# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:34:50 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [[3-(3-cyclohexyl-2-oxidanyl-phenyl)phenyl]-bis(fluoranyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(cccc1c2cccc(c2)C(F)(F)[P](O)(O)=O)C3CCCCC3
#
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
 AY8  AY8  '[[3-(3-cyclohexyl-2-oxidanyl-phenyl)phenyl]-bis(fluoranyl)methyl]phosphonic acid'  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AY8
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
 AY8  C1   C  CR6   0   0.124   0.3571   1.1440   0.3706
 AY8  C2   C  CR16  0  -0.285   0.4798   1.6936   1.6469
 AY8  C3   C  CR16  0  -0.356   1.5117   0.7276  -0.2880
 AY8  C4   C  CR6   0  -0.097   2.7621   0.8565   0.3090
 AY8  C5   C  CR16  0  -0.291   2.8702   1.3962   1.5852
 AY8  C6   C  CR16  0  -0.225   1.7244   1.8179   2.2432
 AY8  C7   C  CT    0   0.550   3.9781   0.3722  -0.4156
 AY8  C14  C  CR6   0  -0.047  -0.9461   1.0458  -0.3237
 AY8  C15  C  CR16  0  -0.317  -3.3613   0.8724  -1.6793
 AY8  C16  C  CR16  0  -0.256  -2.2762   1.4753  -2.2925
 AY8  C17  C  CR16  0  -0.305  -1.0732   1.5571  -1.6107
 AY8  C18  C  CR6   0   0.240  -2.0540   0.4280   0.2772
 AY8  C19  C  CR6   0   0.098  -3.2807   0.3378  -0.3949
 AY8  C21  C  CH1   0  -0.364  -4.5011  -0.3195   0.2107
 AY8  C22  C  CH2   0  -0.400  -4.9118  -1.5832  -0.5558
 AY8  C23  C  CH2   0  -0.437  -6.1324  -2.2437   0.0766
 AY8  C24  C  CH2   0  -0.430  -7.3006  -1.2700   0.1894
 AY8  C25  C  CH2   0  -0.436  -6.8977  -0.0089   0.9473
 AY8  C26  C  CH2   0  -0.403  -5.6801   0.6551   0.3144
 AY8  P8   P  P     0   1.309   4.3573  -1.4340  -0.1983
 AY8  O9   O  O     0  -0.684   5.5061  -1.9012  -0.9985
 AY8  O10  O  OH1   0  -0.734   4.4685  -1.4807   1.3899
 AY8  O11  O  OH1   0  -0.733   3.0120  -2.1828  -0.6248
 AY8  F12  F  F     0  -0.333   3.8437   0.5633  -1.7578
 AY8  F13  F  F     0  -0.329   5.0835   1.0622  -0.0278
 AY8  O20  O  OH1   0  -0.619  -1.8511  -0.0840   1.5093
 AY8  H1   H  HCR6  0   0.259  -0.3977   2.0464   2.1714
 AY8  H2   H  HCR6  0   0.274   1.4179   0.3044  -1.2802
 AY8  H3   H  HCR6  0   0.270   3.8308   1.5004   2.0705
 AY8  H4   H  HCR6  0   0.267   1.8059   2.2549   3.2296
 AY8  H5   H  HCR6  0   0.254  -4.2999   0.8155  -2.2182
 AY8  H6   H  HCR6  0   0.251  -2.3701   1.8847  -3.2893
 AY8  H7   H  HCR6  0   0.255  -0.2207   2.0405  -2.0718
 AY8  H8   H  HCH1  0   0.213  -4.2943  -0.6477   1.2373
 AY8  H9   H  HCH2  0   0.218  -5.1376  -1.3176  -1.5940
 AY8  H10  H  HCH2  0   0.236  -4.0737  -2.2839  -0.5876
 AY8  H11  H  HCH2  0   0.230  -6.4239  -3.1198  -0.5081
 AY8  H12  H  HCH2  0   0.213  -5.8691  -2.6138   1.0737
 AY8  H13  H  HCH2  0   0.210  -7.6393  -0.9940  -0.8154
 AY8  H14  H  HCH2  0   0.229  -8.1486  -1.7521   0.6816
 AY8  H15  H  HCH2  0   0.230  -7.7301   0.6981   0.9773
 AY8  H16  H  HCH2  0   0.212  -6.6725  -0.2653   1.9883
 AY8  H17  H  HCH2  0   0.236  -5.3799   1.5333   0.8919
 AY8  H18  H  HCH2  0   0.219  -5.9462   1.0140  -0.6851
 AY8  H19  H  HOH1  0   0.510   4.8648  -2.2850   1.7560
 AY8  H20  H  HOH1  0   0.501   2.2676  -2.1334  -0.0100
 AY8  H21  H  HOH1  0   0.474  -2.6738  -0.4129   1.8866

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
 AY8  O9   P8   double    1.476  0.020  1.476
 AY8  F13  C7   single    1.360  0.020  1.360
 AY8  O11  P8   single    1.598  0.020  1.598
 AY8  P8   C7   single    1.858  0.020  1.858
 AY8  P8   O10  single    1.593  0.020  1.593
 AY8  C7   F12  single    1.362  0.020  1.362
 AY8  C7   C4   single    1.496  0.020  1.496
 AY8  C5   C4   aromatic  1.390  0.020  1.390
 AY8  C5   C6   aromatic  1.387  0.020  1.387
 AY8  C4   C3   aromatic  1.392  0.020  1.392
 AY8  C6   C2   aromatic  1.386  0.020  1.386
 AY8  C3   C1   aromatic  1.393  0.020  1.393
 AY8  C2   C1   aromatic  1.395  0.020  1.395
 AY8  C1   C14  single    1.480  0.020  1.480
 AY8  C14  C17  aromatic  1.391  0.020  1.391
 AY8  C14  C18  aromatic  1.404  0.020  1.404
 AY8  O20  C18  single    1.350  0.020  1.350
 AY8  C17  C16  aromatic  1.385  0.020  1.385
 AY8  C18  C19  aromatic  1.402  0.020  1.402
 AY8  C16  C15  aromatic  1.385  0.020  1.385
 AY8  C19  C15  aromatic  1.394  0.020  1.394
 AY8  C19  C21  single    1.513  0.020  1.513
 AY8  C22  C21  single    1.534  0.020  1.534
 AY8  C22  C23  single    1.525  0.020  1.525
 AY8  C21  C26  single    1.533  0.020  1.533
 AY8  C26  C25  single    1.524  0.020  1.524
 AY8  C23  C24  single    1.525  0.020  1.525
 AY8  C24  C25  single    1.525  0.020  1.525
 AY8  C2   H1   single    0.930  0.020  1.080
 AY8  C3   H2   single    0.930  0.020  1.080
 AY8  C5   H3   single    0.930  0.020  1.080
 AY8  C6   H4   single    0.930  0.020  1.080
 AY8  C15  H5   single    0.930  0.020  1.080
 AY8  C16  H6   single    0.930  0.020  1.080
 AY8  C17  H7   single    0.930  0.020  1.080
 AY8  C21  H8   single    0.970  0.020  1.090
 AY8  C22  H9   single    0.970  0.020  1.090
 AY8  C22  H10  single    0.970  0.020  1.090
 AY8  C23  H11  single    0.970  0.020  1.090
 AY8  C23  H12  single    0.970  0.020  1.090
 AY8  C24  H13  single    0.970  0.020  1.090
 AY8  C24  H14  single    0.970  0.020  1.090
 AY8  C25  H15  single    0.970  0.020  1.090
 AY8  C25  H16  single    0.970  0.020  1.090
 AY8  C26  H17  single    0.970  0.020  1.090
 AY8  C26  H18  single    0.970  0.020  1.090
 AY8  O10  H19  single    0.850  0.020  0.980
 AY8  O11  H20  single    0.850  0.020  0.980
 AY8  O20  H21  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
 AY8  C14  C1   C3   119.23  3.000
 AY8  C14  C1   C2   122.20  3.000
 AY8  C3   C1   C2   118.52  3.000
 AY8  H1   C2   C6   119.40  3.000
 AY8  H1   C2   C1   120.06  3.000
 AY8  C6   C2   C1   120.54  3.000
 AY8  H2   C3   C4   120.48  3.000
 AY8  H2   C3   C1   118.57  3.000
 AY8  C4   C3   C1   120.95  3.000
 AY8  C7   C4   C5   120.48  3.000
 AY8  C5   C4   C3   119.99  3.000
 AY8  C7   C4   C3   119.51  3.000
 AY8  H3   C5   C6   119.45  3.000
 AY8  H3   C5   C4   121.25  3.000
 AY8  C6   C5   C4   119.31  3.000
 AY8  H4   C6   C5   119.55  3.000
 AY8  H4   C6   C2   119.75  3.000
 AY8  C5   C6   C2   120.70  3.000
 AY8  F13  C7   F12  106.86  3.000
 AY8  F12  C7   P8   105.76  3.000
 AY8  F13  C7   P8   107.10  3.000
 AY8  F12  C7   C4   110.58  3.000
 AY8  P8   C7   C4   115.08  3.000
 AY8  F13  C7   C4   111.00  3.000
 AY8  C18  C14  C17  119.07  3.000
 AY8  C18  C14  C1   121.56  3.000
 AY8  C17  C14  C1   119.36  3.000
 AY8  H5   C15  C19  119.23  3.000
 AY8  H5   C15  C16  118.77  3.000
 AY8  C19  C15  C16  122.00  3.000
 AY8  H6   C16  C17  120.44  3.000
 AY8  H6   C16  C15  120.33  3.000
 AY8  C17  C16  C15  119.23  3.000
 AY8  H7   C17  C16  120.02  3.000
 AY8  H7   C17  C14  119.09  3.000
 AY8  C16  C17  C14  120.88  3.000
 AY8  O20  C18  C19  123.02  3.000
 AY8  C19  C18  C14  120.92  3.000
 AY8  O20  C18  C14  116.05  3.000
 AY8  C21  C19  C18  122.82  3.000
 AY8  C21  C19  C15  119.27  3.000
 AY8  C18  C19  C15  117.90  3.000
 AY8  H8   C21  C26  105.76  3.000
 AY8  H8   C21  C22  105.76  3.000
 AY8  C26  C21  C22  110.58  3.000
 AY8  H8   C21  C19  110.64  3.000
 AY8  C26  C21  C19  111.80  3.000
 AY8  C22  C21  C19  111.96  3.000
 AY8  H10  C22  H9   106.63  3.000
 AY8  H10  C22  C23  110.37  3.000
 AY8  H9   C22  C23  109.46  3.000
 AY8  H10  C22  C21  109.72  3.000
 AY8  H9   C22  C21  109.21  3.000
 AY8  C23  C22  C21  111.34  3.000
 AY8  H12  C23  H11  106.27  3.000
 AY8  H12  C23  C24  109.42  3.000
 AY8  H11  C23  C24  110.31  3.000
 AY8  H12  C23  C22  109.35  3.000
 AY8  H11  C23  C22  109.80  3.000
 AY8  C24  C23  C22  111.54  3.000
 AY8  H14  C24  H13  106.52  3.000
 AY8  H14  C24  C25  110.23  3.000
 AY8  H13  C24  C25  109.21  3.000
 AY8  H14  C24  C23  110.25  3.000
 AY8  H13  C24  C23  109.26  3.000
 AY8  C25  C24  C23  111.24  3.000
 AY8  H16  C25  H15  106.38  3.000
 AY8  H16  C25  C26  109.40  3.000
 AY8  H15  C25  C26  109.75  3.000
 AY8  H16  C25  C24  109.45  3.000
 AY8  H15  C25  C24  110.33  3.000
 AY8  C26  C25  C24  111.39  3.000
 AY8  H18  C26  H17  106.60  3.000
 AY8  H18  C26  C25  109.13  3.000
 AY8  H17  C26  C25  110.49  3.000
 AY8  H18  C26  C21  109.48  3.000
 AY8  H17  C26  C21  109.59  3.000
 AY8  C25  C26  C21  111.43  3.000
 AY8  O11  P8   O10  108.13  3.000
 AY8  O10  P8   O9   118.49  3.000
 AY8  O11  P8   O9   111.24  3.000
 AY8  O10  P8   C7    99.17  3.000
 AY8  O11  P8   C7   104.62  3.000
 AY8  O9   P8   C7   113.77  3.000
 AY8  H19  O10  P8   115.46  3.000
 AY8  H20  O11  P8   117.05  3.000
 AY8  H21  O20  C18  111.03  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
 AY8  CONST_01  C5   C4   C3   C1     0.00   0.0  0
 AY8  CONST_02  C5   C6   C2   C1     0.00   0.0  0
 AY8  CONST_03  C16  C17  C14  C1   180.00   0.0  0
 AY8  CONST_04  C19  C18  C14  C1   180.00   0.0  0
 AY8  CONST_05  C4   C5   C6   C2     0.00   0.0  0
 AY8  CONST_06  C4   C3   C1   C2     0.00   0.0  0
 AY8  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 AY8  CONST_10  C6   C2   C1   C3     0.00   0.0  0
 AY8  CONST_13  C14  C1   C3   C4   180.00   0.0  0
 AY8  CONST_14  C14  C1   C2   C6   180.00   0.0  0
 AY8  CONST_15  C15  C16  C17  C14    0.00   0.0  0
 AY8  CONST_16  C15  C19  C18  C14    0.00   0.0  0
 AY8  CONST_17  C18  C14  C17  C16    0.00   0.0  0
 AY8  CONST_18  C18  C19  C15  C16    0.00   0.0  0
 AY8  CONST_19  C19  C18  C14  C17    0.00   0.0  0
 AY8  CONST_20  C19  C15  C16  C17    0.00   0.0  0
 AY8  CONST_21  C21  C19  C18  C14  180.00   0.0  0
 AY8  CONST_22  C21  C19  C15  C16  180.00   0.0  0
 AY8  CONST_23  C7   C4   C3   C1   180.00   0.0  0
 AY8  CONST_24  O20  C18  C14  C1     0.00   0.0  0
 AY8  CONST_25  C7   C4   C5   C6   180.00   0.0  0
 AY8  CONST_26  O20  C18  C19  C15  180.00   0.0  0
 AY8  CONST_27  O20  C18  C14  C17  180.00   0.0  0
 AY8  CONST_28  O20  C18  C19  C21    0.00   0.0  0
 AY8  CONST_29  H4   C6   C2   C1   180.00   0.0  0
 AY8  CONST_30  H7   C17  C14  C1     0.00   0.0  0
 AY8  CONST_31  H3   C5   C6   C2   180.00   0.0  0
 AY8  CONST_32  H2   C3   C1   C2   180.00   0.0  0
 AY8  CONST_33  H1   C2   C1   C3   180.00   0.0  0
 AY8  CONST_34  H6   C16  C17  C14  180.00   0.0  0
 AY8  CONST_35  H5   C15  C16  C17  180.00   0.0  0
 AY8  Var_01    C24  C23  C22  C21   55.44  30.0  1
 AY8  Var_02    C24  C25  C26  C21  -55.63  30.0  1
 AY8  Var_03    C25  C24  C23  C22  -55.07  30.0  1
 AY8  Var_04    C26  C25  C24  C23   55.10  30.0  1
 AY8  Var_05    F13  C7   C4   C3   152.92  30.0  2
 AY8  Var_06    O9   P8   C7   C4   175.99  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AY8  chir_01  C21  C19  C22  C26  positiv

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
 AY8  plan-1  C1   0.020
 AY8  plan-1  C2   0.020
 AY8  plan-1  C3   0.020
 AY8  plan-1  C4   0.020
 AY8  plan-1  C5   0.020
 AY8  plan-1  C6   0.020
 AY8  plan-1  C7   0.020
 AY8  plan-1  C14  0.020
 AY8  plan-1  H1   0.020
 AY8  plan-1  H2   0.020
 AY8  plan-1  H3   0.020
 AY8  plan-1  H4   0.020
 AY8  plan-2  C1   0.020
 AY8  plan-2  C14  0.020
 AY8  plan-2  C15  0.020
 AY8  plan-2  C16  0.020
 AY8  plan-2  C17  0.020
 AY8  plan-2  C18  0.020
 AY8  plan-2  C19  0.020
 AY8  plan-2  C21  0.020
 AY8  plan-2  O20  0.020
 AY8  plan-2  H5   0.020
 AY8  plan-2  H6   0.020
 AY8  plan-2  H7   0.020

