# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 19:31:32 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: propan-2-yl (R)-dodec-11-en-1-ylphosphonofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[P@](F)(=O)CCCCCCCCCCC=C
#
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
 TO4  TO4  'propan-2-yl (R)-dodec-11-en-1-ylphosphonofluoridate'  ligand  49  19  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TO4
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
 TO4  P1   P  P     0   1.463    4.3231   0.2952   0.3782
 TO4  O1   O  O     0  -0.700    4.4874   0.0984   1.8339
 TO4  O2   O  O2    0  -0.593    5.4749  -0.2634  -0.5598
 TO4  CM   C  CH1   0   0.010    6.8746  -0.2424  -0.1572
 TO4  CM2  C  CH3   0  -0.661    7.2693  -1.6360   0.2807
 TO4  CM1  C  CH3   0  -0.661    7.6753   0.2614  -1.3380
 TO4  C1   C  CH2   0  -0.753    2.8125  -0.2955  -0.3795
 TO4  C2   C  CH2   0  -0.440    1.5583   0.2976   0.2636
 TO4  C3   C  CH2   0  -0.409    0.2883  -0.2821  -0.3457
 TO4  C4   C  CH2   0  -0.415   -0.9765   0.3046   0.2666
 TO4  C5   C  CH2   0  -0.414   -2.2540  -0.2669  -0.3343
 TO4  C6   C  CH2   0  -0.413   -3.5191   0.3282   0.2704
 TO4  C7   C  CH2   0  -0.413   -4.7988  -0.2346  -0.3345
 TO4  C8   C  CH2   0  -0.414   -6.0624   0.3655   0.2681
 TO4  C9   C  CH2   0  -0.416   -7.3410  -0.1824  -0.3522
 TO4  C10  C  CH2   0  -0.483   -8.6048   0.4131   0.2699
 TO4  C11  C  C1    0  -0.152   -9.8510  -0.0614  -0.4064
 TO4  C12  C  C2    0  -0.541  -10.7975  -0.8012   0.1604
 TO4  H2   H  HCH1  0   0.241    6.9978   0.4486   0.6813
 TO4  H3   H  HCH3  0   0.233    7.1478  -2.3516  -0.5336
 TO4  H4   H  HCH3  0   0.237    8.3164  -1.6437   0.5836
 TO4  H5   H  HCH3  0   0.242    6.6730  -1.9685   1.1301
 TO4  H6   H  HCH3  0   0.243    7.3557   1.2591  -1.6388
 TO4  H7   H  HCH3  0   0.237    8.7290   0.3157  -1.0647
 TO4  H8   H  HCH3  0   0.232    7.5845  -0.4093  -2.1938
 TO4  H9   H  HCH2  0   0.294    2.8422  -0.0798  -1.4499
 TO4  H10  H  HCH2  0   0.294    2.8125  -1.3838  -0.2743
 TO4  H11  H  HCH2  0   0.238    1.5657   0.1040   1.3393
 TO4  H12  H  HCH2  0   0.238    1.5544   1.3839   0.1423
 TO4  H13  H  HCH2  0   0.218    0.2886  -0.1036  -1.4260
 TO4  H14  H  HCH2  0   0.218    0.2883  -1.3696  -0.2165
 TO4  H15  H  HCH2  0   0.211   -0.9724   0.1288   1.3479
 TO4  H16  H  HCH2  0   0.211   -0.9701   1.3925   0.1378
 TO4  H17  H  HCH2  0   0.208   -2.2541  -0.0961  -1.4166
 TO4  H18  H  HCH2  0   0.209   -2.2641  -1.3544  -0.2011
 TO4  H19  H  HCH2  0   0.208   -3.5211   0.1551   1.3523
 TO4  H20  H  HCH2  0   0.207   -3.5053   1.4161   0.1403
 TO4  H21  H  HCH2  0   0.208   -4.7951  -0.0611  -1.4164
 TO4  H22  H  HCH2  0   0.208   -4.8152  -1.3223  -0.2045
 TO4  H23  H  HCH2  0   0.210   -6.0733   0.1815   1.3481
 TO4  H24  H  HCH2  0   0.210   -6.0408   1.4544   0.1483
 TO4  H25  H  HCH2  0   0.215   -7.3361   0.0159  -1.4293
 TO4  H26  H  HCH2  0   0.217   -7.3663  -1.2713  -0.2439
 TO4  H27  H  HCH2  0   0.227   -8.6412   0.1709   1.3359
 TO4  H28  H  HCH2  0   0.228   -8.5495   1.5051   0.1975
 TO4  H29  H  H     0   0.236   -9.9612   0.2207  -1.4509
 TO4  H30  H  H     0   0.229  -10.7327  -1.1124   1.1970
 TO4  H31  H  H     0   0.233  -11.6719  -1.1242  -0.3898
 TO4  F1   F  F     0  -0.432    4.3189   1.8573   0.0287

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
 TO4  CM2  CM   single  1.513  0.020  1.513
 TO4  CM   CM1  single  1.513  0.020  1.513
 TO4  CM   O2   single  1.457  0.020  1.457
 TO4  O2   P1   single  1.587  0.020  1.587
 TO4  O1   P1   double  1.478  0.020  1.478
 TO4  P1   C1   single  1.790  0.020  1.790
 TO4  C1   C2   single  1.529  0.020  1.529
 TO4  C12  C11  double  1.328  0.020  1.328
 TO4  C2   C3   single  1.523  0.020  1.523
 TO4  C9   C8   single  1.523  0.020  1.523
 TO4  C9   C10  single  1.529  0.020  1.529
 TO4  C8   C7   single  1.523  0.020  1.523
 TO4  C11  C10  single  1.495  0.020  1.495
 TO4  C3   C4   single  1.523  0.020  1.523
 TO4  C4   C5   single  1.523  0.020  1.523
 TO4  C7   C6   single  1.523  0.020  1.523
 TO4  C6   C5   single  1.523  0.020  1.523
 TO4  CM   H2   single  0.970  0.020  1.090
 TO4  CM2  H3   single  0.970  0.020  1.090
 TO4  CM2  H4   single  0.970  0.020  1.090
 TO4  CM2  H5   single  0.970  0.020  1.090
 TO4  CM1  H6   single  0.970  0.020  1.090
 TO4  CM1  H7   single  0.970  0.020  1.090
 TO4  CM1  H8   single  0.970  0.020  1.090
 TO4  C1   H9   single  0.970  0.020  1.090
 TO4  C1   H10  single  0.970  0.020  1.090
 TO4  C2   H11  single  0.970  0.020  1.090
 TO4  C2   H12  single  0.970  0.020  1.090
 TO4  C3   H13  single  0.970  0.020  1.090
 TO4  C3   H14  single  0.970  0.020  1.090
 TO4  C4   H15  single  0.970  0.020  1.090
 TO4  C4   H16  single  0.970  0.020  1.090
 TO4  C5   H17  single  0.970  0.020  1.090
 TO4  C5   H18  single  0.970  0.020  1.090
 TO4  C6   H19  single  0.970  0.020  1.090
 TO4  C6   H20  single  0.970  0.020  1.090
 TO4  C7   H21  single  0.970  0.020  1.090
 TO4  C7   H22  single  0.970  0.020  1.090
 TO4  C8   H23  single  0.970  0.020  1.090
 TO4  C8   H24  single  0.970  0.020  1.090
 TO4  C9   H25  single  0.970  0.020  1.090
 TO4  C9   H26  single  0.970  0.020  1.090
 TO4  C10  H27  single  0.970  0.020  1.090
 TO4  C10  H28  single  0.970  0.020  1.090
 TO4  C11  H29  single  0.930  0.020  1.080
 TO4  C12  H30  single  0.930  0.020  1.080
 TO4  C12  H31  single  0.930  0.020  1.080
 TO4  P1   F1   single  1.601  0.020  1.601

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
 TO4  F1   P1   C1   103.15  3.000
 TO4  F1   P1   O2   102.49  3.000
 TO4  C1   P1   O2   104.25  3.000
 TO4  F1   P1   O1   110.19  3.000
 TO4  C1   P1   O1   117.82  3.000
 TO4  O2   P1   O1   117.04  3.000
 TO4  CM   O2   P1   121.94  3.000
 TO4  H2   CM   CM1  109.17  3.000
 TO4  H2   CM   CM2  109.31  3.000
 TO4  CM1  CM   CM2  113.23  3.000
 TO4  H2   CM   O2   109.23  3.000
 TO4  CM1  CM   O2   107.31  3.000
 TO4  CM2  CM   O2   108.50  3.000
 TO4  H5   CM2  H4   107.87  3.000
 TO4  H5   CM2  H3   108.71  3.000
 TO4  H4   CM2  H3   108.05  3.000
 TO4  H5   CM2  CM   111.34  3.000
 TO4  H4   CM2  CM   109.72  3.000
 TO4  H3   CM2  CM   111.05  3.000
 TO4  H8   CM1  H7   107.92  3.000
 TO4  H8   CM1  H6   108.77  3.000
 TO4  H7   CM1  H6   107.88  3.000
 TO4  H8   CM1  CM   111.31  3.000
 TO4  H7   CM1  CM   109.42  3.000
 TO4  H6   CM1  CM   111.41  3.000
 TO4  H10  C1   H9   106.90  3.000
 TO4  H10  C1   C2   110.22  3.000
 TO4  H9   C1   C2   110.97  3.000
 TO4  H10  C1   P1   106.72  3.000
 TO4  H9   C1   P1   109.06  3.000
 TO4  C2   C1   P1   112.71  3.000
 TO4  H12  C2   H11  106.58  3.000
 TO4  H12  C2   C3   109.32  3.000
 TO4  H11  C2   C3   109.38  3.000
 TO4  H12  C2   C1   109.98  3.000
 TO4  H11  C2   C1   109.85  3.000
 TO4  C3   C2   C1   111.59  3.000
 TO4  H14  C3   H13  106.16  3.000
 TO4  H14  C3   C4   109.58  3.000
 TO4  H13  C3   C4   109.51  3.000
 TO4  H14  C3   C2   109.32  3.000
 TO4  H13  C3   C2   109.41  3.000
 TO4  C4   C3   C2   112.65  3.000
 TO4  H16  C4   H15  105.98  3.000
 TO4  H16  C4   C5   109.34  3.000
 TO4  H15  C4   C5   109.41  3.000
 TO4  H16  C4   C3   109.30  3.000
 TO4  H15  C4   C3   109.39  3.000
 TO4  C5   C4   C3   113.17  3.000
 TO4  H18  C5   H17  105.95  3.000
 TO4  H18  C5   C6   109.38  3.000
 TO4  H17  C5   C6   109.34  3.000
 TO4  H18  C5   C4   109.40  3.000
 TO4  H17  C5   C4   109.35  3.000
 TO4  C6   C5   C4   113.17  3.000
 TO4  H20  C6   H19  105.91  3.000
 TO4  H20  C6   C7   109.29  3.000
 TO4  H19  C6   C7   109.40  3.000
 TO4  H20  C6   C5   109.29  3.000
 TO4  H19  C6   C5   109.38  3.000
 TO4  C7   C6   C5   113.31  3.000
 TO4  H22  C7   H21  105.93  3.000
 TO4  H22  C7   C8   109.38  3.000
 TO4  H21  C7   C8   109.34  3.000
 TO4  H22  C7   C6   109.41  3.000
 TO4  H21  C7   C6   109.31  3.000
 TO4  C8   C7   C6   113.22  3.000
 TO4  H24  C8   H23  105.95  3.000
 TO4  H24  C8   C9   109.24  3.000
 TO4  H23  C8   C9   109.44  3.000
 TO4  H24  C8   C7   109.38  3.000
 TO4  H23  C8   C7   109.40  3.000
 TO4  C9   C8   C7   113.18  3.000
 TO4  H26  C9   H25  106.11  3.000
 TO4  H26  C9   C10  109.15  3.000
 TO4  H25  C9   C10  109.47  3.000
 TO4  H26  C9   C8   109.69  3.000
 TO4  H25  C9   C8   109.37  3.000
 TO4  C10  C9   C8   112.83  3.000
 TO4  H28  C10  H27  106.67  3.000
 TO4  H28  C10  C11  109.18  3.000
 TO4  H27  C10  C11  110.05  3.000
 TO4  H28  C10  C9   108.63  3.000
 TO4  H27  C10  C9   109.74  3.000
 TO4  C11  C10  C9   112.40  3.000
 TO4  H29  C11  C12  118.82  3.000
 TO4  H29  C11  C10  115.89  3.000
 TO4  C12  C11  C10  125.28  3.000
 TO4  H31  C12  H30  116.66  3.000
 TO4  H31  C12  C11  121.66  3.000
 TO4  H30  C12  C11  121.68  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
 TO4  Var_01  CM2  CM   O2   P1    102.53  30.0  1
 TO4  Var_02  C3   C2   C1   P1   -176.71  30.0  3
 TO4  Var_03  C2   C1   P1   O1     56.39  30.0  3
 TO4  Var_04  C1   P1   O2   CM   -167.29  30.0  3
 TO4  Var_05  C4   C3   C2   C1   -179.33  30.0  3
 TO4  Var_06  C5   C4   C3   C2    180.00  30.0  3
 TO4  Var_07  C6   C5   C4   C3   -179.54  30.0  3
 TO4  Var_08  C7   C6   C5   C4    179.63  30.0  1
 TO4  Var_09  C8   C7   C6   C5   -179.80  30.0  1
 TO4  Var_10  C9   C8   C7   C6    179.12  30.0  1
 TO4  Var_11  C10  C9   C8   C7    179.32  30.0  1
 TO4  Var_12  C11  C10  C9   C8    176.17  30.0  3
 TO4  Var_13  C12  C11  C10  C9    115.54  30.0  1
 TO4  Var_14  H30  C12  C11  C10     0.81   0.0  2
 TO4  Var_15  H3   CM2  CM   O2     60.43  30.0  3
 TO4  Var_16  H6   CM1  CM   O2     59.32  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
 TO4  chir_01  P1  O1  C1  F1  both

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
 TO4  plan-1  C10  0.020
 TO4  plan-1  C11  0.020
 TO4  plan-1  C12  0.020
 TO4  plan-1  H29  0.020
 TO4  plan-1  H30  0.020
 TO4  plan-1  H31  0.020

