# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 06:27:19 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-thiophosphono-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cn(cn1)[P@@](O)(S)=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
 PSH  PSH  1-thiophosphono-L-histidine  L-peptide  23  15  .  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_PSH
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
 PSH  N    N  NH2    0  -0.833  -17.4646  32.8768  21.2811
 PSH  CA   C  CH1    0  -0.187  -18.1735  32.5052  20.0615
 PSH  CB   C  CH2    0  -0.534  -19.5316  33.2183  19.9498
 PSH  CG   C  CR5    0   0.126  -19.4061  34.6948  19.7820
 PSH  CD2  C  CR15   0  -0.126  -19.3926  35.4182  18.6246
 PSH  ND1  N  N      0  -0.466  -19.2249  35.5412  20.8500
 PSH  CE1  C  CR15   0   0.083  -19.1021  36.7372  20.3390
 PSH  NE2  N  NR5    0  -0.570  -19.2010  36.7298  18.9878
 PSH  C    C  C      0   0.404  -17.3503  32.7412  18.7664
 PSH  O    O  O      0  -0.598  -16.2345  33.2853  18.8886
 PSH  P    P  P      0   1.151  -18.9709  38.1065  17.9226
 PSH  S    S  S2     0  -0.472  -16.8438  38.1895  17.7654
 PSH  O1   O  OP    -1  -0.737  -19.3255  39.3172  18.7148
 PSH  O2   O  O      0  -0.726  -19.5559  37.7145  16.6108
 PSH  OXT  O  OC    -1  -0.611  -17.8805  32.3504  17.7072
 PSH  HN1  H  HNH2   0   0.328  -16.5315  33.1561  20.9986
 PSH  HN2  H  HNH2   0   0.333  -17.8790  33.7099  21.6815
 PSH  HA   H  HCH1   0   0.200  -18.3973  31.4289  20.0895
 PSH  HB1  H  HCH2   0   0.232  -20.1210  33.0044  20.8467
 PSH  HB2  H  HCH2   0   0.235  -20.0784  32.7948  19.1079
 PSH  HD2  H  HCR5   0   0.274  -19.4996  35.1138  17.5975
 PSH  HE1  H  HCR5   0   0.270  -18.9444  37.6453  20.9006
 PSH  HS   H  HSH1   0   0.225  -16.6804  37.1248  16.9701

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
 PSH  O2   P    deloc     1.489  0.020  1.489
 PSH  O1   P    deloc     1.490  0.020  1.490
 PSH  OXT  C    deloc     1.247  0.020  1.247
 PSH  P    S    single    2.135  0.020  2.135
 PSH  P    NE2  single    1.756  0.020  1.756
 PSH  O    C    deloc     1.231  0.020  1.231
 PSH  CD2  NE2  aromatic  1.374  0.020  1.374
 PSH  CD2  CG   aromatic  1.365  0.020  1.365
 PSH  C    CA   single    1.525  0.021  1.525
 PSH  NE2  CE1  aromatic  1.355  0.020  1.355
 PSH  CG   CB   single    1.491  0.020  1.491
 PSH  CG   ND1  aromatic  1.375  0.020  1.375
 PSH  CE1  ND1  aromatic  1.306  0.020  1.306
 PSH  CA   CB   single    1.530  0.020  1.530
 PSH  CA   N    single    1.458  0.019  1.458
 PSH  N    HN1  single    0.890  0.020  1.040
 PSH  N    HN2  single    0.890  0.020  1.040
 PSH  CA   HA   single    0.970  0.020  0.970
 PSH  CB   HB1  single    0.970  0.020  1.090
 PSH  CB   HB2  single    0.970  0.020  1.090
 PSH  CD2  HD2  single    0.930  0.020  1.080
 PSH  CE1  HE1  single    0.930  0.020  1.080
 PSH  S    HS   single    1.200  0.020  1.300

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
 PSH  HN2  N    HN1  105.07  3.000
 PSH  HN2  N    CA   109.95  3.000
 PSH  HN1  N    CA   106.52  3.000
 PSH  HA   CA   C    109.00  3.000
 PSH  HA   CA   CB   109.00  3.000
 PSH  C    CA   CB   110.10  1.900
 PSH  HA   CA   N    110.00  3.000
 PSH  CB   CA   N    110.50  1.700
 PSH  C    CA   N    111.00  2.800
 PSH  HB2  CB   HB1  106.68  3.000
 PSH  HB2  CB   CG   109.89  3.000
 PSH  HB1  CB   CG   109.33  3.000
 PSH  HB2  CB   CA   108.61  3.000
 PSH  HB1  CB   CA   108.99  3.000
 PSH  CG   CB   CA   113.14  3.000
 PSH  ND1  CG   CD2  109.34  3.000
 PSH  ND1  CG   CB   122.23  3.000
 PSH  CD2  CG   CB   128.38  3.000
 PSH  HD2  CD2  NE2  122.40  3.000
 PSH  HD2  CD2  CG   131.16  3.000
 PSH  NE2  CD2  CG   106.44  3.000
 PSH  CE1  ND1  CG   105.79  3.000
 PSH  HE1  CE1  NE2  122.29  3.000
 PSH  HE1  CE1  ND1  125.49  3.000
 PSH  NE2  CE1  ND1  112.22  3.000
 PSH  P    NE2  CE1  126.24  3.000
 PSH  CE1  NE2  CD2  106.20  3.000
 PSH  P    NE2  CD2  127.32  3.000
 PSH  OXT  C    O    126.88  3.000
 PSH  O    C    CA   120.80  1.700
 PSH  OXT  C    CA   115.81  3.000
 PSH  O2   P    O1   126.09  3.000
 PSH  O1   P    S    104.17  3.000
 PSH  O2   P    S    109.69  3.000
 PSH  S    P    NE2  101.88  3.000
 PSH  O1   P    NE2  106.47  3.000
 PSH  O2   P    NE2  106.05  3.000
 PSH  HS   S    P     97.72  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
 PSH  CONST_01  CE1  NE2  CD2  CG     0.00   0.0  0
 PSH  CONST_02  NE2  CE1  ND1  CG     0.00   0.0  0
 PSH  CONST_03  ND1  CE1  NE2  CD2    0.00   0.0  0
 PSH  CONST_04  CE1  ND1  CG   CD2    0.00   0.0  0
 PSH  CONST_05  NE2  CD2  CG   ND1    0.00   0.0  0
 PSH  CONST_06  NE2  CD2  CG   CB   180.00   0.0  0
 PSH  CONST_07  CE1  ND1  CG   CB   180.00   0.0  0
 PSH  CONST_08  P    NE2  CD2  CG   180.00   0.0  0
 PSH  CONST_09  P    NE2  CE1  ND1  180.00   0.0  0
 PSH  CONST_10  HE1  CE1  ND1  CG   180.00   0.0  0
 PSH  CONST_11  HD2  CD2  CG   ND1  180.00   0.0  0
 PSH  Var_01    CD2  CG   CB   CA    94.34  30.0  1
 PSH  Var_02    O2   P    NE2  CD2   22.41  30.0  2

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
 PSH  chir_01  CA  C  CB  N  positiv

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
 PSH  plan-1  CB   0.020
 PSH  plan-1  CG   0.020
 PSH  plan-1  CD2  0.020
 PSH  plan-1  ND1  0.020
 PSH  plan-1  CE1  0.020
 PSH  plan-1  NE2  0.020
 PSH  plan-1  P    0.020
 PSH  plan-1  HD2  0.020
 PSH  plan-1  HE1  0.020
 PSH  plan-2  CA   0.020
 PSH  plan-2  C    0.020
 PSH  plan-2  O    0.020
 PSH  plan-2  OXT  0.020

