# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:49:40 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: [(1R)-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
 PPH  PPH  '[(1R)-1-amino-2-phenylethyl]phosphonic acid'  peptide  23  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PPH
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
 PPH  O1   O  O      0  -0.905   1.9159   0.8967   1.3869
 PPH  P1   P  P      0   1.173   1.8139   0.6565  -0.1301
 PPH  O2   O  OP    -1  -0.909   3.1886   0.6137  -0.8288
 PPH  C1   C  CH1    0  -0.336   1.2013  -1.1045  -0.3014
 PPH  N1   N  NH2    0  -0.815   2.2708  -2.0784  -0.0150
 PPH  C2   C  CH2    0  -0.500   0.0136  -1.4610   0.5949
 PPH  C3   C  CR6    0   0.143  -1.2601  -0.7143   0.3205
 PPH  C4   C  CR16   0  -0.332  -2.2248  -1.2446  -0.5323
 PPH  C5   C  CR16   0  -0.249  -3.4197  -0.5756  -0.7741
 PPH  C6   C  CR16   0  -0.280  -3.6723   0.6381  -0.1501
 PPH  C7   C  CR16   0  -0.258  -2.7159   1.1784   0.7035
 PPH  C8   C  CR16   0  -0.259  -1.5184   0.5153   0.9239
 PPH  O3   O  OP    -1  -0.894   0.8070   1.5591  -0.8500
 PPH  H2   H  HCH1   0   0.175   0.8929  -1.2652  -1.3444
 PPH  H3   H  HNH2   0   0.322   3.0985  -1.7284  -0.4876
 PPH  H4   H  HNH2   0   0.315   2.5044  -1.9807   0.9691
 PPH  H5   H  HCH2   0   0.209  -0.1799  -2.5352   0.4974
 PPH  H6   H  HCH2   0   0.213   0.3129  -1.2905   1.6337
 PPH  H7   H  HCR6   0   0.234  -2.0428  -2.2018  -1.0089
 PPH  H8   H  HCR6   0   0.242  -4.1546  -1.0086  -1.4414
 PPH  H9   H  HCR6   0   0.243  -4.6069   1.1572  -0.3227
 PPH  H10  H  HCR6   0   0.239  -2.9048   2.1264   1.1924
 PPH  H11  H  HCR6   0   0.229  -0.7626   0.9464   1.5674

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
 PPH  O1  P1   deloc     1.539  0.020  1.539
 PPH  P1  O2   deloc     1.543  0.020  1.543
 PPH  P1  C1   single    1.872  0.020  1.872
 PPH  C1  N1   single    1.475  0.020  1.475
 PPH  C1  C2   single    1.530  0.020  1.530
 PPH  C2  C3   single    1.502  0.020  1.502
 PPH  C3  C4   aromatic  1.393  0.020  1.393
 PPH  C4  C5   aromatic  1.391  0.020  1.391
 PPH  C5  C6   aromatic  1.388  0.020  1.388
 PPH  C6  C7   aromatic  1.391  0.020  1.391
 PPH  C7  C8   aromatic  1.386  0.020  1.386
 PPH  C3  C8   aromatic  1.394  0.020  1.394
 PPH  P1  O3   deloc     1.532  0.020  1.532
 PPH  C1  H2   single    0.970  0.020  1.090
 PPH  N1  H3   single    0.890  0.020  1.040
 PPH  N1  H4   single    0.890  0.020  1.040
 PPH  C2  H5   single    0.970  0.020  1.090
 PPH  C2  H6   single    0.970  0.020  1.090
 PPH  C4  H7   single    0.930  0.020  1.080
 PPH  C5  H8   single    0.930  0.020  1.080
 PPH  C6  H9   single    0.930  0.020  1.080
 PPH  C7  H10  single    0.930  0.020  1.080
 PPH  C8  H11  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
 PPH  O3   P1  C1  107.22  3.000
 PPH  O3   P1  O2  112.91  3.000
 PPH  C1   P1  O2  102.95  3.000
 PPH  O3   P1  O1  114.50  3.000
 PPH  C1   P1  O1  104.98  3.000
 PPH  O2   P1  O1  113.06  3.000
 PPH  H2   C1  C2  107.69  3.000
 PPH  H2   C1  N1  106.93  3.000
 PPH  C2   C1  N1  107.18  3.000
 PPH  H2   C1  P1  108.42  3.000
 PPH  C2   C1  P1  114.81  3.000
 PPH  N1   C1  P1  111.48  3.000
 PPH  H4   N1  H3  103.31  3.000
 PPH  H4   N1  C1  106.94  3.000
 PPH  H3   N1  C1  105.85  3.000
 PPH  H6   C2  H5  106.58  3.000
 PPH  H6   C2  C3  109.14  3.000
 PPH  H5   C2  C3  108.75  3.000
 PPH  H6   C2  C1  107.91  3.000
 PPH  H5   C2  C1  108.26  3.000
 PPH  C3   C2  C1  115.82  3.000
 PPH  C8   C3  C4  118.21  3.000
 PPH  C8   C3  C2  121.12  3.000
 PPH  C4   C3  C2  120.67  3.000
 PPH  H7   C4  C5  119.50  3.000
 PPH  H7   C4  C3  119.27  3.000
 PPH  C5   C4  C3  121.23  3.000
 PPH  H8   C5  C6  120.21  3.000
 PPH  H8   C5  C4  119.85  3.000
 PPH  C6   C5  C4  119.93  3.000
 PPH  H9   C6  C7  120.32  3.000
 PPH  H9   C6  C5  120.31  3.000
 PPH  C7   C6  C5  119.37  3.000
 PPH  H10  C7  C8  119.83  3.000
 PPH  H10  C7  C6  119.80  3.000
 PPH  C8   C7  C6  120.37  3.000
 PPH  H11  C8  C7  120.48  3.000
 PPH  H11  C8  C3  118.64  3.000
 PPH  C7   C8  C3  120.88  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
 PPH  CONST_01  C6   C5  C4  C3    0.00   0.0  0
 PPH  CONST_02  C6   C7  C8  C3    0.00   0.0  0
 PPH  CONST_03  C7   C8  C3  C4    0.00   0.0  0
 PPH  CONST_04  C7   C6  C5  C4    0.00   0.0  0
 PPH  CONST_05  C8   C3  C4  C5    0.00   0.0  0
 PPH  CONST_06  C8   C7  C6  C5    0.00   0.0  0
 PPH  CONST_07  C5   C4  C3  C2  180.00   0.0  0
 PPH  CONST_08  C7   C8  C3  C2  180.00   0.0  0
 PPH  CONST_09  H8   C5  C4  C3  180.00   0.0  0
 PPH  CONST_10  H10  C7  C8  C3  180.00   0.0  0
 PPH  CONST_11  H11  C8  C3  C4  180.00   0.0  0
 PPH  CONST_12  H9   C6  C5  C4  180.00   0.0  0
 PPH  CONST_13  H7   C4  C5  C6  180.00   0.0  0
 PPH  Var_01    C4   C3  C2  C1   93.38  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
 PPH  chir_01  C1  P1  N1  C2  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
 PPH  plan-1  C2   0.020
 PPH  plan-1  C3   0.020
 PPH  plan-1  C4   0.020
 PPH  plan-1  C5   0.020
 PPH  plan-1  C6   0.020
 PPH  plan-1  C7   0.020
 PPH  plan-1  C8   0.020
 PPH  plan-1  H7   0.020
 PPH  plan-1  H8   0.020
 PPH  plan-1  H9   0.020
 PPH  plan-1  H10  0.020
 PPH  plan-1  H11  0.020

