# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 16:01:53 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)[P](O)(=O)C[C@H](C)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
 2D8  2D8  '(2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid'  ligand  24  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2D8
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
 2D8  C4   C  CH2    0  -0.680   0.3475  -0.4762  -0.1161
 2D8  C5   C  CH1    0  -0.365   1.6303   0.3420   0.0117
 2D8  C6   C  C      0   0.419   2.9038  -0.5217   0.1800
 2D8  C7   C  CH3    0  -0.657   1.8156   1.2942  -1.1714
 2D8  N1   N  NH2    0  -0.802  -2.5873  -1.6219  -1.0157
 2D8  P    P  P      0   1.162  -1.1978   0.4930   0.1424
 2D8  C1   C  CH3    0  -0.661  -3.8474  -0.2246   0.5407
 2D8  C2   C  CH1    0  -0.329  -2.4911  -0.8381   0.2186
 2D8  O31  O  O      0  -0.833  -1.1124   1.1768   1.4984
 2D8  O32  O  OP    -1  -0.830  -1.5143   1.3465  -1.0782
 2D8  O61  O  OC    -1  -0.631   3.9661   0.1097   0.3725
 2D8  O62  O  O      0  -0.606   2.7978  -1.7622   0.1097
 2D8  H1   H  HCH2   0   0.208   0.3202  -0.9741  -1.0911
 2D8  H2   H  HCH2   0   0.221   0.3516  -1.2759   0.6304
 2D8  H3   H  HCH1   0   0.207   1.5499   0.9569   0.9171
 2D8  H4   H  HCH3   0   0.223   0.9696   1.9720  -1.2745
 2D8  H5   H  HCH3   0   0.212   2.7204   1.8899  -1.0589
 2D8  H6   H  HCH3   0   0.200   1.8971   0.7357  -2.1082
 2D8  H10  H  HCH3   0   0.221  -4.6210  -0.9930   0.5900
 2D8  H11  H  HCH3   0   0.221  -3.8256   0.2992   1.4962
 2D8  H12  H  HCH3   0   0.211  -4.1401   0.4971  -0.2253
 2D8  H13  H  HCH1   0   0.217  -2.2279  -1.5313   1.0255
 2D8  H7   H  HNH2   0   0.328  -2.6690  -0.9788  -1.7962
 2D8  H8   H  HNH2   0   0.343  -1.7171  -2.1170  -1.1704

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
 2D8  C1   C2   single  1.523  0.020  1.523
 2D8  C2   N1   single  1.465  0.020  1.465
 2D8  C2   P    single  1.858  0.020  1.858
 2D8  O62  C6   deloc   1.247  0.020  1.247
 2D8  C4   P    single  1.842  0.020  1.842
 2D8  C4   C5   single  1.527  0.020  1.527
 2D8  P    O31  deloc   1.521  0.020  1.521
 2D8  P    O32  deloc   1.523  0.020  1.523
 2D8  C6   C5   single  1.548  0.020  1.548
 2D8  C6   O61  deloc   1.251  0.020  1.251
 2D8  C7   C5   single  1.530  0.020  1.530
 2D8  C4   H1   single  0.970  0.020  1.090
 2D8  C4   H2   single  0.970  0.020  1.090
 2D8  C5   H3   single  0.970  0.020  1.090
 2D8  C7   H4   single  0.970  0.020  1.090
 2D8  C7   H5   single  0.970  0.020  1.090
 2D8  C7   H6   single  0.970  0.020  1.090
 2D8  N1   H7   single  0.890  0.020  1.040
 2D8  N1   H8   single  0.890  0.020  1.040
 2D8  C1   H10  single  0.970  0.020  1.090
 2D8  C1   H11  single  0.970  0.020  1.090
 2D8  C1   H12  single  0.970  0.020  1.090
 2D8  C2   H13  single  0.970  0.020  1.090

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
 2D8  H2   C4  H1   105.98  3.000
 2D8  H2   C4  P    106.98  3.000
 2D8  H1   C4  P    110.07  3.000
 2D8  H2   C4  C5   109.36  3.000
 2D8  H1   C4  C5   109.82  3.000
 2D8  P    C4  C5   114.27  3.000
 2D8  H3   C5  C7   107.35  3.000
 2D8  H3   C5  C6   106.45  3.000
 2D8  C7   C5  C6   109.37  3.000
 2D8  H3   C5  C4   107.92  3.000
 2D8  C7   C5  C4   111.75  3.000
 2D8  C6   C5  C4   113.66  3.000
 2D8  O62  C6  O61  125.67  3.000
 2D8  O61  C6  C5   115.71  3.000
 2D8  O62  C6  C5   118.62  3.000
 2D8  H6   C7  H5   107.81  3.000
 2D8  H6   C7  H4   107.14  3.000
 2D8  H5   C7  H4   108.34  3.000
 2D8  H6   C7  C5   110.71  3.000
 2D8  H5   C7  C5   111.17  3.000
 2D8  H4   C7  C5   111.50  3.000
 2D8  H8   N1  H7   105.15  3.000
 2D8  H8   N1  C2   109.49  3.000
 2D8  H7   N1  C2   108.31  3.000
 2D8  O32  P   O31  118.32  3.000
 2D8  O32  P   C2   106.85  3.000
 2D8  O31  P   C2   108.94  3.000
 2D8  O32  P   C4   110.91  3.000
 2D8  O31  P   C4   108.33  3.000
 2D8  C2   P   C4   102.28  3.000
 2D8  H12  C1  H11  107.61  3.000
 2D8  H12  C1  H10  107.87  3.000
 2D8  H11  C1  H10  108.24  3.000
 2D8  H12  C1  C2   110.88  3.000
 2D8  H11  C1  C2   111.17  3.000
 2D8  H10  C1  C2   110.93  3.000
 2D8  H13  C2  C1   108.24  3.000
 2D8  H13  C2  P    108.44  3.000
 2D8  C1   C2  P    109.88  3.000
 2D8  H13  C2  N1   107.31  3.000
 2D8  P    C2  N1   113.24  3.000
 2D8  C1   C2  N1   109.58  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
 2D8  Var_01  C2  P  C4  C5  -170.33  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
 2D8  chir_01  C5  C4  C6  C7  negativ
 2D8  chir_03  C2  C1  N1  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
 2D8  plan-1  C5   0.020
 2D8  plan-1  C6   0.020
 2D8  plan-1  O61  0.020
 2D8  plan-1  O62  0.020

