# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Nov 18 11:13:06 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[4-(2-acetamidoethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCc1cn(nn1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
#
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
 QMK  QMK  "~{N}-[2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,2,3-triazol-4-yl]ethyl]ethanamide"  ligand  43  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QMK
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
 QMK  C4   C  CH2   0  -0.515  33.2956  -11.9673  26.1689
 QMK  C5   C  CR5   0   0.159  33.1757  -13.3048  26.8100
 QMK  C6   C  CR15  0  -0.095  33.3243  -14.5569  26.2721
 QMK  C11  C  CH1   0  -0.031  31.8812  -17.4570  26.7270
 QMK  C7   C  CH1   0   0.217  33.1380  -16.8308  27.3501
 QMK  C8   C  CH1   0  -0.046  33.8201  -18.4265  25.8094
 QMK  C9   C  CH2   0  -0.167  33.8182  -18.0802  24.3360
 QMK  C10  C  CH1   0  -0.034  32.4284  -18.8145  26.2940
 QMK  N1   N  NH1   0  -0.626  34.6897   -9.9150  26.0698
 QMK  N2   N  NR5   0  -0.295  33.1501  -15.3857  27.3194
 QMK  C3   C  CH2   0  -0.283  34.5850  -11.2553  26.5939
 QMK  N3   N  N     0  -0.095  32.9128  -14.7051  28.4277
 QMK  C1   C  CH3   0  -0.774  34.3234   -7.5291  25.9590
 QMK  C2   C  C     0   0.517  34.1141   -8.8503  26.6573
 QMK  N4   N  N     0  -0.314  32.9236  -13.4539  28.1324
 QMK  O1   O  O     0  -0.500  33.4754   -8.9355  27.6977
 QMK  O2   O  O2    0  -0.484  34.2152  -17.3043  26.5997
 QMK  O3   O  O2    0  -0.585  35.1213  -17.6164  23.9874
 QMK  O4   O  OH1   0  -0.725  36.9683  -16.8850  22.5092
 QMK  O5   O  O     0  -0.701  34.9185  -18.1226  21.4462
 QMK  O7   O  OH1   0  -0.659  32.5724  -19.6838  27.3849
 QMK  O8   O  OH1   0  -0.651  30.8105  -17.6020  27.6038
 QMK  P1   P  P     0   1.449  35.4036  -17.1827  22.4747
 QMK  H1   H  HCH2  0   0.257  32.4381  -11.3512  26.4475
 QMK  H2   H  HCH2  0   0.254  33.2753  -12.0763  25.0837
 QMK  H3   H  HCR5  0   0.312  33.5407  -14.8919  25.2714
 QMK  H4   H  HCH1  0   0.252  31.5991  -16.8834  25.8333
 QMK  H5   H  HCH1  0   0.267  33.2177  -17.1049  28.4076
 QMK  H6   H  HCH1  0   0.274  34.5329  -19.2379  25.9833
 QMK  H7   H  HCH2  0   0.243  33.0693  -17.3147  24.1102
 QMK  H8   H  HCH2  0   0.255  33.5648  -18.9789  23.7679
 QMK  H9   H  HCH1  0   0.262  31.8235  -19.2580  25.4925
 QMK  H10  H  HNH1  0   0.400  35.1707   -9.7884  25.1950
 QMK  H11  H  HCH2  0   0.258  35.4494  -11.8204  26.2447
 QMK  H12  H  HCH2  0   0.246  34.6441  -11.2199  27.6822
 QMK  H13  H  HCH3  0   0.264  34.8704   -6.8562  26.6198
 QMK  H14  H  HCH3  0   0.247  34.8712   -7.6093  25.0219
 QMK  H15  H  HCH3  0   0.262  33.3571   -7.0681  25.7566
 QMK  H16  H  HOH1  0   0.500  37.5258  -17.6512  22.3160
 QMK  H18  H  HOH1  0   0.455  31.7082  -19.8122  27.7911
 QMK  H19  H  HOH1  0   0.466  30.3949  -16.7451  27.7446
 QMK  O6   O  OH1   0  -0.736  34.7867  -15.7114  22.4492
 QMK  H21  H  HOH1  0   0.499  34.5814  -15.3767  21.5657

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
 QMK  O5   P1   double    1.475  0.020  1.475
 QMK  P1   O4   single    1.593  0.020  1.593
 QMK  P1   O3   single    1.599  0.020  1.599
 QMK  O3   C9   single    1.426  0.020  1.426
 QMK  C9   C8   single    1.513  0.020  1.513
 QMK  C8   C10  single    1.524  0.020  1.524
 QMK  C8   O2   single    1.428  0.020  1.428
 QMK  N1   C3   single    1.443  0.020  1.443
 QMK  N1   C2   single    1.345  0.020  1.345
 QMK  C10  C11  single    1.526  0.020  1.526
 QMK  C10  O7   single    1.402  0.020  1.402
 QMK  C3   C4   single    1.533  0.020  1.533
 QMK  O2   C7   single    1.396  0.020  1.396
 QMK  C11  C7   single    1.536  0.020  1.536
 QMK  C11  O8   single    1.391  0.020  1.391
 QMK  C1   C2   single    1.509  0.020  1.509
 QMK  C2   O1   double    1.224  0.020  1.224
 QMK  C6   C5   aromatic  1.371  0.020  1.371
 QMK  C6   N2   aromatic  1.347  0.020  1.347
 QMK  C4   C5   single    1.488  0.020  1.488
 QMK  C7   N2   single    1.446  0.020  1.446
 QMK  C5   N4   aromatic  1.355  0.020  1.355
 QMK  N2   N3   aromatic  1.322  0.020  1.322
 QMK  N4   N3   aromatic  1.286  0.020  1.286
 QMK  C4   H1   single    0.970  0.020  1.090
 QMK  C4   H2   single    0.970  0.020  1.090
 QMK  C6   H3   single    0.930  0.020  1.080
 QMK  C11  H4   single    0.970  0.020  1.090
 QMK  C7   H5   single    0.970  0.020  1.090
 QMK  C8   H6   single    0.970  0.020  1.090
 QMK  C9   H7   single    0.970  0.020  1.090
 QMK  C9   H8   single    0.970  0.020  1.090
 QMK  C10  H9   single    0.970  0.020  1.090
 QMK  N1   H10  single    0.860  0.020  1.020
 QMK  C3   H11  single    0.970  0.020  1.090
 QMK  C3   H12  single    0.970  0.020  1.090
 QMK  C1   H13  single    0.970  0.020  1.090
 QMK  C1   H14  single    0.970  0.020  1.090
 QMK  C1   H15  single    0.970  0.020  1.090
 QMK  O4   H16  single    0.850  0.020  0.980
 QMK  O7   H18  single    0.850  0.020  0.980
 QMK  O8   H19  single    0.850  0.020  0.980
 QMK  P1   O6   single    1.596  0.020  1.596
 QMK  O6   H21  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
 QMK  H2   C4   H1   107.19  3.000
 QMK  H2   C4   C3   109.75  3.000
 QMK  H1   C4   C3   109.13  3.000
 QMK  H2   C4   C5   109.70  3.000
 QMK  H1   C4   C5   109.51  3.000
 QMK  C3   C4   C5   111.46  3.000
 QMK  N4   C5   C6   107.62  3.000
 QMK  N4   C5   C4   122.31  3.000
 QMK  C6   C5   C4   130.03  3.000
 QMK  H3   C6   N2   123.85  3.000
 QMK  H3   C6   C5   132.09  3.000
 QMK  N2   C6   C5   104.06  3.000
 QMK  H4   C11  O8   111.67  3.000
 QMK  H4   C11  C10  109.00  3.000
 QMK  O8   C11  C10  111.22  3.000
 QMK  H4   C11  C7   109.10  3.000
 QMK  O8   C11  C7   114.61  3.000
 QMK  C10  C11  C7   100.62  3.000
 QMK  H5   C7   O2   112.22  3.000
 QMK  H5   C7   N2   105.67  3.000
 QMK  O2   C7   N2   108.74  3.000
 QMK  H5   C7   C11  110.43  3.000
 QMK  N2   C7   C11  113.94  3.000
 QMK  O2   C7   C11  105.97  3.000
 QMK  H6   C8   O2   108.33  3.000
 QMK  H6   C8   C10  110.83  3.000
 QMK  O2   C8   C10  106.07  3.000
 QMK  H6   C8   C9   108.98  3.000
 QMK  O2   C8   C9   111.05  3.000
 QMK  C10  C8   C9   111.51  3.000
 QMK  H8   C9   H7   108.01  3.000
 QMK  H8   C9   O3   110.61  3.000
 QMK  H7   C9   O3   110.32  3.000
 QMK  H8   C9   C8   108.55  3.000
 QMK  H7   C9   C8   111.21  3.000
 QMK  O3   C9   C8   108.13  3.000
 QMK  H9   C10  O7   111.97  3.000
 QMK  H9   C10  C8   111.96  3.000
 QMK  O7   C10  C8   108.14  3.000
 QMK  H9   C10  C11  111.66  3.000
 QMK  O7   C10  C11  111.56  3.000
 QMK  C8   C10  C11  101.02  3.000
 QMK  H10  N1   C2   118.98  3.000
 QMK  H10  N1   C3   117.86  3.000
 QMK  C2   N1   C3   123.05  3.000
 QMK  N3   N2   C7   119.69  3.000
 QMK  N3   N2   C6   111.00  3.000
 QMK  C7   N2   C6   129.26  3.000
 QMK  H12  C3   H11  107.07  3.000
 QMK  H12  C3   N1   109.17  3.000
 QMK  H11  C3   N1   107.92  3.000
 QMK  H12  C3   C4   109.71  3.000
 QMK  H11  C3   C4   109.71  3.000
 QMK  N1   C3   C4   113.06  3.000
 QMK  N4   N3   N2   107.87  3.000
 QMK  H15  C1   H14  108.52  3.000
 QMK  H15  C1   H13  107.24  3.000
 QMK  H14  C1   H13  108.34  3.000
 QMK  H15  C1   C2   109.48  3.000
 QMK  H14  C1   C2   113.81  3.000
 QMK  H13  C1   C2   109.24  3.000
 QMK  O1   C2   C1   121.79  3.000
 QMK  O1   C2   N1   122.64  3.000
 QMK  C1   C2   N1   115.56  3.000
 QMK  N3   N4   C5   109.45  3.000
 QMK  C8   O2   C7   110.52  3.000
 QMK  P1   O3   C9   118.73  3.000
 QMK  H16  O4   P1   114.44  3.000
 QMK  H18  O7   C10  108.57  3.000
 QMK  H19  O8   C11  109.36  3.000
 QMK  O6   P1   O5   116.69  3.000
 QMK  O6   P1   O4   101.99  3.000
 QMK  O5   P1   O4   117.20  3.000
 QMK  O6   P1   O3   101.36  3.000
 QMK  O4   P1   O3   101.75  3.000
 QMK  O5   P1   O3   115.39  3.000
 QMK  H21  O6   P1   114.58  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
 QMK  CONST_01  N3   N2  C6  C5     0.00   0.0  0
 QMK  CONST_02  N2   N3  N4  C5     0.00   0.0  0
 QMK  CONST_03  N3   N4  C5  C6     0.00   0.0  0
 QMK  CONST_04  N4   N3  N2  C6     0.00   0.0  0
 QMK  CONST_05  N4   C5  C6  N2     0.00   0.0  0
 QMK  CONST_06  C7   N2  C6  C5   180.00   0.0  0
 QMK  CONST_07  N4   N3  N2  C7   180.00   0.0  0
 QMK  CONST_08  N2   C6  C5  C4   180.00   0.0  0
 QMK  CONST_09  N3   N4  C5  C4   180.00   0.0  0
 QMK  CONST_10  H3   C6  N2  C7     0.00   0.0  0
 QMK  CONST_11  H3   C6  N2  N3   180.00   0.0  0
 QMK  CONST_12  H3   C6  C5  N4   180.00   0.0  0
 QMK  CONST_13  C1   C2  N1  C3   180.00   0.0  0
 QMK  CONST_14  O1   C2  N1  C3     0.00   0.0  0
 QMK  CONST_15  H10  N1  C2  C1     0.00   0.0  0
 QMK  CONST_16  H10  N1  C2  O1   180.00   0.0  0
 QMK  Var_01    C3   C4  C5  C6  -106.84  30.0  1
 QMK  Var_02    N4   C5  C4  C3    70.81  30.0  2
 QMK  Var_03    H1   C4  C5  C6   132.30  30.0  1
 QMK  Var_04    H2   C4  C5  C6    14.92  30.0  1
 QMK  Var_05    H1   C4  C5  N4   -50.05  30.0  1
 QMK  Var_06    H2   C4  C5  N4  -167.43  30.0  1
 QMK  Var_07    N1   C3  C4  C5  -175.73  30.0  2
 QMK  Var_08    P1   O3  C9  C8   179.81  30.0  2
 QMK  Var_09    H11  C3  C4  C5    63.75  30.0  2
 QMK  Var_10    H12  C3  C4  C5   -53.61  30.0  2
 QMK  Var_11    C2   N1  C3  C4    83.68  30.0  2
 QMK  Var_12    O5   P1  O3  C9   -46.71  30.0  1
 QMK  Var_13    O4   P1  O3  C9  -174.69  30.0  1
 QMK  Var_14    O6   P1  O3  C9    80.34  30.0  1
 QMK  Var_15    H10  N1  C3  C4   -92.57  30.0  2
 QMK  Var_16    H1   C4  C3  N1   -54.66  30.0  3
 QMK  Var_17    H2   C4  C3  N1    62.53  30.0  3
 QMK  Var_18    H13  C1  C2  N1  -117.73  30.0  3
 QMK  Var_19    H14  C1  C2  N1     3.50  30.0  3
 QMK  Var_20    H15  C1  C2  N1   125.12  30.0  3
 QMK  Var_21    H11  C3  N1  C2  -154.79  30.0  3
 QMK  Var_22    H12  C3  N1  C2   -38.74  30.0  3
 QMK  Var_23    H13  C1  C2  O1    61.42  30.0  3
 QMK  Var_24    H14  C1  C2  O1  -177.36  30.0  3
 QMK  Var_25    H15  C1  C2  O1   -55.74  30.0  3
 QMK  Var_26    H7   C9  O3  P1   -58.38  30.0  3
 QMK  Var_27    H8   C9  O3  P1    61.07  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
 QMK  chir_01  C11  C10  C7   O8   positiv
 QMK  chir_02  C7   O2   N2   C11  negativ
 QMK  chir_03  C8   O2   C9   C10  positiv
 QMK  chir_04  C10  O7   C11  C8   negativ

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
 QMK  plan-1  C4   0.020
 QMK  plan-1  C5   0.020
 QMK  plan-1  C6   0.020
 QMK  plan-1  C7   0.020
 QMK  plan-1  N2   0.020
 QMK  plan-1  N3   0.020
 QMK  plan-1  N4   0.020
 QMK  plan-1  H3   0.020
 QMK  plan-2  N1   0.020
 QMK  plan-2  C3   0.020
 QMK  plan-2  C1   0.020
 QMK  plan-2  C2   0.020
 QMK  plan-2  O1   0.020
 QMK  plan-2  H10  0.020

