# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 12:16:31 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-[[1-[(2~{S},3~{S},5~{R})-2-(hydroxymethyl)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-3-yl]-1,2,3-triazol-4-yl]methoxy]benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@@H]([C@@H](CO)O2)n3cc(COc4ccc(cc4)[S](N)(=O)=O)nn3)C(=O)NC1=O
#
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
 P75  P75  4-[[1-[(2~{S},3~{S},5~{R})-2-(hydroxymethyl)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-3-yl]-1,2,3-triazol-4-yl]methoxy]benzenesulfonamide  ligand  55  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P75
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
 P75  C1   C  CR6   0  -0.188   -7.9543  10.1796   7.3567
 P75  C2   C  CH3   0  -0.707   -8.3722   9.1384   6.3699
 P75  C3   C  CR16  0   0.038   -6.6927  10.2846   7.8141
 P75  C4   C  CR15  0   0.190   -4.9110  11.2755   9.2491
 P75  C5   C  CH2   0  -0.498   -4.7626  10.4984  10.5562
 P75  C10  C  CR16  0  -0.334   -5.2877   4.7243  15.7727
 P75  C11  C  CR16  0  -0.217   -5.8125   3.6445  16.4512
 P75  C15  C  CR15  0  -0.056   -3.8901   7.0862  11.4104
 P75  C16  C  CR15  0   0.045   -3.3649   9.5688   8.8888
 P75  C17  C  CH2   0  -0.177   -3.0995   8.5175   7.8387
 P75  C18  C  CR6   0   0.728   -7.1785  12.1322   9.2510
 P75  O1   O  O2    0  -0.459   -3.7968   5.6605  14.2682
 P75  C6   C  CR15  0  -0.133   -4.2658   9.1500  10.0538
 P75  C7   C  CR5   0   0.140   -2.9765   6.7976  12.3909
 P75  C8   C  CH2   0  -0.276   -2.8552   5.5606  13.2013
 P75  C9   C  CR6   0   0.412   -4.2014   4.5577  14.9095
 P75  C13  C  CR16  0  -0.201   -4.1525   2.2128  15.4473
 P75  C14  C  CR16  0  -0.371   -3.6193   3.2957  14.7672
 P75  C12  C  CR6   0  -0.238   -5.2519   2.3838  16.2774
 P75  N1   N  NR5   0  -0.277   -3.5966   8.3437  11.0489
 P75  O6   O  O     0  -0.481   -6.8629  12.9500  10.0929
 P75  N5   N  NR16  0  -0.733   -8.4528  12.0355   8.7600
 P75  C    C  CR6   0   0.555   -8.9414  11.1219   7.8401
 P75  O    O  O     0  -0.449  -10.1101  11.1515   7.5010
 P75  N    N  NR6   0  -0.565   -6.2905  11.2267   8.7216
 P75  O5   O  O     0  -0.489   -4.0442  10.6871   8.3268
 P75  O4   O  OH1   0  -0.656   -4.3139   7.9785   7.3817
 P75  N3   N  N     0  -0.293   -2.1925   7.8850  12.5568
 P75  N2   N  N     0  -0.101   -2.5699   8.8083  11.7449
 P75  S    S  S     0   1.357   -5.9625   0.9935  17.0982
 P75  N4   N  NC2   0  -0.888   -6.6909   0.2151  15.8299
 P75  H1   H  HCH3  0   0.245   -7.5343   8.4943   6.1087
 P75  H2   H  HCH3  0   0.244   -9.1664   8.5073   6.7713
 P75  H3   H  HCH3  0   0.244   -8.7506   9.5863   5.4500
 P75  H4   H  HCR6  0   0.325   -5.9261   9.6071   7.4670
 P75  H5   H  HCR5  0   0.285   -4.6643  12.3295   9.3728
 P75  H6   H  HCH2  0   0.282   -4.0068  10.9747  11.1822
 P75  H7   H  HCH2  0   0.295   -5.6885  10.4372  11.1243
 P75  H9   H  HCR6  0   0.283   -6.6620   3.7892  17.1040
 P75  H10  H  HCR5  0   0.320   -4.6915   6.5183  10.9678
 P75  H11  H  HCR5  0   0.262   -2.3927   9.8904   9.2836
 P75  H12  H  HCH2  0   0.218   -2.4561   7.7552   8.2968
 P75  H13  H  HCH2  0   0.234   -2.5188   8.9732   7.0277
 P75  H14  H  HCR5  0   0.306   -5.0995   8.5460   9.6936
 P75  H15  H  HCH2  0   0.257   -3.0731   4.6900  12.5772
 P75  H16  H  HCH2  0   0.259   -1.8407   5.4538  13.5950
 P75  H17  H  HCR6  0   0.286   -3.6991   1.2383  15.3190
 P75  H18  H  HCR6  0   0.296   -2.7570   3.1388  14.1336
 P75  H19  H  HNR6  0   0.422   -9.1143  12.7038   9.1368
 P75  H20  H  HOH1  0   0.467   -4.1334   7.3791   6.6515
 P75  H21  H  HNC2  0   0.414   -6.9257  -0.7436  16.0723
 P75  H22  H  HNC2  0   0.412   -7.5156   0.7030  15.4941
 P75  H8   H  HCR6  0   0.276   -5.7257   5.7066  15.8928
 P75  O2   O  OS    0  -0.664   -4.9217   0.0874  17.5608
 P75  O3   O  OS    0  -0.649   -6.9193   1.4966  18.0754

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
 P75  C2   C1   single    1.494  0.020  1.494
 P75  O    C    double    1.217  0.020  1.217
 P75  C1   C    single    1.448  0.020  1.448
 P75  C1   C3   double    1.346  0.020  1.346
 P75  O4   C17  single    1.405  0.020  1.405
 P75  C    N5   single    1.385  0.020  1.385
 P75  C17  C16  single    1.509  0.020  1.509
 P75  C3   N    single    1.369  0.020  1.369
 P75  N5   C18  single    1.369  0.020  1.369
 P75  O5   C16  single    1.424  0.020  1.424
 P75  O5   C4   single    1.396  0.020  1.396
 P75  N    C18  single    1.374  0.020  1.374
 P75  N    C4   single    1.478  0.020  1.478
 P75  C18  O6   double    1.215  0.020  1.215
 P75  C16  C6   single    1.531  0.020  1.531
 P75  C4   C5   single    1.528  0.020  1.528
 P75  C6   C5   single    1.522  0.020  1.522
 P75  C6   N1   single    1.445  0.020  1.445
 P75  N1   C15  aromatic  1.341  0.020  1.341
 P75  N1   N2   aromatic  1.325  0.020  1.325
 P75  C15  C7   aromatic  1.371  0.020  1.371
 P75  N2   N3   aromatic  1.286  0.020  1.286
 P75  C7   N3   aromatic  1.351  0.020  1.351
 P75  C7   C8   single    1.484  0.020  1.484
 P75  C8   O1   single    1.426  0.020  1.426
 P75  O1   C9   single    1.338  0.020  1.338
 P75  C9   C14  aromatic  1.397  0.020  1.397
 P75  C9   C10  aromatic  1.397  0.020  1.397
 P75  C14  C13  aromatic  1.385  0.020  1.385
 P75  C10  C11  aromatic  1.379  0.020  1.379
 P75  C13  C12  aromatic  1.388  0.020  1.388
 P75  C11  C12  aromatic  1.391  0.020  1.391
 P75  C12  S    single    1.764  0.020  1.764
 P75  N4   S    single    1.657  0.020  1.657
 P75  O3   S    double    1.457  0.020  1.457
 P75  S    O2   double    1.455  0.020  1.455
 P75  C2   H1   single    0.970  0.020  1.090
 P75  C2   H2   single    0.970  0.020  1.090
 P75  C2   H3   single    0.970  0.020  1.090
 P75  C3   H4   single    0.930  0.020  1.080
 P75  C4   H5   single    0.970  0.020  1.090
 P75  C5   H6   single    0.970  0.020  1.090
 P75  C5   H7   single    0.970  0.020  1.090
 P75  C10  H8   single    0.930  0.020  1.080
 P75  C11  H9   single    0.930  0.020  1.080
 P75  C15  H10  single    0.930  0.020  1.080
 P75  C16  H11  single    0.970  0.020  1.090
 P75  C17  H12  single    0.970  0.020  1.090
 P75  C17  H13  single    0.970  0.020  1.090
 P75  C6   H14  single    0.970  0.020  1.090
 P75  C8   H15  single    0.970  0.020  1.090
 P75  C8   H16  single    0.970  0.020  1.090
 P75  C13  H17  single    0.930  0.020  1.080
 P75  C14  H18  single    0.930  0.020  1.080
 P75  N5   H19  single    0.860  0.020  1.020
 P75  O4   H20  single    0.850  0.020  0.980
 P75  N4   H21  single    0.890  0.020  1.040
 P75  N4   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
 P75  C    C1   C3   118.35  3.000
 P75  C3   C1   C2   122.75  3.000
 P75  C    C1   C2   118.90  3.000
 P75  H3   C2   H2   107.17  3.000
 P75  H3   C2   H1   107.91  3.000
 P75  H2   C2   H1   107.83  3.000
 P75  H3   C2   C1   111.58  3.000
 P75  H2   C2   C1   111.33  3.000
 P75  H1   C2   C1   110.82  3.000
 P75  H4   C3   N    115.87  3.000
 P75  H4   C3   C1   120.46  3.000
 P75  N    C3   C1   123.67  3.000
 P75  H5   C4   O5   110.01  3.000
 P75  H5   C4   N    106.49  3.000
 P75  O5   C4   N    109.27  3.000
 P75  H5   C4   C5   111.89  3.000
 P75  N    C4   C5   112.29  3.000
 P75  O5   C4   C5   106.89  3.000
 P75  H7   C5   H6   108.34  3.000
 P75  H7   C5   C6   113.59  3.000
 P75  H6   C5   C6   110.48  3.000
 P75  H7   C5   C4   113.12  3.000
 P75  H6   C5   C4   109.65  3.000
 P75  C6   C5   C4   101.53  3.000
 P75  H8   C10  C9   119.43  3.000
 P75  H8   C10  C11  120.14  3.000
 P75  C9   C10  C11  120.43  3.000
 P75  H9   C11  C12  120.90  3.000
 P75  H9   C11  C10  119.43  3.000
 P75  C12  C11  C10  119.67  3.000
 P75  H10  C15  N1   123.12  3.000
 P75  H10  C15  C7   132.73  3.000
 P75  N1   C15  C7   104.15  3.000
 P75  H11  C16  O5   109.54  3.000
 P75  H11  C16  C6   109.13  3.000
 P75  O5   C16  C6   103.56  3.000
 P75  H11  C16  C17  107.37  3.000
 P75  C6   C16  C17  116.25  3.000
 P75  O5   C16  C17  110.87  3.000
 P75  H13  C17  H12  106.67  3.000
 P75  H13  C17  O4   112.12  3.000
 P75  H12  C17  O4   112.08  3.000
 P75  H13  C17  C16  108.55  3.000
 P75  H12  C17  C16  107.25  3.000
 P75  O4   C17  C16  109.97  3.000
 P75  N    C18  N5   114.63  3.000
 P75  N    C18  O6   122.85  3.000
 P75  N5   C18  O6   122.52  3.000
 P75  C9   O1   C8   120.02  3.000
 P75  H14  C6   N1   105.81  3.000
 P75  H14  C6   C16  110.48  3.000
 P75  N1   C6   C16  113.84  3.000
 P75  H14  C6   C5   110.49  3.000
 P75  N1   C6   C5   114.72  3.000
 P75  C16  C6   C5   101.58  3.000
 P75  N3   C7   C8   123.82  3.000
 P75  C8   C7   C15  128.36  3.000
 P75  N3   C7   C15  107.77  3.000
 P75  H16  C8   H15  108.22  3.000
 P75  H16  C8   C7   110.73  3.000
 P75  H15  C8   C7   109.62  3.000
 P75  H16  C8   O1   110.49  3.000
 P75  H15  C8   O1   110.56  3.000
 P75  C7   C8   O1   107.23  3.000
 P75  C14  C9   O1   124.72  3.000
 P75  C14  C9   C10  119.63  3.000
 P75  O1   C9   C10  115.65  3.000
 P75  H17  C13  C12  120.90  3.000
 P75  H17  C13  C14  118.97  3.000
 P75  C12  C13  C14  120.13  3.000
 P75  H18  C14  C13  118.75  3.000
 P75  H18  C14  C9   121.53  3.000
 P75  C13  C14  C9   119.72  3.000
 P75  S    C12  C13  120.01  3.000
 P75  S    C12  C11  119.60  3.000
 P75  C13  C12  C11  120.38  3.000
 P75  N2   N1   C6   121.68  3.000
 P75  N2   N1   C15  110.91  3.000
 P75  C6   N1   C15  127.41  3.000
 P75  H19  N5   C    116.86  3.000
 P75  H19  N5   C18  115.33  3.000
 P75  C    N5   C18  127.80  3.000
 P75  O    C    N5   120.50  3.000
 P75  N5   C    C1   114.24  3.000
 P75  O    C    C1   125.27  3.000
 P75  C18  N    C4   116.36  3.000
 P75  C4   N    C3   122.26  3.000
 P75  C18  N    C3   121.27  3.000
 P75  C16  O5   C4   111.50  3.000
 P75  H20  O4   C17  108.90  3.000
 P75  N2   N3   C7   109.28  3.000
 P75  N3   N2   N1   107.90  3.000
 P75  N4   S    O3   112.76  3.000
 P75  O3   S    C12  107.73  3.000
 P75  N4   S    C12  101.02  3.000
 P75  O3   S    O2   118.12  3.000
 P75  N4   S    O2   105.38  3.000
 P75  C12  S    O2   110.52  3.000
 P75  H22  N4   H21  110.15  3.000
 P75  H22  N4   S    112.62  3.000
 P75  H21  N4   S    111.23  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
 P75  CONST_01  C13  C14  C9   C10    0.00   0.0  0
 P75  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 P75  CONST_03  C14  C9   C10  C11    0.00   0.0  0
 P75  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 P75  CONST_05  N3   N2   N1   C15    0.00   0.0  0
 P75  CONST_06  N2   N3   C7   C15    0.00   0.0  0
 P75  CONST_07  N2   N1   C15  C7     0.00   0.0  0
 P75  CONST_08  N1   N2   N3   C7     0.00   0.0  0
 P75  CONST_09  C12  C13  C14  C9     0.00   0.0  0
 P75  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 P75  CONST_11  N3   C7   C15  N1     0.00   0.0  0
 P75  CONST_12  C7   C15  N1   C6   180.00   0.0  0
 P75  CONST_13  N3   N2   N1   C6   180.00   0.0  0
 P75  CONST_14  N5   C18  N    C3     0.00   0.0  0
 P75  CONST_15  N5   C18  N    C4   180.00   0.0  0
 P75  CONST_16  N    C18  N5   C      0.00   0.0  0
 P75  CONST_17  S    C12  C11  C10  180.00   0.0  0
 P75  CONST_18  O1   C9   C10  C11  180.00   0.0  0
 P75  CONST_19  C13  C14  C9   O1   180.00   0.0  0
 P75  CONST_20  N1   C15  C7   C8   180.00   0.0  0
 P75  CONST_21  N2   N3   C7   C8   180.00   0.0  0
 P75  CONST_22  S    C12  C13  C14  180.00   0.0  0
 P75  CONST_23  O6   C18  N    C3   180.00   0.0  0
 P75  CONST_24  O6   C18  N    C4     0.00   0.0  0
 P75  CONST_25  C    N5   C18  O6   180.00   0.0  0
 P75  CONST_26  H18  C14  C9   C10  180.00   0.0  0
 P75  CONST_27  H17  C13  C12  C11  180.00   0.0  0
 P75  CONST_28  H10  C15  N1   C6     0.00   0.0  0
 P75  CONST_29  H9   C11  C10  C9   180.00   0.0  0
 P75  CONST_30  H8   C10  C9   C14  180.00   0.0  0
 P75  CONST_31  H19  N5   C18  N    180.00   0.0  0
 P75  Var_01    N4   S    C12  C11  107.03  30.0  2
 P75  Var_02    O1   C8   C7   C15  -82.05  30.0  2
 P75  Var_03    C14  C9   O1   C8    10.67  30.0  2
 P75  Var_04    H1   C2   C1   C3     1.16  30.0  3
 P75  Var_05    H21  N4   S    C12  163.72  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
 P75  chir_01  C4   O5  N   C5   negativ
 P75  chir_02  C16  O5  C6  C17  negativ
 P75  chir_03  C6   N1  C5  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
 P75  plan-1  C15  0.020
 P75  plan-1  C6   0.020
 P75  plan-1  C7   0.020
 P75  plan-1  C8   0.020
 P75  plan-1  N1   0.020
 P75  plan-1  N3   0.020
 P75  plan-1  N2   0.020
 P75  plan-1  H10  0.020
 P75  plan-2  C1   0.020
 P75  plan-2  C2   0.020
 P75  plan-2  C3   0.020
 P75  plan-2  C4   0.020
 P75  plan-2  C18  0.020
 P75  plan-2  O6   0.020
 P75  plan-2  N5   0.020
 P75  plan-2  C    0.020
 P75  plan-2  O    0.020
 P75  plan-2  N    0.020
 P75  plan-2  H4   0.020
 P75  plan-2  H19  0.020
 P75  plan-3  C10  0.020
 P75  plan-3  C11  0.020
 P75  plan-3  O1   0.020
 P75  plan-3  C9   0.020
 P75  plan-3  C13  0.020
 P75  plan-3  C14  0.020
 P75  plan-3  C12  0.020
 P75  plan-3  S    0.020
 P75  plan-3  H9   0.020
 P75  plan-3  H17  0.020
 P75  plan-3  H18  0.020
 P75  plan-3  H8   0.020

