# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 12:14:52 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: 2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCCC(=O)OCCO[P](O)(=O)OCCN
#
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
 VVA  VVA  '2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate'  ligand  73  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VVA
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
 VVA  O1P  O  O     0  -0.712   -9.6159  -0.5983   1.4135
 VVA  P    P  P     0   1.478   -8.3578   0.1308   1.1690
 VVA  O2P  O  OH1   0  -0.742   -7.6067   0.3777   2.5580
 VVA  O4P  O  O2    0  -0.585   -8.4486   1.5290   0.4184
 VVA  C4   C  CH2   0  -0.174   -9.3799   2.5367   0.8596
 VVA  C5   C  CH2   0  -0.319   -9.3793   3.6522  -0.1558
 VVA  N6   N  NH2   0  -0.799   -9.8915   3.2021  -1.4381
 VVA  O3P  O  O2    0  -0.581   -7.3113  -0.5573   0.1812
 VVA  C1   C  CH2   0  -0.205   -7.0183  -1.9520   0.3217
 VVA  C2   C  CH2   0  -0.207   -5.9027  -2.3035  -0.6203
 VVA  O2   O  O2    0  -0.460   -4.7282  -1.6136  -0.1932
 VVA  C31  C  C     0   0.609   -3.6048  -1.8250  -0.8741
 VVA  O31  O  O     0  -0.452   -3.5401  -2.5703  -1.8192
 VVA  C32  C  CH2   0  -0.582   -2.4620  -1.0193  -0.3208
 VVA  C33  C  CH2   0  -0.418   -1.1032  -1.4438  -0.8559
 VVA  C34  C  CH2   0  -0.416    0.0297  -0.6356  -0.2360
 VVA  C35  C  CH2   0  -0.413    1.4030  -1.0613  -0.7389
 VVA  C36  C  CH2   0  -0.412    2.5448  -0.2786  -0.1033
 VVA  C37  C  CH2   0  -0.412    3.9190  -0.7093  -0.6005
 VVA  C38  C  CH2   0  -0.412    5.0633   0.0558   0.0521
 VVA  C39  C  CH2   0  -0.412    6.4379  -0.3789  -0.4407
 VVA  H1   H  HOH1  0   0.496   -6.7660   0.8524   2.5072
 VVA  H2   H  HCH2  0   0.236  -10.3796   2.1051   0.9458
 VVA  H3   H  HCH2  0   0.242   -9.0759   2.9169   1.8375
 VVA  H4   H  HCH2  0   0.239  -10.0423   4.4277   0.2340
 VVA  H5   H  HCH2  0   0.211   -8.3754   4.0967  -0.1989
 VVA  H6   H  HNH2  0   0.354   -9.9902   3.9963  -2.0564
 VVA  H7   H  HNH2  0   0.344   -9.2158   2.5929  -1.8809
 VVA  H9   H  HCH2  0   0.250   -6.7388  -2.1900   1.3516
 VVA  H10  H  HCH2  0   0.258   -7.8924  -2.5512   0.0589
 VVA  H11  H  HCH2  0   0.254   -5.7511  -3.3847  -0.5864
 VVA  H12  H  HCH2  0   0.252   -6.1597  -2.0284  -1.6458
 VVA  H13  H  HCH2  0   0.279   -2.6515   0.0336  -0.5573
 VVA  H14  H  HCH2  0   0.268   -2.4843  -1.0829   0.7706
 VVA  H15  H  HCH2  0   0.225   -0.9437  -2.5061  -0.6505
 VVA  H16  H  HCH2  0   0.226   -1.0777  -1.3314  -1.9428
 VVA  H17  H  HCH2  0   0.213   -0.1201   0.4292  -0.4448
 VVA  H18  H  HCH2  0   0.212   -0.0053  -0.7385   0.8543
 VVA  H19  H  HCH2  0   0.208    1.5425  -2.1303  -0.5435
 VVA  H20  H  HCH2  0   0.209    1.4446  -0.9450  -1.8276
 VVA  H21  H  HCH2  0   0.207    2.4079   0.7908  -0.2982
 VVA  H22  H  HCH2  0   0.207    2.5001  -0.3952   0.9854
 VVA  H23  H  HCH2  0   0.206    4.0486  -1.7819  -0.4178
 VVA  H24  H  HCH2  0   0.207    3.9697  -0.5806  -1.6875
 VVA  H25  H  HCH2  0   0.206    4.9358   1.1285  -0.1309
 VVA  H26  H  HCH2  0   0.206    5.0102  -0.0729   1.1390
 VVA  H27  H  HCH2  0   0.206    6.5625  -1.4527  -0.2618
 VVA  H28  H  HCH2  0   0.206    6.4939  -0.2459  -1.5270
 VVA  C40  C  CH2   0  -0.412    7.5820   0.3794   0.2198
 VVA  C41  C  CH2   0  -0.412    8.9576  -0.0581  -0.2678
 VVA  C42  C  CH2   0  -0.412   10.1009   0.6944   0.4009
 VVA  C43  C  CH2   0  -0.412   11.4775   0.2536  -0.0807
 VVA  C44  C  CH2   0  -0.412   12.6199   0.9999   0.5965
 VVA  C45  C  CH2   0  -0.406   13.9971   0.5563   0.1197
 VVA  C46  C  CH2   0  -0.420   15.1401   1.2965   0.8033
 VVA  C47  C  CH3   0  -0.661   16.5116   0.8409   0.3246
 VVA  H8   H  HCH2  0   0.206    7.4591   1.4533   0.0399
 VVA  H29  H  HCH2  0   0.206    7.5236   0.2474   1.3061
 VVA  H30  H  HCH2  0   0.206    9.0781  -1.1330  -0.0921
 VVA  H31  H  HCH2  0   0.206    9.0191   0.0785  -1.3533
 VVA  H32  H  HCH2  0   0.206    9.9823   1.7691   0.2234
 VVA  H33  H  HCH2  0   0.206   10.0363   0.5595   1.4865
 VVA  H34  H  HCH2  0   0.206   11.5935  -0.8222   0.0920
 VVA  H35  H  HCH2  0   0.206   11.5452   0.3936  -1.1655
 VVA  H36  H  HCH2  0   0.206   12.5054   2.0756   0.4222
 VVA  H37  H  HCH2  0   0.206   12.5497   0.8613   1.6812
 VVA  H38  H  HCH2  0   0.205   14.1097  -0.5205   0.2891
 VVA  H39  H  HCH2  0   0.206   14.0702   0.6997  -0.9644
 VVA  H40  H  HCH2  0   0.210   15.0296   2.3715   0.6296
 VVA  H41  H  HCH2  0   0.210   15.0640   1.1565   1.8860
 VVA  H42  H  HCH3  0   0.215   16.6274   1.0014  -0.7490
 VVA  H43  H  HCH3  0   0.225   17.3138   1.3822   0.8275
 VVA  H44  H  HCH3  0   0.215   16.6608  -0.2236   0.5143

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
 VVA  C37  C38  single  1.523  0.020  1.523
 VVA  C37  C36  single  1.524  0.020  1.524
 VVA  C38  C39  single  1.524  0.020  1.524
 VVA  O31  C31  double  1.205  0.020  1.205
 VVA  C35  C36  single  1.523  0.020  1.523
 VVA  C35  C34  single  1.523  0.020  1.523
 VVA  C33  C32  single  1.521  0.020  1.521
 VVA  C33  C34  single  1.523  0.020  1.523
 VVA  C31  C32  single  1.504  0.020  1.504
 VVA  C31  O2   single  1.331  0.020  1.331
 VVA  O2   C2   single  1.428  0.020  1.428
 VVA  C2   C1   single  1.502  0.020  1.502
 VVA  C1   O3P  single  1.432  0.020  1.432
 VVA  O3P  P    single  1.595  0.020  1.595
 VVA  O1P  P    double  1.475  0.020  1.475
 VVA  O2P  P    single  1.598  0.020  1.598
 VVA  P    O4P  single  1.590  0.020  1.590
 VVA  O4P  C4   single  1.441  0.020  1.441
 VVA  C4   C5   single  1.508  0.020  1.508
 VVA  C5   N6   single  1.452  0.020  1.452
 VVA  O2P  H1   single  0.850  0.020  0.980
 VVA  C4   H2   single  0.970  0.020  1.090
 VVA  C4   H3   single  0.970  0.020  1.090
 VVA  C5   H4   single  0.970  0.020  1.090
 VVA  C5   H5   single  0.970  0.020  1.090
 VVA  N6   H6   single  0.890  0.020  1.040
 VVA  N6   H7   single  0.890  0.020  1.040
 VVA  C1   H9   single  0.970  0.020  1.090
 VVA  C1   H10  single  0.970  0.020  1.090
 VVA  C2   H11  single  0.970  0.020  1.090
 VVA  C2   H12  single  0.970  0.020  1.090
 VVA  C32  H13  single  0.970  0.020  1.090
 VVA  C32  H14  single  0.970  0.020  1.090
 VVA  C33  H15  single  0.970  0.020  1.090
 VVA  C33  H16  single  0.970  0.020  1.090
 VVA  C34  H17  single  0.970  0.020  1.090
 VVA  C34  H18  single  0.970  0.020  1.090
 VVA  C35  H19  single  0.970  0.020  1.090
 VVA  C35  H20  single  0.970  0.020  1.090
 VVA  C36  H21  single  0.970  0.020  1.090
 VVA  C36  H22  single  0.970  0.020  1.090
 VVA  C37  H23  single  0.970  0.020  1.090
 VVA  C37  H24  single  0.970  0.020  1.090
 VVA  C38  H25  single  0.970  0.020  1.090
 VVA  C38  H26  single  0.970  0.020  1.090
 VVA  C39  H27  single  0.970  0.020  1.090
 VVA  C39  H28  single  0.970  0.020  1.090
 VVA  C39  C40  single  1.523  0.020  1.523
 VVA  C40  C41  single  1.524  0.020  1.524
 VVA  C41  C42  single  1.523  0.020  1.523
 VVA  C42  C43  single  1.524  0.020  1.524
 VVA  C43  C44  single  1.523  0.020  1.523
 VVA  C44  C45  single  1.523  0.020  1.523
 VVA  C45  C46  single  1.524  0.020  1.524
 VVA  C46  C47  single  1.522  0.020  1.522
 VVA  C40  H8   single  0.970  0.020  1.090
 VVA  C40  H29  single  0.970  0.020  1.090
 VVA  C41  H30  single  0.970  0.020  1.090
 VVA  C41  H31  single  0.970  0.020  1.090
 VVA  C42  H32  single  0.970  0.020  1.090
 VVA  C42  H33  single  0.970  0.020  1.090
 VVA  C43  H34  single  0.970  0.020  1.090
 VVA  C43  H35  single  0.970  0.020  1.090
 VVA  C44  H36  single  0.970  0.020  1.090
 VVA  C44  H37  single  0.970  0.020  1.090
 VVA  C45  H38  single  0.970  0.020  1.090
 VVA  C45  H39  single  0.970  0.020  1.090
 VVA  C46  H40  single  0.970  0.020  1.090
 VVA  C46  H41  single  0.970  0.020  1.090
 VVA  C47  H42  single  0.970  0.020  1.090
 VVA  C47  H43  single  0.970  0.020  1.090
 VVA  C47  H44  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
 VVA  O3P  P    O4P   97.15  3.000
 VVA  O4P  P    O2P  107.54  3.000
 VVA  O3P  P    O2P  107.25  3.000
 VVA  O4P  P    O1P  117.68  3.000
 VVA  O2P  P    O1P  109.47  3.000
 VVA  O3P  P    O1P  116.68  3.000
 VVA  H1   O2P  P    116.04  3.000
 VVA  C4   O4P  P    120.49  3.000
 VVA  H3   C4   H2   108.76  3.000
 VVA  H3   C4   C5   110.18  3.000
 VVA  H2   C4   C5   110.22  3.000
 VVA  H3   C4   O4P  109.73  3.000
 VVA  H2   C4   O4P  109.84  3.000
 VVA  C5   C4   O4P  108.10  3.000
 VVA  H5   C5   H4   106.35  3.000
 VVA  H5   C5   N6   114.39  3.000
 VVA  H4   C5   N6   108.73  3.000
 VVA  H5   C5   C4   109.02  3.000
 VVA  H4   C5   C4   106.53  3.000
 VVA  N6   C5   C4   111.40  3.000
 VVA  H7   N6   H6   105.69  3.000
 VVA  H7   N6   C5   109.73  3.000
 VVA  H6   N6   C5   109.32  3.000
 VVA  C1   O3P  P    119.58  3.000
 VVA  H10  C1   H9   108.18  3.000
 VVA  H10  C1   C2   108.37  3.000
 VVA  H9   C1   C2   110.49  3.000
 VVA  H10  C1   O3P  110.31  3.000
 VVA  H9   C1   O3P  110.90  3.000
 VVA  C2   C1   O3P  108.56  3.000
 VVA  H12  C2   H11  108.12  3.000
 VVA  H12  C2   O2   110.65  3.000
 VVA  H11  C2   O2   110.79  3.000
 VVA  H12  C2   C1   110.80  3.000
 VVA  H11  C2   C1   108.38  3.000
 VVA  O2   C2   C1   108.08  3.000
 VVA  C31  O2   C2   117.69  3.000
 VVA  C32  C31  O31  125.38  3.000
 VVA  C32  C31  O2   111.61  3.000
 VVA  O31  C31  O2   123.01  3.000
 VVA  H14  C32  H13  105.53  3.000
 VVA  H14  C32  C33  110.68  3.000
 VVA  H13  C32  C33  110.29  3.000
 VVA  H14  C32  C31  108.70  3.000
 VVA  H13  C32  C31  107.70  3.000
 VVA  C33  C32  C31  113.58  3.000
 VVA  H16  C33  H15  106.45  3.000
 VVA  H16  C33  C34  109.44  3.000
 VVA  H15  C33  C34  109.30  3.000
 VVA  H16  C33  C32  110.00  3.000
 VVA  H15  C33  C32  109.59  3.000
 VVA  C34  C33  C32  111.91  3.000
 VVA  H18  C34  H17  106.06  3.000
 VVA  H18  C34  C35  109.33  3.000
 VVA  H17  C34  C35  109.39  3.000
 VVA  H18  C34  C33  109.35  3.000
 VVA  H17  C34  C33  109.66  3.000
 VVA  C35  C34  C33  112.82  3.000
 VVA  H20  C35  H19  106.02  3.000
 VVA  H20  C35  C36  109.37  3.000
 VVA  H19  C35  C36  109.36  3.000
 VVA  H20  C35  C34  109.42  3.000
 VVA  H19  C35  C34  109.18  3.000
 VVA  C36  C35  C34  113.23  3.000
 VVA  H22  C36  H21  105.99  3.000
 VVA  H22  C36  C37  109.33  3.000
 VVA  H21  C36  C37  109.31  3.000
 VVA  H22  C36  C35  109.23  3.000
 VVA  H21  C36  C35  109.49  3.000
 VVA  C37  C36  C35  113.24  3.000
 VVA  H24  C37  H23  105.96  3.000
 VVA  H24  C37  C38  109.34  3.000
 VVA  H23  C37  C38  109.36  3.000
 VVA  H24  C37  C36  109.40  3.000
 VVA  H23  C37  C36  109.21  3.000
 VVA  C38  C37  C36  113.31  3.000
 VVA  H26  C38  H25  105.96  3.000
 VVA  H26  C38  C39  109.33  3.000
 VVA  H25  C38  C39  109.28  3.000
 VVA  H26  C38  C37  109.24  3.000
 VVA  H25  C38  C37  109.44  3.000
 VVA  C39  C38  C37  113.32  3.000
 VVA  C40  C39  H28  109.33  3.000
 VVA  C40  C39  H27  109.37  3.000
 VVA  H28  C39  H27  105.96  3.000
 VVA  C40  C39  C38  113.29  3.000
 VVA  H28  C39  C38  109.39  3.000
 VVA  H27  C39  C38  109.23  3.000
 VVA  H29  C40  H8   105.95  3.000
 VVA  H29  C40  C41  109.32  3.000
 VVA  H8   C40  C41  109.28  3.000
 VVA  H29  C40  C39  109.25  3.000
 VVA  H8   C40  C39  109.42  3.000
 VVA  C41  C40  C39  113.35  3.000
 VVA  H31  C41  H30  105.96  3.000
 VVA  H31  C41  C42  109.33  3.000
 VVA  H30  C41  C42  109.37  3.000
 VVA  H31  C41  C40  109.39  3.000
 VVA  H30  C41  C40  109.25  3.000
 VVA  C42  C41  C40  113.28  3.000
 VVA  H33  C42  H32  105.95  3.000
 VVA  H33  C42  C43  109.32  3.000
 VVA  H32  C42  C43  109.29  3.000
 VVA  H33  C42  C41  109.26  3.000
 VVA  H32  C42  C41  109.40  3.000
 VVA  C43  C42  C41  113.36  3.000
 VVA  H35  C43  H34  105.96  3.000
 VVA  H35  C43  C44  109.34  3.000
 VVA  H34  C43  C44  109.36  3.000
 VVA  H35  C43  C42  109.38  3.000
 VVA  H34  C43  C42  109.26  3.000
 VVA  C44  C43  C42  113.29  3.000
 VVA  H37  C44  H36  105.95  3.000
 VVA  H37  C44  C45  109.32  3.000
 VVA  H36  C44  C45  109.30  3.000
 VVA  H37  C44  C43  109.27  3.000
 VVA  H36  C44  C43  109.38  3.000
 VVA  C45  C44  C43  113.34  3.000
 VVA  H39  C45  H38  105.94  3.000
 VVA  H39  C45  C46  109.28  3.000
 VVA  H38  C45  C46  109.32  3.000
 VVA  H39  C45  C44  109.38  3.000
 VVA  H38  C45  C44  109.30  3.000
 VVA  C46  C45  C44  113.35  3.000
 VVA  H41  C46  H40  106.00  3.000
 VVA  H41  C46  C47  109.60  3.000
 VVA  H40  C46  C47  109.57  3.000
 VVA  H41  C46  C45  109.24  3.000
 VVA  H40  C46  C45  109.28  3.000
 VVA  C47  C46  C45  112.91  3.000
 VVA  H44  C47  H43  107.66  3.000
 VVA  H44  C47  H42  107.44  3.000
 VVA  H43  C47  H42  107.61  3.000
 VVA  H44  C47  C46  111.12  3.000
 VVA  H43  C47  C46  111.66  3.000
 VVA  H42  C47  C46  111.15  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
 VVA  Var_01  C2   C1   O3P  P    -173.78  30.0  1
 VVA  Var_02  C5   C4   O4P  P    -171.80  30.0  3
 VVA  Var_03  N6   C5   C4   O4P    65.10  30.0  3
 VVA  Var_04  O3P  P    O4P  C4    175.09  30.0  1
 VVA  Var_05  O2   C2   C1   O3P    65.63  30.0  1
 VVA  Var_06  O31  C31  O2   C2     -0.37  30.0  1
 VVA  Var_07  C33  C32  C31  O2    167.37  30.0  3
 VVA  Var_08  C34  C33  C32  C31  -178.07  30.0  1
 VVA  Var_09  C35  C34  C33  C32   178.95  30.0  3
 VVA  Var_10  C36  C35  C34  C33  -178.81  30.0  1
 VVA  Var_11  C37  C36  C35  C34   179.69  30.0  3
 VVA  Var_12  C38  C37  C36  C35  -179.00  30.0  1
 VVA  Var_13  C39  C38  C37  C36   179.76  30.0  3
 VVA  Var_14  C40  C39  C38  C37  -179.57  30.0  3
 VVA  Var_15  C41  C40  C39  C38   179.76  30.0  3
 VVA  Var_16  C42  C41  C40  C39  -179.60  30.0  3
 VVA  Var_17  C43  C42  C41  C40   179.73  30.0  3
 VVA  Var_18  C44  C43  C42  C41  -179.57  30.0  3
 VVA  Var_19  C45  C44  C43  C42   179.78  30.0  3
 VVA  Var_20  C46  C45  C44  C43  -179.64  30.0  3
 VVA  Var_21  C47  C46  C45  C44   179.72  30.0  3
 VVA  Var_22  H6   N6   C5   C4    172.71  30.0  3
 VVA  Var_23  H42  C47  C46  C45    59.90  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
 VVA  chir_01  P  O1P  O2P  O4P  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
 VVA  plan-1  O2   0.020
 VVA  plan-1  C31  0.020
 VVA  plan-1  O31  0.020
 VVA  plan-1  C32  0.020

