# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:50:23 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2,4,5-triphosphonooxyphenyl) dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc(O[P](O)(O)=O)c(O[P](O)(O)=O)cc1O[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
 K2Y  K2Y  '(2,4,5-triphosphonooxyphenyl) dihydrogen phosphate'  ligand  28  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K2Y
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
 K2Y  OAE  O  OP    -1  -0.905  -2.7284   1.5546  -2.4200
 K2Y  PAW  P  P      0   1.200  -2.8535   2.4428  -1.1918
 K2Y  OAF  O  O      0  -0.867  -1.9267   3.6544  -1.1916
 K2Y  OAA  O  OP    -1  -0.970  -4.2788   2.7431  -0.7433
 K2Y  OAO  O  O2     0  -0.660  -2.3300   1.4673   0.1240
 K2Y  CAS  C  CR6    0   0.330  -1.1782   0.7609   0.0624
 K2Y  CAM  C  CR16   0  -0.374   0.0640   1.3922   0.0260
 K2Y  CAT  C  CR6    0   0.293   1.2621   0.6788   0.0472
 K2Y  OAP  O  O2     0  -0.550   2.4705   1.2784  -0.0121
 K2Y  PAX  P  P      0   1.135   2.8822   2.6280   0.9769
 K2Y  OAG  O  OP    -1  -0.826   2.1861   3.8255   0.3392
 K2Y  OAH  O  O      0  -0.967   2.3792   2.2614   2.3651
 K2Y  OAB  O  OP    -1  -0.959   4.3960   2.6236   0.8104
 K2Y  CAV  C  CR6    0   0.216   1.2089  -0.7205   0.1097
 K2Y  OAR  O  O2     0  -0.673   2.3618  -1.4206   0.2076
 K2Y  PAZ  P  P      0   1.185   2.8540  -2.4961  -1.0413
 K2Y  OAK  O  OP    -1  -0.863   1.9706  -3.7290  -0.8815
 K2Y  OAL  O  O      0  -0.944   2.6331  -1.7248  -2.3337
 K2Y  OAD  O  OP    -1  -0.922   4.3103  -2.7139  -0.6493
 K2Y  CAN  C  CR16   0  -0.367  -0.0335  -1.3532   0.1195
 K2Y  CAU  C  CR6    0   0.184  -1.2319  -0.6396   0.0947
 K2Y  OAQ  O  O2     0  -0.582  -2.4420  -1.2369   0.0784
 K2Y  PAY  P  P      0   1.155  -2.8543  -2.5452   1.1204
 K2Y  OAI  O  OP    -1  -0.962  -2.3549  -2.1229   2.4936
 K2Y  OAJ  O  OP    -1  -0.995  -4.3677  -2.5474   0.9503
 K2Y  OAC  O  O      0  -0.773  -2.1559  -3.7670   0.5328
 K2Y  H3   H  HCR6   0   0.228   0.0981   2.4725  -0.0263
 K2Y  H8   H  HCR6   0   0.235  -0.0675  -2.4348   0.1400

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
 K2Y  OAC  PAY  deloc     1.525  0.020  1.525
 K2Y  OAL  PAZ  deloc     1.521  0.020  1.521
 K2Y  PAY  OAJ  deloc     1.523  0.020  1.523
 K2Y  PAY  OAI  deloc     1.521  0.020  1.521
 K2Y  PAY  OAQ  single    1.723  0.020  1.723
 K2Y  PAZ  OAD  deloc     1.524  0.020  1.524
 K2Y  PAZ  OAR  single    1.720  0.020  1.720
 K2Y  PAZ  OAK  deloc     1.525  0.020  1.525
 K2Y  OAQ  CAU  single    1.350  0.020  1.350
 K2Y  CAN  CAU  aromatic  1.395  0.020  1.395
 K2Y  CAN  CAV  aromatic  1.394  0.020  1.394
 K2Y  OAR  CAV  single    1.352  0.020  1.352
 K2Y  CAU  CAS  aromatic  1.402  0.020  1.402
 K2Y  CAV  CAT  aromatic  1.402  0.020  1.402
 K2Y  CAS  OAO  single    1.353  0.020  1.353
 K2Y  CAS  CAM  aromatic  1.394  0.020  1.394
 K2Y  CAT  CAM  aromatic  1.395  0.020  1.395
 K2Y  CAT  OAP  single    1.350  0.020  1.350
 K2Y  OAO  PAW  single    1.719  0.020  1.719
 K2Y  OAP  PAX  single    1.723  0.020  1.723
 K2Y  OAH  PAX  deloc     1.521  0.020  1.521
 K2Y  OAF  PAW  deloc     1.525  0.020  1.525
 K2Y  PAW  OAA  deloc     1.524  0.020  1.524
 K2Y  PAW  OAE  deloc     1.521  0.020  1.521
 K2Y  PAX  OAG  deloc     1.525  0.020  1.525
 K2Y  PAX  OAB  deloc     1.523  0.020  1.523
 K2Y  CAM  H3   single    0.930  0.020  1.080
 K2Y  CAN  H8   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
 K2Y  OAO  PAW  OAA   99.87  3.000
 K2Y  OAA  PAW  OAF  114.30  3.000
 K2Y  OAO  PAW  OAF  105.40  3.000
 K2Y  OAA  PAW  OAE  115.44  3.000
 K2Y  OAF  PAW  OAE  114.46  3.000
 K2Y  OAO  PAW  OAE  105.17  3.000
 K2Y  CAS  OAO  PAW  121.37  3.000
 K2Y  CAU  CAS  CAM  119.15  3.000
 K2Y  CAM  CAS  OAO  121.57  3.000
 K2Y  CAU  CAS  OAO  119.21  3.000
 K2Y  H3   CAM  CAT  118.97  3.000
 K2Y  H3   CAM  CAS  118.78  3.000
 K2Y  CAT  CAM  CAS  122.25  3.000
 K2Y  CAV  CAT  OAP  118.63  3.000
 K2Y  OAP  CAT  CAM  122.76  3.000
 K2Y  CAV  CAT  CAM  118.60  3.000
 K2Y  PAX  OAP  CAT  122.44  3.000
 K2Y  OAB  PAX  OAH  115.33  3.000
 K2Y  OAB  PAX  OAG  114.22  3.000
 K2Y  OAH  PAX  OAG  114.83  3.000
 K2Y  OAB  PAX  OAP   99.93  3.000
 K2Y  OAG  PAX  OAP  105.42  3.000
 K2Y  OAH  PAX  OAP  104.83  3.000
 K2Y  CAN  CAV  OAR  121.61  3.000
 K2Y  OAR  CAV  CAT  119.19  3.000
 K2Y  CAN  CAV  CAT  119.15  3.000
 K2Y  PAZ  OAR  CAV  121.01  3.000
 K2Y  OAD  PAZ  OAL  115.46  3.000
 K2Y  OAD  PAZ  OAK  114.27  3.000
 K2Y  OAL  PAZ  OAK  114.50  3.000
 K2Y  OAK  PAZ  OAR  105.28  3.000
 K2Y  OAD  PAZ  OAR  100.14  3.000
 K2Y  OAL  PAZ  OAR  104.97  3.000
 K2Y  H8   CAN  CAU  118.98  3.000
 K2Y  H8   CAN  CAV  118.79  3.000
 K2Y  CAU  CAN  CAV  122.22  3.000
 K2Y  OAQ  CAU  CAN  122.96  3.000
 K2Y  CAN  CAU  CAS  118.59  3.000
 K2Y  OAQ  CAU  CAS  118.44  3.000
 K2Y  PAY  OAQ  CAU  122.92  3.000
 K2Y  OAC  PAY  OAJ  114.26  3.000
 K2Y  OAJ  PAY  OAI  115.31  3.000
 K2Y  OAC  PAY  OAI  114.83  3.000
 K2Y  OAI  PAY  OAQ  104.87  3.000
 K2Y  OAJ  PAY  OAQ   99.87  3.000
 K2Y  OAC  PAY  OAQ  105.41  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
 K2Y  CONST_01  CAV  CAN  CAU  CAS     0.00   0.0  0
 K2Y  CONST_02  CAV  CAT  CAM  CAS     0.00   0.0  0
 K2Y  CONST_03  CAN  CAU  CAS  CAM     0.00   0.0  0
 K2Y  CONST_04  CAN  CAV  CAT  CAM     0.00   0.0  0
 K2Y  CONST_05  CAU  CAN  CAV  CAT     0.00   0.0  0
 K2Y  CONST_06  CAU  CAS  CAM  CAT     0.00   0.0  0
 K2Y  CONST_07  CAN  CAU  CAS  OAO   180.00   0.0  0
 K2Y  CONST_08  CAT  CAM  CAS  OAO   180.00   0.0  0
 K2Y  CONST_09  OAP  CAT  CAM  CAS   180.00   0.0  0
 K2Y  CONST_10  OAQ  CAU  CAS  CAM   180.00   0.0  0
 K2Y  CONST_11  OAR  CAV  CAT  CAM   180.00   0.0  0
 K2Y  CONST_12  CAN  CAV  CAT  OAP   180.00   0.0  0
 K2Y  CONST_13  OAQ  CAU  CAN  CAV   180.00   0.0  0
 K2Y  CONST_14  CAU  CAN  CAV  OAR   180.00   0.0  0
 K2Y  CONST_15  H8   CAN  CAU  CAS   180.00   0.0  0
 K2Y  CONST_16  H3   CAM  CAT  CAV   180.00   0.0  0
 K2Y  Var_01    CAU  CAS  OAO  PAW  -115.31  30.0  2
 K2Y  Var_02    CAV  CAT  OAP  PAX  -133.33  30.0  2
 K2Y  Var_03    CAN  CAV  OAR  PAZ    66.27  30.0  2
 K2Y  Var_04    OAH  PAX  OAP  CAT    44.66  30.0  3
 K2Y  Var_05    OAL  PAZ  OAR  CAV    45.46  30.0  3
 K2Y  Var_06    OAC  PAY  OAQ  CAU   -76.00  30.0  3

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
 K2Y  plan-1  OAO  0.020
 K2Y  plan-1  CAS  0.020
 K2Y  plan-1  CAM  0.020
 K2Y  plan-1  CAT  0.020
 K2Y  plan-1  OAP  0.020
 K2Y  plan-1  CAV  0.020
 K2Y  plan-1  OAR  0.020
 K2Y  plan-1  CAN  0.020
 K2Y  plan-1  CAU  0.020
 K2Y  plan-1  OAQ  0.020
 K2Y  plan-1  H3   0.020
 K2Y  plan-1  H8   0.020

