# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:09:38 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: hexadecyl hydrogen (R)-(3-azidopropyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCCO[P](O)(=O)CCCN=[N+]=[N-]
#
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
 1R1  1R1  'hexadecyl hydrogen (R)-(3-azidopropyl)phosphonate'  ligand  66  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1R1
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
 1R1  C16  C  CH3    0  -0.662   15.3699   0.7495   0.0643
 1R1  C15  C  CH2    0  -0.419   14.0980   0.0986   0.5898
 1R1  C14  C  CH2    0  -0.406   12.8355   0.6435  -0.0669
 1R1  C13  C  CH2    0  -0.411   11.5593  -0.0110   0.4463
 1R1  C12  C  CH2    0  -0.412   10.2955   0.5253  -0.2142
 1R1  C11  C  CH2    0  -0.412    9.0236  -0.1385   0.2979
 1R1  C10  C  CH2    0  -0.412    7.7549   0.3890  -0.3605
 1R1  C9   C  CH2    0  -0.412    6.4891  -0.2770   0.1636
 1R1  C8   C  CH2    0  -0.413    5.2118   0.2448  -0.4825
 1R1  C7   C  CH2    0  -0.412    3.9558  -0.4275   0.0567
 1R1  C6   C  CH2    0  -0.413    2.6663   0.0950  -0.5638
 1R1  C5   C  CH2    0  -0.412    1.4225  -0.5779   0.0025
 1R1  C4   C  CH2    0  -0.413    0.1198  -0.0479  -0.5819
 1R1  C3   C  CH2    0  -0.428   -1.1092  -0.7144   0.0232
 1R1  C2   C  CH2    0  -0.463   -2.4201  -0.1554  -0.5169
 1R1  C1   C  CH2    0  -0.150   -3.6084  -0.8282   0.1337
 1R1  O1   O  O2     0  -0.601   -4.8130  -0.2051  -0.3433
 1R1  P1   P  P      0   1.392   -6.2459  -0.7995   0.0685
 1R1  O2   O  O      0  -0.720   -6.3601  -1.2756   1.4685
 1R1  C1H  C  CH2    0  -0.756   -7.3488   0.5427  -0.4053
 1R1  C2H  C  CH2    0  -0.450   -8.8111   0.2072  -0.1213
 1R1  C3H  C  CH2    0  -0.296   -9.7035   1.3874  -0.4827
 1R1  N1   N  N      0  -0.361  -11.1262   1.0992  -0.2709
 1R1  N2   N  N      1   0.355  -11.5124   1.1009   0.8829
 1R1  N3   N  N     -1  -0.225  -11.9689   1.0822   1.9107
 1R1  H1   H  HCH3   0   0.215   15.4751   0.5966  -1.0115
 1R1  H2   H  HCH3   0   0.215   15.3649   1.8265   0.2424
 1R1  H3   H  HCH3   0   0.225   16.2589   0.3395   0.5450
 1R1  H4   H  HCH2   0   0.210   14.1481  -0.9833   0.4318
 1R1  H5   H  HCH2   0   0.210   14.0330   0.2422   1.6729
 1R1  H6   H  HCH2   0   0.206   12.7804   1.7258   0.0950
 1R1  H7   H  HCH2   0   0.205   12.9035   0.5047  -1.1518
 1R1  H8   H  HCH2   0   0.206   11.6191  -1.0936   0.2877
 1R1  H9   H  HCH2   0   0.206   11.4897   0.1305   1.5307
 1R1  H10  H  HCH2   0   0.206   10.2316   1.6071  -0.0526
 1R1  H11  H  HCH2   0   0.206   10.3661   0.3864  -1.2988
 1R1  H12  H  HCH2   0   0.206    9.0910  -1.2205   0.1383
 1R1  H13  H  HCH2   0   0.206    8.9533   0.0014   1.3825
 1R1  H14  H  HCH2   0   0.206    7.6875   1.4716  -0.2047
 1R1  H15  H  HCH2   0   0.206    7.8205   0.2439  -1.4446
 1R1  H16  H  HCH2   0   0.206    6.5581  -1.3593   0.0062
 1R1  H17  H  HCH2   0   0.206    6.4285  -0.1349   1.2485
 1R1  H18  H  HCH2   0   0.206    5.1410   1.3270  -0.3254
 1R1  H19  H  HCH2   0   0.206    5.2666   0.1004  -1.5673
 1R1  H20  H  HCH2   0   0.207    4.0248  -1.5087  -0.1076
 1R1  H21  H  HCH2   0   0.206    3.9125  -0.2915   1.1432
 1R1  H22  H  HCH2   0   0.207    2.5983   1.1769  -0.4036
 1R1  H23  H  HCH2   0   0.207    2.6982  -0.0480  -1.6495
 1R1  H24  H  HCH2   0   0.208    1.4849  -1.6583  -0.1683
 1R1  H25  H  HCH2   0   0.207    1.4070  -0.4466   1.0904
 1R1  H26  H  HCH2   0   0.210    0.0619   1.0339  -0.4192
 1R1  H27  H  HCH2   0   0.211    0.1175  -0.1916  -1.6677
 1R1  H28  H  HCH2   0   0.218   -1.0637  -1.7933  -0.1594
 1R1  H29  H  HCH2   0   0.216   -1.0838  -0.5905   1.1113
 1R1  H30  H  HCH2   0   0.229   -2.4635   0.9210  -0.3264
 1R1  H31  H  HCH2   0   0.230   -2.4661  -0.2910  -1.6012
 1R1  H32  H  HCH2   0   0.226   -3.6154  -1.8968  -0.1011
 1R1  H33  H  HCH2   0   0.230   -3.5535  -0.7266   1.2205
 1R1  H35  H  HCH2   0   0.291   -7.0432   1.4266   0.1606
 1R1  H36  H  HCH2   0   0.291   -7.2014   0.7780  -1.4624
 1R1  H37  H  HCH2   0   0.253   -9.1231  -0.6680  -0.6949
 1R1  H38  H  HCH2   0   0.249   -8.9335  -0.0398   0.9361
 1R1  H39  H  HCH2   0   0.253   -9.4017   2.2786   0.0760
 1R1  H40  H  HCH2   0   0.261   -9.6075   1.6191  -1.5419
 1R1  O3   O  OH1    0  -0.750   -6.5349  -2.0331  -0.9260
 1R1  H34  H  HOH1   0   0.489   -6.4691  -1.8324  -1.8687

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
 1R1  C10  C11  single  1.524  0.020  1.524
 1R1  C10  C9   single  1.523  0.020  1.523
 1R1  C12  C11  single  1.523  0.020  1.523
 1R1  C12  C13  single  1.524  0.020  1.524
 1R1  C7   C8   single  1.523  0.020  1.523
 1R1  C7   C6   single  1.523  0.020  1.523
 1R1  C8   C9   single  1.524  0.020  1.524
 1R1  C15  C14  single  1.524  0.020  1.524
 1R1  C15  C16  single  1.522  0.020  1.522
 1R1  C5   C6   single  1.523  0.020  1.523
 1R1  C5   C4   single  1.523  0.020  1.523
 1R1  C13  C14  single  1.523  0.020  1.523
 1R1  C3   C4   single  1.523  0.020  1.523
 1R1  C3   C2   single  1.524  0.020  1.524
 1R1  C1   C2   single  1.513  0.020  1.513
 1R1  C1   O1   single  1.438  0.020  1.438
 1R1  O1   P1   single  1.605  0.020  1.605
 1R1  P1   C1H  single  1.801  0.020  1.801
 1R1  P1   O2   double  1.483  0.020  1.483
 1R1  C1H  C2H  single  1.527  0.020  1.527
 1R1  C2H  C3H  single  1.523  0.020  1.523
 1R1  N1   C3H  single  1.467  0.020  1.467
 1R1  N1   N2   double  1.217  0.020  1.217
 1R1  N2   N3   double  1.125  0.020  1.125
 1R1  C16  H1   single  0.970  0.020  1.090
 1R1  C16  H2   single  0.970  0.020  1.090
 1R1  C16  H3   single  0.970  0.020  1.090
 1R1  C15  H4   single  0.970  0.020  1.090
 1R1  C15  H5   single  0.970  0.020  1.090
 1R1  C14  H6   single  0.970  0.020  1.090
 1R1  C14  H7   single  0.970  0.020  1.090
 1R1  C13  H8   single  0.970  0.020  1.090
 1R1  C13  H9   single  0.970  0.020  1.090
 1R1  C12  H10  single  0.970  0.020  1.090
 1R1  C12  H11  single  0.970  0.020  1.090
 1R1  C11  H12  single  0.970  0.020  1.090
 1R1  C11  H13  single  0.970  0.020  1.090
 1R1  C10  H14  single  0.970  0.020  1.090
 1R1  C10  H15  single  0.970  0.020  1.090
 1R1  C9   H16  single  0.970  0.020  1.090
 1R1  C9   H17  single  0.970  0.020  1.090
 1R1  C8   H18  single  0.970  0.020  1.090
 1R1  C8   H19  single  0.970  0.020  1.090
 1R1  C7   H20  single  0.970  0.020  1.090
 1R1  C7   H21  single  0.970  0.020  1.090
 1R1  C6   H22  single  0.970  0.020  1.090
 1R1  C6   H23  single  0.970  0.020  1.090
 1R1  C5   H24  single  0.970  0.020  1.090
 1R1  C5   H25  single  0.970  0.020  1.090
 1R1  C4   H26  single  0.970  0.020  1.090
 1R1  C4   H27  single  0.970  0.020  1.090
 1R1  C3   H28  single  0.970  0.020  1.090
 1R1  C3   H29  single  0.970  0.020  1.090
 1R1  C2   H30  single  0.970  0.020  1.090
 1R1  C2   H31  single  0.970  0.020  1.090
 1R1  C1   H32  single  0.970  0.020  1.090
 1R1  C1   H33  single  0.970  0.020  1.090
 1R1  C1H  H35  single  0.970  0.020  1.090
 1R1  C1H  H36  single  0.970  0.020  1.090
 1R1  C2H  H37  single  0.970  0.020  1.090
 1R1  C2H  H38  single  0.970  0.020  1.090
 1R1  C3H  H39  single  0.970  0.020  1.090
 1R1  C3H  H40  single  0.970  0.020  1.090
 1R1  P1   O3   single  1.611  0.020  1.611
 1R1  O3   H34  single  0.850  0.020  0.980

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
 1R1  H3   C16  H2   107.62  3.000
 1R1  H3   C16  H1   107.65  3.000
 1R1  H2   C16  H1   107.41  3.000
 1R1  H3   C16  C15  111.61  3.000
 1R1  H2   C16  C15  111.20  3.000
 1R1  H1   C16  C15  111.15  3.000
 1R1  H5   C15  H4   105.98  3.000
 1R1  H5   C15  C14  109.29  3.000
 1R1  H4   C15  C14  109.22  3.000
 1R1  H5   C15  C16  109.58  3.000
 1R1  H4   C15  C16  109.55  3.000
 1R1  C14  C15  C16  112.99  3.000
 1R1  H7   C14  H6   105.93  3.000
 1R1  H7   C14  C13  109.34  3.000
 1R1  H6   C14  C13  109.41  3.000
 1R1  H7   C14  C15  109.27  3.000
 1R1  H6   C14  C15  109.34  3.000
 1R1  C13  C14  C15  113.29  3.000
 1R1  H9   C13  H8   105.92  3.000
 1R1  H9   C13  C12  109.32  3.000
 1R1  H8   C13  C12  109.28  3.000
 1R1  H9   C13  C14  109.34  3.000
 1R1  H8   C13  C14  109.27  3.000
 1R1  C12  C13  C14  113.44  3.000
 1R1  H11  C12  H10  105.95  3.000
 1R1  H11  C12  C11  109.35  3.000
 1R1  H10  C12  C11  109.39  3.000
 1R1  H11  C12  C13  109.33  3.000
 1R1  H10  C12  C13  109.39  3.000
 1R1  C11  C12  C13  113.18  3.000
 1R1  H13  C11  H12  105.91  3.000
 1R1  H13  C11  C10  109.27  3.000
 1R1  H12  C11  C10  109.28  3.000
 1R1  H13  C11  C12  109.31  3.000
 1R1  H12  C11  C12  109.26  3.000
 1R1  C10  C11  C12  113.52  3.000
 1R1  H15  C10  H14  105.97  3.000
 1R1  H15  C10  C9   109.40  3.000
 1R1  H14  C10  C9   109.39  3.000
 1R1  H15  C10  C11  109.38  3.000
 1R1  H14  C10  C11  109.38  3.000
 1R1  C9   C10  C11  113.07  3.000
 1R1  H17  C9   H16  105.89  3.000
 1R1  H17  C9   C8   109.21  3.000
 1R1  H16  C9   C8   109.28  3.000
 1R1  H17  C9   C10  109.26  3.000
 1R1  H16  C9   C10  109.28  3.000
 1R1  C8   C9   C10  113.64  3.000
 1R1  H19  C8   H18  105.98  3.000
 1R1  H19  C8   C7   109.48  3.000
 1R1  H18  C8   C7   109.38  3.000
 1R1  H19  C8   C9   109.44  3.000
 1R1  H18  C8   C9   109.37  3.000
 1R1  C7   C8   C9   112.95  3.000
 1R1  H21  C7   H20  105.88  3.000
 1R1  H21  C7   C6   109.14  3.000
 1R1  H20  C7   C6   109.31  3.000
 1R1  H21  C7   C8   109.19  3.000
 1R1  H20  C7   C8   109.29  3.000
 1R1  C6   C7   C8   113.73  3.000
 1R1  H23  C6   H22  106.00  3.000
 1R1  H23  C6   C5   109.54  3.000
 1R1  H22  C6   C5   109.34  3.000
 1R1  H23  C6   C7   109.52  3.000
 1R1  H22  C6   C7   109.36  3.000
 1R1  C5   C6   C7   112.84  3.000
 1R1  H25  C5   H24  105.88  3.000
 1R1  H25  C5   C4   109.09  3.000
 1R1  H24  C5   C4   109.40  3.000
 1R1  H25  C5   C6   109.12  3.000
 1R1  H24  C5   C6   109.34  3.000
 1R1  C4   C5   C6   113.70  3.000
 1R1  H27  C4   H26  106.06  3.000
 1R1  H27  C4   C3   109.55  3.000
 1R1  H26  C4   C3   109.29  3.000
 1R1  H27  C4   C5   109.67  3.000
 1R1  H26  C4   C5   109.38  3.000
 1R1  C3   C4   C5   112.66  3.000
 1R1  H29  C3   H28  106.03  3.000
 1R1  H29  C3   C2   109.30  3.000
 1R1  H28  C3   C2   109.75  3.000
 1R1  H29  C3   C4   109.05  3.000
 1R1  H28  C3   C4   109.35  3.000
 1R1  C2   C3   C4   113.12  3.000
 1R1  H31  C2   H30  107.03  3.000
 1R1  H31  C2   C1   109.77  3.000
 1R1  H30  C2   C1   109.37  3.000
 1R1  H31  C2   C3   110.00  3.000
 1R1  H30  C2   C3   109.47  3.000
 1R1  C1   C2   C3   111.11  3.000
 1R1  H33  C1   H32  107.73  3.000
 1R1  H33  C1   O1   109.37  3.000
 1R1  H32  C1   O1   110.29  3.000
 1R1  H33  C1   C2   110.30  3.000
 1R1  H32  C1   C2   110.31  3.000
 1R1  O1   C1   C2   108.83  3.000
 1R1  P1   O1   C1   120.16  3.000
 1R1  O3   P1   C1H  107.37  3.000
 1R1  O3   P1   O2   108.85  3.000
 1R1  C1H  P1   O2   116.13  3.000
 1R1  O3   P1   O1   106.58  3.000
 1R1  O2   P1   O1   115.45  3.000
 1R1  C1H  P1   O1   101.73  3.000
 1R1  H36  C1H  H35  106.79  3.000
 1R1  H36  C1H  C2H  110.87  3.000
 1R1  H35  C1H  C2H  110.43  3.000
 1R1  H36  C1H  P1   109.41  3.000
 1R1  H35  C1H  P1   107.18  3.000
 1R1  C2H  C1H  P1   111.96  3.000
 1R1  H38  C2H  H37  107.17  3.000
 1R1  H38  C2H  C3H  109.82  3.000
 1R1  H37  C2H  C3H  109.21  3.000
 1R1  H38  C2H  C1H  109.69  3.000
 1R1  H37  C2H  C1H  110.62  3.000
 1R1  C3H  C2H  C1H  110.29  3.000
 1R1  H40  C3H  H39  107.40  3.000
 1R1  H40  C3H  N1   105.54  3.000
 1R1  H39  C3H  N1   110.72  3.000
 1R1  H40  C3H  C2H  110.13  3.000
 1R1  H39  C3H  C2H  110.39  3.000
 1R1  N1   C3H  C2H  112.44  3.000
 1R1  N2   N1   C3H  116.39  3.000
 1R1  N3   N2   N1   174.46  3.000
 1R1  H34  O3   P1   115.54  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
 1R1  Var_01  C13  C14  C15  C16   179.55  30.0  3
 1R1  Var_02  C12  C13  C14  C15  -179.65  30.0  1
 1R1  Var_03  C11  C12  C13  C14   179.69  30.0  1
 1R1  Var_04  C10  C11  C12  C13  -179.83  30.0  3
 1R1  Var_05  C9   C10  C11  C12  -179.74  30.0  1
 1R1  Var_06  C8   C9   C10  C11   179.78  30.0  3
 1R1  Var_07  C7   C8   C9   C10  -179.77  30.0  1
 1R1  Var_08  C6   C7   C8   C9    179.20  30.0  1
 1R1  Var_09  C5   C6   C7   C8   -179.26  30.0  3
 1R1  Var_10  C4   C5   C6   C7    178.70  30.0  1
 1R1  Var_11  C3   C4   C5   C6   -178.70  30.0  3
 1R1  Var_12  C2   C3   C4   C5    177.87  30.0  1
 1R1  Var_13  C1   C2   C3   C4   -178.84  30.0  3
 1R1  Var_14  O1   C1   C2   C3    176.21  30.0  1
 1R1  Var_15  C1H  P1   O1   C1    166.01  30.0  3
 1R1  Var_16  C2H  C1H  P1   O1    179.37  30.0  3
 1R1  Var_17  C3H  C2H  C1H  P1    177.70  30.0  3
 1R1  Var_18  N1   C3H  C2H  C1H   178.05  30.0  3
 1R1  Var_19  H1   C16  C15  C14   -59.50  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
 1R1  chir_01  P1  C1H  O2  O3  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
 1R1  plan-1  C3H  0.020
 1R1  plan-1  N1   0.020
 1R1  plan-1  N2   0.020
 1R1  plan-1  N3   0.020

