# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 12:24:29 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: methyl (S)-(9Z,12Z,15Z)-octadeca-9,12,15-trien-1-ylphosphonofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C/C=C\C\C=C/CCCCCCCC[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
 GJY  GJY  'methyl (S)-(9Z,12Z,15Z)-octadeca-9,12,15-trien-1-ylphosphonofluoridate'  ligand  57  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GJY
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
 GJY  O1   O  O     0  -0.699   -8.3664   1.7828  -1.3237
 GJY  P1   P  P     0   1.470   -8.1578   0.5873  -0.4817
 GJY  O2   O  O2    0  -0.583   -9.3178   0.2258   0.5454
 GJY  CM   C  CH3   0  -0.411  -10.6971   0.4596   0.2278
 GJY  C1   C  CH2   0  -0.755   -6.6683   0.5024   0.5062
 GJY  C2   C  CH2   0  -0.439   -5.3943   0.6707  -0.3225
 GJY  C3   C  CH2   0  -0.408   -4.1554   0.6908   0.5647
 GJY  C4   C  CH2   0  -0.415   -2.8657   0.8557  -0.2280
 GJY  C5   C  CH2   0  -0.414   -1.6270   0.9218   0.6568
 GJY  C6   C  CH2   0  -0.414   -0.3364   1.0927  -0.1340
 GJY  C7   C  CH2   0  -0.415    0.8991   1.2027   0.7502
 GJY  C8   C  CH2   0  -0.488    2.1871   1.3872  -0.0532
 GJY  C9   C  C1    0  -0.206    3.3743   1.6265   0.8245
 GJY  C10  C  C1    0  -0.209    4.5014   0.9207   0.8968
 GJY  C11  C  CH2   0  -0.580    4.8836  -0.2858   0.0877
 GJY  C12  C  C1    0  -0.210    5.9352   0.0810  -0.9216
 GJY  C13  C  C1    0  -0.200    7.2467  -0.1312  -0.8286
 GJY  C14  C  CH2   0  -0.576    7.9798  -0.8164   0.2885
 GJY  C15  C  C1    0  -0.205    8.5914  -2.1059  -0.1802
 GJY  C16  C  C1    0  -0.211    9.8863  -2.3647  -0.3557
 GJY  C17  C  CH2   0  -0.490   11.0441  -1.4505  -0.1003
 GJY  C18  C  CH3   0  -0.658   11.9463  -1.9715   1.0170
 GJY  F1   F  F     0  -0.431   -8.0787  -0.7300  -1.3843
 GJY  H1   H  HCH3  0   0.244  -10.8718   1.5051  -0.0210
 GJY  H2   H  HCH3  0   0.242  -11.0223  -0.1695  -0.6005
 GJY  H3   H  HCH3  0   0.257  -11.2686   0.2010   1.1145
 GJY  H4   H  HCH2  0   0.295   -6.7430   1.3001   1.2505
 GJY  H5   H  HCH2  0   0.295   -6.6572  -0.4439   1.0523
 GJY  H6   H  HCH2  0   0.239   -5.3092  -0.1416  -1.0487
 GJY  H7   H  HCH2  0   0.238   -5.4439   1.6004  -0.8954
 GJY  H8   H  HCH2  0   0.218   -4.2465   1.5072   1.2890
 GJY  H9   H  HCH2  0   0.218   -4.1116  -0.2340   1.1498
 GJY  H10  H  HCH2  0   0.212   -2.7641   0.0264  -0.9364
 GJY  H11  H  HCH2  0   0.211   -2.9257   1.7668  -0.8338
 GJY  H12  H  HCH2  0   0.209   -1.7329   1.7530   1.3627
 GJY  H13  H  HCH2  0   0.210   -1.5648   0.0132   1.2662
 GJY  H14  H  HCH2  0   0.210   -0.2173   0.2509  -0.8249
 GJY  H15  H  HCH2  0   0.209   -0.4112   1.9891  -0.7601
 GJY  H16  H  HCH2  0   0.214    0.7768   2.0455   1.4391
 GJY  H17  H  HCH2  0   0.217    0.9871   0.3088   1.3764
 GJY  H18  H  HCH2  0   0.230    2.3367   0.5245  -0.7069
 GJY  H19  H  HCH2  0   0.229    2.0617   2.2511  -0.7163
 GJY  H20  H  H     0   0.230    3.2849   2.4857   1.4849
 GJY  H21  H  H     0   0.234    5.2648   1.2573   1.5927
 GJY  H22  H  HCH2  0   0.251    5.2490  -1.0665   0.7585
 GJY  H23  H  HCH2  0   0.254    4.0167  -0.7005  -0.4295
 GJY  H24  H  H     0   0.238    5.5687   0.6100  -1.7965
 GJY  H25  H  H     0   0.238    7.8749   0.2144  -1.6450
 GJY  H26  H  HCH2  0   0.253    8.7502  -0.1439   0.6728
 GJY  H27  H  HCH2  0   0.250    7.3071  -1.0189   1.1252
 GJY  H28  H  H     0   0.235    7.8784  -2.8914  -0.4146
 GJY  H29  H  H     0   0.231   10.1556  -3.3579  -0.7067
 GJY  H30  H  HCH2  0   0.233   11.6331  -1.3619  -1.0184
 GJY  H31  H  HCH2  0   0.232   10.7042  -0.4424   0.1423
 GJY  H32  H  HCH3  0   0.223   11.4035  -2.0348   1.9609
 GJY  H33  H  HCH3  0   0.222   12.3276  -2.9679   0.7869
 GJY  H34  H  HCH3  0   0.230   12.8042  -1.3153   1.1666

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
 GJY  C1   P1   single  1.789  0.020  1.789
 GJY  C1   C2   single  1.529  0.020  1.529
 GJY  P1   O2   single  1.591  0.020  1.591
 GJY  P1   O1   double  1.477  0.020  1.477
 GJY  O2   CM   single  1.435  0.020  1.435
 GJY  C2   C3   single  1.524  0.020  1.524
 GJY  C3   C4   single  1.523  0.020  1.523
 GJY  C4   C5   single  1.524  0.020  1.524
 GJY  C5   C6   single  1.523  0.020  1.523
 GJY  C6   C7   single  1.523  0.020  1.523
 GJY  C8   C7   single  1.529  0.020  1.529
 GJY  C8   C9   single  1.496  0.020  1.496
 GJY  C9   C10  double  1.332  0.020  1.332
 GJY  C10  C11  single  1.502  0.020  1.502
 GJY  C12  C11  single  1.503  0.020  1.503
 GJY  C12  C13  double  1.332  0.020  1.332
 GJY  C18  C17  single  1.528  0.020  1.528
 GJY  C13  C14  single  1.502  0.020  1.502
 GJY  C17  C16  single  1.497  0.020  1.497
 GJY  C14  C15  single  1.502  0.020  1.502
 GJY  C16  C15  double  1.332  0.020  1.332
 GJY  P1   F1   single  1.599  0.020  1.599
 GJY  CM   H1   single  0.970  0.020  1.090
 GJY  CM   H2   single  0.970  0.020  1.090
 GJY  CM   H3   single  0.970  0.020  1.090
 GJY  C1   H4   single  0.970  0.020  1.090
 GJY  C1   H5   single  0.970  0.020  1.090
 GJY  C2   H6   single  0.970  0.020  1.090
 GJY  C2   H7   single  0.970  0.020  1.090
 GJY  C3   H8   single  0.970  0.020  1.090
 GJY  C3   H9   single  0.970  0.020  1.090
 GJY  C4   H10  single  0.970  0.020  1.090
 GJY  C4   H11  single  0.970  0.020  1.090
 GJY  C5   H12  single  0.970  0.020  1.090
 GJY  C5   H13  single  0.970  0.020  1.090
 GJY  C6   H14  single  0.970  0.020  1.090
 GJY  C6   H15  single  0.970  0.020  1.090
 GJY  C7   H16  single  0.970  0.020  1.090
 GJY  C7   H17  single  0.970  0.020  1.090
 GJY  C8   H18  single  0.970  0.020  1.090
 GJY  C8   H19  single  0.970  0.020  1.090
 GJY  C9   H20  single  0.930  0.020  1.080
 GJY  C10  H21  single  0.930  0.020  1.080
 GJY  C11  H22  single  0.970  0.020  1.090
 GJY  C11  H23  single  0.970  0.020  1.090
 GJY  C12  H24  single  0.930  0.020  1.080
 GJY  C13  H25  single  0.930  0.020  1.080
 GJY  C14  H26  single  0.970  0.020  1.090
 GJY  C14  H27  single  0.970  0.020  1.090
 GJY  C15  H28  single  0.930  0.020  1.080
 GJY  C16  H29  single  0.930  0.020  1.080
 GJY  C17  H30  single  0.970  0.020  1.090
 GJY  C17  H31  single  0.970  0.020  1.090
 GJY  C18  H32  single  0.970  0.020  1.090
 GJY  C18  H33  single  0.970  0.020  1.090
 GJY  C18  H34  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
 GJY  F1   P1   C1   103.38  3.000
 GJY  F1   P1   O2   102.32  3.000
 GJY  C1   P1   O2   103.87  3.000
 GJY  F1   P1   O1   110.61  3.000
 GJY  O2   P1   O1   116.68  3.000
 GJY  C1   P1   O1   118.08  3.000
 GJY  CM   O2   P1   121.40  3.000
 GJY  H3   CM   H2   109.02  3.000
 GJY  H3   CM   H1   109.31  3.000
 GJY  H2   CM   H1   109.44  3.000
 GJY  H3   CM   O2   106.64  3.000
 GJY  H2   CM   O2   111.17  3.000
 GJY  H1   CM   O2   111.19  3.000
 GJY  H5   C1   H4   107.00  3.000
 GJY  H5   C1   C2   110.96  3.000
 GJY  H4   C1   C2   110.21  3.000
 GJY  H5   C1   P1   109.00  3.000
 GJY  H4   C1   P1   106.52  3.000
 GJY  C2   C1   P1   112.90  3.000
 GJY  H7   C2   H6   106.70  3.000
 GJY  H7   C2   C3   109.31  3.000
 GJY  H6   C2   C3   109.47  3.000
 GJY  H7   C2   C1   109.87  3.000
 GJY  H6   C2   C1   110.07  3.000
 GJY  C3   C2   C1   111.30  3.000
 GJY  H9   C3   H8   106.23  3.000
 GJY  H9   C3   C4   109.61  3.000
 GJY  H8   C3   C4   109.51  3.000
 GJY  H9   C3   C2   109.41  3.000
 GJY  H8   C3   C2   109.10  3.000
 GJY  C4   C3   C2   112.76  3.000
 GJY  H11  C4   H10  106.08  3.000
 GJY  H11  C4   C5   109.24  3.000
 GJY  H10  C4   C5   109.45  3.000
 GJY  H11  C4   C3   109.36  3.000
 GJY  H10  C4   C3   109.47  3.000
 GJY  C5   C4   C3   113.01  3.000
 GJY  H13  C5   H12  106.04  3.000
 GJY  H13  C5   C6   109.49  3.000
 GJY  H12  C5   C6   109.34  3.000
 GJY  H13  C5   C4   109.46  3.000
 GJY  H12  C5   C4   109.17  3.000
 GJY  C6   C5   C4   113.09  3.000
 GJY  H15  C6   H14  106.00  3.000
 GJY  H15  C6   C7   109.14  3.000
 GJY  H14  C6   C7   109.47  3.000
 GJY  H15  C6   C5   109.30  3.000
 GJY  H14  C6   C5   109.47  3.000
 GJY  C7   C6   C5   113.20  3.000
 GJY  H17  C7   H16  106.11  3.000
 GJY  H17  C7   C8   109.34  3.000
 GJY  H16  C7   C8   109.37  3.000
 GJY  H17  C7   C6   109.77  3.000
 GJY  H16  C7   C6   109.27  3.000
 GJY  C8   C7   C6   112.76  3.000
 GJY  H19  C8   H18  106.02  3.000
 GJY  H19  C8   C9   108.64  3.000
 GJY  H18  C8   C9   111.64  3.000
 GJY  H19  C8   C7   108.45  3.000
 GJY  H18  C8   C7   109.53  3.000
 GJY  C9   C8   C7   112.31  3.000
 GJY  H20  C9   C10  117.09  3.000
 GJY  H20  C9   C8   114.68  3.000
 GJY  C10  C9   C8   128.23  3.000
 GJY  H21  C10  C11  114.52  3.000
 GJY  H21  C10  C9   117.73  3.000
 GJY  C11  C10  C9   127.72  3.000
 GJY  H23  C11  H22  106.58  3.000
 GJY  H23  C11  C12  109.29  3.000
 GJY  H22  C11  C12  110.66  3.000
 GJY  H23  C11  C10  111.00  3.000
 GJY  H22  C11  C10  109.17  3.000
 GJY  C12  C11  C10  110.10  3.000
 GJY  H24  C12  C13  117.79  3.000
 GJY  H24  C12  C11  115.07  3.000
 GJY  C13  C12  C11  127.10  3.000
 GJY  H25  C13  C14  114.95  3.000
 GJY  H25  C13  C12  117.79  3.000
 GJY  C14  C13  C12  127.26  3.000
 GJY  H27  C14  H26  106.20  3.000
 GJY  H27  C14  C15  109.30  3.000
 GJY  H26  C14  C15  110.55  3.000
 GJY  H27  C14  C13  110.71  3.000
 GJY  H26  C14  C13  108.97  3.000
 GJY  C15  C14  C13  111.00  3.000
 GJY  H28  C15  C16  117.97  3.000
 GJY  H28  C15  C14  114.88  3.000
 GJY  C16  C15  C14  127.13  3.000
 GJY  H29  C16  C17  114.92  3.000
 GJY  H29  C16  C15  117.44  3.000
 GJY  C17  C16  C15  127.63  3.000
 GJY  H31  C17  H30  106.23  3.000
 GJY  H31  C17  C18  109.66  3.000
 GJY  H30  C17  C18  108.86  3.000
 GJY  H31  C17  C16  111.17  3.000
 GJY  H30  C17  C16  108.82  3.000
 GJY  C18  C17  C16  111.91  3.000
 GJY  H34  C18  H33  107.67  3.000
 GJY  H34  C18  H32  107.92  3.000
 GJY  H33  C18  H32  107.66  3.000
 GJY  H34  C18  C17  111.08  3.000
 GJY  H33  C18  C17  111.32  3.000
 GJY  H32  C18  C17  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
 GJY  Var_01  C11  C10  C9   C8      1.54   0.0  2
 GJY  Var_02  C14  C13  C12  C11     1.65   0.0  2
 GJY  Var_03  C17  C16  C15  C14     1.54   0.0  2
 GJY  Var_04  C2   C1   P1   O1    -55.23  30.0  1
 GJY  Var_05  C3   C2   C1   P1    176.00  30.0  3
 GJY  Var_06  C1   P1   O2   CM    166.40  30.0  1
 GJY  Var_07  C4   C3   C2   C1    179.93  30.0  3
 GJY  Var_08  C5   C4   C3   C2    178.14  30.0  3
 GJY  Var_09  C6   C5   C4   C3   -179.75  30.0  3
 GJY  Var_10  C7   C6   C5   C4    178.20  30.0  3
 GJY  Var_11  C8   C7   C6   C5   -179.46  30.0  3
 GJY  Var_12  C9   C8   C7   C6    174.45  30.0  1
 GJY  Var_13  C10  C9   C8   C7    122.03  30.0  3
 GJY  Var_14  C12  C11  C10  C9    106.90  30.0  3
 GJY  Var_15  C13  C12  C11  C10   100.28  30.0  1
 GJY  Var_16  C15  C14  C13  C12   113.73  30.0  3
 GJY  Var_17  C16  C15  C14  C13   109.54  30.0  3
 GJY  Var_18  C18  C17  C16  C15   115.48  30.0  1
 GJY  Var_19  H1   CM   O2   P1    -56.70  30.0  3
 GJY  Var_20  H32  C18  C17  C16   -62.00  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
 GJY  chir_01  P1  O2  O1  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
 GJY  plan-1  C8   0.020
 GJY  plan-1  C9   0.020
 GJY  plan-1  C10  0.020
 GJY  plan-1  C11  0.020
 GJY  plan-1  H20  0.020
 GJY  plan-1  H21  0.020
 GJY  plan-2  C11  0.020
 GJY  plan-2  C12  0.020
 GJY  plan-2  C13  0.020
 GJY  plan-2  C14  0.020
 GJY  plan-2  H24  0.020
 GJY  plan-2  H25  0.020
 GJY  plan-3  C14  0.020
 GJY  plan-3  C15  0.020
 GJY  plan-3  C16  0.020
 GJY  plan-3  C17  0.020
 GJY  plan-3  H28  0.020
 GJY  plan-3  H29  0.020

