# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 12:58:23 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (R)-[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)[P@@H](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
 MPJ  MPJ  '(R)-[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphinic acid'  L-peptide  21  9  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MPJ
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
 MPJ  N    N  NH2   0  -0.798  1.1467   1.2326  -2.1039
 MPJ  CA   C  CH1   0  -0.350  1.7706   0.9203  -0.8259
 MPJ  CB   C  CH2   0  -0.445  1.1684  -0.2976  -0.1190
 MPJ  CG   C  CH2   0  -0.558  1.7373  -0.5855   1.2636
 MPJ  SD   S  S2    0  -0.041  0.7299  -1.8669   2.0631
 MPJ  CE   C  CH3   0  -0.763  1.6505  -2.0713   3.6029
 MPJ  P    P  P     0   1.044  3.5383   0.7499  -1.2489
 MPJ  H    H  HNH2  0   0.354  1.0124   0.3843  -2.6405
 MPJ  HN2  H  HNH2  0   0.367  0.2279   1.6287  -1.9543
 MPJ  HA   H  HCH1  0   0.280  1.6792   1.8020  -0.1827
 MPJ  HB1  H  HCH2  0   0.245  1.2818  -1.1777  -0.7581
 MPJ  HB2  H  HCH2  0   0.254  0.0941  -0.1094  -0.0346
 MPJ  HG1  H  HCH2  0   0.260  1.7255   0.3148   1.8824
 MPJ  HG2  H  HCH2  0   0.266  2.7665  -0.9398   1.2071
 MPJ  HE1  H  HCH3  0   0.261  1.6736  -1.1442   4.1738
 MPJ  HE2  H  HCH3  0   0.261  2.6700  -2.4037   3.4119
 MPJ  HE3  H  HCH3  0   0.273  1.1415  -2.8308   4.1937
 MPJ  HO2  H  HOH1  0   0.491  4.3531   1.6284   0.6036
 MPJ  HP   H  H     0   0.077  3.8217   1.9595  -1.9140
 MPJ  O1   O  O     0  -0.726  3.8506  -0.4868  -2.0201
 MPJ  O2   O  OH1   0  -0.752  4.4198   0.8034   0.1050

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
 MPJ  N   CA   single  1.458  0.019  1.458
 MPJ  N   H    single  0.860  0.020  0.860
 MPJ  N   HN2  single  0.868  0.020  1.013
 MPJ  CA  CB   single  1.521  0.033  1.521
 MPJ  CA  P    single  1.826  0.020  1.826
 MPJ  CA  HA   single  0.970  0.020  0.970
 MPJ  CB  CG   single  1.523  0.020  1.523
 MPJ  CB  HB1  single  0.939  0.020  1.096
 MPJ  CB  HB2  single  0.939  0.020  1.096
 MPJ  CG  SD   single  1.815  0.020  1.815
 MPJ  CG  HG1  single  0.939  0.020  1.096
 MPJ  CG  HG2  single  0.939  0.020  1.096
 MPJ  SD  CE   single  1.806  0.020  1.806
 MPJ  CE  HE1  single  0.939  0.020  1.096
 MPJ  CE  HE2  single  0.939  0.020  1.096
 MPJ  CE  HE3  single  0.939  0.020  1.096
 MPJ  O1  P    double  1.490  0.020  1.490
 MPJ  O2  P    single  1.616  0.020  1.616
 MPJ  O2  HO2  single  0.832  0.020  0.971
 MPJ  P   HP   single  1.209  0.020  1.412

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
 MPJ  HN2  N   H    106.61  3.000
 MPJ  HN2  N   CA   110.08  3.000
 MPJ  H    N   CA   114.00  3.000
 MPJ  HA   CA  P    106.98  3.000
 MPJ  HA   CA  CB   109.00  3.000
 MPJ  P    CA  CB   114.42  3.000
 MPJ  HA   CA  N    110.00  3.000
 MPJ  P    CA  N    103.39  3.000
 MPJ  CB   CA  N    110.40  1.500
 MPJ  HB2  CB  HB1  106.58  3.000
 MPJ  HB2  CB  CG   109.23  3.000
 MPJ  HB1  CB  CG   109.86  3.000
 MPJ  HB2  CB  CA   106.56  3.000
 MPJ  HB1  CB  CA   109.24  3.000
 MPJ  CG   CB  CA   115.00  3.000
 MPJ  HG2  CG  HG1  107.90  3.000
 MPJ  HG2  CG  SD   108.50  3.000
 MPJ  HG1  CG  SD   109.04  3.000
 MPJ  HG2  CG  CB   111.54  3.000
 MPJ  HG1  CG  CB   110.76  3.000
 MPJ  SD   CG  CB   109.03  3.000
 MPJ  CE   SD  CG    99.94  3.000
 MPJ  HE3  CE  HE2  108.65  3.000
 MPJ  HE3  CE  HE1  108.63  3.000
 MPJ  HE2  CE  HE1  109.38  3.000
 MPJ  HE3  CE  SD   107.66  3.000
 MPJ  HE2  CE  SD   111.24  3.000
 MPJ  HE1  CE  SD   111.19  3.000
 MPJ  HP   P   O2   104.90  3.000
 MPJ  HP   P   O1   115.20  3.000
 MPJ  O2   P   O1   110.28  3.000
 MPJ  HP   P   CA   102.94  3.000
 MPJ  O2   P   CA   109.32  3.000
 MPJ  O1   P   CA   113.59  3.000
 MPJ  HO2  O2  P    115.02  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
 MPJ  Var_01  SD   CG  CB  CA  170.45  30.0  3
 MPJ  Var_02  HE1  CE  SD  CG   61.08  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
 MPJ  chir_01  CA  N   CB  P   negativ
 MPJ  chir_02  P   CA  O1  O2  both

