# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 03:27:38 2020
#   Inital geometry file: a 168 line input string
#   Ligand name: (2R)-2,3-bis(decanoyloxy)propyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)OC[C@H](CO[P](O)([O-])=O)OC(=O)CCCCCCCCC
#
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
 XPA  XPA  '(2R)-2,3-bis(decanoyloxy)propyl hydrogen phosphate'  ligand  76  32  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XPA
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
 XPA  O1   O  OP    -1  -0.806   -0.3423   3.8878  -2.7224
 XPA  O2   O  O      0  -0.810   -1.9045   4.7832  -0.8356
 XPA  P1   P  P      0   1.335   -1.1780   3.6560  -1.4997
 XPA  O3   O  OH1    0  -0.779   -2.2861   2.4901  -1.7965
 XPA  O4   O  O2     0  -0.610   -0.2650   2.8557  -0.3864
 XPA  C1   C  CH2    0  -0.165    0.3974   3.5586   0.6320
 XPA  C2   C  CH1    0  -0.052    0.7929   2.6193   1.7588
 XPA  C3   C  CH2    0  -0.195   -0.3633   2.0495   2.5503
 XPA  O5   O  O2     0  -0.443   -1.1508   1.2127   1.7122
 XPA  C4   C  C      0   0.606   -2.3871   0.9161   2.0906
 XPA  O6   O  O      0  -0.458   -2.8525   1.2433   3.1546
 XPA  C5   C  CH2    0  -0.590   -3.1141   0.1558   1.0164
 XPA  C6   C  CH2    0  -0.417   -4.4943  -0.3282   1.4288
 XPA  C7   C  CH2    0  -0.415   -5.2143  -1.0266   0.2822
 XPA  C8   C  CH2    0  -0.412   -6.5977  -1.5337   0.6690
 XPA  C9   C  CH2    0  -0.411   -7.3299  -2.2093  -0.4836
 XPA  C10  C  CH2    0  -0.411   -8.7138  -2.7207  -0.1025
 XPA  C11  C  CH2    0  -0.406   -9.4455  -3.3897  -1.2592
 XPA  C12  C  CH2    0  -0.418  -10.8359  -3.8904  -0.8870
 XPA  C13  C  CH3    0  -0.662  -11.5525  -4.5639  -2.0493
 XPA  O7   O  O2     0  -0.466    1.5585   1.5126   1.2702
 XPA  C14  C  C      0   0.611    2.8676   1.6579   1.0812
 XPA  O8   O  O      0  -0.451    3.4672   2.6775   1.3132
 XPA  C15  C  CH2    0  -0.584    3.4813   0.3970   0.5375
 XPA  C16  C  CH2    0  -0.417    5.0014   0.3926   0.5665
 XPA  C17  C  CH2    0  -0.415    5.5719  -0.9168   0.0364
 XPA  C18  C  CH2    0  -0.412    7.0936  -0.9643   0.0818
 XPA  C19  C  CH2    0  -0.411    7.6657  -2.2766  -0.4396
 XPA  C20  C  CH2    0  -0.411    9.1866  -2.3387  -0.3781
 XPA  C21  C  CH2    0  -0.406    9.7549  -3.6547  -0.8943
 XPA  C22  C  CH2    0  -0.419   11.2751  -3.7272  -0.8222
 XPA  C23  C  CH3    0  -0.662   11.8280  -5.0497  -1.3355
 XPA  H1   H  HOH1   0   0.464   -1.9578   1.7981  -2.3807
 XPA  H2   H  HCH2   0   0.222   -0.2320   4.3426   1.0663
 XPA  H3   H  HCH2   0   0.223    1.2984   4.0518   0.2488
 XPA  H4   H  HCH1   0   0.269    1.3839   3.2057   2.4696
 XPA  H5   H  HCH2   0   0.246   -0.9518   2.8811   2.9440
 XPA  H6   H  HCH2   0   0.255    0.0126   1.4760   3.4021
 XPA  H7   H  HCH2   0   0.267   -2.4901  -0.6845   0.6966
 XPA  H8   H  HCH2   0   0.278   -3.1779   0.8163   0.1449
 XPA  H9   H  HCH2   0   0.222   -4.4089  -1.0133   2.2770
 XPA  H10  H  HCH2   0   0.223   -5.0972   0.5166   1.7724
 XPA  H11  H  HCH2   0   0.211   -4.6083  -1.8660  -0.0764
 XPA  H12  H  HCH2   0   0.211   -5.3048  -0.3350  -0.5624
 XPA  H13  H  HCH2   0   0.208   -7.1997  -0.6971   1.0411
 XPA  H14  H  HCH2   0   0.208   -6.5058  -2.2370   1.5037
 XPA  H15  H  HCH2   0   0.206   -6.7261  -3.0434  -0.8586
 XPA  H16  H  HCH2   0   0.207   -7.4219  -1.5034  -1.3163
 XPA  H17  H  HCH2   0   0.206   -9.3166  -1.8875   0.2757
 XPA  H18  H  HCH2   0   0.206   -8.6223  -3.4299   0.7274
 XPA  H19  H  HCH2   0   0.205   -8.8465  -4.2287  -1.6313
 XPA  H20  H  HCH2   0   0.206   -9.5281  -2.6838  -2.0930
 XPA  H21  H  HCH2   0   0.209  -11.4355  -3.0513  -0.5200
 XPA  H22  H  HCH2   0   0.210  -10.7555  -4.5925  -0.0515
 XPA  H23  H  HCH3   0   0.216  -10.9968  -5.4356  -2.3999
 XPA  H24  H  HCH3   0   0.225  -12.5501  -4.9016  -1.7660
 XPA  H25  H  HCH3   0   0.215  -11.6617  -3.8823  -2.8951
 XPA  H26  H  HCH2   0   0.268    3.0828  -0.4565   1.0930
 XPA  H27  H  HCH2   0   0.277    3.1203   0.2706  -0.4896
 XPA  H28  H  HCH2   0   0.225    5.3904   1.2252  -0.0250
 XPA  H29  H  HCH2   0   0.224    5.3494   0.5517   1.5910
 XPA  H30  H  HCH2   0   0.212    5.1659  -1.7527   0.6168
 XPA  H31  H  HCH2   0   0.212    5.2337  -1.0719  -0.9941
 XPA  H32  H  HCH2   0   0.209    7.5027  -0.1314  -0.5006
 XPA  H33  H  HCH2   0   0.208    7.4296  -0.8064   1.1127
 XPA  H34  H  HCH2   0   0.207    7.2453  -3.1085   0.1366
 XPA  H35  H  HCH2   0   0.207    7.3375  -2.4300  -1.4737
 XPA  H36  H  HCH2   0   0.206    9.6089  -1.5085  -0.9554
 XPA  H37  H  HCH2   0   0.206    9.5136  -2.1837   0.6563
 XPA  H38  H  HCH2   0   0.205    9.3253  -4.4845  -0.3216
 XPA  H39  H  HCH2   0   0.205    9.4345  -3.8073  -1.9312
 XPA  H40  H  HCH2   0   0.210   11.7044  -2.9010  -1.3979
 XPA  H41  H  HCH2   0   0.209   11.5959  -3.5726   0.2130
 XPA  H42  H  HCH3   0   0.216   11.5691  -5.2046  -2.3845
 XPA  H43  H  HCH3   0   0.225   12.9150  -5.0902  -1.2553
 XPA  H44  H  HCH3   0   0.215   11.4229  -5.8910  -0.7697

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
 XPA  O1   P1   single  1.499  0.020  1.499
 XPA  O2   P1   double  1.496  0.020  1.496
 XPA  P1   O3   single  1.636  0.020  1.636
 XPA  P1   O4   single  1.647  0.020  1.647
 XPA  O3   H1   single  0.850  0.020  0.980
 XPA  O4   C1   single  1.404  0.020  1.404
 XPA  C1   C2   single  1.519  0.020  1.519
 XPA  C1   H2   single  0.970  0.020  1.090
 XPA  C1   H3   single  0.970  0.020  1.090
 XPA  C2   C3   single  1.513  0.020  1.513
 XPA  C2   O7   single  1.432  0.020  1.432
 XPA  C2   H4   single  0.970  0.020  1.090
 XPA  C3   O5   single  1.422  0.020  1.422
 XPA  C3   H5   single  0.970  0.020  1.090
 XPA  C3   H6   single  0.970  0.020  1.090
 XPA  O5   C4   single  1.326  0.020  1.326
 XPA  C4   O6   double  1.207  0.020  1.207
 XPA  C4   C5   single  1.503  0.020  1.503
 XPA  C5   C6   single  1.520  0.020  1.520
 XPA  C5   H7   single  0.970  0.020  1.090
 XPA  C5   H8   single  0.970  0.020  1.090
 XPA  C6   C7   single  1.523  0.020  1.523
 XPA  C6   H9   single  0.970  0.020  1.090
 XPA  C6   H10  single  0.970  0.020  1.090
 XPA  C7   C8   single  1.523  0.020  1.523
 XPA  C7   H11  single  0.970  0.020  1.090
 XPA  C7   H12  single  0.970  0.020  1.090
 XPA  C8   C9   single  1.523  0.020  1.523
 XPA  C8   H13  single  0.970  0.020  1.090
 XPA  C8   H14  single  0.970  0.020  1.090
 XPA  C9   C10  single  1.524  0.020  1.524
 XPA  C9   H15  single  0.970  0.020  1.090
 XPA  C9   H16  single  0.970  0.020  1.090
 XPA  C10  C11  single  1.523  0.020  1.523
 XPA  C10  H17  single  0.970  0.020  1.090
 XPA  C10  H18  single  0.970  0.020  1.090
 XPA  C11  C12  single  1.524  0.020  1.524
 XPA  C11  H19  single  0.970  0.020  1.090
 XPA  C11  H20  single  0.970  0.020  1.090
 XPA  C12  C13  single  1.523  0.020  1.523
 XPA  C12  H21  single  0.970  0.020  1.090
 XPA  C12  H22  single  0.970  0.020  1.090
 XPA  C13  H23  single  0.970  0.020  1.090
 XPA  C13  H24  single  0.970  0.020  1.090
 XPA  C13  H25  single  0.970  0.020  1.090
 XPA  O7   C14  single  1.331  0.020  1.331
 XPA  C14  O8   double  1.205  0.020  1.205
 XPA  C14  C15  single  1.504  0.020  1.504
 XPA  C15  C16  single  1.520  0.020  1.520
 XPA  C15  H26  single  0.970  0.020  1.090
 XPA  C15  H27  single  0.970  0.020  1.090
 XPA  C16  C17  single  1.523  0.020  1.523
 XPA  C16  H28  single  0.970  0.020  1.090
 XPA  C16  H29  single  0.970  0.020  1.090
 XPA  C17  C18  single  1.523  0.020  1.523
 XPA  C17  H30  single  0.970  0.020  1.090
 XPA  C17  H31  single  0.970  0.020  1.090
 XPA  C18  C19  single  1.524  0.020  1.524
 XPA  C18  H32  single  0.970  0.020  1.090
 XPA  C18  H33  single  0.970  0.020  1.090
 XPA  C19  C20  single  1.523  0.020  1.523
 XPA  C19  H34  single  0.970  0.020  1.090
 XPA  C19  H35  single  0.970  0.020  1.090
 XPA  C20  C21  single  1.524  0.020  1.524
 XPA  C20  H36  single  0.970  0.020  1.090
 XPA  C20  H37  single  0.970  0.020  1.090
 XPA  C21  C22  single  1.524  0.020  1.524
 XPA  C21  H38  single  0.970  0.020  1.090
 XPA  C21  H39  single  0.970  0.020  1.090
 XPA  C22  C23  single  1.523  0.020  1.523
 XPA  C22  H40  single  0.970  0.020  1.090
 XPA  C22  H41  single  0.970  0.020  1.090
 XPA  C23  H42  single  0.970  0.020  1.090
 XPA  C23  H43  single  0.970  0.020  1.090
 XPA  C23  H44  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
 XPA  O4   P1   O3    98.73  3.000
 XPA  O4   P1   O2   109.58  3.000
 XPA  O3   P1   O2   106.77  3.000
 XPA  O4   P1   O1   108.50  3.000
 XPA  O3   P1   O1   109.87  3.000
 XPA  O2   P1   O1   121.08  3.000
 XPA  H1   O3   P1   113.03  3.000
 XPA  C1   O4   P1   120.57  3.000
 XPA  H3   C1   H2   106.79  3.000
 XPA  H3   C1   C2   108.86  3.000
 XPA  H2   C1   C2   107.34  3.000
 XPA  H3   C1   O4   111.08  3.000
 XPA  H2   C1   O4   112.02  3.000
 XPA  C2   C1   O4   110.57  3.000
 XPA  H4   C2   O7   110.31  3.000
 XPA  H4   C2   C3   105.94  3.000
 XPA  O7   C2   C3   107.22  3.000
 XPA  H4   C2   C1   106.92  3.000
 XPA  O7   C2   C1   111.35  3.000
 XPA  C3   C2   C1   114.96  3.000
 XPA  H6   C3   H5   107.68  3.000
 XPA  H6   C3   O5   109.93  3.000
 XPA  H5   C3   O5   111.22  3.000
 XPA  H6   C3   C2   110.03  3.000
 XPA  H5   C3   C2   108.28  3.000
 XPA  O5   C3   C2   109.66  3.000
 XPA  C4   O5   C3   118.65  3.000
 XPA  C5   C4   O6   125.50  3.000
 XPA  C5   C4   O5   111.10  3.000
 XPA  O6   C4   O5   123.40  3.000
 XPA  H8   C5   H7   105.29  3.000
 XPA  H8   C5   C6   110.80  3.000
 XPA  H7   C5   C6   110.64  3.000
 XPA  H8   C5   C4   106.96  3.000
 XPA  H7   C5   C4   108.75  3.000
 XPA  C6   C5   C4   113.98  3.000
 XPA  H10  C6   H9   106.45  3.000
 XPA  H10  C6   C7   109.28  3.000
 XPA  H9   C6   C7   109.48  3.000
 XPA  H10  C6   C5   109.88  3.000
 XPA  H9   C6   C5   109.82  3.000
 XPA  C7   C6   C5   111.78  3.000
 XPA  H12  C7   H11  106.08  3.000
 XPA  H12  C7   C8   109.33  3.000
 XPA  H11  C7   C8   109.29  3.000
 XPA  H12  C7   C6   109.27  3.000
 XPA  H11  C7   C6   109.64  3.000
 XPA  C8   C7   C6   113.00  3.000
 XPA  H14  C8   H13  106.11  3.000
 XPA  H14  C8   C9   109.40  3.000
 XPA  H13  C8   C9   109.36  3.000
 XPA  H14  C8   C7   109.33  3.000
 XPA  H13  C8   C7   109.33  3.000
 XPA  C9   C8   C7   113.08  3.000
 XPA  H16  C9   H15  106.06  3.000
 XPA  H16  C9   C10  109.27  3.000
 XPA  H15  C9   C10  109.30  3.000
 XPA  H16  C9   C8   109.25  3.000
 XPA  H15  C9   C8   109.37  3.000
 XPA  C10  C9   C8   113.34  3.000
 XPA  H18  C10  H17  106.07  3.000
 XPA  H18  C10  C11  109.33  3.000
 XPA  H17  C10  C11  109.37  3.000
 XPA  H18  C10  C9   109.32  3.000
 XPA  H17  C10  C9   109.31  3.000
 XPA  C11  C10  C9   113.18  3.000
 XPA  H20  C11  H19  106.03  3.000
 XPA  H20  C11  C12  109.20  3.000
 XPA  H19  C11  C12  109.27  3.000
 XPA  H20  C11  C10  109.34  3.000
 XPA  H19  C11  C10  109.36  3.000
 XPA  C12  C11  C10  113.39  3.000
 XPA  H22  C12  H21  106.03  3.000
 XPA  H22  C12  C13  109.49  3.000
 XPA  H21  C12  C13  109.71  3.000
 XPA  H22  C12  C11  109.28  3.000
 XPA  H21  C12  C11  109.26  3.000
 XPA  C13  C12  C11  112.85  3.000
 XPA  H25  C13  H24  107.64  3.000
 XPA  H25  C13  H23  107.50  3.000
 XPA  H24  C13  H23  107.57  3.000
 XPA  H25  C13  C12  111.24  3.000
 XPA  H24  C13  C12  111.66  3.000
 XPA  H23  C13  C12  111.03  3.000
 XPA  C14  O7   C2   119.35  3.000
 XPA  C15  C14  O8   125.15  3.000
 XPA  C15  C14  O7   111.18  3.000
 XPA  O8   C14  O7   123.67  3.000
 XPA  H27  C15  H26  105.43  3.000
 XPA  H27  C15  C16  110.30  3.000
 XPA  H26  C15  C16  110.63  3.000
 XPA  H27  C15  C14  107.52  3.000
 XPA  H26  C15  C14  108.78  3.000
 XPA  C16  C15  C14  113.80  3.000
 XPA  H29  C16  H28  106.43  3.000
 XPA  H29  C16  C17  109.38  3.000
 XPA  H28  C16  C17  109.46  3.000
 XPA  H29  C16  C15  109.61  3.000
 XPA  H28  C16  C15  110.08  3.000
 XPA  C17  C16  C15  111.73  3.000
 XPA  H31  C17  H30  106.01  3.000
 XPA  H31  C17  C18  109.40  3.000
 XPA  H30  C17  C18  109.31  3.000
 XPA  H31  C17  C16  109.47  3.000
 XPA  H30  C17  C16  109.42  3.000
 XPA  C18  C17  C16  112.99  3.000
 XPA  H33  C18  H32  106.02  3.000
 XPA  H33  C18  C19  109.33  3.000
 XPA  H32  C18  C19  109.43  3.000
 XPA  H33  C18  C17  109.27  3.000
 XPA  H32  C18  C17  109.48  3.000
 XPA  C19  C18  C17  113.07  3.000
 XPA  H35  C19  H34  105.96  3.000
 XPA  H35  C19  C20  109.35  3.000
 XPA  H34  C19  C20  109.32  3.000
 XPA  H35  C19  C18  109.34  3.000
 XPA  H34  C19  C18  109.27  3.000
 XPA  C20  C19  C18  113.34  3.000
 XPA  H37  C20  H36  105.97  3.000
 XPA  H37  C20  C21  109.31  3.000
 XPA  H36  C20  C21  109.40  3.000
 XPA  H37  C20  C19  109.28  3.000
 XPA  H36  C20  C19  109.43  3.000
 XPA  C21  C20  C19  113.20  3.000
 XPA  H39  C21  H38  105.93  3.000
 XPA  H39  C21  C22  109.25  3.000
 XPA  H38  C21  C22  109.29  3.000
 XPA  H39  C21  C20  109.38  3.000
 XPA  H38  C21  C20  109.32  3.000
 XPA  C22  C21  C20  113.41  3.000
 XPA  H41  C22  H40  106.01  3.000
 XPA  H41  C22  C23  109.58  3.000
 XPA  H40  C22  C23  109.63  3.000
 XPA  H41  C22  C21  109.29  3.000
 XPA  H40  C22  C21  109.30  3.000
 XPA  C23  C22  C21  112.81  3.000
 XPA  H44  C23  H43  107.64  3.000
 XPA  H44  C23  H42  107.49  3.000
 XPA  H43  C23  H42  107.57  3.000
 XPA  H44  C23  C22  111.09  3.000
 XPA  H43  C23  C22  111.68  3.000
 XPA  H42  C23  C22  111.17  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
 XPA  Var_01  C2   C1   O4   P1    162.12  30.0  3
 XPA  Var_02  O8   C14  O7   C2      0.87  30.0  3
 XPA  Var_03  O6   C4   O5   C3     -5.24  30.0  3
 XPA  Var_04  C6   C5   C4   O5    174.72  30.0  3
 XPA  Var_05  C7   C6   C5   C4    176.99  30.0  3
 XPA  Var_06  C8   C7   C6   C5    179.53  30.0  3
 XPA  Var_07  C9   C8   C7   C6    178.92  30.0  3
 XPA  Var_08  C10  C9   C8   C7    179.91  30.0  3
 XPA  Var_09  C11  C10  C9   C8    179.72  30.0  3
 XPA  Var_10  C12  C11  C10  C9   -179.41  30.0  3
 XPA  Var_11  C13  C12  C11  C10  -179.66  30.0  3
 XPA  Var_12  C16  C15  C14  O7   -168.10  30.0  3
 XPA  Var_13  C17  C16  C15  C14   178.67  30.0  3
 XPA  Var_14  C18  C17  C16  C15  -178.71  30.0  3
 XPA  Var_15  C19  C18  C17  C16   179.63  30.0  3
 XPA  Var_16  C20  C19  C18  C17  -179.16  30.0  3
 XPA  Var_17  C21  C20  C19  C18   179.73  30.0  3
 XPA  Var_18  C22  C21  C20  C19  -179.43  30.0  3
 XPA  Var_19  C23  C22  C21  C20   179.75  30.0  3
 XPA  Var_20  H5   C3   O5   C4    -41.96  30.0  1
 XPA  Var_21  H23  C13  C12  C11    60.78  30.0  3
 XPA  Var_22  H42  C23  C22  C21    61.10  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
 XPA  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
 XPA  plan-1  O5   0.020
 XPA  plan-1  C4   0.020
 XPA  plan-1  O6   0.020
 XPA  plan-1  C5   0.020
 XPA  plan-2  O7   0.020
 XPA  plan-2  C14  0.020
 XPA  plan-2  O8   0.020
 XPA  plan-2  C15  0.020

