# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:13:58 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S)-2,3-dihydroxypropyl (2R)-2-(octanoyloxy)-3-(pentanoyloxy)propyl phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)O[C@H](COC(=O)CCCC)CO[P]([O-])(=O)OC[C@@H](O)CO
#
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
 AGA  AGA  '(2S)-2,3-dihydroxypropyl (2R)-2-(octanoyloxy)-3-(pentanoyloxy)propyl phosphate'  ligand  66  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AGA
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
 AGA  O1    O  OH1    0  -0.669    5.5316  -0.0280  -4.2882
 AGA  C1    C  CH2    0  -0.160    5.4009  -0.7875  -3.1112
 AGA  C2    C  CH1    0  -0.042    4.1064  -0.4036  -2.4118
 AGA  O2    O  OH1    0  -0.650    4.0678   0.9649  -2.0799
 AGA  C3    C  CH2    0  -0.159    3.9000  -1.2986  -1.2009
 AGA  P1    P  P      0   1.351    2.1095  -2.0339   0.5382
 AGA  O3    O  OP    -1  -0.794    1.4419  -3.1929  -0.1389
 AGA  O4    O  O      0  -0.804    3.1479  -2.2946   1.5862
 AGA  O5    O  O2     0  -0.604    2.6698  -0.9815  -0.5871
 AGA  O6    O  O2     0  -0.606    0.9709  -0.9925   1.0986
 AGA  C4    C  CH2    0  -0.169    0.2988  -1.3586   2.2802
 AGA  C5    C  CH1    0  -0.029   -0.8439  -0.4051   2.5577
 AGA  C6    C  CH2    0  -0.231   -0.4378   1.0168   2.8991
 AGA  O7    O  O2     0  -0.462    0.2171   1.6769   1.8218
 AGA  C7    C  C      0   0.628    1.5470   1.7843   1.8339
 AGA  O8    O  O      0  -0.456    2.2412   1.4058   2.7423
 AGA  C8    C  CH2    0  -0.586    2.0524   2.4576   0.5901
 AGA  C9    C  CH2    0  -0.417    3.4079   3.1277   0.7785
 AGA  C10   C  CH2    0  -0.433    3.7697   4.0336  -0.3925
 AGA  C11   C  CH3    0  -0.660    5.1474   4.6619  -0.2351
 AGA  O9    O  O2     0  -0.466   -1.7084  -0.4408   1.4168
 AGA  C12   C  C      0   0.612   -3.0097  -0.2113   1.5797
 AGA  O10   O  O      0  -0.451   -3.5103   0.0653   2.6408
 AGA  C13   C  CH2    0  -0.586   -3.7546  -0.3559   0.2810
 AGA  C14   C  CH2    0  -0.418   -5.2381  -0.0448   0.3873
 AGA  C15   C  CH2    0  -0.416   -5.9608  -0.2610  -0.9363
 AGA  C16   C  CH2    0  -0.412   -7.4505   0.0442  -0.8519
 AGA  C17   C  CH2    0  -0.407   -8.1896  -0.2001  -2.1610
 AGA  C18   C  CH2    0  -0.419   -9.6800   0.1045  -2.0764
 AGA  C19   C  CH3    0  -0.662  -10.4128  -0.1528  -3.3856
 AGA  HO1   H  HOH1   0   0.455    6.3663  -0.2656  -4.7011
 AGA  H11   H  HCH2   0   0.199    5.3785  -1.8641  -3.3249
 AGA  H12   H  HCH2   0   0.194    6.2442  -0.6202  -2.4247
 AGA  H2    H  HCH1   0   0.231    3.2750  -0.5621  -3.1068
 AGA  HO2   H  HOH1   0   0.442    4.7509   1.1434  -1.4245
 AGA  H31   H  HCH2   0   0.210    3.9264  -2.3437  -1.5335
 AGA  H32   H  HCH2   0   0.208    4.7303  -1.1647  -0.4956
 AGA  H41   H  HCH2   0   0.230   -0.1111  -2.3735   2.2085
 AGA  H42   H  HCH2   0   0.224    0.9677  -1.3401   3.1470
 AGA  H5    H  HCH1   0   0.265   -1.3642  -0.7912   3.4401
 AGA  H61   H  HCH2   0   0.265   -1.3218   1.6115   3.1282
 AGA  H62   H  HCH2   0   0.253    0.1860   0.9944   3.7941
 AGA  H81   H  HCH2   0   0.287    2.1248   1.6910  -0.1884
 AGA  H82   H  HCH2   0   0.252    1.3103   3.1806   0.2434
 AGA  H91   H  HCH2   0   0.223    3.4064   3.7240   1.6956
 AGA  H92   H  HCH2   0   0.218    4.1817   2.3658   0.9085
 AGA  H101  H  HCH2   0   0.218    3.7268   3.4679  -1.3270
 AGA  H102  H  HCH2   0   0.217    3.0161   4.8219  -0.4816
 AGA  H111  H  HCH3   0   0.217    5.2089   5.2501   0.6826
 AGA  H112  H  HCH3   0   0.216    5.9272   3.8994  -0.1891
 AGA  H113  H  HCH3   0   0.227    5.3819   5.3249  -1.0686
 AGA  H131  H  HCH2   0   0.274   -3.2773   0.2858  -0.4660
 AGA  H132  H  HCH2   0   0.275   -3.6032  -1.3796  -0.0773
 AGA  H141  H  HCH2   0   0.224   -5.6957  -0.6748   1.1544
 AGA  H142  H  HCH2   0   0.225   -5.3774   0.9895   0.7140
 AGA  H151  H  HCH2   0   0.213   -5.5041   0.3629  -1.7124
 AGA  H152  H  HCH2   0   0.212   -5.8209  -1.2978  -1.2614
 AGA  H161  H  HCH2   0   0.208   -7.9013  -0.5664  -0.0616
 AGA  H162  H  HCH2   0   0.209   -7.5899   1.0864  -0.5438
 AGA  H171  H  HCH2   0   0.207   -7.7392   0.4078  -2.9537
 AGA  H172  H  HCH2   0   0.206   -8.0509  -1.2432  -2.4667
 AGA  H181  H  HCH2   0   0.210  -10.1266  -0.4990  -1.2800
 AGA  H182  H  HCH2   0   0.210   -9.8184   1.1482  -1.7773
 AGA  H191  H  HCH3   0   0.225  -11.4751   0.0804  -3.3043
 AGA  H192  H  HCH3   0   0.215  -10.0016   0.4557  -4.1935
 AGA  H193  H  HCH3   0   0.215  -10.3264  -1.1986  -3.6871

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
 AGA  O1   C1    single  1.407  0.020  1.407
 AGA  O1   HO1   single  0.850  0.020  0.980
 AGA  C1   C2    single  1.521  0.020  1.521
 AGA  C1   H11   single  0.970  0.020  1.090
 AGA  C1   H12   single  0.970  0.020  1.090
 AGA  C2   O2    single  1.409  0.020  1.409
 AGA  C2   C3    single  1.520  0.020  1.520
 AGA  C2   H2    single  0.970  0.020  1.090
 AGA  O2   HO2   single  0.850  0.020  0.980
 AGA  C3   O5    single  1.411  0.020  1.411
 AGA  C3   H31   single  0.970  0.020  1.090
 AGA  C3   H32   single  0.970  0.020  1.090
 AGA  P1   O3    deloc   1.499  0.020  1.499
 AGA  P1   O4    deloc   1.498  0.020  1.498
 AGA  P1   O5    single  1.639  0.020  1.639
 AGA  P1   O6    single  1.642  0.020  1.642
 AGA  O6   C4    single  1.408  0.020  1.408
 AGA  C4   C5    single  1.514  0.020  1.514
 AGA  C4   H41   single  0.970  0.020  1.090
 AGA  C4   H42   single  0.970  0.020  1.090
 AGA  C5   C6    single  1.518  0.020  1.518
 AGA  C5   O9    single  1.432  0.020  1.432
 AGA  C5   H5    single  0.970  0.020  1.090
 AGA  C6   O7    single  1.423  0.020  1.423
 AGA  C6   H61   single  0.970  0.020  1.090
 AGA  C6   H62   single  0.970  0.020  1.090
 AGA  O7   C7    single  1.334  0.020  1.334
 AGA  C7   O8    double  1.204  0.020  1.204
 AGA  C7   C8    single  1.502  0.020  1.502
 AGA  C8   C9    single  1.524  0.020  1.524
 AGA  C8   H81   single  0.970  0.020  1.090
 AGA  C8   H82   single  0.970  0.020  1.090
 AGA  C9   C10   single  1.524  0.020  1.524
 AGA  C9   H91   single  0.970  0.020  1.090
 AGA  C9   H92   single  0.970  0.020  1.090
 AGA  C10  C11   single  1.522  0.020  1.522
 AGA  C10  H101  single  0.970  0.020  1.090
 AGA  C10  H102  single  0.970  0.020  1.090
 AGA  C11  H111  single  0.970  0.020  1.090
 AGA  C11  H112  single  0.970  0.020  1.090
 AGA  C11  H113  single  0.970  0.020  1.090
 AGA  O9   C12   single  1.331  0.020  1.331
 AGA  C12  O10   double  1.205  0.020  1.205
 AGA  C12  C13   single  1.504  0.020  1.504
 AGA  C13  C14   single  1.520  0.020  1.520
 AGA  C13  H131  single  0.970  0.020  1.090
 AGA  C13  H132  single  0.970  0.020  1.090
 AGA  C14  C15   single  1.523  0.020  1.523
 AGA  C14  H141  single  0.970  0.020  1.090
 AGA  C14  H142  single  0.970  0.020  1.090
 AGA  C15  C16   single  1.523  0.020  1.523
 AGA  C15  H151  single  0.970  0.020  1.090
 AGA  C15  H152  single  0.970  0.020  1.090
 AGA  C16  C17   single  1.523  0.020  1.523
 AGA  C16  H161  single  0.970  0.020  1.090
 AGA  C16  H162  single  0.970  0.020  1.090
 AGA  C17  C18   single  1.524  0.020  1.524
 AGA  C17  H171  single  0.970  0.020  1.090
 AGA  C17  H172  single  0.970  0.020  1.090
 AGA  C18  C19   single  1.522  0.020  1.522
 AGA  C18  H181  single  0.970  0.020  1.090
 AGA  C18  H182  single  0.970  0.020  1.090
 AGA  C19  H191  single  0.970  0.020  1.090
 AGA  C19  H192  single  0.970  0.020  1.090
 AGA  C19  H193  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
 AGA  HO1   O1   C1    107.85  3.000
 AGA  H12   C1   H11   106.64  3.000
 AGA  H12   C1   C2    109.09  3.000
 AGA  H11   C1   C2    108.64  3.000
 AGA  H12   C1   O1    111.64  3.000
 AGA  H11   C1   O1    111.63  3.000
 AGA  C2    C1   O1    109.12  3.000
 AGA  H2    C2   C3    108.50  3.000
 AGA  H2    C2   O2    105.62  3.000
 AGA  C3    C2   O2    112.38  3.000
 AGA  H2    C2   C1    108.53  3.000
 AGA  C3    C2   C1    109.48  3.000
 AGA  O2    C2   C1    112.15  3.000
 AGA  HO2   O2   C2    108.71  3.000
 AGA  H32   C3   H31   107.03  3.000
 AGA  H32   C3   O5    110.64  3.000
 AGA  H31   C3   O5    111.53  3.000
 AGA  H32   C3   C2    109.72  3.000
 AGA  H31   C3   C2    108.44  3.000
 AGA  O5    C3   C2    109.43  3.000
 AGA  O6    P1   O5     93.68  3.000
 AGA  O6    P1   O4    110.63  3.000
 AGA  O5    P1   O4    110.79  3.000
 AGA  O6    P1   O3    109.61  3.000
 AGA  O5    P1   O3    109.78  3.000
 AGA  O4    P1   O3    119.34  3.000
 AGA  P1    O5   C3    116.89  3.000
 AGA  C4    O6   P1    116.92  3.000
 AGA  H42   C4   H41   107.19  3.000
 AGA  H42   C4   C5    107.78  3.000
 AGA  H41   C4   C5    108.22  3.000
 AGA  H42   C4   O6    111.61  3.000
 AGA  H41   C4   O6    111.35  3.000
 AGA  C5    C4   O6    110.51  3.000
 AGA  H5    C5   O9    110.28  3.000
 AGA  H5    C5   C6    106.04  3.000
 AGA  O9    C5   C6    111.35  3.000
 AGA  H5    C5   C4    106.52  3.000
 AGA  O9    C5   C4    107.10  3.000
 AGA  C6    C5   C4    115.42  3.000
 AGA  H62   C6   H61   107.60  3.000
 AGA  H62   C6   O7    111.55  3.000
 AGA  H61   C6   O7    106.22  3.000
 AGA  H62   C6   C5    108.56  3.000
 AGA  H61   C6   C5    109.97  3.000
 AGA  O7    C6   C5    112.80  3.000
 AGA  C7    O7   C6    119.29  3.000
 AGA  C8    C7   O8    124.86  3.000
 AGA  C8    C7   O7    111.34  3.000
 AGA  O8    C7   O7    123.79  3.000
 AGA  H82   C8   H81   106.42  3.000
 AGA  H82   C8   C9    110.64  3.000
 AGA  H81   C8   C9    109.69  3.000
 AGA  H82   C8   C7    109.32  3.000
 AGA  H81   C8   C7    107.29  3.000
 AGA  C9    C8   C7    113.20  3.000
 AGA  H92   C9   H91   106.33  3.000
 AGA  H92   C9   C10   109.72  3.000
 AGA  H91   C9   C10   108.69  3.000
 AGA  H92   C9   C8    109.74  3.000
 AGA  H91   C9   C8    110.01  3.000
 AGA  C10   C9   C8    112.18  3.000
 AGA  H102  C10  H101  106.03  3.000
 AGA  H102  C10  C11   109.53  3.000
 AGA  H101  C10  C11   109.72  3.000
 AGA  H102  C10  C9    109.11  3.000
 AGA  H101  C10  C9    109.87  3.000
 AGA  C11   C10  C9    112.37  3.000
 AGA  H113  C11  H112  107.65  3.000
 AGA  H113  C11  H111  107.62  3.000
 AGA  H112  C11  H111  107.50  3.000
 AGA  H113  C11  C10   111.50  3.000
 AGA  H112  C11  C10   111.26  3.000
 AGA  H111  C11  C10   111.12  3.000
 AGA  C12   O9   C5    119.23  3.000
 AGA  C13   C12  O10   125.20  3.000
 AGA  C13   C12  O9    111.21  3.000
 AGA  O10   C12  O9    123.58  3.000
 AGA  H132  C13  H131  105.33  3.000
 AGA  H132  C13  C14   110.44  3.000
 AGA  H131  C13  C14   110.69  3.000
 AGA  H132  C13  C12   107.70  3.000
 AGA  H131  C13  C12   108.49  3.000
 AGA  C14   C13  C12   113.79  3.000
 AGA  H142  C14  H141  106.39  3.000
 AGA  H142  C14  C15   109.47  3.000
 AGA  H141  C14  C15   109.23  3.000
 AGA  H142  C14  C13   109.81  3.000
 AGA  H141  C14  C13   109.86  3.000
 AGA  C15   C14  C13   111.92  3.000
 AGA  H152  C15  H151  105.98  3.000
 AGA  H152  C15  C16   109.33  3.000
 AGA  H151  C15  C16   109.45  3.000
 AGA  H152  C15  C14   109.36  3.000
 AGA  H151  C15  C14   109.69  3.000
 AGA  C16   C15  C14   112.80  3.000
 AGA  H162  C16  H161  105.96  3.000
 AGA  H162  C16  C17   109.42  3.000
 AGA  H161  C16  C17   109.32  3.000
 AGA  H162  C16  C15   109.31  3.000
 AGA  H161  C16  C15   109.31  3.000
 AGA  C17   C16  C15   113.26  3.000
 AGA  H172  C17  H171  105.92  3.000
 AGA  H172  C17  C18   109.25  3.000
 AGA  H171  C17  C18   109.35  3.000
 AGA  H172  C17  C16   109.34  3.000
 AGA  H171  C17  C16   109.47  3.000
 AGA  C18   C17  C16   113.26  3.000
 AGA  H182  C18  H181  105.98  3.000
 AGA  H182  C18  C19   109.59  3.000
 AGA  H181  C18  C19   109.64  3.000
 AGA  H182  C18  C17   109.24  3.000
 AGA  H181  C18  C17   109.23  3.000
 AGA  C19   C18  C17   112.92  3.000
 AGA  H193  C19  H192  107.44  3.000
 AGA  H193  C19  H191  107.61  3.000
 AGA  H192  C19  H191  107.63  3.000
 AGA  H193  C19  C18   111.18  3.000
 AGA  H192  C19  C18   111.15  3.000
 AGA  H191  C19  C18   111.63  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
 AGA  Var_01  O3    P1   O5   C3    -80.74  30.0  1
 AGA  Var_02  C5    C4   O6   P1   -171.99  30.0  3
 AGA  Var_03  O10   C12  O9   C5      2.12  30.0  3
 AGA  Var_04  O8    C7   O7   C6     -3.54  30.0  3
 AGA  Var_05  C9    C8   C7   O7    155.62  30.0  3
 AGA  Var_06  C10   C9   C8   C7   -168.45  30.0  3
 AGA  Var_07  C11   C10  C9   C8   -177.71  30.0  3
 AGA  Var_08  C14   C13  C12  O9   -177.39  30.0  3
 AGA  Var_09  C15   C14  C13  C12  -177.60  30.0  3
 AGA  Var_10  C16   C15  C14  C13   179.95  30.0  3
 AGA  Var_11  C17   C16  C15  C14  -178.64  30.0  3
 AGA  Var_12  C18   C17  C16  C15   179.97  30.0  3
 AGA  Var_13  C19   C18  C17  C16  -179.54  30.0  3
 AGA  Var_14  H31   C3   O5   P1     47.43  30.0  1
 AGA  Var_15  H61   C6   O7   C7    138.37  30.0  1
 AGA  Var_16  H111  C11  C10  C9    -58.61  30.0  3
 AGA  Var_17  H191  C19  C18  C17  -179.48  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
 AGA  chir_01  C2  C1  O2  C3  positiv
 AGA  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
 AGA  plan-1  O7   0.020
 AGA  plan-1  C7   0.020
 AGA  plan-1  O8   0.020
 AGA  plan-1  C8   0.020
 AGA  plan-2  O9   0.020
 AGA  plan-2  C12  0.020
 AGA  plan-2  O10  0.020
 AGA  plan-2  C13  0.020

