# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:25:25 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: methyl (R)-(6Z,9Z,12Z)-octadeca-6,9,12-trien-1-ylphosphonofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C/C=C\C\C=C/CCCCC[P@@](F)(=O)OC
#
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
 7FA  7FA  'methyl (R)-(6Z,9Z,12Z)-octadeca-6,9,12-trien-1-ylphosphonofluoridate'  ligand  57  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7FA
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
 7FA  C1   C  CH2   0  -0.753   -6.0795   0.7428  -0.6444
 7FA  P1   P  P     0   1.469   -7.4662  -0.3077  -0.2255
 7FA  C2   C  CH2   0  -0.440   -4.9441   0.6532   0.3763
 7FA  O2   O  O2    0  -0.583   -8.4433  -0.1697  -1.4732
 7FA  C3   C  CH2   0  -0.409   -3.7965   1.5895   0.0190
 7FA  C4   C  CH2   0  -0.414   -2.6390   1.4918   1.0033
 7FA  C5   C  CH2   0  -0.492   -1.4853   2.4365   0.6607
 7FA  C6   C  C1    0  -0.215   -0.3558   2.3025   1.6334
 7FA  C7   C  C1    0  -0.203    0.8656   1.8251   1.3987
 7FA  C8   C  CH2   0  -0.575    1.4240   1.3488   0.0880
 7FA  C9   C  C1    0  -0.206    2.6163   2.1697  -0.3114
 7FA  CM   C  CH3   0  -0.411   -9.7997  -0.6332  -1.4118
 7FA  C10  C  C1    0  -0.204    3.8762   1.7594  -0.4505
 7FA  C11  C  CH2   0  -0.576    4.4119   0.3666  -0.2849
 7FA  C12  C  C1    0  -0.205    4.9767  -0.1416  -1.5811
 7FA  C13  C  C1    0  -0.214    6.2471  -0.4467  -1.8427
 7FA  C14  C  CH2   0  -0.490    7.4061  -0.4015  -0.8964
 7FA  C15  C  CH2   0  -0.411    7.9267  -1.8020  -0.5654
 7FA  C16  C  CH2   0  -0.407    9.1077  -1.7859   0.3967
 7FA  C17  C  CH2   0  -0.420    9.6239  -3.1794   0.7347
 7FA  C18  C  CH3   0  -0.662   10.7777  -3.1600   1.7280
 7FA  O1   O  O     0  -0.699   -8.0743  -0.1611   1.1125
 7FA  F1   F  F     0  -0.432   -6.8779  -1.7830  -0.4140
 7FA  H1   H  HCH2  0   0.295   -5.7272   0.4822  -1.6450
 7FA  H2   H  HCH2  0   0.296   -6.4642   1.7648  -0.6966
 7FA  H3   H  HCH2  0   0.239   -5.3218   0.9022   1.3712
 7FA  H4   H  HCH2  0   0.239   -4.5701  -0.3726   0.4298
 7FA  H5   H  HCH2  0   0.220   -3.4372   1.3576  -0.9889
 7FA  H6   H  HCH2  0   0.221   -4.1669   2.6194  -0.0154
 7FA  H7   H  HCH2  0   0.219   -2.9987   1.7082   2.0146
 7FA  H8   H  HCH2  0   0.220   -2.2630   0.4642   1.0247
 7FA  H9   H  HCH2  0   0.231   -1.1503   2.2467  -0.3616
 7FA  H10  H  HCH2  0   0.232   -1.8565   3.4668   0.6774
 7FA  H11  H  H     0   0.232   -0.5885   2.5998   2.6528
 7FA  H12  H  H     0   0.236    1.5592   1.7739   2.2333
 7FA  H13  H  HCH2  0   0.251    1.6938   0.2937   0.1768
 7FA  H14  H  HCH2  0   0.252    0.6672   1.4058  -0.6975
 7FA  H15  H  H     0   0.238    2.4087   3.2225  -0.4807
 7FA  H16  H  HCH3  0   0.244  -10.3493  -0.1336  -0.6155
 7FA  H17  H  HCH3  0   0.257  -10.2540  -0.3907  -2.3681
 7FA  H18  H  HCH3  0   0.241   -9.8431  -1.7116  -1.2610
 7FA  H19  H  H     0   0.238    4.6180   2.5002  -0.7367
 7FA  H20  H  HCH2  0   0.252    5.1776   0.3663   0.4944
 7FA  H21  H  HCH2  0   0.251    3.6269  -0.3124   0.0565
 7FA  H22  H  H     0   0.235    4.2516  -0.2479  -2.3830
 7FA  H24  H  H     0   0.231    6.4813  -0.8005  -2.8434
 7FA  H26  H  HCH2  0   0.230    8.2170   0.1805  -1.3468
 7FA  H27  H  HCH2  0   0.229    7.1369   0.1129   0.0290
 7FA  H28  H  HCH2  0   0.215    7.1118  -2.3907  -0.1324
 7FA  H29  H  HCH2  0   0.213    8.2146  -2.3126  -1.4905
 7FA  H30  H  HCH2  0   0.209    9.9217  -1.1911  -0.0324
 7FA  H31  H  HCH2  0   0.208    8.8128  -1.2751   1.3201
 7FA  H32  H  HCH2  0   0.211    8.8030  -3.7798   1.1389
 7FA  H33  H  HCH2  0   0.211    9.9415  -3.6811  -0.1847
 7FA  H34  H  HCH3  0   0.216   11.6270  -2.5964   1.3371
 7FA  H35  H  HCH3  0   0.216   10.4803  -2.6938   2.6690
 7FA  H36  H  HCH3  0   0.226   11.1286  -4.1673   1.9548

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
 7FA  O1   P1   double  1.477  0.020  1.477
 7FA  O2   CM   single  1.435  0.020  1.435
 7FA  O2   P1   single  1.591  0.020  1.591
 7FA  P1   C1   single  1.789  0.020  1.789
 7FA  C1   C2   single  1.529  0.020  1.529
 7FA  C2   C3   single  1.524  0.020  1.524
 7FA  C3   C4   single  1.523  0.020  1.523
 7FA  C4   C5   single  1.530  0.020  1.530
 7FA  C5   C6   single  1.497  0.020  1.497
 7FA  C6   C7   double  1.332  0.020  1.332
 7FA  C7   C8   single  1.502  0.020  1.502
 7FA  C8   C9   single  1.502  0.020  1.502
 7FA  C9   C10  double  1.332  0.020  1.332
 7FA  C18  C17  single  1.523  0.020  1.523
 7FA  C10  C11  single  1.501  0.020  1.501
 7FA  C11  C12  single  1.502  0.020  1.502
 7FA  C17  C16  single  1.524  0.020  1.524
 7FA  C16  C15  single  1.523  0.020  1.523
 7FA  C12  C13  double  1.332  0.020  1.332
 7FA  C13  C14  single  1.497  0.020  1.497
 7FA  C15  C14  single  1.530  0.020  1.530
 7FA  P1   F1   single  1.599  0.020  1.599
 7FA  C1   H1   single  0.970  0.020  1.090
 7FA  C1   H2   single  0.970  0.020  1.090
 7FA  C2   H3   single  0.970  0.020  1.090
 7FA  C2   H4   single  0.970  0.020  1.090
 7FA  C3   H5   single  0.970  0.020  1.090
 7FA  C3   H6   single  0.970  0.020  1.090
 7FA  C4   H7   single  0.970  0.020  1.090
 7FA  C4   H8   single  0.970  0.020  1.090
 7FA  C5   H9   single  0.970  0.020  1.090
 7FA  C5   H10  single  0.970  0.020  1.090
 7FA  C6   H11  single  0.930  0.020  1.080
 7FA  C7   H12  single  0.930  0.020  1.080
 7FA  C8   H13  single  0.970  0.020  1.090
 7FA  C8   H14  single  0.970  0.020  1.090
 7FA  C9   H15  single  0.930  0.020  1.080
 7FA  CM   H16  single  0.970  0.020  1.090
 7FA  CM   H17  single  0.970  0.020  1.090
 7FA  CM   H18  single  0.970  0.020  1.090
 7FA  C10  H19  single  0.930  0.020  1.080
 7FA  C11  H20  single  0.970  0.020  1.090
 7FA  C11  H21  single  0.970  0.020  1.090
 7FA  C12  H22  single  0.930  0.020  1.080
 7FA  C13  H24  single  0.930  0.020  1.080
 7FA  C14  H26  single  0.970  0.020  1.090
 7FA  C14  H27  single  0.970  0.020  1.090
 7FA  C15  H28  single  0.970  0.020  1.090
 7FA  C15  H29  single  0.970  0.020  1.090
 7FA  C16  H30  single  0.970  0.020  1.090
 7FA  C16  H31  single  0.970  0.020  1.090
 7FA  C17  H32  single  0.970  0.020  1.090
 7FA  C17  H33  single  0.970  0.020  1.090
 7FA  C18  H34  single  0.970  0.020  1.090
 7FA  C18  H35  single  0.970  0.020  1.090
 7FA  C18  H36  single  0.970  0.020  1.090

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
 7FA  H2   C1   H1   107.02  3.000
 7FA  H2   C1   C2   110.36  3.000
 7FA  H1   C1   C2   110.98  3.000
 7FA  H2   C1   P1   106.69  3.000
 7FA  H1   C1   P1   108.92  3.000
 7FA  C2   C1   P1   112.62  3.000
 7FA  F1   P1   O1   110.48  3.000
 7FA  F1   P1   O2   102.32  3.000
 7FA  O1   P1   O2   116.68  3.000
 7FA  F1   P1   C1   103.23  3.000
 7FA  O2   P1   C1   103.97  3.000
 7FA  O1   P1   C1   118.22  3.000
 7FA  H4   C2   H3   106.70  3.000
 7FA  H4   C2   C3   109.30  3.000
 7FA  H3   C2   C3   109.49  3.000
 7FA  H4   C2   C1   109.98  3.000
 7FA  H3   C2   C1   109.73  3.000
 7FA  C3   C2   C1   111.51  3.000
 7FA  CM   O2   P1   121.27  3.000
 7FA  H6   C3   H5   106.34  3.000
 7FA  H6   C3   C4   109.75  3.000
 7FA  H5   C3   C4   109.39  3.000
 7FA  H6   C3   C2   109.31  3.000
 7FA  H5   C3   C2   109.44  3.000
 7FA  C4   C3   C2   112.43  3.000
 7FA  H8   C4   H7   106.28  3.000
 7FA  H8   C4   C5   108.97  3.000
 7FA  H7   C4   C5   109.42  3.000
 7FA  H8   C4   C3   109.52  3.000
 7FA  H7   C4   C3   109.55  3.000
 7FA  C5   C4   C3   112.88  3.000
 7FA  H10  C5   H9   106.35  3.000
 7FA  H10  C5   C6   109.27  3.000
 7FA  H9   C5   C6   111.17  3.000
 7FA  H10  C5   C4   108.78  3.000
 7FA  H9   C5   C4   109.48  3.000
 7FA  C6   C5   C4   111.61  3.000
 7FA  H11  C6   C7   117.35  3.000
 7FA  H11  C6   C5   115.05  3.000
 7FA  C7   C6   C5   127.56  3.000
 7FA  H12  C7   C8   114.71  3.000
 7FA  H12  C7   C6   117.83  3.000
 7FA  C8   C7   C6   127.45  3.000
 7FA  H14  C8   H13  106.26  3.000
 7FA  H14  C8   C9   109.29  3.000
 7FA  H13  C8   C9   110.70  3.000
 7FA  H14  C8   C7   110.69  3.000
 7FA  H13  C8   C7   109.08  3.000
 7FA  C9   C8   C7   110.73  3.000
 7FA  H15  C9   C10  117.57  3.000
 7FA  H15  C9   C8   114.80  3.000
 7FA  C10  C9   C8   127.61  3.000
 7FA  H18  CM   H17  109.03  3.000
 7FA  H18  CM   H16  109.43  3.000
 7FA  H17  CM   H16  109.28  3.000
 7FA  H18  CM   O2   111.31  3.000
 7FA  H17  CM   O2   106.60  3.000
 7FA  H16  CM   O2   111.12  3.000
 7FA  H19  C10  C11  114.70  3.000
 7FA  H19  C10  C9   117.59  3.000
 7FA  C11  C10  C9   127.70  3.000
 7FA  H21  C11  H20  106.29  3.000
 7FA  H21  C11  C12  109.24  3.000
 7FA  H20  C11  C12  110.60  3.000
 7FA  H21  C11  C10  110.77  3.000
 7FA  H20  C11  C10  109.20  3.000
 7FA  C12  C11  C10  110.66  3.000
 7FA  H22  C12  C13  117.97  3.000
 7FA  H22  C12  C11  114.77  3.000
 7FA  C13  C12  C11  127.25  3.000
 7FA  H24  C13  C14  115.15  3.000
 7FA  H24  C13  C12  117.43  3.000
 7FA  C14  C13  C12  127.39  3.000
 7FA  H27  C14  H26  106.30  3.000
 7FA  H27  C14  C15  109.36  3.000
 7FA  H26  C14  C15  108.87  3.000
 7FA  H27  C14  C13  111.03  3.000
 7FA  H26  C14  C13  109.23  3.000
 7FA  C15  C14  C13  111.87  3.000
 7FA  H29  C15  H28  106.20  3.000
 7FA  H29  C15  C16  109.55  3.000
 7FA  H28  C15  C16  109.45  3.000
 7FA  H29  C15  C14  109.47  3.000
 7FA  H28  C15  C14  108.94  3.000
 7FA  C16  C15  C14  113.00  3.000
 7FA  H31  C16  H30  106.08  3.000
 7FA  H31  C16  C17  109.30  3.000
 7FA  H30  C16  C17  109.37  3.000
 7FA  H31  C16  C15  109.18  3.000
 7FA  H30  C16  C15  109.53  3.000
 7FA  C17  C16  C15  113.14  3.000
 7FA  H33  C17  H32  106.05  3.000
 7FA  H33  C17  C18  109.51  3.000
 7FA  H32  C17  C18  109.54  3.000
 7FA  H33  C17  C16  109.33  3.000
 7FA  H32  C17  C16  109.24  3.000
 7FA  C18  C17  C16  112.93  3.000
 7FA  H36  C18  H35  107.63  3.000
 7FA  H36  C18  H34  107.52  3.000
 7FA  H35  C18  H34  107.47  3.000
 7FA  H36  C18  C17  111.58  3.000
 7FA  H35  C18  C17  111.18  3.000
 7FA  H34  C18  C17  111.26  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
 7FA  Var_01  C8   C7   C6   C5      2.35   0.0  2
 7FA  Var_02  C11  C10  C9   C8      2.08   0.0  2
 7FA  Var_03  C14  C13  C12  C11     2.30   0.0  2
 7FA  Var_04  C4   C3   C2   C1   -178.58  30.0  3
 7FA  Var_05  C3   C2   C1   P1   -178.20  30.0  3
 7FA  Var_06  O1   P1   C1   C2     54.27  30.0  1
 7FA  Var_07  C5   C4   C3   C2   -179.53  30.0  3
 7FA  Var_08  C6   C5   C4   C3   -179.15  30.0  3
 7FA  Var_09  C7   C6   C5   C4    112.74  30.0  3
 7FA  Var_10  C9   C8   C7   C6    119.33  30.0  3
 7FA  Var_11  C10  C9   C8   C7    115.96  30.0  3
 7FA  Var_12  C12  C11  C10  C9    116.82  30.0  3
 7FA  Var_13  C13  C12  C11  C10   115.22  30.0  3
 7FA  Var_14  C15  C14  C13  C12   111.08  30.0  3
 7FA  Var_15  C16  C15  C14  C13   180.00  30.0  1
 7FA  Var_16  C17  C16  C15  C14   179.68  30.0  1
 7FA  Var_17  C18  C17  C16  C15  -178.32  30.0  1
 7FA  Var_18  H16  CM   O2   P1     58.99  30.0  3
 7FA  Var_19  H34  C18  C17  C16   -59.99  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
 7FA  chir_01  P1  O2  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
 7FA  plan-1  C5   0.020
 7FA  plan-1  C6   0.020
 7FA  plan-1  C7   0.020
 7FA  plan-1  C8   0.020
 7FA  plan-1  H11  0.020
 7FA  plan-1  H12  0.020
 7FA  plan-2  C8   0.020
 7FA  plan-2  C9   0.020
 7FA  plan-2  C10  0.020
 7FA  plan-2  C11  0.020
 7FA  plan-2  H15  0.020
 7FA  plan-2  H19  0.020
 7FA  plan-3  C11  0.020
 7FA  plan-3  C12  0.020
 7FA  plan-3  C13  0.020
 7FA  plan-3  C14  0.020
 7FA  plan-3  H22  0.020
 7FA  plan-3  H24  0.020

