# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:50:48 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: [(1R)-1-aminopropyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](N)[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
 3V2  3V2  '[(1R)-1-aminopropyl]phosphonic acid'  ligand  18  8  .  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_3V2
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
 3V2  N    N  NH2   0  -0.792  -0.4987   2.0925   0.1162
 3V2  CA   C  CH1   0  -0.366  -0.6779   0.6718   0.3870
 3V2  CB   C  CH2   0  -0.449  -1.9367   0.0797  -0.2616
 3V2  CG   C  CH3   0  -0.677  -2.3159  -1.3380   0.1469
 3V2  P1   P  P     0   1.369   0.8648  -0.1284  -0.1593
 3V2  O2   O  OH1   0  -0.745   0.8353  -1.6782   0.2822
 3V2  O3   O  O     0  -0.721   1.1217  -0.0433  -1.6185
 3V2  O1   O  OH1   0  -0.745   1.9517   0.5738   0.7948
 3V2  H1   H  HNH2  0   0.349  -0.6015   2.2648  -0.8771
 3V2  H2   H  HNH2  0   0.361  -1.2437   2.6092   0.5668
 3V2  H4   H  HCH1  0   0.277  -0.7456   0.5428   1.4727
 3V2  H5   H  HCH2  0   0.243  -2.7530   0.7543   0.0116
 3V2  H6   H  HCH2  0   0.230  -1.8445   0.1458  -1.3498
 3V2  H7   H  HCH3  0   0.230  -1.6452  -2.0871  -0.2691
 3V2  H8   H  HCH3  0   0.222  -2.3164  -1.4532   1.2324
 3V2  H9   H  HCH3  0   0.235  -3.3204  -1.5708  -0.2057
 3V2  H10  H  HOH1  0   0.488   0.7041  -1.8392   1.2256
 3V2  H11  H  HOH1  0   0.491   2.8647   0.3286   0.5916

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
 3V2  N   CA   single  1.457  0.020  1.457
 3V2  O3  P1   double  1.484  0.020  1.484
 3V2  P1  CA   single  1.822  0.020  1.822
 3V2  P1  O2   single  1.612  0.020  1.612
 3V2  CA  CB   single  1.535  0.020  1.535
 3V2  CB  CG   single  1.523  0.020  1.523
 3V2  P1  O1   single  1.608  0.020  1.608
 3V2  N   H1   single  0.890  0.020  1.040
 3V2  N   H2   single  0.890  0.020  1.040
 3V2  CA  H4   single  0.970  0.020  1.090
 3V2  CB  H5   single  0.970  0.020  1.090
 3V2  CB  H6   single  0.970  0.020  1.090
 3V2  CG  H7   single  0.970  0.020  1.090
 3V2  CG  H8   single  0.970  0.020  1.090
 3V2  CG  H9   single  0.970  0.020  1.090
 3V2  O2  H10  single  0.850  0.020  0.980
 3V2  O1  H11  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
 3V2  H2   N   H1  105.96  3.000
 3V2  H2   N   CA  108.93  3.000
 3V2  H1   N   CA  109.60  3.000
 3V2  H4   CA  P1  107.33  3.000
 3V2  H4   CA  CB  108.83  3.000
 3V2  P1   CA  CB  113.47  3.000
 3V2  H4   CA  N   107.86  3.000
 3V2  CB   CA  N   113.48  3.000
 3V2  P1   CA  N   105.57  3.000
 3V2  H6   CB  H5  105.91  3.000
 3V2  H6   CB  CG  110.12  3.000
 3V2  H5   CB  CG  108.74  3.000
 3V2  H6   CB  CA  109.15  3.000
 3V2  H5   CB  CA  105.58  3.000
 3V2  CG   CB  CA  116.73  3.000
 3V2  H9   CG  H8  107.38  3.000
 3V2  H9   CG  H7  107.31  3.000
 3V2  H8   CG  H7  107.93  3.000
 3V2  H9   CG  CB  109.96  3.000
 3V2  H8   CG  CB  111.41  3.000
 3V2  H7   CG  CB  112.63  3.000
 3V2  O1   P1  O3  116.19  3.000
 3V2  O1   P1  O2  105.65  3.000
 3V2  O3   P1  O2  109.12  3.000
 3V2  O1   P1  CA  101.69  3.000
 3V2  O2   P1  CA  108.95  3.000
 3V2  O3   P1  CA  114.60  3.000
 3V2  H10  O2  P1  115.49  3.000
 3V2  H11  O1  P1  113.76  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
 3V2  Var_01  H7  CG  CB  CA  -72.25  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
 3V2  chir_01  CA  N  P1  CB  positiv

