# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:21:50 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5'-O-[(2,3-dihydroxybenzoyl)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(O)c4O)[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
 HP8  HP8  5'-O-[(2,3-dihydroxybenzoyl)sulfamoyl]adenosine  ligand  51  33  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HP8
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
 HP8  S     S  S     0   1.632  -2.9797  -2.4316  -0.4254
 HP8  N1    N  N     0  -0.471   4.7047   2.8050  -0.7565
 HP8  C2    C  CR16  0   0.049   5.1793   1.5620  -0.7526
 HP8  N3    N  N     0  -0.452   4.5251   0.4310  -0.5476
 HP8  C4    C  CR56  0   0.487   3.2317   0.6454  -0.3314
 HP8  C5    C  CR56  0   0.052   2.5971   1.8757  -0.3115
 HP8  C6    C  CR6   0   0.478   3.4014   3.0070  -0.5375
 HP8  N6    N  NH2   0  -0.814   2.9145   4.2470  -0.5434
 HP8  N7    N  N     0  -0.544   1.2557   1.7162  -0.0785
 HP8  C8    C  CR15  0   0.175   1.0889   0.4308   0.0437
 HP8  N9    N  NR5   0  -0.536   2.2436  -0.2725  -0.0966
 HP8  O9    O  O     0  -0.392  -2.4188   0.1349  -1.8652
 HP8  C1'   C  CH1   0   0.210   2.3767  -1.7096  -0.0469
 HP8  C1S   C  CR6   0  -0.148  -2.9313   1.5363   0.0110
 HP8  C2'   C  CH1   0  -0.046   2.2939  -2.2847   1.3673
 HP8  O2'   O  OH1   0  -0.649   3.5541  -2.2606   1.9621
 HP8  C21   C  C     0   0.555  -2.7349   0.2509  -0.7096
 HP8  C2S   C  CR6   0   0.264  -2.0517   2.5954  -0.2249
 HP8  O2S   O  OH1   0  -0.662  -1.0772   2.5069  -1.1455
 HP8  C3'   C  CH1   0  -0.032   1.7373  -3.6840   1.0893
 HP8  O3'   O  OH1   0  -0.663   2.7389  -4.5373   0.6085
 HP8  C3S   C  CR6   0   0.288  -2.1955   3.7771   0.5220
 HP8  O3S   O  OH1   0  -0.620  -1.2858   4.7428   0.2956
 HP8  C4'   C  CH1   0  -0.050   0.7671  -3.3922  -0.0510
 HP8  O4'   O  O2    0  -0.487   1.3120  -2.2780  -0.7570
 HP8  C4S   C  CR16  0  -0.372  -3.2372   3.9048   1.4279
 HP8  C5'   C  CH2   0  -0.199  -0.6210  -3.0846   0.4711
 HP8  O5'   O  OC2   0  -0.571  -1.4507  -2.7936  -0.6705
 HP8  C5S   C  CR16  0  -0.252  -4.1332   2.8602   1.6200
 HP8  C6S   C  CR16  0  -0.302  -3.9778   1.6754   0.9286
 HP8  NHS   N  NC1   0  -0.846  -2.9322  -0.8582   0.1088
 HP8  OS1   O  OS    0  -0.601  -3.5849  -2.4987  -1.7235
 HP8  OS2   O  OS    0  -0.628  -3.4890  -3.1879   0.6907
 HP8  HN6   H  HNH2  0   0.407   1.9447   4.4308  -0.3541
 HP8  HN6A  H  HNH2  0   0.408   3.5232   5.0311  -0.7043
 HP8  H8    H  HCR5  0   0.287   0.1411  -0.0503   0.2261
 HP8  H1'   H  HCH1  0   0.276   3.3437  -1.9488  -0.5013
 HP8  H2'   H  HCH1  0   0.256   1.5606  -1.7144   1.9522
 HP8  HO2'  H  HOH1  0   0.472   3.4503  -2.3268   2.9168
 HP8  HO2S  H  HOH1  0   0.480  -0.1886   2.4495  -0.7121
 HP8  H3'   H  HCH1  0   0.264   1.2283  -4.1026   1.9670
 HP8  HO3'  H  HOH1  0   0.453   3.5112  -4.4400   1.1785
 HP8  HO3S  H  HOH1  0   0.478  -1.4619   5.5045   0.8595
 HP8  H4'   H  HCH1  0   0.288   0.7059  -4.2425  -0.7361
 HP8  H4S   H  HCR6  0   0.282  -3.3537   4.8267   1.9867
 HP8  H5'   H  HCH2  0   0.287  -1.0045  -3.9598   0.9969
 HP8  H5'A  H  HCH2  0   0.249  -0.6196  -2.2358   1.1622
 HP8  H5S   H  HCR6  0   0.269  -4.9511   2.9783   2.3172
 HP8  H6S   H  HCR6  0   0.273  -4.6830   0.8694   1.0852
 HP8  HNHS  H  HNC1  0   0.459  -3.1089  -0.7340   1.0990
 HP8  H2    H  HCR6  0   0.257   6.2434   1.4697  -0.9410

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
 HP8  OS1  S     deloc     1.434  0.020  1.434
 HP8  NHS  S     single    1.662  0.020  1.662
 HP8  S    OS2   deloc     1.441  0.020  1.441
 HP8  S    O5'   single    1.590  0.020  1.590
 HP8  C6   N1    aromatic  1.337  0.020  1.337
 HP8  N1   C2    aromatic  1.331  0.020  1.331
 HP8  N3   C2    aromatic  1.323  0.020  1.323
 HP8  C2   H2    single    0.930  0.020  1.080
 HP8  C4   N3    aromatic  1.329  0.020  1.329
 HP8  N9   C4    aromatic  1.369  0.020  1.369
 HP8  C5   C4    aromatic  1.385  0.020  1.385
 HP8  N7   C5    aromatic  1.371  0.020  1.371
 HP8  C5   C6    aromatic  1.406  0.020  1.406
 HP8  N6   C6    single    1.332  0.020  1.332
 HP8  N6   HN6   single    0.860  0.020  1.020
 HP8  N6   HN6A  single    0.860  0.020  1.020
 HP8  C8   N7    aromatic  1.302  0.020  1.302
 HP8  C8   N9    aromatic  1.359  0.020  1.359
 HP8  C8   H8    single    0.930  0.020  1.080
 HP8  C1'  N9    single    1.444  0.020  1.444
 HP8  C21  O9    double    1.204  0.020  1.204
 HP8  O4'  C1'   single    1.400  0.020  1.400
 HP8  C2'  C1'   single    1.529  0.020  1.529
 HP8  C1'  H1'   single    0.970  0.020  1.090
 HP8  C2S  C1S   aromatic  1.397  0.020  1.397
 HP8  C1S  C21   single    1.487  0.020  1.487
 HP8  C1S  C6S   aromatic  1.399  0.020  1.399
 HP8  C3'  C2'   single    1.531  0.020  1.531
 HP8  C2'  O2'   single    1.394  0.020  1.394
 HP8  C2'  H2'   single    0.970  0.020  1.090
 HP8  O2'  HO2'  single    0.850  0.020  0.980
 HP8  NHS  C21   single    1.392  0.020  1.392
 HP8  O2S  C2S   single    1.343  0.020  1.343
 HP8  C3S  C2S   aromatic  1.405  0.020  1.405
 HP8  O2S  HO2S  single    0.850  0.020  0.980
 HP8  O3'  C3'   single    1.401  0.020  1.401
 HP8  C3'  C4'   single    1.525  0.020  1.525
 HP8  C3'  H3'   single    0.970  0.020  1.090
 HP8  O3'  HO3'  single    0.850  0.020  0.980
 HP8  O3S  C3S   single    1.346  0.020  1.346
 HP8  C3S  C4S   aromatic  1.386  0.020  1.386
 HP8  O3S  HO3S  single    0.850  0.020  0.980
 HP8  C5'  C4'   single    1.515  0.020  1.515
 HP8  C4'  O4'   single    1.427  0.020  1.427
 HP8  C4'  H4'   single    0.970  0.020  1.090
 HP8  C4S  C5S   aromatic  1.390  0.020  1.390
 HP8  C4S  H4S   single    0.930  0.020  1.080
 HP8  C5'  O5'   single    1.441  0.020  1.441
 HP8  C5'  H5'   single    0.970  0.020  1.090
 HP8  C5'  H5'A  single    0.970  0.020  1.090
 HP8  C5S  C6S   aromatic  1.381  0.020  1.381
 HP8  C5S  H5S   single    0.930  0.020  1.080
 HP8  C6S  H6S   single    0.930  0.020  1.080
 HP8  NHS  HNHS  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
 HP8  OS2   S    OS1  121.83  3.000
 HP8  OS2   S    NHS  104.95  3.000
 HP8  OS1   S    NHS  110.32  3.000
 HP8  OS2   S    O5'  109.86  3.000
 HP8  NHS   S    O5'  103.74  3.000
 HP8  OS1   S    O5'  104.81  3.000
 HP8  C6    N1   C2   119.24  3.000
 HP8  H2    C2   N3   116.07  3.000
 HP8  H2    C2   N1   115.40  3.000
 HP8  N3    C2   N1   128.53  3.000
 HP8  C4    N3   C2   111.64  3.000
 HP8  N9    C4   C5   105.22  3.000
 HP8  C5    C4   N3   126.29  3.000
 HP8  N9    C4   N3   128.49  3.000
 HP8  N7    C5   C6   132.89  3.000
 HP8  C6    C5   C4   116.77  3.000
 HP8  N7    C5   C4   110.34  3.000
 HP8  N6    C6   C5   122.71  3.000
 HP8  N6    C6   N1   119.75  3.000
 HP8  C5    C6   N1   117.54  3.000
 HP8  HN6A  N6   HN6  118.14  3.000
 HP8  HN6A  N6   C6   120.35  3.000
 HP8  HN6   N6   C6   121.47  3.000
 HP8  C8    N7   C5   104.85  3.000
 HP8  H8    C8   N9   122.22  3.000
 HP8  H8    C8   N7   124.68  3.000
 HP8  N9    C8   N7   113.10  3.000
 HP8  C1'   N9   C8   126.13  3.000
 HP8  C1'   N9   C4   127.35  3.000
 HP8  C8    N9   C4   106.49  3.000
 HP8  H1'   C1'  O4'  111.86  3.000
 HP8  H1'   C1'  C2'  110.46  3.000
 HP8  O4'   C1'  C2'  105.97  3.000
 HP8  H1'   C1'  N9   106.53  3.000
 HP8  C2'   C1'  N9   113.65  3.000
 HP8  O4'   C1'  N9   108.45  3.000
 HP8  C6S   C1S  C2S  120.43  3.000
 HP8  C6S   C1S  C21  120.19  3.000
 HP8  C2S   C1S  C21  119.38  3.000
 HP8  H2'   C2'  C3'  109.19  3.000
 HP8  H2'   C2'  O2'  111.57  3.000
 HP8  C3'   C2'  O2'  114.96  3.000
 HP8  H2'   C2'  C1'  109.48  3.000
 HP8  O2'   C2'  C1'  109.83  3.000
 HP8  C3'   C2'  C1'  101.27  3.000
 HP8  HO2'  O2'  C2'  108.94  3.000
 HP8  NHS   C21  C1S  112.65  3.000
 HP8  NHS   C21  O9   121.65  3.000
 HP8  C1S   C21  O9   125.69  3.000
 HP8  C3S   C2S  O2S  119.59  3.000
 HP8  C3S   C2S  C1S  118.91  3.000
 HP8  O2S   C2S  C1S  121.50  3.000
 HP8  HO2S  O2S  C2S  110.78  3.000
 HP8  H3'   C3'  C4'  112.08  3.000
 HP8  H3'   C3'  O3'  111.95  3.000
 HP8  C4'   C3'  O3'  108.34  3.000
 HP8  H3'   C3'  C2'  111.83  3.000
 HP8  C4'   C3'  C2'  101.08  3.000
 HP8  O3'   C3'  C2'  111.04  3.000
 HP8  HO3'  O3'  C3'  107.95  3.000
 HP8  C4S   C3S  O3S  123.49  3.000
 HP8  C4S   C3S  C2S  120.10  3.000
 HP8  O3S   C3S  C2S  116.41  3.000
 HP8  HO3S  O3S  C3S  110.18  3.000
 HP8  H4'   C4'  C5'  108.81  3.000
 HP8  H4'   C4'  O4'  108.58  3.000
 HP8  C5'   C4'  O4'  111.22  3.000
 HP8  H4'   C4'  C3'  110.81  3.000
 HP8  O4'   C4'  C3'  106.04  3.000
 HP8  C5'   C4'  C3'  111.35  3.000
 HP8  C4'   O4'  C1'  110.88  3.000
 HP8  H4S   C4S  C5S  119.91  3.000
 HP8  H4S   C4S  C3S  119.72  3.000
 HP8  C5S   C4S  C3S  120.37  3.000
 HP8  H5'A  C5'  H5'  108.57  3.000
 HP8  H5'A  C5'  O5'  110.14  3.000
 HP8  H5'   C5'  O5'  109.97  3.000
 HP8  H5'A  C5'  C4'  111.96  3.000
 HP8  H5'   C5'  C4'  109.00  3.000
 HP8  O5'   C5'  C4'  107.19  3.000
 HP8  C5'   O5'  S    118.52  3.000
 HP8  H5S   C5S  C6S  120.13  3.000
 HP8  H5S   C5S  C4S  119.66  3.000
 HP8  C6S   C5S  C4S  120.22  3.000
 HP8  H6S   C6S  C5S  119.55  3.000
 HP8  H6S   C6S  C1S  120.56  3.000
 HP8  C5S   C6S  C1S  119.88  3.000
 HP8  HNHS  NHS  C21  120.09  3.000
 HP8  HNHS  NHS  S    115.15  3.000
 HP8  C21   NHS  S    124.69  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
 HP8  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 HP8  CONST_02  N7    C5   C6   N1   180.00   0.0  0
 HP8  CONST_03  C4    N3   C2   N1     0.00   0.0  0
 HP8  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 HP8  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 HP8  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 HP8  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 HP8  CONST_08  C8    N9   C4   N3   180.00   0.0  0
 HP8  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 HP8  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 HP8  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 HP8  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 HP8  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 HP8  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 HP8  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 HP8  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 HP8  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 HP8  CONST_18  C4S   C3S  C2S  C1S    0.00   0.0  0
 HP8  CONST_19  C4S   C5S  C6S  C1S    0.00   0.0  0
 HP8  CONST_20  C5S   C6S  C1S  C2S    0.00   0.0  0
 HP8  CONST_21  C5S   C4S  C3S  C2S    0.00   0.0  0
 HP8  CONST_22  C6S   C1S  C2S  C3S    0.00   0.0  0
 HP8  CONST_23  C6S   C5S  C4S  C3S    0.00   0.0  0
 HP8  CONST_24  C1'   N9   C4   N3     0.00   0.0  0
 HP8  CONST_25  C1'   N9   C4   C5   180.00   0.0  0
 HP8  CONST_26  C1'   N9   C8   N7   180.00   0.0  0
 HP8  CONST_27  N6    C6   N1   C2   180.00   0.0  0
 HP8  CONST_28  N6    C6   C5   C4   180.00   0.0  0
 HP8  CONST_29  N7    C5   C6   N6     0.00   0.0  0
 HP8  CONST_30  O3S   C3S  C2S  C1S  180.00   0.0  0
 HP8  CONST_31  C3S   C2S  C1S  C21  180.00   0.0  0
 HP8  CONST_32  C5S   C6S  C1S  C21  180.00   0.0  0
 HP8  CONST_33  C6S   C1S  C2S  O2S  180.00   0.0  0
 HP8  CONST_34  C4S   C3S  C2S  O2S  180.00   0.0  0
 HP8  CONST_35  C5S   C4S  C3S  O3S  180.00   0.0  0
 HP8  CONST_36  H2    C2   N3   C4   180.00   0.0  0
 HP8  CONST_37  H8    C8   N9   C4   180.00   0.0  0
 HP8  CONST_38  H5S   C5S  C6S  C1S  180.00   0.0  0
 HP8  CONST_39  H6S   C6S  C1S  C2S  180.00   0.0  0
 HP8  CONST_40  H4S   C4S  C3S  C2S  180.00   0.0  0
 HP8  CONST_41  HN6   N6   C6   N1   180.00   0.0  0
 HP8  CONST_42  HN6A  N6   C6   N1     0.00   0.0  0
 HP8  CONST_43  C1S   C21  NHS  S    180.00   0.0  0
 HP8  CONST_44  HNHS  NHS  C21  C1S    0.00   0.0  0
 HP8  CONST_45  O9    C21  NHS  S      0.00   0.0  0
 HP8  Var_01    C2S   C1S  C21  O9   -40.19  30.0  2
 HP8  Var_02    C4'   C5'  O5'  S    179.96  30.0  2
 HP8  Var_03    OS1   S    NHS  C21  -34.86  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
 HP8  chir_01  C1'  N9   O4'  C2'  positiv
 HP8  chir_02  C2'  O2'  C1'  C3'  negativ
 HP8  chir_03  C3'  O3'  C4'  C2'  positiv
 HP8  chir_04  C4'  O4'  C3'  C5'  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
 HP8  plan-1  C1S   0.020
 HP8  plan-1  C21   0.020
 HP8  plan-1  C2S   0.020
 HP8  plan-1  O2S   0.020
 HP8  plan-1  C3S   0.020
 HP8  plan-1  O3S   0.020
 HP8  plan-1  C4S   0.020
 HP8  plan-1  C5S   0.020
 HP8  plan-1  C6S   0.020
 HP8  plan-1  H4S   0.020
 HP8  plan-1  H5S   0.020
 HP8  plan-1  H6S   0.020
 HP8  plan-2  N1    0.020
 HP8  plan-2  C2    0.020
 HP8  plan-2  N3    0.020
 HP8  plan-2  C4    0.020
 HP8  plan-2  C5    0.020
 HP8  plan-2  C6    0.020
 HP8  plan-2  N6    0.020
 HP8  plan-2  N7    0.020
 HP8  plan-2  C8    0.020
 HP8  plan-2  N9    0.020
 HP8  plan-2  C1'   0.020
 HP8  plan-2  H8    0.020
 HP8  plan-2  H2    0.020
 HP8  plan-3  C6    0.020
 HP8  plan-3  N6    0.020
 HP8  plan-3  HN6   0.020
 HP8  plan-3  HN6A  0.020
 HP8  plan-4  S     0.020
 HP8  plan-4  O9    0.020
 HP8  plan-4  C1S   0.020
 HP8  plan-4  C21   0.020
 HP8  plan-4  NHS   0.020
 HP8  plan-4  HNHS  0.020

