# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 06:55:55 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  27  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 OK
;

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  OP    -1  -0.927  -1.8598  -2.4888   0.8123
 HRX  P14  P  P      0   1.159  -2.0936  -1.4248  -0.3126
 HRX  O16  O  O      0  -0.908  -1.4799  -1.8520  -1.6517
 HRX  O15  O  OP    -1  -0.893  -3.5660  -1.0274  -0.4162
 HRX  C8   C  CT     0  -0.293  -1.0586  -0.0273   0.4278
 HRX  P9   P  P      0   1.167  -1.6554   1.6925   0.0228
 HRX  O11  O  OP    -1  -0.927  -1.7420   1.7301  -1.5115
 HRX  O12  O  O      0  -0.923  -2.9983   1.8894   0.7395
 HRX  O10  O  OP    -1  -0.912  -0.5950   2.6823   0.5650
 HRX  O13  O  OH1    0  -0.758  -1.1443  -0.2399   1.8467
 HRX  C7   C  CH2    0  -0.412   0.3926  -0.2610  -0.0194
 HRX  C9   C  CH2    0  -0.516   1.4640   0.4737   0.7938
 HRX  C6   C  CR6    0   0.054   2.8368   0.1342   0.3065
 HRX  C5   C  CR16   0  -0.205   3.4025   0.7609  -0.8014
 HRX  C2   C  CR16   0  -0.319   4.6598   0.3793  -1.2419
 HRX  C3   C  CR16   0  -0.086   5.3228  -0.6306  -0.5596
 HRX  N4   N  N      0  -0.404   4.8056  -1.2448   0.4979
 HRX  C1   C  CR16   0  -0.121   3.6001  -0.8654   0.9070
 HRX  H5   H  HOH1   0   0.398  -1.3423  -1.2053   1.8677
 HRX  H6   H  HCH2   0   0.170   0.6204  -1.3337   0.0311
 HRX  H7   H  HCH2   0   0.190   0.4879   0.0151  -1.0720
 HRX  H8   H  HCH2   0   0.248   1.2720   1.5440   0.7213
 HRX  H9   H  HCH2   0   0.203   1.3688   0.1926   1.8454
 HRX  H10  H  HCR6   0   0.256   2.8577   1.5464  -1.3127
 HRX  H11  H  HCR6   0   0.262   5.1231   0.8540  -2.0966
 HRX  H12  H  HCR6   0   0.253   6.3082  -0.9531  -0.8780
 HRX  H13  H  HCR6   0   0.244   3.2043  -1.3854   1.7754

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   deloc     1.535  0.020  1.535
 HRX  N4   C1   aromatic  1.328  0.020  1.328
 HRX  N4   C3   aromatic  1.328  0.020  1.328
 HRX  C1   C6   aromatic  1.394  0.020  1.394
 HRX  C3   C2   aromatic  1.387  0.020  1.387
 HRX  O10  P9   deloc     1.549  0.020  1.549
 HRX  P9   O11  deloc     1.537  0.020  1.537
 HRX  P9   C8   single    1.865  0.020  1.865
 HRX  O13  C8   single    1.437  0.020  1.437
 HRX  C7   C8   single    1.536  0.020  1.536
 HRX  C7   C9   single    1.533  0.020  1.533
 HRX  C6   C9   single    1.496  0.020  1.496
 HRX  C6   C5   aromatic  1.393  0.020  1.393
 HRX  C2   C5   aromatic  1.386  0.020  1.386
 HRX  C8   P14  single    1.890  0.020  1.890
 HRX  P14  O16  deloc     1.534  0.020  1.534
 HRX  P14  O15  deloc     1.529  0.020  1.529
 HRX  P14  O17  deloc     1.566  0.020  1.566
 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  C8   P14  O15  111.21  3.000
 HRX  O15  P14  O16  113.50  3.000
 HRX  C8   P14  O16  109.20  3.000
 HRX  O15  P14  O17  111.66  3.000
 HRX  O16  P14  O17  112.23  3.000
 HRX  C8   P14  O17   98.00  3.000
 HRX  C7   C8   O13  108.73  3.000
 HRX  C7   C8   P9   112.29  3.000
 HRX  O13  C8   P9   109.38  3.000
 HRX  C7   C8   P14  106.90  3.000
 HRX  O13  C8   P14  104.16  3.000
 HRX  P9   C8   P14  114.94  3.000
 HRX  O10  P9   O12  110.71  3.000
 HRX  O10  P9   O11  111.87  3.000
 HRX  O12  P9   O11  114.43  3.000
 HRX  O11  P9   C8   104.91  3.000
 HRX  O10  P9   C8   107.11  3.000
 HRX  O12  P9   C8   107.27  3.000
 HRX  H5   O13  C8   100.25  3.000
 HRX  H7   C7   H6   105.86  3.000
 HRX  H7   C7   C9   109.22  3.000
 HRX  H6   C7   C9   107.39  3.000
 HRX  H7   C7   C8   108.93  3.000
 HRX  H6   C7   C8   109.35  3.000
 HRX  C9   C7   C8   115.65  3.000
 HRX  H9   C9   H8   107.54  3.000
 HRX  H9   C9   C6   109.58  3.000
 HRX  H8   C9   C6   111.27  3.000
 HRX  H9   C9   C7   109.06  3.000
 HRX  H8   C9   C7   108.20  3.000
 HRX  C6   C9   C7   111.09  3.000
 HRX  C1   C6   C5   116.29  3.000
 HRX  C5   C6   C9   121.99  3.000
 HRX  C1   C6   C9   121.67  3.000
 HRX  H10  C5   C2   120.36  3.000
 HRX  H10  C5   C6   119.80  3.000
 HRX  C2   C5   C6   119.83  3.000
 HRX  H11  C2   C3   120.22  3.000
 HRX  H11  C2   C5   121.25  3.000
 HRX  C3   C2   C5   118.53  3.000
 HRX  H12  C3   N4   116.75  3.000
 HRX  H12  C3   C2   120.41  3.000
 HRX  N4   C3   C2   122.84  3.000
 HRX  C1   N4   C3   117.82  3.000
 HRX  H13  C1   N4   116.10  3.000
 HRX  H13  C1   C6   119.21  3.000
 HRX  N4   C1   C6   124.70  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    -95.69  30.0  2
 HRX  Var_02    C6   C9  C7   C8    177.84  30.0  3
 HRX  Var_03    P9   C8  P14  O17  -149.24  30.0  3
 HRX  Var_04    O12  P9  C8   P14    67.85  30.0  3
 HRX  Var_05    C9   C7  C8   P14  -161.77  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
 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

