# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 09:04:35 2021
#   Inital geometry file: a 169 line input string
#   Ligand name: (2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P](O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O
#
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
 LPY  LPY  '(2R)-2-hydroxy-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl tridecanoate'  ligand  78  35  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LPY
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
 LPY  P    P  P     0   1.476  -11.2853   3.4479  21.4293
 LPY  O1   O  OH1   0  -0.676   -9.0295  -0.3627  25.7501
 LPY  O2   O  OH1   0  -0.661   -8.9408   0.7725  23.1685
 LPY  O3   O  O2    0  -0.593  -10.5122   2.9711  22.7327
 LPY  O4   O  OH1   0  -0.711  -11.8560   4.8654  21.8565
 LPY  O5   O  O     0  -0.716  -12.2776   2.4850  20.8877
 LPY  O7   O  O     0  -0.454   -6.9758  -0.1414  16.5576
 LPY  O8   O  OH1   0  -0.686  -10.5151   0.9857  19.2954
 LPY  O9   O  O2    0  -0.452   -9.0075   0.6570  17.0189
 LPY  O10  O  O2    0  -0.573  -10.1001   3.8460  20.4457
 LPY  O11  O  OH1   0  -0.662  -11.3822   3.4695  25.2962
 LPY  O12  O  OH1   0  -0.675  -13.3326   1.7812  26.4114
 LPY  C15  C  CH1   0  -0.039   -9.6757   2.0152  18.8455
 LPY  C16  C  CH2   0  -0.210   -9.1335   2.8964  19.9683
 LPY  C17  C  CH1   0  -0.001  -11.1898   0.6597  26.1860
 LPY  C20  C  CH1   0   0.012  -12.4011   1.2695  25.4919
 LPY  C26  C  CH1   0  -0.016  -10.1968   0.1488  25.1459
 LPY  C29  C  CH3   0  -0.662  -10.8404   1.8003   1.4808
 LPY  C30  C  CH2   0  -0.419  -10.7972   0.8398   2.6615
 LPY  C31  C  CH2   0  -0.406  -10.6239   1.5533   3.9970
 LPY  C32  C  CH2   0  -0.411  -10.5776   0.6030   5.1868
 LPY  C33  C  CH2   0  -0.411  -10.3677   1.3123   6.5191
 LPY  C34  C  CH2   0  -0.412  -10.3126   0.3550   7.7032
 LPY  C35  C  CH2   0  -0.412  -10.0291   1.0454   9.0319
 LPY  C36  C  CH2   0  -0.412   -9.9691   0.0733  10.2043
 LPY  C37  C  CH2   0  -0.414   -9.5321   0.7219  11.5117
 LPY  C38  C  CH2   0  -0.415   -9.4628  -0.2650  12.6710
 LPY  C39  C  CH2   0  -0.433   -8.8912   0.3533  13.9398
 LPY  C40  C  CH2   0  -0.541   -8.8077  -0.6612  15.0868
 LPY  C41  C  CH1   0   0.035   -9.7529   1.2660  24.2027
 LPY  C42  C  C     0   0.574   -8.1492  -0.0503  16.2913
 LPY  C43  C  CH1   0   0.005  -10.9756   1.9011  23.5606
 LPY  C44  C  CH1   0  -0.029  -11.9770   2.4190  24.5815
 LPY  C45  C  CH2   0  -0.175   -8.4968   1.3700  18.1429
 LPY  H1   H  HOH1  0   0.459   -9.2127  -1.2497  26.0732
 LPY  H2   H  HOH1  0   0.452   -8.1837   0.3347  23.5723
 LPY  H3   H  HOH1  0   0.507  -12.5754   5.1935  21.2995
 LPY  H4   H  HOH1  0   0.457  -11.3011   1.3715  19.7128
 LPY  H5   H  HOH1  0   0.455  -11.9918   3.7377  25.9925
 LPY  H6   H  HOH1  0   0.453  -13.4726   1.1142  27.0931
 LPY  H7   H  HOH1  0   0.461  -11.0971  -0.4494  27.7887
 LPY  H8   H  HCH1  0   0.227  -10.1879   2.6726  18.1263
 LPY  H9   H  HCH2  0   0.253   -8.7599   2.2858  20.7951
 LPY  H10  H  HCH2  0   0.257   -8.3098   3.5044  19.5953
 LPY  H11  H  HCH1  0   0.228  -10.7002   1.4323  26.7934
 LPY  H12  H  HCH1  0   0.217  -12.8641   0.4955  24.8590
 LPY  H13  H  HCH1  0   0.221  -10.6905  -0.6308  24.5454
 LPY  H14  H  HCH3  0   0.225  -10.9518   1.2709   0.5338
 LPY  H15  H  HCH3  0   0.216  -11.6759   2.4965   1.5714
 LPY  H16  H  HCH3  0   0.215   -9.9243   2.3914   1.4223
 LPY  H17  H  HCH2  0   0.210  -11.7151   0.2438   2.6842
 LPY  H18  H  HCH2  0   0.210   -9.9779   0.1268   2.5254
 LPY  H19  H  HCH2  0   0.205   -9.7036   2.1482   3.9720
 LPY  H20  H  HCH2  0   0.206  -11.4422   2.2691   4.1346
 LPY  H21  H  HCH2  0   0.206  -11.5067   0.0229   5.2241
 LPY  H22  H  HCH2  0   0.205   -9.7727  -0.1252   5.0367
 LPY  H23  H  HCH2  0   0.205   -9.4379   1.8911   6.4785
 LPY  H24  H  HCH2  0   0.207  -11.1710   2.0408   6.6749
 LPY  H25  H  HCH2  0   0.207  -11.2578  -0.1957   7.7688
 LPY  H26  H  HCH2  0   0.206   -9.5368  -0.3971   7.5219
 LPY  H27  H  HCH2  0   0.205   -9.0772   1.5837   8.9610
 LPY  H28  H  HCH2  0   0.208  -10.7943   1.8058   9.2218
 LPY  H29  H  HCH2  0   0.209  -10.9482  -0.4005  10.3350
 LPY  H30  H  HCH2  0   0.206   -9.2720  -0.7363   9.9612
 LPY  H31  H  HCH2  0   0.208   -8.5472   1.1805  11.3713
 LPY  H32  H  HCH2  0   0.211  -10.2142   1.5398  11.7671
 LPY  H33  H  HCH2  0   0.216  -10.4619  -0.6642  12.8740
 LPY  H34  H  HCH2  0   0.214   -8.8451  -1.1210  12.3787
 LPY  H35  H  HCH2  0   0.231   -7.8916   0.7450  13.7304
 LPY  H36  H  HCH2  0   0.233   -9.5043   1.2056  14.2454
 LPY  H37  H  HCH2  0   0.259   -9.8087  -1.0145  15.3416
 LPY  H38  H  HCH2  0   0.259   -8.2165  -1.5221  14.7720
 LPY  H39  H  HCH1  0   0.226   -9.2205   2.0267  24.7920
 LPY  H40  H  HCH1  0   0.268  -11.4782   1.1492  22.9418
 LPY  H41  H  HCH1  0   0.248  -12.8707   2.7662  24.0402
 LPY  H42  H  HCH2  0   0.242   -7.9695   0.6938  18.8216
 LPY  H43  H  HCH2  0   0.245   -7.7930   2.1366  17.8109
 LPY  O13  O  OH1   0  -0.680  -11.6530  -0.3933  27.0071

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
 LPY  C29  C30  single  1.523  0.020  1.523
 LPY  C30  C31  single  1.524  0.020  1.524
 LPY  C31  C32  single  1.523  0.020  1.523
 LPY  C32  C33  single  1.524  0.020  1.524
 LPY  C33  C34  single  1.524  0.020  1.524
 LPY  C34  C35  single  1.524  0.020  1.524
 LPY  C35  C36  single  1.524  0.020  1.524
 LPY  C36  C37  single  1.523  0.020  1.523
 LPY  C37  C38  single  1.524  0.020  1.524
 LPY  C38  C39  single  1.523  0.020  1.523
 LPY  C39  C40  single  1.534  0.020  1.534
 LPY  C40  C42  single  1.502  0.020  1.502
 LPY  C42  O7   double  1.207  0.020  1.207
 LPY  C42  O9   single  1.329  0.020  1.329
 LPY  O9   C45  single  1.426  0.020  1.426
 LPY  C45  C15  single  1.516  0.020  1.516
 LPY  O8   C15  single  1.402  0.020  1.402
 LPY  C15  C16  single  1.527  0.020  1.527
 LPY  C16  O10  single  1.437  0.020  1.437
 LPY  O10  P    single  1.591  0.020  1.591
 LPY  O5   P    double  1.485  0.020  1.485
 LPY  P    O3   single  1.589  0.020  1.589
 LPY  P    O4   single  1.587  0.020  1.587
 LPY  O3   C43  single  1.430  0.020  1.430
 LPY  O2   C41  single  1.404  0.020  1.404
 LPY  C43  C41  single  1.520  0.020  1.520
 LPY  C43  C44  single  1.521  0.020  1.521
 LPY  C41  C26  single  1.528  0.020  1.528
 LPY  C44  O11  single  1.403  0.020  1.403
 LPY  C44  C20  single  1.526  0.020  1.526
 LPY  C26  O1   single  1.410  0.020  1.410
 LPY  C26  C17  single  1.526  0.020  1.526
 LPY  C20  C17  single  1.523  0.020  1.523
 LPY  C20  O12  single  1.405  0.020  1.405
 LPY  C17  O13  single  1.413  0.020  1.413
 LPY  O1   H1   single  0.850  0.020  0.980
 LPY  O2   H2   single  0.850  0.020  0.980
 LPY  O4   H3   single  0.850  0.020  0.980
 LPY  O8   H4   single  0.850  0.020  0.980
 LPY  O11  H5   single  0.850  0.020  0.980
 LPY  O12  H6   single  0.850  0.020  0.980
 LPY  O13  H7   single  0.850  0.020  0.980
 LPY  C15  H8   single  0.970  0.020  1.090
 LPY  C16  H9   single  0.970  0.020  1.090
 LPY  C16  H10  single  0.970  0.020  1.090
 LPY  C17  H11  single  0.970  0.020  1.090
 LPY  C20  H12  single  0.970  0.020  1.090
 LPY  C26  H13  single  0.970  0.020  1.090
 LPY  C29  H14  single  0.970  0.020  1.090
 LPY  C29  H15  single  0.970  0.020  1.090
 LPY  C29  H16  single  0.970  0.020  1.090
 LPY  C30  H17  single  0.970  0.020  1.090
 LPY  C30  H18  single  0.970  0.020  1.090
 LPY  C31  H19  single  0.970  0.020  1.090
 LPY  C31  H20  single  0.970  0.020  1.090
 LPY  C32  H21  single  0.970  0.020  1.090
 LPY  C32  H22  single  0.970  0.020  1.090
 LPY  C33  H23  single  0.970  0.020  1.090
 LPY  C33  H24  single  0.970  0.020  1.090
 LPY  C34  H25  single  0.970  0.020  1.090
 LPY  C34  H26  single  0.970  0.020  1.090
 LPY  C35  H27  single  0.970  0.020  1.090
 LPY  C35  H28  single  0.970  0.020  1.090
 LPY  C36  H29  single  0.970  0.020  1.090
 LPY  C36  H30  single  0.970  0.020  1.090
 LPY  C37  H31  single  0.970  0.020  1.090
 LPY  C37  H32  single  0.970  0.020  1.090
 LPY  C38  H33  single  0.970  0.020  1.090
 LPY  C38  H34  single  0.970  0.020  1.090
 LPY  C39  H35  single  0.970  0.020  1.090
 LPY  C39  H36  single  0.970  0.020  1.090
 LPY  C40  H37  single  0.970  0.020  1.090
 LPY  C40  H38  single  0.970  0.020  1.090
 LPY  C41  H39  single  0.970  0.020  1.090
 LPY  C43  H40  single  0.970  0.020  1.090
 LPY  C44  H41  single  0.970  0.020  1.090
 LPY  C45  H42  single  0.970  0.020  1.090
 LPY  C45  H43  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
 LPY  O10  P    O5   115.76  3.000
 LPY  O5   P    O4   115.92  3.000
 LPY  O10  P    O4   102.17  3.000
 LPY  O4   P    O3   102.84  3.000
 LPY  O5   P    O3   115.46  3.000
 LPY  O10  P    O3   102.70  3.000
 LPY  H1   O1   C26  108.72  3.000
 LPY  H2   O2   C41  107.79  3.000
 LPY  C43  O3   P    122.80  3.000
 LPY  H3   O4   P    114.55  3.000
 LPY  H4   O8   C15  109.33  3.000
 LPY  C45  O9   C42  117.80  3.000
 LPY  C16  O10  P    122.77  3.000
 LPY  H5   O11  C44  107.95  3.000
 LPY  H6   O12  C20  107.88  3.000
 LPY  H8   C15  C45  108.25  3.000
 LPY  H8   C15  C16  107.52  3.000
 LPY  C45  C15  C16  108.07  3.000
 LPY  H8   C15  O8   111.68  3.000
 LPY  C16  C15  O8   113.59  3.000
 LPY  C45  C15  O8   107.55  3.000
 LPY  H10  C16  H9   108.19  3.000
 LPY  H10  C16  C15  109.80  3.000
 LPY  H9   C16  C15  110.80  3.000
 LPY  H10  C16  O10  104.68  3.000
 LPY  H9   C16  O10  110.35  3.000
 LPY  C15  C16  O10  112.77  3.000
 LPY  H11  C17  C26  108.81  3.000
 LPY  H11  C17  C20  108.96  3.000
 LPY  C26  C17  C20  109.93  3.000
 LPY  H11  C17  O13  110.43  3.000
 LPY  C20  C17  O13  107.60  3.000
 LPY  C26  C17  O13  111.09  3.000
 LPY  H12  C20  C44  107.65  3.000
 LPY  H12  C20  C17  108.34  3.000
 LPY  C44  C20  C17  110.63  3.000
 LPY  H12  C20  O12  110.68  3.000
 LPY  C17  C20  O12  112.00  3.000
 LPY  C44  C20  O12  107.47  3.000
 LPY  H13  C26  C41  108.14  3.000
 LPY  H13  C26  C17  108.48  3.000
 LPY  C41  C26  C17  111.41  3.000
 LPY  H13  C26  O1   110.36  3.000
 LPY  C17  C26  O1   111.59  3.000
 LPY  C41  C26  O1   106.81  3.000
 LPY  H16  C29  H15  107.54  3.000
 LPY  H16  C29  H14  107.57  3.000
 LPY  H15  C29  H14  107.67  3.000
 LPY  H16  C29  C30  111.06  3.000
 LPY  H15  C29  C30  111.09  3.000
 LPY  H14  C29  C30  111.72  3.000
 LPY  H18  C30  H17  106.00  3.000
 LPY  H18  C30  C31  109.20  3.000
 LPY  H17  C30  C31  109.39  3.000
 LPY  H18  C30  C29  109.61  3.000
 LPY  H17  C30  C29  109.62  3.000
 LPY  C31  C30  C29  112.79  3.000
 LPY  H20  C31  H19  105.98  3.000
 LPY  H20  C31  C32  109.39  3.000
 LPY  H19  C31  C32  109.32  3.000
 LPY  H20  C31  C30  109.33  3.000
 LPY  H19  C31  C30  109.24  3.000
 LPY  C32  C31  C30  113.32  3.000
 LPY  H22  C32  H21  106.00  3.000
 LPY  H22  C32  C33  109.15  3.000
 LPY  H21  C32  C33  109.47  3.000
 LPY  H22  C32  C31  109.26  3.000
 LPY  H21  C32  C31  109.33  3.000
 LPY  C33  C32  C31  113.37  3.000
 LPY  H24  C33  H23  106.03  3.000
 LPY  H24  C33  C34  109.49  3.000
 LPY  H23  C33  C34  109.26  3.000
 LPY  H24  C33  C32  109.44  3.000
 LPY  H23  C33  C32  109.29  3.000
 LPY  C34  C33  C32  113.08  3.000
 LPY  H26  C34  H25  106.00  3.000
 LPY  H26  C34  C35  108.88  3.000
 LPY  H25  C34  C35  109.63  3.000
 LPY  H26  C34  C33  109.16  3.000
 LPY  H25  C34  C33  109.34  3.000
 LPY  C35  C34  C33  113.56  3.000
 LPY  H28  C35  H27  106.08  3.000
 LPY  H28  C35  C36  109.69  3.000
 LPY  H27  C35  C36  109.20  3.000
 LPY  H28  C35  C34  109.61  3.000
 LPY  H27  C35  C34  109.13  3.000
 LPY  C36  C35  C34  112.90  3.000
 LPY  H30  C36  H29  105.99  3.000
 LPY  H30  C36  C37  108.82  3.000
 LPY  H29  C36  C37  109.76  3.000
 LPY  H30  C36  C35  109.01  3.000
 LPY  H29  C36  C35  109.41  3.000
 LPY  C37  C36  C35  113.57  3.000
 LPY  H32  C37  H31  106.09  3.000
 LPY  H32  C37  C38  109.54  3.000
 LPY  H31  C37  C38  109.13  3.000
 LPY  H32  C37  C36  109.85  3.000
 LPY  H31  C37  C36  109.03  3.000
 LPY  C38  C37  C36  112.96  3.000
 LPY  H34  C38  H33  106.21  3.000
 LPY  H34  C38  C39  109.15  3.000
 LPY  H33  C38  C39  109.64  3.000
 LPY  H34  C38  C37  109.19  3.000
 LPY  H33  C38  C37  109.61  3.000
 LPY  C39  C38  C37  112.82  3.000
 LPY  H36  C39  H35  106.67  3.000
 LPY  H36  C39  C40  109.70  3.000
 LPY  H35  C39  C40  109.28  3.000
 LPY  H36  C39  C38  109.81  3.000
 LPY  H35  C39  C38  109.20  3.000
 LPY  C40  C39  C38  112.02  3.000
 LPY  H38  C40  H37  107.99  3.000
 LPY  H38  C40  C42  108.35  3.000
 LPY  H37  C40  C42  110.26  3.000
 LPY  H38  C40  C39  109.62  3.000
 LPY  H37  C40  C39  109.79  3.000
 LPY  C42  C40  C39  110.77  3.000
 LPY  H39  C41  C43  109.07  3.000
 LPY  H39  C41  C26  108.40  3.000
 LPY  C43  C41  C26  109.43  3.000
 LPY  H39  C41  O2   110.96  3.000
 LPY  C26  C41  O2   111.45  3.000
 LPY  C43  C41  O2   107.51  3.000
 LPY  C40  C42  O9   111.85  3.000
 LPY  O9   C42  O7   123.19  3.000
 LPY  C40  C42  O7   124.92  3.000
 LPY  H40  C43  C44  108.10  3.000
 LPY  H40  C43  C41  108.71  3.000
 LPY  C44  C43  C41  112.85  3.000
 LPY  H40  C43  O3   109.58  3.000
 LPY  C44  C43  O3   110.32  3.000
 LPY  C41  C43  O3   107.25  3.000
 LPY  H41  C44  C43  108.16  3.000
 LPY  H41  C44  C20  107.77  3.000
 LPY  C43  C44  C20  109.08  3.000
 LPY  H41  C44  O11  111.01  3.000
 LPY  C20  C44  O11  112.20  3.000
 LPY  C43  C44  O11  108.53  3.000
 LPY  H43  C45  H42  108.17  3.000
 LPY  H43  C45  C15  110.07  3.000
 LPY  H42  C45  C15  110.51  3.000
 LPY  H43  C45  O9   110.01  3.000
 LPY  H42  C45  O9   110.65  3.000
 LPY  C15  C45  O9   107.43  3.000
 LPY  H7   O13  C17  109.05  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
 LPY  Var_01  C15  C16  O10  P      77.81  30.0  2
 LPY  Var_02  C39  C40  C42  O7    -94.86  30.0  1
 LPY  Var_03  C32  C31  C30  C29  -179.93  30.0  3
 LPY  Var_04  C33  C32  C31  C30   178.49  30.0  3
 LPY  Var_05  C34  C33  C32  C31  -179.60  30.0  3
 LPY  Var_06  C35  C34  C33  C32   176.93  30.0  3
 LPY  Var_07  C36  C35  C34  C33  -179.66  30.0  3
 LPY  Var_08  C37  C36  C35  C34   173.47  30.0  3
 LPY  Var_09  C38  C37  C36  C35  -179.40  30.0  3
 LPY  Var_10  C39  C38  C37  C36   174.15  30.0  3
 LPY  Var_11  C40  C39  C38  C37  -179.03  30.0  3
 LPY  Var_12  C42  C40  C39  C38   175.88  30.0  3
 LPY  Var_13  H14  C29  C30  C31   179.26  30.0  3
 LPY  Var_14  H42  C45  O9   C42   -55.80  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
 LPY  chir_02  C15  C45  O8   C16  negativ
 LPY  chir_03  C17  C26  C20  O13  negativ
 LPY  chir_04  C20  O12  C17  C44  positiv
 LPY  chir_05  C26  O1   C17  C41  negativ
 LPY  chir_06  C41  O2   C26  C43  positiv
 LPY  chir_07  C43  O3   C44  C41  positiv
 LPY  chir_08  C44  O11  C43  C20  negativ
 LPY  chir_09  P    O5   O3   O4   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
 LPY  plan-1  O7   0.020
 LPY  plan-1  O9   0.020
 LPY  plan-1  C40  0.020
 LPY  plan-1  C42  0.020

