# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:33:30 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: S-(phosphonomethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC[P](O)(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
 CYQ  CYQ  S-(phosphonomethyl)-L-cysteine  L-peptide  19  12  .  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_CYQ
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
 CYQ  N    N  NH2    0  -0.807  29.1169   3.4546  10.6937
 CYQ  CA   C  CH1    0  -0.160  28.0190   2.7603  10.0163
 CYQ  CB   C  CH2    0  -0.555  28.5154   1.3721   9.6364
 CYQ  SG   S  S2     0  -0.087  27.2904   0.3385   8.7906
 CYQ  CD   C  CH2    0  -0.816  27.0238   1.2329   7.2377
 CYQ  C    C  C      0   0.395  26.7896   2.6695  10.9539
 CYQ  O    O  O      0  -0.608  26.9570   2.0661  12.0316
 CYQ  OXT  O  OC    -1  -0.611  25.7389   3.2123  10.5552
 CYQ  P    P  P      0   1.173  26.1648   0.1440   5.9587
 CYQ  O1P  O  O      0  -0.897  25.8329   1.1360   4.8385
 CYQ  O2P  O  OP    -1  -0.898  24.9438  -0.4091   6.7013
 CYQ  O3P  O  OP    -1  -0.898  27.2007  -0.9154   5.5694
 CYQ  H    H  HNH2   0   0.336  28.8235   4.3946  10.9328
 CYQ  H2   H  HNH2   0   0.332  29.8784   3.5764  10.0358
 CYQ  HA   H  HCH1   0   0.183  27.7113   3.2787   9.0979
 CYQ  HB2  H  HCH2   0   0.239  29.4077   1.4480   9.0063
 CYQ  HB3  H  HCH2   0   0.245  28.8012   0.8314  10.5412
 CYQ  HD2  H  HCH2   0   0.217  26.4255   2.1246   7.4404
 CYQ  HD3  H  HCH2   0   0.217  27.9942   1.5707   6.8615

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
 CYQ  N   CA   single  1.458  0.019  1.458
 CYQ  N   H    single  0.860  0.020  0.860
 CYQ  N   H2   single  0.890  0.020  1.040
 CYQ  CA  CB   single  1.530  0.020  1.530
 CYQ  CA  C    single  1.525  0.021  1.525
 CYQ  CA  HA   single  0.970  0.020  0.970
 CYQ  CB  SG   single  1.812  0.020  1.812
 CYQ  CB  HB2  single  0.970  0.020  1.090
 CYQ  CB  HB3  single  0.970  0.020  1.090
 CYQ  SG  CD   single  1.812  0.020  1.812
 CYQ  CD  P    single  1.887  0.020  1.887
 CYQ  CD  HD2  single  0.970  0.020  1.090
 CYQ  CD  HD3  single  0.970  0.020  1.090
 CYQ  C   O    deloc   1.231  0.020  1.231
 CYQ  C   OXT  deloc   1.248  0.020  1.248
 CYQ  P   O1P  deloc   1.533  0.020  1.533
 CYQ  P   O2P  deloc   1.532  0.020  1.532
 CYQ  P   O3P  deloc   1.532  0.020  1.532

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
 CYQ  H2   N   H    105.02  3.000
 CYQ  H2   N   CA   108.65  3.000
 CYQ  H    N   CA   114.00  3.000
 CYQ  HA   CA  C    109.00  3.000
 CYQ  HA   CA  CB   109.00  3.000
 CYQ  C    CA  CB   110.10  1.900
 CYQ  HA   CA  N    110.00  3.000
 CYQ  C    CA  N    111.00  2.800
 CYQ  CB   CA  N    110.50  1.700
 CYQ  HB3  CB  HB2  107.33  3.000
 CYQ  HB3  CB  SG   106.33  3.000
 CYQ  HB2  CB  SG   108.77  3.000
 CYQ  HB3  CB  CA   109.27  3.000
 CYQ  HB2  CB  CA   110.25  3.000
 CYQ  SG   CB  CA   114.59  3.000
 CYQ  CD   SG  CB   102.58  3.000
 CYQ  HD3  CD  HD2  107.30  3.000
 CYQ  HD3  CD  P    110.42  3.000
 CYQ  HD2  CD  P    110.33  3.000
 CYQ  HD3  CD  SG   108.46  3.000
 CYQ  HD2  CD  SG   108.93  3.000
 CYQ  P    CD  SG   111.29  3.000
 CYQ  OXT  C   O    126.86  3.000
 CYQ  OXT  C   CA   116.70  3.000
 CYQ  O    C   CA   120.80  1.700
 CYQ  O3P  P   O2P  114.36  3.000
 CYQ  O3P  P   O1P  114.09  3.000
 CYQ  O2P  P   O1P  114.53  3.000
 CYQ  O3P  P   CD   105.28  3.000
 CYQ  O2P  P   CD   104.04  3.000
 CYQ  O1P  P   CD   102.74  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
 CYQ  Var_01  P    CD  SG  CB  164.02  30.0  3
 CYQ  Var_02  O1P  P   CD  SG  171.06  30.0  3
 CYQ  Var_03  HB2  CB  SG  CD  -58.87  30.0  1

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
 CYQ  chir_01  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
 CYQ  plan-1  CA   0.020
 CYQ  plan-1  C    0.020
 CYQ  plan-1  O    0.020
 CYQ  plan-1  OXT  0.020

