# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:43:43 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2S)-2-amino-3-phenylpropan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)Cc1ccccc1
#
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
 PHL  PHL  (2S)-2-amino-3-phenylpropan-1-ol  L-peptide  24  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 PERFECT
;

data_comp_PHL
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
 PHL  N    N  NH2   0  -0.780  -10.7900  16.5324   8.7076
 PHL  CA   C  CH1   0  -0.120  -11.3503  17.1503   9.8974
 PHL  C    C  CH2   0  -0.172  -10.9848  18.6356   9.9958
 PHL  O    O  OH1   0  -0.664  -11.6240  19.3252  11.0464
 PHL  CB   C  CH2   0  -0.530  -10.9004  16.3759  11.1405
 PHL  CG   C  CR6   0   0.166  -11.3843  14.9545  11.1497
 PHL  CD1  C  CR16  0  -0.306  -12.6870  14.6610  11.5490
 PHL  CD2  C  CR16  0  -0.316  -10.5667  13.9043  10.7401
 PHL  CE1  C  CR16  0  -0.240  -13.1637  13.3573  11.5353
 PHL  CE2  C  CR16  0  -0.241  -11.0362  12.5972  10.7284
 PHL  CZ   C  CR16  0  -0.274  -12.3381  12.3188  11.1231
 PHL  H    H  HNH2  0   0.346  -11.1121  17.0219   7.8812
 PHL  H2   H  HNH2  0   0.336   -9.7805  16.6293   8.7156
 PHL  HA   H  HCH1  0   0.228  -12.4416  17.0753   9.8263
 PHL  HC1  H  HCH2  0   0.190   -9.8904  18.7276  10.0531
 PHL  HC2  H  HCH2  0   0.220  -11.2952  19.1261   9.0689
 PHL  HO   H  HOH1  0   0.448  -11.2006  19.0876  11.8758
 PHL  HB2  H  HCH2  0   0.240   -9.8068  16.4042  11.1960
 PHL  HB3  H  HCH2  0   0.241  -11.2725  16.8815  12.0353
 PHL  HD1  H  HCR6  0   0.241  -13.3368  15.4645  11.8781
 PHL  HD2  H  HCR6  0   0.240   -9.5485  14.1108  10.4324
 PHL  HE1  H  HCR6  0   0.249  -14.1786  13.1512  11.8514
 PHL  HE2  H  HCR6  0   0.248  -10.3839  11.7944  10.4082
 PHL  HZ   H  HCR6  0   0.249  -12.7054  11.3005  11.1141

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
 PHL  N    CA   single    1.458  0.019  1.458
 PHL  N    H    single    0.860  0.020  0.860
 PHL  N    H2   single    0.890  0.020  1.040
 PHL  CA   C    single    1.525  0.021  1.525
 PHL  CA   CB   single    1.530  0.020  1.530
 PHL  CA   HA   single    0.970  0.020  0.970
 PHL  C    O    single    1.231  0.020  1.231
 PHL  C    HC1  single    0.970  0.020  1.090
 PHL  C    HC2  single    0.970  0.020  1.090
 PHL  O    HO   single    0.850  0.020  0.980
 PHL  CB   CG   single    1.502  0.020  1.502
 PHL  CB   HB2  single    0.970  0.020  1.090
 PHL  CB   HB3  single    0.970  0.020  1.090
 PHL  CG   CD1  aromatic  1.394  0.020  1.394
 PHL  CG   CD2  aromatic  1.393  0.020  1.393
 PHL  CD1  CE1  aromatic  1.388  0.020  1.388
 PHL  CD1  HD1  single    0.930  0.020  1.080
 PHL  CD2  CE2  aromatic  1.389  0.020  1.389
 PHL  CD2  HD2  single    0.930  0.020  1.080
 PHL  CE1  CZ   aromatic  1.389  0.020  1.389
 PHL  CE1  HE1  single    0.930  0.020  1.080
 PHL  CE2  CZ   aromatic  1.389  0.020  1.389
 PHL  CE2  HE2  single    0.930  0.020  1.080
 PHL  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
 PHL  H2   N    H    106.07  3.000
 PHL  H2   N    CA   109.68  3.000
 PHL  H    N    CA   114.00  3.000
 PHL  HA   CA   CB   109.00  3.000
 PHL  HA   CA   C    109.00  3.000
 PHL  CB   CA   C    110.10  1.900
 PHL  HA   CA   N    110.00  3.000
 PHL  CB   CA   N    110.50  1.700
 PHL  C    CA   N    111.00  2.800
 PHL  HC2  C    HC1  106.80  3.000
 PHL  HC2  C    O    106.47  3.000
 PHL  HC1  C    O    111.80  3.000
 PHL  HC2  C    CA   108.21  3.000
 PHL  HC1  C    CA   108.76  3.000
 PHL  O    C    CA   120.80  1.700
 PHL  HO   O    C    108.81  3.000
 PHL  HB3  CB   HB2  106.65  3.000
 PHL  HB3  CB   CG   108.86  3.000
 PHL  HB2  CB   CG   110.24  3.000
 PHL  HB3  CB   CA   109.29  3.000
 PHL  HB2  CB   CA   108.73  3.000
 PHL  CG   CB   CA   112.88  3.000
 PHL  CD2  CG   CD1  118.31  3.000
 PHL  CD2  CG   CB   121.53  3.000
 PHL  CD1  CG   CB   120.15  3.000
 PHL  HD1  CD1  CE1  119.55  3.000
 PHL  HD1  CD1  CG   119.40  3.000
 PHL  CE1  CD1  CG   121.06  3.000
 PHL  HD2  CD2  CE2  119.64  3.000
 PHL  HD2  CD2  CG   119.44  3.000
 PHL  CE2  CD2  CG   120.92  3.000
 PHL  HE1  CE1  CZ   120.09  3.000
 PHL  HE1  CE1  CD1  119.85  3.000
 PHL  CZ   CE1  CD1  120.06  3.000
 PHL  HE2  CE2  CZ   120.02  3.000
 PHL  HE2  CE2  CD2  119.77  3.000
 PHL  CZ   CE2  CD2  120.21  3.000
 PHL  HZ   CZ   CE2  120.28  3.000
 PHL  HZ   CZ   CE1  120.27  3.000
 PHL  CE2  CZ   CE1  119.45  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
 PHL  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PHL  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PHL  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PHL  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PHL  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PHL  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PHL  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PHL  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PHL  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 PHL  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 PHL  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 PHL  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 PHL  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 PHL  Var_01    CD1  CG   CB   CA   -80.54  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
 PHL  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
 PHL  plan-1  CB   0.020
 PHL  plan-1  CG   0.020
 PHL  plan-1  CD1  0.020
 PHL  plan-1  CD2  0.020
 PHL  plan-1  CE1  0.020
 PHL  plan-1  CE2  0.020
 PHL  plan-1  CZ   0.020
 PHL  plan-1  HD1  0.020
 PHL  plan-1  HD2  0.020
 PHL  plan-1  HE1  0.020
 PHL  plan-1  HE2  0.020
 PHL  plan-1  HZ   0.020

