# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:36:39 2022
#   Inital geometry file: a 182 line input string
#   Ligand name: O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO[P](O)(=O)OC[C@H](N)C(O)=O
#
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
 S12  S12  O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine  L-peptide  79  35  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_S12
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
 S12  C     C  C      0   0.409   8.7866   9.4742   -4.8680
 S12  N     N  NH2    0  -0.813   8.1566   9.9733   -7.2260
 S12  P     P  P      0   1.357   7.4714   5.6733   -6.9584
 S12  OG    O  O2     0  -0.614   7.9739   7.1566   -6.4876
 S12  C2    C  CH2    0  -0.137   5.4237   5.6839   -8.6675
 S12  O2    O  O2     0  -0.632   6.7436   6.0819   -8.3859
 S12  C3    C  CH1    0  -0.046   5.0260   6.2532  -10.0148
 S12  O3    O  O      0  -0.805   6.4321   5.1401   -6.0182
 S12  C4    C  CH2    0  -0.180   3.5665   5.9293  -10.2918
 S12  O4    O  OP    -1  -0.777   8.7137   4.9063   -7.2773
 S12  C5    C  C      0   0.578   2.1072   6.1971  -12.1521
 S12  C6    C  CH2    0  -0.548   2.0100   6.8295  -13.5140
 S12  C7    C  CH2    0  -0.432   3.1335   6.3917  -14.4564
 S12  C8    C  CH2    0  -0.410   3.0146   7.0342  -15.8320
 S12  C9    C  CH2    0  -0.419   4.1532   6.6288  -16.7593
 S12  CA    C  CH1    0  -0.250   7.6698   9.4848   -5.9456
 S12  CB    C  CH2    0  -0.136   7.0133   8.1249   -6.1010
 S12  C10   C  CH2    0  -0.421   4.0763   7.2904  -18.1310
 S12  C11   C  CH2    0  -0.424   5.1784   6.8541  -19.0931
 S12  O11   O  OH1    0  -0.664   5.8682   5.7011  -10.9982
 S12  C12   C  CH2    0  -0.485   6.5781   7.3069  -18.6712
 S12  C13   C  C1     0  -0.207   7.6469   6.8121  -19.5931
 S12  C14   C  C1     0  -0.210   8.4547   7.5801  -20.3194
 S12  O51   O  O      0  -0.442   1.2703   5.4942  -11.6443
 S12  O52   O  O2     0  -0.463   3.2566   6.5089  -11.5595
 S12  O     O  O      0  -0.607   8.5172   8.8789   -3.8072
 S12  OXT   O  OC    -1  -0.601   9.8337  10.0977   -5.1311
 S12  H     H  HNH2   0   0.328   7.4033  10.4143   -7.7369
 S12  H2    H  HNH2   0   0.332   8.8529  10.6846   -7.0488
 S12  H2B   H  HCH2   0   0.205   5.3263   4.5910   -8.6922
 S12  H2A   H  HCH2   0   0.207   4.7207   6.0521   -7.9132
 S12  H3    H  HCH1   0   0.216   5.1348   7.3473   -9.9699
 S12  H4    H  HCH2   0   0.236   3.4124   4.8473  -10.3185
 S12  H4A   H  HCH2   0   0.236   2.9203   6.3503   -9.5174
 S12  H6    H  HCH2   0   0.256   1.0378   6.5779  -13.9387
 S12  H6A   H  HCH2   0   0.264   2.0416   7.9169  -13.3950
 S12  H7    H  HCH2   0   0.233   4.1025   6.6529  -14.0245
 S12  H8    H  HCH2   0   0.214   2.0543   6.7647  -16.2839
 S12  H9    H  HCH2   0   0.215   5.1026   6.8776  -16.2758
 S12  H9A   H  HCH2   0   0.209   4.1520   5.5404  -16.8844
 S12  HA    H  HCH1   0   0.200   6.8779  10.1334   -5.5300
 S12  HB2   H  HCH2   0   0.195   6.2154   8.2022   -6.8515
 S12  HB3   H  HCH2   0   0.191   6.5393   7.8460   -5.1567
 S12  H10   H  HCH2   0   0.219   3.1039   7.0626  -18.5784
 S12  H11   H  HCH2   0   0.211   5.1619   5.7633  -19.1922
 S12  HO11  H  HOH1   0   0.451   5.7057   6.1545  -11.8311
 S12  H12   H  HCH2   0   0.224   6.6065   8.3995  -18.6169
 S12  H14   H  H      0   0.223   8.3457   8.6619  -20.2587
 S12  C15   C  CH2    0  -0.478   9.5268   7.0745  -21.2319
 S12  C16   C  CH2    0  -0.412   9.3330   7.4976  -22.6878
 S12  C17   C  CH2    0  -0.411  10.4509   6.9912  -23.5903
 S12  C18   C  CH2    0  -0.410  10.3133   7.4278  -25.0427
 S12  C19   C  CH2    0  -0.409  11.4322   6.8947  -25.9290
 S12  C20   C  CH2    0  -0.405  11.3297   7.3462  -27.3797
 S12  C21   C  CH2    0  -0.417  12.4518   6.8052  -28.2575
 S12  C22   C  CH3    0  -0.659  12.3529   7.2694  -29.7037
 S12  H23   H  HCH2   0   0.228   3.1219   5.3028  -14.5614
 S12  H24   H  HCH2   0   0.213   3.0063   8.1238  -15.7211
 S12  H25   H  HCH2   0   0.208   4.1078   8.3789  -18.0124
 S12  H26   H  HCH2   0   0.223   4.9684   7.2530  -20.0894
 S12  H27   H  HCH2   0   0.229   6.7872   6.9405  -17.6611
 S12  H28   H  H      0   0.223   7.7548   5.7304  -19.6600
 S12  H30   H  HCH2   0   0.222  10.4984   7.4505  -20.8910
 S12  H31   H  HCH2   0   0.224   9.5801   5.9833  -21.1705
 S12  H32   H  HCH2   0   0.213   8.3689   7.1263  -23.0493
 S12  H33   H  HCH2   0   0.211   9.2819   8.5901  -22.7460
 S12  H34   H  HCH2   0   0.207  11.4137   7.3390  -23.1997
 S12  H35   H  HCH2   0   0.207  10.4840   5.8972  -23.5418
 S12  H36   H  HCH2   0   0.206   9.3466   7.0942  -25.4357
 S12  H37   H  HCH2   0   0.206  10.2997   8.5220  -25.0936
 S12  H38   H  HCH2   0   0.205  12.3982   7.2115  -25.5200
 S12  H39   H  HCH2   0   0.205  11.4331   5.7999  -25.8886
 S12  H40   H  HCH2   0   0.205  10.3639   7.0337  -27.7923
 S12  H41   H  HCH2   0   0.205  11.3352   8.4412  -27.4211
 S12  H42   H  HCH2   0   0.209  13.4159   7.1116  -27.8397
 S12  H43   H  HCH2   0   0.209  12.4421   5.7114  -28.2216
 S12  H44   H  HCH3   0   0.224  13.1658   6.8689  -30.3105
 S12  H45   H  HCH3   0   0.214  11.4134   6.9491  -30.1582
 S12  H46   H  HCH3   0   0.215  12.3957   8.3580  -29.7727

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
 S12  C    CA    single  1.525  0.021  1.525
 S12  C    O     deloc   1.231  0.020  1.231
 S12  C    OXT   deloc   1.247  0.020  1.247
 S12  N    CA    single  1.458  0.019  1.458
 S12  N    H     single  0.860  0.020  0.860
 S12  N    H2    single  0.890  0.020  1.040
 S12  P    OG    single  1.635  0.020  1.635
 S12  P    O2    single  1.654  0.020  1.654
 S12  P    O3    deloc   1.499  0.020  1.499
 S12  P    O4    deloc   1.494  0.020  1.494
 S12  OG   CB    single  1.418  0.020  1.418
 S12  C2   O2    single  1.407  0.020  1.407
 S12  C2   C3    single  1.516  0.020  1.516
 S12  C2   H2B   single  0.970  0.020  1.090
 S12  C2   H2A   single  0.970  0.020  1.090
 S12  C3   C4    single  1.520  0.020  1.520
 S12  C3   O11   single  1.408  0.020  1.408
 S12  C3   H3    single  0.970  0.020  1.090
 S12  C4   O52   single  1.428  0.020  1.428
 S12  C4   H4    single  0.970  0.020  1.090
 S12  C4   H4A   single  0.970  0.020  1.090
 S12  C5   C6    single  1.505  0.020  1.505
 S12  C5   O51   double  1.205  0.020  1.205
 S12  C5   O52   single  1.330  0.020  1.330
 S12  C6   C7    single  1.530  0.020  1.530
 S12  C6   H6    single  0.970  0.020  1.090
 S12  C6   H6A   single  0.970  0.020  1.090
 S12  C7   C8    single  1.523  0.020  1.523
 S12  C7   H7    single  0.970  0.020  1.090
 S12  C8   C9    single  1.523  0.020  1.523
 S12  C8   H8    single  0.970  0.020  1.090
 S12  C9   C10   single  1.525  0.020  1.525
 S12  C9   H9    single  0.970  0.020  1.090
 S12  C9   H9A   single  0.970  0.020  1.090
 S12  CA   CB    single  1.530  0.020  1.530
 S12  CA   HA    single  0.970  0.020  0.970
 S12  CB   HB2   single  0.970  0.020  1.090
 S12  CB   HB3   single  0.970  0.020  1.090
 S12  C10  C11   single  1.527  0.020  1.527
 S12  C10  H10   single  0.970  0.020  1.090
 S12  C11  C12   single  1.530  0.020  1.530
 S12  C11  H11   single  0.970  0.020  1.090
 S12  O11  HO11  single  0.850  0.020  0.980
 S12  C12  C13   single  1.496  0.020  1.496
 S12  C12  H12   single  0.970  0.020  1.090
 S12  C13  C14   double  1.330  0.020  1.330
 S12  C14  H14   single  0.930  0.020  1.080
 S12  C14  C15   single  1.496  0.020  1.496
 S12  C15  C16   single  1.528  0.020  1.528
 S12  C16  C17   single  1.523  0.020  1.523
 S12  C17  C18   single  1.523  0.020  1.523
 S12  C18  C19   single  1.524  0.020  1.524
 S12  C19  C20   single  1.523  0.020  1.523
 S12  C20  C21   single  1.524  0.020  1.524
 S12  C21  C22   single  1.522  0.020  1.522
 S12  C7   H23   single  0.970  0.020  1.090
 S12  C8   H24   single  0.970  0.020  1.090
 S12  C10  H25   single  0.970  0.020  1.090
 S12  C11  H26   single  0.970  0.020  1.090
 S12  C12  H27   single  0.970  0.020  1.090
 S12  C13  H28   single  0.930  0.020  1.080
 S12  C15  H30   single  0.970  0.020  1.090
 S12  C15  H31   single  0.970  0.020  1.090
 S12  C16  H32   single  0.970  0.020  1.090
 S12  C16  H33   single  0.970  0.020  1.090
 S12  C17  H34   single  0.970  0.020  1.090
 S12  C17  H35   single  0.970  0.020  1.090
 S12  C18  H36   single  0.970  0.020  1.090
 S12  C18  H37   single  0.970  0.020  1.090
 S12  C19  H38   single  0.970  0.020  1.090
 S12  C19  H39   single  0.970  0.020  1.090
 S12  C20  H40   single  0.970  0.020  1.090
 S12  C20  H41   single  0.970  0.020  1.090
 S12  C21  H42   single  0.970  0.020  1.090
 S12  C21  H43   single  0.970  0.020  1.090
 S12  C22  H44   single  0.970  0.020  1.090
 S12  C22  H45   single  0.970  0.020  1.090
 S12  C22  H46   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
 S12  OXT   C    O    126.89  3.000
 S12  OXT   C    CA   117.03  3.000
 S12  O     C    CA   120.80  1.700
 S12  H2    N    H    107.14  3.000
 S12  H2    N    CA   108.21  3.000
 S12  H     N    CA   114.00  3.000
 S12  O4    P    O3   121.84  3.000
 S12  O4    P    O2   107.96  3.000
 S12  O3    P    O2   108.91  3.000
 S12  O4    P    OG   105.76  3.000
 S12  O3    P    OG   110.79  3.000
 S12  O2    P    OG    99.18  3.000
 S12  CB    OG   P    119.33  3.000
 S12  H2A   C2   H2B  107.05  3.000
 S12  H2A   C2   C3   108.52  3.000
 S12  H2B   C2   C3   109.31  3.000
 S12  H2A   C2   O2   111.68  3.000
 S12  H2B   C2   O2   111.68  3.000
 S12  C3    C2   O2   108.53  3.000
 S12  C2    O2   P    121.05  3.000
 S12  H3    C3   O11  111.06  3.000
 S12  H3    C3   C4   108.31  3.000
 S12  O11   C3   C4   111.31  3.000
 S12  H3    C3   C2   108.13  3.000
 S12  O11   C3   C2   108.46  3.000
 S12  C4    C3   C2   109.50  3.000
 S12  H4A   C4   H4   108.37  3.000
 S12  H4A   C4   O52  110.14  3.000
 S12  H4    C4   O52  110.46  3.000
 S12  H4A   C4   C3   110.88  3.000
 S12  H4    C4   C3   110.52  3.000
 S12  O52   C4   C3   106.48  3.000
 S12  O52   C5   O51  123.30  3.000
 S12  O52   C5   C6   111.13  3.000
 S12  O51   C5   C6   125.57  3.000
 S12  H6A   C6   H6   107.30  3.000
 S12  H6A   C6   C7   109.27  3.000
 S12  H6    C6   C7   110.41  3.000
 S12  H6A   C6   C5   108.50  3.000
 S12  H6    C6   C5   108.25  3.000
 S12  C7    C6   C5   112.94  3.000
 S12  H23   C7   H7   106.57  3.000
 S12  H23   C7   C8   109.42  3.000
 S12  H7    C7   C8   109.00  3.000
 S12  H23   C7   C6   109.64  3.000
 S12  H7    C7   C6   109.83  3.000
 S12  C8    C7   C6   112.23  3.000
 S12  H24   C8   H8   106.27  3.000
 S12  H24   C8   C9   109.39  3.000
 S12  H8    C8   C9   109.80  3.000
 S12  H24   C8   C7   109.20  3.000
 S12  H8    C8   C7   109.72  3.000
 S12  C9    C8   C7   112.28  3.000
 S12  H9A   C9   H9   106.10  3.000
 S12  H9A   C9   C10  109.16  3.000
 S12  H9    C9   C10  110.04  3.000
 S12  H9A   C9   C8   109.46  3.000
 S12  H9    C9   C8   108.61  3.000
 S12  C10   C9   C8   113.23  3.000
 S12  HA    CA   CB   109.00  3.000
 S12  HA    CA   N    110.00  3.000
 S12  CB    CA   N    110.50  1.700
 S12  HA    CA   C    109.00  3.000
 S12  CB    CA   C    110.10  1.900
 S12  N     CA   C    111.00  2.800
 S12  HB3   CB   HB2  107.07  3.000
 S12  HB3   CB   CA   109.14  3.000
 S12  HB2   CB   CA   108.73  3.000
 S12  HB3   CB   OG   110.81  3.000
 S12  HB2   CB   OG   110.73  3.000
 S12  CA    CB   OG   110.29  3.000
 S12  H25   C10  H10  106.06  3.000
 S12  H25   C10  C11  109.36  3.000
 S12  H10   C10  C11  108.93  3.000
 S12  H25   C10  C9   109.40  3.000
 S12  H10   C10  C9   108.80  3.000
 S12  C11   C10  C9   113.98  3.000
 S12  H26   C11  H11  106.13  3.000
 S12  H26   C11  C12  108.59  3.000
 S12  H11   C11  C12  109.47  3.000
 S12  H26   C11  C10  109.35  3.000
 S12  H11   C11  C10  109.31  3.000
 S12  C12   C11  C10  113.70  3.000
 S12  HO11  O11  C3   108.60  3.000
 S12  H27   C12  H12  106.47  3.000
 S12  H27   C12  C13  108.75  3.000
 S12  H12   C12  C13  110.02  3.000
 S12  H27   C12  C11  109.27  3.000
 S12  H12   C12  C11  109.44  3.000
 S12  C13   C12  C11  112.69  3.000
 S12  H28   C13  C14  118.67  3.000
 S12  H28   C13  C12  115.92  3.000
 S12  C14   C13  C12  125.41  3.000
 S12  C15   C14  H14  116.20  3.000
 S12  C15   C14  C13  124.97  3.000
 S12  H14   C14  C13  118.84  3.000
 S12  C5    O52  C4   119.20  3.000
 S12  H31   C15  H30  106.35  3.000
 S12  H31   C15  C16  109.61  3.000
 S12  H30   C15  C16  108.28  3.000
 S12  H31   C15  C14  109.74  3.000
 S12  H30   C15  C14  109.25  3.000
 S12  C16   C15  C14  113.37  3.000
 S12  H33   C16  H32  106.24  3.000
 S12  H33   C16  C17  109.53  3.000
 S12  H32   C16  C17  109.75  3.000
 S12  H33   C16  C15  109.43  3.000
 S12  H32   C16  C15  109.41  3.000
 S12  C17   C16  C15  112.29  3.000
 S12  H35   C17  H34  105.94  3.000
 S12  H35   C17  C18  109.34  3.000
 S12  H34   C17  C18  109.17  3.000
 S12  H35   C17  C16  109.14  3.000
 S12  H34   C17  C16  109.16  3.000
 S12  C18   C17  C16  113.80  3.000
 S12  H37   C18  H36  106.05  3.000
 S12  H37   C18  C19  109.36  3.000
 S12  H36   C18  C19  109.44  3.000
 S12  H37   C18  C17  109.38  3.000
 S12  H36   C18  C17  109.55  3.000
 S12  C19   C18  C17  112.84  3.000
 S12  H39   C19  H38  105.93  3.000
 S12  H39   C19  C20  109.36  3.000
 S12  H38   C19  C20  109.22  3.000
 S12  H39   C19  C18  109.19  3.000
 S12  H38   C19  C18  109.21  3.000
 S12  C20   C19  C18  113.64  3.000
 S12  H41   C20  H40  105.97  3.000
 S12  H41   C20  C21  109.23  3.000
 S12  H40   C20  C21  109.32  3.000
 S12  H41   C20  C19  109.39  3.000
 S12  H40   C20  C19  109.48  3.000
 S12  C21   C20  C19  113.20  3.000
 S12  H43   C21  H42  105.97  3.000
 S12  H43   C21  C22  109.59  3.000
 S12  H42   C21  C22  109.54  3.000
 S12  H43   C21  C20  109.24  3.000
 S12  H42   C21  C20  109.23  3.000
 S12  C22   C21  C20  113.03  3.000
 S12  H46   C22  H45  107.46  3.000
 S12  H46   C22  H44  107.56  3.000
 S12  H45   C22  H44  107.58  3.000
 S12  H46   C22  C21  111.20  3.000
 S12  H45   C22  C21  111.23  3.000
 S12  H44   C22  C21  111.60  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
 S12  Var_01  C15  C14  C13  C12   179.57   0.0  2
 S12  Var_02  CA   CB   OG   P    -169.89  30.0  3
 S12  Var_03  C3   C2   O2   P     177.78  30.0  2
 S12  Var_04  O3   P    O2   C2    -12.12  30.0  1
 S12  Var_05  C6   C5   O52  C4   -176.02  30.0  1
 S12  Var_06  C8   C7   C6   C5    179.64  30.0  3
 S12  Var_07  C9   C8   C7   C6    178.45  30.0  3
 S12  Var_08  C10  C9   C8   C7   -178.42  30.0  3
 S12  Var_09  C11  C10  C9   C8   -177.72  30.0  3
 S12  Var_10  C12  C11  C10  C9    -66.83  30.0  3
 S12  Var_11  C13  C12  C11  C10   177.24  30.0  3
 S12  Var_12  C14  C13  C12  C11   117.92  30.0  3
 S12  Var_13  C16  C15  C14  C13   119.95  30.0  3
 S12  Var_14  C17  C16  C15  C14   178.96  30.0  3
 S12  Var_15  C18  C17  C16  C15  -178.31  30.0  3
 S12  Var_16  C19  C18  C17  C16  -179.26  30.0  3
 S12  Var_17  C20  C19  C18  C17  -178.70  30.0  3
 S12  Var_18  C21  C20  C19  C18  -179.88  30.0  3
 S12  Var_19  C22  C21  C20  C19  -179.46  30.0  3
 S12  Var_20  H4   C4   O52  C5     49.13  30.0  1
 S12  Var_21  H44  C22  C21  C20  -179.98  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
 S12  chir_02  C3  C2  C4  O11  positiv
 S12  chir_03  CA  C   N   CB   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
 S12  plan-1  C    0.020
 S12  plan-1  CA   0.020
 S12  plan-1  O    0.020
 S12  plan-1  OXT  0.020
 S12  plan-2  C5   0.020
 S12  plan-2  C6   0.020
 S12  plan-2  O51  0.020
 S12  plan-2  O52  0.020
 S12  plan-3  C12  0.020
 S12  plan-3  C13  0.020
 S12  plan-3  C14  0.020
 S12  plan-3  H14  0.020
 S12  plan-3  C15  0.020
 S12  plan-3  H28  0.020

