# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:10:30 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-O-[(pyridine-3-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)c4cccnc4)[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
 SFH  SFH  5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine  ligand  48  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SFH
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
 SFH  C1S  C  CH1   0   0.164  -1.3899   1.1690  -0.0528
 SFH  C2N  C  CR16  0  -0.066   1.4995  -2.5434  -0.1415
 SFH  C2S  C  CH1   0  -0.039  -2.1183   2.3281   0.6333
 SFH  C2X  C  CR16  0   0.039  -3.4044  -2.5998  -0.7246
 SFH  C3N  C  CR6   0  -0.143   1.2787  -1.5320  -1.0736
 SFH  C3S  C  CH1   0  -0.043  -0.9664   3.0621   1.3337
 SFH  C4N  C  CR16  0  -0.142   0.3408  -1.7632  -2.0766
 SFH  C4S  C  CH1   0   0.025   0.1775   2.8507   0.3415
 SFH  C4X  C  CR56  0   0.502  -2.0956  -1.1984   0.3400
 SFH  C5N  C  CR16  0  -0.308  -0.3278  -2.9715  -2.0983
 SFH  C5S  C  CH2   0  -0.211   1.5253   2.8694   1.0155
 SFH  C5X  C  CR56  0   0.005  -1.7522  -2.1454   1.2902
 SFH  C6N  C  CR16  0  -0.053  -0.0264  -3.9114  -1.1227
 SFH  C6X  C  CR6   0   0.464  -2.3262  -3.4204   1.1351
 SFH  C7N  C  C     0   0.602   2.0416  -0.2590  -1.1067
 SFH  C8X  C  CR15  0   0.099  -0.6938  -0.3971   1.8133
 SFH  N1N  N  N     0  -0.386   0.8698  -3.7074  -0.1651
 SFH  N1X  N  N     0  -0.468  -3.1612  -3.6091   0.1071
 SFH  N3X  N  N     0  -0.453  -2.9220  -1.3698  -0.6877
 SFH  N6X  N  NH2   0  -0.815  -2.0770  -4.4289   1.9707
 SFH  N7N  N  NC1   0  -0.863   2.6794   0.0913   0.0684
 SFH  N7X  N  N     0  -0.442  -0.8730  -1.6237   2.2021
 SFH  N9X  N  NR5   0  -0.532  -1.4068  -0.0717   0.6906
 SFH  O1'  O  OS    0  -0.625   4.0611   1.4399   1.5943
 SFH  O2'  O  OS    0  -0.606   4.5098   1.6012  -0.8683
 SFH  O2S  O  OH1   0  -0.662  -2.6694   3.1256  -0.3776
 SFH  O3S  O  OH1   0  -0.652  -1.1956   4.4261   1.5284
 SFH  O4S  O  O2    0  -0.493  -0.0569   1.5735  -0.2238
 SFH  O5S  O  OC2   0  -0.564   2.5557   2.6458   0.0273
 SFH  O7N  O  O     0  -0.412   2.1205   0.4278  -2.0953
 SFH  S1   S  S     0   1.615   3.5969   1.4707   0.2303
 SFH  H1   H  HCH1  0   0.284  -1.8564   0.9474  -1.0165
 SFH  H3   H  HCH1  0   0.266  -2.8809   1.9708   1.3354
 SFH  H4   H  HCR6  0   0.254  -4.0882  -2.8202  -1.5374
 SFH  H5   H  HCH1  0   0.249  -0.7371   2.5579   2.2818
 SFH  H6   H  HCR6  0   0.287   0.1423  -1.0093  -2.8263
 SFH  H7   H  HCH1  0   0.268   0.1419   3.6213  -0.4382
 SFH  H8   H  HCR6  0   0.283  -1.0649  -3.1882  -2.8582
 SFH  H9   H  HCH2  0   0.292   1.7109   3.8474   1.4586
 SFH  H10  H  HCH2  0   0.252   1.5748   2.1261   1.8144
 SFH  H11  H  HCR6  0   0.281  -0.5287  -4.8718  -1.1177
 SFH  H12  H  HCR5  0   0.289  -0.0570   0.3119   2.3189
 SFH  H13  H  HNH2  0   0.410  -1.3795  -4.3402   2.6884
 SFH  H14  H  HNH2  0   0.403  -2.4431  -5.3453   1.7777
 SFH  H15  H  HNC1  0   0.450   2.5682  -0.4511   0.9153
 SFH  H16  H  HOH1  0   0.454  -2.7087   4.0337  -0.0523
 SFH  H17  H  HOH1  0   0.473  -1.6860   4.5456   2.3484
 SFH  H2   H  HCR6  0   0.266   2.2421  -2.4367   0.6421

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
 SFH  C2X  N3X  aromatic  1.322  0.020  1.322
 SFH  C2X  N1X  aromatic  1.330  0.020  1.330
 SFH  O2S  C2S  single    1.401  0.020  1.401
 SFH  N3X  C4X  aromatic  1.330  0.020  1.330
 SFH  N1X  C6X  aromatic  1.338  0.020  1.338
 SFH  C2S  C1S  single    1.531  0.020  1.531
 SFH  C2S  C3S  single    1.535  0.020  1.535
 SFH  O3S  C3S  single    1.397  0.020  1.397
 SFH  C4X  N9X  aromatic  1.366  0.020  1.366
 SFH  C4X  C5X  aromatic  1.385  0.020  1.385
 SFH  C1S  N9X  single    1.446  0.020  1.446
 SFH  C1S  O4S  single    1.403  0.020  1.403
 SFH  C6X  C5X  aromatic  1.407  0.020  1.407
 SFH  C6X  N6X  single    1.333  0.020  1.333
 SFH  C3S  C4S  single    1.529  0.020  1.529
 SFH  N9X  C8X  aromatic  1.369  0.020  1.369
 SFH  C5X  N7X  aromatic  1.370  0.020  1.370
 SFH  C4S  O4S  single    1.416  0.020  1.416
 SFH  C4S  C5S  single    1.507  0.020  1.507
 SFH  C8X  N7X  aromatic  1.299  0.020  1.299
 SFH  C5S  O5S  single    1.445  0.020  1.445
 SFH  O5S  S1   single    1.583  0.020  1.583
 SFH  S1   O2'  deloc     1.434  0.020  1.434
 SFH  S1   O1'  deloc     1.441  0.020  1.441
 SFH  S1   N7N  single    1.665  0.020  1.665
 SFH  O7N  C7N  double    1.206  0.020  1.206
 SFH  C7N  N7N  single    1.382  0.020  1.382
 SFH  C7N  C3N  single    1.484  0.020  1.484
 SFH  C2N  C3N  aromatic  1.393  0.020  1.393
 SFH  C2N  N1N  aromatic  1.324  0.020  1.324
 SFH  C3N  C4N  aromatic  1.392  0.020  1.392
 SFH  N1N  C6N  aromatic  1.327  0.020  1.327
 SFH  C4N  C5N  aromatic  1.381  0.020  1.381
 SFH  C6N  C5N  aromatic  1.388  0.020  1.388
 SFH  C1S  H1   single    0.970  0.020  1.090
 SFH  C2N  H2   single    0.930  0.020  1.080
 SFH  C2S  H3   single    0.970  0.020  1.090
 SFH  C2X  H4   single    0.930  0.020  1.080
 SFH  C3S  H5   single    0.970  0.020  1.090
 SFH  C4N  H6   single    0.930  0.020  1.080
 SFH  C4S  H7   single    0.970  0.020  1.090
 SFH  C5N  H8   single    0.930  0.020  1.080
 SFH  C5S  H9   single    0.970  0.020  1.090
 SFH  C5S  H10  single    0.970  0.020  1.090
 SFH  C6N  H11  single    0.930  0.020  1.080
 SFH  C8X  H12  single    0.930  0.020  1.080
 SFH  N6X  H13  single    0.860  0.020  1.020
 SFH  N6X  H14  single    0.860  0.020  1.020
 SFH  N7N  H15  single    0.860  0.020  1.020
 SFH  O2S  H16  single    0.850  0.020  0.980
 SFH  O3S  H17  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
 SFH  H1   C1S  O4S  110.87  3.000
 SFH  H1   C1S  N9X  105.91  3.000
 SFH  O4S  C1S  N9X  108.72  3.000
 SFH  H1   C1S  C2S  110.21  3.000
 SFH  O4S  C1S  C2S  106.75  3.000
 SFH  N9X  C1S  C2S  114.42  3.000
 SFH  H2   C2N  N1N  115.15  3.000
 SFH  H2   C2N  C3N  121.36  3.000
 SFH  N1N  C2N  C3N  123.45  3.000
 SFH  H3   C2S  O2S  111.96  3.000
 SFH  H3   C2S  C3S  112.68  3.000
 SFH  O2S  C2S  C3S  110.63  3.000
 SFH  H3   C2S  C1S  111.79  3.000
 SFH  C3S  C2S  C1S  102.09  3.000
 SFH  O2S  C2S  C1S  107.14  3.000
 SFH  H4   C2X  N3X  116.11  3.000
 SFH  H4   C2X  N1X  115.44  3.000
 SFH  N3X  C2X  N1X  128.45  3.000
 SFH  C7N  C3N  C4N  118.20  3.000
 SFH  C4N  C3N  C2N  117.91  3.000
 SFH  C7N  C3N  C2N  123.78  3.000
 SFH  H5   C3S  O3S  111.24  3.000
 SFH  H5   C3S  C4S  109.91  3.000
 SFH  O3S  C3S  C4S  110.38  3.000
 SFH  H5   C3S  C2S  109.34  3.000
 SFH  C4S  C3S  C2S  101.49  3.000
 SFH  O3S  C3S  C2S  114.05  3.000
 SFH  H6   C4N  C5N  120.67  3.000
 SFH  H6   C4N  C3N  120.47  3.000
 SFH  C5N  C4N  C3N  118.86  3.000
 SFH  H7   C4S  O4S  110.15  3.000
 SFH  H7   C4S  C5S  109.77  3.000
 SFH  O4S  C4S  C5S  109.74  3.000
 SFH  H7   C4S  C3S  109.87  3.000
 SFH  C5S  C4S  C3S  112.16  3.000
 SFH  O4S  C4S  C3S  105.06  3.000
 SFH  N9X  C4X  N3X  128.16  3.000
 SFH  N9X  C4X  C5X  105.24  3.000
 SFH  N3X  C4X  C5X  126.60  3.000
 SFH  H8   C5N  C6N  120.44  3.000
 SFH  H8   C5N  C4N  121.11  3.000
 SFH  C6N  C5N  C4N  118.44  3.000
 SFH  H10  C5S  H9   107.79  3.000
 SFH  H10  C5S  O5S  111.25  3.000
 SFH  H9   C5S  O5S  107.19  3.000
 SFH  H10  C5S  C4S  111.05  3.000
 SFH  H9   C5S  C4S  110.21  3.000
 SFH  O5S  C5S  C4S  109.27  3.000
 SFH  N7X  C5X  C6X  132.88  3.000
 SFH  N7X  C5X  C4X  110.82  3.000
 SFH  C6X  C5X  C4X  116.29  3.000
 SFH  H11  C6N  N1N  116.47  3.000
 SFH  H11  C6N  C5N  120.18  3.000
 SFH  N1N  C6N  C5N  123.35  3.000
 SFH  N6X  C6X  N1X  119.45  3.000
 SFH  N6X  C6X  C5X  122.70  3.000
 SFH  N1X  C6X  C5X  117.85  3.000
 SFH  O7N  C7N  N7N  121.48  3.000
 SFH  N7N  C7N  C3N  115.82  3.000
 SFH  O7N  C7N  C3N  122.69  3.000
 SFH  H12  C8X  N9X  122.38  3.000
 SFH  H12  C8X  N7X  124.17  3.000
 SFH  N9X  C8X  N7X  113.45  3.000
 SFH  C6N  N1N  C2N  117.98  3.000
 SFH  C6X  N1X  C2X  119.18  3.000
 SFH  C4X  N3X  C2X  111.61  3.000
 SFH  H14  N6X  H13  118.05  3.000
 SFH  H14  N6X  C6X  120.07  3.000
 SFH  H13  N6X  C6X  120.71  3.000
 SFH  H15  N7N  S1   115.05  3.000
 SFH  H15  N7N  C7N  121.67  3.000
 SFH  S1   N7N  C7N  123.16  3.000
 SFH  C8X  N7X  C5X  104.41  3.000
 SFH  C8X  N9X  C4X  106.08  3.000
 SFH  C8X  N9X  C1S  128.25  3.000
 SFH  C4X  N9X  C1S  125.55  3.000
 SFH  H16  O2S  C2S  107.96  3.000
 SFH  H17  O3S  C3S  108.87  3.000
 SFH  C4S  O4S  C1S  111.62  3.000
 SFH  S1   O5S  C5S  119.75  3.000
 SFH  O5S  S1   O2'  104.65  3.000
 SFH  O2'  S1   O1'  121.46  3.000
 SFH  O5S  S1   O1'  110.43  3.000
 SFH  O1'  S1   N7N  104.58  3.000
 SFH  O2'  S1   N7N  110.59  3.000
 SFH  O5S  S1   N7N  103.89  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
 SFH  CONST_01  C5N  C4N  C3N  C2N     0.00   0.0  0
 SFH  CONST_02  C5N  C6N  N1N  C2N     0.00   0.0  0
 SFH  CONST_03  N9X  C4X  N3X  C2X   180.00   0.0  0
 SFH  CONST_04  C5X  C4X  N3X  C2X     0.00   0.0  0
 SFH  CONST_05  C5X  C6X  N1X  C2X     0.00   0.0  0
 SFH  CONST_06  C6N  N1N  C2N  C3N     0.00   0.0  0
 SFH  CONST_07  C6N  C5N  C4N  C3N     0.00   0.0  0
 SFH  CONST_08  N1N  C2N  C3N  C4N     0.00   0.0  0
 SFH  CONST_09  N1N  C6N  C5N  C4N     0.00   0.0  0
 SFH  CONST_10  N1X  C2X  N3X  C4X     0.00   0.0  0
 SFH  CONST_11  N7X  C8X  N9X  C4X     0.00   0.0  0
 SFH  CONST_12  N1X  C6X  C5X  C4X     0.00   0.0  0
 SFH  CONST_13  C8X  N7X  C5X  C4X     0.00   0.0  0
 SFH  CONST_14  C8X  N9X  C4X  C5X     0.00   0.0  0
 SFH  CONST_15  N9X  C8X  N7X  C5X     0.00   0.0  0
 SFH  CONST_16  N3X  C2X  N1X  C6X     0.00   0.0  0
 SFH  CONST_17  N3X  C4X  C5X  C6X     0.00   0.0  0
 SFH  CONST_18  N9X  C4X  C5X  C6X   180.00   0.0  0
 SFH  CONST_19  C8X  N7X  C5X  C6X   180.00   0.0  0
 SFH  CONST_20  N3X  C4X  N9X  C8X   180.00   0.0  0
 SFH  CONST_21  N7X  C5X  C6X  N1X   180.00   0.0  0
 SFH  CONST_22  N7X  C5X  C4X  N3X   180.00   0.0  0
 SFH  CONST_23  N9X  C4X  C5X  N7X     0.00   0.0  0
 SFH  CONST_24  N3X  C4X  N9X  C1S     0.00   0.0  0
 SFH  CONST_25  C5X  C4X  N9X  C1S   180.00   0.0  0
 SFH  CONST_26  N7X  C8X  N9X  C1S   180.00   0.0  0
 SFH  CONST_27  N6X  C6X  N1X  C2X   180.00   0.0  0
 SFH  CONST_28  N6X  C6X  C5X  C4X   180.00   0.0  0
 SFH  CONST_29  C7N  C3N  C4N  C5N   180.00   0.0  0
 SFH  CONST_30  N1N  C2N  C3N  C7N   180.00   0.0  0
 SFH  CONST_31  N7X  C5X  C6X  N6X     0.00   0.0  0
 SFH  CONST_32  H12  C8X  N9X  C1S     0.00   0.0  0
 SFH  CONST_33  H6   C4N  C3N  C2N   180.00   0.0  0
 SFH  CONST_34  H11  C6N  N1N  C2N   180.00   0.0  0
 SFH  CONST_35  H8   C5N  C4N  C3N   180.00   0.0  0
 SFH  CONST_36  H2   C2N  C3N  C4N   180.00   0.0  0
 SFH  CONST_37  H4   C2X  N3X  C4X   180.00   0.0  0
 SFH  CONST_38  H13  N6X  C6X  C5X     0.00   0.0  0
 SFH  CONST_39  H14  N6X  C6X  C5X   180.00   0.0  0
 SFH  CONST_40  S1   N7N  C7N  C3N   180.00   0.0  0
 SFH  CONST_41  H15  N7N  C7N  C3N     0.00   0.0  0
 SFH  CONST_42  S1   N7N  C7N  O7N     0.00   0.0  0
 SFH  Var_01    O7N  C7N  C3N  C2N   158.55  30.0  2
 SFH  Var_02    O2'  S1   O5S  C5S  -176.08  30.0  3
 SFH  Var_03    O5S  S1   N7N  C7N    64.04  30.0  1
 SFH  Var_04    H9   C5S  O5S  S1    115.37  30.0  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
 SFH  chir_01  C1S  C2S  N9X  O4S  positiv
 SFH  chir_02  C2S  O2S  C3S  C1S  positiv
 SFH  chir_03  C3S  O3S  C4S  C2S  positiv
 SFH  chir_04  C4S  O4S  C3S  C5S  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
 SFH  plan-1  C2N  0.020
 SFH  plan-1  C3N  0.020
 SFH  plan-1  C4N  0.020
 SFH  plan-1  C5N  0.020
 SFH  plan-1  C6N  0.020
 SFH  plan-1  C7N  0.020
 SFH  plan-1  N1N  0.020
 SFH  plan-1  H6   0.020
 SFH  plan-1  H8   0.020
 SFH  plan-1  H11  0.020
 SFH  plan-1  H2   0.020
 SFH  plan-2  C1S  0.020
 SFH  plan-2  C2X  0.020
 SFH  plan-2  C4X  0.020
 SFH  plan-2  C5X  0.020
 SFH  plan-2  C6X  0.020
 SFH  plan-2  C8X  0.020
 SFH  plan-2  N1X  0.020
 SFH  plan-2  N3X  0.020
 SFH  plan-2  N6X  0.020
 SFH  plan-2  N7X  0.020
 SFH  plan-2  N9X  0.020
 SFH  plan-2  H4   0.020
 SFH  plan-2  H12  0.020
 SFH  plan-3  C6X  0.020
 SFH  plan-3  N6X  0.020
 SFH  plan-3  H13  0.020
 SFH  plan-3  H14  0.020
 SFH  plan-4  C3N  0.020
 SFH  plan-4  C7N  0.020
 SFH  plan-4  N7N  0.020
 SFH  plan-4  O7N  0.020
 SFH  plan-4  S1   0.020
 SFH  plan-4  H15  0.020

