# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:32:42 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  36  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  OH1   0  -0.727  -3.2145   0.7142  -2.3497
 K2Y  PAW  P  P     0   1.442  -3.0853   1.9441  -1.3491
 K2Y  OAF  O  O     0  -0.678  -2.3229   3.0372  -1.9703
 K2Y  OAA  O  OH1   0  -0.717  -4.5104   2.2563  -0.7298
 K2Y  OAO  O  O2    0  -0.610  -2.4464   1.3349   0.0131
 K2Y  CAS  C  CR6   0   0.314  -1.2446   0.6821  -0.0299
 K2Y  CAM  C  CR16  0  -0.396  -0.0510   1.3817  -0.0546
 K2Y  CAT  C  CR6   0   0.322   1.1442   0.6837  -0.0397
 K2Y  OAP  O  O2    0  -0.601   2.3361   1.3479  -0.1056
 K2Y  PAX  P  P     0   1.448   3.0539   1.8311   1.2656
 K2Y  OAG  O  OH1   0  -0.727   2.3019   3.1644   1.7030
 K2Y  OAH  O  O     0  -0.684   3.0408   0.8514   2.3614
 K2Y  OAB  O  OH1   0  -0.721   4.4336   2.2300   0.5922
 K2Y  CAV  C  CR6   0   0.323   1.1445  -0.7058   0.0142
 K2Y  OAR  O  O2    0  -0.601   2.3370  -1.3689   0.0821
 K2Y  PAZ  P  P     0   1.448   3.0513  -1.8585  -1.2888
 K2Y  OAK  O  OH1   0  -0.727   2.3118  -3.2049  -1.7066
 K2Y  OAL  O  O     0  -0.684   3.0192  -0.8896  -2.3939
 K2Y  OAD  O  OH1   0  -0.721   4.4402  -2.2347  -0.6209
 K2Y  CAN  C  CR16  0  -0.396  -0.0499  -1.4050   0.0251
 K2Y  CAU  C  CR6   0   0.315  -1.2442  -0.7067  -0.0044
 K2Y  OAQ  O  O2    0  -0.610  -2.4453  -1.3600  -0.0549
 K2Y  PAY  P  P     0   1.443  -3.0894  -1.9805   1.2995
 K2Y  OAI  O  OH1   0  -0.727  -3.2366  -0.7567   2.3048
 K2Y  OAJ  O  OH1   0  -0.717  -4.5062  -2.3028   0.6657
 K2Y  OAC  O  O     0  -0.678  -2.3238  -3.0706   1.9223
 K2Y  H1   H  HOH1  0   0.498  -3.7778  -0.0218  -2.0737
 K2Y  H2   H  HOH1  0   0.513  -5.0449   2.8761  -1.2458
 K2Y  H3   H  HCR6  0   0.308  -0.0533   2.4633  -0.0845
 K2Y  H4   H  HOH1  0   0.502   2.3346   3.9020   1.0781
 K2Y  H5   H  HOH1  0   0.512   5.1289   2.4740   1.2190
 K2Y  H6   H  HOH1  0   0.502   2.3583  -3.9345  -1.0731
 K2Y  H7   H  HOH1  0   0.512   5.1285  -2.4946  -1.2490
 K2Y  H8   H  HCR6  0   0.308  -0.0511  -2.4866   0.0541
 K2Y  H9   H  HOH1  0   0.498  -3.7938  -0.0185   2.0223
 K2Y  H10  H  HOH1  0   0.513  -5.0434  -2.9213   1.1800

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  double    1.470  0.020  1.470
 K2Y  OAL  PAZ  double    1.470  0.020  1.470
 K2Y  PAY  OAJ  single    1.585  0.020  1.585
 K2Y  PAY  OAI  single    1.591  0.020  1.591
 K2Y  PAY  OAQ  single    1.623  0.020  1.623
 K2Y  PAZ  OAD  single    1.586  0.020  1.586
 K2Y  PAZ  OAR  single    1.622  0.020  1.622
 K2Y  PAZ  OAK  single    1.592  0.020  1.592
 K2Y  OAQ  CAU  single    1.368  0.020  1.368
 K2Y  CAN  CAU  aromatic  1.384  0.020  1.384
 K2Y  CAN  CAV  aromatic  1.384  0.020  1.384
 K2Y  OAR  CAV  single    1.366  0.020  1.366
 K2Y  CAU  CAS  aromatic  1.389  0.020  1.389
 K2Y  CAV  CAT  aromatic  1.391  0.020  1.391
 K2Y  CAS  OAO  single    1.368  0.020  1.368
 K2Y  CAS  CAM  aromatic  1.384  0.020  1.384
 K2Y  CAT  CAM  aromatic  1.384  0.020  1.384
 K2Y  CAT  OAP  single    1.366  0.020  1.366
 K2Y  OAO  PAW  single    1.623  0.020  1.623
 K2Y  OAP  PAX  single    1.621  0.020  1.621
 K2Y  OAH  PAX  double    1.470  0.020  1.470
 K2Y  OAF  PAW  double    1.470  0.020  1.470
 K2Y  PAW  OAA  single    1.585  0.020  1.585
 K2Y  PAW  OAE  single    1.591  0.020  1.591
 K2Y  PAX  OAG  single    1.592  0.020  1.592
 K2Y  PAX  OAB  single    1.586  0.020  1.586
 K2Y  OAE  H1   single    0.850  0.020  0.980
 K2Y  OAA  H2   single    0.850  0.020  0.980
 K2Y  CAM  H3   single    0.930  0.020  1.080
 K2Y  OAG  H4   single    0.850  0.020  0.980
 K2Y  OAB  H5   single    0.850  0.020  0.980
 K2Y  OAK  H6   single    0.850  0.020  0.980
 K2Y  OAD  H7   single    0.850  0.020  0.980
 K2Y  CAN  H8   single    0.930  0.020  1.080
 K2Y  OAI  H9   single    0.850  0.020  0.980
 K2Y  OAJ  H10  single    0.850  0.020  0.980

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  H1   OAE  PAW  117.14  3.000
 K2Y  OAO  PAW  OAA   95.74  3.000
 K2Y  OAA  PAW  OAF  119.00  3.000
 K2Y  OAO  PAW  OAF  115.43  3.000
 K2Y  OAA  PAW  OAE  108.97  3.000
 K2Y  OAF  PAW  OAE  110.56  3.000
 K2Y  OAO  PAW  OAE  105.64  3.000
 K2Y  H2   OAA  PAW  114.49  3.000
 K2Y  CAS  OAO  PAW  119.89  3.000
 K2Y  CAU  CAS  CAM  120.37  3.000
 K2Y  CAM  CAS  OAO  121.13  3.000
 K2Y  CAU  CAS  OAO  118.46  3.000
 K2Y  H3   CAM  CAT  120.42  3.000
 K2Y  H3   CAM  CAS  120.27  3.000
 K2Y  CAT  CAM  CAS  119.32  3.000
 K2Y  CAV  CAT  OAP  119.18  3.000
 K2Y  OAP  CAT  CAM  120.51  3.000
 K2Y  CAV  CAT  CAM  120.30  3.000
 K2Y  PAX  OAP  CAT  119.36  3.000
 K2Y  OAB  PAX  OAH  119.46  3.000
 K2Y  OAB  PAX  OAG  108.48  3.000
 K2Y  OAH  PAX  OAG  110.43  3.000
 K2Y  OAB  PAX  OAP   95.80  3.000
 K2Y  OAG  PAX  OAP  105.84  3.000
 K2Y  OAH  PAX  OAP  115.33  3.000
 K2Y  H4   OAG  PAX  116.43  3.000
 K2Y  H5   OAB  PAX  114.43  3.000
 K2Y  CAN  CAV  OAR  120.51  3.000
 K2Y  OAR  CAV  CAT  119.15  3.000
 K2Y  CAN  CAV  CAT  120.33  3.000
 K2Y  PAZ  OAR  CAV  119.28  3.000
 K2Y  OAD  PAZ  OAL  119.47  3.000
 K2Y  OAD  PAZ  OAK  108.46  3.000
 K2Y  OAL  PAZ  OAK  110.48  3.000
 K2Y  OAK  PAZ  OAR  105.82  3.000
 K2Y  OAD  PAZ  OAR   95.81  3.000
 K2Y  OAL  PAZ  OAR  115.28  3.000
 K2Y  H6   OAK  PAZ  116.34  3.000
 K2Y  H7   OAD  PAZ  114.41  3.000
 K2Y  H8   CAN  CAU  120.27  3.000
 K2Y  H8   CAN  CAV  120.41  3.000
 K2Y  CAU  CAN  CAV  119.32  3.000
 K2Y  OAQ  CAU  CAN  121.16  3.000
 K2Y  CAN  CAU  CAS  120.34  3.000
 K2Y  OAQ  CAU  CAS  118.46  3.000
 K2Y  PAY  OAQ  CAU  120.01  3.000
 K2Y  OAC  PAY  OAJ  118.95  3.000
 K2Y  OAJ  PAY  OAI  109.05  3.000
 K2Y  OAC  PAY  OAI  110.54  3.000
 K2Y  OAI  PAY  OAQ  105.66  3.000
 K2Y  OAJ  PAY  OAQ   95.67  3.000
 K2Y  OAC  PAY  OAQ  115.48  3.000
 K2Y  H9   OAI  PAY  117.13  3.000
 K2Y  H10  OAJ  PAY  114.45  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
 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  -101.59  30.0  2
 K2Y  Var_02    CAV  CAT  OAP  PAX   -91.94  30.0  2
 K2Y  Var_03    CAN  CAV  OAR  PAZ    88.93  30.0  2
 K2Y  Var_04    OAH  PAX  OAP  CAT    42.84  30.0  3
 K2Y  Var_05    OAL  PAZ  OAR  CAV    42.11  30.0  2
 K2Y  Var_06    OAC  PAY  OAQ  CAU   -64.72  30.0  1

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

