# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:28:34 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: [1-fluoro-2-(imidazo[1,2-a]pyridin-3-yl)ethane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(F)(Cc1cnc2ccccn12)[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
 39L  39L  '[1-fluoro-2-(imidazo[1,2-a]pyridin-3-yl)ethane-1,1-diyl]bis(phosphonic acid)'  ligand  31  20  .  2022-07-22  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_39L
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
 39L  O4   O  OH1   0  -0.734   2.4942  -2.5586  -1.0071
 39L  P2   P  P     0   1.376   2.7116  -1.2052  -0.1796
 39L  O6   O  O     0  -0.676   3.4503  -1.4917   1.0630
 39L  O5   O  OH1   0  -0.742   3.2786  -0.1100  -1.1912
 39L  C9   C  CT    0  -0.131   1.0226  -0.4845   0.0833
 39L  F    F  F     0  -0.358   0.5095  -1.2301   1.1458
 39L  P1   P  P     0   1.376   1.1710   1.2508   0.7267
 39L  O3   O  OH1   0  -0.735   1.1750   2.2039  -0.5558
 39L  O1   O  OH1   0  -0.729  -0.2515   1.3929   1.4319
 39L  O2   O  O     0  -0.678   2.3748   1.4660   1.5532
 39L  C8   C  CH2   0  -0.626   0.1255  -0.6526  -1.1465
 39L  C2   C  CR5   0   0.281  -1.1816   0.0561  -1.1317
 39L  C1   C  CR15  0  -0.282  -1.5933   1.1493  -1.8542
 39L  N1   N  N     0  -0.467  -2.8692   1.4972  -1.5782
 39L  C7   C  CR56  0   0.523  -3.2824   0.6150  -0.6880
 39L  N2   N  N     0  -0.553  -2.2830  -0.2986  -0.3889
 39L  C3   C  CR16  0   0.032  -2.4883  -1.3359   0.4751
 39L  C4   C  CR16  0  -0.389  -3.6975  -1.4744   1.0719
 39L  C5   C  CR16  0  -0.153  -4.7381  -0.5461   0.8132
 39L  C6   C  CR16  0  -0.396  -4.5363   0.4832  -0.0560
 39L  H1   H  HOH1  0   0.500   2.2583  -2.4771  -1.9407
 39L  H2   H  HOH1  0   0.508   4.2170  -0.1894  -1.4180
 39L  H3   H  HOH1  0   0.499   0.3077   2.3979  -0.9385
 39L  H4   H  HOH1  0   0.505  -0.3435   2.1636   2.0113
 39L  H5   H  HCH2  0   0.314   0.6653  -0.2859  -2.0219
 39L  H6   H  HCH2  0   0.311  -0.0236  -1.7242  -1.3097
 39L  H7   H  HCR5  0   0.282  -1.0110   1.6816  -2.5949
 39L  H8   H  HCR6  0   0.303  -1.6725  -2.0205   0.6372
 39L  H9   H  HCR6  0   0.282  -3.8528  -2.3022   1.7480
 39L  H10  H  HCR6  0   0.275  -5.6937  -0.6646   1.3050
 39L  H11  H  HCR6  0   0.281  -5.3094   1.2033  -0.2850

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
 39L  O6  P2   double    1.474  0.020  1.474
 39L  C4  C3   aromatic  1.355  0.020  1.355
 39L  C4  C5   aromatic  1.418  0.020  1.418
 39L  C3  N2   aromatic  1.366  0.020  1.366
 39L  O5  P2   single    1.595  0.020  1.595
 39L  C5  C6   aromatic  1.362  0.020  1.362
 39L  P2  O4   single    1.601  0.020  1.601
 39L  P2  C9   single    1.855  0.020  1.855
 39L  C8  C2   single    1.487  0.020  1.487
 39L  C8  C9   single    1.531  0.020  1.531
 39L  N2  C2   aromatic  1.375  0.020  1.375
 39L  N2  C7   aromatic  1.387  0.020  1.387
 39L  C2  C1   aromatic  1.373  0.020  1.373
 39L  C6  C7   aromatic  1.410  0.020  1.410
 39L  C9  F    single    1.396  0.020  1.396
 39L  C9  P1   single    1.857  0.020  1.857
 39L  C7  N1   aromatic  1.320  0.020  1.320
 39L  O2  P1   double    1.476  0.020  1.476
 39L  C1  N1   aromatic  1.351  0.020  1.351
 39L  P1  O1   single    1.594  0.020  1.594
 39L  P1  O3   single    1.598  0.020  1.598
 39L  O4  H1   single    0.850  0.020  0.980
 39L  O5  H2   single    0.850  0.020  0.980
 39L  O3  H3   single    0.850  0.020  0.980
 39L  O1  H4   single    0.850  0.020  0.980
 39L  C8  H5   single    0.970  0.020  1.090
 39L  C8  H6   single    0.970  0.020  1.090
 39L  C1  H7   single    0.930  0.020  1.080
 39L  C3  H8   single    0.930  0.020  1.080
 39L  C4  H9   single    0.930  0.020  1.080
 39L  C5  H10  single    0.930  0.020  1.080
 39L  C6  H11  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
 39L  H1   O4  P2  117.46  3.000
 39L  C9   P2  O5   98.44  3.000
 39L  C9   P2  O6  114.36  3.000
 39L  O5   P2  O6  119.34  3.000
 39L  C9   P2  O4  106.14  3.000
 39L  O5   P2  O4  107.51  3.000
 39L  O6   P2  O4  109.84  3.000
 39L  H2   O5  P2  115.89  3.000
 39L  C8   C9  P1  115.32  3.000
 39L  P1   C9  F   105.36  3.000
 39L  C8   C9  F   109.71  3.000
 39L  P1   C9  P2  109.84  3.000
 39L  F    C9  P2  103.59  3.000
 39L  C8   C9  P2  112.14  3.000
 39L  O2   P1  O1  117.84  3.000
 39L  O1   P1  O3  107.71  3.000
 39L  O2   P1  O3  111.13  3.000
 39L  O3   P1  C9  106.23  3.000
 39L  O1   P1  C9   99.51  3.000
 39L  O2   P1  C9  113.30  3.000
 39L  H3   O3  P1  115.77  3.000
 39L  H4   O1  P1  114.86  3.000
 39L  H6   C8  H5  106.06  3.000
 39L  H6   C8  C2  110.40  3.000
 39L  H5   C8  C2  106.40  3.000
 39L  H6   C8  C9  107.88  3.000
 39L  H5   C8  C9  108.50  3.000
 39L  C2   C8  C9  117.04  3.000
 39L  N2   C2  C1  104.44  3.000
 39L  C1   C2  C8  129.62  3.000
 39L  N2   C2  C8  125.91  3.000
 39L  H7   C1  N1  121.42  3.000
 39L  H7   C1  C2  126.17  3.000
 39L  N1   C1  C2  112.37  3.000
 39L  C7   N1  C1  105.15  3.000
 39L  C6   C7  N2  118.85  3.000
 39L  C6   C7  N1  130.03  3.000
 39L  N2   C7  N1  111.12  3.000
 39L  C3   N2  C7  121.91  3.000
 39L  C7   N2  C2  106.90  3.000
 39L  C3   N2  C2  131.17  3.000
 39L  H8   C3  C4  122.98  3.000
 39L  H8   C3  N2  117.64  3.000
 39L  C4   C3  N2  119.36  3.000
 39L  H9   C4  C5  120.69  3.000
 39L  H9   C4  C3  118.83  3.000
 39L  C5   C4  C3  120.48  3.000
 39L  H10  C5  C6  120.27  3.000
 39L  H10  C5  C4  119.58  3.000
 39L  C6   C5  C4  120.15  3.000
 39L  H11  C6  C5  122.17  3.000
 39L  H11  C6  C7  118.59  3.000
 39L  C5   C6  C7  119.23  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
 39L  CONST_01  C4   C3  N2  C2   180.00   0.0  0
 39L  CONST_02  C6   C7  N2  C2   180.00   0.0  0
 39L  CONST_03  N1   C7  N2  C2     0.00   0.0  0
 39L  CONST_04  C7   N1  C1  C2     0.00   0.0  0
 39L  CONST_05  C3   N2  C2  C1   180.00   0.0  0
 39L  CONST_06  C7   N2  C2  C1     0.00   0.0  0
 39L  CONST_07  N2   C7  N1  C1     0.00   0.0  0
 39L  CONST_08  C6   C7  N1  C1   180.00   0.0  0
 39L  CONST_09  C3   N2  C7  N1   180.00   0.0  0
 39L  CONST_10  C5   C6  C7  N1   180.00   0.0  0
 39L  CONST_11  N2   C2  C1  N1     0.00   0.0  0
 39L  CONST_12  C4   C3  N2  C7     0.00   0.0  0
 39L  CONST_13  C4   C5  C6  C7     0.00   0.0  0
 39L  CONST_14  C5   C4  C3  N2     0.00   0.0  0
 39L  CONST_15  C5   C6  C7  N2     0.00   0.0  0
 39L  CONST_16  C6   C5  C4  C3     0.00   0.0  0
 39L  CONST_17  C6   C7  N2  C3     0.00   0.0  0
 39L  CONST_18  C3   N2  C2  C8     0.00   0.0  0
 39L  CONST_19  C7   N2  C2  C8   180.00   0.0  0
 39L  CONST_20  N1   C1  C2  C8   180.00   0.0  0
 39L  CONST_21  H8   C3  N2  C2     0.00   0.0  0
 39L  CONST_22  H11  C6  C7  N1     0.00   0.0  0
 39L  CONST_23  H10  C5  C6  C7   180.00   0.0  0
 39L  CONST_24  H7   C1  N1  C7   180.00   0.0  0
 39L  CONST_25  H9   C4  C3  N2   180.00   0.0  0
 39L  Var_01    N2   C2  C8  C9   -73.67  30.0  2
 39L  Var_02    C2   C8  C9  P2  -171.34  30.0  2
 39L  Var_03    C8   C9  P2  O4   -38.93  30.0  3
 39L  Var_04    O2   P1  C9  P2   -30.96  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
 39L  plan-1  C8   0.020
 39L  plan-1  C2   0.020
 39L  plan-1  C1   0.020
 39L  plan-1  N1   0.020
 39L  plan-1  C7   0.020
 39L  plan-1  N2   0.020
 39L  plan-1  C3   0.020
 39L  plan-1  C4   0.020
 39L  plan-1  C5   0.020
 39L  plan-1  C6   0.020
 39L  plan-1  H7   0.020
 39L  plan-1  H8   0.020
 39L  plan-1  H9   0.020
 39L  plan-1  H10  0.020
 39L  plan-1  H11  0.020

