# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:52:32 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2S)-2-amino-3-phenylpropane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)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
 HPH  HPH  (2S)-2-amino-3-phenylpropane-1,1-diol  peptide  25  12  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HPH
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
 HPH  C    C  CH1   0   0.295  -12.4876  17.1896  28.3423
 HPH  O    O  OH1   0  -0.665  -12.9396  17.0311  27.0406
 HPH  CA   C  CH1   0  -0.161  -12.4006  15.8139  29.0171
 HPH  N    N  NH2   0  -0.818  -12.1002  16.0710  30.4195
 HPH  CB   C  CH2   0  -0.503  -13.7093  15.0243  28.9044
 HPH  CG   C  CR6   0   0.110  -13.5964  13.6517  29.5098
 HPH  CD1  C  CR16  0  -0.298  -12.9061  12.6421  28.8387
 HPH  CD2  C  CR16  0  -0.315  -14.1519  13.3586  30.7528
 HPH  CE1  C  CR16  0  -0.238  -12.7753  11.3770  29.3922
 HPH  CE2  C  CR16  0  -0.239  -14.0237  12.0921  31.3122
 HPH  CZ   C  CR16  0  -0.270  -13.3343  11.0973  30.6338
 HPH  OXT  O  OH1   0  -0.680  -13.3571  18.0228  29.0574
 HPH  HO   H  HOH1  0   0.459  -12.7395  17.8256  26.5357
 HPH  HA   H  HCH1  0   0.228  -11.6108  15.2428  28.5087
 HPH  H    H  HNH2  0   0.366  -12.1786  15.2223  30.9661
 HPH  H2   H  HNH2  0   0.357  -11.1407  16.3803  30.5223
 HPH  HB2  H  HCH2  0   0.240  -14.5131  15.5817  29.3912
 HPH  HB3  H  HCH2  0   0.256  -13.9753  14.9310  27.8507
 HPH  HD1  H  HCR6  0   0.245  -12.4713  12.8503  27.8674
 HPH  HD2  H  HCR6  0   0.249  -14.6976  14.1275  31.2877
 HPH  HE1  H  HCR6  0   0.251  -12.2392  10.6063  28.8530
 HPH  HE2  H  HCR6  0   0.251  -14.4657  11.8841  32.2784
 HPH  HZ   H  HCR6  0   0.252  -13.2351  10.1100  31.0661
 HPH  HC   H  HCH1  0   0.187  -11.4747  17.6299  28.3367
 HPH  HXT  H  HOH1  0   0.440  -13.2512  17.7505  29.9842

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
 HPH  C    O    single    1.231  0.020  1.231
 HPH  C    CA   single    1.525  0.021  1.525
 HPH  C    OXT  single    1.401  0.020  1.401
 HPH  O    HO   single    0.850  0.020  0.980
 HPH  CA   N    single    1.458  0.019  1.458
 HPH  CA   CB   single    1.530  0.020  1.530
 HPH  CA   HA   single    0.970  0.020  0.970
 HPH  N    H    single    0.860  0.020  0.860
 HPH  N    H2   single    0.890  0.020  1.040
 HPH  CB   CG   single    1.504  0.020  1.504
 HPH  CB   HB2  single    0.970  0.020  1.090
 HPH  CB   HB3  single    0.970  0.020  1.090
 HPH  CG   CD1  aromatic  1.395  0.020  1.395
 HPH  CG   CD2  aromatic  1.393  0.020  1.393
 HPH  CD1  CE1  aromatic  1.387  0.020  1.387
 HPH  CD1  HD1  single    0.930  0.020  1.080
 HPH  CD2  CE2  aromatic  1.390  0.020  1.390
 HPH  CD2  HD2  single    0.930  0.020  1.080
 HPH  CE1  CZ   aromatic  1.390  0.020  1.390
 HPH  CE1  HE1  single    0.930  0.020  1.080
 HPH  CE2  CZ   aromatic  1.387  0.020  1.387
 HPH  CE2  HE2  single    0.930  0.020  1.080
 HPH  CZ   HZ   single    0.930  0.020  1.080
 HPH  C    HC   single    0.970  0.020  1.090
 HPH  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
 HPH  HC   C    OXT  109.56  3.000
 HPH  HC   C    CA   107.91  3.000
 HPH  OXT  C    CA   110.12  3.000
 HPH  HC   C    O    109.86  3.000
 HPH  OXT  C    O    110.17  3.000
 HPH  CA   C    O    120.80  1.700
 HPH  HO   O    C    109.29  3.000
 HPH  HA   CA   CB   109.00  3.000
 HPH  HA   CA   N    110.00  3.000
 HPH  CB   CA   N    110.50  1.700
 HPH  HA   CA   C    109.00  3.000
 HPH  CB   CA   C    110.10  1.900
 HPH  N    CA   C    111.00  2.800
 HPH  H2   N    H    105.93  3.000
 HPH  H2   N    CA   110.28  3.000
 HPH  H    N    CA   114.00  3.000
 HPH  HB3  CB   HB2  107.14  3.000
 HPH  HB3  CB   CG   109.21  3.000
 HPH  HB2  CB   CG   109.95  3.000
 HPH  HB3  CB   CA   108.87  3.000
 HPH  HB2  CB   CA   109.43  3.000
 HPH  CG   CB   CA   112.11  3.000
 HPH  CD2  CG   CD1  118.32  3.000
 HPH  CD2  CG   CB   121.42  3.000
 HPH  CD1  CG   CB   120.25  3.000
 HPH  HD1  CD1  CE1  119.66  3.000
 HPH  HD1  CD1  CG   119.36  3.000
 HPH  CE1  CD1  CG   120.98  3.000
 HPH  HD2  CD2  CE2  119.60  3.000
 HPH  HD2  CD2  CG   119.46  3.000
 HPH  CE2  CD2  CG   120.93  3.000
 HPH  HE1  CE1  CZ   120.05  3.000
 HPH  HE1  CE1  CD1  119.81  3.000
 HPH  CZ   CE1  CD1  120.14  3.000
 HPH  HE2  CE2  CZ   120.10  3.000
 HPH  HE2  CE2  CD2  119.76  3.000
 HPH  CZ   CE2  CD2  120.14  3.000
 HPH  HZ   CZ   CE2  120.29  3.000
 HPH  HZ   CZ   CE1  120.23  3.000
 HPH  CE2  CZ   CE1  119.49  3.000
 HPH  HXT  OXT  C    104.63  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
 HPH  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 HPH  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 HPH  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 HPH  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 HPH  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 HPH  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 HPH  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 HPH  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 HPH  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 HPH  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 HPH  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 HPH  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 HPH  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 HPH  Var_01    CD1  CG   CB   CA   -75.24  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
 HPH  chir_01  CA  C  N  CB  negativ

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
 HPH  plan-1  CB   0.020
 HPH  plan-1  CG   0.020
 HPH  plan-1  CD1  0.020
 HPH  plan-1  CD2  0.020
 HPH  plan-1  CE1  0.020
 HPH  plan-1  CE2  0.020
 HPH  plan-1  CZ   0.020
 HPH  plan-1  HD1  0.020
 HPH  plan-1  HD2  0.020
 HPH  plan-1  HE1  0.020
 HPH  plan-1  HE2  0.020
 HPH  plan-1  HZ   0.020

