# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:53:59 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  45  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   0.027   0.3175   1.1945   0.3644
 AY8  C2   C  CR16   0  -0.334   0.3896   1.7736   1.6341
 AY8  C3   C  CR16   0  -0.329   1.4919   0.7487  -0.2380
 AY8  C4   C  CR6    0  -0.019   2.7234   0.8777   0.3961
 AY8  C5   C  CR16   0  -0.318   2.7738   1.4318   1.6712
 AY8  C6   C  CR16   0  -0.225   1.6118   1.8824   2.2801
 AY8  C7   C  CT     0   0.452   3.9558   0.3698  -0.2823
 AY8  C14  C  CR6    0  -0.024  -0.9726   1.0794  -0.3546
 AY8  C15  C  CR16   0  -0.317  -3.3865   0.8988  -1.7169
 AY8  C16  C  CR16   0  -0.256  -2.3011   1.5132  -2.3238
 AY8  C17  C  CR16   0  -0.310  -1.1017   1.6029  -1.6381
 AY8  C18  C  CR6    0   0.240  -2.0740   0.4342   0.2284
 AY8  C19  C  CR6    0   0.091  -3.3018   0.3516  -0.4401
 AY8  C21  C  CH1    0  -0.327  -4.5046  -0.3114   0.1891
 AY8  C22  C  CH2    0  -0.407  -4.9003  -1.5994  -0.5443
 AY8  C23  C  CH2    0  -0.434  -6.0998  -2.2684   0.1201
 AY8  C24  C  CH2    0  -0.430  -7.2871  -1.3166   0.2237
 AY8  C25  C  CH2    0  -0.434  -6.8998  -0.0246   0.9363
 AY8  C26  C  CH2    0  -0.410  -5.7027   0.6424   0.2679
 AY8  P8   P  P      0   1.103   4.1947  -1.4995  -0.1744
 AY8  O9   O  O      0  -0.886   5.5252  -1.7332  -0.8854
 AY8  O10  O  OP    -1  -0.877   4.2141  -1.7408   1.3304
 AY8  O11  O  OP    -1  -0.874   2.9712  -2.0388  -0.9095
 AY8  F12  F  F      0  -0.380   3.9236   0.7772  -1.6048
 AY8  F13  F  F      0  -0.376   5.0532   1.0190   0.2482
 AY8  O20  O  OH1    0  -0.619  -1.9888  -0.1412   1.4494
 AY8  H1   H  HCR6   0   0.267  -0.5012   2.1698   2.1069
 AY8  H2   H  HCR6   0   0.247   1.4373   0.2841  -1.2130
 AY8  H3   H  HCR6   0   0.252   3.7149   1.5281   2.1942
 AY8  H4   H  HCR6   0   0.256   1.6599   2.3325   3.2633
 AY8  H5   H  HCR6   0   0.247  -4.3248   0.8437  -2.2568
 AY8  H6   H  HCR6   0   0.247  -2.3954   1.9291  -3.3181
 AY8  H7   H  HCR6   0   0.253  -0.2518   2.0991  -2.0904
 AY8  H8   H  HCH1   0   0.236  -4.2552  -0.5947   1.2148
 AY8  H9   H  HCH2   0   0.211  -5.1435  -1.3654  -1.5867
 AY8  H10  H  HCH2   0   0.231  -4.0503  -2.2864  -0.5688
 AY8  H11  H  HCH2   0   0.227  -6.3814  -3.1664  -0.4358
 AY8  H12  H  HCH2   0   0.210  -5.8155  -2.6043   1.1234
 AY8  H13  H  HCH2   0   0.208  -7.6494  -1.0790  -0.7829
 AY8  H14  H  HCH2   0   0.226  -8.1161  -1.8017   0.7450
 AY8  H15  H  HCH2   0   0.227  -7.7468   0.6655   0.9566
 AY8  H16  H  HCH2   0   0.210  -6.6547  -0.2444   1.9812
 AY8  H17  H  HCH2   0   0.231  -5.4179   1.5465   0.8126
 AY8  H18  H  HCH2   0   0.212  -5.9880   0.9627  -0.7397
 AY8  H21  H  HOH1   0   0.475  -1.0764  -0.1315   1.7639

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   deloc     1.527  0.020  1.527
 AY8  F13  C7   single    1.381  0.020  1.381
 AY8  O11  P8   deloc     1.526  0.020  1.526
 AY8  P8   C7   single    1.888  0.020  1.888
 AY8  P8   O10  deloc     1.524  0.020  1.524
 AY8  C7   F12  single    1.384  0.020  1.384
 AY8  C7   C4   single    1.496  0.020  1.496
 AY8  C5   C4   aromatic  1.391  0.020  1.391
 AY8  C5   C6   aromatic  1.387  0.020  1.387
 AY8  C4   C3   aromatic  1.391  0.020  1.391
 AY8  C6   C2   aromatic  1.387  0.020  1.387
 AY8  C3   C1   aromatic  1.393  0.020  1.393
 AY8  C2   C1   aromatic  1.397  0.020  1.397
 AY8  C1   C14  single    1.481  0.020  1.481
 AY8  C14  C17  aromatic  1.392  0.020  1.392
 AY8  C14  C18  aromatic  1.403  0.020  1.403
 AY8  O20  C18  single    1.352  0.020  1.352
 AY8  C17  C16  aromatic  1.384  0.020  1.384
 AY8  C18  C19  aromatic  1.400  0.020  1.400
 AY8  C16  C15  aromatic  1.387  0.020  1.387
 AY8  C19  C15  aromatic  1.392  0.020  1.392
 AY8  C19  C21  single    1.511  0.020  1.511
 AY8  C22  C21  single    1.534  0.020  1.534
 AY8  C22  C23  single    1.526  0.020  1.526
 AY8  C21  C26  single    1.533  0.020  1.533
 AY8  C26  C25  single    1.525  0.020  1.525
 AY8  C23  C24  single    1.525  0.020  1.525
 AY8  C24  C25  single    1.526  0.020  1.526
 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  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   119.96  3.000
 AY8  C14  C1   C2   121.21  3.000
 AY8  C3   C1   C2   118.81  3.000
 AY8  H1   C2   C6   119.51  3.000
 AY8  H1   C2   C1   120.37  3.000
 AY8  C6   C2   C1   120.08  3.000
 AY8  H2   C3   C4   119.70  3.000
 AY8  H2   C3   C1   119.00  3.000
 AY8  C4   C3   C1   121.30  3.000
 AY8  C7   C4   C5   121.41  3.000
 AY8  C5   C4   C3   119.12  3.000
 AY8  C7   C4   C3   119.42  3.000
 AY8  H3   C5   C6   119.21  3.000
 AY8  H3   C5   C4   120.70  3.000
 AY8  C6   C5   C4   120.09  3.000
 AY8  H4   C6   C5   119.77  3.000
 AY8  H4   C6   C2   119.67  3.000
 AY8  C5   C6   C2   120.56  3.000
 AY8  F13  C7   F12  104.31  3.000
 AY8  F12  C7   P8   110.43  3.000
 AY8  F13  C7   P8   110.07  3.000
 AY8  F12  C7   C4   108.31  3.000
 AY8  P8   C7   C4   114.50  3.000
 AY8  F13  C7   C4   108.71  3.000
 AY8  C18  C14  C17  118.89  3.000
 AY8  C18  C14  C1   121.17  3.000
 AY8  C17  C14  C1   119.94  3.000
 AY8  H5   C15  C19  119.32  3.000
 AY8  H5   C15  C16  118.81  3.000
 AY8  C19  C15  C16  121.87  3.000
 AY8  H6   C16  C17  120.38  3.000
 AY8  H6   C16  C15  120.28  3.000
 AY8  C17  C16  C15  119.33  3.000
 AY8  H7   C17  C16  120.17  3.000
 AY8  H7   C17  C14  118.98  3.000
 AY8  C16  C17  C14  120.84  3.000
 AY8  O20  C18  C19  117.46  3.000
 AY8  C19  C18  C14  121.13  3.000
 AY8  O20  C18  C14  121.41  3.000
 AY8  C21  C19  C18  121.68  3.000
 AY8  C21  C19  C15  120.41  3.000
 AY8  C18  C19  C15  117.91  3.000
 AY8  H8   C21  C26  106.93  3.000
 AY8  H8   C21  C22  106.85  3.000
 AY8  C26  C21  C22  110.20  3.000
 AY8  H8   C21  C19  108.84  3.000
 AY8  C26  C21  C19  111.75  3.000
 AY8  C22  C21  C19  112.01  3.000
 AY8  H10  C22  H9   106.59  3.000
 AY8  H10  C22  C23  110.21  3.000
 AY8  H9   C22  C23  109.47  3.000
 AY8  H10  C22  C21  109.74  3.000
 AY8  H9   C22  C21  109.44  3.000
 AY8  C23  C22  C21  111.27  3.000
 AY8  H12  C23  H11  106.30  3.000
 AY8  H12  C23  C24  109.33  3.000
 AY8  H11  C23  C24  110.28  3.000
 AY8  H12  C23  C22  109.22  3.000
 AY8  H11  C23  C22  109.96  3.000
 AY8  C24  C23  C22  111.59  3.000
 AY8  H14  C24  H13  106.48  3.000
 AY8  H14  C24  C25  110.22  3.000
 AY8  H13  C24  C25  109.23  3.000
 AY8  H14  C24  C23  110.24  3.000
 AY8  H13  C24  C23  109.28  3.000
 AY8  C25  C24  C23  111.26  3.000
 AY8  H16  C25  H15  106.40  3.000
 AY8  H16  C25  C26  109.28  3.000
 AY8  H15  C25  C26  109.91  3.000
 AY8  H16  C25  C24  109.42  3.000
 AY8  H15  C25  C24  110.29  3.000
 AY8  C26  C25  C24  111.41  3.000
 AY8  H18  C26  H17  106.52  3.000
 AY8  H18  C26  C25  109.07  3.000
 AY8  H17  C26  C25  110.36  3.000
 AY8  H18  C26  C21  109.76  3.000
 AY8  H17  C26  C21  109.66  3.000
 AY8  C25  C26  C21  111.34  3.000
 AY8  O11  P8   O10  115.46  3.000
 AY8  O10  P8   O9   115.12  3.000
 AY8  O11  P8   O9   114.86  3.000
 AY8  O10  P8   C7   102.41  3.000
 AY8  O11  P8   C7   102.77  3.000
 AY8  O9   P8   C7   103.61  3.000
 AY8  H21  O20  C18  110.46  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    55.63  30.0  1
 AY8  Var_02    C24  C25  C26  C21   -55.97  30.0  1
 AY8  Var_03    C25  C24  C23  C22   -54.68  30.0  1
 AY8  Var_04    C26  C25  C24  C23    54.78  30.0  1
 AY8  Var_05    F13  C7   C4   C3    157.92  30.0  2
 AY8  Var_06    O9   P8   C7   C4   -177.90  30.0  2

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

