# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 20:50:55 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)[C@@H]4CCN4)[C@@H](O)[C@H]3O
#
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
 8X1  8X1  5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine  ligand  48  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8X1
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
 8X1  O2S  O  OS    0  -0.631   4.5285   1.8743   0.0325
 8X1  S    S  S     0   1.632   3.6234   1.0336  -0.7097
 8X1  O1S  O  OS    0  -0.609   3.9604   0.5364  -2.0137
 8X1  N3S  N  NC1   0  -0.835   3.2659  -0.2200   0.3224
 8X1  C    C  C     0   0.567   2.4212  -1.2708   0.0132
 8X1  CA   C  C     0  -0.226   2.4817  -2.3889   1.0309
 8X1  CB   C  C     0  -0.494   3.5229  -3.4540   0.5952
 8X1  CG   C  C     0  -0.266   2.3113  -4.2737   0.1232
 8X1  N    N  N     0  -0.604   1.4433  -3.3962   0.9195
 8X1  O    O  O     0  -0.406   1.7380  -1.2751  -0.9802
 8X1  O5'  O  OC2   0  -0.565   2.2303   1.7561  -0.9110
 8X1  C5'  C  CH2   0  -0.194   1.6176   2.4307   0.2032
 8X1  C4'  C  CR15  0  -0.042   0.2764   2.9353  -0.2876
 8X1  C3'  C  CR15  0  -0.036  -0.5263   3.5821   0.8374
 8X1  O3'  O  OH1   0  -0.663  -1.3610   4.5591   0.2778
 8X1  C2'  C  CR15  0  -0.053  -1.3405   2.3876   1.3443
 8X1  O2'  O  OH1   0  -0.650  -2.5308   2.7159   1.9906
 8X1  C1'  C  CR15  0   0.208  -1.6445   1.6622   0.0353
 8X1  O4'  O  O     0  -0.480  -0.5164   1.8584  -0.7773
 8X1  N9   N  NR5   0  -0.542  -1.8847   0.2532   0.1819
 8X1  C4   C  CR56  0   0.490  -2.9154  -0.4554  -0.3727
 8X1  C5   C  CR56  0   0.005  -2.6612  -1.7778  -0.0510
 8X1  N7   N  N     0  -0.459  -1.5004  -1.8879   0.6730
 8X1  C8   C  CR15  0   0.133  -1.0726  -0.6680   0.7849
 8X1  N3   N  N     0  -0.456  -3.9500   0.0050  -1.0691
 8X1  C2   C  CR16  0   0.048  -4.7601  -0.9713  -1.4425
 8X1  N1   N  N     0  -0.473  -4.6486  -2.2749  -1.2036
 8X1  C6   C  CR6   0   0.466  -3.6007  -2.7227  -0.5027
 8X1  N6   N  NH2   0  -0.816  -3.4811  -4.0282  -0.2636
 8X1  H1   H  HNC1  0   0.458   3.8009  -0.2359   1.1836
 8X1  H2   H  H     0   0.277   2.6139  -1.9685   2.0338
 8X1  H3   H  H     0   0.261   4.2590  -3.1630  -0.1521
 8X1  H4   H  H     0   0.267   4.0363  -3.8882   1.4507
 8X1  H5   H  H     0   0.222   2.1558  -4.2099  -0.9572
 8X1  H6   H  H     0   0.227   2.2867  -5.3251   0.4152
 8X1  H7   H  H     0   0.362   0.5630  -3.1036   0.5107
 8X1  H9   H  HCH2  0   0.250   1.5155   1.7410   1.0463
 8X1  H10  H  HCH2  0   0.282   2.2320   3.2762   0.5169
 8X1  H11  H  HCR5  0   0.284   0.4444   3.6506  -1.0980
 8X1  H12  H  HCR5  0   0.263   0.1208   3.9985   1.6208
 8X1  H13  H  HOH1  0   0.453  -2.0844   4.7213   0.8949
 8X1  H14  H  HCR5  0   0.253  -0.6956   1.7662   1.9785
 8X1  H15  H  HOH1  0   0.472  -2.3453   2.8949   2.9180
 8X1  H16  H  HCR5  0   0.268  -2.5461   2.0773  -0.4274
 8X1  H17  H  HCR5  0   0.283  -0.1733  -0.3767   1.3054
 8X1  H18  H  HCR6  0   0.254  -5.6312  -0.6759  -2.0175
 8X1  H19  H  HNH2  0   0.405  -4.1887  -4.6698  -0.5775
 8X1  H20  H  HNH2  0   0.412  -2.7212  -4.3879   0.2865

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
 8X1  CG   N    single    1.469  0.020  1.469
 8X1  CG   CB   single    1.537  0.020  1.537
 8X1  N    CA   single    1.451  0.020  1.451
 8X1  CB   CA   single    1.552  0.020  1.552
 8X1  O    C    double    1.206  0.020  1.206
 8X1  CA   C    single    1.513  0.020  1.513
 8X1  C    N3S  single    1.383  0.020  1.383
 8X1  N1   C2   aromatic  1.330  0.020  1.330
 8X1  N1   C6   aromatic  1.338  0.020  1.338
 8X1  C2   N3   aromatic  1.322  0.020  1.322
 8X1  N6   C6   single    1.333  0.020  1.333
 8X1  C6   C5   aromatic  1.407  0.020  1.407
 8X1  N3   C4   aromatic  1.329  0.020  1.329
 8X1  O4'  C4'  single    1.424  0.020  1.424
 8X1  O4'  C1'  single    1.404  0.020  1.404
 8X1  C5   C4   aromatic  1.384  0.020  1.384
 8X1  C5   N7   aromatic  1.372  0.020  1.372
 8X1  N3S  S    single    1.663  0.020  1.663
 8X1  C4   N9   aromatic  1.368  0.020  1.368
 8X1  C5'  O5'  single    1.439  0.020  1.439
 8X1  C5'  C4'  single    1.515  0.020  1.515
 8X1  O5'  S    single    1.582  0.020  1.582
 8X1  N7   C8   aromatic  1.298  0.020  1.298
 8X1  N9   C1'  single    1.437  0.020  1.437
 8X1  N9   C8   aromatic  1.368  0.020  1.368
 8X1  C4'  C3'  single    1.526  0.020  1.526
 8X1  C1'  C2'  single    1.527  0.020  1.527
 8X1  O1S  S    deloc     1.436  0.020  1.436
 8X1  S    O2S  deloc     1.441  0.020  1.441
 8X1  C3'  C2'  single    1.532  0.020  1.532
 8X1  C3'  O3'  single    1.402  0.020  1.402
 8X1  C2'  O2'  single    1.394  0.020  1.394
 8X1  N3S  H1   single    0.860  0.020  1.020
 8X1  CA   H2   single    0.970  0.020  1.090
 8X1  CB   H3   single    0.970  0.020  1.090
 8X1  CB   H4   single    0.970  0.020  1.090
 8X1  CG   H5   single    0.970  0.020  1.090
 8X1  CG   H6   single    0.970  0.020  1.090
 8X1  N    H7   single    0.890  0.020  1.040
 8X1  C5'  H9   single    0.970  0.020  1.090
 8X1  C5'  H10  single    0.970  0.020  1.090
 8X1  C4'  H11  single    0.970  0.020  1.090
 8X1  C3'  H12  single    0.970  0.020  1.090
 8X1  O3'  H13  single    0.850  0.020  0.980
 8X1  C2'  H14  single    0.970  0.020  1.090
 8X1  O2'  H15  single    0.850  0.020  0.980
 8X1  C1'  H16  single    0.970  0.020  1.090
 8X1  C8   H17  single    0.930  0.020  1.080
 8X1  C2   H18  single    0.930  0.020  1.080
 8X1  N6   H19  single    0.860  0.020  1.020
 8X1  N6   H20  single    0.860  0.020  1.020

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
 8X1  O5'  S    N3S  103.53  3.000
 8X1  O5'  S    O1S  104.43  3.000
 8X1  N3S  S    O1S  110.68  3.000
 8X1  O1S  S    O2S  121.49  3.000
 8X1  O5'  S    O2S  110.62  3.000
 8X1  N3S  S    O2S  104.79  3.000
 8X1  H1   N3S  C    120.01  3.000
 8X1  H1   N3S  S    115.19  3.000
 8X1  C    N3S  S    124.43  3.000
 8X1  O    C    CA   125.04  3.000
 8X1  CA   C    N3S  112.74  3.000
 8X1  O    C    N3S  122.20  3.000
 8X1  H2   CA   N    115.03  3.000
 8X1  H2   CA   CB   116.07  3.000
 8X1  N    CA   CB    88.98  3.000
 8X1  H2   CA   C    109.70  3.000
 8X1  CB   CA   C    110.19  3.000
 8X1  N    CA   C    115.65  3.000
 8X1  H4   CB   H3   109.11  3.000
 8X1  H4   CB   CG   113.61  3.000
 8X1  H3   CB   CG   117.69  3.000
 8X1  H4   CB   CA   111.70  3.000
 8X1  H3   CB   CA   117.58  3.000
 8X1  CG   CB   CA    85.60  3.000
 8X1  H6   CG   H5   108.51  3.000
 8X1  H6   CG   N    114.65  3.000
 8X1  H5   CG   N    114.63  3.000
 8X1  H6   CG   CB   116.70  3.000
 8X1  H5   CG   CB   112.61  3.000
 8X1  N    CG   CB    88.90  3.000
 8X1  H7   N    CG   117.83  3.000
 8X1  H7   N    CA   116.87  3.000
 8X1  CG   N    CA    91.92  3.000
 8X1  C5'  O5'  S    119.36  3.000
 8X1  H10  C5'  H9   108.63  3.000
 8X1  H10  C5'  C4'  109.48  3.000
 8X1  H9   C5'  C4'  112.15  3.000
 8X1  H10  C5'  O5'  110.24  3.000
 8X1  H9   C5'  O5'  109.93  3.000
 8X1  C4'  C5'  O5'  106.39  3.000
 8X1  H11  C4'  O4'  108.98  3.000
 8X1  H11  C4'  C3'  110.48  3.000
 8X1  O4'  C4'  C3'  106.33  3.000
 8X1  H11  C4'  C5'  108.78  3.000
 8X1  C3'  C4'  C5'  111.60  3.000
 8X1  O4'  C4'  C5'  110.63  3.000
 8X1  H12  C3'  C2'  111.89  3.000
 8X1  H12  C3'  O3'  111.81  3.000
 8X1  C2'  C3'  O3'  111.05  3.000
 8X1  H12  C3'  C4'  112.13  3.000
 8X1  O3'  C3'  C4'  108.32  3.000
 8X1  C2'  C3'  C4'  101.13  3.000
 8X1  H13  O3'  C3'  107.96  3.000
 8X1  H14  C2'  C1'  110.09  3.000
 8X1  H14  C2'  O2'  111.55  3.000
 8X1  C1'  C2'  O2'  109.84  3.000
 8X1  H14  C2'  C3'  108.69  3.000
 8X1  O2'  C2'  C3'  115.07  3.000
 8X1  C1'  C2'  C3'  101.10  3.000
 8X1  H15  O2'  C2'  109.02  3.000
 8X1  H16  C1'  N9   106.10  3.000
 8X1  H16  C1'  O4'  111.35  3.000
 8X1  N9   C1'  O4'  109.29  3.000
 8X1  H16  C1'  C2'  110.24  3.000
 8X1  N9   C1'  C2'  114.30  3.000
 8X1  O4'  C1'  C2'  105.65  3.000
 8X1  C1'  O4'  C4'  110.73  3.000
 8X1  C8   N9   C4   106.09  3.000
 8X1  C8   N9   C1'  127.31  3.000
 8X1  C4   N9   C1'  126.33  3.000
 8X1  N3   C4   C5   126.54  3.000
 8X1  C5   C4   N9   105.20  3.000
 8X1  N3   C4   N9   128.26  3.000
 8X1  C6   C5   N7   132.86  3.000
 8X1  N7   C5   C4   110.77  3.000
 8X1  C6   C5   C4   116.37  3.000
 8X1  C8   N7   C5   104.41  3.000
 8X1  H17  C8   N7   124.76  3.000
 8X1  H17  C8   N9   121.70  3.000
 8X1  N7   C8   N9   113.54  3.000
 8X1  C2   N3   C4   111.65  3.000
 8X1  H18  C2   N1   115.43  3.000
 8X1  H18  C2   N3   116.14  3.000
 8X1  N1   C2   N3   128.43  3.000
 8X1  C6   N1   C2   119.20  3.000
 8X1  N6   C6   N1   119.48  3.000
 8X1  N6   C6   C5   122.71  3.000
 8X1  N1   C6   C5   117.80  3.000
 8X1  H20  N6   H19  118.34  3.000
 8X1  H20  N6   C6   121.12  3.000
 8X1  H19  N6   C6   120.40  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
 8X1  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 8X1  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 8X1  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 8X1  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 8X1  CONST_05  N1   C2   N3   C4      0.00   0.0  0
 8X1  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 8X1  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 8X1  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 8X1  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 8X1  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 8X1  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 8X1  CONST_12  N1   C6   C5   N7    180.00   0.0  0
 8X1  CONST_13  N3   C4   C5   N7    180.00   0.0  0
 8X1  CONST_14  C6   C5   N7   C8    180.00   0.0  0
 8X1  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 8X1  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 8X1  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 8X1  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 8X1  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 8X1  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 8X1  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 8X1  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 8X1  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 8X1  CONST_24  H17  C8   N9   C1'     0.00   0.0  0
 8X1  CONST_25  H18  C2   N3   C4    180.00   0.0  0
 8X1  CONST_26  H19  N6   C6   C5    180.00   0.0  0
 8X1  CONST_27  H20  N6   C6   C5      0.00   0.0  0
 8X1  CONST_28  CA   C    N3S  S     180.00   0.0  0
 8X1  CONST_29  H1   N3S  C    CA      0.00   0.0  0
 8X1  CONST_30  O    C    N3S  S       0.00   0.0  0
 8X1  Var_01    CB   CG   N    CA     16.68  30.0  1
 8X1  Var_02    C4'  C5'  O5'  S    -176.57  30.0  1
 8X1  Var_03    C    N3S  S    O2S   179.99  30.0  1

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
 8X1  chir_01  CA   N    CB   C    negativ
 8X1  chir_02  C4'  O4'  C5'  C3'  positiv
 8X1  chir_03  C3'  O3'  C4'  C2'  positiv
 8X1  chir_04  C2'  O2'  C3'  C1'  positiv
 8X1  chir_05  C1'  O4'  N9   C2'  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
 8X1  plan-1  S    0.020
 8X1  plan-1  N3S  0.020
 8X1  plan-1  C    0.020
 8X1  plan-1  CA   0.020
 8X1  plan-1  O    0.020
 8X1  plan-1  H1   0.020
 8X1  plan-2  C6   0.020
 8X1  plan-2  N6   0.020
 8X1  plan-2  H19  0.020
 8X1  plan-2  H20  0.020
 8X1  plan-3  C1'  0.020
 8X1  plan-3  N9   0.020
 8X1  plan-3  C4   0.020
 8X1  plan-3  C5   0.020
 8X1  plan-3  N7   0.020
 8X1  plan-3  C8   0.020
 8X1  plan-3  N3   0.020
 8X1  plan-3  C2   0.020
 8X1  plan-3  N1   0.020
 8X1  plan-3  C6   0.020
 8X1  plan-3  N6   0.020
 8X1  plan-3  H17  0.020
 8X1  plan-3  H18  0.020

