# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 11:41:04 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: O-[(S)-{[(2R)-2,3-bis(hexanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)OC[C@H](CO[P@](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCC
#
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
 PSF  PSF  O-[(S)-{[(2R)-2,3-bis(hexanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine  ligand  64  30  .  2021-08-20  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PSF
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
 PSF  O2    O  O2    0  -0.581   4.3189   -8.7039   5.7871
 PSF  O1    O  O2    0  -0.604   4.9069   -7.1959   3.9359
 PSF  P     P  P     0   1.515   5.5764   -8.2456   4.9238
 PSF  O4    O  O     0  -0.688   6.6794   -7.7765   5.7804
 PSF  O3    O  OH1   0  -0.740   5.9211   -9.4356   3.9158
 PSF  C2    C  CH2   0  -0.219   3.1164   -9.2037   5.2010
 PSF  C3    C  CH1   0  -0.065   2.0212   -9.1939   6.2480
 PSF  O11   O  O2    0  -0.452   1.8223   -7.8901   6.7973
 PSF  O12   O  O     0  -0.456   0.6743   -7.1963   5.0124
 PSF  C1    C  C     0   0.594   1.1303   -6.9858   6.1104
 PSF  C4    C  CH2   0  -0.172   2.3424  -10.1053   7.4130
 PSF  C5    C  C     0   0.608   1.2050  -10.9464   9.3034
 PSF  O51   O  O     0  -0.449   2.1366  -11.6645   9.5642
 PSF  O52   O  O2    0  -0.463   1.1914  -10.1288   8.2524
 PSF  C6    C  CH2   0  -0.583  -0.0659  -10.8361  10.0986
 PSF  C7    C  CH2   0  -0.418  -0.1821  -11.8582  11.2180
 PSF  C13   C  CH2   0  -0.562   0.9544   -5.7043   6.8780
 PSF  C14   C  CH2   0  -0.429   2.2090   -5.1725   7.5675
 PSF  C15   C  CH2   0  -0.432   3.3695   -4.9247   6.6135
 PSF  N     N  NH2   0  -0.783   5.4162   -4.9229   1.1476
 PSF  CA    C  CH1   0  -0.245   4.7149   -5.9168   1.9235
 PSF  CB    C  CH2   0  -0.160   5.6498   -6.3675   3.0433
 PSF  C     C  C     0   0.540   3.4114   -5.4172   2.5396
 PSF  OT1   O  O     0  -0.437   3.2740   -4.3045   2.9824
 PSF  OT2   O  OH1   0  -0.584   2.4596   -6.3373   2.5408
 PSF  C8    C  CH2   0  -0.410  -1.4756  -11.6854  12.0042
 PSF  C9    C  CH2   0  -0.420  -1.6322  -12.7045  13.1258
 PSF  C10   C  CH3   0  -0.662  -2.9190  -12.5145  13.9162
 PSF  C16   C  CH2   0  -0.415   4.5520   -4.2325   7.2797
 PSF  C17   C  CH3   0  -0.674   5.7433   -4.0859   6.3430
 PSF  HO3   H  HOH1  0   0.501   6.5209  -10.1017   4.2786
 PSF  H21   H  HCH2  0   0.272   2.8166   -8.6012   4.3435
 PSF  H22   H  HCH2  0   0.266   3.2605  -10.2302   4.8549
 PSF  H31   H  HCH1  0   0.281   1.1090   -9.5464   5.7567
 PSF  H41   H  HCH2  0   0.254   3.2136   -9.7511   7.9680
 PSF  H42   H  HCH2  0   0.252   2.5621  -11.1045   7.0302
 PSF  H61   H  HCH2  0   0.272  -0.9144  -10.9175   9.4135
 PSF  H62   H  HCH2  0   0.277  -0.1156   -9.8199  10.5050
 PSF  H71   H  HCH2  0   0.225   0.6710  -11.7671  11.8952
 PSF  H72   H  HCH2  0   0.225  -0.1414  -12.8689  10.8024
 PSF  H131  H  HCH2  0   0.284   0.1745   -5.8839   7.6255
 PSF  H132  H  HCH2  0   0.261   0.5550   -4.9620   6.1862
 PSF  H141  H  HCH2  0   0.228   2.5193   -5.8498   8.3667
 PSF  H142  H  HCH2  0   0.234   1.9342   -4.2345   8.0575
 PSF  H151  H  HCH2  0   0.218   3.0288   -4.3205   5.7672
 PSF  H152  H  HCH2  0   0.219   3.7086   -5.8729   6.1864
 PSF  H2    H  HNH2  0   0.367   4.9081   -4.7176   0.2979
 PSF  HA    H  HCH1  0   0.282   4.5005   -6.7739   1.2818
 PSF  HB1   H  HCH2  0   0.245   6.0252   -5.4984   3.5889
 PSF  HB2   H  HCH2  0   0.266   6.4972   -6.8983   2.6058
 PSF  HXT   H  HOH1  0   0.475   1.6721   -6.0190   3.0095
 PSF  H81   H  HCH2  0   0.212  -2.3312  -11.7631  11.3246
 PSF  H82   H  HCH2  0   0.212  -1.5144  -10.6744  12.4251
 PSF  H91   H  HCH2  0   0.212  -1.6055  -13.7135  12.7027
 PSF  H92   H  HCH2  0   0.212  -0.7731  -12.6348  13.7995
 PSF  H101  H  HCH3  0   0.216  -2.9527  -11.5277  14.3822
 PSF  H102  H  HCH3  0   0.216  -3.7957  -12.6017  13.2712
 PSF  H103  H  HCH3  0   0.227  -3.0177  -13.2571  14.7088
 PSF  H161  H  HCH2  0   0.212   4.2372   -3.2475   7.6373
 PSF  H162  H  HCH2  0   0.211   4.8517   -4.7963   8.1686
 PSF  H171  H  HCH3  0   0.222   6.1238   -5.0641   6.0432
 PSF  H172  H  HCH3  0   0.214   5.4641   -3.5485   5.4342
 PSF  H173  H  HCH3  0   0.226   6.5624   -3.5407   6.8129
 PSF  H1    H  HNH2  0   0.351   5.4822   -4.0541   1.6640

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
 PSF  O2   P     single  1.593  0.020  1.593
 PSF  O2   C2    single  1.428  0.020  1.428
 PSF  O1   P     single  1.589  0.020  1.589
 PSF  O1   CB    single  1.426  0.020  1.426
 PSF  P    O4    double  1.473  0.020  1.473
 PSF  P    O3    single  1.597  0.020  1.597
 PSF  O3   HO3   single  0.850  0.020  0.980
 PSF  C2   C3    single  1.515  0.020  1.515
 PSF  C2   H21   single  0.970  0.020  1.090
 PSF  C2   H22   single  0.970  0.020  1.090
 PSF  C3   O11   single  1.429  0.020  1.429
 PSF  C3   C4    single  1.514  0.020  1.514
 PSF  C3   H31   single  0.970  0.020  1.090
 PSF  O11  C1    single  1.330  0.020  1.330
 PSF  O12  C1    double  1.207  0.020  1.207
 PSF  C1   C13   single  1.504  0.020  1.504
 PSF  C4   O52   single  1.425  0.020  1.425
 PSF  C4   H41   single  0.970  0.020  1.090
 PSF  C4   H42   single  0.970  0.020  1.090
 PSF  C5   O51   double  1.205  0.020  1.205
 PSF  C5   O52   single  1.332  0.020  1.332
 PSF  C5   C6    single  1.503  0.020  1.503
 PSF  C6   C7    single  1.520  0.020  1.520
 PSF  C6   H61   single  0.970  0.020  1.090
 PSF  C6   H62   single  0.970  0.020  1.090
 PSF  C7   C8    single  1.523  0.020  1.523
 PSF  C7   H71   single  0.970  0.020  1.090
 PSF  C7   H72   single  0.970  0.020  1.090
 PSF  C13  C14   single  1.527  0.020  1.527
 PSF  C13  H131  single  0.970  0.020  1.090
 PSF  C13  H132  single  0.970  0.020  1.090
 PSF  C14  C15   single  1.522  0.020  1.522
 PSF  C14  H141  single  0.970  0.020  1.090
 PSF  C14  H142  single  0.970  0.020  1.090
 PSF  C15  C16   single  1.524  0.020  1.524
 PSF  C15  H151  single  0.970  0.020  1.090
 PSF  C15  H152  single  0.970  0.020  1.090
 PSF  N    CA    single  1.443  0.020  1.443
 PSF  N    H1    single  0.890  0.020  1.040
 PSF  N    H2    single  0.890  0.020  1.040
 PSF  CA   CB    single  1.527  0.020  1.527
 PSF  CA   C     single  1.526  0.020  1.526
 PSF  CA   HA    single  0.970  0.020  1.090
 PSF  CB   HB1   single  0.970  0.020  1.090
 PSF  CB   HB2   single  0.970  0.020  1.090
 PSF  C    OT1   double  1.205  0.020  1.205
 PSF  C    OT2   single  1.324  0.020  1.324
 PSF  OT2  HXT   single  0.850  0.020  0.980
 PSF  C8   C9    single  1.524  0.020  1.524
 PSF  C8   H81   single  0.970  0.020  1.090
 PSF  C8   H82   single  0.970  0.020  1.090
 PSF  C9   C10   single  1.522  0.020  1.522
 PSF  C9   H91   single  0.970  0.020  1.090
 PSF  C9   H92   single  0.970  0.020  1.090
 PSF  C10  H101  single  0.970  0.020  1.090
 PSF  C10  H102  single  0.970  0.020  1.090
 PSF  C10  H103  single  0.970  0.020  1.090
 PSF  C16  C17   single  1.522  0.020  1.522
 PSF  C16  H161  single  0.970  0.020  1.090
 PSF  C16  H162  single  0.970  0.020  1.090
 PSF  C17  H171  single  0.970  0.020  1.090
 PSF  C17  H172  single  0.970  0.020  1.090
 PSF  C17  H173  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
 PSF  C2    O2   P     122.89  3.000
 PSF  CB    O1   P     123.58  3.000
 PSF  O3    P    O4    116.27  3.000
 PSF  O3    P    O1    100.99  3.000
 PSF  O4    P    O1    117.81  3.000
 PSF  O3    P    O2    107.34  3.000
 PSF  O4    P    O2    111.57  3.000
 PSF  O1    P    O2    101.21  3.000
 PSF  HO3   O3   P     114.22  3.000
 PSF  H22   C2   H21   107.84  3.000
 PSF  H22   C2   C3    108.67  3.000
 PSF  H21   C2   C3    109.95  3.000
 PSF  H22   C2   O2    110.35  3.000
 PSF  H21   C2   O2    111.16  3.000
 PSF  C3    C2   O2    108.83  3.000
 PSF  H31   C3   C4    109.17  3.000
 PSF  H31   C3   O11   110.52  3.000
 PSF  C4    C3   O11   106.44  3.000
 PSF  H31   C3   C2    106.87  3.000
 PSF  C4    C3   C2    112.00  3.000
 PSF  O11   C3   C2    111.85  3.000
 PSF  C1    O11  C3    119.63  3.000
 PSF  C13   C1   O12   124.64  3.000
 PSF  C13   C1   O11   112.13  3.000
 PSF  O12   C1   O11   123.21  3.000
 PSF  H42   C4   H41   108.32  3.000
 PSF  H42   C4   O52   110.72  3.000
 PSF  H41   C4   O52   110.51  3.000
 PSF  H42   C4   C3    108.89  3.000
 PSF  H41   C4   C3    111.42  3.000
 PSF  O52   C4   C3    106.98  3.000
 PSF  C6    C5   O52   111.34  3.000
 PSF  C6    C5   O51   125.66  3.000
 PSF  O52   C5   O51   123.00  3.000
 PSF  C5    O52  C4    117.83  3.000
 PSF  H62   C6   H61   105.44  3.000
 PSF  H62   C6   C7    110.30  3.000
 PSF  H61   C6   C7    110.61  3.000
 PSF  H62   C6   C5    107.61  3.000
 PSF  H61   C6   C5    108.61  3.000
 PSF  C7    C6   C5    113.88  3.000
 PSF  H72   C7   H71   106.46  3.000
 PSF  H72   C7   C8    109.43  3.000
 PSF  H71   C7   C8    109.48  3.000
 PSF  H72   C7   C6    109.79  3.000
 PSF  H71   C7   C6    109.91  3.000
 PSF  C8    C7   C6    111.63  3.000
 PSF  H132  C13  H131  106.49  3.000
 PSF  H132  C13  C14   110.50  3.000
 PSF  H131  C13  C14   109.52  3.000
 PSF  H132  C13  C1    107.40  3.000
 PSF  H131  C13  C1    106.97  3.000
 PSF  C14   C13  C1    115.53  3.000
 PSF  H142  C14  H141  105.99  3.000
 PSF  H142  C14  C15   109.44  3.000
 PSF  H141  C14  C15   110.04  3.000
 PSF  H142  C14  C13   107.13  3.000
 PSF  H141  C14  C13   110.34  3.000
 PSF  C15   C14  C13   113.58  3.000
 PSF  H152  C15  H151  105.85  3.000
 PSF  H152  C15  C16   108.90  3.000
 PSF  H151  C15  C16   109.20  3.000
 PSF  H152  C15  C14   109.87  3.000
 PSF  H151  C15  C14   109.71  3.000
 PSF  C16   C15  C14   113.05  3.000
 PSF  H2    N    H1    106.68  3.000
 PSF  H2    N    CA    110.33  3.000
 PSF  H1    N    CA    110.39  3.000
 PSF  HA    CA   C     109.06  3.000
 PSF  HA    CA   CB    108.63  3.000
 PSF  C     CA   CB    108.88  3.000
 PSF  HA    CA   N     108.67  3.000
 PSF  C     CA   N     114.00  3.000
 PSF  CB    CA   N     107.46  3.000
 PSF  HB2   CB   HB1   108.67  3.000
 PSF  HB2   CB   CA    108.96  3.000
 PSF  HB1   CB   CA    109.99  3.000
 PSF  HB2   CB   O1    111.89  3.000
 PSF  HB1   CB   O1    109.17  3.000
 PSF  CA    CB   O1    108.15  3.000
 PSF  OT2   C    OT1   124.00  3.000
 PSF  OT2   C    CA    112.77  3.000
 PSF  OT1   C    CA    123.23  3.000
 PSF  HXT   OT2  C     110.86  3.000
 PSF  H82   C8   H81   106.03  3.000
 PSF  H82   C8   C9    109.31  3.000
 PSF  H81   C8   C9    109.21  3.000
 PSF  H82   C8   C7    109.45  3.000
 PSF  H81   C8   C7    109.57  3.000
 PSF  C9    C8   C7    113.03  3.000
 PSF  H92   C9   H91   106.12  3.000
 PSF  H92   C9   C10   109.64  3.000
 PSF  H91   C9   C10   109.66  3.000
 PSF  H92   C9   C8    109.27  3.000
 PSF  H91   C9   C8    109.25  3.000
 PSF  C10   C9   C8    112.68  3.000
 PSF  H103  C10  H102  107.59  3.000
 PSF  H103  C10  H101  107.61  3.000
 PSF  H102  C10  H101  107.43  3.000
 PSF  H103  C10  C9    111.64  3.000
 PSF  H102  C10  C9    111.23  3.000
 PSF  H101  C10  C9    111.13  3.000
 PSF  H162  C16  H161  106.08  3.000
 PSF  H162  C16  C17   109.57  3.000
 PSF  H161  C16  C17   109.85  3.000
 PSF  H162  C16  C15   109.49  3.000
 PSF  H161  C16  C15   109.18  3.000
 PSF  C17   C16  C15   112.46  3.000
 PSF  H173  C17  H172  107.73  3.000
 PSF  H173  C17  H171  107.73  3.000
 PSF  H172  C17  H171  107.55  3.000
 PSF  H173  C17  C16   111.77  3.000
 PSF  H172  C17  C16   111.06  3.000
 PSF  H171  C17  C16   110.82  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
 PSF  CONST_01  HXT   OT2  C    CA    180.00   0.0  0
 PSF  Var_01    C3    C2   O2   P    -165.12  30.0  3
 PSF  Var_02    CA    CB   O1   P     158.48  30.0  3
 PSF  Var_03    O12   C1   O11  C3     -1.70  30.0  3
 PSF  Var_04    C14   C13  C1   O11    45.47  30.0  3
 PSF  Var_05    C15   C14  C13  C1     57.65  30.0  3
 PSF  Var_06    O51   C5   O52  C4     -0.51  30.0  2
 PSF  Var_07    C8    C7   C6   C5    179.03  30.0  3
 PSF  Var_08    C7    C6   C5   O51    -7.27  30.0  3
 PSF  Var_09    C9    C8   C7   C6    179.36  30.0  3
 PSF  Var_10    C10   C9   C8   C7    179.33  30.0  3
 PSF  Var_11    C16   C15  C14  C13   172.76  30.0  3
 PSF  Var_12    C17   C16  C15  C14   175.67  30.0  3
 PSF  Var_13    H41   C4   O52  C5    -63.17  30.0  1
 PSF  Var_14    H171  C17  C16  C15   -62.98  30.0  3
 PSF  Var_15    H101  C10  C9   C8    -60.31  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
 PSF  chir_02  C3  C2  O11  C4  positiv
 PSF  chir_03  CA  N   CB   C   negativ
 PSF  chir_04  P   O1  O4   O3  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
 PSF  plan-1  CA   0.020
 PSF  plan-1  C    0.020
 PSF  plan-1  OT1  0.020
 PSF  plan-1  OT2  0.020
 PSF  plan-1  HXT  0.020
 PSF  plan-2  O11  0.020
 PSF  plan-2  O12  0.020
 PSF  plan-2  C1   0.020
 PSF  plan-2  C13  0.020
 PSF  plan-3  C5   0.020
 PSF  plan-3  O51  0.020
 PSF  plan-3  O52  0.020
 PSF  plan-3  C6   0.020

