# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:36:34 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  20  10  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.807  -2.1853   0.3747  -1.6914
 MPH  CA   C  CH1    0  -0.323  -0.9584   0.5460  -0.9126
 MPH  CB   C  CH2    0  -0.437  -1.0817  -0.0835   0.4829
 MPH  CG   C  CH2    0  -0.545  -0.0237   0.3782   1.4726
 MPH  SD   S  S2     0  -0.070  -0.3715  -0.3071   3.1206
 MPH  CE   C  CH3    0  -0.762   1.0084   0.3984   4.0484
 MPH  P    P  P      0   1.167   0.4612  -0.1521  -1.9218
 MPH  H    H  HNH2   0   0.316  -2.9951   0.4958  -1.0921
 MPH  HN2  H  HNH2   0   0.316  -2.2133  -0.5884  -2.0066
 MPH  HA   H  HCH1   0   0.168  -0.7942   1.6244  -0.7743
 MPH  HB1  H  HCH2   0   0.205  -1.0545  -1.1738   0.3853
 MPH  HB2  H  HCH2   0   0.200  -2.0698   0.1656   0.8921
 MPH  HG1  H  HCH2   0   0.232  -0.0252   1.4696   1.5458
 MPH  HG2  H  HCH2   0   0.268   0.9616   0.0632   1.1357
 MPH  HE1  H  HCH3   0   0.267   0.9064   0.0955   5.0891
 MPH  HE2  H  HCH3   0   0.256   1.9644   0.0365   3.6723
 MPH  HE3  H  HCH3   0   0.255   0.9954   1.4870   4.0017
 MPH  O1   O  O      0  -0.909   0.0079  -1.5924  -2.2187
 MPH  O2   O  OP    -1  -0.908   0.5574   0.7350  -3.1682
 MPH  O3   O  OP    -1  -0.888   1.7116  -0.0737  -1.0314

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  1.876  0.020  1.876
 MPH  CA  HA   single  0.970  0.020  0.970
 MPH  CB  CG   single  1.520  0.020  1.520
 MPH  CB  HB1  single  0.970  0.020  1.090
 MPH  CB  HB2  single  0.970  0.020  1.090
 MPH  CG  SD   single  1.818  0.020  1.818
 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    deloc   1.539  0.020  1.539
 MPH  O2  P    deloc   1.533  0.020  1.533
 MPH  O3  P    deloc   1.537  0.020  1.537

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    105.96  3.000
 MPH  HN2  N   CA   107.45  3.000
 MPH  H    N   CA   114.00  3.000
 MPH  HA   CA  P    108.63  3.000
 MPH  HA   CA  CB   109.00  3.000
 MPH  P    CA  CB   113.38  3.000
 MPH  HA   CA  N    110.00  3.000
 MPH  P    CA  N    107.73  3.000
 MPH  CB   CA  N    110.40  1.500
 MPH  HB2  CB  HB1  106.34  3.000
 MPH  HB2  CB  CG   108.34  3.000
 MPH  HB1  CB  CG   110.07  3.000
 MPH  HB2  CB  CA   108.53  3.000
 MPH  HB1  CB  CA   108.97  3.000
 MPH  CG   CB  CA   114.27  3.000
 MPH  HG2  CG  HG1  108.11  3.000
 MPH  HG2  CG  SD   110.16  3.000
 MPH  HG1  CG  SD   108.37  3.000
 MPH  HG2  CG  CB   109.92  3.000
 MPH  HG1  CG  CB   110.22  3.000
 MPH  SD   CG  CB   110.02  3.000
 MPH  CE   SD  CG    99.92  3.000
 MPH  HE3  CE  HE2  109.12  3.000
 MPH  HE3  CE  HE1  108.53  3.000
 MPH  HE2  CE  HE1  108.65  3.000
 MPH  HE3  CE  SD   111.05  3.000
 MPH  HE2  CE  SD   111.31  3.000
 MPH  HE1  CE  SD   108.11  3.000
 MPH  O3   P   O2   112.98  3.000
 MPH  O3   P   O1   113.53  3.000
 MPH  O2   P   O1   113.78  3.000
 MPH  O3   P   CA   106.55  3.000
 MPH  O2   P   CA   105.63  3.000
 MPH  O1   P   CA   103.25  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  174.49  30.0  3
 MPH  Var_02  HE1  CE  SD  CG  177.85  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

