# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 17:03:34 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: ({3-hydroxy-2-oxo-4-[2-(phosphonooxy)ethyl]pyridin-1(2H)-yl}methyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(CCO[P](O)(O)=O)C=CN(C[P](O)(O)=O)C1=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
 HDX  HDX  '({3-hydroxy-2-oxo-4-[2-(phosphonooxy)ethyl]pyridin-1(2H)-yl}methyl)phosphonic acid'  ligand  33  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HDX
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
 HDX  OAA   O  O     0  -0.579  -2.5172   1.3795   1.4578
 HDX  OAB   O  OH1   0  -0.770  -4.3903  -0.4039   1.9057
 HDX  OAC   O  OH1   0  -0.741   4.8764  -0.3712   1.8040
 HDX  OAD   O  OH1   0  -0.616   0.1276   1.8979   1.4153
 HDX  OAE   O  O     0  -0.699  -3.5808  -2.2067   0.1826
 HDX  OAF   O  OH1   0  -0.735  -5.9765  -1.1562   0.2053
 HDX  OAG   O  OH1   0  -0.731   6.2251  -0.0715  -0.3752
 HDX  OAH   O  O     0  -0.711   4.6630  -2.1451   0.0395
 HDX  CAI   C  CR16  0  -0.415  -0.4439   0.4937  -1.8846
 HDX  CAJ   C  CR16  0   0.032  -1.7761   0.2763  -1.8144
 HDX  CAK   C  CH2   0  -0.153   2.4602   0.0708  -0.3073
 HDX  CAL   C  CH2   0  -0.536   1.7327   1.2823  -0.8677
 HDX  CAM   C  CH2   0  -0.627  -3.9185   0.3979  -0.6580
 HDX  OAN   O  O2    0  -0.589   3.8679   0.2953  -0.4593
 HDX  CAO   C  CR6   0   0.529  -1.8764   1.1259   0.4163
 HDX  CAP   C  CR6   0   0.091   0.2500   1.0686  -0.7919
 HDX  CAQ   C  CR6   0   0.190  -0.4632   1.3721   0.3329
 HDX  NAR   N  NR6   0  -0.501  -2.4775   0.6062  -0.6912
 HDX  PAS   P  P     0   1.351  -4.3979  -0.9966   0.4301
 HDX  PAT   P  P     0   1.455   4.8979  -0.7033   0.2403
 HDX  HOAD  H  HOH1  0   0.475  -0.5424   2.0479   2.0981
 HDX  HAI   H  HCR6  0   0.282   0.0860   0.2322  -2.7892
 HDX  HAJ   H  HCR6  0   0.319  -2.3455  -0.1464  -2.6274
 HDX  HAK   H  HCH2  0   0.243   2.2041  -0.0682   0.7465
 HDX  HAKA  H  HCH2  0   0.249   2.1705  -0.8321  -0.8492
 HDX  HAL   H  HCH2  0   0.271   2.0281   2.1763  -0.3163
 HDX  HALA  H  HCH2  0   0.272   2.0223   1.4286  -1.9101
 HDX  HAM   H  HCH2  0   0.326  -4.4255   1.3158  -0.3580
 HDX  HAMA  H  HCH2  0   0.320  -4.2475   0.1622  -1.6687
 HDX  H10   H  HOH1  0   0.499  -3.7260   0.3312   1.9625
 HDX  H11   H  HOH1  0   0.496   5.0756   0.5444   2.0413
 HDX  H12   H  HOH1  0   0.499  -6.2084  -1.8136  -0.4638
 HDX  H13   H  HOH1  0   0.505   7.0211  -0.5914  -0.1999

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
 HDX  OAA  CAO   double  1.249  0.020  1.249
 HDX  OAB  PAS   single  1.590  0.020  1.590
 HDX  OAC  PAT   single  1.599  0.020  1.599
 HDX  OAD  CAQ   single  1.341  0.020  1.341
 HDX  OAD  HOAD  single  0.850  0.020  0.980
 HDX  OAE  PAS   double  1.481  0.020  1.481
 HDX  OAF  PAS   single  1.602  0.020  1.602
 HDX  OAG  PAT   single  1.594  0.020  1.594
 HDX  OAH  PAT   double  1.475  0.020  1.475
 HDX  CAI  CAJ   double  1.352  0.020  1.352
 HDX  CAI  CAP   single  1.416  0.020  1.416
 HDX  CAI  HAI   single  0.930  0.020  1.080
 HDX  CAJ  NAR   single  1.365  0.020  1.365
 HDX  CAJ  HAJ   single  0.930  0.020  1.080
 HDX  CAK  CAL   single  1.520  0.020  1.520
 HDX  CAK  OAN   single  1.434  0.020  1.434
 HDX  CAK  HAK   single  0.970  0.020  1.090
 HDX  CAK  HAKA  single  0.970  0.020  1.090
 HDX  CAL  CAP   single  1.500  0.020  1.500
 HDX  CAL  HAL   single  0.970  0.020  1.090
 HDX  CAL  HALA  single  0.970  0.020  1.090
 HDX  CAM  NAR   single  1.456  0.020  1.456
 HDX  CAM  PAS   single  1.833  0.020  1.833
 HDX  CAM  HAM   single  0.970  0.020  1.090
 HDX  CAM  HAMA  single  0.970  0.020  1.090
 HDX  OAN  PAT   single  1.596  0.020  1.596
 HDX  CAO  CAQ   single  1.437  0.020  1.437
 HDX  CAO  NAR   single  1.363  0.020  1.363
 HDX  CAP  CAQ   double  1.366  0.020  1.366
 HDX  OAB  H10   single  0.850  0.020  0.980
 HDX  OAC  H11   single  0.850  0.020  0.980
 HDX  OAF  H12   single  0.850  0.020  0.980
 HDX  OAG  H13   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
 HDX  H10   OAB  PAS  109.42  3.000
 HDX  H11   OAC  PAT  115.73  3.000
 HDX  HOAD  OAD  CAQ  108.98  3.000
 HDX  H12   OAF  PAS  113.66  3.000
 HDX  H13   OAG  PAT  113.74  3.000
 HDX  HAI   CAI  CAP  120.26  3.000
 HDX  HAI   CAI  CAJ  119.21  3.000
 HDX  CAP   CAI  CAJ  120.54  3.000
 HDX  HAJ   CAJ  NAR  116.34  3.000
 HDX  HAJ   CAJ  CAI  122.96  3.000
 HDX  NAR   CAJ  CAI  120.69  3.000
 HDX  HAKA  CAK  HAK  108.12  3.000
 HDX  HAKA  CAK  OAN  109.72  3.000
 HDX  HAK   CAK  OAN  110.62  3.000
 HDX  HAKA  CAK  CAL  110.42  3.000
 HDX  HAK   CAK  CAL  110.15  3.000
 HDX  OAN   CAK  CAL  107.82  3.000
 HDX  HALA  CAL  HAL  107.52  3.000
 HDX  HALA  CAL  CAP  109.24  3.000
 HDX  HAL   CAL  CAP  111.03  3.000
 HDX  HALA  CAL  CAK  109.38  3.000
 HDX  HAL   CAL  CAK  109.70  3.000
 HDX  CAP   CAL  CAK  109.93  3.000
 HDX  HAMA  CAM  HAM  107.28  3.000
 HDX  HAMA  CAM  PAS  107.91  3.000
 HDX  HAM   CAM  PAS  110.82  3.000
 HDX  HAMA  CAM  NAR  107.98  3.000
 HDX  HAM   CAM  NAR  110.23  3.000
 HDX  PAS   CAM  NAR  112.41  3.000
 HDX  PAT   OAN  CAK  119.28  3.000
 HDX  NAR   CAO  CAQ  116.87  3.000
 HDX  NAR   CAO  OAA  121.92  3.000
 HDX  CAQ   CAO  OAA  121.22  3.000
 HDX  CAQ   CAP  CAL  121.74  3.000
 HDX  CAQ   CAP  CAI  118.01  3.000
 HDX  CAL   CAP  CAI  120.21  3.000
 HDX  CAP   CAQ  CAO  121.55  3.000
 HDX  CAP   CAQ  OAD  121.46  3.000
 HDX  CAO   CAQ  OAD  116.98  3.000
 HDX  CAO   NAR  CAM  118.19  3.000
 HDX  CAO   NAR  CAJ  122.29  3.000
 HDX  CAM   NAR  CAJ  119.52  3.000
 HDX  CAM   PAS  OAF  104.49  3.000
 HDX  CAM   PAS  OAE  112.22  3.000
 HDX  OAF   PAS  OAE  116.02  3.000
 HDX  CAM   PAS  OAB  105.43  3.000
 HDX  OAF   PAS  OAB   99.90  3.000
 HDX  OAE   PAS  OAB  117.19  3.000
 HDX  OAN   PAT  OAH  116.70  3.000
 HDX  OAN   PAT  OAG   96.89  3.000
 HDX  OAH   PAT  OAG  117.89  3.000
 HDX  OAN   PAT  OAC  106.86  3.000
 HDX  OAH   PAT  OAC  109.53  3.000
 HDX  OAG   PAT  OAC  107.86  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
 HDX  CONST_01  CAQ  CAO  NAR  CAJ    0.00   0.0  0
 HDX  CONST_02  CAJ  NAR  CAO  OAA  180.00   0.0  0
 HDX  CONST_03  CAQ  CAO  NAR  CAM  180.00   0.0  0
 HDX  CONST_04  CAM  NAR  CAO  OAA    0.00   0.0  0
 HDX  Var_01    CAK  CAL  CAP  CAI  -91.68  30.0  2
 HDX  Var_02    PAS  CAM  NAR  CAJ  108.20  30.0  2
 HDX  Var_03    NAR  CAM  PAS  OAB   81.07  30.0  2
 HDX  Var_04    CAP  CAL  CAK  OAN  177.31  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
 HDX  plan-1  OAA  0.020
 HDX  plan-1  OAD  0.020
 HDX  plan-1  CAI  0.020
 HDX  plan-1  CAJ  0.020
 HDX  plan-1  CAL  0.020
 HDX  plan-1  CAM  0.020
 HDX  plan-1  CAO  0.020
 HDX  plan-1  CAP  0.020
 HDX  plan-1  CAQ  0.020
 HDX  plan-1  NAR  0.020
 HDX  plan-1  HAI  0.020
 HDX  plan-1  HAJ  0.020

