# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 20:58:50 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(3~{S})-2-azanylidene-3-oxidanyl-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCC(=N)[C@@H](O)C=C)[C@H](O)[C@@H](O[S](O)(=O)=O)[C@H]1O
#
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
 QAH  QAH  '[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(3~{S})-2-azanylidene-3-oxidanyl-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate'  ligand  41  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QAH
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
 QAH  C1   C  CH1    0   0.281   7.9571  -4.8164  12.9030
 QAH  C2   C  CH1    0  -0.005   9.4709  -4.6285  13.0147
 QAH  C2'  C  CH2    0  -0.234   6.1366  -5.2667  14.3490
 QAH  C3   C  CH1    0   0.018  10.0029  -4.0923  11.6910
 QAH  C3'  C  C      0   0.202   5.9524  -4.4470  15.6000
 QAH  C4   C  CH1    0  -0.044   9.5391  -4.9689  10.5178
 QAH  C4'  C  CH1    0  -0.066   6.6463  -4.9159  16.8725
 QAH  C5   C  CH1    0  -0.011   8.0248  -5.1179  10.5885
 QAH  C5'  C  C1     0  -0.208   7.9519  -4.1843  17.0440
 QAH  C6   C  CH2    0  -0.156   7.4841  -5.9999   9.4840
 QAH  C6'  C  C2     0  -0.557   9.1476  -4.7545  17.1378
 QAH  N1   N  N      0  -0.551   5.2432  -3.4026  15.5347
 QAH  O1   O  O2     0  -0.494   7.5169  -5.4160  14.0652
 QAH  O1S  O  OS     0  -0.738  12.4768  -4.7901   9.7329
 QAH  O2   O  OH1    0  -0.669   9.7842  -3.7104  14.0271
 QAH  O2S  O  OS     0  -0.725  11.6880  -2.4681   9.9150
 QAH  O3   O  OC2    0  -0.625  11.4164  -4.0340  11.8327
 QAH  O3S  O  OS    -1  -0.712  13.6080  -3.2401  11.2635
 QAH  O4   O  OH1    0  -0.682  10.1413  -6.2353  10.5340
 QAH  O4'  O  OH1    0  -0.655   6.7695  -6.3072  16.8289
 QAH  O5   O  O2     0  -0.489   7.6293  -5.6567  11.8325
 QAH  O6   O  OH1    0  -0.666   6.0798  -5.8961   9.4764
 QAH  S    S  S      0   1.579  12.3712  -3.5826  10.5721
 QAH  H1   H  HCH1   0   0.189   7.4835  -3.8263  12.7592
 QAH  H2   H  HCH1   0   0.218   9.9205  -5.6148  13.2024
 QAH  H3   H  HCH2   0   0.248   5.6027  -4.7684  13.5358
 QAH  H4   H  HCH2   0   0.252   5.6922  -6.2573  14.4746
 QAH  H5   H  HCH1   0   0.231   9.6010  -3.0818  11.5361
 QAH  H6   H  HCH1   0   0.235   9.7550  -4.4371   9.5820
 QAH  H7   H  HCH1   0   0.258   6.0028  -4.6027  17.7097
 QAH  H8   H  HCH1   0   0.227   7.5964  -4.1096  10.4603
 QAH  H9   H  H      0   0.268   7.8579  -3.1064  17.1368
 QAH  H10  H  HCH2   0   0.206   7.8159  -7.0323   9.6397
 QAH  H11  H  HCH2   0   0.201   7.9219  -5.6590   8.5366
 QAH  H12  H  H      0   0.258  10.0332  -4.1581  17.3130
 QAH  H13  H  H      0   0.248   9.2920  -5.8244  17.0576
 QAH  H14  H  H      0   0.340   5.1645  -2.9462  16.4426
 QAH  H15  H  HOH1   0   0.462   9.4562  -4.0595  14.8661
 QAH  H16  H  HOH1   0   0.451  11.0586  -6.1017  10.2531
 QAH  H17  H  HOH1   0   0.462   7.1043  -6.6139  17.6784
 QAH  H18  H  HOH1   0   0.454   5.7403  -6.5038   8.8137

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
 QAH  O1S  S    deloc   1.474  0.020  1.474
 QAH  C6   O6   single  1.408  0.020  1.408
 QAH  C6   C5   single  1.513  0.020  1.513
 QAH  O2S  S    deloc   1.463  0.020  1.463
 QAH  S    O3S  deloc   1.458  0.020  1.458
 QAH  S    O3   single  1.645  0.020  1.645
 QAH  C4   C5   single  1.523  0.020  1.523
 QAH  C4   O4   single  1.402  0.020  1.402
 QAH  C4   C3   single  1.536  0.020  1.536
 QAH  C5   O5   single  1.412  0.020  1.412
 QAH  O3   C3   single  1.422  0.020  1.422
 QAH  C3   C2   single  1.524  0.020  1.524
 QAH  O5   C1   single  1.400  0.020  1.400
 QAH  C2   C1   single  1.530  0.020  1.530
 QAH  C2   O2   single  1.402  0.020  1.402
 QAH  C1   O1   single  1.380  0.020  1.380
 QAH  O1   C2'  single  1.417  0.020  1.417
 QAH  C2'  C3'  single  1.507  0.020  1.507
 QAH  C3'  N1   double  1.264  0.020  1.264
 QAH  C3'  C4'  single  1.523  0.020  1.523
 QAH  O4'  C4'  single  1.397  0.020  1.397
 QAH  C4'  C5'  single  1.506  0.020  1.506
 QAH  C5'  C6'  double  1.328  0.020  1.328
 QAH  C1   H1   single  0.970  0.020  1.090
 QAH  C2   H2   single  0.970  0.020  1.090
 QAH  C2'  H3   single  0.970  0.020  1.090
 QAH  C2'  H4   single  0.970  0.020  1.090
 QAH  C3   H5   single  0.970  0.020  1.090
 QAH  C4   H6   single  0.970  0.020  1.090
 QAH  C4'  H7   single  0.970  0.020  1.090
 QAH  C5   H8   single  0.970  0.020  1.090
 QAH  C5'  H9   single  0.930  0.020  1.080
 QAH  C6   H10  single  0.970  0.020  1.090
 QAH  C6   H11  single  0.970  0.020  1.090
 QAH  C6'  H12  single  0.930  0.020  1.080
 QAH  C6'  H13  single  0.930  0.020  1.080
 QAH  N1   H14  single  0.890  0.020  1.040
 QAH  O2   H15  single  0.850  0.020  0.980
 QAH  O4   H16  single  0.850  0.020  0.980
 QAH  O4'  H17  single  0.850  0.020  0.980
 QAH  O6   H18  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
 QAH  H1   C1   O5   109.72  3.000
 QAH  H1   C1   O1   111.20  3.000
 QAH  O5   C1   O1   107.97  3.000
 QAH  H1   C1   C2   108.85  3.000
 QAH  O1   C1   C2   107.91  3.000
 QAH  O5   C1   C2   111.18  3.000
 QAH  H2   C2   O2   111.87  3.000
 QAH  H2   C2   C3   108.73  3.000
 QAH  O2   C2   C3   108.58  3.000
 QAH  H2   C2   C1   107.87  3.000
 QAH  O2   C2   C1   110.75  3.000
 QAH  C3   C2   C1   108.98  3.000
 QAH  H4   C2'  H3   107.46  3.000
 QAH  H4   C2'  O1   108.88  3.000
 QAH  H3   C2'  O1   112.01  3.000
 QAH  H4   C2'  C3'  110.36  3.000
 QAH  H3   C2'  C3'  108.05  3.000
 QAH  O1   C2'  C3'  110.04  3.000
 QAH  H5   C3   O3   109.88  3.000
 QAH  H5   C3   C4   107.86  3.000
 QAH  O3   C3   C4   113.55  3.000
 QAH  H5   C3   C2   108.57  3.000
 QAH  O3   C3   C2   105.96  3.000
 QAH  C4   C3   C2   110.92  3.000
 QAH  N1   C3'  C4'  123.57  3.000
 QAH  C4'  C3'  C2'  118.06  3.000
 QAH  N1   C3'  C2'  118.37  3.000
 QAH  H6   C4   O4   111.27  3.000
 QAH  H6   C4   C5   106.40  3.000
 QAH  O4   C4   C5   109.75  3.000
 QAH  H6   C4   C3   108.38  3.000
 QAH  O4   C4   C3   112.14  3.000
 QAH  C5   C4   C3   108.69  3.000
 QAH  H7   C4'  O4'  110.99  3.000
 QAH  H7   C4'  C5'  106.36  3.000
 QAH  O4'  C4'  C5'  114.25  3.000
 QAH  H7   C4'  C3'  106.34  3.000
 QAH  C5'  C4'  C3'  109.91  3.000
 QAH  O4'  C4'  C3'  108.69  3.000
 QAH  H8   C5   O5   110.02  3.000
 QAH  H8   C5   C6   108.00  3.000
 QAH  O5   C5   C6   108.69  3.000
 QAH  H8   C5   C4   106.94  3.000
 QAH  O5   C5   C4   110.89  3.000
 QAH  C6   C5   C4   112.23  3.000
 QAH  H9   C5'  C6'  119.87  3.000
 QAH  H9   C5'  C4'  114.63  3.000
 QAH  C6'  C5'  C4'  125.44  3.000
 QAH  H11  C6   H10  107.12  3.000
 QAH  H11  C6   O6   111.73  3.000
 QAH  H10  C6   O6   111.86  3.000
 QAH  H11  C6   C5   107.84  3.000
 QAH  H10  C6   C5   109.71  3.000
 QAH  O6   C6   C5   108.50  3.000
 QAH  H13  C6'  H12  116.59  3.000
 QAH  H13  C6'  C5'  122.63  3.000
 QAH  H12  C6'  C5'  120.78  3.000
 QAH  H14  N1   C3'  111.55  3.000
 QAH  C2'  O1   C1   115.70  3.000
 QAH  H15  O2   C2   108.33  3.000
 QAH  S    O3   C3   120.80  3.000
 QAH  H16  O4   C4   106.18  3.000
 QAH  H17  O4'  C4'  108.67  3.000
 QAH  C5   O5   C1   112.27  3.000
 QAH  H18  O6   C6   108.02  3.000
 QAH  O3S  S    O3   101.15  3.000
 QAH  O3   S    O2S  106.39  3.000
 QAH  O3S  S    O2S  115.48  3.000
 QAH  O3   S    O1S  104.66  3.000
 QAH  O3S  S    O1S  113.69  3.000
 QAH  O2S  S    O1S  113.69  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
 QAH  Var_01  C3'  C2'  O1   C1   -114.66  30.0  3
 QAH  Var_02  O1S  S    O3   C3    -79.69  30.0  3
 QAH  Var_03  O1   C2'  C3'  C4'   -55.46  30.0  2
 QAH  Var_04  H12  C6'  C5'  C4'  -176.71   0.0  2

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
 QAH  chir_01  C1   O5   C2   O1   positiv
 QAH  chir_02  C2   O2   C1   C3   negativ
 QAH  chir_03  C3   O3   C4   C2   negativ
 QAH  chir_04  C4   O4   C3   C5   positiv
 QAH  chir_05  C4'  C3'  O4'  C5'  negativ
 QAH  chir_06  C5   O5   C4   C6   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
 QAH  plan-1  C2'  0.020
 QAH  plan-1  C3'  0.020
 QAH  plan-1  C4'  0.020
 QAH  plan-1  N1   0.020
 QAH  plan-1  H14  0.020
 QAH  plan-2  C4'  0.020
 QAH  plan-2  C5'  0.020
 QAH  plan-2  C6'  0.020
 QAH  plan-2  H9   0.020
 QAH  plan-2  H12  0.020
 QAH  plan-2  H13  0.020

