# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 12:21:49 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: O-[(R)-hydroxy{[(2R)-2-hydroxy-3-{[(1R)-1-hydroxypentadecyl]oxy}propyl]oxy}phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCC[C@H](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
 LPS  LPS  O-[(R)-hydroxy{[(2R)-2-hydroxy-3-{[(1R)-1-hydroxypentadecyl]oxy}propyl]oxy}phosphoryl]-L-serine  L-peptide  76  32  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LPS
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
 LPS  OT2   O  OH1   0  -0.592   1.6512  -1.1161  -11.8759
 LPS  C     C  C     0   0.545   2.2763  -0.0741  -11.3432
 LPS  OT1   O  O     0  -0.427   2.9028   0.7280  -11.9831
 LPS  C12   C  CH1   0  -0.260   2.0924  -0.0214   -9.8366
 LPS  N     N  NH2   0  -0.777   2.9432   0.9989   -9.2792
 LPS  C11   C  CH2   0  -0.165   0.6011   0.1266   -9.5142
 LPS  O12   O  O2    0  -0.581   0.4873   0.0788   -8.0880
 LPS  P     P  P     0   1.474  -0.9279   0.2756   -7.3812
 LPS  O13   O  O     0  -0.704  -1.6877   1.4932   -7.7163
 LPS  O14   O  OH1   0  -0.744  -1.8093  -1.0148   -7.7135
 LPS  O11   O  O2    0  -0.577  -0.4084   0.1317   -5.8834
 LPS  C1    C  CH2   0  -0.184  -1.3366   0.1872   -4.7957
 LPS  C2    C  CH1   0  -0.056  -0.5733  -0.1030   -3.5135
 LPS  O21   O  OH1   0  -0.652   0.1051  -1.3313   -3.5711
 LPS  C3    C  CH2   0  -0.161  -1.5349  -0.0227   -2.3376
 LPS  O31   O  O2    0  -0.499  -0.8027  -0.2031   -1.1503
 LPS  C31   C  CH1   0   0.309  -1.5555  -0.1123    0.0291
 LPS  O32   O  OH1   0  -0.661  -2.5040  -1.1333    0.1248
 LPS  C32   C  CH2   0  -0.506  -0.5719  -0.1080    1.1875
 LPS  C33   C  CH2   0  -0.418  -1.2472   0.0150    2.5475
 LPS  C34   C  CH2   0  -0.413  -0.2466   0.0309    3.6964
 LPS  C35   C  CH2   0  -0.412  -0.9127   0.1135    5.0640
 LPS  C36   C  CH2   0  -0.412   0.0807   0.1101    6.2191
 LPS  C37   C  CH2   0  -0.412  -0.5892   0.1552    7.5868
 LPS  C38   C  CH2   0  -0.412   0.4006   0.1449    8.7452
 LPS  C39   C  CH2   0  -0.412  -0.2743   0.1591   10.1111
 LPS  C40   C  CH2   0  -0.412   0.7111   0.1461   11.2732
 LPS  C41   C  CH2   0  -0.411   0.0301   0.1397   12.6362
 LPS  C42   C  CH2   0  -0.412   1.0099   0.1264   13.8029
 LPS  C43   C  CH2   0  -0.406   0.3223   0.1090   15.1624
 LPS  C44   C  CH2   0  -0.419   1.2959   0.0974   16.3347
 LPS  C45   C  CH3   0  -0.661   0.5917   0.0742   17.6845
 LPS  HT2   H  HOH1  0   0.486   1.7665  -1.1196  -12.8383
 LPS  H12   H  HCH1  0   0.292   2.4182  -0.9908   -9.4433
 LPS  HN1   H  HNH2  0   0.349   2.6404   1.9195   -9.5736
 LPS  HN2   H  HNH2  0   0.361   2.8786   0.9805   -8.2703
 LPS  H111  H  HCH2  0   0.252   0.0139  -0.6777   -9.9612
 LPS  H112  H  HCH2  0   0.249   0.2285   1.0842   -9.8903
 LPS  H14   H  HOH1  0   0.497  -1.3944  -1.8708   -7.5413
 LPS  H11   H  HCH2  0   0.249  -1.7990   1.1757   -4.7445
 LPS  H12A  H  HCH2  0   0.239  -2.1312  -0.5532   -4.9365
 LPS  H2    H  HCH1  0   0.246   0.1991   0.6624   -3.3888
 LPS  H21   H  HOH1  0   0.446  -0.5417  -2.0440   -3.6229
 LPS  H31A  H  HCH2  0   0.212  -2.0414   0.9526   -2.3415
 LPS  H32A  H  HCH2  0   0.210  -2.3130  -0.7887   -2.4513
 LPS  H31   H  HCH1  0   0.196  -2.1419   0.8179    0.0282
 LPS  H32   H  HOH1  0   0.449  -2.0480  -1.9667    0.2947
 LPS  H321  H  HCH2  0   0.229   0.0267  -1.0267    1.1507
 LPS  H322  H  HCH2  0   0.234   0.1255   0.7230    1.0496
 LPS  H331  H  HCH2  0   0.214  -1.8499   0.9295    2.5778
 LPS  H332  H  HCH2  0   0.215  -1.9446  -0.8147    2.6929
 LPS  H341  H  HCH2  0   0.209   0.3721  -0.8724    3.6493
 LPS  H342  H  HCH2  0   0.210   0.4410   0.8747    3.5727
 LPS  H351  H  HCH2  0   0.208  -1.5286   1.0184    5.1161
 LPS  H352  H  HCH2  0   0.207  -1.6040  -0.7288    5.1799
 LPS  H361  H  HCH2  0   0.206   0.7091  -0.7855    6.1534
 LPS  H362  H  HCH2  0   0.207   0.7606   0.9633    6.1170
 LPS  H371  H  HCH2  0   0.206  -1.2189   1.0495    7.6550
 LPS  H372  H  HCH2  0   0.206  -1.2685  -0.6992    7.6847
 LPS  H381  H  HCH2  0   0.206   1.0410  -0.7410    8.6667
 LPS  H382  H  HCH2  0   0.206   1.0695   1.0086    8.6593
 LPS  H391  H  HCH2  0   0.206  -0.9168   1.0433   10.1904
 LPS  H392  H  HCH2  0   0.206  -0.9418  -0.7061   10.1939
 LPS  H401  H  HCH2  0   0.206   1.3605  -0.7326   11.1881
 LPS  H402  H  HCH2  0   0.206   1.3716   1.0173   11.1994
 LPS  H411  H  HCH2  0   0.206  -0.6222   1.0163   12.7208
 LPS  H412  H  HCH2  0   0.206  -0.6287  -0.7332   12.7075
 LPS  H421  H  HCH2  0   0.206   1.6656  -0.7474   13.7162
 LPS  H422  H  HCH2  0   0.206   1.6650   1.0024   13.7370
 LPS  H431  H  HCH2  0   0.205  -0.3359   0.9811   15.2482
 LPS  H432  H  HCH2  0   0.205  -0.3314  -0.7683   15.2275
 LPS  H441  H  HCH2  0   0.210   1.9543  -0.7726   16.2488
 LPS  H442  H  HCH2  0   0.210   1.9459   0.9757   16.2735
 LPS  H451  H  HCH3  0   0.225   1.3026   0.0679   18.5115
 LPS  H452  H  HCH3  0   0.215  -0.0512   0.9483   17.8077
 LPS  H453  H  HCH3  0   0.215  -0.0386  -0.8120   17.7835

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
 LPS  OT2  C     single  1.327  0.020  1.327
 LPS  OT2  HT2   single  0.850  0.020  0.980
 LPS  C    OT1   double  1.202  0.020  1.202
 LPS  C    C12   single  1.519  0.020  1.519
 LPS  C12  N     single  1.441  0.020  1.441
 LPS  C12  C11   single  1.533  0.020  1.533
 LPS  C12  H12   single  0.970  0.020  1.090
 LPS  N    HN1   single  0.890  0.020  1.040
 LPS  N    HN2   single  0.890  0.020  1.040
 LPS  C11  O12   single  1.432  0.020  1.432
 LPS  C11  H111  single  0.970  0.020  1.090
 LPS  C11  H112  single  0.970  0.020  1.090
 LPS  O12  P     single  1.594  0.020  1.594
 LPS  P    O13   double  1.474  0.020  1.474
 LPS  P    O14   single  1.598  0.020  1.598
 LPS  P    O11   single  1.592  0.020  1.592
 LPS  O14  H14   single  0.850  0.020  0.980
 LPS  O11  C1    single  1.431  0.020  1.431
 LPS  C1   C2    single  1.520  0.020  1.520
 LPS  C1   H11   single  0.970  0.020  1.090
 LPS  C1   H12A  single  0.970  0.020  1.090
 LPS  C2   O21   single  1.404  0.020  1.404
 LPS  C2   C3    single  1.521  0.020  1.521
 LPS  C2   H2    single  0.970  0.020  1.090
 LPS  O21  H21   single  0.850  0.020  0.980
 LPS  C3   O31   single  1.406  0.020  1.406
 LPS  C3   H31A  single  0.970  0.020  1.090
 LPS  C3   H32A  single  0.970  0.020  1.090
 LPS  O31  C31   single  1.402  0.020  1.402
 LPS  C31  O32   single  1.397  0.020  1.397
 LPS  C31  C32   single  1.520  0.020  1.520
 LPS  C31  H31   single  0.970  0.020  1.090
 LPS  O32  H32   single  0.850  0.020  0.980
 LPS  C32  C33   single  1.523  0.020  1.523
 LPS  C32  H321  single  0.970  0.020  1.090
 LPS  C32  H322  single  0.970  0.020  1.090
 LPS  C33  C34   single  1.524  0.020  1.524
 LPS  C33  H331  single  0.970  0.020  1.090
 LPS  C33  H332  single  0.970  0.020  1.090
 LPS  C34  C35   single  1.523  0.020  1.523
 LPS  C34  H341  single  0.970  0.020  1.090
 LPS  C34  H342  single  0.970  0.020  1.090
 LPS  C35  C36   single  1.524  0.020  1.524
 LPS  C35  H351  single  0.970  0.020  1.090
 LPS  C35  H352  single  0.970  0.020  1.090
 LPS  C36  C37   single  1.524  0.020  1.524
 LPS  C36  H361  single  0.970  0.020  1.090
 LPS  C36  H362  single  0.970  0.020  1.090
 LPS  C37  C38   single  1.524  0.020  1.524
 LPS  C37  H371  single  0.970  0.020  1.090
 LPS  C37  H372  single  0.970  0.020  1.090
 LPS  C38  C39   single  1.524  0.020  1.524
 LPS  C38  H381  single  0.970  0.020  1.090
 LPS  C38  H382  single  0.970  0.020  1.090
 LPS  C39  C40   single  1.524  0.020  1.524
 LPS  C39  H391  single  0.970  0.020  1.090
 LPS  C39  H392  single  0.970  0.020  1.090
 LPS  C40  C41   single  1.524  0.020  1.524
 LPS  C40  H401  single  0.970  0.020  1.090
 LPS  C40  H402  single  0.970  0.020  1.090
 LPS  C41  C42   single  1.524  0.020  1.524
 LPS  C41  H411  single  0.970  0.020  1.090
 LPS  C41  H412  single  0.970  0.020  1.090
 LPS  C42  C43   single  1.524  0.020  1.524
 LPS  C42  H421  single  0.970  0.020  1.090
 LPS  C42  H422  single  0.970  0.020  1.090
 LPS  C43  C44   single  1.524  0.020  1.524
 LPS  C43  H431  single  0.970  0.020  1.090
 LPS  C43  H432  single  0.970  0.020  1.090
 LPS  C44  C45   single  1.523  0.020  1.523
 LPS  C44  H441  single  0.970  0.020  1.090
 LPS  C44  H442  single  0.970  0.020  1.090
 LPS  C45  H451  single  0.970  0.020  1.090
 LPS  C45  H452  single  0.970  0.020  1.090
 LPS  C45  H453  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
 LPS  HT2   OT2  C     110.20  3.000
 LPS  C12   C    OT1   124.61  3.000
 LPS  C12   C    OT2   111.62  3.000
 LPS  OT1   C    OT2   123.77  3.000
 LPS  H12   C12  C11   107.41  3.000
 LPS  H12   C12  N     108.19  3.000
 LPS  C11   C12  N     115.13  3.000
 LPS  H12   C12  C     106.82  3.000
 LPS  C11   C12  C     109.26  3.000
 LPS  N     C12  C     109.69  3.000
 LPS  HN2   N    HN1   106.71  3.000
 LPS  HN2   N    C12   109.60  3.000
 LPS  HN1   N    C12   110.78  3.000
 LPS  H112  C11  H111  108.72  3.000
 LPS  H112  C11  O12   110.16  3.000
 LPS  H111  C11  O12   109.91  3.000
 LPS  H112  C11  C12   110.09  3.000
 LPS  H111  C11  C12   111.47  3.000
 LPS  O12   C11  C12   106.48  3.000
 LPS  P     O12  C11   120.54  3.000
 LPS  O11   P    O14   107.62  3.000
 LPS  O11   P    O13   117.19  3.000
 LPS  O14   P    O13   109.61  3.000
 LPS  O11   P    O12    96.68  3.000
 LPS  O14   P    O12   107.33  3.000
 LPS  O13   P    O12   117.31  3.000
 LPS  H14   O14  P     116.19  3.000
 LPS  C1    O11  P     120.00  3.000
 LPS  H12A  C1   H11   108.09  3.000
 LPS  H12A  C1   C2    110.10  3.000
 LPS  H11   C1   C2    110.23  3.000
 LPS  H12A  C1   O11   110.29  3.000
 LPS  H11   C1   O11   110.20  3.000
 LPS  C2    C1   O11   107.94  3.000
 LPS  H2    C2   C3    108.73  3.000
 LPS  H2    C2   O21   105.98  3.000
 LPS  C3    C2   O21   112.53  3.000
 LPS  H2    C2   C1    108.48  3.000
 LPS  C3    C2   C1    108.94  3.000
 LPS  O21   C2   C1    112.02  3.000
 LPS  H21   O21  C2    108.95  3.000
 LPS  H32A  C3   H31A  106.99  3.000
 LPS  H32A  C3   O31   111.53  3.000
 LPS  H31A  C3   O31   110.90  3.000
 LPS  H32A  C3   C2    109.34  3.000
 LPS  H31A  C3   C2    109.60  3.000
 LPS  O31   C3   C2    108.47  3.000
 LPS  C31   O31  C3    114.98  3.000
 LPS  H31   C31  C32   110.08  3.000
 LPS  H31   C31  O32   104.85  3.000
 LPS  C32   C31  O32   112.91  3.000
 LPS  H31   C31  O31   109.90  3.000
 LPS  C32   C31  O31   107.09  3.000
 LPS  O32   C31  O31   112.02  3.000
 LPS  H32   O32  C31   108.81  3.000
 LPS  H322  C32  H321  106.51  3.000
 LPS  H322  C32  C33   109.51  3.000
 LPS  H321  C32  C33   109.84  3.000
 LPS  H322  C32  C31   108.59  3.000
 LPS  H321  C32  C31   108.97  3.000
 LPS  C33   C32  C31   113.19  3.000
 LPS  H332  C33  H331  106.19  3.000
 LPS  H332  C33  C34   109.06  3.000
 LPS  H331  C33  C34   109.37  3.000
 LPS  H332  C33  C32   109.88  3.000
 LPS  H331  C33  C32   109.62  3.000
 LPS  C34   C33  C32   112.51  3.000
 LPS  H342  C34  H341  106.00  3.000
 LPS  H342  C34  C35   109.52  3.000
 LPS  H341  C34  C35   109.27  3.000
 LPS  H342  C34  C33   109.58  3.000
 LPS  H341  C34  C33   109.25  3.000
 LPS  C35   C34  C33   112.98  3.000
 LPS  H352  C35  H351  105.97  3.000
 LPS  H352  C35  C36   109.23  3.000
 LPS  H351  C35  C36   109.40  3.000
 LPS  H352  C35  C34   109.22  3.000
 LPS  H351  C35  C34   109.46  3.000
 LPS  C36   C35  C34   113.29  3.000
 LPS  H362  C36  H361  105.96  3.000
 LPS  H362  C36  C37   109.48  3.000
 LPS  H361  C36  C37   109.27  3.000
 LPS  H362  C36  C35   109.40  3.000
 LPS  H361  C36  C35   109.28  3.000
 LPS  C37   C36  C35   113.19  3.000
 LPS  H372  C37  H371  105.93  3.000
 LPS  H372  C37  C38   109.24  3.000
 LPS  H371  C37  C38   109.35  3.000
 LPS  H372  C37  C36   109.25  3.000
 LPS  H371  C37  C36   109.43  3.000
 LPS  C38   C37  C36   113.37  3.000
 LPS  H382  C38  H381  105.95  3.000
 LPS  H382  C38  C39   109.47  3.000
 LPS  H381  C38  C39   109.30  3.000
 LPS  H382  C38  C37   109.37  3.000
 LPS  H381  C38  C37   109.31  3.000
 LPS  C39   C38  C37   113.19  3.000
 LPS  H392  C39  H391  105.93  3.000
 LPS  H392  C39  C40   109.24  3.000
 LPS  H391  C39  C40   109.32  3.000
 LPS  H392  C39  C38   109.28  3.000
 LPS  H391  C39  C38   109.40  3.000
 LPS  C40   C39  C38   113.40  3.000
 LPS  H402  C40  H401  105.97  3.000
 LPS  H402  C40  C41   109.45  3.000
 LPS  H401  C40  C41   109.33  3.000
 LPS  H402  C40  C39   109.37  3.000
 LPS  H401  C40  C39   109.32  3.000
 LPS  C41   C40  C39   113.16  3.000
 LPS  H412  C41  H411  105.92  3.000
 LPS  H412  C41  C42   109.26  3.000
 LPS  H411  C41  C42   109.30  3.000
 LPS  H412  C41  C40   109.28  3.000
 LPS  H411  C41  C40   109.38  3.000
 LPS  C42   C41  C40   113.43  3.000
 LPS  H422  C42  H421  105.96  3.000
 LPS  H422  C42  C43   109.43  3.000
 LPS  H421  C42  C43   109.36  3.000
 LPS  H422  C42  C41   109.35  3.000
 LPS  H421  C42  C41   109.34  3.000
 LPS  C43   C42  C41   113.15  3.000
 LPS  H432  C43  H431  105.91  3.000
 LPS  H432  C43  C44   109.23  3.000
 LPS  H431  C43  C44   109.24  3.000
 LPS  H432  C43  C42   109.35  3.000
 LPS  H431  C43  C42   109.38  3.000
 LPS  C44   C43  C42   113.46  3.000
 LPS  H442  C44  H441  106.04  3.000
 LPS  H442  C44  C45   109.66  3.000
 LPS  H441  C44  C45   109.62  3.000
 LPS  H442  C44  C43   109.29  3.000
 LPS  H441  C44  C43   109.27  3.000
 LPS  C45   C44  C43   112.74  3.000
 LPS  H453  C45  H452  107.43  3.000
 LPS  H453  C45  H451  107.63  3.000
 LPS  H452  C45  H451  107.63  3.000
 LPS  H453  C45  C44   111.08  3.000
 LPS  H452  C45  C44   111.10  3.000
 LPS  H451  C45  C44   111.77  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
 LPS  CONST_01  HT2   OT2  C    OT1     0.00   0.0  0
 LPS  Var_01    O13   P    O12  C11   -54.32  30.0  3
 LPS  Var_02    C2    C1   O11  P     174.97  30.0  3
 LPS  Var_03    C34   C33  C32  C31  -179.46  30.0  3
 LPS  Var_04    C35   C34  C33  C32  -178.35  30.0  3
 LPS  Var_05    C36   C35  C34  C33   179.19  30.0  3
 LPS  Var_06    C37   C36  C35  C34  -178.46  30.0  3
 LPS  Var_07    C38   C37  C36  C35   179.71  30.0  3
 LPS  Var_08    C39   C38  C37  C36  -178.73  30.0  3
 LPS  Var_09    C40   C39  C38  C37   179.88  30.0  3
 LPS  Var_10    C41   C40  C39  C38  -179.15  30.0  3
 LPS  Var_11    C42   C41  C40  C39   179.99  30.0  3
 LPS  Var_12    C43   C42  C41  C40  -179.55  30.0  3
 LPS  Var_13    C44   C43  C42  C41  -179.93  30.0  3
 LPS  Var_14    C45   C44  C43  C42  -179.76  30.0  3
 LPS  Var_15    H111  C11  O12  P     -62.16  30.0  1
 LPS  Var_16    H31A  C3   O31  C31    57.70  30.0  1
 LPS  Var_17    H451  C45  C44  C43  -179.90  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
 LPS  chir_01  C12  C    N    C11  negativ
 LPS  chir_03  C2   O21  C1   C3   negativ
 LPS  chir_04  C31  O31  O32  C32  negativ
 LPS  chir_05  P    O13  O14  O11  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
 LPS  plan-1  OT2  0.020
 LPS  plan-1  C    0.020
 LPS  plan-1  OT1  0.020
 LPS  plan-1  C12  0.020
 LPS  plan-1  HT2  0.020

