# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:13:36 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [(2~{R})-1-ethanoylsulfanyl-6-phenyl-hexan-2-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)SC[C@@H](CCCCc1ccccc1)[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
 8XW  8XW  '[(2~{R})-1-ethanoylsulfanyl-6-phenyl-hexan-2-yl]phosphonic acid'  ligand  39  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8XW
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
 8XW  CAA  C  CH3    0  -0.749   6.2767   2.0790   0.5540
 8XW  CAB  C  C      0   0.229   4.8743   1.9748   0.0072
 8XW  OAC  O  O      0  -0.423   4.2572   2.9502  -0.3626
 8XW  SAD  S  S2     0   0.024   4.2938   0.3147  -0.0173
 8XW  CAE  C  CH2    0  -0.561   2.6146   0.5068  -0.6918
 8XW  CAF  C  CH1    0  -0.470   1.5671  -0.2700   0.0988
 8XW  PAQ  P  P      0   1.192   1.8336  -2.1067  -0.1449
 8XW  OAS  O  O      0  -0.880   3.3610  -2.2606  -0.0267
 8XW  OAT  O  OP    -1  -0.899   1.0657  -2.8237   0.9732
 8XW  OAR  O  OP    -1  -0.905   1.3031  -2.3981  -1.5553
 8XW  CAG  C  CH2    0  -0.394   0.1804   0.2083  -0.3359
 8XW  CAH  C  CH2    0  -0.415  -0.9805  -0.3736   0.4609
 8XW  CAI  C  CH2    0  -0.408  -2.3261   0.2012   0.0385
 8XW  CAJ  C  CH2    0  -0.505  -3.4959  -0.4144   0.8091
 8XW  CAK  C  CR6    0   0.141  -4.8209   0.1635   0.3997
 8XW  CAL  C  CR16   0  -0.316  -5.5533  -0.3944  -0.6465
 8XW  CAM  C  CR16   0  -0.240  -6.7591   0.1630  -1.0516
 8XW  CAN  C  CR16   0  -0.276  -7.2545   1.2937  -0.4147
 8XW  CAO  C  CR16   0  -0.239  -6.5337   1.8610   0.6286
 8XW  CAP  C  CR16   0  -0.314  -5.3285   1.2993   1.0288
 8XW  HAB  H  HCH3   0   0.270   6.9243   2.5279  -0.2002
 8XW  HAC  H  HCH3   0   0.269   6.2768   2.7391   1.4225
 8XW  HAA  H  HCH3   0   0.250   6.6983   1.1191   0.8462
 8XW  HAG  H  HCH1   0   0.187   1.6963  -0.0240   1.1614
 8XW  HAH  H  HCH2   0   0.187   0.1308   1.3036  -0.2660
 8XW  HAI  H  HCH2   0   0.196   0.0431  -0.0339  -1.3945
 8XW  HAJ  H  HCH2   0   0.218  -0.9885  -1.4591   0.3552
 8XW  HAK  H  HCH2   0   0.192  -0.8262  -0.1789   1.5283
 8XW  HAL  H  HCH2   0   0.212  -2.3310   1.2870   0.1841
 8XW  HAM  H  HCH2   0   0.213  -2.4753   0.0376  -1.0340
 8XW  HAN  H  HCH2   0   0.234  -3.4971  -1.4964   0.6502
 8XW  HAO  H  HCH2   0   0.233  -3.3415  -0.2568   1.8806
 8XW  HAP  H  HCR6   0   0.244  -5.1778  -1.2791  -1.1486
 8XW  HAQ  H  HCR6   0   0.251  -7.3154  -0.2888  -1.8633
 8XW  HAR  H  HCR6   0   0.251  -8.1961   1.7274  -0.7261
 8XW  HAS  H  HCR6   0   0.251  -6.9120   2.7403   1.1348
 8XW  HAT  H  HCR6   0   0.243  -4.7720   1.7465   1.8449
 8XW  HAE  H  HCH2   0   0.260   2.4078   1.5787  -0.6899
 8XW  HAF  H  HCH2   0   0.251   2.6288   0.1774  -1.7326

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
 8XW  CAA  CAB  single    1.509  0.020  1.509
 8XW  CAB  OAC  double    1.212  0.020  1.212
 8XW  CAB  SAD  single    1.759  0.020  1.759
 8XW  SAD  CAE  single    1.820  0.020  1.820
 8XW  CAE  CAF  single    1.525  0.020  1.525
 8XW  CAF  PAQ  single    1.872  0.020  1.872
 8XW  CAF  CAG  single    1.530  0.020  1.530
 8XW  PAQ  OAS  deloc     1.540  0.020  1.540
 8XW  PAQ  OAT  deloc     1.534  0.020  1.534
 8XW  PAQ  OAR  deloc     1.535  0.020  1.535
 8XW  CAG  CAH  single    1.524  0.020  1.524
 8XW  CAH  CAI  single    1.523  0.020  1.523
 8XW  CAI  CAJ  single    1.530  0.020  1.530
 8XW  CAJ  CAK  single    1.502  0.020  1.502
 8XW  CAK  CAL  aromatic  1.394  0.020  1.394
 8XW  CAK  CAP  aromatic  1.394  0.020  1.394
 8XW  CAL  CAM  aromatic  1.389  0.020  1.389
 8XW  CAM  CAN  aromatic  1.389  0.020  1.389
 8XW  CAN  CAO  aromatic  1.389  0.020  1.389
 8XW  CAO  CAP  aromatic  1.389  0.020  1.389
 8XW  CAA  HAB  single    0.970  0.020  1.090
 8XW  CAA  HAC  single    0.970  0.020  1.090
 8XW  CAA  HAA  single    0.970  0.020  1.090
 8XW  CAE  HAE  single    0.970  0.020  1.090
 8XW  CAE  HAF  single    0.970  0.020  1.090
 8XW  CAF  HAG  single    0.970  0.020  1.090
 8XW  CAG  HAH  single    0.970  0.020  1.090
 8XW  CAG  HAI  single    0.970  0.020  1.090
 8XW  CAH  HAJ  single    0.970  0.020  1.090
 8XW  CAH  HAK  single    0.970  0.020  1.090
 8XW  CAI  HAL  single    0.970  0.020  1.090
 8XW  CAI  HAM  single    0.970  0.020  1.090
 8XW  CAJ  HAN  single    0.970  0.020  1.090
 8XW  CAJ  HAO  single    0.970  0.020  1.090
 8XW  CAL  HAP  single    0.930  0.020  1.080
 8XW  CAM  HAQ  single    0.930  0.020  1.080
 8XW  CAN  HAR  single    0.930  0.020  1.080
 8XW  CAO  HAS  single    0.930  0.020  1.080
 8XW  CAP  HAT  single    0.930  0.020  1.080

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
 8XW  HAA  CAA  HAC  108.66  3.000
 8XW  HAA  CAA  HAB  108.58  3.000
 8XW  HAC  CAA  HAB  107.54  3.000
 8XW  HAA  CAA  CAB  113.36  3.000
 8XW  HAC  CAA  CAB  109.30  3.000
 8XW  HAB  CAA  CAB  109.25  3.000
 8XW  SAD  CAB  OAC  125.96  3.000
 8XW  SAD  CAB  CAA  112.15  3.000
 8XW  OAC  CAB  CAA  121.89  3.000
 8XW  CAE  SAD  CAB  102.13  3.000
 8XW  HAF  CAE  HAE  107.48  3.000
 8XW  HAF  CAE  CAF  110.46  3.000
 8XW  HAE  CAE  CAF  111.66  3.000
 8XW  HAF  CAE  SAD  108.03  3.000
 8XW  HAE  CAE  SAD  106.13  3.000
 8XW  CAF  CAE  SAD  112.83  3.000
 8XW  HAG  CAF  CAG  108.15  3.000
 8XW  HAG  CAF  PAQ  109.21  3.000
 8XW  CAG  CAF  PAQ  113.51  3.000
 8XW  HAG  CAF  CAE  107.86  3.000
 8XW  CAG  CAF  CAE  108.42  3.000
 8XW  PAQ  CAF  CAE  109.54  3.000
 8XW  OAR  PAQ  OAT  114.08  3.000
 8XW  OAR  PAQ  OAS  113.23  3.000
 8XW  OAT  PAQ  OAS  113.20  3.000
 8XW  OAR  PAQ  CAF  104.87  3.000
 8XW  OAT  PAQ  CAF  107.00  3.000
 8XW  OAS  PAQ  CAF  103.26  3.000
 8XW  HAI  CAG  HAH  106.05  3.000
 8XW  HAI  CAG  CAH  109.01  3.000
 8XW  HAH  CAG  CAH  108.25  3.000
 8XW  HAI  CAG  CAF  108.62  3.000
 8XW  HAH  CAG  CAF  109.54  3.000
 8XW  CAH  CAG  CAF  115.00  3.000
 8XW  HAK  CAH  HAJ  105.80  3.000
 8XW  HAK  CAH  CAI  109.11  3.000
 8XW  HAJ  CAH  CAI  110.01  3.000
 8XW  HAK  CAH  CAG  109.53  3.000
 8XW  HAJ  CAH  CAG  109.57  3.000
 8XW  CAI  CAH  CAG  112.58  3.000
 8XW  HAM  CAI  HAL  106.12  3.000
 8XW  HAM  CAI  CAJ  109.21  3.000
 8XW  HAL  CAI  CAJ  109.17  3.000
 8XW  HAM  CAI  CAH  109.61  3.000
 8XW  HAL  CAI  CAH  109.95  3.000
 8XW  CAJ  CAI  CAH  112.58  3.000
 8XW  HAO  CAJ  HAN  106.56  3.000
 8XW  HAO  CAJ  CAK  109.63  3.000
 8XW  HAN  CAJ  CAK  109.87  3.000
 8XW  HAO  CAJ  CAI  109.11  3.000
 8XW  HAN  CAJ  CAI  109.01  3.000
 8XW  CAK  CAJ  CAI  112.47  3.000
 8XW  CAP  CAK  CAL  118.27  3.000
 8XW  CAP  CAK  CAJ  120.76  3.000
 8XW  CAL  CAK  CAJ  120.94  3.000
 8XW  HAP  CAL  CAM  119.54  3.000
 8XW  HAP  CAL  CAK  119.49  3.000
 8XW  CAM  CAL  CAK  120.97  3.000
 8XW  HAQ  CAM  CAN  120.01  3.000
 8XW  HAQ  CAM  CAL  119.82  3.000
 8XW  CAN  CAM  CAL  120.17  3.000
 8XW  HAR  CAN  CAO  120.25  3.000
 8XW  HAR  CAN  CAM  120.29  3.000
 8XW  CAO  CAN  CAM  119.45  3.000
 8XW  HAS  CAO  CAP  119.80  3.000
 8XW  HAS  CAO  CAN  120.09  3.000
 8XW  CAP  CAO  CAN  120.10  3.000
 8XW  HAT  CAP  CAO  119.70  3.000
 8XW  HAT  CAP  CAK  119.26  3.000
 8XW  CAO  CAP  CAK  121.03  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
 8XW  CONST_01  CAN  CAM  CAL  CAK     0.00   0.0  0
 8XW  CONST_02  CAN  CAO  CAP  CAK     0.00   0.0  0
 8XW  CONST_03  CAO  CAP  CAK  CAL     0.00   0.0  0
 8XW  CONST_04  CAO  CAN  CAM  CAL     0.00   0.0  0
 8XW  CONST_05  CAP  CAK  CAL  CAM     0.00   0.0  0
 8XW  CONST_06  CAP  CAO  CAN  CAM     0.00   0.0  0
 8XW  CONST_07  CAM  CAL  CAK  CAJ   180.00   0.0  0
 8XW  CONST_08  CAO  CAP  CAK  CAJ   180.00   0.0  0
 8XW  CONST_09  HAQ  CAM  CAL  CAK   180.00   0.0  0
 8XW  CONST_10  HAS  CAO  CAP  CAK   180.00   0.0  0
 8XW  CONST_11  HAT  CAP  CAK  CAL   180.00   0.0  0
 8XW  CONST_12  HAR  CAN  CAM  CAL   180.00   0.0  0
 8XW  CONST_13  HAP  CAL  CAM  CAN   180.00   0.0  0
 8XW  Var_01    CAL  CAK  CAJ  CAI    89.15  30.0  2
 8XW  Var_02    CAK  CAJ  CAI  CAH   179.47  30.0  3
 8XW  Var_03    CAF  CAE  SAD  CAB  -133.36  30.0  3
 8XW  Var_04    CAI  CAH  CAG  CAF   176.58  30.0  3
 8XW  Var_05    CAJ  CAI  CAH  CAG   178.25  30.0  3
 8XW  Var_06    HAB  CAA  CAB  OAC   -58.91  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
 8XW  chir_01  CAF  CAE  PAQ  CAG  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
 8XW  plan-1  CAJ  0.020
 8XW  plan-1  CAK  0.020
 8XW  plan-1  CAL  0.020
 8XW  plan-1  CAM  0.020
 8XW  plan-1  CAN  0.020
 8XW  plan-1  CAO  0.020
 8XW  plan-1  CAP  0.020
 8XW  plan-1  HAP  0.020
 8XW  plan-1  HAQ  0.020
 8XW  plan-1  HAR  0.020
 8XW  plan-1  HAS  0.020
 8XW  plan-1  HAT  0.020
 8XW  plan-2  CAA  0.020
 8XW  plan-2  CAB  0.020
 8XW  plan-2  OAC  0.020
 8XW  plan-2  SAD  0.020

