# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:50:39 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  23  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.473  -0.1546  -2.5006   0.5484
 P9T  C03  C  CR16   0  -0.483   0.7812  -1.4292   0.6453
 P9T  C04  C  CR6    0   0.253   0.4507  -0.1192   0.4929
 P9T  C05  C  CH2    0  -0.848   1.5176   0.8855   0.6928
 P9T  C10  C  CR66   0  -0.312  -0.9285   0.1785   0.1420
 P9T  C11  C  CR6    0   0.481  -1.4721   1.4405  -0.1317
 P9T  C13  C  CR16   0  -0.455  -2.8002   1.6539  -0.4152
 P9T  C14  C  CR6    0   0.499  -3.6341   0.5496  -0.4496
 P9T  C16  C  CR16   0  -0.510  -3.1849  -0.7279  -0.2220
 P9T  C17  C  CR66   0   0.583  -1.8363  -0.8900   0.0668
 P9T  F12  F  F      0  -0.326  -0.6869   2.5134  -0.1306
 P9T  F15  F  F      0  -0.328  -4.9253   0.7404  -0.7251
 P9T  O01  O  O      0  -0.595   0.0840  -3.6862   0.6305
 P9T  O07  O  O      0  -0.896   1.9816   0.7622  -2.0215
 P9T  O08  O  OP    -1  -0.959   3.6057   2.0999  -0.5567
 P9T  O09  O  OP    -1  -0.900   3.6169  -0.4523  -0.4546
 P9T  O18  O  O      0  -0.260  -1.4432  -2.1611   0.2764
 P9T  P06  P  P      0   1.194   2.7960   0.8078  -0.7235
 P9T  H1   H  HCR6   0   0.279   1.8022  -1.6827   0.8554
 P9T  H2   H  HCH2   0   0.269   1.1501   1.9021   0.7683
 P9T  H3   H  HCH2   0   0.222   2.0509   0.6646   1.6204
 P9T  H4   H  HCR6   0   0.322  -3.1704   2.6514  -0.6134
 P9T  H5   H  HCR6   0   0.301  -3.8512  -1.5790  -0.2680

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    1.334  0.020  1.334
 P9T  C13  C14  aromatic  1.384  0.020  1.384
 P9T  C13  C11  aromatic  1.375  0.020  1.375
 P9T  C14  C16  aromatic  1.373  0.020  1.373
 P9T  F12  C11  single    1.330  0.020  1.330
 P9T  C11  C10  aromatic  1.401  0.020  1.401
 P9T  C16  C17  aromatic  1.389  0.020  1.389
 P9T  O07  P06  deloc     1.533  0.020  1.533
 P9T  C10  C17  aromatic  1.404  0.020  1.404
 P9T  C10  C04  single    1.454  0.020  1.454
 P9T  C17  O18  single    1.347  0.020  1.347
 P9T  O09  P06  deloc     1.528  0.020  1.528
 P9T  P06  C05  single    1.910  0.020  1.910
 P9T  P06  O08  deloc     1.534  0.020  1.534
 P9T  C05  C04  single    1.479  0.020  1.479
 P9T  C04  C03  double    1.360  0.020  1.360
 P9T  O18  C02  single    1.360  0.020  1.360
 P9T  C03  C02  single    1.426  0.020  1.426
 P9T  C02  O01  double    1.212  0.020  1.212
 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

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  116.37  3.000
 P9T  O01  C02  C03  126.95  3.000
 P9T  O18  C02  C03  116.61  3.000
 P9T  H1   C03  C04  118.75  3.000
 P9T  H1   C03  C02  117.42  3.000
 P9T  C04  C03  C02  123.83  3.000
 P9T  C10  C04  C05  125.29  3.000
 P9T  C05  C04  C03  117.65  3.000
 P9T  C10  C04  C03  117.06  3.000
 P9T  H3   C05  H2   107.22  3.000
 P9T  H3   C05  P06  107.14  3.000
 P9T  H2   C05  P06  108.47  3.000
 P9T  H3   C05  C04  109.24  3.000
 P9T  H2   C05  C04  113.71  3.000
 P9T  P06  C05  C04  110.80  3.000
 P9T  C17  C10  C11  115.09  3.000
 P9T  C17  C10  C04  118.06  3.000
 P9T  C11  C10  C04  126.84  3.000
 P9T  F12  C11  C13  116.46  3.000
 P9T  F12  C11  C10  119.84  3.000
 P9T  C13  C11  C10  123.71  3.000
 P9T  H4   C13  C14  121.65  3.000
 P9T  H4   C13  C11  120.75  3.000
 P9T  C14  C13  C11  117.60  3.000
 P9T  F15  C14  C16  118.94  3.000
 P9T  C16  C14  C13  122.75  3.000
 P9T  F15  C14  C13  118.30  3.000
 P9T  H5   C16  C17  121.00  3.000
 P9T  H5   C16  C14  121.56  3.000
 P9T  C17  C16  C14  117.44  3.000
 P9T  O18  C17  C16  115.21  3.000
 P9T  O18  C17  C10  121.41  3.000
 P9T  C16  C17  C10  123.38  3.000
 P9T  C17  O18  C02  122.90  3.000
 P9T  O09  P06  O08  113.08  3.000
 P9T  O08  P06  O07  113.42  3.000
 P9T  O09  P06  O07  114.20  3.000
 P9T  O08  P06  C05  103.80  3.000
 P9T  O09  P06  C05  105.23  3.000
 P9T  O07  P06  C05  105.88  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   178.88  30.0  1
 P9T  Var_02    C10  C04  C03  C02    -3.34  30.0  1
 P9T  Var_03    C11  C10  C04  C03  -176.41  30.0  1
 P9T  Var_04    O18  C02  C03  C04     0.54  30.0  1
 P9T  Var_05    P06  C05  C04  C03    69.98  30.0  2
 P9T  Var_06    O07  P06  C05  C04    46.85  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

