# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  2 05:56:45 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 5'-O-{[4-(2-carboxyphenyl)-4-oxobutanoyl]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)CCC(=O)c4ccccc4C(O)=O)[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
 4YB  4YB  5'-O-{[4-(2-carboxyphenyl)-4-oxobutanoyl]sulfamoyl}adenosine  ligand  59  38  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4YB
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
 4YB  C1   C  CR5    0   0.482  -1.4384   1.9352   0.1435
 4YB  C2   C  CR5    0  -0.011  -0.3715   2.3554  -0.6362
 4YB  C3   C  C      0   0.461   0.1496   3.6333  -0.3438
 4YB  C4   C  CR15   0   0.093  -0.9304   0.4606  -1.3907
 4YB  N1   N  N      0  -0.475  -0.4258   4.3208   0.6544
 4YB  N2   N  N      0  -0.463  -2.0067   2.6018   1.1447
 4YB  O1   O  O      0  -0.585   5.3940   2.3923  -1.7238
 4YB  O2   O  OC    -1  -0.582   3.3040   2.9047  -2.3179
 4YB  C6   C  CR6    0  -0.037   3.7964   2.8080  -0.0344
 4YB  C7   C  CR16   0  -0.284   4.1476   4.0037   0.5849
 4YB  C8   C  CR16   0  -0.239   3.7032   4.3116   1.8618
 4YB  C9   C  CR16   0  -0.249   2.8988   3.4144   2.5503
 4YB  C10  C  CR16   0  -0.288   2.5689   2.2079   1.9591
 4YB  C11  C  CR6    0  -0.035   3.0145   1.8850   0.6749
 4YB  C12  C  C      0   0.388   2.7192   0.5550   0.0829
 4YB  O3   O  O      0  -0.400   3.2525   0.2006  -0.9462
 4YB  C13  C  CH2    0  -0.586   1.7817  -0.3723   0.8242
 4YB  C14  C  CH2    0  -0.599   1.5765  -1.6817   0.0906
 4YB  C15  C  C      0   0.615   0.6509  -2.6160   0.8212
 4YB  O4   O  O      0  -0.413   0.1858  -2.4309   1.9160
 4YB  N3   N  NC1    0  -0.844   0.3716  -3.7641   0.0928
 4YB  S1   S  S      0   1.617  -0.6905  -4.9424   0.5764
 4YB  O5   O  OS     0  -0.631  -0.6940  -5.9052  -0.4965
 4YB  O6   O  OS     0  -0.610  -0.4393  -5.3394   1.9327
 4YB  O7   O  OC2    0  -0.568  -2.0751  -4.1750   0.6344
 4YB  C16  C  CH2    0  -0.201  -2.6109  -3.6085  -0.5800
 4YB  C17  C  CH1    0   0.006  -3.3332  -2.3429  -0.2091
 4YB  O8   O  O2     0  -0.487  -2.4084  -1.4114   0.3162
 4YB  C18  C  CH1    0  -0.026  -3.9335  -1.6230  -1.4126
 4YB  O9   O  OH1    0  -0.654  -5.1504  -2.2013  -1.7822
 4YB  C19  C  CH1    0  -0.058  -4.0666  -0.1927  -0.8649
 4YB  O10  O  OH1    0  -0.662  -5.2472  -0.0511  -0.1249
 4YB  C20  C  CH1    0   0.182  -2.8819  -0.1014   0.1149
 4YB  N4   N  NR5    0  -0.534  -1.7865   0.7093  -0.3509
 4YB  N5   N  N      0  -0.431  -0.0703   1.4143  -1.5884
 4YB  C21  C  C1     0   0.042  -1.4347   3.7807   1.3262
 4YB  N6   N  NH2    0  -0.843   1.1370   4.1985  -1.0376
 4YB  H1   H  HCR5   0   0.292  -0.9896  -0.4453  -1.9757
 4YB  H5   H  HCR6   0   0.257   2.5384   3.6474   3.5432
 4YB  H6   H  HCR6   0   0.260   1.9584   1.5124   2.5192
 4YB  H7   H  HCH2   0   0.290   2.1936  -0.5577   1.8198
 4YB  H8   H  HCH2   0   0.276   0.8279   0.1332   0.9940
 4YB  H9   H  HCH2   0   0.284   1.1786  -1.5083  -0.9123
 4YB  H10  H  HCH2   0   0.305   2.5280  -2.2004  -0.0574
 4YB  H11  H  HNC1   0   0.457   0.7927  -3.9031  -0.8185
 4YB  H12  H  HCH2   0   0.252  -1.8162  -3.3919  -1.2989
 4YB  H13  H  HCH2   0   0.286  -3.3023  -4.3215  -1.0291
 4YB  H14  H  HCH1   0   0.262  -4.1244  -2.5641   0.5200
 4YB  H15  H  HCH1   0   0.252  -3.2139  -1.6297  -2.2421
 4YB  H16  H  HOH1   0   0.473  -5.3306  -1.9944  -2.7049
 4YB  H17  H  HCH1   0   0.262  -3.9925   0.5636  -1.6552
 4YB  H18  H  HOH1   0   0.452  -5.9356  -0.5615  -0.5698
 4YB  H19  H  HCH1   0   0.276  -3.2161   0.3514   1.0532
 4YB  H20  H  H      0   0.248  -1.8441   4.3899   2.1255
 4YB  H21  H  HNH2   0   0.425   1.8032   3.6278  -1.5735
 4YB  H22  H  HNH2   0   0.380   1.5134   5.0508  -0.6543
 4YB  H3   H  HCR6   0   0.257   4.7593   4.7207   0.0501
 4YB  C5   C  C      0   0.405   4.2073   2.6511  -1.4887
 4YB  H4   H  HCR6   0   0.259   3.9807   5.2544   2.3159

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
 4YB  O1   C5   deloc     1.237  0.020  1.237
 4YB  C5   O2   deloc     1.252  0.020  1.252
 4YB  C5   C6   single    1.519  0.020  1.519
 4YB  C7   C6   aromatic  1.392  0.020  1.392
 4YB  C7   C8   aromatic  1.387  0.020  1.387
 4YB  C6   C11  aromatic  1.402  0.020  1.402
 4YB  O3   C12  double    1.212  0.020  1.212
 4YB  C8   C9   aromatic  1.388  0.020  1.388
 4YB  C11  C12  single    1.485  0.020  1.485
 4YB  C11  C10  aromatic  1.397  0.020  1.397
 4YB  C12  C13  single    1.513  0.020  1.513
 4YB  C9   C10  aromatic  1.384  0.020  1.384
 4YB  C13  C14  single    1.515  0.020  1.515
 4YB  C14  C15  single    1.504  0.020  1.504
 4YB  C15  N3   single    1.388  0.020  1.388
 4YB  C15  O4   double    1.204  0.020  1.204
 4YB  N3   S1   single    1.658  0.020  1.658
 4YB  O5   S1   deloc     1.442  0.020  1.442
 4YB  O6   S1   deloc     1.435  0.020  1.435
 4YB  S1   O7   single    1.584  0.020  1.584
 4YB  O7   C16  single    1.443  0.020  1.443
 4YB  C16  C17  single    1.504  0.020  1.504
 4YB  N5   C4   aromatic  1.299  0.020  1.299
 4YB  N5   C2   aromatic  1.372  0.020  1.372
 4YB  C4   N4   aromatic  1.370  0.020  1.370
 4YB  N6   C3   single    1.333  0.020  1.333
 4YB  C2   C3   aromatic  1.411  0.020  1.411
 4YB  C2   C1   aromatic  1.387  0.020  1.387
 4YB  O8   C17  single    1.414  0.020  1.414
 4YB  O8   C20  single    1.407  0.020  1.407
 4YB  C17  C18  single    1.525  0.020  1.525
 4YB  N4   C1   aromatic  1.367  0.020  1.367
 4YB  N4   C20  single    1.440  0.020  1.440
 4YB  C3   N1   aromatic  1.342  0.020  1.342
 4YB  C18  O9   single    1.397  0.020  1.397
 4YB  C18  C19  single    1.537  0.020  1.537
 4YB  C1   N2   aromatic  1.330  0.020  1.330
 4YB  C20  C19  single    1.540  0.020  1.540
 4YB  C19  O10  single    1.400  0.020  1.400
 4YB  N1   C21  aromatic  1.327  0.020  1.327
 4YB  N2   C21  aromatic  1.323  0.020  1.323
 4YB  C4   H1   single    0.930  0.020  1.080
 4YB  C7   H3   single    0.930  0.020  1.080
 4YB  C8   H4   single    0.930  0.020  1.080
 4YB  C9   H5   single    0.930  0.020  1.080
 4YB  C10  H6   single    0.930  0.020  1.080
 4YB  C13  H7   single    0.970  0.020  1.090
 4YB  C13  H8   single    0.970  0.020  1.090
 4YB  C14  H9   single    0.970  0.020  1.090
 4YB  C14  H10  single    0.970  0.020  1.090
 4YB  N3   H11  single    0.860  0.020  1.020
 4YB  C16  H12  single    0.970  0.020  1.090
 4YB  C16  H13  single    0.970  0.020  1.090
 4YB  C17  H14  single    0.970  0.020  1.090
 4YB  C18  H15  single    0.970  0.020  1.090
 4YB  O9   H16  single    0.850  0.020  0.980
 4YB  C19  H17  single    0.970  0.020  1.090
 4YB  O10  H18  single    0.850  0.020  0.980
 4YB  C20  H19  single    0.970  0.020  1.090
 4YB  C21  H20  single    0.930  0.020  1.080
 4YB  N6   H21  single    0.890  0.020  1.040
 4YB  N6   H22  single    0.890  0.020  1.040

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
 4YB  N4   C1   N2   127.79  3.000
 4YB  N2   C1   C2   126.88  3.000
 4YB  N4   C1   C2   105.33  3.000
 4YB  N5   C2   C3   133.16  3.000
 4YB  C3   C2   C1   116.24  3.000
 4YB  N5   C2   C1   110.56  3.000
 4YB  N6   C3   N1   119.20  3.000
 4YB  N1   C3   C2   117.39  3.000
 4YB  N6   C3   C2   123.36  3.000
 4YB  H1   C4   N5   124.72  3.000
 4YB  H1   C4   N4   121.96  3.000
 4YB  N5   C4   N4   113.32  3.000
 4YB  C21  N1   C3   119.62  3.000
 4YB  C21  N2   C1   111.41  3.000
 4YB  C11  C6   C7   118.76  3.000
 4YB  C11  C6   C5   124.54  3.000
 4YB  C7   C6   C5   116.52  3.000
 4YB  H3   C7   C8   119.25  3.000
 4YB  H3   C7   C6   119.42  3.000
 4YB  C8   C7   C6   121.31  3.000
 4YB  H4   C8   C9   120.22  3.000
 4YB  H4   C8   C7   119.83  3.000
 4YB  C9   C8   C7   119.94  3.000
 4YB  H5   C9   C10  120.04  3.000
 4YB  H5   C9   C8   120.62  3.000
 4YB  C10  C9   C8   119.34  3.000
 4YB  H6   C10  C11  120.49  3.000
 4YB  H6   C10  C9   118.30  3.000
 4YB  C11  C10  C9   121.22  3.000
 4YB  C12  C11  C10  120.65  3.000
 4YB  C10  C11  C6   119.38  3.000
 4YB  C12  C11  C6   119.91  3.000
 4YB  C13  C12  O3   120.63  3.000
 4YB  C13  C12  C11  118.48  3.000
 4YB  O3   C12  C11  120.84  3.000
 4YB  H8   C13  H7   105.41  3.000
 4YB  H8   C13  C14  110.90  3.000
 4YB  H7   C13  C14  110.21  3.000
 4YB  H8   C13  C12  109.49  3.000
 4YB  H7   C13  C12  108.47  3.000
 4YB  C14  C13  C12  112.12  3.000
 4YB  H10  C14  H9   105.53  3.000
 4YB  H10  C14  C15  107.84  3.000
 4YB  H9   C14  C15  108.68  3.000
 4YB  H10  C14  C13  110.95  3.000
 4YB  H9   C14  C13  110.89  3.000
 4YB  C15  C14  C13  112.64  3.000
 4YB  N3   C15  O4   121.78  3.000
 4YB  O4   C15  C14  125.72  3.000
 4YB  N3   C15  C14  112.49  3.000
 4YB  H11  N3   S1   115.52  3.000
 4YB  H11  N3   C15  120.11  3.000
 4YB  S1   N3   C15  124.30  3.000
 4YB  O7   S1   O6   104.62  3.000
 4YB  O7   S1   O5   110.41  3.000
 4YB  O6   S1   O5   121.26  3.000
 4YB  O7   S1   N3   103.08  3.000
 4YB  O6   S1   N3   111.10  3.000
 4YB  O5   S1   N3   105.01  3.000
 4YB  C16  O7   S1   118.94  3.000
 4YB  H13  C16  H12  108.64  3.000
 4YB  H13  C16  C17  110.33  3.000
 4YB  H12  C16  C17  110.16  3.000
 4YB  H13  C16  O7   108.99  3.000
 4YB  H12  C16  O7   111.18  3.000
 4YB  C17  C16  O7   107.53  3.000
 4YB  H14  C17  C18  109.59  3.000
 4YB  H14  C17  O8   110.93  3.000
 4YB  C18  C17  O8   103.86  3.000
 4YB  H14  C17  C16  109.89  3.000
 4YB  C18  C17  C16  113.06  3.000
 4YB  O8   C17  C16  109.39  3.000
 4YB  C20  O8   C17  109.89  3.000
 4YB  H15  C18  C19  109.36  3.000
 4YB  H15  C18  O9   111.62  3.000
 4YB  C19  C18  O9   113.83  3.000
 4YB  H15  C18  C17  109.58  3.000
 4YB  C19  C18  C17  101.07  3.000
 4YB  O9   C18  C17  110.87  3.000
 4YB  H16  O9   C18  109.12  3.000
 4YB  H17  C19  C20  111.45  3.000
 4YB  H17  C19  O10  111.60  3.000
 4YB  C20  C19  O10  107.84  3.000
 4YB  H17  C19  C18  112.28  3.000
 4YB  O10  C19  C18  110.81  3.000
 4YB  C20  C19  C18  102.43  3.000
 4YB  H18  O10  C19  107.70  3.000
 4YB  H19  C20  N4   106.07  3.000
 4YB  H19  C20  C19  109.58  3.000
 4YB  N4   C20  C19  114.37  3.000
 4YB  H19  C20  O8   111.43  3.000
 4YB  C19  C20  O8   107.13  3.000
 4YB  N4   C20  O8   108.32  3.000
 4YB  C20  N4   C4   128.22  3.000
 4YB  C20  N4   C1   125.56  3.000
 4YB  C4   N4   C1   106.16  3.000
 4YB  C4   N5   C2   104.63  3.000
 4YB  H20  C21  N2   115.99  3.000
 4YB  H20  C21  N1   115.55  3.000
 4YB  N2   C21  N1   128.46  3.000
 4YB  H22  N6   H21  115.21  3.000
 4YB  H22  N6   C3   115.95  3.000
 4YB  H21  N6   C3   121.07  3.000
 4YB  C6   C5   O2   114.70  3.000
 4YB  C6   C5   O1   117.58  3.000
 4YB  O2   C5   O1   127.48  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
 4YB  CONST_01  C4   N5   C2   C1      0.00   0.0  0
 4YB  CONST_02  N1   C3   C2   C1      0.00   0.0  0
 4YB  CONST_03  N5   C4   N4   C1      0.00   0.0  0
 4YB  CONST_04  N1   C21  N2   C1      0.00   0.0  0
 4YB  CONST_05  N4   C4   N5   C2      0.00   0.0  0
 4YB  CONST_06  C21  N1   C3   C2      0.00   0.0  0
 4YB  CONST_07  C4   N4   C1   C2      0.00   0.0  0
 4YB  CONST_08  C21  N2   C1   C2      0.00   0.0  0
 4YB  CONST_09  C4   N5   C2   C3    180.00   0.0  0
 4YB  CONST_10  N4   C1   C2   C3    180.00   0.0  0
 4YB  CONST_11  N2   C1   C2   C3      0.00   0.0  0
 4YB  CONST_12  N2   C21  N1   C3      0.00   0.0  0
 4YB  CONST_13  N2   C1   N4   C4    180.00   0.0  0
 4YB  CONST_14  N5   C2   C3   N1    180.00   0.0  0
 4YB  CONST_15  N5   C2   C1   N2    180.00   0.0  0
 4YB  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 4YB  CONST_17  C9   C10  C11  C6      0.00   0.0  0
 4YB  CONST_18  C10  C11  C6   C7      0.00   0.0  0
 4YB  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 4YB  CONST_20  C11  C6   C7   C8      0.00   0.0  0
 4YB  CONST_21  C11  C10  C9   C8      0.00   0.0  0
 4YB  CONST_22  N5   C2   C1   N4      0.00   0.0  0
 4YB  CONST_23  C21  N2   C1   N4    180.00   0.0  0
 4YB  CONST_24  C20  N4   C1   C2    180.00   0.0  0
 4YB  CONST_25  C20  N4   C1   N2      0.00   0.0  0
 4YB  CONST_26  N5   C4   N4   C20   180.00   0.0  0
 4YB  CONST_27  N6   C3   C2   C1    180.00   0.0  0
 4YB  CONST_28  C8   C7   C6   C5    180.00   0.0  0
 4YB  CONST_29  C10  C11  C6   C5    180.00   0.0  0
 4YB  CONST_30  C12  C11  C6   C7    180.00   0.0  0
 4YB  CONST_31  C12  C11  C10  C9    180.00   0.0  0
 4YB  CONST_32  N6   C3   C2   N5      0.00   0.0  0
 4YB  CONST_33  N6   C3   N1   C21   180.00   0.0  0
 4YB  CONST_34  H1   C4   N4   C1    180.00   0.0  0
 4YB  CONST_35  H20  C21  N2   C1    180.00   0.0  0
 4YB  CONST_36  H4   C8   C7   C6    180.00   0.0  0
 4YB  CONST_37  H6   C10  C11  C6    180.00   0.0  0
 4YB  CONST_38  H5   C9   C8   C7    180.00   0.0  0
 4YB  CONST_39  H3   C7   C8   C9    180.00   0.0  0
 4YB  CONST_41  H22  N6   C3   C2    180.00   0.0  0
 4YB  CONST_42  S1   N3   C15  C14   180.00   0.0  0
 4YB  CONST_43  S1   N3   C15  O4      0.00   0.0  0
 4YB  CONST_44  H11  N3   C15  C14     0.00   0.0  0
 4YB  Var_01    C7   C6   C5   O1     76.55  30.0  2
 4YB  Var_02    O3   C12  C11  C6      7.44  30.0  2
 4YB  Var_03    C14  C13  C12  C11   179.68  30.0  3
 4YB  Var_04    C17  C16  O7   S1   -145.89  30.0  3
 4YB  Var_05    C15  C14  C13  C12   179.72  30.0  3
 4YB  Var_06    N3   C15  C14  C13   174.68  30.0  3
 4YB  Var_07    O5   S1   N3   C15   178.16  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
 4YB  chir_01  C17  C16  O8   C18  negativ
 4YB  chir_02  C18  O9   C17  C19  positiv
 4YB  chir_03  C19  O10  C18  C20  positiv
 4YB  chir_04  C20  O8   N4   C19  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
 4YB  plan-1  C6   0.020
 4YB  plan-1  C7   0.020
 4YB  plan-1  C8   0.020
 4YB  plan-1  C9   0.020
 4YB  plan-1  C10  0.020
 4YB  plan-1  C11  0.020
 4YB  plan-1  C12  0.020
 4YB  plan-1  H5   0.020
 4YB  plan-1  H6   0.020
 4YB  plan-1  H3   0.020
 4YB  plan-1  C5   0.020
 4YB  plan-1  H4   0.020
 4YB  plan-2  C1   0.020
 4YB  plan-2  C2   0.020
 4YB  plan-2  C3   0.020
 4YB  plan-2  C4   0.020
 4YB  plan-2  N1   0.020
 4YB  plan-2  N2   0.020
 4YB  plan-2  C20  0.020
 4YB  plan-2  N4   0.020
 4YB  plan-2  N5   0.020
 4YB  plan-2  C21  0.020
 4YB  plan-2  N6   0.020
 4YB  plan-2  H1   0.020
 4YB  plan-2  H20  0.020
 4YB  plan-3  C3   0.020
 4YB  plan-3  N6   0.020
 4YB  plan-3  H21  0.020
 4YB  plan-3  H22  0.020
 4YB  plan-4  C11  0.020
 4YB  plan-4  C12  0.020
 4YB  plan-4  O3   0.020
 4YB  plan-4  C13  0.020
 4YB  plan-5  C14  0.020
 4YB  plan-5  C15  0.020
 4YB  plan-5  O4   0.020
 4YB  plan-5  N3   0.020
 4YB  plan-5  S1   0.020
 4YB  plan-5  H11  0.020
 4YB  plan-6  O1   0.020
 4YB  plan-6  O2   0.020
 4YB  plan-6  C6   0.020
 4YB  plan-6  C5   0.020

