# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 13:54:04 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R)-2,3-bis(octanoyloxy)propyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@H](CO[P](O)([O-])=O)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
 PA8  PA8  '(2R)-2,3-bis(octanoyloxy)propyl hydrogen phosphate'  ligand  64  28  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PA8
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
 PA8  O1   O  OP    -1  -0.785    1.8446   2.1511  -1.4605
 PA8  O2   O  O      0  -0.809    0.7104   4.4906  -1.5021
 PA8  P1   P  P      0   1.326    0.6145   3.0003  -1.3637
 PA8  O3   O  OH1    0  -0.783   -0.4683   2.3809  -2.4157
 PA8  O4   O  O2     0  -0.606   -0.2033   2.6491   0.0239
 PA8  C1   C  CH2    0  -0.195    0.3974   2.9984   1.2465
 PA8  C2   C  CH1    0  -0.034    0.6530   1.7811   2.1248
 PA8  C3   C  CH2    0  -0.198   -0.5871   1.1265   2.6883
 PA8  O5   O  O2     0  -0.446   -1.3653   0.5747   1.6303
 PA8  C4   C  C      0   0.609   -2.5356   0.0328   1.9438
 PA8  O6   O  O      0  -0.457   -2.9743   0.0097   3.0675
 PA8  C5   C  CH2    0  -0.582   -3.2180  -0.5419   0.7325
 PA8  C6   C  CH2    0  -0.417   -4.6055  -1.0931   1.0193
 PA8  C7   C  CH2    0  -0.415   -5.2511  -1.6944  -0.2223
 PA8  C8   C  CH2    0  -0.412   -6.6444  -2.2481   0.0499
 PA8  C9   C  CH2    0  -0.406   -7.2992  -2.8632  -1.1799
 PA8  C10  C  CH2    0  -0.419   -8.6964  -3.4083  -0.9075
 PA8  C11  C  CH3    0  -0.662   -9.3393  -4.0299  -2.1395
 PA8  O7   O  O2     0  -0.465    1.3779   0.7720   1.4231
 PA8  C12  C  C      0   0.625    2.6898   0.9188   1.2519
 PA8  O8   O  O      0  -0.460    3.3233   1.8285   1.7265
 PA8  C13  C  CH2    0  -0.586    3.2623  -0.1926   0.4195
 PA8  C14  C  CH2    0  -0.420    4.7782  -0.2899   0.4881
 PA8  C15  C  CH2    0  -0.414    5.3161  -1.4135  -0.3887
 PA8  C16  C  CH2    0  -0.412    6.8317  -1.5489  -0.3155
 PA8  C17  C  CH2    0  -0.406    7.3795  -2.6638  -1.1972
 PA8  C18  C  CH2    0  -0.418    8.8947  -2.8051  -1.1174
 PA8  C19  C  CH3    0  -0.662    9.4347  -3.9219  -2.0000
 PA8  H1   H  HOH1   0   0.466   -1.2283   2.9571  -2.5516
 PA8  H2   H  HCH2   0   0.231   -0.2610   3.6753   1.8019
 PA8  H3   H  HCH2   0   0.228    1.3410   3.5349   1.1100
 PA8  H4   H  HCH1   0   0.262    1.2221   2.1277   2.9946
 PA8  H5   H  HCH2   0   0.245   -1.1559   1.8795   3.2392
 PA8  H6   H  HCH2   0   0.254   -0.3057   0.3407   3.3943
 PA8  H7   H  HCH2   0   0.274   -2.5730  -1.3277   0.3247
 PA8  H8   H  HCH2   0   0.270   -3.2596   0.2313  -0.0407
 PA8  H9   H  HCH2   0   0.224   -4.5446  -1.8552   1.8006
 PA8  H10  H  HCH2   0   0.224   -5.2454  -0.2979   1.4118
 PA8  H11  H  HCH2   0   0.212   -4.6131  -2.4934  -0.6163
 PA8  H12  H  HCH2   0   0.212   -5.3100  -0.9359  -1.0104
 PA8  H13  H  HCH2   0   0.208   -7.2820  -1.4464   0.4392
 PA8  H14  H  HCH2   0   0.208   -6.5847  -3.0005   0.8439
 PA8  H15  H  HCH2   0   0.206   -6.6648  -3.6695  -1.5652
 PA8  H16  H  HCH2   0   0.206   -7.3542  -2.1139  -1.9773
 PA8  H17  H  HCH2   0   0.210   -9.3302  -2.6008  -0.5275
 PA8  H18  H  HCH2   0   0.210   -8.6437  -4.1530  -0.1076
 PA8  H19  H  HCH3   0   0.216   -8.7462  -4.8680  -2.5104
 PA8  H20  H  HCH3   0   0.225  -10.3407  -4.4052  -1.9252
 PA8  H21  H  HCH3   0   0.215   -9.4252  -3.3039  -2.9503
 PA8  H22  H  HCH2   0   0.257    2.8010  -1.1388   0.7150
 PA8  H23  H  HCH2   0   0.279    2.9356  -0.0033  -0.6074
 PA8  H24  H  HCH2   0   0.222    5.2267   0.6574   0.1786
 PA8  H25  H  HCH2   0   0.220    5.0916  -0.4566   1.5229
 PA8  H26  H  HCH2   0   0.210    4.8528  -2.3617  -0.0944
 PA8  H27  H  HCH2   0   0.211    5.0152  -1.2389  -1.4275
 PA8  H28  H  HCH2   0   0.208    7.2952  -0.5984  -0.6022
 PA8  H29  H  HCH2   0   0.208    7.1293  -1.7297   0.7233
 PA8  H30  H  HCH2   0   0.206    6.9123  -3.6138  -0.9141
 PA8  H31  H  HCH2   0   0.206    7.0868  -2.4810  -2.2371
 PA8  H32  H  HCH2   0   0.210    9.3616  -1.8563  -1.4001
 PA8  H33  H  HCH2   0   0.210    9.1865  -2.9879  -0.0785
 PA8  H34  H  HCH3   0   0.225   10.5208  -3.9960  -1.9323
 PA8  H35  H  HCH3   0   0.216    9.0191  -4.8889  -1.7107
 PA8  H36  H  HCH3   0   0.215    9.1794  -3.7561  -3.0483

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
 PA8  O1   P1   single  1.498  0.020  1.498
 PA8  O2   P1   double  1.500  0.020  1.500
 PA8  P1   O3   single  1.632  0.020  1.632
 PA8  P1   O4   single  1.649  0.020  1.649
 PA8  O3   H1   single  0.850  0.020  0.980
 PA8  O4   C1   single  1.406  0.020  1.406
 PA8  C1   C2   single  1.523  0.020  1.523
 PA8  C1   H2   single  0.970  0.020  1.090
 PA8  C1   H3   single  0.970  0.020  1.090
 PA8  C2   C3   single  1.511  0.020  1.511
 PA8  C2   O7   single  1.427  0.020  1.427
 PA8  C2   H4   single  0.970  0.020  1.090
 PA8  C3   O5   single  1.425  0.020  1.425
 PA8  C3   H5   single  0.970  0.020  1.090
 PA8  C3   H6   single  0.970  0.020  1.090
 PA8  O5   C4   single  1.327  0.020  1.327
 PA8  C4   O6   double  1.207  0.020  1.207
 PA8  C4   C5   single  1.504  0.020  1.504
 PA8  C5   C6   single  1.520  0.020  1.520
 PA8  C5   H7   single  0.970  0.020  1.090
 PA8  C5   H8   single  0.970  0.020  1.090
 PA8  C6   C7   single  1.523  0.020  1.523
 PA8  C6   H9   single  0.970  0.020  1.090
 PA8  C6   H10  single  0.970  0.020  1.090
 PA8  C7   C8   single  1.524  0.020  1.524
 PA8  C7   H11  single  0.970  0.020  1.090
 PA8  C7   H12  single  0.970  0.020  1.090
 PA8  C8   C9   single  1.523  0.020  1.523
 PA8  C8   H13  single  0.970  0.020  1.090
 PA8  C8   H14  single  0.970  0.020  1.090
 PA8  C9   C10  single  1.524  0.020  1.524
 PA8  C9   H15  single  0.970  0.020  1.090
 PA8  C9   H16  single  0.970  0.020  1.090
 PA8  C10  C11  single  1.522  0.020  1.522
 PA8  C10  H17  single  0.970  0.020  1.090
 PA8  C10  H18  single  0.970  0.020  1.090
 PA8  C11  H19  single  0.970  0.020  1.090
 PA8  C11  H20  single  0.970  0.020  1.090
 PA8  C11  H21  single  0.970  0.020  1.090
 PA8  O7   C12  single  1.331  0.020  1.331
 PA8  C12  O8   double  1.206  0.020  1.206
 PA8  C12  C13  single  1.502  0.020  1.502
 PA8  C13  C14  single  1.521  0.020  1.521
 PA8  C13  H22  single  0.970  0.020  1.090
 PA8  C13  H23  single  0.970  0.020  1.090
 PA8  C14  C15  single  1.523  0.020  1.523
 PA8  C14  H24  single  0.970  0.020  1.090
 PA8  C14  H25  single  0.970  0.020  1.090
 PA8  C15  C16  single  1.523  0.020  1.523
 PA8  C15  H26  single  0.970  0.020  1.090
 PA8  C15  H27  single  0.970  0.020  1.090
 PA8  C16  C17  single  1.523  0.020  1.523
 PA8  C16  H28  single  0.970  0.020  1.090
 PA8  C16  H29  single  0.970  0.020  1.090
 PA8  C17  C18  single  1.524  0.020  1.524
 PA8  C17  H30  single  0.970  0.020  1.090
 PA8  C17  H31  single  0.970  0.020  1.090
 PA8  C18  C19  single  1.522  0.020  1.522
 PA8  C18  H32  single  0.970  0.020  1.090
 PA8  C18  H33  single  0.970  0.020  1.090
 PA8  C19  H34  single  0.970  0.020  1.090
 PA8  C19  H35  single  0.970  0.020  1.090
 PA8  C19  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
 PA8  O4   P1   O3    97.62  3.000
 PA8  O4   P1   O2   108.73  3.000
 PA8  O3   P1   O2   111.11  3.000
 PA8  O4   P1   O1   109.94  3.000
 PA8  O3   P1   O1   106.74  3.000
 PA8  O2   P1   O1   120.32  3.000
 PA8  H1   O3   P1   112.79  3.000
 PA8  C1   O4   P1   117.83  3.000
 PA8  H3   C1   H2   106.18  3.000
 PA8  H3   C1   C2   108.62  3.000
 PA8  H2   C1   C2   107.60  3.000
 PA8  H3   C1   O4   112.45  3.000
 PA8  H2   C1   O4   109.72  3.000
 PA8  C2   C1   O4   112.00  3.000
 PA8  H4   C2   O7   110.50  3.000
 PA8  H4   C2   C3   105.50  3.000
 PA8  O7   C2   C3   107.09  3.000
 PA8  H4   C2   C1   106.99  3.000
 PA8  O7   C2   C1   111.53  3.000
 PA8  C3   C2   C1   115.07  3.000
 PA8  H6   C3   H5   107.68  3.000
 PA8  H6   C3   O5   109.99  3.000
 PA8  H5   C3   O5   110.91  3.000
 PA8  H6   C3   C2   109.94  3.000
 PA8  H5   C3   C2   108.46  3.000
 PA8  O5   C3   C2   109.82  3.000
 PA8  C4   O5   C3   117.67  3.000
 PA8  C5   C4   O6   125.29  3.000
 PA8  C5   C4   O5   111.46  3.000
 PA8  O6   C4   O5   123.25  3.000
 PA8  H8   C5   H7   105.44  3.000
 PA8  H8   C5   C6   110.79  3.000
 PA8  H7   C5   C6   110.34  3.000
 PA8  H8   C5   C4   108.43  3.000
 PA8  H7   C5   C4   107.86  3.000
 PA8  C6   C5   C4   113.61  3.000
 PA8  H10  C6   H9   106.44  3.000
 PA8  H10  C6   C7   109.37  3.000
 PA8  H9   C6   C7   109.33  3.000
 PA8  H10  C6   C5   109.76  3.000
 PA8  H9   C6   C5   109.68  3.000
 PA8  C7   C6   C5   112.09  3.000
 PA8  H12  C7   H11  106.12  3.000
 PA8  H12  C7   C8   109.33  3.000
 PA8  H11  C7   C8   109.37  3.000
 PA8  H12  C7   C6   109.62  3.000
 PA8  H11  C7   C6   109.52  3.000
 PA8  C8   C7   C6   112.67  3.000
 PA8  H14  C8   H13  106.06  3.000
 PA8  H14  C8   C9   109.34  3.000
 PA8  H13  C8   C9   109.40  3.000
 PA8  H14  C8   C7   109.22  3.000
 PA8  H13  C8   C7   109.25  3.000
 PA8  C9   C8   C7   113.31  3.000
 PA8  H16  C9   H15  106.04  3.000
 PA8  H16  C9   C10  109.18  3.000
 PA8  H15  C9   C10  109.29  3.000
 PA8  H16  C9   C8   109.46  3.000
 PA8  H15  C9   C8   109.40  3.000
 PA8  C10  C9   C8   113.22  3.000
 PA8  H18  C10  H17  106.03  3.000
 PA8  H18  C10  C11  109.52  3.000
 PA8  H17  C10  C11  109.74  3.000
 PA8  H18  C10  C9   109.26  3.000
 PA8  H17  C10  C9   109.21  3.000
 PA8  C11  C10  C9   112.86  3.000
 PA8  H21  C11  H20  107.61  3.000
 PA8  H21  C11  H19  107.51  3.000
 PA8  H20  C11  H19  107.55  3.000
 PA8  H21  C11  C10  111.26  3.000
 PA8  H20  C11  C10  111.67  3.000
 PA8  H19  C11  C10  111.04  3.000
 PA8  C12  O7   C2   119.07  3.000
 PA8  C13  C12  O8   125.18  3.000
 PA8  C13  C12  O7   111.42  3.000
 PA8  O8   C12  O7   123.40  3.000
 PA8  H23  C13  H22  106.10  3.000
 PA8  H23  C13  C14  110.55  3.000
 PA8  H22  C13  C14  110.67  3.000
 PA8  H23  C13  C12  106.16  3.000
 PA8  H22  C13  C12  109.26  3.000
 PA8  C14  C13  C12  113.73  3.000
 PA8  H25  C14  H24  106.40  3.000
 PA8  H25  C14  C15  109.32  3.000
 PA8  H24  C14  C15  109.35  3.000
 PA8  H25  C14  C13  109.76  3.000
 PA8  H24  C14  C13  109.93  3.000
 PA8  C15  C14  C13  111.92  3.000
 PA8  H27  C15  H26  106.05  3.000
 PA8  H27  C15  C16  109.46  3.000
 PA8  H26  C15  C16  109.32  3.000
 PA8  H27  C15  C14  109.34  3.000
 PA8  H26  C15  C14  109.54  3.000
 PA8  C16  C15  C14  112.90  3.000
 PA8  H29  C16  H28  106.05  3.000
 PA8  H29  C16  C17  109.29  3.000
 PA8  H28  C16  C17  109.35  3.000
 PA8  H29  C16  C15  109.30  3.000
 PA8  H28  C16  C15  109.34  3.000
 PA8  C17  C16  C15  113.26  3.000
 PA8  H31  C17  H30  106.01  3.000
 PA8  H31  C17  C18  109.32  3.000
 PA8  H30  C17  C18  109.27  3.000
 PA8  H31  C17  C16  109.34  3.000
 PA8  H30  C17  C16  109.37  3.000
 PA8  C18  C17  C16  113.28  3.000
 PA8  H33  C18  H32  106.04  3.000
 PA8  H33  C18  C19  109.46  3.000
 PA8  H32  C18  C19  109.57  3.000
 PA8  H33  C18  C17  109.28  3.000
 PA8  H32  C18  C17  109.28  3.000
 PA8  C19  C18  C17  112.98  3.000
 PA8  H36  C19  H35  107.45  3.000
 PA8  H36  C19  H34  107.63  3.000
 PA8  H35  C19  H34  107.61  3.000
 PA8  H36  C19  C18  111.25  3.000
 PA8  H35  C19  C18  111.17  3.000
 PA8  H34  C19  C18  111.54  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
 PA8  Var_01  C2   C1   O4   P1   -119.02  30.0  3
 PA8  Var_02  O8   C12  O7   C2      4.42  30.0  3
 PA8  Var_03  O6   C4   O5   C3      1.41  30.0  3
 PA8  Var_04  C6   C5   C4   O5   -176.13  30.0  3
 PA8  Var_05  C7   C6   C5   C4   -178.69  30.0  3
 PA8  Var_06  C8   C7   C6   C5   -179.86  30.0  3
 PA8  Var_07  C9   C8   C7   C6   -179.54  30.0  3
 PA8  Var_08  C10  C9   C8   C7   -179.63  30.0  3
 PA8  Var_09  C11  C10  C9   C8   -179.59  30.0  3
 PA8  Var_10  C14  C13  C12  O7   -164.87  30.0  3
 PA8  Var_11  C15  C14  C13  C12  -179.01  30.0  3
 PA8  Var_12  C16  C15  C14  C13  -178.86  30.0  3
 PA8  Var_13  C17  C16  C15  C14  -179.58  30.0  3
 PA8  Var_14  C18  C17  C16  C15  -179.64  30.0  3
 PA8  Var_15  C19  C18  C17  C16   179.94  30.0  3
 PA8  Var_16  H5   C3   O5   C4    -56.01  30.0  1
 PA8  Var_17  H19  C11  C10  C9     60.49  30.0  3
 PA8  Var_18  H34  C19  C18  C17   179.46  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
 PA8  chir_01  C2  C1  C3  O7  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
 PA8  plan-1  O5   0.020
 PA8  plan-1  C4   0.020
 PA8  plan-1  O6   0.020
 PA8  plan-1  C5   0.020
 PA8  plan-2  O7   0.020
 PA8  plan-2  C12  0.020
 PA8  plan-2  O8   0.020
 PA8  plan-2  C13  0.020

