# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 04:42:07 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: N-({(3S)-1-[6-tert-butyl-5-methoxy-8-(2-oxo-1,2-dihydropyridin-3-yl)quinolin-3-yl]pyrrolidin-3-yl}methyl)methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c2cc(cnc2c(cc1C(C)(C)C)C3=CC=CNC3=O)N4CC[C@H](CN[S](C)(=O)=O)C4
#
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
 28M  28M  N-({(3S)-1-[6-tert-butyl-5-methoxy-8-(2-oxo-1,2-dihydropyridin-3-yl)quinolin-3-yl]pyrrolidin-3-yl}methyl)methanesulfonamide  ligand  66  34  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_28M
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
 28M  C1   C  CR6   0   0.096   3.6633  -0.1614   0.0004
 28M  C2   C  CR16  0  -0.393   4.1264   1.1173   0.1925
 28M  C3   C  CR6   0   0.078   3.2931   2.2538   0.3151
 28M  C4   C  CR6   0   0.231   1.9306   2.0443   0.2068
 28M  C5   C  CR66  0   0.072   1.3907   0.7328   0.0949
 28M  C6   C  CR66  0   0.106   2.2623  -0.3743  -0.0377
 28M  N7   N  N     0  -0.405   1.7756  -1.6254  -0.1960
 28M  C8   C  CR16  0  -0.164   0.4933  -1.8313  -0.1720
 28M  C9   C  CR6   0   0.344  -0.4796  -0.8057   0.0335
 28M  C10  C  CR16  0  -0.348   0.0030   0.4841   0.1432
 28M  N11  N  NR5   0  -0.540  -1.8025  -1.1185   0.1255
 28M  C12  C  CH2   0  -0.278  -2.3291  -2.4026  -0.3124
 28M  C13  C  CH2   0  -0.496  -3.8527  -2.2373  -0.2696
 28M  C14  C  CR15  0  -0.272  -4.1085  -0.8740   0.3872
 28M  C15  C  CH2   0  -0.266  -2.8219  -0.0958   0.1423
 28M  C16  C  CH2   0  -0.287  -5.3270  -0.1501  -0.1575
 28M  N17  N  NC1   0  -0.745  -6.5392  -0.8806   0.2028
 28M  S18  S  S     0   1.341  -7.9898  -0.1053   0.2369
 28M  O19  O  OS    0  -0.673  -8.9704  -1.0911   0.6656
 28M  O20  O  OS    0  -0.674  -7.8102   1.1092   1.0193
 28M  C21  C  CH3   0  -0.797  -8.3723   0.3713  -1.4335
 28M  O22  O  O2    0  -0.488   1.0484   3.0837   0.2594
 28M  C23  C  CH3   0  -0.428   0.4800   3.4422  -0.9963
 28M  C24  C  CT    0  -0.143   3.9067   3.6245   0.6326
 28M  C25  C  CH3   0  -0.651   3.5502   4.6870  -0.4167
 28M  C26  C  CH3   0  -0.637   3.4227   4.0768   2.0191
 28M  C27  C  CH3   0  -0.678   5.4380   3.5597   0.6918
 28M  C28  C  CR6   0  -0.195   4.6115  -1.2836  -0.1298
 28M  C29  C  CR6   0   0.512   5.6260  -1.2068  -1.1626
 28M  O30  O  O     0  -0.495   5.7723  -0.2846  -1.9607
 28M  N31  N  NR16  0  -0.653   6.4698  -2.2991  -1.2106
 28M  C33  C  CR16  0   0.046   6.4126  -3.3790  -0.4017
 28M  C34  C  CR16  0  -0.389   5.4645  -3.4551   0.5648
 28M  C35  C  CR16  0  -0.140   4.5564  -2.3792   0.6852
 28M  H1   H  HCR6  0   0.249   5.1949   1.2518   0.2547
 28M  H2   H  HCR6  0   0.270   0.1716  -2.8580  -0.3112
 28M  H3   H  HCR6  0   0.275  -0.6786   1.3078   0.2968
 28M  H4   H  HCH2  0   0.237  -1.9931  -2.6446  -1.3263
 28M  H5   H  HCH2  0   0.244  -1.9891  -3.2097   0.3408
 28M  H6   H  HCH2  0   0.248  -4.2603  -2.2608  -1.2828
 28M  H7   H  HCH2  0   0.263  -4.3245  -3.0463   0.2867
 28M  H8   H  HCR5  0   0.266  -4.2406  -1.0020   1.4647
 28M  H9   H  HCH2  0   0.255  -2.6423   0.6319   0.9368
 28M  H10  H  HCH2  0   0.225  -2.8557   0.4612  -0.8069
 28M  H11  H  HCH2  0   0.271  -5.3874   0.8479   0.2764
 28M  H12  H  HCH2  0   0.242  -5.2310  -0.0351  -1.2431
 28M  H13  H  HNC1  0   0.417  -6.6169  -1.7987  -0.2221
 28M  H14  H  HCH3  0   0.292  -8.4268  -0.5190  -2.0555
 28M  H15  H  HCH3  0   0.304  -9.3346   0.8810  -1.4271
 28M  H16  H  HCH3  0   0.291  -7.6040   1.0452  -1.8067
 28M  H17  H  HCH3  0   0.229   1.2515   3.6936  -1.7272
 28M  H18  H  HCH3  0   0.228  -0.1400   2.6446  -1.4123
 28M  H19  H  HCH3  0   0.244  -0.1445   4.3168  -0.8258
 28M  H20  H  HCH3  0   0.225   3.7794   4.3422  -1.4268
 28M  H21  H  HCH3  0   0.246   2.5049   4.9812  -0.3823
 28M  H22  H  HCH3  0   0.228   4.1388   5.5887  -0.2342
 28M  H23  H  HCH3  0   0.223   3.8816   5.0326   2.2807
 28M  H24  H  HCH3  0   0.237   2.3424   4.2043   2.0607
 28M  H25  H  HCH3  0   0.223   3.7096   3.3523   2.7837
 28M  H26  H  HCH3  0   0.232   5.7987   2.8767   1.4626
 28M  H27  H  HCH3  0   0.232   5.8820   3.2666  -0.2617
 28M  H28  H  HCH3  0   0.241   5.8249   4.5501   0.9362
 28M  H29  H  HNR6  0   0.421   7.1848  -2.2740  -1.9248
 28M  H30  H  HCR6  0   0.310   7.1524  -4.1452  -0.5796
 28M  H31  H  HCR6  0   0.275   5.4128  -4.3120   1.2183
 28M  H32  H  HCR6  0   0.266   3.8011  -2.4237   1.4588

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
 28M  C25  C24  single    1.535  0.020  1.535
 28M  C34  C33  double    1.356  0.020  1.356
 28M  C34  C35  single    1.413  0.020  1.413
 28M  C33  N31  single    1.350  0.020  1.350
 28M  C35  C28  double    1.367  0.020  1.367
 28M  C24  C27  single    1.534  0.020  1.534
 28M  C24  C26  single    1.537  0.020  1.537
 28M  C24  C3   single    1.535  0.020  1.535
 28M  N31  C29  single    1.381  0.020  1.381
 28M  C2   C3   aromatic  1.415  0.020  1.415
 28M  C2   C1   aromatic  1.373  0.020  1.373
 28M  C28  C29  single    1.450  0.020  1.450
 28M  C28  C1   single    1.475  0.020  1.475
 28M  C29  O30  double    1.228  0.020  1.228
 28M  C3   C4   aromatic  1.383  0.020  1.383
 28M  C1   C6   aromatic  1.418  0.020  1.418
 28M  C4   O22  single    1.364  0.020  1.364
 28M  C4   C5   aromatic  1.423  0.020  1.423
 28M  C6   C5   aromatic  1.415  0.020  1.415
 28M  C6   N7   aromatic  1.352  0.020  1.352
 28M  O22  C23  single    1.424  0.020  1.424
 28M  C5   C10  aromatic  1.411  0.020  1.411
 28M  N7   C8   aromatic  1.299  0.020  1.299
 28M  C10  C9   aromatic  1.381  0.020  1.381
 28M  C8   C9   aromatic  1.428  0.020  1.428
 28M  C9   N11  single    1.363  0.020  1.363
 28M  N11  C12  single    1.455  0.020  1.455
 28M  N11  C15  single    1.444  0.020  1.444
 28M  C12  C13  single    1.533  0.020  1.533
 28M  C15  C14  single    1.523  0.020  1.523
 28M  C13  C14  single    1.535  0.020  1.535
 28M  C14  C16  single    1.518  0.020  1.518
 28M  C16  N17  single    1.460  0.020  1.460
 28M  N17  S18  single    1.645  0.020  1.645
 28M  O20  S18  double    1.456  0.020  1.456
 28M  S18  C21  single    1.779  0.020  1.779
 28M  S18  O19  double    1.455  0.020  1.455
 28M  C2   H1   single    0.930  0.020  1.080
 28M  C8   H2   single    0.930  0.020  1.080
 28M  C10  H3   single    0.930  0.020  1.080
 28M  C12  H4   single    0.970  0.020  1.090
 28M  C12  H5   single    0.970  0.020  1.090
 28M  C13  H6   single    0.970  0.020  1.090
 28M  C13  H7   single    0.970  0.020  1.090
 28M  C14  H8   single    0.970  0.020  1.090
 28M  C15  H9   single    0.970  0.020  1.090
 28M  C15  H10  single    0.970  0.020  1.090
 28M  C16  H11  single    0.970  0.020  1.090
 28M  C16  H12  single    0.970  0.020  1.090
 28M  N17  H13  single    0.890  0.020  1.040
 28M  C21  H14  single    0.970  0.020  1.090
 28M  C21  H15  single    0.970  0.020  1.090
 28M  C21  H16  single    0.970  0.020  1.090
 28M  C23  H17  single    0.970  0.020  1.090
 28M  C23  H18  single    0.970  0.020  1.090
 28M  C23  H19  single    0.970  0.020  1.090
 28M  C25  H20  single    0.970  0.020  1.090
 28M  C25  H21  single    0.970  0.020  1.090
 28M  C25  H22  single    0.970  0.020  1.090
 28M  C26  H23  single    0.970  0.020  1.090
 28M  C26  H24  single    0.970  0.020  1.090
 28M  C26  H25  single    0.970  0.020  1.090
 28M  C27  H26  single    0.970  0.020  1.090
 28M  C27  H27  single    0.970  0.020  1.090
 28M  C27  H28  single    0.970  0.020  1.090
 28M  N31  H29  single    0.860  0.020  1.020
 28M  C33  H30  single    0.930  0.020  1.080
 28M  C34  H31  single    0.930  0.020  1.080
 28M  C35  H32  single    0.930  0.020  1.080

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
 28M  C28  C1   C6   121.24  3.000
 28M  C6   C1   C2   118.48  3.000
 28M  C28  C1   C2   120.26  3.000
 28M  H1   C2   C3   118.57  3.000
 28M  H1   C2   C1   117.27  3.000
 28M  C3   C2   C1   124.16  3.000
 28M  C24  C3   C4   123.05  3.000
 28M  C4   C3   C2   116.86  3.000
 28M  C24  C3   C2   119.99  3.000
 28M  O22  C4   C5   117.39  3.000
 28M  C5   C4   C3   121.31  3.000
 28M  O22  C4   C3   121.24  3.000
 28M  C10  C5   C6   118.11  3.000
 28M  C10  C5   C4   122.21  3.000
 28M  C6   C5   C4   119.66  3.000
 28M  N7   C6   C5   120.88  3.000
 28M  N7   C6   C1   119.87  3.000
 28M  C5   C6   C1   119.25  3.000
 28M  C8   N7   C6   119.99  3.000
 28M  H2   C8   C9   119.73  3.000
 28M  H2   C8   N7   116.12  3.000
 28M  C9   C8   N7   124.14  3.000
 28M  N11  C9   C10  123.24  3.000
 28M  N11  C9   C8   120.41  3.000
 28M  C10  C9   C8   116.35  3.000
 28M  H3   C10  C9   120.19  3.000
 28M  H3   C10  C5   119.42  3.000
 28M  C9   C10  C5   120.37  3.000
 28M  C15  N11  C12  111.89  3.000
 28M  C15  N11  C9   121.57  3.000
 28M  C12  N11  C9   122.25  3.000
 28M  H5   C12  H4   107.15  3.000
 28M  H5   C12  C13  111.85  3.000
 28M  H4   C12  C13  110.77  3.000
 28M  H5   C12  N11  111.05  3.000
 28M  H4   C12  N11  111.25  3.000
 28M  C13  C12  N11  104.83  3.000
 28M  H7   C13  H6   107.22  3.000
 28M  H7   C13  C14  111.65  3.000
 28M  H6   C13  C14  110.72  3.000
 28M  H7   C13  C12  111.38  3.000
 28M  H6   C13  C12  110.03  3.000
 28M  C14  C13  C12  105.87  3.000
 28M  H8   C14  C16  108.20  3.000
 28M  H8   C14  C15  108.68  3.000
 28M  C16  C14  C15  112.12  3.000
 28M  H8   C14  C13  109.75  3.000
 28M  C16  C14  C13  113.81  3.000
 28M  C15  C14  C13  104.14  3.000
 28M  H10  C15  H9   107.17  3.000
 28M  H10  C15  C14  111.79  3.000
 28M  H9   C15  C14  111.24  3.000
 28M  H10  C15  N11  111.71  3.000
 28M  H9   C15  N11  111.35  3.000
 28M  C14  C15  N11  103.67  3.000
 28M  H12  C16  H11  107.64  3.000
 28M  H12  C16  N17  111.69  3.000
 28M  H11  C16  N17  108.29  3.000
 28M  H12  C16  C14  109.57  3.000
 28M  H11  C16  C14  109.77  3.000
 28M  N17  C16  C14  109.83  3.000
 28M  H13  N17  S18  111.56  3.000
 28M  H13  N17  C16  114.39  3.000
 28M  S18  N17  C16  120.09  3.000
 28M  C21  S18  O20  107.92  3.000
 28M  C21  S18  O19  108.26  3.000
 28M  O20  S18  O19  119.35  3.000
 28M  O19  S18  N17  106.32  3.000
 28M  C21  S18  N17  107.24  3.000
 28M  O20  S18  N17  107.19  3.000
 28M  H16  C21  H15  109.65  3.000
 28M  H16  C21  H14  110.26  3.000
 28M  H15  C21  H14  110.02  3.000
 28M  H16  C21  S18  109.65  3.000
 28M  H15  C21  S18  108.05  3.000
 28M  H14  C21  S18  109.18  3.000
 28M  C23  O22  C4   114.57  3.000
 28M  H19  C23  H18  108.71  3.000
 28M  H19  C23  H17  108.98  3.000
 28M  H18  C23  H17  108.31  3.000
 28M  H19  C23  O22  107.05  3.000
 28M  H18  C23  O22  112.24  3.000
 28M  H17  C23  O22  111.47  3.000
 28M  C27  C24  C26  106.98  3.000
 28M  C26  C24  C25  109.87  3.000
 28M  C27  C24  C25  106.70  3.000
 28M  C26  C24  C3   108.88  3.000
 28M  C27  C24  C3   111.68  3.000
 28M  C25  C24  C3   112.57  3.000
 28M  H22  C25  H21  106.84  3.000
 28M  H22  C25  H20  107.59  3.000
 28M  H21  C25  H20  108.47  3.000
 28M  H22  C25  C24  109.39  3.000
 28M  H21  C25  C24  112.91  3.000
 28M  H20  C25  C24  111.41  3.000
 28M  H25  C26  H24  108.17  3.000
 28M  H25  C26  H23  107.61  3.000
 28M  H24  C26  H23  107.78  3.000
 28M  H25  C26  C24  110.72  3.000
 28M  H24  C26  C24  112.43  3.000
 28M  H23  C26  C24  109.96  3.000
 28M  H28  C27  H27  107.16  3.000
 28M  H28  C27  H26  107.02  3.000
 28M  H27  C27  H26  108.32  3.000
 28M  H28  C27  C24  108.93  3.000
 28M  H27  C27  C24  112.56  3.000
 28M  H26  C27  C24  112.56  3.000
 28M  C35  C28  C29  119.70  3.000
 28M  C29  C28  C1   118.20  3.000
 28M  C35  C28  C1   122.10  3.000
 28M  N31  C29  O30  119.90  3.000
 28M  O30  C29  C28  125.86  3.000
 28M  N31  C29  C28  114.23  3.000
 28M  H29  N31  C33  118.23  3.000
 28M  H29  N31  C29  115.91  3.000
 28M  C33  N31  C29  125.86  3.000
 28M  H30  C33  C34  123.82  3.000
 28M  H30  C33  N31  116.09  3.000
 28M  C34  C33  N31  120.09  3.000
 28M  H31  C34  C35  121.49  3.000
 28M  H31  C34  C33  120.65  3.000
 28M  C35  C34  C33  117.86  3.000
 28M  H32  C35  C34  118.57  3.000
 28M  H32  C35  C28  119.17  3.000
 28M  C34  C35  C28  122.26  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
 28M  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 28M  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 28M  CONST_03  C10  C5   C6   C1    180.00   0.0  0
 28M  CONST_04  C8   N7   C6   C1    180.00   0.0  0
 28M  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 28M  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 28M  CONST_07  N7   C6   C1   C2    180.00   0.0  0
 28M  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 28M  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 28M  CONST_10  C10  C5   C4   C3    180.00   0.0  0
 28M  CONST_11  N7   C6   C5   C4    180.00   0.0  0
 28M  CONST_12  C9   C10  C5   C4    180.00   0.0  0
 28M  CONST_13  C8   N7   C6   C5      0.00   0.0  0
 28M  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 28M  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 28M  CONST_16  C9   C8   N7   C6      0.00   0.0  0
 28M  CONST_17  C10  C5   C6   N7      0.00   0.0  0
 28M  CONST_18  C10  C9   C8   N7      0.00   0.0  0
 28M  CONST_19  C28  C1   C2   C3    180.00   0.0  0
 28M  CONST_20  C28  C1   C6   C5    180.00   0.0  0
 28M  CONST_21  N11  C9   C10  C5    180.00   0.0  0
 28M  CONST_22  C28  C1   C6   N7      0.00   0.0  0
 28M  CONST_23  N11  C9   C8   N7    180.00   0.0  0
 28M  CONST_24  C33  N31  C29  C28     0.00   0.0  0
 28M  CONST_25  C24  C3   C2   C1    180.00   0.0  0
 28M  CONST_26  O22  C4   C3   C2    180.00   0.0  0
 28M  CONST_27  C24  C3   C4   C5    180.00   0.0  0
 28M  CONST_28  O22  C4   C5   C6    180.00   0.0  0
 28M  CONST_29  O22  C4   C5   C10     0.00   0.0  0
 28M  CONST_30  C33  N31  C29  O30   180.00   0.0  0
 28M  CONST_31  H1   C2   C3   C4    180.00   0.0  0
 28M  CONST_32  H3   C10  C5   C4      0.00   0.0  0
 28M  CONST_33  H2   C8   N7   C6    180.00   0.0  0
 28M  CONST_34  H29  N31  C29  C28   180.00   0.0  0
 28M  Var_01    C35  C28  C1   C2    123.96  30.0  2
 28M  Var_02    C12  N11  C9   C8    -16.21  30.0  2
 28M  Var_03    C13  C12  N11  C9   -170.11  30.0  1
 28M  Var_04    C14  C15  N11  C9   -174.78  30.0  1
 28M  Var_05    C14  C13  C12  N11    -7.33  30.0  1
 28M  Var_06    C25  C24  C3   C2    123.52  30.0  3
 28M  Var_07    S18  N17  C16  C14   158.02  30.0  3
 28M  Var_08    H20  C25  C24  C3    -51.97  30.0  3
 28M  Var_09    H26  C27  C24  C3    -60.51  30.0  3
 28M  Var_10    H23  C26  C24  C3    177.69  30.0  3
 28M  Var_11    H17  C23  O22  C4    -57.12  30.0  3
 28M  Var_12    O20  S18  N17  C16   -49.64  30.0  3
 28M  Var_13    H14  C21  S18  N17    60.01  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
 28M  chir_01  C14  C15  C13  C16  positiv

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
 28M  plan-1  C1   0.020
 28M  plan-1  C28  0.020
 28M  plan-1  C29  0.020
 28M  plan-1  O30  0.020
 28M  plan-1  N31  0.020
 28M  plan-1  C33  0.020
 28M  plan-1  C34  0.020
 28M  plan-1  C35  0.020
 28M  plan-1  H29  0.020
 28M  plan-1  H30  0.020
 28M  plan-1  H31  0.020
 28M  plan-1  H32  0.020
 28M  plan-2  C1   0.020
 28M  plan-2  C2   0.020
 28M  plan-2  C3   0.020
 28M  plan-2  C4   0.020
 28M  plan-2  C5   0.020
 28M  plan-2  C6   0.020
 28M  plan-2  N7   0.020
 28M  plan-2  C8   0.020
 28M  plan-2  C9   0.020
 28M  plan-2  C10  0.020
 28M  plan-2  N11  0.020
 28M  plan-2  O22  0.020
 28M  plan-2  C24  0.020
 28M  plan-2  C28  0.020
 28M  plan-2  H1   0.020
 28M  plan-2  H2   0.020
 28M  plan-2  H3   0.020

