# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:14:44 2020
#   Inital geometry file: a 165 line input string
#   Ligand name: (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octyloxy)methyl]ethyl hydrogen (S)-heptylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOC[C@H](CO[P@@](O)(=O)OCCN)O[P@](O)(=O)CCCCCCC
#
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
 GEL  GEL  '(1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octyloxy)methyl]ethyl hydrogen (S)-heptylphosphonate'  ligand  76  31  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GEL
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
 GEL  C1    C  CH2   0  -0.170  -0.9148   3.3329   0.5563
 GEL  O1    O  O2    0  -0.531  -0.6771   2.2437   1.4244
 GEL  C11   C  CH2   0  -0.136   0.4262   2.3903   2.3125
 GEL  C12   C  CH2   0  -0.473   0.7169   1.0391   2.9295
 GEL  C13   C  CH2   0  -0.422   1.8165   1.1046   3.9811
 GEL  C14   C  CH2   0  -0.413   2.1959  -0.2735   4.5085
 GEL  C15   C  CH2   0  -0.411   3.2454  -0.2267   5.6111
 GEL  C16   C  CH2   0  -0.406   3.6536  -1.6066   6.1104
 GEL  C17   C  CH2   0  -0.418   4.7036  -1.5646   7.2137
 GEL  C18   C  CH3   0  -0.663   5.1142  -2.9487   7.6969
 GEL  C2    C  CH1   0  -0.026  -1.6154   2.8762  -0.7095
 GEL  O2    O  O2    0  -0.593  -0.7803   1.9249  -1.3718
 GEL  P2    P  P     0   1.386  -0.4067   2.0914  -2.9292
 GEL  O1P   O  O     0  -0.715  -1.5238   2.5398  -3.7963
 GEL  O2P   O  OH1   0  -0.750   0.7706   3.1888  -2.9905
 GEL  C22   C  CH2   0  -0.748   0.3138   0.4876  -3.3040
 GEL  C23   C  CH2   0  -0.434   0.8676   0.4224  -4.7274
 GEL  C24   C  CH2   0  -0.408   1.3478  -0.9764  -5.0927
 GEL  C25   C  CH2   0  -0.413   1.8957  -1.0512  -6.5125
 GEL  C26   C  CH2   0  -0.407   2.3406  -2.4504  -6.9164
 GEL  C27   C  CH2   0  -0.419   2.8746  -2.5198  -8.3423
 GEL  C28   C  CH3   0  -0.662   3.3106  -3.9212  -8.7458
 GEL  C3    C  CH2   0  -0.206  -3.0063   2.2836  -0.5551
 GEL  O3    O  O2    0  -0.576  -2.9557   0.9677  -0.0059
 GEL  P3    P  P     0   1.440  -3.5967   0.6080   1.4127
 GEL  O3P   O  O     0  -0.710  -5.0701   0.5769   1.5040
 GEL  O4P   O  OH1   0  -0.782  -2.9754   1.6295   2.4580
 GEL  O5P   O  O2    0  -0.587  -2.8616  -0.7958   1.5978
 GEL  C31   C  CH2   0  -0.172  -3.2431  -1.6597   2.6834
 GEL  C32   C  CH2   0  -0.318  -2.1915  -2.7327   2.8258
 GEL  N3    N  NH2   0  -0.794  -0.9241  -2.1794   3.2705
 GEL  H11   H  HCH2  0   0.241  -1.5250   4.1029   1.0430
 GEL  H12   H  HCH2  0   0.251   0.0342   3.8006   0.2738
 GEL  H111  H  HCH2  0   0.219   0.1995   3.1368   3.0836
 GEL  H112  H  HCH2  0   0.231   1.2955   2.7513   1.7523
 GEL  H121  H  HCH2  0   0.226   1.0040   0.3423   2.1357
 GEL  H122  H  HCH2  0   0.226  -0.1923   0.6370   3.3858
 GEL  H131  H  HCH2  0   0.217   1.4885   1.7385   4.8118
 GEL  H132  H  HCH2  0   0.216   2.7049   1.5875   3.5606
 GEL  H141  H  HCH2  0   0.208   2.5678  -0.8831   3.6775
 GEL  H142  H  HCH2  0   0.212   1.2984  -0.7831   4.8753
 GEL  H151  H  HCH2  0   0.207   2.8642   0.3658   6.4504
 GEL  H152  H  HCH2  0   0.207   4.1323   0.3030   5.2456
 GEL  H161  H  HCH2  0   0.206   4.0350  -2.1967   5.2695
 GEL  H162  H  HCH2  0   0.206   2.7674  -2.1386   6.4743
 GEL  H171  H  HCH2  0   0.210   4.3195  -0.9816   8.0568
 GEL  H172  H  HCH2  0   0.209   5.5860  -1.0267   6.8530
 GEL  H181  H  HCH3  0   0.226   5.8670  -2.8917   8.4837
 GEL  H182  H  HCH3  0   0.216   4.2597  -3.4976   8.0972
 GEL  H183  H  HCH3  0   0.215   5.5322  -3.5431   6.8822
 GEL  H2    H  HCH1  0   0.271  -1.7491   3.7855  -1.3081
 GEL  HOP2  H  HOH1  0   0.489   1.5595   2.9832  -2.4719
 GEL  H221  H  HCH2  0   0.286   1.0925   0.2592  -2.5716
 GEL  H222  H  HCH2  0   0.285  -0.4761  -0.2564  -3.1691
 GEL  H231  H  HCH2  0   0.234   0.0956   0.7326  -5.4369
 GEL  H232  H  HCH2  0   0.234   1.6921   1.1313  -4.8365
 GEL  H241  H  HCH2  0   0.216   2.1184  -1.2986  -4.3844
 GEL  H242  H  HCH2  0   0.216   0.5180  -1.6825  -4.9837
 GEL  H251  H  HCH2  0   0.209   1.1294  -0.6987  -7.2120
 GEL  H252  H  HCH2  0   0.211   2.7378  -0.3582  -6.6129
 GEL  H261  H  HCH2  0   0.207   3.1117  -2.8049  -6.2231
 GEL  H262  H  HCH2  0   0.207   1.4989  -3.1438  -6.8118
 GEL  H271  H  HCH2  0   0.210   2.1036  -2.1620  -9.0319
 GEL  H272  H  HCH2  0   0.211   3.7167  -1.8286  -8.4468
 GEL  H281  H  HCH3  0   0.226   3.6811  -3.9470  -9.7712
 GEL  H282  H  HCH3  0   0.216   4.1084  -4.2886  -8.0974
 GEL  H283  H  HCH3  0   0.216   2.4809  -4.6267  -8.6757
 GEL  H31   H  HCH2  0   0.254  -3.6237   2.9654   0.0366
 GEL  H32   H  HCH2  0   0.269  -3.4668   2.2011  -1.5397
 GEL  HOP4  H  HOH1  0   0.505  -2.0380   1.8712   2.2206
 GEL  H311  H  HCH2  0   0.230  -3.3175  -1.0934   3.6159
 GEL  H312  H  HCH2  0   0.241  -4.2154  -2.1071   2.4690
 GEL  H321  H  HCH2  0   0.236  -2.5552  -3.4276   3.5860
 GEL  H322  H  HCH2  0   0.210  -2.1343  -3.3027   1.8881
 GEL  HN31  H  HNH2  0   0.352  -0.2694  -2.9303   3.4453
 GEL  HN32  H  HNH2  0   0.347  -0.5122  -1.6240   2.5328

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
 GEL  C1   O1    single  1.413  0.020  1.413
 GEL  C1   C2    single  1.517  0.020  1.517
 GEL  C1   H11   single  0.970  0.020  1.090
 GEL  C1   H12   single  0.970  0.020  1.090
 GEL  O1   C11   single  1.424  0.020  1.424
 GEL  C11  C12   single  1.514  0.020  1.514
 GEL  C11  H111  single  0.970  0.020  1.090
 GEL  C11  H112  single  0.970  0.020  1.090
 GEL  C12  C13   single  1.523  0.020  1.523
 GEL  C12  H121  single  0.970  0.020  1.090
 GEL  C12  H122  single  0.970  0.020  1.090
 GEL  C13  C14   single  1.524  0.020  1.524
 GEL  C13  H131  single  0.970  0.020  1.090
 GEL  C13  H132  single  0.970  0.020  1.090
 GEL  C14  C15   single  1.523  0.020  1.523
 GEL  C14  H141  single  0.970  0.020  1.090
 GEL  C14  H142  single  0.970  0.020  1.090
 GEL  C15  C16   single  1.523  0.020  1.523
 GEL  C15  H151  single  0.970  0.020  1.090
 GEL  C15  H152  single  0.970  0.020  1.090
 GEL  C16  C17   single  1.524  0.020  1.524
 GEL  C16  H161  single  0.970  0.020  1.090
 GEL  C16  H162  single  0.970  0.020  1.090
 GEL  C17  C18   single  1.522  0.020  1.522
 GEL  C17  H171  single  0.970  0.020  1.090
 GEL  C17  H172  single  0.970  0.020  1.090
 GEL  C18  H181  single  0.970  0.020  1.090
 GEL  C18  H182  single  0.970  0.020  1.090
 GEL  C18  H183  single  0.970  0.020  1.090
 GEL  C2   O2    single  1.429  0.020  1.429
 GEL  C2   C3    single  1.520  0.020  1.520
 GEL  C2   H2    single  0.970  0.020  1.090
 GEL  O2   P2    single  1.610  0.020  1.610
 GEL  P2   O1P   double  1.484  0.020  1.484
 GEL  P2   O2P   single  1.611  0.020  1.611
 GEL  P2   C22   single  1.798  0.020  1.798
 GEL  O2P  HOP2  single  0.850  0.020  0.980
 GEL  C22  C23   single  1.529  0.020  1.529
 GEL  C22  H221  single  0.970  0.020  1.090
 GEL  C22  H222  single  0.970  0.020  1.090
 GEL  C23  C24   single  1.523  0.020  1.523
 GEL  C23  H231  single  0.970  0.020  1.090
 GEL  C23  H232  single  0.970  0.020  1.090
 GEL  C24  C25   single  1.524  0.020  1.524
 GEL  C24  H241  single  0.970  0.020  1.090
 GEL  C24  H242  single  0.970  0.020  1.090
 GEL  C25  C26   single  1.523  0.020  1.523
 GEL  C25  H251  single  0.970  0.020  1.090
 GEL  C25  H252  single  0.970  0.020  1.090
 GEL  C26  C27   single  1.524  0.020  1.524
 GEL  C26  H261  single  0.970  0.020  1.090
 GEL  C26  H262  single  0.970  0.020  1.090
 GEL  C27  C28   single  1.522  0.020  1.522
 GEL  C27  H271  single  0.970  0.020  1.090
 GEL  C27  H272  single  0.970  0.020  1.090
 GEL  C28  H281  single  0.970  0.020  1.090
 GEL  C28  H282  single  0.970  0.020  1.090
 GEL  C28  H283  single  0.970  0.020  1.090
 GEL  C3   O3    single  1.427  0.020  1.427
 GEL  C3   H31   single  0.970  0.020  1.090
 GEL  C3   H32   single  0.970  0.020  1.090
 GEL  O3   P3    single  1.598  0.020  1.598
 GEL  P3   O3P   double  1.477  0.020  1.477
 GEL  P3   O4P   single  1.588  0.020  1.588
 GEL  P3   O5P   single  1.595  0.020  1.595
 GEL  O4P  HOP4  single  0.850  0.020  0.980
 GEL  O5P  C31   single  1.439  0.020  1.439
 GEL  C31  C32   single  1.509  0.020  1.509
 GEL  C31  H311  single  0.970  0.020  1.090
 GEL  C31  H312  single  0.970  0.020  1.090
 GEL  C32  N3    single  1.453  0.020  1.453
 GEL  C32  H321  single  0.970  0.020  1.090
 GEL  C32  H322  single  0.970  0.020  1.090
 GEL  N3   HN31  single  0.890  0.020  1.040
 GEL  N3   HN32  single  0.890  0.020  1.040

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
 GEL  H12   C1   H11   107.27  3.000
 GEL  H12   C1   C2    108.27  3.000
 GEL  H11   C1   C2    108.95  3.000
 GEL  H12   C1   O1    110.00  3.000
 GEL  H11   C1   O1    111.24  3.000
 GEL  C2    C1   O1    110.99  3.000
 GEL  C11   O1   C1    115.73  3.000
 GEL  H112  C11  H111  107.41  3.000
 GEL  H112  C11  C12   110.51  3.000
 GEL  H111  C11  C12   111.14  3.000
 GEL  H112  C11  O1    109.26  3.000
 GEL  H111  C11  O1    110.39  3.000
 GEL  C12   C11  O1    108.13  3.000
 GEL  H122  C12  H121  106.65  3.000
 GEL  H122  C12  C13   109.14  3.000
 GEL  H121  C12  C13   109.80  3.000
 GEL  H122  C12  C11   109.79  3.000
 GEL  H121  C12  C11   108.85  3.000
 GEL  C13   C12  C11   112.44  3.000
 GEL  H132  C13  H131  106.20  3.000
 GEL  H132  C13  C14   109.25  3.000
 GEL  H131  C13  C14   109.61  3.000
 GEL  H132  C13  C12   109.85  3.000
 GEL  H131  C13  C12   109.42  3.000
 GEL  C14   C13  C12   112.33  3.000
 GEL  H142  C14  H141  105.86  3.000
 GEL  H142  C14  C15   109.66  3.000
 GEL  H141  C14  C15   109.41  3.000
 GEL  H142  C14  C13   109.43  3.000
 GEL  H141  C14  C13   108.98  3.000
 GEL  C15   C14  C13   113.23  3.000
 GEL  H152  C15  H151  106.01  3.000
 GEL  H152  C15  C16   109.29  3.000
 GEL  H151  C15  C16   109.39  3.000
 GEL  H152  C15  C14   109.33  3.000
 GEL  H151  C15  C14   109.36  3.000
 GEL  C16   C15  C14   113.21  3.000
 GEL  H162  C16  H161  105.95  3.000
 GEL  H162  C16  C17   109.28  3.000
 GEL  H161  C16  C17   109.30  3.000
 GEL  H162  C16  C15   109.39  3.000
 GEL  H161  C16  C15   109.25  3.000
 GEL  C17   C16  C15   113.40  3.000
 GEL  H172  C17  H171  105.97  3.000
 GEL  H172  C17  C18   109.51  3.000
 GEL  H171  C17  C18   109.54  3.000
 GEL  H172  C17  C16   109.29  3.000
 GEL  H171  C17  C16   109.30  3.000
 GEL  C18   C17  C16   112.99  3.000
 GEL  H183  C18  H182  107.44  3.000
 GEL  H183  C18  H181  107.62  3.000
 GEL  H182  C18  H181  107.58  3.000
 GEL  H183  C18  C17   111.19  3.000
 GEL  H182  C18  C17   111.25  3.000
 GEL  H181  C18  C17   111.57  3.000
 GEL  H2    C2   C3    105.49  3.000
 GEL  H2    C2   O2    111.73  3.000
 GEL  C3    C2   O2    108.81  3.000
 GEL  H2    C2   C1    105.20  3.000
 GEL  C3    C2   C1    117.08  3.000
 GEL  O2    C2   C1    108.50  3.000
 GEL  P2    O2   C2    121.01  3.000
 GEL  C22   P2   O2P   107.87  3.000
 GEL  C22   P2   O1P   116.72  3.000
 GEL  O2P   P2   O1P   108.80  3.000
 GEL  C22   P2   O2    101.68  3.000
 GEL  O2P   P2   O2    106.07  3.000
 GEL  O1P   P2   O2    114.95  3.000
 GEL  HOP2  O2P  P2    115.55  3.000
 GEL  H222  C22  H221  106.84  3.000
 GEL  H222  C22  C23   110.34  3.000
 GEL  H221  C22  C23   110.91  3.000
 GEL  H222  C22  P2    106.96  3.000
 GEL  H221  C22  P2    109.40  3.000
 GEL  C23   C22  P2    112.18  3.000
 GEL  H232  C23  H231  106.49  3.000
 GEL  H232  C23  C24   109.51  3.000
 GEL  H231  C23  C24   109.12  3.000
 GEL  H232  C23  C22   109.79  3.000
 GEL  H231  C23  C22   109.65  3.000
 GEL  C24   C23  C22   112.13  3.000
 GEL  H242  C24  H241  106.21  3.000
 GEL  H242  C24  C25   109.49  3.000
 GEL  H241  C24  C25   109.59  3.000
 GEL  H242  C24  C23   109.23  3.000
 GEL  H241  C24  C23   109.68  3.000
 GEL  C25   C24  C23   112.45  3.000
 GEL  H252  C25  H251  106.00  3.000
 GEL  H252  C25  C26   109.41  3.000
 GEL  H251  C25  C26   109.30  3.000
 GEL  H252  C25  C24   109.32  3.000
 GEL  H251  C25  C24   109.12  3.000
 GEL  C26   C25  C24   113.41  3.000
 GEL  H262  C26  H261  105.99  3.000
 GEL  H262  C26  C27   109.25  3.000
 GEL  H261  C26  C27   109.30  3.000
 GEL  H262  C26  C25   109.37  3.000
 GEL  H261  C26  C25   109.57  3.000
 GEL  C27   C26  C25   113.10  3.000
 GEL  H272  C27  H271  105.99  3.000
 GEL  H272  C27  C28   109.62  3.000
 GEL  H271  C27  C28   109.62  3.000
 GEL  H272  C27  C26   109.28  3.000
 GEL  H271  C27  C26   109.13  3.000
 GEL  C28   C27  C26   112.97  3.000
 GEL  H283  C28  H282  107.46  3.000
 GEL  H283  C28  H281  107.66  3.000
 GEL  H282  C28  H281  107.59  3.000
 GEL  H283  C28  C27   111.12  3.000
 GEL  H282  C28  C27   111.21  3.000
 GEL  H281  C28  C27   111.61  3.000
 GEL  H32   C3   H31   107.30  3.000
 GEL  H32   C3   O3    107.03  3.000
 GEL  H31   C3   O3    112.75  3.000
 GEL  H32   C3   C2    108.93  3.000
 GEL  H31   C3   C2    109.18  3.000
 GEL  O3    C3   C2    111.49  3.000
 GEL  P3    O3   C3    122.35  3.000
 GEL  O5P   P3   O4P   108.02  3.000
 GEL  O5P   P3   O3P   115.72  3.000
 GEL  O4P   P3   O3P   111.30  3.000
 GEL  O5P   P3   O3     96.68  3.000
 GEL  O4P   P3   O3    106.42  3.000
 GEL  O3P   P3   O3    117.38  3.000
 GEL  HOP4  O4P  P3    111.54  3.000
 GEL  C31   O5P  P3    119.58  3.000
 GEL  H312  C31  H311  108.61  3.000
 GEL  H312  C31  C32   110.35  3.000
 GEL  H311  C31  C32   109.59  3.000
 GEL  H312  C31  O5P   109.51  3.000
 GEL  H311  C31  O5P   110.52  3.000
 GEL  C32   C31  O5P   108.26  3.000
 GEL  H322  C32  H321  106.34  3.000
 GEL  H322  C32  N3    114.42  3.000
 GEL  H321  C32  N3    108.65  3.000
 GEL  H322  C32  C31   108.94  3.000
 GEL  H321  C32  C31   106.62  3.000
 GEL  N3    C32  C31   111.47  3.000
 GEL  HN32  N3   HN31  105.68  3.000
 GEL  HN32  N3   C32   109.95  3.000
 GEL  HN31  N3   C32   109.57  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
 GEL  Var_01  C12   C11  O1   C1   -167.50  30.0  3
 GEL  Var_02  C13   C12  C11  O1   -175.60  30.0  3
 GEL  Var_03  C2    C1   O1   C11   153.65  30.0  1
 GEL  Var_04  C14   C13  C12  C11  -174.75  30.0  3
 GEL  Var_05  C15   C14  C13  C12  -177.15  30.0  3
 GEL  Var_06  C16   C15  C14  C13  -178.35  30.0  3
 GEL  Var_07  C17   C16  C15  C14   179.99  30.0  3
 GEL  Var_08  C18   C17  C16  C15  -179.47  30.0  3
 GEL  Var_09  O1P   P2   O2   C2    -40.85  30.0  3
 GEL  Var_10  C23   C22  P2   O2   -175.28  30.0  3
 GEL  Var_11  C24   C23  C22  P2   -174.13  30.0  3
 GEL  Var_12  C25   C24  C23  C22   179.74  30.0  3
 GEL  Var_13  C26   C25  C24  C23  -178.14  30.0  3
 GEL  Var_14  C27   C26  C25  C24   179.44  30.0  3
 GEL  Var_15  C28   C27  C26  C25  -179.65  30.0  3
 GEL  Var_16  O3P   P3   O3   C3     71.48  30.0  3
 GEL  Var_17  C32   C31  O5P  P3   -166.48  30.0  3
 GEL  Var_18  N3    C32  C31  O5P    67.12  30.0  3
 GEL  Var_19  H181  C18  C17  C16   179.88  30.0  3
 GEL  Var_20  H281  C28  C27  C26   179.55  30.0  3
 GEL  Var_21  H31   C3   O3   P3     -6.85  30.0  1
 GEL  Var_22  HN31  N3   C32  C31   174.36  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
 GEL  chir_01  C2  C1   O2   C3   negativ
 GEL  chir_02  P2  O1P  O2P  C22  both
 GEL  chir_03  P3  O3P  O4P  O5P  both

