# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:35:56 2020
#   Inital geometry file: a 166 line input string
#   Ligand name: (2R)-2,3-bis(octanoyloxy)propyl (2R)-2,3-dihydroxypropyl phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@H](CO[P]([O-])(=O)OC[C@H](O)CO)OC(=O)CCCCCCC
#
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
 PG8  PG8  '(2R)-2,3-bis(octanoyloxy)propyl (2R)-2,3-dihydroxypropyl phosphate'  ligand  75  33  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PG8
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
 PG8  O1   O  OP    -1  -0.797    0.1608  -2.6875   1.2539
 PG8  O2   O  O      0  -0.796    2.2538  -1.6291   2.3452
 PG8  P1   P  P      0   1.371    1.0745  -1.5114   1.4293
 PG8  O3   O  O2     0  -0.611    1.5490  -0.9417  -0.0352
 PG8  C1   C  CH2    0  -0.163    2.5870  -1.6504  -0.6779
 PG8  C2   C  CH1    0  -0.054    2.8421  -1.0468  -2.0488
 PG8  C3   C  CH2    0  -0.170    4.0501  -1.7187  -2.6825
 PG8  O4   O  OH1    0  -0.666    4.3525  -1.0725  -3.8958
 PG8  O5   O  OH1    0  -0.657    1.7047  -1.0903  -2.8769
 PG8  O6   O  O2     0  -0.608    0.1878  -0.1750   1.7832
 PG8  C4   C  CH2    0  -0.184   -0.6103  -0.2232   2.9444
 PG8  C5   C  CH1    0  -0.021   -1.4600   1.0322   3.0450
 PG8  C6   C  CH2    0  -0.232   -0.7014   2.3109   3.3387
 PG8  O7   O  O2     0  -0.466    0.2485   2.6166   2.3259
 PG8  C7   C  C      0   0.631    1.5203   2.2434   2.4941
 PG8  O8   O  O      0  -0.453    1.9660   1.8428   3.5381
 PG8  C8   C  CH2    0  -0.581    2.3064   2.4332   1.2299
 PG8  C9   C  CH2    0  -0.429    3.6656   1.7534   1.2427
 PG8  C10  C  CH2    0  -0.428    4.3978   1.9664  -0.0761
 PG8  C11  C  CH2    0  -0.423    5.5959   1.0454  -0.2610
 PG8  C12  C  CH2    0  -0.416    6.2477   1.1845  -1.6303
 PG8  C13  C  CH2    0  -0.423    7.4174   0.2321  -1.8451
 PG8  C14  C  CH3    0  -0.662    7.9969   0.3234  -3.2497
 PG8  O9   O  O2     0  -0.466   -2.1906   1.2483   1.8316
 PG8  C15  C  C      0   0.611   -3.3332   0.5952   1.6377
 PG8  O10  O  O      0  -0.452   -3.8066  -0.1716   2.4388
 PG8  C16  C  CH2    0  -0.583   -3.9395   0.9287   0.3020
 PG8  C17  C  CH2    0  -0.418   -5.4140   0.5677   0.2018
 PG8  C18  C  CH2    0  -0.415   -6.0083   0.9506  -1.1476
 PG8  C19  C  CH2    0  -0.412   -7.4976   0.6423  -1.2411
 PG8  C20  C  CH2    0  -0.406   -8.1117   1.0378  -2.5779
 PG8  C21  C  CH2    0  -0.418   -9.6069   0.7537  -2.6609
 PG8  C22  C  CH3    0  -0.663  -10.2116   1.1608  -3.9974
 PG8  H1   H  HCH2   0   0.212    3.5098  -1.6094  -0.0887
 PG8  H2   H  HCH2   0   0.209    2.3281  -2.7131  -0.7921
 PG8  H3   H  HCH1   0   0.234    3.0739   0.0161  -1.9208
 PG8  H4   H  HCH2   0   0.199    4.8908  -1.6662  -1.9784
 PG8  H5   H  HCH2   0   0.205    3.8345  -2.7864  -2.8378
 PG8  H6   H  HOH1   0   0.456    5.1290  -1.4963  -4.2717
 PG8  H7   H  HOH1   0   0.442    1.4582  -2.0120  -3.0115
 PG8  H8   H  HCH2   0   0.228   -0.0010  -0.2897   3.8535
 PG8  H9   H  HCH2   0   0.235   -1.2659  -1.0991   2.9295
 PG8  H10  H  HCH1   0   0.267   -2.1504   0.8911   3.8826
 PG8  H11  H  HCH2   0   0.250   -0.2333   2.2275   4.3200
 PG8  H12  H  HCH2   0   0.264   -1.3989   3.1482   3.3729
 PG8  H13  H  HCH2   0   0.268    2.4107   3.5092   1.0505
 PG8  H14  H  HCH2   0   0.262    1.7118   2.0458   0.3995
 PG8  H15  H  HCH2   0   0.240    3.5210   0.6849   1.4196
 PG8  H16  H  HCH2   0   0.218    4.2744   2.1286   2.0689
 PG8  H17  H  HCH2   0   0.218    4.7168   3.0108  -0.1600
 PG8  H18  H  HCH2   0   0.212    3.6982   1.8048  -0.9032
 PG8  H19  H  HCH2   0   0.205    5.2695   0.0079  -0.1237
 PG8  H20  H  HCH2   0   0.214    6.3361   1.2327   0.5248
 PG8  H21  H  HCH2   0   0.210    6.5873   2.2166  -1.7722
 PG8  H22  H  HCH2   0   0.211    5.4961   1.0034  -2.4068
 PG8  H23  H  HCH2   0   0.210    7.0866  -0.7942  -1.6544
 PG8  H24  H  HCH2   0   0.213    8.1981   0.4382  -1.1064
 PG8  H25  H  HCH3   0   0.226    8.8327  -0.3632  -3.3885
 PG8  H26  H  HCH3   0   0.212    7.2402   0.0786  -3.9981
 PG8  H27  H  HCH3   0   0.216    8.3559   1.3317  -3.4642
 PG8  H28  H  HCH2   0   0.265   -3.7857   1.9902   0.0934
 PG8  H29  H  HCH2   0   0.278   -3.3654   0.3916  -0.4618
 PG8  H30  H  HCH2   0   0.226   -5.5470  -0.5040   0.3682
 PG8  H31  H  HCH2   0   0.224   -5.9686   1.0760   0.9958
 PG8  H32  H  HCH2   0   0.212   -5.8492   2.0194  -1.3274
 PG8  H33  H  HCH2   0   0.213   -5.4754   0.4250  -1.9474
 PG8  H34  H  HCH2   0   0.209   -7.6590  -0.4273  -1.0676
 PG8  H35  H  HCH2   0   0.208   -8.0234   1.1631  -0.4331
 PG8  H36  H  HCH2   0   0.206   -7.9374   2.1047  -2.7565
 PG8  H37  H  HCH2   0   0.207   -7.5970   0.5080  -3.3872
 PG8  H38  H  HCH2   0   0.210   -9.7828  -0.3122  -2.4862
 PG8  H39  H  HCH2   0   0.210  -10.1188   1.2817  -1.8503
 PG8  H40  H  HCH3   0   0.216   -9.7384   0.6266  -4.8235
 PG8  H41  H  HCH3   0   0.226  -11.2809   0.9498  -4.0371
 PG8  H42  H  HCH3   0   0.216  -10.0800   2.2292  -4.1794

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
 PG8  O1   P1   deloc   1.500  0.020  1.500
 PG8  O2   P1   deloc   1.498  0.020  1.498
 PG8  P1   O3   single  1.642  0.020  1.642
 PG8  P1   O6   single  1.642  0.020  1.642
 PG8  O3   C1   single  1.412  0.020  1.412
 PG8  C1   C2   single  1.519  0.020  1.519
 PG8  C1   H1   single  0.970  0.020  1.090
 PG8  C1   H2   single  0.970  0.020  1.090
 PG8  C2   C3   single  1.521  0.020  1.521
 PG8  C2   O5   single  1.408  0.020  1.408
 PG8  C2   H3   single  0.970  0.020  1.090
 PG8  C3   O4   single  1.408  0.020  1.408
 PG8  C3   H4   single  0.970  0.020  1.090
 PG8  C3   H5   single  0.970  0.020  1.090
 PG8  O4   H6   single  0.850  0.020  0.980
 PG8  O5   H7   single  0.850  0.020  0.980
 PG8  O6   C4   single  1.410  0.020  1.410
 PG8  C4   C5   single  1.519  0.020  1.519
 PG8  C4   H8   single  0.970  0.020  1.090
 PG8  C4   H9   single  0.970  0.020  1.090
 PG8  C5   C6   single  1.516  0.020  1.516
 PG8  C5   O9   single  1.433  0.020  1.433
 PG8  C5   H10  single  0.970  0.020  1.090
 PG8  C6   O7   single  1.422  0.020  1.422
 PG8  C6   H11  single  0.970  0.020  1.090
 PG8  C6   H12  single  0.970  0.020  1.090
 PG8  O7   C7   single  1.336  0.020  1.336
 PG8  C7   O8   double  1.204  0.020  1.204
 PG8  C7   C8   single  1.501  0.020  1.501
 PG8  C8   C9   single  1.520  0.020  1.520
 PG8  C8   H13  single  0.970  0.020  1.090
 PG8  C8   H14  single  0.970  0.020  1.090
 PG8  C9   C10  single  1.523  0.020  1.523
 PG8  C9   H15  single  0.970  0.020  1.090
 PG8  C9   H16  single  0.970  0.020  1.090
 PG8  C10  C11  single  1.522  0.020  1.522
 PG8  C10  H17  single  0.970  0.020  1.090
 PG8  C10  H18  single  0.970  0.020  1.090
 PG8  C11  C12  single  1.523  0.020  1.523
 PG8  C11  H19  single  0.970  0.020  1.090
 PG8  C11  H20  single  0.970  0.020  1.090
 PG8  C12  C13  single  1.524  0.020  1.524
 PG8  C12  H21  single  0.970  0.020  1.090
 PG8  C12  H22  single  0.970  0.020  1.090
 PG8  C13  C14  single  1.522  0.020  1.522
 PG8  C13  H23  single  0.970  0.020  1.090
 PG8  C13  H24  single  0.970  0.020  1.090
 PG8  C14  H25  single  0.970  0.020  1.090
 PG8  C14  H26  single  0.970  0.020  1.090
 PG8  C14  H27  single  0.970  0.020  1.090
 PG8  O9   C15  single  1.330  0.020  1.330
 PG8  C15  O10  double  1.206  0.020  1.206
 PG8  C15  C16  single  1.504  0.020  1.504
 PG8  C16  C17  single  1.521  0.020  1.521
 PG8  C16  H28  single  0.970  0.020  1.090
 PG8  C16  H29  single  0.970  0.020  1.090
 PG8  C17  C18  single  1.523  0.020  1.523
 PG8  C17  H30  single  0.970  0.020  1.090
 PG8  C17  H31  single  0.970  0.020  1.090
 PG8  C18  C19  single  1.524  0.020  1.524
 PG8  C18  H32  single  0.970  0.020  1.090
 PG8  C18  H33  single  0.970  0.020  1.090
 PG8  C19  C20  single  1.523  0.020  1.523
 PG8  C19  H34  single  0.970  0.020  1.090
 PG8  C19  H35  single  0.970  0.020  1.090
 PG8  C20  C21  single  1.524  0.020  1.524
 PG8  C20  H36  single  0.970  0.020  1.090
 PG8  C20  H37  single  0.970  0.020  1.090
 PG8  C21  C22  single  1.522  0.020  1.522
 PG8  C21  H38  single  0.970  0.020  1.090
 PG8  C21  H39  single  0.970  0.020  1.090
 PG8  C22  H40  single  0.970  0.020  1.090
 PG8  C22  H41  single  0.970  0.020  1.090
 PG8  C22  H42  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
 PG8  O6   P1   O3    93.78  3.000
 PG8  O6   P1   O2   110.93  3.000
 PG8  O3   P1   O2   110.20  3.000
 PG8  O6   P1   O1   109.54  3.000
 PG8  O3   P1   O1   110.12  3.000
 PG8  O2   P1   O1   119.32  3.000
 PG8  C1   O3   P1   116.39  3.000
 PG8  H2   C1   H1   106.88  3.000
 PG8  H2   C1   C2   109.25  3.000
 PG8  H1   C1   C2   109.20  3.000
 PG8  H2   C1   O3   111.05  3.000
 PG8  H1   C1   O3   110.84  3.000
 PG8  C2   C1   O3   109.56  3.000
 PG8  H3   C2   O5   105.65  3.000
 PG8  H3   C2   C3   108.01  3.000
 PG8  O5   C2   C3   112.53  3.000
 PG8  H3   C2   C1   108.40  3.000
 PG8  O5   C2   C1   112.51  3.000
 PG8  C3   C2   C1   109.50  3.000
 PG8  H5   C3   H4   106.68  3.000
 PG8  H5   C3   O4   111.46  3.000
 PG8  H4   C3   O4   111.50  3.000
 PG8  H5   C3   C2   109.38  3.000
 PG8  H4   C3   C2   108.66  3.000
 PG8  O4   C3   C2   109.09  3.000
 PG8  H6   O4   C3   107.95  3.000
 PG8  H7   O5   C2   108.57  3.000
 PG8  C4   O6   P1   117.08  3.000
 PG8  H9   C4   H8   107.19  3.000
 PG8  H9   C4   C5   109.10  3.000
 PG8  H8   C4   C5   107.82  3.000
 PG8  H9   C4   O6   110.82  3.000
 PG8  H8   C4   O6   111.74  3.000
 PG8  C5   C4   O6   110.06  3.000
 PG8  H10  C5   O9   110.24  3.000
 PG8  H10  C5   C6   106.03  3.000
 PG8  O9   C5   C6   106.98  3.000
 PG8  H10  C5   C4   107.27  3.000
 PG8  O9   C5   C4   110.72  3.000
 PG8  C6   C5   C4   115.47  3.000
 PG8  H12  C6   H11  107.76  3.000
 PG8  H12  C6   O7   106.54  3.000
 PG8  H11  C6   O7   111.76  3.000
 PG8  H12  C6   C5   109.50  3.000
 PG8  H11  C6   C5   108.95  3.000
 PG8  O7   C6   C5   112.20  3.000
 PG8  C7   O7   C6   119.09  3.000
 PG8  C8   C7   O8   125.36  3.000
 PG8  C8   C7   O7   110.93  3.000
 PG8  O8   C7   O7   123.68  3.000
 PG8  H14  C8   H13  106.00  3.000
 PG8  H14  C8   C9   109.55  3.000
 PG8  H13  C8   C9   110.82  3.000
 PG8  H14  C8   C7   108.08  3.000
 PG8  H13  C8   C7   108.18  3.000
 PG8  C9   C8   C7   113.88  3.000
 PG8  H16  C9   H15  106.69  3.000
 PG8  H16  C9   C10  109.80  3.000
 PG8  H15  C9   C10  109.91  3.000
 PG8  H16  C9   C8   110.55  3.000
 PG8  H15  C9   C8   108.69  3.000
 PG8  C10  C9   C8   111.10  3.000
 PG8  H18  C10  H17  105.60  3.000
 PG8  H18  C10  C11  108.77  3.000
 PG8  H17  C10  C11  109.78  3.000
 PG8  H18  C10  C9   109.03  3.000
 PG8  H17  C10  C9   109.85  3.000
 PG8  C11  C10  C9   113.50  3.000
 PG8  H20  C11  H19  105.85  3.000
 PG8  H20  C11  C12  109.89  3.000
 PG8  H19  C11  C12  109.06  3.000
 PG8  H20  C11  C10  109.95  3.000
 PG8  H19  C11  C10  108.84  3.000
 PG8  C12  C11  C10  113.00  3.000
 PG8  H22  C12  H21  106.05  3.000
 PG8  H22  C12  C13  108.87  3.000
 PG8  H21  C12  C13  109.43  3.000
 PG8  H22  C12  C11  109.18  3.000
 PG8  H21  C12  C11  109.58  3.000
 PG8  C13  C12  C11  113.47  3.000
 PG8  H24  C13  H23  105.93  3.000
 PG8  H24  C13  C14  109.88  3.000
 PG8  H23  C13  C14  109.39  3.000
 PG8  H24  C13  C12  109.55  3.000
 PG8  H23  C13  C12  109.23  3.000
 PG8  C14  C13  C12  112.64  3.000
 PG8  H27  C14  H26  107.47  3.000
 PG8  H27  C14  H25  107.72  3.000
 PG8  H26  C14  H25  107.62  3.000
 PG8  H27  C14  C13  111.22  3.000
 PG8  H26  C14  C13  110.81  3.000
 PG8  H25  C14  C13  111.81  3.000
 PG8  C15  O9   C5   119.17  3.000
 PG8  C16  C15  O10  124.94  3.000
 PG8  C16  C15  O9   111.51  3.000
 PG8  O10  C15  O9   123.55  3.000
 PG8  H29  C16  H28  105.62  3.000
 PG8  H29  C16  C17  110.21  3.000
 PG8  H28  C16  C17  110.75  3.000
 PG8  H29  C16  C15  107.40  3.000
 PG8  H28  C16  C15  109.16  3.000
 PG8  C17  C16  C15  113.36  3.000
 PG8  H31  C17  H30  106.47  3.000
 PG8  H31  C17  C18  109.17  3.000
 PG8  H30  C17  C18  109.51  3.000
 PG8  H31  C17  C16  109.47  3.000
 PG8  H30  C17  C16  109.92  3.000
 PG8  C18  C17  C16  112.14  3.000
 PG8  H33  C18  H32  106.13  3.000
 PG8  H33  C18  C19  109.48  3.000
 PG8  H32  C18  C19  109.23  3.000
 PG8  H33  C18  C17  109.65  3.000
 PG8  H32  C18  C17  109.51  3.000
 PG8  C19  C18  C17  112.63  3.000
 PG8  H35  C19  H34  106.05  3.000
 PG8  H35  C19  C20  109.29  3.000
 PG8  H34  C19  C20  109.45  3.000
 PG8  H35  C19  C18  109.12  3.000
 PG8  H34  C19  C18  109.38  3.000
 PG8  C20  C19  C18  113.29  3.000
 PG8  H37  C20  H36  106.00  3.000
 PG8  H37  C20  C21  109.29  3.000
 PG8  H36  C20  C21  109.18  3.000
 PG8  H37  C20  C19  109.47  3.000
 PG8  H36  C20  C19  109.37  3.000
 PG8  C21  C20  C19  113.26  3.000
 PG8  H39  C21  H38  106.05  3.000
 PG8  H39  C21  C22  109.60  3.000
 PG8  H38  C21  C22  109.68  3.000
 PG8  H39  C21  C20  109.18  3.000
 PG8  H38  C21  C20  109.30  3.000
 PG8  C22  C21  C20  112.81  3.000
 PG8  H42  C22  H41  107.55  3.000
 PG8  H42  C22  H40  107.49  3.000
 PG8  H41  C22  H40  107.63  3.000
 PG8  H42  C22  C21  111.11  3.000
 PG8  H41  C22  C21  111.70  3.000
 PG8  H40  C22  C21  111.18  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
 PG8  Var_01  C2   C1   O3   P1    176.52  30.0  3
 PG8  Var_02  C5   C4   O6   P1   -174.47  30.0  3
 PG8  Var_03  O6   P1   O3   C1    168.00  30.0  1
 PG8  Var_04  O10  C15  O9   C5      0.71  30.0  3
 PG8  Var_05  O8   C7   O7   C6    -11.86  30.0  3
 PG8  Var_06  C9   C8   C7   O7   -167.17  30.0  3
 PG8  Var_07  C10  C9   C8   C7    179.05  30.0  3
 PG8  Var_08  C11  C10  C9   C8   -165.91  30.0  3
 PG8  Var_09  C12  C11  C10  C9    175.10  30.0  3
 PG8  Var_10  C13  C12  C11  C10  -177.94  30.0  3
 PG8  Var_11  C14  C13  C12  C11   176.28  30.0  3
 PG8  Var_12  C17  C16  C15  O9   -162.19  30.0  3
 PG8  Var_13  C18  C17  C16  C15   178.48  30.0  3
 PG8  Var_14  C19  C18  C17  C16  -177.82  30.0  3
 PG8  Var_15  C20  C19  C18  C17   179.18  30.0  3
 PG8  Var_16  C21  C20  C19  C18  -178.89  30.0  3
 PG8  Var_17  C22  C21  C20  C19   179.64  30.0  3
 PG8  Var_18  H11  C6   O7   C7     26.94  30.0  1
 PG8  Var_19  H25  C14  C13  C12   179.98  30.0  3
 PG8  Var_20  H40  C22  C21  C20    59.76  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
 PG8  chir_01  C2  C1  C3  O5  negativ
 PG8  chir_02  C5  O9  C4  C6  negativ

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
 PG8  plan-1  O7   0.020
 PG8  plan-1  C7   0.020
 PG8  plan-1  O8   0.020
 PG8  plan-1  C8   0.020
 PG8  plan-2  O9   0.020
 PG8  plan-2  C15  0.020
 PG8  plan-2  O10  0.020
 PG8  plan-2  C16  0.020

