# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 05:37:38 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC(=O)NC1=CC(=O)N(C)C=C1)[S](=O)(=O)c2cc(C)cc3cn[nH]c23
#
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
 WPM  WPM  N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide  ligand  46  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WPM
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
 WPM  C1   C  CR6   0   0.564   4.9134  25.2686  11.6400
 WPM  C10  C  CR56  0   0.093  -4.2612  30.5544  10.5243
 WPM  C11  C  CR16  0  -0.391  -5.2669  30.4401  11.4891
 WPM  C12  C  CR6   0   0.176  -5.5950  29.1974  11.9913
 WPM  C13  C  CR16  0  -0.297  -4.9007  28.0640  11.5242
 WPM  C14  C  CR6   0  -0.212  -3.8983  28.1520  10.5813
 WPM  C15  C  CR15  0  -0.144  -3.6868  31.6257   9.7878
 WPM  C16  C  CH3   0  -0.539   7.2328  26.0098  11.6508
 WPM  C2   C  CR16  0   0.025   5.4067  27.5935  11.3425
 WPM  C3   C  CR16  0  -0.461   4.1009  27.9293  11.2365
 WPM  C4   C  CR6   0   0.355   3.1192  26.9053  11.3311
 WPM  C5   C  CR16  0  -0.418   3.5255  25.6129  11.5271
 WPM  C6   C  C     0   0.513   0.6736  26.5619  11.1707
 WPM  C7   C  CH2   0  -0.441  -0.5950  27.3923  11.0047
 WPM  C9   C  CR56  0   0.368  -3.5785  29.4168  10.0613
 WPM  N1   N  NR6   0  -0.447   5.8168  26.3202  11.5363
 WPM  N2   N  NH1   0  -0.672   1.8004  27.3259  11.2305
 WPM  N3   N  N     0  -0.520  -1.7539  26.5404  11.1586
 WPM  N4   N  NR15  0  -0.541  -2.7000  29.8610   9.1355
 WPM  N5   N  N     0  -0.222  -2.7675  31.1853   8.9713
 WPM  O3   O  O     0  -0.433   0.6588  25.3542  11.2298
 WPM  O4   O  O     0  -0.574   5.3284  24.1255  11.8225
 WPM  S1   S  S     0   1.302  -3.0134  26.7102  10.1019
 WPM  H1   H  HCR6  0   0.252  -5.7860  31.3240  11.8384
 WPM  H2   H  HCR6  0   0.266  -5.1807  27.0940  11.9174
 WPM  H3   H  HCR5  0   0.285  -3.9257  32.6768   9.8407
 WPM  H4   H  HCH3  0   0.237   7.8078  26.9167  11.4903
 WPM  H5   H  HCH3  0   0.278   7.4621  25.6190  12.6404
 WPM  H6   H  HCH3  0   0.278   7.5248  25.2713  10.9077
 WPM  H7   H  HCH3  0   0.241  -7.4586  28.3557  12.6623
 WPM  H8   H  HCH3  0   0.230  -6.2783  28.5925  13.9409
 WPM  H9   H  HCH3  0   0.302  -7.1367  29.9774  13.2705
 WPM  H10  H  HCR6  0   0.300   6.1845  28.3397  11.2726
 WPM  H11  H  HCR6  0   0.286   3.8271  28.9604  11.0761
 WPM  H12  H  HCR6  0   0.294   2.8301  24.7962  11.6128
 WPM  H13  H  HCH2  0   0.278  -0.5996  28.2191  11.7245
 WPM  H14  H  HCH2  0   0.306  -0.5625  27.8412  10.0106
 WPM  H15  H  HCH3  0   0.268  -1.2038  25.8812  13.0493
 WPM  H16  H  HCH3  0   0.280  -2.4887  27.0967  13.0782
 WPM  H17  H  HCH3  0   0.233  -2.8277  25.4217  12.5836
 WPM  H18  H  HNH1  0   0.433   1.6731  28.3275  11.1537
 WPM  H19  H  HNR5  0   0.400  -2.0800  29.3205   8.5562
 WPM  C17  C  CH3   0  -0.787  -6.6739  29.0241  13.0202
 WPM  C8   C  CH3   0  -0.523  -2.1004  26.2266  12.5409
 WPM  O1   O  OS    0  -0.523  -2.4406  26.9629   8.7870
 WPM  O2   O  OS    0  -0.695  -3.8662  25.5545  10.3079

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
 WPM  N5   N4   aromatic  1.336  0.020  1.336
 WPM  N5   C15  aromatic  1.306  0.020  1.306
 WPM  O1   S1   double    1.456  0.020  1.456
 WPM  N4   C9   aromatic  1.351  0.020  1.351
 WPM  C15  C10  aromatic  1.421  0.020  1.421
 WPM  C9   C10  aromatic  1.405  0.020  1.405
 WPM  C9   C14  aromatic  1.404  0.020  1.404
 WPM  S1   O2   double    1.451  0.020  1.451
 WPM  S1   C14  single    1.758  0.020  1.758
 WPM  S1   N3   single    1.653  0.020  1.653
 WPM  C10  C11  aromatic  1.398  0.020  1.398
 WPM  C14  C13  aromatic  1.379  0.020  1.379
 WPM  O3   C6   double    1.209  0.020  1.209
 WPM  C11  C12  aromatic  1.380  0.020  1.380
 WPM  C6   C7   single    1.525  0.020  1.525
 WPM  C6   N2   single    1.363  0.020  1.363
 WPM  O4   C1   double    1.230  0.020  1.230
 WPM  C16  N1   single    1.454  0.020  1.454
 WPM  C1   N1   single    1.390  0.020  1.390
 WPM  C1   C5   single    1.434  0.020  1.434
 WPM  N1   C2   single    1.352  0.020  1.352
 WPM  C7   N3   single    1.447  0.020  1.447
 WPM  C5   C4   double    1.369  0.020  1.369
 WPM  C2   C3   double    1.352  0.020  1.352
 WPM  C4   C3   single    1.422  0.020  1.422
 WPM  C4   N2   single    1.388  0.020  1.388
 WPM  C13  C12  aromatic  1.409  0.020  1.409
 WPM  N3   C8   single    1.459  0.020  1.459
 WPM  C12  C17  single    1.501  0.020  1.501
 WPM  C11  H1   single    0.930  0.020  1.080
 WPM  C13  H2   single    0.930  0.020  1.080
 WPM  C15  H3   single    0.930  0.020  1.080
 WPM  C16  H4   single    0.970  0.020  1.090
 WPM  C16  H5   single    0.970  0.020  1.090
 WPM  C16  H6   single    0.970  0.020  1.090
 WPM  C17  H7   single    0.970  0.020  1.090
 WPM  C17  H8   single    0.970  0.020  1.090
 WPM  C17  H9   single    0.970  0.020  1.090
 WPM  C2   H10  single    0.930  0.020  1.080
 WPM  C3   H11  single    0.930  0.020  1.080
 WPM  C5   H12  single    0.930  0.020  1.080
 WPM  C7   H13  single    0.970  0.020  1.090
 WPM  C7   H14  single    0.970  0.020  1.090
 WPM  C8   H15  single    0.970  0.020  1.090
 WPM  C8   H16  single    0.970  0.020  1.090
 WPM  C8   H17  single    0.970  0.020  1.090
 WPM  N2   H18  single    0.860  0.020  1.020
 WPM  N4   H19  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
 WPM  O4   C1   N1   119.67  3.000
 WPM  N1   C1   C5   116.18  3.000
 WPM  O4   C1   C5   124.15  3.000
 WPM  C9   C10  C15  104.07  3.000
 WPM  C9   C10  C11  120.70  3.000
 WPM  C15  C10  C11  135.22  3.000
 WPM  H1   C11  C12  120.24  3.000
 WPM  H1   C11  C10  120.04  3.000
 WPM  C12  C11  C10  119.72  3.000
 WPM  C17  C12  C13  119.26  3.000
 WPM  C17  C12  C11  121.62  3.000
 WPM  C13  C12  C11  119.12  3.000
 WPM  H2   C13  C14  119.54  3.000
 WPM  H2   C13  C12  118.20  3.000
 WPM  C14  C13  C12  122.25  3.000
 WPM  S1   C14  C9   121.53  3.000
 WPM  S1   C14  C13  119.99  3.000
 WPM  C9   C14  C13  118.43  3.000
 WPM  H3   C15  N5   120.99  3.000
 WPM  H3   C15  C10  128.26  3.000
 WPM  N5   C15  C10  110.75  3.000
 WPM  H6   C16  H5   108.72  3.000
 WPM  H6   C16  H4   108.90  3.000
 WPM  H5   C16  H4   108.83  3.000
 WPM  H6   C16  N1   110.65  3.000
 WPM  H5   C16  N1   110.69  3.000
 WPM  H4   C16  N1   109.01  3.000
 WPM  H10  C2   N1   116.20  3.000
 WPM  H10  C2   C3   121.24  3.000
 WPM  N1   C2   C3   122.55  3.000
 WPM  H11  C3   C4   121.54  3.000
 WPM  H11  C3   C2   119.60  3.000
 WPM  C4   C3   C2   118.85  3.000
 WPM  N2   C4   C5   125.35  3.000
 WPM  N2   C4   C3   115.66  3.000
 WPM  C5   C4   C3   118.99  3.000
 WPM  H12  C5   C4   122.42  3.000
 WPM  H12  C5   C1   115.90  3.000
 WPM  C4   C5   C1   121.68  3.000
 WPM  O3   C6   N2   124.61  3.000
 WPM  N2   C6   C7   112.79  3.000
 WPM  O3   C6   C7   122.60  3.000
 WPM  H14  C7   H13  106.74  3.000
 WPM  H14  C7   N3   111.28  3.000
 WPM  H13  C7   N3   111.78  3.000
 WPM  H14  C7   C6   107.36  3.000
 WPM  H13  C7   C6   110.04  3.000
 WPM  N3   C7   C6   109.52  3.000
 WPM  N4   C9   C14  134.24  3.000
 WPM  C14  C9   C10  119.77  3.000
 WPM  N4   C9   C10  105.99  3.000
 WPM  C2   N1   C16  120.52  3.000
 WPM  C2   N1   C1   121.75  3.000
 WPM  C16  N1   C1   117.73  3.000
 WPM  H18  N2   C6   116.57  3.000
 WPM  H18  N2   C4   115.13  3.000
 WPM  C6   N2   C4   128.25  3.000
 WPM  S1   N3   C8   116.53  3.000
 WPM  C8   N3   C7   114.68  3.000
 WPM  S1   N3   C7   118.82  3.000
 WPM  H19  N4   N5   119.53  3.000
 WPM  H19  N4   C9   128.21  3.000
 WPM  N5   N4   C9   112.15  3.000
 WPM  N4   N5   C15  107.04  3.000
 WPM  O2   S1   O1   119.84  3.000
 WPM  O2   S1   N3   105.98  3.000
 WPM  O1   S1   N3   107.18  3.000
 WPM  N3   S1   C14  107.06  3.000
 WPM  O2   S1   C14  108.58  3.000
 WPM  O1   S1   C14  107.56  3.000
 WPM  H9   C17  H8   107.85  3.000
 WPM  H9   C17  H7   107.83  3.000
 WPM  H8   C17  H7   107.17  3.000
 WPM  H9   C17  C12  111.23  3.000
 WPM  H8   C17  C12  111.31  3.000
 WPM  H7   C17  C12  111.27  3.000
 WPM  H17  C8   H16  109.43  3.000
 WPM  H17  C8   H15  107.37  3.000
 WPM  H16  C8   H15  108.41  3.000
 WPM  H17  C8   N3   110.84  3.000
 WPM  H16  C8   N3   112.25  3.000
 WPM  H15  C8   N3   108.39  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
 WPM  CONST_01  N4   N5   C15  C10     0.00   0.0  0
 WPM  CONST_02  N5   N4   C9   C10     0.00   0.0  0
 WPM  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 WPM  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 WPM  CONST_05  N5   C15  C10  C11   180.00   0.0  0
 WPM  CONST_06  N4   C9   C10  C11   180.00   0.0  0
 WPM  CONST_07  C14  C9   C10  C11     0.00   0.0  0
 WPM  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 WPM  CONST_09  C15  C10  C11  C12   180.00   0.0  0
 WPM  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 WPM  CONST_11  C9   C14  C13  C12     0.00   0.0  0
 WPM  CONST_12  N4   C9   C14  C13   180.00   0.0  0
 WPM  CONST_13  N5   N4   C9   C14   180.00   0.0  0
 WPM  CONST_14  C15  C10  C9   C14   180.00   0.0  0
 WPM  CONST_15  C9   N4   N5   C15     0.00   0.0  0
 WPM  CONST_16  N4   C9   C10  C15     0.00   0.0  0
 WPM  CONST_17  N5   C15  C10  C9      0.00   0.0  0
 WPM  CONST_18  C5   C1   N1   C2      0.00   0.0  0
 WPM  CONST_19  S1   C14  C9   C10   180.00   0.0  0
 WPM  CONST_20  C17  C12  C11  C10   180.00   0.0  0
 WPM  CONST_21  S1   C14  C13  C12   180.00   0.0  0
 WPM  CONST_22  C17  C12  C13  C14   180.00   0.0  0
 WPM  CONST_23  S1   C14  C9   N4      0.00   0.0  0
 WPM  CONST_24  C5   C1   N1   C16   180.00   0.0  0
 WPM  CONST_25  O4   C1   N1   C2    180.00   0.0  0
 WPM  CONST_26  H19  N4   C9   C10   180.00   0.0  0
 WPM  CONST_27  H3   C15  C10  C11     0.00   0.0  0
 WPM  CONST_28  H2   C13  C12  C11   180.00   0.0  0
 WPM  CONST_29  H1   C11  C12  C13   180.00   0.0  0
 WPM  CONST_30  O4   C1   N1   C16     0.00   0.0  0
 WPM  CONST_31  O3   C6   N2   C4      0.00   0.0  0
 WPM  CONST_32  C7   C6   N2   C4    180.00   0.0  0
 WPM  CONST_33  H18  N2   C6   C7      0.00   0.0  0
 WPM  Var_01    O1   S1   C14  C13   157.61  30.0  2
 WPM  Var_02    C6   N2   C4   C3    173.82  30.0  2
 WPM  Var_03    H4   C16  N1   C1    176.64  30.0  3
 WPM  Var_04    H7   C17  C12  C11   121.37  30.0  2
 WPM  Var_05    C7   N3   S1   C14   -76.73  30.0  3
 WPM  Var_06    S1   N3   C7   C6   -136.43  30.0  3
 WPM  Var_07    N3   C7   C6   N2   -171.13  30.0  3
 WPM  Var_08    H15  C8   N3   C7    -49.88  30.0  3

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
 WPM  plan-1  C1   0.020
 WPM  plan-1  C16  0.020
 WPM  plan-1  C2   0.020
 WPM  plan-1  C3   0.020
 WPM  plan-1  C4   0.020
 WPM  plan-1  C5   0.020
 WPM  plan-1  N1   0.020
 WPM  plan-1  N2   0.020
 WPM  plan-1  O4   0.020
 WPM  plan-1  H10  0.020
 WPM  plan-1  H11  0.020
 WPM  plan-1  H12  0.020
 WPM  plan-2  C10  0.020
 WPM  plan-2  C11  0.020
 WPM  plan-2  C12  0.020
 WPM  plan-2  C13  0.020
 WPM  plan-2  C14  0.020
 WPM  plan-2  C15  0.020
 WPM  plan-2  C9   0.020
 WPM  plan-2  N4   0.020
 WPM  plan-2  N5   0.020
 WPM  plan-2  S1   0.020
 WPM  plan-2  H1   0.020
 WPM  plan-2  H2   0.020
 WPM  plan-2  H3   0.020
 WPM  plan-2  H19  0.020
 WPM  plan-2  C17  0.020
 WPM  plan-3  C4   0.020
 WPM  plan-3  C6   0.020
 WPM  plan-3  C7   0.020
 WPM  plan-3  N2   0.020
 WPM  plan-3  O3   0.020
 WPM  plan-3  H18  0.020

