# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 10:39:45 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(C[n+]1cccc(F)c1)([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
 NI9  NI9  3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium  ligand  29  18  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NI9
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
 NI9  C1   C  CT    0  -0.303   0.8921  -1.7560  -1.0527
 NI9  O1   O  OH1   0  -0.729   3.4285  -2.3893  -0.4876
 NI9  O2   O  OH1   0  -0.647  -0.0280  -1.7745  -2.1167
 NI9  C2   C  CH2   0  -0.364   0.9629  -0.3129  -0.5416
 NI9  O3   O  OH1   0  -0.734   3.0940  -0.9089  -2.4640
 NI9  C3   C  CR16  0  -0.091  -0.3236   0.1933   1.4512
 NI9  P1   P  P     0   1.386   0.2348  -2.8974   0.2521
 NI9  P2   P  P     0   1.400   2.5285  -2.2458  -1.7869
 NI9  O4   O  OH1   0  -0.734   1.2460  -2.6071   1.4530
 NI9  O5   O  O     0  -0.679   2.3824  -3.3974  -2.7019
 NI9  O6   O  O     0  -0.680  -1.1998  -2.6842   0.5473
 NI9  O7   O  OH1   0  -0.726   0.6109  -4.3276  -0.3481
 NI9  N    N  NR6   1  -0.401  -0.2850   0.1205   0.1134
 NI9  C4   C  CR16  0  -0.247  -2.6342   0.8256   1.3396
 NI9  C5   C  CR16  0   0.091  -1.3601   0.3963  -0.6367
 NI9  C6   C  CR16  0  -0.323  -2.5481   0.7515  -0.0392
 NI9  C7   C  CR6   0   0.469  -1.4967   0.5467   2.0713
 NI9  HO1  H  HOH1  0   0.509   4.3446  -2.6652  -0.6402
 NI9  HO2  H  HOH1  0   0.475  -0.0468  -2.6435  -2.5401
 NI9  H21  H  HCH2  0   0.336   1.7694  -0.1844   0.1759
 NI9  H22  H  HCH2  0   0.344   1.1434   0.3654  -1.3738
 NI9  HO3  H  HOH1  0   0.505   2.9306  -0.8424  -3.4150
 NI9  H3   H  HCR6  0   0.373   0.5813  -0.0194   2.0014
 NI9  HO4  H  HOH1  0   0.505   0.9752  -2.9648   2.3114
 NI9  HO7  H  HOH1  0   0.506  -0.0511  -5.0159  -0.1893
 NI9  H4   H  HCR6  0   0.342  -3.5557   1.1065   1.8314
 NI9  H5   H  HCR6  0   0.358  -1.2446   0.3477  -1.7070
 NI9  H6   H  HCR6  0   0.331  -3.4019   0.9736  -0.6607
 NI9  F    F  F     0  -0.273  -1.5118   0.6200   3.3932

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
 NI9  C1  P2   single    1.859  0.020  1.859
 NI9  C1  O2   single    1.407  0.020  1.407
 NI9  C1  C2   single    1.533  0.020  1.533
 NI9  C1  P1   single    1.854  0.020  1.854
 NI9  O1  P2   single    1.587  0.020  1.587
 NI9  O1  HO1  single    0.850  0.020  0.980
 NI9  O2  HO2  single    0.850  0.020  0.980
 NI9  C2  N    single    1.474  0.020  1.474
 NI9  C2  H21  single    0.970  0.020  1.090
 NI9  C2  H22  single    0.970  0.020  1.090
 NI9  O3  P2   single    1.602  0.020  1.602
 NI9  O3  HO3  single    0.850  0.020  0.980
 NI9  C3  N    aromatic  1.340  0.020  1.340
 NI9  C3  C7   aromatic  1.373  0.020  1.373
 NI9  C3  H3   single    0.930  0.020  1.080
 NI9  P1  O6   double    1.480  0.020  1.480
 NI9  P1  O7   single    1.596  0.020  1.596
 NI9  P1  O4   single    1.597  0.020  1.597
 NI9  P2  O5   double    1.478  0.020  1.478
 NI9  O4  HO4  single    0.850  0.020  0.980
 NI9  O7  HO7  single    0.850  0.020  0.980
 NI9  N   C5   aromatic  1.340  0.020  1.340
 NI9  F   C7   single    1.324  0.020  1.324
 NI9  C4  C7   aromatic  1.381  0.020  1.381
 NI9  C4  C6   aromatic  1.384  0.020  1.384
 NI9  C4  H4   single    0.930  0.020  1.080
 NI9  C5  C6   aromatic  1.376  0.020  1.376
 NI9  C5  H5   single    0.930  0.020  1.080
 NI9  C6  H6   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
 NI9  P2   C1  P1   115.33  3.000
 NI9  P1   C1  C2   111.18  3.000
 NI9  P2   C1  C2   109.82  3.000
 NI9  P1   C1  O2   107.00  3.000
 NI9  C2   C1  O2   107.15  3.000
 NI9  P2   C1  O2   105.87  3.000
 NI9  HO1  O1  P2   115.66  3.000
 NI9  HO2  O2  C1   110.84  3.000
 NI9  H22  C2  H21  107.93  3.000
 NI9  H22  C2  N    107.26  3.000
 NI9  H21  C2  N    107.45  3.000
 NI9  H22  C2  C1   109.84  3.000
 NI9  H21  C2  C1   111.45  3.000
 NI9  N    C2  C1   112.69  3.000
 NI9  HO3  O3  P2   114.42  3.000
 NI9  H3   C3  C7   122.44  3.000
 NI9  H3   C3  N    118.27  3.000
 NI9  C7   C3  N    119.29  3.000
 NI9  O7   P1  O6   115.63  3.000
 NI9  O7   P1  O4   107.25  3.000
 NI9  O6   P1  O4   115.96  3.000
 NI9  O4   P1  C1   101.12  3.000
 NI9  O7   P1  C1   101.74  3.000
 NI9  O6   P1  C1   113.29  3.000
 NI9  O5   P2  O3   115.05  3.000
 NI9  O5   P2  O1   119.50  3.000
 NI9  O3   P2  O1   102.79  3.000
 NI9  O5   P2  C1   111.27  3.000
 NI9  O3   P2  C1   104.94  3.000
 NI9  O1   P2  C1   101.52  3.000
 NI9  HO4  O4  P1   114.98  3.000
 NI9  HO7  O7  P1   114.48  3.000
 NI9  C5   N   C3   121.64  3.000
 NI9  C5   N   C2   119.40  3.000
 NI9  C3   N   C2   118.93  3.000
 NI9  H4   C4  C7   120.89  3.000
 NI9  H4   C4  C6   121.33  3.000
 NI9  C7   C4  C6   117.77  3.000
 NI9  H5   C5  C6   122.36  3.000
 NI9  H5   C5  N    117.44  3.000
 NI9  C6   C5  N    120.18  3.000
 NI9  H6   C6  C5   119.08  3.000
 NI9  H6   C6  C4   120.91  3.000
 NI9  C5   C6  C4   120.01  3.000
 NI9  C4   C7  F    120.56  3.000
 NI9  C4   C7  C3   121.09  3.000
 NI9  F    C7  C3   118.35  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
 NI9  CONST_01  C6  C5  N   C3     0.00   0.0  0
 NI9  CONST_02  C6  C4  C7  C3     0.00   0.0  0
 NI9  CONST_03  C4  C7  C3  N      0.00   0.0  0
 NI9  CONST_04  C4  C6  C5  N      0.00   0.0  0
 NI9  CONST_05  C7  C3  N   C5     0.00   0.0  0
 NI9  CONST_06  C7  C4  C6  C5     0.00   0.0  0
 NI9  CONST_07  C7  C3  N   C2   180.00   0.0  0
 NI9  CONST_08  C6  C5  N   C2   180.00   0.0  0
 NI9  CONST_09  F   C7  C3  N    180.00   0.0  0
 NI9  CONST_10  C6  C4  C7  F    180.00   0.0  0
 NI9  CONST_11  H5  C5  N   C3   180.00   0.0  0
 NI9  CONST_12  H4  C4  C7  C3   180.00   0.0  0
 NI9  CONST_13  H6  C6  C5  N    180.00   0.0  0
 NI9  CONST_14  H3  C3  C7  C4   180.00   0.0  0
 NI9  Var_01    C3  N   C2  C1   104.05  30.0  2
 NI9  Var_02    N   C2  C1  O2    68.20  30.0  3
 NI9  Var_03    O2  C1  P2  O1  -172.44  30.0  3
 NI9  Var_04    O6  P1  C1  O2   -47.20  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
 NI9  plan-1  C2  0.020
 NI9  plan-1  C3  0.020
 NI9  plan-1  N   0.020
 NI9  plan-1  C4  0.020
 NI9  plan-1  C5  0.020
 NI9  plan-1  C6  0.020
 NI9  plan-1  C7  0.020
 NI9  plan-1  H3  0.020
 NI9  plan-1  H4  0.020
 NI9  plan-1  H5  0.020
 NI9  plan-1  H6  0.020
 NI9  plan-1  F   0.020

