# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:48:25 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: [(2S,3R,4S)-2,4-dihydroxy-3-methylhexyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](O)[C@@H](C)[C@H](O)C[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
 PSX  PSX  '[(2S,3R,4S)-2,4-dihydroxy-3-methylhexyl]phosphonic acid'  ligand  28  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PSX
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
 PSX  CAA   C  CH3    0  -0.664   5.1167  -0.4116   0.8709
 PSX  C6    C  CH2    0  -0.440   3.9915   0.5605   0.5402
 PSX  C5    C  CH1    0   0.087   2.6692  -0.1304   0.2376
 PSX  OC5   O  OH1    0  -0.713   2.8305  -0.9219  -0.9220
 PSX  C4    C  CH1    0  -0.273   1.4851   0.8448   0.1032
 PSX  CAB   C  CH3    0  -0.674   1.6495   1.8112  -1.0664
 PSX  C3    C  CH1    0   0.084   0.1658   0.0585   0.0578
 PSX  OC3   O  OH1    0  -0.755   0.1825  -0.8135  -1.0583
 PSX  C2    C  CH2    0  -0.768  -1.0974   0.9176   0.0313
 PSX  P1    P  P      0   1.197  -2.6257  -0.1427   0.0516
 PSX  O2P   O  O      0  -0.897  -2.2798  -1.2077  -1.0438
 PSX  O1P   O  OP    -1  -0.887  -2.7138  -0.7543   1.4488
 PSX  O3P   O  OP    -1  -0.881  -3.8028   0.7449  -0.3426
 PSX  HAA1  H  HCH3   0   0.213   4.8721  -1.0179   1.7456
 PSX  HAA2  H  HCH3   0   0.221   5.3171  -1.0911   0.0420
 PSX  HAA3  H  HCH3   0   0.224   6.0430   0.1207   1.0905
 PSX  H61   H  HCH2   0   0.214   3.8376   1.2424   1.3816
 PSX  H62   H  HCH2   0   0.213   4.2860   1.1817  -0.3104
 PSX  H5    H  HCH1   0   0.168   2.4418  -0.7768   1.1059
 PSX  HOC5  H  HOH1   0   0.445   1.9244  -1.1422  -1.2058
 PSX  H4    H  HCH1   0   0.209   1.4576   1.4306   1.0307
 PSX  HAB1  H  HCH3   0   0.215   1.6802   1.2907  -2.0235
 PSX  HAB2  H  HCH3   0   0.227   0.8275   2.5257  -1.1065
 PSX  HAB3  H  HCH3   0   0.225   2.5679   2.3932  -0.9789
 PSX  H3    H  HCH1   0   0.164   0.1291  -0.5311   0.9925
 PSX  HOC3  H  HOH1   0   0.442  -0.7967  -1.1064  -1.1653
 PSX  H21   H  HCH2   0   0.201  -1.0973   1.6033   0.8849
 PSX  H22   H  HCH2   0   0.203  -1.1016   1.5403  -0.8697

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
 PSX  CAA  C6    single  1.523  0.020  1.523
 PSX  CAA  HAA1  single  0.970  0.020  1.090
 PSX  CAA  HAA2  single  0.970  0.020  1.090
 PSX  CAA  HAA3  single  0.970  0.020  1.090
 PSX  C6   C5    single  1.522  0.020  1.522
 PSX  C6   H61   single  0.970  0.020  1.090
 PSX  C6   H62   single  0.970  0.020  1.090
 PSX  C5   OC5   single  1.413  0.020  1.413
 PSX  C5   C4    single  1.540  0.020  1.540
 PSX  C5   H5    single  0.970  0.020  1.090
 PSX  OC5  HOC5  single  0.850  0.020  0.980
 PSX  C4   CAB   single  1.526  0.020  1.526
 PSX  C4   C3    single  1.537  0.020  1.537
 PSX  C4   H4    single  0.970  0.020  1.090
 PSX  CAB  HAB1  single  0.970  0.020  1.090
 PSX  CAB  HAB2  single  0.970  0.020  1.090
 PSX  CAB  HAB3  single  0.970  0.020  1.090
 PSX  C3   OC3   single  1.417  0.020  1.417
 PSX  C3   C2    single  1.528  0.020  1.528
 PSX  C3   H3    single  0.970  0.020  1.090
 PSX  OC3  HOC3  single  0.850  0.020  0.980
 PSX  C2   P1    single  1.860  0.020  1.860
 PSX  C2   H21   single  0.970  0.020  1.090
 PSX  C2   H22   single  0.970  0.020  1.090
 PSX  P1   O2P   deloc   1.566  0.020  1.566
 PSX  P1   O1P   deloc   1.528  0.020  1.528
 PSX  P1   O3P   deloc   1.526  0.020  1.526

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
 PSX  HAA3  CAA  HAA2  107.53  3.000
 PSX  HAA3  CAA  HAA1  107.45  3.000
 PSX  HAA2  CAA  HAA1  107.70  3.000
 PSX  HAA3  CAA  C6    111.08  3.000
 PSX  HAA2  CAA  C6    111.62  3.000
 PSX  HAA1  CAA  C6    111.27  3.000
 PSX  H62   C6   H61   106.39  3.000
 PSX  H62   C6   C5    109.70  3.000
 PSX  H61   C6   C5    108.28  3.000
 PSX  H62   C6   CAA   109.41  3.000
 PSX  H61   C6   CAA   109.56  3.000
 PSX  C5    C6   CAA   113.27  3.000
 PSX  H5    C5   C4    106.29  3.000
 PSX  H5    C5   OC5   109.90  3.000
 PSX  C4    C5   OC5   111.77  3.000
 PSX  H5    C5   C6    106.72  3.000
 PSX  C4    C5   C6    113.44  3.000
 PSX  OC5   C5   C6    108.55  3.000
 PSX  HOC5  OC5  C5    105.03  3.000
 PSX  H4    C4   C3    106.05  3.000
 PSX  H4    C4   CAB   108.21  3.000
 PSX  C3    C4   CAB   113.20  3.000
 PSX  H4    C4   C5    106.48  3.000
 PSX  C3    C4   C5    109.80  3.000
 PSX  CAB   C4   C5    112.65  3.000
 PSX  HAB3  CAB  HAB2  106.75  3.000
 PSX  HAB3  CAB  HAB1  107.55  3.000
 PSX  HAB2  CAB  HAB1  107.58  3.000
 PSX  HAB3  CAB  C4    111.54  3.000
 PSX  HAB2  CAB  C4    111.23  3.000
 PSX  HAB1  CAB  C4    111.94  3.000
 PSX  H3    C3   C2    106.68  3.000
 PSX  H3    C3   OC3   109.77  3.000
 PSX  C2    C3   OC3   110.01  3.000
 PSX  H3    C3   C4    106.05  3.000
 PSX  C2    C3   C4    115.00  3.000
 PSX  OC3   C3   C4    109.16  3.000
 PSX  HOC3  OC3  C3    104.26  3.000
 PSX  H22   C2   H21   106.58  3.000
 PSX  H22   C2   P1    109.26  3.000
 PSX  H21   C2   P1    110.40  3.000
 PSX  H22   C2   C3    109.70  3.000
 PSX  H21   C2   C3    109.79  3.000
 PSX  P1    C2   C3    111.01  3.000
 PSX  O3P   P1   O1P   115.12  3.000
 PSX  O3P   P1   O2P   112.65  3.000
 PSX  O1P   P1   O2P   112.34  3.000
 PSX  O3P   P1   C2    107.42  3.000
 PSX  O1P   P1   C2    106.60  3.000
 PSX  O2P   P1   C2    101.45  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
 PSX  Var_01  O2P   P1   C2  C3  -47.01  30.0  3
 PSX  Var_02  HAA1  CAA  C6  C5  -59.80  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
 PSX  chir_01  C5  C6   OC5  C4  positiv
 PSX  chir_02  C4  C5   CAB  C3  negativ
 PSX  chir_03  C3  OC3  C4   C2  negativ

