# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:35:41 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  62  30  .  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_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  -0.610   4.1598   -8.0289   6.3224
 PSF  O1    O  O2     0  -0.611   5.3480   -6.6552   4.6102
 PSF  P     P  P      0   1.379   5.6278   -7.9226   5.6057
 PSF  O4    O  O      0  -0.795   6.5673   -7.5047   6.6938
 PSF  O3    O  OP    -1  -0.815   5.9000   -9.1558   4.7947
 PSF  C2    C  CH2    0  -0.209   3.0258   -8.3888   5.5653
 PSF  C3    C  CH1    0  -0.059   1.8688   -8.6259   6.5184
 PSF  O11   O  O2     0  -0.457   1.6775   -7.4791   7.3496
 PSF  O12   O  O      0  -0.449   0.3682   -6.4441   5.8597
 PSF  C1    C  C      0   0.578   1.0051   -6.4302   6.8835
 PSF  C4    C  CH2    0  -0.175   2.1424   -9.7916   7.4409
 PSF  C5    C  C      0   0.608   1.0091  -10.9921   9.1246
 PSF  O51   O  O      0  -0.452   1.9522  -11.7332   9.2468
 PSF  O52   O  O2     0  -0.464   0.9788   -9.9972   8.2422
 PSF  C6    C  CH2    0  -0.583  -0.2573  -11.0569   9.9333
 PSF  C7    C  CH2    0  -0.417  -0.2794  -12.2002  10.9352
 PSF  C13   C  CH2    0  -0.552   1.1792   -5.2397   7.7853
 PSF  C14   C  CH2    0  -0.440   2.6335   -4.7543   7.7961
 PSF  C15   C  CH2    0  -0.423   3.1321   -4.2864   6.4348
 PSF  N     N  NH2    0  -0.804   5.6960   -6.8965   0.9615
 PSF  CA    C  CH1    0  -0.241   4.9816   -7.0367   2.2321
 PSF  CB    C  CH2    0  -0.144   5.9400   -6.5959   3.3268
 PSF  C     C  C      0   0.426   3.6757   -6.2142   2.2746
 PSF  OT1   O  O      0  -0.619   3.8045   -4.9885   2.0594
 PSF  OT2   O  OC    -1  -0.607   2.6046   -6.8194   2.4782
 PSF  C8    C  CH2    0  -0.410  -1.5427  -12.1898  11.7869
 PSF  C9    C  CH2    0  -0.420  -1.5849  -13.3346  12.7913
 PSF  C10   C  CH3    0  -0.662  -2.8253  -13.3042  13.6734
 PSF  C16   C  CH2    0  -0.411   4.5699   -3.7854   6.4756
 PSF  C17   C  CH3    0  -0.688   5.0176   -3.1973   5.1455
 PSF  H21   H  HCH2   0   0.272   2.7702   -7.6123   4.8390
 PSF  H22   H  HCH2   0   0.216   3.1925   -9.3117   4.9966
 PSF  H31   H  HCH1   0   0.262   0.9717   -8.8302   5.9268
 PSF  H41   H  HCH2   0   0.248   3.0105   -9.6023   8.0752
 PSF  H42   H  HCH2   0   0.245   2.3489  -10.6772   6.8353
 PSF  H61   H  HCH2   0   0.274  -1.1054  -11.1295   9.2458
 PSF  H62   H  HCH2   0   0.273  -0.3775  -10.0963  10.4451
 PSF  H71   H  HCH2   0   0.224   0.5951  -12.1373  11.5879
 PSF  H72   H  HCH2   0   0.224  -0.2038  -13.1557  10.4087
 PSF  H131  H  HCH2   0   0.271   0.8767   -5.5096   8.8002
 PSF  H132  H  HCH2   0   0.252   0.5166   -4.4445   7.4417
 PSF  H141  H  HCH2   0   0.230   3.2823   -5.5499   8.1695
 PSF  H142  H  HCH2   0   0.230   2.7063   -3.9319   8.5121
 PSF  H151  H  HCH2   0   0.200   2.4748   -3.4923   6.0620
 PSF  H152  H  HCH2   0   0.243   3.0791   -5.1025   5.7070
 PSF  HA    H  HCH1   0   0.203   4.7574   -8.0963   2.3800
 PSF  HB1   H  HCH2   0   0.199   6.2281   -5.5549   3.1512
 PSF  HB2   H  HCH2   0   0.201   6.8502   -7.2014   3.2674
 PSF  H81   H  HCH2   0   0.212  -2.4252  -12.2419  11.1400
 PSF  H82   H  HCH2   0   0.211  -1.6133  -11.2352  12.3202
 PSF  H91   H  HCH2   0   0.212  -1.5388  -14.2871  12.2544
 PSF  H92   H  HCH2   0   0.212  -0.6891  -13.2965  13.4185
 PSF  H101  H  HCH3   0   0.216  -2.8706  -12.3817  14.2553
 PSF  H102  H  HCH3   0   0.216  -3.7376  -13.3599  13.0764
 PSF  H103  H  HCH3   0   0.226  -2.8379  -14.1394  14.3744
 PSF  H161  H  HCH2   0   0.197   4.6764   -3.0330   7.2646
 PSF  H162  H  HCH2   0   0.218   5.2241   -4.6184   6.7486
 PSF  H171  H  HCH3   0   0.256   4.8852   -3.9161   4.3369
 PSF  H172  H  HCH3   0   0.203   4.4373   -2.3069   4.8929
 PSF  H173  H  HCH3   0   0.211   6.0690   -2.9056   5.1709
 PSF  H1    H  HNH2   0   0.326   5.6927   -5.9126   0.7149
 PSF  H2    H  HNH2   0   0.341   5.1710   -7.3574   0.2285

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  1.637  0.020  1.637
 PSF  O2   C2    single  1.410  0.020  1.410
 PSF  O1   P     single  1.636  0.020  1.636
 PSF  O1   CB    single  1.415  0.020  1.415
 PSF  P    O4    deloc   1.497  0.020  1.497
 PSF  P    O3    deloc   1.501  0.020  1.501
 PSF  C2   C3    single  1.518  0.020  1.518
 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  1.512  0.020  1.512
 PSF  C3   H31   single  0.970  0.020  1.090
 PSF  O11  C1    single  1.330  0.020  1.330
 PSF  O12  C1    double  1.206  0.020  1.206
 PSF  C1   C13   single  1.504  0.020  1.504
 PSF  C4   O52   single  1.428  0.020  1.428
 PSF  C4   H41   single  0.970  0.020  1.090
 PSF  C4   H42   single  0.970  0.020  1.090
 PSF  C5   O51   double  1.206  0.020  1.206
 PSF  C5   O52   single  1.330  0.020  1.330
 PSF  C5   C6    single  1.504  0.020  1.504
 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  1.524  0.020  1.524
 PSF  C7   H71   single  0.970  0.020  1.090
 PSF  C7   H72   single  0.970  0.020  1.090
 PSF  C13  C14   single  1.533  0.020  1.533
 PSF  C13  H131  single  0.970  0.020  1.090
 PSF  C13  H132  single  0.970  0.020  1.090
 PSF  C14  C15   single  1.523  0.020  1.523
 PSF  C14  H141  single  0.970  0.020  1.090
 PSF  C14  H142  single  0.970  0.020  1.090
 PSF  C15  C16   single  1.523  0.020  1.523
 PSF  C15  H151  single  0.970  0.020  1.090
 PSF  C15  H152  single  0.970  0.020  1.090
 PSF  N    CA    single  1.464  0.020  1.464
 PSF  N    H1    single  0.890  0.020  1.040
 PSF  N    H2    single  0.890  0.020  1.040
 PSF  CA   CB    single  1.520  0.020  1.520
 PSF  CA   C     single  1.544  0.020  1.544
 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   deloc   1.251  0.020  1.251
 PSF  C    OT2   deloc   1.247  0.020  1.247
 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     120.17  3.000
 PSF  CB    O1   P     120.86  3.000
 PSF  O3    P    O4    120.55  3.000
 PSF  O3    P    O1    109.81  3.000
 PSF  O4    P    O1    109.48  3.000
 PSF  O3    P    O2    110.23  3.000
 PSF  O4    P    O2    105.23  3.000
 PSF  O1    P    O2     99.40  3.000
 PSF  H22   C2   H21   106.78  3.000
 PSF  H22   C2   C3    108.06  3.000
 PSF  H21   C2   C3    110.48  3.000
 PSF  H22   C2   O2    111.77  3.000
 PSF  H21   C2   O2    111.30  3.000
 PSF  C3    C2   O2    108.41  3.000
 PSF  H31   C3   C4    109.54  3.000
 PSF  H31   C3   O11   110.77  3.000
 PSF  C4    C3   O11   106.75  3.000
 PSF  H31   C3   C2    108.34  3.000
 PSF  C4    C3   C2    111.45  3.000
 PSF  O11   C3   C2    109.99  3.000
 PSF  C1    O11  C3    119.77  3.000
 PSF  C13   C1   O12   125.42  3.000
 PSF  C13   C1   O11   110.83  3.000
 PSF  O12   C1   O11   123.74  3.000
 PSF  H42   C4   H41   108.20  3.000
 PSF  H42   C4   O52   110.39  3.000
 PSF  H41   C4   O52   110.30  3.000
 PSF  H42   C4   C3    108.73  3.000
 PSF  H41   C4   C3    111.40  3.000
 PSF  O52   C4   C3    107.82  3.000
 PSF  C6    C5   O52   111.70  3.000
 PSF  C6    C5   O51   125.29  3.000
 PSF  O52   C5   O51   123.02  3.000
 PSF  C5    O52  C4    117.48  3.000
 PSF  H62   C6   H61   105.47  3.000
 PSF  H62   C6   C7    110.49  3.000
 PSF  H61   C6   C7    110.66  3.000
 PSF  H62   C6   C5    107.82  3.000
 PSF  H61   C6   C5    108.52  3.000
 PSF  C7    C6   C5    113.52  3.000
 PSF  H72   C7   H71   106.41  3.000
 PSF  H72   C7   C8    109.41  3.000
 PSF  H71   C7   C8    109.22  3.000
 PSF  H72   C7   C6    109.80  3.000
 PSF  H71   C7   C6    109.79  3.000
 PSF  C8    C7   C6    112.05  3.000
 PSF  H132  C13  H131  107.72  3.000
 PSF  H132  C13  C14   110.34  3.000
 PSF  H131  C13  C14   109.52  3.000
 PSF  H132  C13  C1    108.54  3.000
 PSF  H131  C13  C1    109.23  3.000
 PSF  C14   C13  C1    111.40  3.000
 PSF  H142  C14  H141  106.53  3.000
 PSF  H142  C14  C15   109.43  3.000
 PSF  H141  C14  C15   109.55  3.000
 PSF  H142  C14  C13   107.83  3.000
 PSF  H141  C14  C13   109.58  3.000
 PSF  C15   C14  C13   113.66  3.000
 PSF  H152  C15  H151  106.55  3.000
 PSF  H152  C15  C16   107.99  3.000
 PSF  H151  C15  C16   109.68  3.000
 PSF  H152  C15  C14   110.44  3.000
 PSF  H151  C15  C14   109.27  3.000
 PSF  C16   C15  C14   112.71  3.000
 PSF  H2    N    H1    105.30  3.000
 PSF  H2    N    CA    109.36  3.000
 PSF  H1    N    CA    107.59  3.000
 PSF  HA    CA   C     109.83  3.000
 PSF  HA    CA   CB    108.24  3.000
 PSF  C     CA   CB    111.04  3.000
 PSF  HA    CA   N     108.07  3.000
 PSF  C     CA   N     112.67  3.000
 PSF  CB    CA   N     106.83  3.000
 PSF  HB2   CB   HB1   107.37  3.000
 PSF  HB2   CB   CA    108.95  3.000
 PSF  HB1   CB   CA    109.04  3.000
 PSF  HB2   CB   O1    111.97  3.000
 PSF  HB1   CB   O1    107.20  3.000
 PSF  CA    CB   O1    112.17  3.000
 PSF  OT2   C    OT1   126.30  3.000
 PSF  OT2   C    CA    118.19  3.000
 PSF  OT1   C    CA    115.48  3.000
 PSF  H82   C8   H81   106.07  3.000
 PSF  H82   C8   C9    109.39  3.000
 PSF  H81   C8   C9    109.34  3.000
 PSF  H82   C8   C7    109.36  3.000
 PSF  H81   C8   C7    109.73  3.000
 PSF  C9    C8   C7    112.73  3.000
 PSF  H92   C9   H91   106.08  3.000
 PSF  H92   C9   C10   109.53  3.000
 PSF  H91   C9   C10   109.64  3.000
 PSF  H92   C9   C8    109.20  3.000
 PSF  H91   C9   C8    109.23  3.000
 PSF  C10   C9   C8    112.93  3.000
 PSF  H103  C10  H102  107.62  3.000
 PSF  H103  C10  H101  107.71  3.000
 PSF  H102  C10  H101  107.45  3.000
 PSF  H103  C10  C9    111.51  3.000
 PSF  H102  C10  C9    111.28  3.000
 PSF  H101  C10  C9    111.07  3.000
 PSF  H162  C16  H161  106.57  3.000
 PSF  H162  C16  C17   109.66  3.000
 PSF  H161  C16  C17   109.60  3.000
 PSF  H162  C16  C15   108.71  3.000
 PSF  H161  C16  C15   109.70  3.000
 PSF  C17   C16  C15   112.42  3.000
 PSF  H173  C17  H172  107.41  3.000
 PSF  H173  C17  H171  108.09  3.000
 PSF  H172  C17  H171  107.55  3.000
 PSF  H173  C17  C16   111.50  3.000
 PSF  H172  C17  C16   111.15  3.000
 PSF  H171  C17  C16   110.97  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  Var_01  C3    C2   O2   P     170.92  30.0  3
 PSF  Var_02  CA    CB   O1   P      99.26  30.0  3
 PSF  Var_03  O12   C1   O11  C3     11.17  30.0  3
 PSF  Var_04  C14   C13  C1   O11    65.42  30.0  3
 PSF  Var_05  C15   C14  C13  C1     61.92  30.0  3
 PSF  Var_06  O51   C5   O52  C4     -1.88  30.0  1
 PSF  Var_07  C8    C7   C6   C5    176.92  30.0  3
 PSF  Var_08  C7    C6   C5   O51    -1.68  30.0  3
 PSF  Var_09  C9    C8   C7   C6    179.66  30.0  3
 PSF  Var_10  C10   C9   C8   C7    178.26  30.0  3
 PSF  Var_11  C16   C15  C14  C13   178.95  30.0  3
 PSF  Var_12  C17   C16  C15  C14  -174.54  30.0  3
 PSF  Var_13  H41   C4   O52  C5    -58.57  30.0  1
 PSF  Var_14  H171  C17  C16  C15   -55.57  30.0  3
 PSF  Var_15  H101  C10  C9   C8    -60.55  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

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-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

