# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:04:09 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: [1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(CCc1cccnc1)([P](O)(O)=O)[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
 HRX  HRX  '[1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid)'  ligand  31  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HRX
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
 HRX  O17  O  OH1   0  -0.748  -1.4847  -2.6542   0.0905
 HRX  P14  P  P     0   1.384  -2.1773  -1.2971  -0.4156
 HRX  O16  O  O     0  -0.695  -2.3199  -1.1228  -1.8773
 HRX  O15  O  OH1   0  -0.734  -3.5964  -1.2278   0.3169
 HRX  C8   C  CT    0  -0.298  -1.0612  -0.0688   0.4153
 HRX  P9   P  P     0   1.390  -1.6717   1.6072  -0.0918
 HRX  O11  O  OH1   0  -0.737  -0.9739   1.9315  -1.4973
 HRX  O12  O  O     0  -0.685  -3.1410   1.7049  -0.2142
 HRX  O10  O  OH1   0  -0.733  -0.9775   2.5334   1.0095
 HRX  O13  O  OH1   0  -0.655  -1.2704  -0.1397   1.8056
 HRX  C7   C  CH2   0  -0.515   0.3942  -0.3434   0.0072
 HRX  C9   C  CH2   0  -0.528   1.4517   0.5346   0.6876
 HRX  C6   C  CR6   0   0.041   2.8250   0.1099   0.2560
 HRX  C5   C  CR16  0  -0.191   3.4034   0.5973  -0.9105
 HRX  C2   C  CR16  0  -0.317   4.6603   0.1518  -1.2858
 HRX  C3   C  CR16  0  -0.073   5.3006  -0.7757  -0.4773
 HRX  N4   N  N     0  -0.400   4.7654  -1.2533   0.6400
 HRX  C1   C  CR16  0  -0.100   3.5614  -0.8166   0.9879
 HRX  H1   H  HOH1  0   0.501  -1.9768  -3.4631  -0.1094
 HRX  H2   H  HOH1  0   0.491  -3.5704  -1.2779   1.2820
 HRX  H3   H  HOH1  0   0.492  -0.0575   2.2342  -1.4789
 HRX  H4   H  HOH1  0   0.502  -1.2998   3.4464   1.0203
 HRX  H5   H  HOH1  0   0.469  -0.8227  -0.9195   2.1575
 HRX  H6   H  HCH2  0   0.287   0.6234  -1.3828   0.2543
 HRX  H7   H  HCH2  0   0.275   0.4885  -0.2740  -1.0788
 HRX  H8   H  HCH2  0   0.256   1.3200   1.5901   0.4469
 HRX  H9   H  HCH2  0   0.265   1.3609   0.4531   1.7716
 HRX  H10  H  HCR6  0   0.265   2.8774   1.3249  -1.5182
 HRX  H11  H  HCR6  0   0.271   5.1391   0.5167  -2.1841
 HRX  H12  H  HCR6  0   0.263   6.2857  -1.1438  -0.7409
 HRX  H13  H  HCR6  0   0.256   3.1511  -1.2198   1.9093

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
 HRX  O12  P9   double    1.478  0.020  1.478
 HRX  N4   C1   aromatic  1.327  0.020  1.327
 HRX  N4   C3   aromatic  1.328  0.020  1.328
 HRX  C1   C6   aromatic  1.392  0.020  1.392
 HRX  C3   C2   aromatic  1.387  0.020  1.387
 HRX  O10  P9   single    1.598  0.020  1.598
 HRX  P9   O11  single    1.602  0.020  1.602
 HRX  P9   C8   single    1.854  0.020  1.854
 HRX  O13  C8   single    1.408  0.020  1.408
 HRX  C7   C8   single    1.536  0.020  1.536
 HRX  C7   C9   single    1.534  0.020  1.534
 HRX  C6   C9   single    1.501  0.020  1.501
 HRX  C6   C5   aromatic  1.390  0.020  1.390
 HRX  C2   C5   aromatic  1.385  0.020  1.385
 HRX  C8   P14  single    1.856  0.020  1.856
 HRX  P14  O16  double    1.479  0.020  1.479
 HRX  P14  O15  single    1.598  0.020  1.598
 HRX  P14  O17  single    1.605  0.020  1.605
 HRX  O17  H1   single    0.850  0.020  0.980
 HRX  O15  H2   single    0.850  0.020  0.980
 HRX  O11  H3   single    0.850  0.020  0.980
 HRX  O10  H4   single    0.850  0.020  0.980
 HRX  O13  H5   single    0.850  0.020  0.980
 HRX  C7   H6   single    0.970  0.020  1.090
 HRX  C7   H7   single    0.970  0.020  1.090
 HRX  C9   H8   single    0.970  0.020  1.090
 HRX  C9   H9   single    0.970  0.020  1.090
 HRX  C5   H10  single    0.930  0.020  1.080
 HRX  C2   H11  single    0.930  0.020  1.080
 HRX  C3   H12  single    0.930  0.020  1.080
 HRX  C1   H13  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
 HRX  H1   O17  P14  114.96  3.000
 HRX  C8   P14  O15  107.46  3.000
 HRX  O15  P14  O16  111.23  3.000
 HRX  C8   P14  O16  114.99  3.000
 HRX  O15  P14  O17  105.98  3.000
 HRX  O16  P14  O17  116.92  3.000
 HRX  C8   P14  O17   99.14  3.000
 HRX  H2   O15  P14  115.55  3.000
 HRX  C7   C8   O13  113.21  3.000
 HRX  C7   C8   P9   113.63  3.000
 HRX  O13  C8   P9   105.47  3.000
 HRX  C7   C8   P14  109.42  3.000
 HRX  O13  C8   P14  108.63  3.000
 HRX  P9   C8   P14  106.12  3.000
 HRX  O10  P9   O12  116.80  3.000
 HRX  O10  P9   O11  107.34  3.000
 HRX  O12  P9   O11  110.31  3.000
 HRX  O11  P9   C8   106.23  3.000
 HRX  O10  P9   C8   101.09  3.000
 HRX  O12  P9   C8   114.19  3.000
 HRX  H3   O11  P9   117.40  3.000
 HRX  H4   O10  P9   114.18  3.000
 HRX  H5   O13  C8   109.37  3.000
 HRX  H7   C7   H6   105.49  3.000
 HRX  H7   C7   C9   110.20  3.000
 HRX  H6   C7   C9   107.44  3.000
 HRX  H7   C7   C8   109.54  3.000
 HRX  H6   C7   C8   107.98  3.000
 HRX  C9   C7   C8   115.66  3.000
 HRX  H9   C9   H8   106.35  3.000
 HRX  H9   C9   C6   109.93  3.000
 HRX  H8   C9   C6   108.72  3.000
 HRX  H9   C9   C7   109.91  3.000
 HRX  H8   C9   C7   111.90  3.000
 HRX  C6   C9   C7   109.96  3.000
 HRX  C1   C6   C5   117.04  3.000
 HRX  C5   C6   C9   121.52  3.000
 HRX  C1   C6   C9   121.42  3.000
 HRX  H10  C5   C2   120.27  3.000
 HRX  H10  C5   C6   120.25  3.000
 HRX  C2   C5   C6   119.47  3.000
 HRX  H11  C2   C3   120.37  3.000
 HRX  H11  C2   C5   121.21  3.000
 HRX  C3   C2   C5   118.42  3.000
 HRX  H12  C3   N4   116.67  3.000
 HRX  H12  C3   C2   120.31  3.000
 HRX  N4   C3   C2   123.02  3.000
 HRX  C1   N4   C3   117.90  3.000
 HRX  H13  C1   N4   116.28  3.000
 HRX  H13  C1   C6   119.57  3.000
 HRX  N4   C1   C6   124.14  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
 HRX  CONST_01  C3   N4  C1   C6      0.00   0.0  0
 HRX  CONST_02  C3   C2  C5   C6      0.00   0.0  0
 HRX  CONST_03  N4   C1  C6   C5      0.00   0.0  0
 HRX  CONST_04  N4   C3  C2   C5      0.00   0.0  0
 HRX  CONST_05  C1   N4  C3   C2      0.00   0.0  0
 HRX  CONST_06  C1   C6  C5   C2      0.00   0.0  0
 HRX  CONST_07  N4   C1  C6   C9    180.00   0.0  0
 HRX  CONST_08  C2   C5  C6   C9    180.00   0.0  0
 HRX  CONST_09  H11  C2  C5   C6    180.00   0.0  0
 HRX  CONST_10  H13  C1  C6   C5    180.00   0.0  0
 HRX  CONST_11  H12  C3  C2   C5    180.00   0.0  0
 HRX  CONST_12  H10  C5  C2   C3    180.00   0.0  0
 HRX  Var_01    C1   C6  C9   C7    -92.79  30.0  3
 HRX  Var_02    C6   C9  C7   C8    176.89  30.0  3
 HRX  Var_03    P9   C8  P14  O17   178.36  30.0  3
 HRX  Var_04    O12  P9  C8   P14    36.43  30.0  2
 HRX  Var_05    C9   C7  C8   P14  -176.11  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
 HRX  plan-1  C9   0.020
 HRX  plan-1  C6   0.020
 HRX  plan-1  C5   0.020
 HRX  plan-1  C2   0.020
 HRX  plan-1  C3   0.020
 HRX  plan-1  N4   0.020
 HRX  plan-1  C1   0.020
 HRX  plan-1  H10  0.020
 HRX  plan-1  H11  0.020
 HRX  plan-1  H12  0.020
 HRX  plan-1  H13  0.020

