# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 12:51:43 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: [(1R)-1-amino-3-(methylsulfanyl)propyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[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
 MPH  MPH  '[(1R)-1-amino-3-(methylsulfanyl)propyl]phosphonic acid'  L-peptide  22  10  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MPH
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
 MPH  N    N  NH2   0  -0.759  -2.1085   0.2573  -1.7478
 MPH  CA   C  CH1   0  -0.391  -0.9375   0.4862  -0.9124
 MPH  CB   C  CH2   0  -0.459  -1.0607  -0.1227   0.4926
 MPH  CG   C  CH2   0  -0.645   0.0080   0.3079   1.4882
 MPH  SD   S  S2    0  -0.006  -0.4619  -0.2530   3.1499
 MPH  CE   C  CH3   0  -0.760   0.9388   0.3885   4.0916
 MPH  P    P  P     0   1.347   0.4712  -0.1801  -1.8589
 MPH  H    H  HNH2  0   0.363  -2.8945   0.7704  -1.3689
 MPH  HN2  H  HNH2  0   0.340  -2.3688  -0.7215  -1.7171
 MPH  HA   H  HCH1  0   0.336  -0.7972   1.5676  -0.8205
 MPH  HB1  H  HCH2  0   0.296  -1.0910  -1.2135   0.4176
 MPH  HB2  H  HCH2  0   0.307  -2.0393   0.1887   0.8705
 MPH  HG1  H  HCH2  0   0.230   0.1040   1.3964   1.4968
 MPH  HG2  H  HCH2  0   0.301   0.9823  -0.1125   1.2422
 MPH  HE1  H  HCH3  0   0.243   0.7907   0.1160   5.1349
 MPH  HE2  H  HCH3  0   0.254   1.8763  -0.0459   3.7473
 MPH  HE3  H  HCH3  0   0.278   0.9957   1.4739   4.0196
 MPH  HO2  H  HOH1  0   0.500   0.9985   0.4197  -3.8955
 MPH  HO3  H  HOH1  0   0.474   2.0202   1.1726  -1.0499
 MPH  O1   O  O     0  -0.803   0.4352  -1.6506  -2.0489
 MPH  O2   O  OH1   0  -0.718   0.4067   0.7165  -3.1905
 MPH  O3   O  OH1   0  -0.728   1.8417   0.2256  -1.1167

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
 MPH  N   CA   single  1.458  0.019  1.458
 MPH  N   H    single  0.860  0.020  0.860
 MPH  N   HN2  single  0.890  0.020  1.040
 MPH  CA  CB   single  1.521  0.033  1.521
 MPH  CA  P    single  1.823  0.020  1.823
 MPH  CA  HA   single  0.970  0.020  0.970
 MPH  CB  CG   single  1.523  0.020  1.523
 MPH  CB  HB1  single  0.970  0.020  1.090
 MPH  CB  HB2  single  0.970  0.020  1.090
 MPH  CG  SD   single  1.816  0.020  1.816
 MPH  CG  HG1  single  0.970  0.020  1.090
 MPH  CG  HG2  single  0.970  0.020  1.090
 MPH  SD  CE   single  1.806  0.020  1.806
 MPH  CE  HE1  single  0.970  0.020  1.090
 MPH  CE  HE2  single  0.970  0.020  1.090
 MPH  CE  HE3  single  0.970  0.020  1.090
 MPH  O1  P    double  1.483  0.020  1.483
 MPH  O2  P    single  1.607  0.020  1.607
 MPH  O2  HO2  single  0.850  0.020  0.980
 MPH  O3  P    single  1.610  0.020  1.610
 MPH  O3  HO3  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
 MPH  HN2  N   H    106.19  3.000
 MPH  HN2  N   CA   109.94  3.000
 MPH  H    N   CA   114.00  3.000
 MPH  HA   CA  P    107.80  3.000
 MPH  HA   CA  CB   109.00  3.000
 MPH  P    CA  CB   113.07  3.000
 MPH  HA   CA  N    110.00  3.000
 MPH  P    CA  N    105.42  3.000
 MPH  CB   CA  N    110.40  1.500
 MPH  HB2  CB  HB1  106.43  3.000
 MPH  HB2  CB  CG   108.74  3.000
 MPH  HB1  CB  CG   110.26  3.000
 MPH  HB2  CB  CA   105.95  3.000
 MPH  HB1  CB  CA   109.56  3.000
 MPH  CG   CB  CA   115.44  3.000
 MPH  HG2  CG  HG1  107.92  3.000
 MPH  HG2  CG  SD   108.60  3.000
 MPH  HG1  CG  SD   108.86  3.000
 MPH  HG2  CG  CB   111.77  3.000
 MPH  HG1  CG  CB   110.39  3.000
 MPH  SD   CG  CB   109.23  3.000
 MPH  CE   SD  CG    99.60  3.000
 MPH  HE3  CE  HE2  109.36  3.000
 MPH  HE3  CE  HE1  108.66  3.000
 MPH  HE2  CE  HE1  108.68  3.000
 MPH  HE3  CE  SD   111.10  3.000
 MPH  HE2  CE  SD   111.17  3.000
 MPH  HE1  CE  SD   107.79  3.000
 MPH  O3   P   O2   105.99  3.000
 MPH  O3   P   O1   109.24  3.000
 MPH  O2   P   O1   116.50  3.000
 MPH  O3   P   CA   109.04  3.000
 MPH  O2   P   CA   101.26  3.000
 MPH  O1   P   CA   114.21  3.000
 MPH  HO2  O2  P    114.10  3.000
 MPH  HO3  O3  P    115.86  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
 MPH  Var_01  SD   CG  CB  CA   169.64  30.0  3
 MPH  Var_02  HE1  CE  SD  CG  -179.76  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
 MPH  chir_01  CA  N  CB  P  negativ

