# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 15:28:25 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: [(1S)-1-amino-2-phenylethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)[P](O)(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
 XPH  XPH  '[(1S)-1-amino-2-phenylethyl]phosphonic acid'  peptide  23  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XPH
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
 XPH  O3   O  OP    -1  -0.909  -3.1564  -0.6331   0.8795
 XPH  P    P  P      0   1.173  -1.8083  -0.6585   0.1305
 XPH  O2   O  O      0  -0.908  -1.9639  -0.8617  -1.3876
 XPH  CA   C  CH1    0  -0.335  -1.1939   1.1013   0.3156
 XPH  CB   C  CH2    0  -0.501  -0.0253   1.4690  -0.6008
 XPH  CG   C  CR6    0   0.144   1.2583   0.7386  -0.3330
 XPH  CD2  C  CR16   0  -0.257   1.5322  -0.4831  -0.9439
 XPH  CE2  C  CR16   0  -0.259   2.7332  -1.1388  -0.7189
 XPH  CZ   C  CR16   0  -0.280   3.6780  -0.5974   0.1467
 XPH  CE1  C  CR16   0  -0.248   3.4110   0.6103   0.7763
 XPH  CD1  C  CR16   0  -0.330   2.2124   1.2711   0.5305
 XPH  N    N  NH2    0  -0.815  -2.2717   2.0753   0.0613
 XPH  O1   O  OP    -1  -0.893  -0.7758  -1.5798   0.7881
 XPH  HA   H  HCH1   0   0.175  -0.8653   1.2512   1.3540
 XPH  HB3  H  HCH2   0   0.214  -0.3369   1.2854  -1.6337
 XPH  HB2  H  HCH2   0   0.209   0.1559   2.5461  -0.5134
 XPH  HD2  H  HCR6   0   0.225   0.7872  -0.9164  -1.5982
 XPH  HE2  H  HCR6   0   0.240   2.9329  -2.0821  -1.2124
 XPH  HG   H  HCR6   0   0.243   4.6145  -1.1111   0.3248
 XPH  HE1  H  HCR6   0   0.242   4.1368   1.0442   1.4528
 XPH  HD1  H  HCR6   0   0.234   2.0188   2.2233   1.0125
 XPH  H    H  HNH2   0   0.315  -2.5295   1.9816  -0.9173
 XPH  H2   H  HNH2   0   0.322  -3.0874   1.7231   0.5525

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
 XPH  CZ   CE1  aromatic  1.388  0.020  1.388
 XPH  CZ   CE2  aromatic  1.391  0.020  1.391
 XPH  CE1  CD1  aromatic  1.391  0.020  1.391
 XPH  CE2  CD2  aromatic  1.387  0.020  1.387
 XPH  CD1  CG   aromatic  1.393  0.020  1.393
 XPH  CD2  CG   aromatic  1.393  0.020  1.393
 XPH  CG   CB   single    1.501  0.020  1.501
 XPH  CB   CA   single    1.521  0.033  1.521
 XPH  CA   N    single    1.458  0.019  1.458
 XPH  CA   P    single    1.873  0.020  1.873
 XPH  P    O2   deloc     1.540  0.020  1.540
 XPH  P    O3   deloc     1.542  0.020  1.542
 XPH  P    O1   deloc     1.532  0.020  1.532
 XPH  CA   HA   single    0.970  0.020  0.970
 XPH  CB   HB3  single    0.970  0.020  1.090
 XPH  CB   HB2  single    0.970  0.020  1.090
 XPH  CD2  HD2  single    0.930  0.020  1.080
 XPH  CE2  HE2  single    0.930  0.020  1.080
 XPH  CZ   HG   single    0.930  0.020  1.080
 XPH  CE1  HE1  single    0.930  0.020  1.080
 XPH  CD1  HD1  single    0.930  0.020  1.080
 XPH  N    H    single    0.860  0.020  0.860
 XPH  N    H2   single    0.890  0.020  1.040

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
 XPH  O1   P    CA   107.55  3.000
 XPH  O1   P    O2   114.33  3.000
 XPH  CA   P    O2   104.75  3.000
 XPH  O1   P    O3   112.98  3.000
 XPH  O2   P    O3   113.12  3.000
 XPH  CA   P    O3   102.90  3.000
 XPH  HA   CA   N    110.00  3.000
 XPH  HA   CA   CB   109.00  3.000
 XPH  N    CA   CB   110.40  1.500
 XPH  HA   CA   P    108.63  3.000
 XPH  N    CA   P    111.33  3.000
 XPH  CB   CA   P    114.65  3.000
 XPH  HB2  CB   HB3  106.70  3.000
 XPH  HB2  CB   CG   108.82  3.000
 XPH  HB3  CB   CG   109.28  3.000
 XPH  HB2  CB   CA   108.35  3.000
 XPH  HB3  CB   CA   107.91  3.000
 XPH  CG   CB   CA   115.43  3.000
 XPH  CD1  CG   CD2  118.19  3.000
 XPH  CD2  CG   CB   121.11  3.000
 XPH  CD1  CG   CB   120.69  3.000
 XPH  HD2  CD2  CE2  120.34  3.000
 XPH  HD2  CD2  CG   118.75  3.000
 XPH  CE2  CD2  CG   120.92  3.000
 XPH  HE2  CE2  CZ   119.82  3.000
 XPH  HE2  CE2  CD2  119.83  3.000
 XPH  CZ   CE2  CD2  120.34  3.000
 XPH  HG   CZ   CE1  120.31  3.000
 XPH  HG   CZ   CE2  120.33  3.000
 XPH  CE1  CZ   CE2  119.36  3.000
 XPH  HE1  CE1  CD1  119.85  3.000
 XPH  HE1  CE1  CZ   120.20  3.000
 XPH  CD1  CE1  CZ   119.95  3.000
 XPH  HD1  CD1  CE1  119.50  3.000
 XPH  HD1  CD1  CG   119.27  3.000
 XPH  CE1  CD1  CG   121.23  3.000
 XPH  H2   N    H    103.30  3.000
 XPH  H2   N    CA   105.93  3.000
 XPH  H    N    CA   114.00  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
 XPH  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 XPH  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 XPH  CONST_03  CE1  CZ   CE2  CD2    0.00   0.0  0
 XPH  CONST_04  CE1  CD1  CG   CD2    0.00   0.0  0
 XPH  CONST_05  CD1  CE1  CZ   CE2    0.00   0.0  0
 XPH  CONST_06  CD1  CG   CD2  CE2    0.00   0.0  0
 XPH  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 XPH  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 XPH  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 XPH  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 XPH  CONST_11  HG   CZ   CE2  CD2  180.00   0.0  0
 XPH  CONST_12  HD1  CD1  CG   CD2  180.00   0.0  0
 XPH  CONST_13  HD2  CD2  CE2  CZ   180.00   0.0  0
 XPH  Var_01    CD1  CG   CB   CA   -91.81  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
 XPH  chir_01  CA  CB  N  P  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
 XPH  plan-1  CB   0.020
 XPH  plan-1  CG   0.020
 XPH  plan-1  CD2  0.020
 XPH  plan-1  CE2  0.020
 XPH  plan-1  CZ   0.020
 XPH  plan-1  CE1  0.020
 XPH  plan-1  CD1  0.020
 XPH  plan-1  HD2  0.020
 XPH  plan-1  HE2  0.020
 XPH  plan-1  HG   0.020
 XPH  plan-1  HE1  0.020
 XPH  plan-1  HD1  0.020

