# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:45:22 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (S)-[(3R,4S)-4-hydroxy-3-methyl-2-oxohexyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](O)[C@@H](C)C(=O)C[P@H](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
 PSK  PSK  '(S)-[(3R,4S)-4-hydroxy-3-methyl-2-oxohexyl]phosphinic acid'  ligand  26  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PSK
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
 PSK  CAA   C  CH3    0  -0.659   4.3316   1.0576  -0.9600
 PSK  CAJ   C  CH2    0  -0.466   3.2144   0.0242  -0.9416
 PSK  CAQ   C  CH1    0   0.049   2.2098   0.2410   0.1890
 PSK  OAG   O  OH1    0  -0.667   2.8362   0.2598   1.4547
 PSK  CAP   C  CH1    0  -0.367   1.0579  -0.7715   0.1139
 PSK  CAB   C  CH3    0  -0.691   1.4577  -2.1656   0.6120
 PSK  CAN   C  C      0   0.415  -0.1820  -0.3132   0.8521
 PSK  OAE   O  O      0  -0.414  -0.1562   0.5518   1.7042
 PSK  CAL   C  CH2    0  -0.835  -1.4727  -0.9338   0.4246
 PSK  P1    P  P      0   0.968  -2.2854   0.1868  -0.8188
 PSK  OAH   O  O      0  -0.797  -1.2463   0.5977  -1.8350
 PSK  OAF   O  OP    -1  -0.802  -3.5808  -0.4497  -1.2579
 PSK  HAA1  H  HCH3   0   0.218   3.9299   2.0706  -1.0265
 PSK  HAA2  H  HCH3   0   0.221   4.9485   1.0044  -0.0633
 PSK  HAA3  H  HCH3   0   0.228   4.9875   0.9074  -1.8178
 PSK  HAJ1  H  HCH2   0   0.227   2.6703   0.0561  -1.8896
 PSK  HAJ2  H  HCH2   0   0.220   3.6438  -0.9822  -0.8790
 PSK  HAQ   H  HCH1   0   0.224   1.7876   1.2433   0.0602
 PSK  HOAG  H  HOH1   0   0.442   3.3840  -0.5280   1.5339
 PSK  HAP   H  HCH1   0   0.258   0.7617  -0.8650  -0.9363
 PSK  HAB1  H  HCH3   0   0.247   2.3177  -2.5427   0.0584
 PSK  HAB2  H  HCH3   0   0.232   1.7099  -2.1630   1.6729
 PSK  HAB3  H  HCH3   0   0.248   0.6513  -2.8847   0.4724
 PSK  HAL1  H  HCH2   0   0.266  -1.3350  -1.9031  -0.0591
 PSK  HAL2  H  HCH2   0   0.277  -2.1561  -1.0518   1.2675
 PSK  HP1   H  H      0  -0.038  -2.5690   1.3025   0.0279

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
 PSK  CAA  CAJ   single  1.522  0.020  1.522
 PSK  CAA  HAA1  single  0.939  0.020  1.096
 PSK  CAA  HAA2  single  0.939  0.020  1.096
 PSK  CAA  HAA3  single  0.939  0.020  1.096
 PSK  CAJ  CAQ   single  1.528  0.020  1.528
 PSK  CAJ  HAJ1  single  0.939  0.020  1.096
 PSK  CAJ  HAJ2  single  0.939  0.020  1.096
 PSK  CAQ  OAG   single  1.412  0.020  1.412
 PSK  CAQ  CAP   single  1.535  0.020  1.535
 PSK  CAQ  HAQ   single  0.939  0.020  1.096
 PSK  OAG  HOAG  single  0.832  0.020  0.971
 PSK  CAP  CAB   single  1.533  0.020  1.533
 PSK  CAP  CAN   single  1.514  0.020  1.514
 PSK  CAP  HAP   single  0.939  0.020  1.096
 PSK  CAB  HAB1  single  0.939  0.020  1.096
 PSK  CAB  HAB2  single  0.939  0.020  1.096
 PSK  CAB  HAB3  single  0.939  0.020  1.096
 PSK  CAN  OAE   double  1.214  0.020  1.214
 PSK  CAN  CAL   single  1.495  0.020  1.495
 PSK  CAL  P1    single  1.861  0.020  1.861
 PSK  CAL  HAL1  single  0.939  0.020  1.096
 PSK  CAL  HAL2  single  0.939  0.020  1.096
 PSK  P1   OAH   deloc   1.510  0.020  1.510
 PSK  P1   OAF   deloc   1.509  0.020  1.509
 PSK  P1   HP1   single  1.209  0.020  1.412

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
 PSK  HAA3  CAA  HAA2  107.47  3.000
 PSK  HAA3  CAA  HAA1  107.54  3.000
 PSK  HAA2  CAA  HAA1  107.68  3.000
 PSK  HAA3  CAA  CAJ   110.95  3.000
 PSK  HAA2  CAA  CAJ   111.87  3.000
 PSK  HAA1  CAA  CAJ   111.14  3.000
 PSK  HAJ2  CAJ  HAJ1  105.74  3.000
 PSK  HAJ2  CAJ  CAQ   110.22  3.000
 PSK  HAJ1  CAJ  CAQ   108.07  3.000
 PSK  HAJ2  CAJ  CAA   109.67  3.000
 PSK  HAJ1  CAJ  CAA   109.57  3.000
 PSK  CAQ   CAJ  CAA   113.28  3.000
 PSK  HAQ   CAQ  CAP   107.97  3.000
 PSK  HAQ   CAQ  OAG   105.32  3.000
 PSK  CAP   CAQ  OAG   112.67  3.000
 PSK  HAQ   CAQ  CAJ   107.23  3.000
 PSK  CAP   CAQ  CAJ   111.32  3.000
 PSK  OAG   CAQ  CAJ   111.92  3.000
 PSK  HOAG  OAG  CAQ   108.37  3.000
 PSK  HAP   CAP  CAN   105.78  3.000
 PSK  HAP   CAP  CAB   107.72  3.000
 PSK  CAN   CAP  CAB   109.29  3.000
 PSK  HAP   CAP  CAQ   107.82  3.000
 PSK  CAN   CAP  CAQ   113.01  3.000
 PSK  CAB   CAP  CAQ   112.83  3.000
 PSK  HAB3  CAB  HAB2  107.30  3.000
 PSK  HAB3  CAB  HAB1  106.89  3.000
 PSK  HAB2  CAB  HAB1  108.21  3.000
 PSK  HAB3  CAB  CAP   111.44  3.000
 PSK  HAB2  CAB  CAP   111.97  3.000
 PSK  HAB1  CAB  CAP   110.81  3.000
 PSK  CAL   CAN  OAE   120.99  3.000
 PSK  CAL   CAN  CAP   116.23  3.000
 PSK  OAE   CAN  CAP   122.70  3.000
 PSK  HAL2  CAL  HAL1  108.97  3.000
 PSK  HAL2  CAL  P1    107.92  3.000
 PSK  HAL1  CAL  P1    107.08  3.000
 PSK  HAL2  CAL  CAN   111.39  3.000
 PSK  HAL1  CAL  CAN   112.73  3.000
 PSK  P1    CAL  CAN   108.55  3.000
 PSK  HP1   P1   OAF   109.35  3.000
 PSK  HP1   P1   OAH   108.83  3.000
 PSK  OAF   P1   OAH   120.65  3.000
 PSK  HP1   P1   CAL    99.26  3.000
 PSK  OAF   P1   CAL   108.38  3.000
 PSK  OAH   P1   CAL   108.24  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
 PSK  Var_01  P1    CAL  CAN  CAP  -94.96  30.0  3
 PSK  Var_02  OAH   P1   CAL  CAN   46.99  30.0  3
 PSK  Var_03  HAA1  CAA  CAJ  CAQ  -56.65  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
 PSK  chir_01  CAQ  CAJ  OAG  CAP  positiv
 PSK  chir_02  CAP  CAN  CAB  CAQ  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
 PSK  plan-1  CAP  0.020
 PSK  plan-1  CAN  0.020
 PSK  plan-1  OAE  0.020
 PSK  plan-1  CAL  0.020

