# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 06:53:17 2021
#   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  60  38  .  2021-08-04  2023-02-16
;
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  CR56  0   0.484   98.2833  -22.9471  -19.2391
 4YB  C2   C  CR56  0   0.011   97.9650  -23.7134  -20.3488
 4YB  C3   C  CR6   0   0.464   96.5949  -23.8222  -20.6534
 4YB  C4   C  CR15  0   0.092  100.0655  -23.8234  -20.1519
 4YB  N1   N  N     0  -0.464   95.7260  -23.1850  -19.8641
 4YB  N2   N  N     0  -0.455   97.4323  -22.2920  -18.4540
 4YB  O1   O  O     0  -0.429   96.8559  -22.5937  -26.0513
 4YB  O2   O  OH1   0  -0.584   97.5354  -24.0707  -24.5170
 4YB  C6   C  CR6   0  -0.000   96.8109  -21.9750  -23.7554
 4YB  C7   C  CR16  0  -0.263   95.4731  -21.7315  -23.4786
 4YB  C8   C  CR16  0  -0.230   95.1141  -20.9185  -22.4137
 4YB  C9   C  CR16  0  -0.226   96.0934  -20.3307  -21.6284
 4YB  C10  C  CR16  0  -0.298   97.4291  -20.5634  -21.9073
 4YB  C11  C  CR6   0   0.005   97.8053  -21.3818  -22.9706
 4YB  C12  C  C     0   0.393   99.2336  -21.5731  -23.3310
 4YB  O3   O  O     0  -0.397   99.5276  -22.0559  -24.4036
 4YB  C13  C  CH2   0  -0.585  100.2933  -21.1245  -22.3574
 4YB  C14  C  CH2   0  -0.602  101.6448  -21.7407  -22.6670
 4YB  C15  C  C     0   0.614  102.7033  -21.3120  -21.6863
 4YB  O4   O  O     0  -0.412  102.6723  -20.3043  -21.0278
 4YB  N3   N  NC1   0  -0.847  103.7597  -22.2043  -21.6123
 4YB  S1   S  S     0   1.619  105.0875  -21.9984  -20.6345
 4YB  O5   O  OS    0  -0.608  105.6390  -20.6804  -20.7721
 4YB  O6   O  OS    0  -0.629  105.8915  -23.1745  -20.8536
 4YB  O7   O  OC2   0  -0.568  104.4579  -22.0162  -19.1832
 4YB  C16  C  CH2   0  -0.200  103.8162  -23.2182  -18.7069
 4YB  C17  C  CH1   0  -0.003  102.6932  -22.7994  -17.7973
 4YB  O8   O  O2    0  -0.490  101.6978  -22.1095  -18.5406
 4YB  C18  C  CH1   0   0.010  101.9557  -23.9844  -17.1773
 4YB  O9   O  OH1   0  -0.652  102.6727  -24.4955  -16.1018
 4YB  C19  C  CH1   0  -0.070  100.6049  -23.3427  -16.8459
 4YB  O10  O  OH1   0  -0.655  100.7552  -22.6055  -15.6682
 4YB  C20  C  CH1   0   0.161  100.4182  -22.4127  -18.0590
 4YB  N4   N  NR5   0  -0.533   99.6426  -23.0232  -19.1247
 4YB  N5   N  N     0  -0.436   99.0960  -24.2472  -20.9091
 4YB  C21  C  CR16  0   0.042   96.1804  -22.4652  -18.8429
 4YB  N6   N  NH2   0  -0.817   96.1347  -24.5737  -21.6591
 4YB  H1   H  HCR5  0   0.286  101.1071  -24.0597  -20.3047
 4YB  H2   H  HOH1  0   0.489   97.6930  -24.6408  -25.2858
 4YB  H4   H  HCR6  0   0.273   94.0682  -20.7452  -22.2000
 4YB  H5   H  HCR6  0   0.272   95.8199  -19.6938  -20.7983
 4YB  H6   H  HCR6  0   0.274   98.1791  -20.0811  -21.2954
 4YB  H7   H  HCH2  0   0.310  100.3472  -20.0320  -22.4039
 4YB  H8   H  HCH2  0   0.269   99.9834  -21.3585  -21.3380
 4YB  H9   H  HCH2  0   0.279  101.5751  -22.8303  -22.6847
 4YB  H10  H  HCH2  0   0.317  101.9890  -21.4470  -23.6631
 4YB  H11  H  HNC1  0   0.459  103.7889  -23.0136  -22.2218
 4YB  H12  H  HCH2  0   0.252  103.4364  -23.8162  -19.5393
 4YB  H13  H  HCH2  0   0.289  104.5451  -23.8131  -18.1563
 4YB  H14  H  HCH1  0   0.268  103.0885  -22.1550  -17.0021
 4YB  H15  H  HCH1  0   0.238  101.7885  -24.7487  -17.9509
 4YB  H16  H  HOH1  0   0.466  102.2899  -25.3403  -15.8454
 4YB  H17  H  HCH1  0   0.273   99.7938  -24.0764  -16.7754
 4YB  H18  H  HOH1  0   0.464   99.8917  -22.2822  -15.3919
 4YB  H19  H  HCH1  0   0.283   99.8827  -21.5024  -17.7748
 4YB  H20  H  HCR6  0   0.253   95.4226  -21.9615  -18.2523
 4YB  H21  H  HNH2  0   0.397   95.1666  -24.4842  -21.9189
 4YB  H22  H  HNH2  0   0.406   96.7663  -24.8797  -22.3796
 4YB  H3   H  HCR6  0   0.277   94.7025  -22.1921  -24.0836
 4YB  C5   C  C     0   0.466   97.1025  -22.8818  -24.9087

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   double    1.204  0.020  1.204
 4YB  C5   O2   single    1.324  0.020  1.324
 4YB  C5   C6   single    1.496  0.020  1.496
 4YB  C7   C6   aromatic  1.388  0.020  1.388
 4YB  C7   C8   aromatic  1.387  0.020  1.387
 4YB  C6   C11  aromatic  1.399  0.020  1.399
 4YB  O3   C12  double    1.212  0.020  1.212
 4YB  C8   C9   aromatic  1.386  0.020  1.386
 4YB  C11  C12  single    1.485  0.020  1.485
 4YB  C11  C10  aromatic  1.394  0.020  1.394
 4YB  C12  C13  single    1.507  0.020  1.507
 4YB  C9   C10  aromatic  1.384  0.020  1.384
 4YB  C13  C14  single    1.517  0.020  1.517
 4YB  C14  C15  single    1.505  0.020  1.505
 4YB  C15  N3   single    1.385  0.020  1.385
 4YB  C15  O4   double    1.204  0.020  1.204
 4YB  N3   S1   single    1.662  0.020  1.662
 4YB  O5   S1   double    1.435  0.020  1.435
 4YB  O6   S1   double    1.441  0.020  1.441
 4YB  S1   O7   single    1.582  0.020  1.582
 4YB  O7   C16  single    1.443  0.020  1.443
 4YB  C16  C17  single    1.505  0.020  1.505
 4YB  N5   C4   aromatic  1.301  0.020  1.301
 4YB  N5   C2   aromatic  1.370  0.020  1.370
 4YB  C4   N4   aromatic  1.369  0.020  1.369
 4YB  N6   C3   single    1.337  0.020  1.337
 4YB  C2   C3   aromatic  1.408  0.020  1.408
 4YB  C2   C1   aromatic  1.386  0.020  1.386
 4YB  O8   C17  single    1.421  0.020  1.421
 4YB  O8   C20  single    1.401  0.020  1.401
 4YB  C17  C18  single    1.527  0.020  1.527
 4YB  N4   C1   aromatic  1.366  0.020  1.366
 4YB  N4   C20  single    1.453  0.020  1.453
 4YB  C3   N1   aromatic  1.336  0.020  1.336
 4YB  C18  O9   single    1.390  0.020  1.390
 4YB  C18  C19  single    1.532  0.020  1.532
 4YB  C1   N2   aromatic  1.330  0.020  1.330
 4YB  C20  C19  single    1.540  0.020  1.540
 4YB  C19  O10  single    1.398  0.020  1.398
 4YB  N1   C21  aromatic  1.329  0.020  1.329
 4YB  N2   C21  aromatic  1.322  0.020  1.322
 4YB  C4   H1   single    0.930  0.020  1.080
 4YB  O2   H2   single    0.850  0.020  0.980
 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   127.92  3.000
 4YB  N2   C1   C2   126.73  3.000
 4YB  N4   C1   C2   105.35  3.000
 4YB  N5   C2   C3   133.21  3.000
 4YB  C3   C2   C1   116.08  3.000
 4YB  N5   C2   C1   110.69  3.000
 4YB  N6   C3   N1   119.26  3.000
 4YB  N1   C3   C2   117.93  3.000
 4YB  N6   C3   C2   122.76  3.000
 4YB  H1   C4   N5   124.44  3.000
 4YB  H1   C4   N4   122.17  3.000
 4YB  N5   C4   N4   113.38  3.000
 4YB  C21  N1   C3   119.33  3.000
 4YB  C21  N2   C1   111.56  3.000
 4YB  H2   O2   C5   110.26  3.000
 4YB  C11  C6   C7   119.93  3.000
 4YB  C11  C6   C5   123.44  3.000
 4YB  C7   C6   C5   116.63  3.000
 4YB  H3   C7   C8   119.62  3.000
 4YB  H3   C7   C6   120.00  3.000
 4YB  C8   C7   C6   120.37  3.000
 4YB  H4   C8   C9   120.23  3.000
 4YB  H4   C8   C7   119.73  3.000
 4YB  C9   C8   C7   120.05  3.000
 4YB  H5   C9   C10  119.85  3.000
 4YB  H5   C9   C8   120.39  3.000
 4YB  C10  C9   C8   119.76  3.000
 4YB  H6   C10  C11  120.43  3.000
 4YB  H6   C10  C9   118.70  3.000
 4YB  C11  C10  C9   120.86  3.000
 4YB  C12  C11  C10  121.36  3.000
 4YB  C10  C11  C6   119.03  3.000
 4YB  C12  C11  C6   119.52  3.000
 4YB  C13  C12  O3   121.29  3.000
 4YB  C13  C12  C11  118.74  3.000
 4YB  O3   C12  C11  119.94  3.000
 4YB  H8   C13  H7   105.54  3.000
 4YB  H8   C13  C14  110.89  3.000
 4YB  H7   C13  C14  110.66  3.000
 4YB  H8   C13  C12  109.88  3.000
 4YB  H7   C13  C12  107.70  3.000
 4YB  C14  C13  C12  111.93  3.000
 4YB  H10  C14  H9   105.85  3.000
 4YB  H10  C14  C15  107.19  3.000
 4YB  H9   C14  C15  109.85  3.000
 4YB  H10  C14  C13  110.92  3.000
 4YB  H9   C14  C13  110.59  3.000
 4YB  C15  C14  C13  112.19  3.000
 4YB  N3   C15  O4   121.98  3.000
 4YB  O4   C15  C14  125.20  3.000
 4YB  N3   C15  C14  112.81  3.000
 4YB  H11  N3   S1   115.45  3.000
 4YB  H11  N3   C15  120.29  3.000
 4YB  S1   N3   C15  124.14  3.000
 4YB  O7   S1   O6   110.62  3.000
 4YB  O7   S1   O5   104.54  3.000
 4YB  O6   S1   O5   121.36  3.000
 4YB  O7   S1   N3   102.73  3.000
 4YB  O6   S1   N3   104.79  3.000
 4YB  O5   S1   N3   111.37  3.000
 4YB  C16  O7   S1   119.27  3.000
 4YB  H13  C16  H12  108.57  3.000
 4YB  H13  C16  C17  110.22  3.000
 4YB  H12  C16  C17  110.69  3.000
 4YB  H13  C16  O7   108.90  3.000
 4YB  H12  C16  O7   111.02  3.000
 4YB  C17  C16  O7   107.43  3.000
 4YB  H14  C17  C18  109.60  3.000
 4YB  H14  C17  O8   110.26  3.000
 4YB  C18  C17  O8   104.53  3.000
 4YB  H14  C17  C16  109.43  3.000
 4YB  C18  C17  C16  112.95  3.000
 4YB  O8   C17  C16  109.99  3.000
 4YB  C20  O8   C17  110.80  3.000
 4YB  H15  C18  C19  108.01  3.000
 4YB  H15  C18  O9   111.53  3.000
 4YB  C19  C18  O9   116.20  3.000
 4YB  H15  C18  C17  109.09  3.000
 4YB  C19  C18  C17  100.87  3.000
 4YB  O9   C18  C17  110.51  3.000
 4YB  H16  O9   C18  108.90  3.000
 4YB  H17  C19  C20  111.42  3.000
 4YB  H17  C19  O10  112.24  3.000
 4YB  C20  C19  O10  111.00  3.000
 4YB  H17  C19  C18  112.71  3.000
 4YB  O10  C19  C18  107.97  3.000
 4YB  C20  C19  C18  100.92  3.000
 4YB  H18  O10  C19  108.82  3.000
 4YB  H19  C20  N4   106.20  3.000
 4YB  H19  C20  C19  110.94  3.000
 4YB  N4   C20  C19  112.88  3.000
 4YB  H19  C20  O8   110.89  3.000
 4YB  C19  C20  O8   106.91  3.000
 4YB  N4   C20  O8   109.06  3.000
 4YB  C20  N4   C4   129.14  3.000
 4YB  C20  N4   C1   124.70  3.000
 4YB  C4   N4   C1   106.09  3.000
 4YB  C4   N5   C2   104.49  3.000
 4YB  H20  C21  N2   116.13  3.000
 4YB  H20  C21  N1   115.52  3.000
 4YB  N2   C21  N1   128.35  3.000
 4YB  H22  N6   H21  116.51  3.000
 4YB  H22  N6   C3   119.58  3.000
 4YB  H21  N6   C3   118.38  3.000
 4YB  C6   C5   O2   112.33  3.000
 4YB  C6   C5   O1   123.14  3.000
 4YB  O2   C5   O1   124.23  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_40  H21  N6   C3   C2    180.00   0.0  0
 4YB  CONST_42  H2   O2   C5   C6    180.00   0.0  0
 4YB  CONST_43  S1   N3   C15  C14   180.00   0.0  0
 4YB  CONST_44  S1   N3   C15  O4      0.00   0.0  0
 4YB  CONST_45  H11  N3   C15  C14     0.00   0.0  0
 4YB  Var_01    C7   C6   C5   O1     66.78  30.0  2
 4YB  Var_02    O3   C12  C11  C6     11.53  30.0  2
 4YB  Var_03    C14  C13  C12  C11   163.22  30.0  3
 4YB  Var_04    C17  C16  O7   S1   -147.51  30.0  3
 4YB  Var_05    C15  C14  C13  C12  -179.18  30.0  3
 4YB  Var_06    N3   C15  C14  C13   156.69  30.0  3
 4YB  Var_07    O5   S1   N3   C15   -48.76  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  H4   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-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  H2   0.020
 4YB  plan-6  C5   0.020

