# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 11:31:17 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5'-O-[(3-cyanobenzene-1-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)c4cccc(c4)C#N)[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
 B1X  B1X  5'-O-[(3-cyanobenzene-1-carbonyl)sulfamoyl]adenosine  ligand  50  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B1X
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
 B1X  C1   C  CR56  0   0.491   3.0849  -0.7769   0.2985
 B1X  C2   C  CR56  0  -0.007   2.5737  -2.0424   0.0602
 B1X  C3   C  CR6   0   0.459   3.3818  -3.1266   0.4516
 B1X  C4   C  CR15  0   0.123   1.1142  -0.6921  -0.6486
 B1X  N1   N  N     0  -0.474   4.5663  -2.8508   1.0111
 B1X  N2   N  N     0  -0.457   4.2570  -0.4880   0.8561
 B1X  N3   N  NS    0  -0.275  -0.0714  -5.3325  -0.1936
 B1X  C6   C  CR6   0   0.033  -1.8635  -3.5165  -0.5684
 B1X  C7   C  CR16  0  -0.241  -1.7846  -2.3347   0.1582
 B1X  C8   C  CR16  0  -0.227  -2.8768  -3.7128  -1.5060
 B1X  C9   C  CR16  0  -0.231  -3.8081  -2.7106  -1.7161
 B1X  C10  C  CR16  0  -0.260  -3.7151  -1.5142  -1.0215
 B1X  C11  C  CR6   0  -0.027  -2.6993  -1.3196  -0.0871
 B1X  C12  C  C     0   0.579  -2.5295  -0.0579   0.6831
 B1X  O1   O  O     0  -0.403  -1.9420  -0.0036   1.7359
 B1X  N4   N  NC1   0  -0.859  -3.0592   1.0662   0.0858
 B1X  S1   S  S     0   1.635  -3.0533   2.5729   0.7984
 B1X  O2   O  OS    0  -0.624  -3.6848   3.4340  -0.1681
 B1X  O3   O  OS    0  -0.604  -3.5212   2.4859   2.1514
 B1X  C13  C  CH2   0  -0.195  -0.7653   3.2021  -0.2770
 B1X  C14  C  CH1   0  -0.032   0.6903   3.2721   0.1240
 B1X  O5   O  O2    0  -0.485   1.1196   2.0117   0.6357
 B1X  C15  C  CH1   0  -0.045   1.5895   3.5934  -1.0716
 B1X  O6   O  OH1   0  -0.664   2.6687   4.3662  -0.6212
 B1X  C16  C  CH1   0  -0.044   2.0514   2.1941  -1.4883
 B1X  O7   O  OH1   0  -0.650   3.2689   2.1540  -2.1654
 B1X  C17  C  CH1   0   0.210   2.1915   1.5202  -0.1267
 B1X  N5   N  NR5   0  -0.544   2.1326   0.0872  -0.1668
 B1X  N6   N  N     0  -0.439   1.3387  -1.9650  -0.5317
 B1X  C18  C  CR16  0   0.048   4.9267  -1.5818   1.1778
 B1X  N7   N  NH2   0  -0.832   3.0246  -4.3991   0.2780
 B1X  H1   H  HCR5  0   0.284   0.2217  -0.2614  -1.0775
 B1X  H8   H  HCR6  0   0.295  -2.9320  -4.6388  -2.0616
 B1X  H9   H  HCR6  0   0.290  -4.6066  -2.8577  -2.4292
 B1X  H10  H  HCR6  0   0.285  -4.4614  -0.7519  -1.2048
 B1X  H11  H  HNC1  0   0.462  -3.4400   1.0348  -0.8523
 B1X  H12  H  HCH2  0   0.252  -0.9347   2.4256  -1.0285
 B1X  H13  H  HCH2  0   0.283  -1.0823   4.1632  -0.6830
 B1X  H14  H  HCH1  0   0.281   0.8089   4.0384   0.8965
 B1X  H15  H  HCH1  0   0.262   1.0383   4.0974  -1.8759
 B1X  H16  H  HOH1  0   0.452   3.3925   4.2584  -1.2499
 B1X  H17  H  HCH1  0   0.254   1.2509   1.7102  -2.0628
 B1X  H18  H  HOH1  0   0.472   3.1106   2.2920  -3.1047
 B1X  H19  H  HCH1  0   0.266   3.1590   1.7745   0.3201
 B1X  H20  H  HCR6  0   0.253   5.8965  -1.4294   1.6394
 B1X  H21  H  HNH2  0   0.423   2.1071  -4.6478  -0.0545
 B1X  H22  H  HNH2  0   0.402   3.6188  -5.1350   0.6195
 B1X  O4   O  OC2   0  -0.566  -1.5129   2.9116   0.9217
 B1X  H7   H  HCR6  0   0.295  -1.0046  -2.2051   0.8935
 B1X  C5   C  CSP   0   0.100  -0.8746  -4.5240  -0.3605

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
 B1X  N3   C5   triple    1.152  0.020  1.152
 B1X  C5   C6   single    1.427  0.020  1.427
 B1X  C8   C6   aromatic  1.394  0.020  1.394
 B1X  C8   C9   aromatic  1.384  0.020  1.384
 B1X  C6   C7   aromatic  1.390  0.020  1.390
 B1X  C9   C10  aromatic  1.387  0.020  1.387
 B1X  C7   C11  aromatic  1.388  0.020  1.388
 B1X  C10  C11  aromatic  1.394  0.020  1.394
 B1X  N7   C3   single    1.333  0.020  1.333
 B1X  C11  C12  single    1.488  0.020  1.488
 B1X  N6   C2   aromatic  1.372  0.020  1.372
 B1X  N6   C4   aromatic  1.298  0.020  1.298
 B1X  C3   C2   aromatic  1.408  0.020  1.408
 B1X  C3   N1   aromatic  1.339  0.020  1.339
 B1X  C2   C1   aromatic  1.386  0.020  1.386
 B1X  C4   N5   aromatic  1.370  0.020  1.370
 B1X  O6   C15  single    1.402  0.020  1.402
 B1X  N1   C18  aromatic  1.330  0.020  1.330
 B1X  N4   C12  single    1.379  0.020  1.379
 B1X  N4   S1   single    1.667  0.020  1.667
 B1X  C12  O1   double    1.207  0.020  1.207
 B1X  C15  C16  single    1.531  0.020  1.531
 B1X  C15  C14  single    1.530  0.020  1.530
 B1X  C1   N5   aromatic  1.368  0.020  1.368
 B1X  C1   N2   aromatic  1.330  0.020  1.330
 B1X  C13  C14  single    1.511  0.020  1.511
 B1X  C13  O4   single    1.442  0.020  1.442
 B1X  N5   C17  single    1.435  0.020  1.435
 B1X  O3   S1   deloc     1.434  0.020  1.434
 B1X  C16  C17  single    1.526  0.020  1.526
 B1X  C16  O7   single    1.394  0.020  1.394
 B1X  C18  N2   aromatic  1.322  0.020  1.322
 B1X  C14  O5   single    1.426  0.020  1.426
 B1X  S1   O4   single    1.582  0.020  1.582
 B1X  S1   O2   deloc     1.440  0.020  1.440
 B1X  C17  O5   single    1.404  0.020  1.404
 B1X  C4   H1   single    0.930  0.020  1.080
 B1X  C7   H7   single    0.930  0.020  1.080
 B1X  C8   H8   single    0.930  0.020  1.080
 B1X  C9   H9   single    0.930  0.020  1.080
 B1X  C10  H10  single    0.930  0.020  1.080
 B1X  N4   H11  single    0.860  0.020  1.020
 B1X  C13  H12  single    0.970  0.020  1.090
 B1X  C13  H13  single    0.970  0.020  1.090
 B1X  C14  H14  single    0.970  0.020  1.090
 B1X  C15  H15  single    0.970  0.020  1.090
 B1X  O6   H16  single    0.850  0.020  0.980
 B1X  C16  H17  single    0.970  0.020  1.090
 B1X  O7   H18  single    0.850  0.020  0.980
 B1X  C17  H19  single    0.970  0.020  1.090
 B1X  C18  H20  single    0.930  0.020  1.080
 B1X  N7   H21  single    0.860  0.020  1.020
 B1X  N7   H22  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
 B1X  N5   C1   N2   128.26  3.000
 B1X  N2   C1   C2   126.57  3.000
 B1X  N5   C1   C2   105.17  3.000
 B1X  N6   C2   C3   132.87  3.000
 B1X  C3   C2   C1   116.35  3.000
 B1X  N6   C2   C1   110.78  3.000
 B1X  N7   C3   N1   119.22  3.000
 B1X  N1   C3   C2   117.74  3.000
 B1X  N7   C3   C2   123.04  3.000
 B1X  H1   C4   N6   124.75  3.000
 B1X  H1   C4   N5   121.82  3.000
 B1X  N6   C4   N5   113.43  3.000
 B1X  C18  N1   C3   119.27  3.000
 B1X  C18  N2   C1   111.64  3.000
 B1X  C8   C6   C7   120.84  3.000
 B1X  C7   C6   C5   119.01  3.000
 B1X  C8   C6   C5   120.14  3.000
 B1X  H7   C7   C11  120.57  3.000
 B1X  H7   C7   C6   119.95  3.000
 B1X  C11  C7   C6   119.48  3.000
 B1X  H8   C8   C9   120.51  3.000
 B1X  H8   C8   C6   120.21  3.000
 B1X  C9   C8   C6   119.28  3.000
 B1X  H9   C9   C10  119.84  3.000
 B1X  H9   C9   C8   119.92  3.000
 B1X  C10  C9   C8   120.24  3.000
 B1X  H10  C10  C11  121.17  3.000
 B1X  H10  C10  C9   118.46  3.000
 B1X  C11  C10  C9   120.35  3.000
 B1X  C12  C11  C10  123.27  3.000
 B1X  C12  C11  C7   116.96  3.000
 B1X  C10  C11  C7   119.77  3.000
 B1X  N4   C12  O1   121.88  3.000
 B1X  O1   C12  C11  123.04  3.000
 B1X  N4   C12  C11  115.05  3.000
 B1X  H11  N4   S1   115.17  3.000
 B1X  H11  N4   C12  121.35  3.000
 B1X  S1   N4   C12  123.40  3.000
 B1X  O4   S1   O3   104.90  3.000
 B1X  O4   S1   O2   110.56  3.000
 B1X  O3   S1   O2   121.76  3.000
 B1X  O2   S1   N4   104.59  3.000
 B1X  O4   S1   N4   103.31  3.000
 B1X  O3   S1   N4   110.32  3.000
 B1X  H13  C13  H12  108.96  3.000
 B1X  H13  C13  C14  109.75  3.000
 B1X  H12  C13  C14  111.37  3.000
 B1X  H13  C13  O4   109.65  3.000
 B1X  H12  C13  O4   110.35  3.000
 B1X  C14  C13  O4   106.74  3.000
 B1X  H14  C14  C15  109.93  3.000
 B1X  H14  C14  O5   109.44  3.000
 B1X  C15  C14  O5   106.79  3.000
 B1X  H14  C14  C13  108.90  3.000
 B1X  O5   C14  C13  110.12  3.000
 B1X  C15  C14  C13  111.61  3.000
 B1X  C17  O5   C14  110.14  3.000
 B1X  H15  C15  C16  111.82  3.000
 B1X  H15  C15  O6   111.65  3.000
 B1X  C16  C15  O6   111.04  3.000
 B1X  H15  C15  C14  111.95  3.000
 B1X  C16  C15  C14  101.42  3.000
 B1X  O6   C15  C14  108.49  3.000
 B1X  H16  O6   C15  107.85  3.000
 B1X  H17  C16  C17  109.83  3.000
 B1X  H17  C16  O7   111.72  3.000
 B1X  C17  C16  O7   109.92  3.000
 B1X  H17  C16  C15  108.98  3.000
 B1X  O7   C16  C15  114.96  3.000
 B1X  C17  C16  C15  100.86  3.000
 B1X  H18  O7   C16  109.04  3.000
 B1X  H19  C17  N5   106.23  3.000
 B1X  H19  C17  C16  110.03  3.000
 B1X  N5   C17  C16  114.36  3.000
 B1X  H19  C17  O5   111.80  3.000
 B1X  C16  C17  O5   105.06  3.000
 B1X  N5   C17  O5   109.47  3.000
 B1X  C17  N5   C4   127.49  3.000
 B1X  C17  N5   C1   126.37  3.000
 B1X  C4   N5   C1   106.13  3.000
 B1X  C4   N6   C2   104.48  3.000
 B1X  H20  C18  N2   116.11  3.000
 B1X  H20  C18  N1   115.45  3.000
 B1X  N2   C18  N1   128.44  3.000
 B1X  H22  N7   H21  118.01  3.000
 B1X  H22  N7   C3   119.74  3.000
 B1X  H21  N7   C3   121.52  3.000
 B1X  C13  O4   S1   118.88  3.000
 B1X  C6   C5   N3   180.00  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
 B1X  CONST_01  C4   N6   C2   C1      0.00   0.0  0
 B1X  CONST_02  N1   C3   C2   C1      0.00   0.0  0
 B1X  CONST_03  N6   C4   N5   C1      0.00   0.0  0
 B1X  CONST_04  N1   C18  N2   C1      0.00   0.0  0
 B1X  CONST_05  N5   C4   N6   C2      0.00   0.0  0
 B1X  CONST_06  C18  N1   C3   C2      0.00   0.0  0
 B1X  CONST_07  C4   N5   C1   C2      0.00   0.0  0
 B1X  CONST_08  C18  N2   C1   C2      0.00   0.0  0
 B1X  CONST_09  C4   N6   C2   C3    180.00   0.0  0
 B1X  CONST_10  N5   C1   C2   C3    180.00   0.0  0
 B1X  CONST_11  N2   C1   C2   C3      0.00   0.0  0
 B1X  CONST_12  N2   C18  N1   C3      0.00   0.0  0
 B1X  CONST_13  N2   C1   N5   C4    180.00   0.0  0
 B1X  CONST_14  N6   C2   C3   N1    180.00   0.0  0
 B1X  CONST_15  N6   C2   C1   N2    180.00   0.0  0
 B1X  CONST_16  C10  C9   C8   C6      0.00   0.0  0
 B1X  CONST_17  C10  C11  C7   C6      0.00   0.0  0
 B1X  CONST_18  C9   C8   C6   C7      0.00   0.0  0
 B1X  CONST_19  C9   C10  C11  C7      0.00   0.0  0
 B1X  CONST_20  C11  C7   C6   C8      0.00   0.0  0
 B1X  CONST_21  C11  C10  C9   C8      0.00   0.0  0
 B1X  CONST_22  N6   C2   C1   N5      0.00   0.0  0
 B1X  CONST_23  C18  N2   C1   N5    180.00   0.0  0
 B1X  CONST_24  C17  N5   C1   C2    180.00   0.0  0
 B1X  CONST_25  C17  N5   C1   N2      0.00   0.0  0
 B1X  CONST_26  N6   C4   N5   C17   180.00   0.0  0
 B1X  CONST_27  N7   C3   C2   C1    180.00   0.0  0
 B1X  CONST_28  C9   C8   C6   C5    180.00   0.0  0
 B1X  CONST_29  C11  C7   C6   C5    180.00   0.0  0
 B1X  CONST_30  C12  C11  C7   C6    180.00   0.0  0
 B1X  CONST_31  C12  C11  C10  C9    180.00   0.0  0
 B1X  CONST_32  N7   C3   C2   N6      0.00   0.0  0
 B1X  CONST_33  N7   C3   N1   C18   180.00   0.0  0
 B1X  CONST_34  H1   C4   N5   C1    180.00   0.0  0
 B1X  CONST_35  H20  C18  N2   C1    180.00   0.0  0
 B1X  CONST_36  H9   C9   C8   C6    180.00   0.0  0
 B1X  CONST_37  H8   C8   C6   C7    180.00   0.0  0
 B1X  CONST_38  H10  C10  C11  C7    180.00   0.0  0
 B1X  CONST_39  H7   C7   C6   C8    180.00   0.0  0
 B1X  CONST_40  H21  N7   C3   C2      0.00   0.0  0
 B1X  CONST_41  H22  N7   C3   C2    180.00   0.0  0
 B1X  CONST_42  S1   N4   C12  C11   180.00   0.0  0
 B1X  CONST_43  H11  N4   C12  C11     0.00   0.0  0
 B1X  CONST_44  S1   N4   C12  O1      0.00   0.0  0
 B1X  Var_01    N4   C12  C11  C7    155.35  30.0  2
 B1X  Var_02    C14  C13  O4   S1   -171.46  30.0  2
 B1X  Var_03    O3   S1   N4   C12   -47.99  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
 B1X  chir_01  C14  C15  C13  O5   negativ
 B1X  chir_02  C15  O6   C14  C16  positiv
 B1X  chir_03  C16  O7   C15  C17  positiv
 B1X  chir_04  C17  O5   N5   C16  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
 B1X  plan-1  N3   0.020
 B1X  plan-1  C6   0.020
 B1X  plan-1  C7   0.020
 B1X  plan-1  C8   0.020
 B1X  plan-1  C9   0.020
 B1X  plan-1  C10  0.020
 B1X  plan-1  C11  0.020
 B1X  plan-1  C12  0.020
 B1X  plan-1  H8   0.020
 B1X  plan-1  H9   0.020
 B1X  plan-1  H10  0.020
 B1X  plan-1  H7   0.020
 B1X  plan-1  C5   0.020
 B1X  plan-2  C1   0.020
 B1X  plan-2  C2   0.020
 B1X  plan-2  C3   0.020
 B1X  plan-2  C4   0.020
 B1X  plan-2  N1   0.020
 B1X  plan-2  N2   0.020
 B1X  plan-2  C17  0.020
 B1X  plan-2  N5   0.020
 B1X  plan-2  N6   0.020
 B1X  plan-2  C18  0.020
 B1X  plan-2  N7   0.020
 B1X  plan-2  H1   0.020
 B1X  plan-2  H20  0.020
 B1X  plan-3  C3   0.020
 B1X  plan-3  N7   0.020
 B1X  plan-3  H21  0.020
 B1X  plan-3  H22  0.020
 B1X  plan-4  C11  0.020
 B1X  plan-4  C12  0.020
 B1X  plan-4  O1   0.020
 B1X  plan-4  N4   0.020
 B1X  plan-4  S1   0.020
 B1X  plan-4  H11  0.020

