# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 07:52:52 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O[P](O)(O)=O)(SC[C@H](N)C(O)=O)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
 QPA  QPA  S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine  L-peptide  25  17  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_QPA
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
 QPA  C    C  C      0   0.414  -73.6575  -3.4480  120.9660
 QPA  N    N  NH2    0  -0.812  -73.9900  -5.3020  119.3887
 QPA  O    O  O      0  -0.591  -74.3033  -2.6814  121.7055
 QPA  C8   C  CT     0   0.029  -77.3821  -1.9884  117.9906
 QPA  C9   C  CH3    0  -0.668  -77.9114  -0.5541  117.9724
 QPA  CA   C  CH1    0  -0.191  -74.3346  -3.9091  119.6526
 QPA  CB   C  CH2    0  -0.534  -75.8502  -3.7710  119.6749
 QPA  SG   S  S2     0  -0.100  -76.4169  -2.0494  119.5905
 QPA  C10  C  C      0   0.427  -76.3437  -2.2571  116.8626
 QPA  O10  O  OC    -1  -0.614  -75.7624  -1.2591  116.3874
 QPA  O11  O  OP    -1  -0.899  -80.8260  -2.2973  117.6379
 QPA  O12  O  OP    -1  -0.892  -79.8951  -4.5744  116.9192
 QPA  O13  O  O      0  -0.890  -79.2119  -2.4416  115.6460
 QPA  O14  O  O2     0  -0.645  -78.3772  -2.9416  118.0647
 QPA  OXT  O  OC    -1  -0.614  -72.4959  -3.8670  121.1581
 QPA  HN   H  HNH2   0   0.328  -74.1324  -5.5031  118.4069
 QPA  HNA  H  HNH2   0   0.330  -73.0016  -5.4175  119.5702
 QPA  H9   H  HCH3   0   0.202  -78.6331  -0.4024  118.7766
 QPA  H9A  H  HCH3   0   0.209  -77.1150   0.1782  118.0903
 QPA  H9B  H  HCH3   0   0.223  -78.4131  -0.3578  117.0263
 QPA  HA   H  HCH1   0   0.193  -73.9580  -3.2371  118.8617
 QPA  HB   H  HCH2   0   0.261  -76.2763  -4.2780  118.8112
 QPA  HBA  H  HCH2   0   0.227  -76.2611  -4.2397  120.5706
 QPA  O9   O  O      0  -0.610  -76.1268  -3.4471  116.5579
 QPA  P2   P  P      0   1.218  -79.6943  -3.0634  116.9553

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
 QPA  OXT  C    deloc   1.250  0.020  1.250
 QPA  CA   C    single  1.525  0.021  1.525
 QPA  C    O    deloc   1.231  0.020  1.231
 QPA  CA   N    single  1.458  0.019  1.458
 QPA  N    HN   single  0.890  0.020  1.040
 QPA  N    HNA  single  0.890  0.020  1.040
 QPA  O13  P2   deloc   1.528  0.020  1.528
 QPA  O12  P2   deloc   1.525  0.020  1.525
 QPA  P2   O11  deloc   1.528  0.020  1.528
 QPA  P2   O14  single  1.726  0.020  1.726
 QPA  C10  C8   single  1.556  0.020  1.556
 QPA  O14  C8   single  1.380  0.020  1.380
 QPA  C9   C8   single  1.529  0.020  1.529
 QPA  C8   SG   single  1.870  0.020  1.870
 QPA  C9   H9   single  0.970  0.020  1.090
 QPA  C9   H9A  single  0.970  0.020  1.090
 QPA  C9   H9B  single  0.970  0.020  1.090
 QPA  O9   C10  deloc   1.247  0.020  1.247
 QPA  CA   CB   single  1.530  0.020  1.530
 QPA  CA   HA   single  0.970  0.020  0.970
 QPA  SG   CB   single  1.814  0.020  1.814
 QPA  CB   HB   single  0.970  0.020  1.090
 QPA  CB   HBA  single  0.970  0.020  1.090
 QPA  O10  C10  deloc   1.249  0.020  1.249

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
 QPA  OXT  C    CA   115.92  3.000
 QPA  CA   C    O    120.80  1.700
 QPA  OXT  C    O    126.65  3.000
 QPA  HNA  N    HN   106.78  3.000
 QPA  HNA  N    CA   107.90  3.000
 QPA  HN   N    CA   109.38  3.000
 QPA  O14  C8   C10  113.63  3.000
 QPA  O14  C8   SG   107.69  3.000
 QPA  C10  C8   SG   105.67  3.000
 QPA  SG   C8   C9   102.68  3.000
 QPA  O14  C8   C9   113.51  3.000
 QPA  C10  C8   C9   112.60  3.000
 QPA  H9B  C9   H9A  108.06  3.000
 QPA  H9B  C9   H9   108.10  3.000
 QPA  H9A  C9   H9   108.09  3.000
 QPA  H9B  C9   C8   109.82  3.000
 QPA  H9A  C9   C8   112.12  3.000
 QPA  H9   C9   C8   110.53  3.000
 QPA  HA   CA   CB   109.00  3.000
 QPA  HA   CA   N    110.00  3.000
 QPA  CB   CA   N    110.50  1.700
 QPA  HA   CA   C    109.00  3.000
 QPA  CB   CA   C    110.10  1.900
 QPA  N    CA   C    111.00  2.800
 QPA  HBA  CB   HB   107.69  3.000
 QPA  HBA  CB   SG   109.15  3.000
 QPA  HB   CB   SG   106.43  3.000
 QPA  HBA  CB   CA   110.37  3.000
 QPA  HB   CB   CA   109.63  3.000
 QPA  SG   CB   CA   113.35  3.000
 QPA  CB   SG   C8   103.41  3.000
 QPA  O10  C10  O9   126.05  3.000
 QPA  O10  C10  C8   116.64  3.000
 QPA  O9   C10  C8   117.24  3.000
 QPA  C8   O14  P2   124.36  3.000
 QPA  O14  P2   O13  106.33  3.000
 QPA  O14  P2   O12  100.70  3.000
 QPA  O13  P2   O12  115.13  3.000
 QPA  O14  P2   O11  104.04  3.000
 QPA  O12  P2   O11  114.20  3.000
 QPA  O13  P2   O11  114.38  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
 QPA  Var_01  O13  P2  O14  C8   25.74  30.0  3
 QPA  Var_02  CA   CB  SG   C8  117.52  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
 QPA  chir_01  C8  O14  C9  SG  negativ
 QPA  chir_02  CA  N    CB  C   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
 QPA  plan-1  C    0.020
 QPA  plan-1  O    0.020
 QPA  plan-1  CA   0.020
 QPA  plan-1  OXT  0.020
 QPA  plan-2  C8   0.020
 QPA  plan-2  C10  0.020
 QPA  plan-2  O10  0.020
 QPA  plan-2  O9   0.020

