# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 20:33:31 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(5,7-difluoro-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CC1=CC(=O)Oc2cc(F)cc(F)c12
#
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
 P9T  P9T  '[(5,7-difluoro-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid'  ligand  25  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P9T
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
 P9T  C02  C  CR6   0   0.566  -0.1508  -2.5491  -0.1392
 P9T  C03  C  CR16  0  -0.577   0.8118  -1.4747  -0.1920
 P9T  C04  C  CR6   0   0.344   0.4633  -0.1719  -0.1478
 P9T  C05  C  CH2   0  -0.840   1.4849   0.9304  -0.1766
 P9T  C10  C  CR66  0  -0.273  -0.9553   0.1505  -0.0765
 P9T  C11  C  CR6   0   0.563  -1.5322   1.4286  -0.0693
 P9T  C13  C  CR16  0  -0.565  -2.8844   1.6562   0.0183
 P9T  C14  C  CR6   0   0.561  -3.7171   0.5535   0.0944
 P9T  C16  C  CR16  0  -0.499  -3.2414  -0.7356   0.0766
 P9T  C17  C  CR66  0   0.424  -1.8690  -0.9130  -0.0128
 P9T  F12  F  F     0  -0.294  -0.7534   2.5068  -0.1596
 P9T  F15  F  F     0  -0.294  -5.0297   0.7543   0.1833
 P9T  O01  O  O     0  -0.421   0.1022  -3.7253  -0.1700
 P9T  O07  O  O     0  -0.705   3.7772  -0.4796  -1.0108
 P9T  O08  O  OH1   0  -0.734   3.8690   1.9328   0.0121
 P9T  O09  O  OH1   0  -0.745   3.4082  -0.1570   1.4623
 P9T  O18  O  O     0  -0.460  -1.4553  -2.1933  -0.0363
 P9T  P06  P  P     0   1.392   3.2301   0.4628  -0.0070
 P9T  H1   H  HCR6  0   0.287   1.8382  -1.7971  -0.2808
 P9T  H2   H  HCH2  0   0.328   1.3959   1.4837  -1.1157
 P9T  H3   H  HCH2  0   0.315   1.2792   1.6492   0.6184
 P9T  H4   H  HCR6  0   0.317  -3.2760   2.6645   0.0234
 P9T  H5   H  HCR6  0   0.315  -3.9081  -1.5856   0.1275
 P9T  H6   H  HOH1  0   0.499   4.8361   1.9445  -0.0212
 P9T  H7   H  HOH1  0   0.493   3.1385   0.4128   2.1949

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
 P9T  F15  C14  single    1.331  0.020  1.331
 P9T  C13  C14  aromatic  1.384  0.020  1.384
 P9T  C13  C11  aromatic  1.374  0.020  1.374
 P9T  C14  C16  aromatic  1.374  0.020  1.374
 P9T  F12  C11  single    1.333  0.020  1.333
 P9T  C11  C10  aromatic  1.402  0.020  1.402
 P9T  C16  C17  aromatic  1.387  0.020  1.387
 P9T  O07  P06  double    1.482  0.020  1.482
 P9T  C10  C17  aromatic  1.404  0.020  1.404
 P9T  C10  C04  single    1.457  0.020  1.457
 P9T  C17  O18  single    1.346  0.020  1.346
 P9T  O09  P06  single    1.605  0.020  1.605
 P9T  P06  C05  single    1.815  0.020  1.815
 P9T  P06  O08  single    1.603  0.020  1.603
 P9T  C05  C04  single    1.503  0.020  1.503
 P9T  C04  C03  double    1.349  0.020  1.349
 P9T  O18  C02  single    1.356  0.020  1.356
 P9T  C03  C02  single    1.444  0.020  1.444
 P9T  C02  O01  double    1.203  0.020  1.203
 P9T  C03  H1   single    0.930  0.020  1.080
 P9T  C05  H2   single    0.970  0.020  1.090
 P9T  C05  H3   single    0.970  0.020  1.090
 P9T  C13  H4   single    0.930  0.020  1.080
 P9T  C16  H5   single    0.930  0.020  1.080
 P9T  O08  H6   single    0.850  0.020  0.980
 P9T  O09  H7   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
 P9T  O18  C02  O01  117.42  3.000
 P9T  O01  C02  C03  125.89  3.000
 P9T  O18  C02  C03  116.68  3.000
 P9T  H1   C03  C04  122.45  3.000
 P9T  H1   C03  C02  114.50  3.000
 P9T  C04  C03  C02  123.04  3.000
 P9T  C10  C04  C05  120.04  3.000
 P9T  C05  C04  C03  122.14  3.000
 P9T  C10  C04  C03  117.83  3.000
 P9T  H3   C05  H2   106.07  3.000
 P9T  H3   C05  P06  106.44  3.000
 P9T  H2   C05  P06  106.79  3.000
 P9T  H3   C05  C04  109.93  3.000
 P9T  H2   C05  C04  109.40  3.000
 P9T  P06  C05  C04  117.57  3.000
 P9T  C17  C10  C11  115.00  3.000
 P9T  C17  C10  C04  117.94  3.000
 P9T  C11  C10  C04  127.06  3.000
 P9T  F12  C11  C13  116.44  3.000
 P9T  F12  C11  C10  119.77  3.000
 P9T  C13  C11  C10  123.79  3.000
 P9T  H4   C13  C14  121.65  3.000
 P9T  H4   C13  C11  120.73  3.000
 P9T  C14  C13  C11  117.63  3.000
 P9T  F15  C14  C16  118.94  3.000
 P9T  C16  C14  C13  122.58  3.000
 P9T  F15  C14  C13  118.48  3.000
 P9T  H5   C16  C17  120.84  3.000
 P9T  H5   C16  C14  121.55  3.000
 P9T  C17  C16  C14  117.61  3.000
 P9T  O18  C17  C16  115.28  3.000
 P9T  O18  C17  C10  121.33  3.000
 P9T  C16  C17  C10  123.38  3.000
 P9T  H6   O08  P06  114.14  3.000
 P9T  H7   O09  P06  115.81  3.000
 P9T  C17  O18  C02  123.14  3.000
 P9T  O09  P06  O08  107.40  3.000
 P9T  O08  P06  O07  116.37  3.000
 P9T  O09  P06  O07  109.50  3.000
 P9T  O08  P06  C05   98.52  3.000
 P9T  O09  P06  C05  106.97  3.000
 P9T  O07  P06  C05  117.11  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
 P9T  CONST_01  C14  C13  C11  C10     0.00   0.0  0
 P9T  CONST_02  C14  C16  C17  C10     0.00   0.0  0
 P9T  CONST_03  C16  C14  C13  C11     0.00   0.0  0
 P9T  CONST_04  C16  C17  C10  C11     0.00   0.0  0
 P9T  CONST_05  C17  C16  C14  C13     0.00   0.0  0
 P9T  CONST_06  C17  C10  C11  C13     0.00   0.0  0
 P9T  CONST_07  F12  C11  C10  C04     0.00   0.0  0
 P9T  CONST_08  F15  C14  C13  C11   180.00   0.0  0
 P9T  CONST_09  F12  C11  C13  C14   180.00   0.0  0
 P9T  CONST_10  F15  C14  C16  C17   180.00   0.0  0
 P9T  CONST_11  F12  C11  C10  C17   180.00   0.0  0
 P9T  CONST_12  H4   C13  C11  C10   180.00   0.0  0
 P9T  CONST_13  H5   C16  C17  C10   180.00   0.0  0
 P9T  Var_01    C16  C17  O18  C02   179.07  30.0  1
 P9T  Var_02    C10  C04  C03  C02    -1.54  30.0  1
 P9T  Var_03    C11  C10  C04  C03  -177.60  30.0  1
 P9T  Var_04    O18  C02  C03  C04    -0.21  30.0  1
 P9T  Var_05    P06  C05  C04  C03    -9.54  30.0  3
 P9T  Var_06    O07  P06  C05  C04    58.40  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
 P9T  plan-1  C02  0.020
 P9T  plan-1  C03  0.020
 P9T  plan-1  O01  0.020
 P9T  plan-1  O18  0.020
 P9T  plan-2  C04  0.020
 P9T  plan-2  C10  0.020
 P9T  plan-2  C11  0.020
 P9T  plan-2  C13  0.020
 P9T  plan-2  C14  0.020
 P9T  plan-2  C16  0.020
 P9T  plan-2  C17  0.020
 P9T  plan-2  F12  0.020
 P9T  plan-2  F15  0.020
 P9T  plan-2  O18  0.020
 P9T  plan-2  H4   0.020
 P9T  plan-2  H5   0.020

