE1  H  HCR6   0   0.242  7.2217  23.9499  16.7253
 HPE  HE2  H  HCR6   0   0.242  4.7349  23.0339  20.0800
 HPE  HZ1  H  HCR6   0   0.249  7.6330  26.1985  17.6414
 HPE  HZ2  H  HCR6   0   0.249  5.1468  25.2800  21.0029
 HPE  HH   H  HCR6   0   0.249  6.5975  26.8777  19.7864

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
 HPE  N    CA   single    1.458  0.019  1.458
 HPE  N    H    single    0.860  0.020  0.860
 HPE  N    H2   single    0.890  0.020  1.040
 HPE  CA   C    single    1.525  0.021  1.525
 HPE  CA   CB   single    1.530  0.020  1.530
 HPE  CA   HA   single    0.970  0.020  0.970
 HPE  C    O    deloc     1.231  0.020  1.231
 HPE  C    OXT  deloc     1.248  0.020  1.248
 HPE  CB   CG   single    1.530  0.020  1.530
 HPE  CB   HB2  single    0.970  0.020  1.090
 HPE  CB   HB3  single    0.970  0.020  1.090
 HPE  CG   CD   single    1.502  0.020  1.502
 HPE  CG   HG2  single    0.970  0.020  1.090
 HPE  CG   HG3  single    0.970  0.020  1.090
 HPE  CD   CE1  aromatic  1.394  0.020  1.394
 HPE  CD   CE2  aromatic  1.394  0.020  1.394
 HPE  CE1  CZ1  aromatic  1.389  0.020  1.389
 HPE  CE1  HE1  single    0.930  0.020  1.080
 HPE  CE2  CZ2  aromatic  1.389  0.020  1.389
 HPE  CE2  HE2  single    0.930  0.020  1.080
 HPE  CZ1  CH   aromatic  1.389  0.020  1.389
 HPE  CZ1  HZ1  single    0.930  0.020  1.080
 HPE  CZ2  CH   aromatic  1.389  0.020  1.389
 HPE  CZ2  HZ2  single    0.930  0.020  1.080
 HPE  CH   HH   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
 HPE  H2   N    H    106.87  3.000
 HPE  H2   N    CA   108.49  3.000
 HPE  H    N    CA   114.00  3.000
 HPE  HA   CA   CB   109.00  3.000
 HPE  HA   CA   C    109.00  3.000
 HPE  CB   CA   C    110.10  1.900
 HPE  HA   CA   N    110.00  3.000
 HPE  CB   CA   N    110.50  1.700
 HPE  C    CA   N    111.00  2.800
 HPE  OXT  C    O    126.87  3.000
 HPE  OXT  C    CA   116.10  3.000
 HPE  O    C    CA   120.80  1.700
 HPE  HB3  CB   HB2  106.60  3.000
 HPE  HB3  CB   CG   108.54  3.000
 HPE  HB2  CB   CG   109.28  3.000
 HPE  HB3  CB   CA   108.98  3.000
 HPE  HB2  CB   CA   109.35  3.000
 HPE  CG   CB   CA   113.85  3.000
 HPE  HG3  CG   HG2  106.82  3.000
 HPE  HG3  CG   CD   109.22  3.000
 HPE  HG2  CG   CD   109.89  3.000
 HPE  HG3  CG   CB   110.01  3.000
 HPE  HG2  CG   CB   109.02  3.000
 HPE  CD   CG   CB   111.75  3.000
 HPE  CE2  CD   CE1  118.27  3.000
 HPE  CE2  CD   CG   120.86  3.000
 HPE  CE1  CD   CG   120.83  3.000
 HPE  HE1  CE1  CZ1  119.61  3.000
 HPE  HE1  CE1  CD   119.42  3.000
 HPE  CZ1  CE1  CD   120.97  3.000
 HPE  HE2  CE2  CZ2  119.65  3.000
 HPE  HE2  CE2  CD   119.33  3.000
 HPE  CZ2  CE2  CD   121.02  3.000
 HPE  HZ1  CZ1  CH   120.01  3.000
 HPE  HZ1  CZ1  CE1  119.81  3.000
 HPE  CH   CZ1  CE1  120.18  3.000
 HPE  HZ2  CZ2  CH   120.08  3.000
 HPE  HZ2  CZ2  CE2  119.79  3.000
 HPE  CH   CZ2  CE2  120.13  3.000
 HPE  HH   CH   CZ2  120.28  3.000
 HPE  HH   CH   CZ1  120.29  3.000
 HPE  CZ2  CH   CZ1  119.43  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
 HPE  CONST_01  CH   CZ1  CE1  CD      0.00   0.0  0
 HPE  CONST_02  CH   CZ2  CE2  CD      0.00   0.0  0
 HPE  CONST_03  CZ2  CE2  CD   CE1     0.00   0.0  0
 HPE  CONST_04  CZ2  CH   CZ1  CE1     0.00   0.0  0
 HPE  CONST_05  CZ1  CE1  CD   CE2     0.00   0.0  0
 HPE  CONST_06  CZ1  CH   CZ2  CE2     0.00   0.0  0
 HPE  CONST_07  CZ1  CE1  CD   CG    180.00   0.0  0
 HPE  CONST_08  CZ2  CE2  CD   CG    180.00   0.0  0
 HPE  CONST_09  HZ1  CZ1  CE1  CD    180.00   0.0  0
 HPE  CONST_10  HZ2  CZ2  CE2  CD    180.00   0.0  0
 HPE  CONST_11  HE2  CE2  CD   CE1   180.00   0.0  0
 HPE  CONST_12  HH   CH   CZ1  CE1   180.00   0.0  0
 HPE  CONST_13  HE1  CE1  CD   CE2   180.00   0.0  0
 HPE  Var_01    CE1  CD   CG   CB    -86.21  30.0  2
 HPE  Var_02    CD   CG   CB   CA   -177.80  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
 HPE  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
 HPE  plan-1  CG   0.020
 HPE  plan-1  CD   0.020
 HPE  plan-1  CE1  0.020
 HPE  plan-1  CE2  0.020
 HPE  plan-1  CZ1  0.020
 HPE  plan-1  CZ2  0.020
 HPE  plan-1  CH   0.020
 HPE  plan-1  HE1  0.020
 HPE  plan-1  HE2  0.020
 HPE  plan-1  HZ1  0.020
 HPE  plan-1  HZ2  0.020
 HPE  plan-1  HH   0.020
 HPE  plan-2  CA   0.020
 HPE  plan-2  C    0.020
 HPE  plan-2  O    0.020
 HPE  plan-2  OXT  0.020

