# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:26:35 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: tetradecyl hydrogen (R)-(3-azidopropyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCO[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
 1QY  1QY  'tetradecyl hydrogen (R)-(3-azidopropyl)phosphonate'  ligand  60  24  .  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_1QY
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
 1QY  C14  C  CH3    0  -0.662  -13.9759   0.9206   0.0464
 1QY  C13  C  CH2    0  -0.419  -12.7309   0.2294  -0.4919
 1QY  C12  C  CH2    0  -0.406  -11.4448   0.7386   0.1472
 1QY  C11  C  CH2    0  -0.411  -10.1944   0.0471  -0.3811
 1QY  C10  C  CH2    0  -0.412   -8.9077   0.5502   0.2609
 1QY  C9   C  CH2    0  -0.412   -7.6608  -0.1465  -0.2688
 1QY  C8   C  CH2    0  -0.412   -6.3693   0.3523   0.3673
 1QY  C7   C  CH2    0  -0.412   -5.1288  -0.3479  -0.1724
 1QY  C6   C  CH2    0  -0.413   -3.8289   0.1501   0.4468
 1QY  C5   C  CH2    0  -0.412   -2.5977  -0.5503  -0.1137
 1QY  C4   C  CH2    0  -0.412   -1.2870  -0.0430   0.4735
 1QY  C3   C  CH2    0  -0.428   -0.0684  -0.7384  -0.1198
 1QY  C2   C  CH2    0  -0.463    1.2495  -0.2062   0.4303
 1QY  C1   C  CH2    0  -0.149    2.4295  -0.9074  -0.2055
 1QY  O1   O  O2     0  -0.601    3.6419  -0.3138   0.2877
 1QY  P1   P  P      0   1.392    5.0684  -0.9278  -0.1169
 1QY  O2   O  O      0  -0.720    5.1872  -1.3951  -1.5195
 1QY  C1H  C  CH2    0  -0.758    6.1865   0.3943   0.3761
 1QY  C2H  C  CH2    0  -0.449    7.6454   0.0457   0.0926
 1QY  C3H  C  CH2    0  -0.282    8.5488   1.2068   0.4709
 1QY  N1   N  N      0  -0.362    9.9487   0.8228   0.2513
 1QY  N2   N  N      1   0.355   10.6695   1.6384  -0.2852
 1QY  N3   N  N     -1  -0.229   11.4119   2.3230  -0.7821
 1QY  H1   H  HCH3   0   0.226  -14.8828   0.5367  -0.4221
 1QY  H2   H  HCH3   0   0.215  -14.0730   0.7749   1.1240
 1QY  H3   H  HCH3   0   0.215  -13.9399   1.9964  -0.1361
 1QY  H4   H  HCH2   0   0.210  -12.8115  -0.8500  -0.3292
 1QY  H5   H  HCH2   0   0.210  -12.6751   0.3675  -1.5762
 1QY  H6   H  HCH2   0   0.206  -11.3608   1.8186  -0.0181
 1QY  H7   H  HCH2   0   0.205  -11.5028   0.6039   1.2332
 1QY  H8   H  HCH2   0   0.206  -10.2819  -1.0330  -0.2186
 1QY  H9   H  HCH2   0   0.206  -10.1353   0.1845  -1.4666
 1QY  H10  H  HCH2   0   0.206   -8.8181   1.6299   0.0971
 1QY  H11  H  HCH2   0   0.206   -8.9664   0.4140   1.3466
 1QY  H12  H  HCH2   0   0.206   -7.7518  -1.2261  -0.1048
 1QY  H13  H  HCH2   0   0.206   -7.6042  -0.0112  -1.3547
 1QY  H14  H  HCH2   0   0.206   -6.2776   1.4319   0.2036
 1QY  H15  H  HCH2   0   0.206   -6.4218   0.2152   1.4532
 1QY  H16  H  HCH2   0   0.207   -5.2197  -1.4270  -0.0052
 1QY  H17  H  HCH2   0   0.206   -5.0837  -0.2151  -1.2593
 1QY  H18  H  HCH2   0   0.207   -3.7390   1.2297   0.2824
 1QY  H19  H  HCH2   0   0.207   -3.8654   0.0121   1.5331
 1QY  H20  H  HCH2   0   0.208   -2.6814  -1.6285   0.0616
 1QY  H21  H  HCH2   0   0.207   -2.5762  -0.4238  -1.2020
 1QY  H22  H  HCH2   0   0.210   -1.2066   1.0362   0.3035
 1QY  H23  H  HCH2   0   0.211   -1.2936  -0.1792   1.5602
 1QY  H24  H  HCH2   0   0.218   -0.1385  -1.8154   0.0664
 1QY  H25  H  HCH2   0   0.216   -0.0816  -0.6176  -1.2084
 1QY  H26  H  HCH2   0   0.229    1.3186   0.8683   0.2367
 1QY  H27  H  HCH2   0   0.229    1.2821  -0.3391   1.5155
 1QY  H28  H  HCH2   0   0.226    2.4074  -1.9759   0.0293
 1QY  H29  H  HCH2   0   0.230    2.3910  -0.8048  -1.2929
 1QY  H31  H  HCH2   0   0.290    5.8922   1.2880  -0.1806
 1QY  H32  H  HCH2   0   0.290    6.0381   0.6194   1.4354
 1QY  H33  H  HCH2   0   0.251    7.9432  -0.8406   0.6570
 1QY  H34  H  HCH2   0   0.253    7.7779  -0.1851  -0.9658
 1QY  H35  H  HCH2   0   0.253    8.2824   2.0957  -0.1074
 1QY  H36  H  HCH2   0   0.256    8.4202   1.4516   1.5283
 1QY  O3   O  OH1    0  -0.751    5.3290  -2.1735   0.8705
 1QY  H30  H  HOH1   0   0.489    5.2561  -1.9792   1.8139

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
 1QY  C2H  C3H  single  1.519  0.020  1.519
 1QY  C2H  C1H  single  1.526  0.020  1.526
 1QY  C3H  N1   single  1.468  0.020  1.468
 1QY  N3   N2   double  1.126  0.020  1.126
 1QY  O2   P1   double  1.483  0.020  1.483
 1QY  N2   N1   double  1.213  0.020  1.213
 1QY  C1H  P1   single  1.800  0.020  1.800
 1QY  P1   O1   single  1.605  0.020  1.605
 1QY  O1   C1   single  1.437  0.020  1.437
 1QY  C3   C4   single  1.523  0.020  1.523
 1QY  C3   C2   single  1.524  0.020  1.524
 1QY  C1   C2   single  1.513  0.020  1.513
 1QY  C4   C5   single  1.523  0.020  1.523
 1QY  C13  C14  single  1.522  0.020  1.522
 1QY  C13  C12  single  1.524  0.020  1.524
 1QY  C7   C6   single  1.524  0.020  1.524
 1QY  C7   C8   single  1.523  0.020  1.523
 1QY  C9   C10  single  1.523  0.020  1.523
 1QY  C9   C8   single  1.524  0.020  1.524
 1QY  C5   C6   single  1.523  0.020  1.523
 1QY  C11  C10  single  1.523  0.020  1.523
 1QY  C11  C12  single  1.523  0.020  1.523
 1QY  C14  H1   single  0.970  0.020  1.090
 1QY  C14  H2   single  0.970  0.020  1.090
 1QY  C14  H3   single  0.970  0.020  1.090
 1QY  C13  H4   single  0.970  0.020  1.090
 1QY  C13  H5   single  0.970  0.020  1.090
 1QY  C12  H6   single  0.970  0.020  1.090
 1QY  C12  H7   single  0.970  0.020  1.090
 1QY  C11  H8   single  0.970  0.020  1.090
 1QY  C11  H9   single  0.970  0.020  1.090
 1QY  C10  H10  single  0.970  0.020  1.090
 1QY  C10  H11  single  0.970  0.020  1.090
 1QY  C9   H12  single  0.970  0.020  1.090
 1QY  C9   H13  single  0.970  0.020  1.090
 1QY  C8   H14  single  0.970  0.020  1.090
 1QY  C8   H15  single  0.970  0.020  1.090
 1QY  C7   H16  single  0.970  0.020  1.090
 1QY  C7   H17  single  0.970  0.020  1.090
 1QY  C6   H18  single  0.970  0.020  1.090
 1QY  C6   H19  single  0.970  0.020  1.090
 1QY  C5   H20  single  0.970  0.020  1.090
 1QY  C5   H21  single  0.970  0.020  1.090
 1QY  C4   H22  single  0.970  0.020  1.090
 1QY  C4   H23  single  0.970  0.020  1.090
 1QY  C3   H24  single  0.970  0.020  1.090
 1QY  C3   H25  single  0.970  0.020  1.090
 1QY  C2   H26  single  0.970  0.020  1.090
 1QY  C2   H27  single  0.970  0.020  1.090
 1QY  C1   H28  single  0.970  0.020  1.090
 1QY  C1   H29  single  0.970  0.020  1.090
 1QY  C1H  H31  single  0.970  0.020  1.090
 1QY  C1H  H32  single  0.970  0.020  1.090
 1QY  C2H  H33  single  0.970  0.020  1.090
 1QY  C2H  H34  single  0.970  0.020  1.090
 1QY  C3H  H35  single  0.970  0.020  1.090
 1QY  C3H  H36  single  0.970  0.020  1.090
 1QY  P1   O3   single  1.611  0.020  1.611
 1QY  O3   H30  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
 1QY  H3   C14  H2   107.42  3.000
 1QY  H3   C14  H1   107.61  3.000
 1QY  H2   C14  H1   107.64  3.000
 1QY  H3   C14  C13  111.18  3.000
 1QY  H2   C14  C13  111.17  3.000
 1QY  H1   C14  C13  111.62  3.000
 1QY  H5   C13  H4   105.99  3.000
 1QY  H5   C13  C12  109.29  3.000
 1QY  H4   C13  C12  109.23  3.000
 1QY  H5   C13  C14  109.55  3.000
 1QY  H4   C13  C14  109.57  3.000
 1QY  C12  C13  C14  112.97  3.000
 1QY  H7   C12  H6   105.94  3.000
 1QY  H7   C12  C11  109.35  3.000
 1QY  H6   C12  C11  109.40  3.000
 1QY  H7   C12  C13  109.27  3.000
 1QY  H6   C12  C13  109.32  3.000
 1QY  C11  C12  C13  113.31  3.000
 1QY  H9   C11  H8   105.95  3.000
 1QY  H9   C11  C10  109.30  3.000
 1QY  H8   C11  C10  109.29  3.000
 1QY  H9   C11  C12  109.32  3.000
 1QY  H8   C11  C12  109.30  3.000
 1QY  C10  C11  C12  113.41  3.000
 1QY  H11  C10  H10  105.96  3.000
 1QY  H11  C10  C9   109.36  3.000
 1QY  H10  C10  C9   109.38  3.000
 1QY  H11  C10  C11  109.34  3.000
 1QY  H10  C10  C11  109.36  3.000
 1QY  C9   C10  C11  113.19  3.000
 1QY  H13  C9   H12  105.92  3.000
 1QY  H13  C9   C8   109.24  3.000
 1QY  H12  C9   C8   109.30  3.000
 1QY  H13  C9   C10  109.29  3.000
 1QY  H12  C9   C10  109.31  3.000
 1QY  C8   C9   C10  113.51  3.000
 1QY  H15  C8   H14  105.99  3.000
 1QY  H15  C8   C7   109.42  3.000
 1QY  H14  C8   C7   109.37  3.000
 1QY  H15  C8   C9   109.40  3.000
 1QY  H14  C8   C9   109.34  3.000
 1QY  C7   C8   C9   113.07  3.000
 1QY  H17  C7   H16  105.91  3.000
 1QY  H17  C7   C6   109.17  3.000
 1QY  H16  C7   C6   109.31  3.000
 1QY  H17  C7   C8   109.22  3.000
 1QY  H16  C7   C8   109.33  3.000
 1QY  C6   C7   C8   113.61  3.000
 1QY  H19  C6   H18  106.00  3.000
 1QY  H19  C6   C5   109.50  3.000
 1QY  H18  C6   C5   109.36  3.000
 1QY  H19  C6   C7   109.48  3.000
 1QY  H18  C6   C7   109.33  3.000
 1QY  C5   C6   C7   112.94  3.000
 1QY  H21  C5   H20  105.90  3.000
 1QY  H21  C5   C4   109.12  3.000
 1QY  H20  C5   C4   109.38  3.000
 1QY  H21  C5   C6   109.16  3.000
 1QY  H20  C5   C6   109.38  3.000
 1QY  C4   C5   C6   113.61  3.000
 1QY  H23  C4   H22  106.08  3.000
 1QY  H23  C4   C3   109.54  3.000
 1QY  H22  C4   C3   109.30  3.000
 1QY  H23  C4   C5   109.63  3.000
 1QY  H22  C4   C5   109.36  3.000
 1QY  C3   C4   C5   112.72  3.000
 1QY  H25  C3   H24  106.06  3.000
 1QY  H25  C3   C2   109.31  3.000
 1QY  H24  C3   C2   109.72  3.000
 1QY  H25  C3   C4   109.09  3.000
 1QY  H24  C3   C4   109.36  3.000
 1QY  C2   C3   C4   113.06  3.000
 1QY  H27  C2   H26  107.04  3.000
 1QY  H27  C2   C1   109.72  3.000
 1QY  H26  C2   C1   109.37  3.000
 1QY  H27  C2   C3   109.96  3.000
 1QY  H26  C2   C3   109.50  3.000
 1QY  C1   C2   C3   111.15  3.000
 1QY  H29  C1   H28  107.73  3.000
 1QY  H29  C1   O1   109.41  3.000
 1QY  H28  C1   O1   110.29  3.000
 1QY  H29  C1   C2   110.31  3.000
 1QY  H28  C1   C2   110.29  3.000
 1QY  O1   C1   C2   108.80  3.000
 1QY  P1   O1   C1   120.35  3.000
 1QY  O3   P1   C1H  107.43  3.000
 1QY  O3   P1   O2   108.85  3.000
 1QY  C1H  P1   O2   116.14  3.000
 1QY  O3   P1   O1   106.57  3.000
 1QY  C1H  P1   O1   101.66  3.000
 1QY  O2   P1   O1   115.48  3.000
 1QY  H32  C1H  H31  106.77  3.000
 1QY  H32  C1H  C2H  110.90  3.000
 1QY  H31  C1H  C2H  110.46  3.000
 1QY  H32  C1H  P1   109.40  3.000
 1QY  H31  C1H  P1   107.08  3.000
 1QY  C2H  C1H  P1   112.02  3.000
 1QY  H34  C2H  H33  107.25  3.000
 1QY  H34  C2H  C3H  109.32  3.000
 1QY  H33  C2H  C3H  109.24  3.000
 1QY  H34  C2H  C1H  110.15  3.000
 1QY  H33  C2H  C1H  110.49  3.000
 1QY  C3H  C2H  C1H  110.34  3.000
 1QY  H36  C3H  H35  107.51  3.000
 1QY  H36  C3H  N1   108.39  3.000
 1QY  H35  C3H  N1   111.46  3.000
 1QY  H36  C3H  C2H  110.01  3.000
 1QY  H35  C3H  C2H  110.17  3.000
 1QY  N1   C3H  C2H  109.26  3.000
 1QY  N2   N1   C3H  117.17  3.000
 1QY  N3   N2   N1   174.74  3.000
 1QY  H30  O3   P1   115.53  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
 1QY  Var_01  C11  C12  C13  C14   179.72  30.0  3
 1QY  Var_02  C10  C11  C12  C13  -179.74  30.0  1
 1QY  Var_03  C9   C10  C11  C12   179.88  30.0  3
 1QY  Var_04  C8   C9   C10  C11   179.93  30.0  1
 1QY  Var_05  C7   C8   C9   C10  -179.82  30.0  3
 1QY  Var_06  C6   C7   C8   C9    179.50  30.0  1
 1QY  Var_07  C5   C6   C7   C8   -179.42  30.0  3
 1QY  Var_08  C4   C5   C6   C7    178.76  30.0  1
 1QY  Var_09  C3   C4   C5   C6   -178.93  30.0  1
 1QY  Var_10  C2   C3   C4   C5    178.19  30.0  1
 1QY  Var_11  C1   C2   C3   C4   -178.94  30.0  3
 1QY  Var_12  O1   C1   C2   C3    176.58  30.0  1
 1QY  Var_13  O2   P1   O1   C1     39.11  30.0  1
 1QY  Var_14  C2H  C1H  P1   O1    179.82  30.0  1
 1QY  Var_15  C3H  C2H  C1H  P1    177.75  30.0  1
 1QY  Var_16  N1   C3H  C2H  C1H   177.23  30.0  3
 1QY  Var_17  H1   C14  C13  C12  -179.74  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
 1QY  chir_01  P1  C1H  O1  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
 1QY  plan-1  C3H  0.020
 1QY  plan-1  N1   0.020
 1QY  plan-1  N2   0.020
 1QY  plan-1  N3   0.020

