# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:51:16 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-phenyl-N-(propan-2-yl)-6-[(thiophen-2-yl)sulfonyl]-4,5,6,7-tetrahydro-1H-pyrrolo[2,3-c]pyridine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)n1c2CN(CCc2cc1c3ccccc3)[S](=O)(=O)c4sccc4
#
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
 9LM  9LM  2-phenyl-N-(propan-2-yl)-6-[(thiophen-2-yl)sulfonyl]-4,5,6,7-tetrahydro-1H-pyrrolo[2,3-c]pyridine-1-carboxamide  ligand  52  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9LM
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
 9LM  C4   C  CR5   0   0.341  -2.7081  -1.4743  -0.2355
 9LM  C7   C  CH2   0  -0.343   1.8655  -1.9295  -0.6443
 9LM  C8   C  CH2   0  -0.494   0.7089  -2.9144  -0.5490
 9LM  C10  C  CR6   0   0.073  -4.1579  -1.3453  -0.3686
 9LM  C13  C  CR16  0  -0.266  -6.9341  -1.1853  -0.6889
 9LM  C15  C  CR16  0  -0.311  -4.9848  -2.3889   0.0493
 9LM  C20  C  CR15  0  -0.162   3.4342   2.1359  -0.3486
 9LM  C21  C  CR15  0  -0.175   3.9945   2.7003  -1.5197
 9LM  C22  C  CR15  0  -0.444   4.6886   1.7875  -2.2584
 9LM  C28  C  CH3   0  -0.668  -0.6255   4.0324   0.4373
 9LM  C27  C  CH1   0  -0.098  -1.8982   3.2290   0.6569
 9LM  C29  C  CH3   0  -0.645  -3.1059   3.8719  -0.0136
 9LM  N26  N  NH1   0  -0.628  -1.6877   1.8732   0.1656
 9LM  O25  O  O     0  -0.447  -3.1120   0.8068   1.5791
 9LM  N5   N  NR5   0  -0.657  -1.8735  -0.4175   0.0803
 9LM  C1   C  CR5   0   0.286  -0.5654  -0.8483   0.0103
 9LM  C9   C  CH2   0  -0.348   0.6379  -0.0382   0.3577
 9LM  N6   N  N     0  -0.573   1.7699  -0.9629   0.4589
 9LM  C2   C  CR5   0   0.030  -0.5619  -2.1582  -0.3643
 9LM  C3   C  CR15  0  -0.440  -1.9159  -2.5551  -0.5208
 9LM  C11  C  CR16  0  -0.302  -4.7438  -0.2226  -0.9581
 9LM  C12  C  CR16  0  -0.241  -6.1191  -0.1420  -1.1106
 9LM  C14  C  CR16  0  -0.240  -6.3603  -2.3114  -0.1136
 9LM  S16  S  S     0   1.383   3.1771  -0.2893   1.0041
 9LM  O17  O  OS    0  -0.641   2.8424   0.5099   2.1674
 9LM  O18  O  OS    0  -0.642   4.1550  -1.3571   1.0960
 9LM  C19  C  CR5   0  -0.429   3.7300   0.8069  -0.2382
 9LM  S23  S  S2    0   0.302   4.6824   0.2356  -1.5474
 9LM  H1   H  HCH2  0   0.285   2.8082  -2.4667  -0.5794
 9LM  H2   H  HCH2  0   0.252   1.8399  -1.4083  -1.6082
 9LM  H3   H  HCH2  0   0.259   0.6847  -3.5142  -1.4611
 9LM  H4   H  HCH2  0   0.254   0.8771  -3.6063   0.2806
 9LM  H5   H  HCR6  0   0.258  -8.0074  -1.1217  -0.8113
 9LM  H6   H  HCR6  0   0.253  -4.5472  -3.2628   0.5152
 9LM  H7   H  HCR5  0   0.295   2.8581   2.6906   0.3782
 9LM  H8   H  HCR5  0   0.287   3.8934   3.7390  -1.7966
 9LM  H9   H  HCR5  0   0.316   5.2183   1.9510  -3.1846
 9LM  H10  H  HCH3  0   0.230  -0.3819   4.1058  -0.6249
 9LM  H11  H  HCH3  0   0.245  -0.7508   5.0453   0.8182
 9LM  H12  H  HCH3  0   0.239   0.2220   3.5803   0.9539
 9LM  H13  H  HCH1  0   0.256  -2.0848   3.1537   1.7291
 9LM  H14  H  HCH3  0   0.225  -2.9518   3.9632  -1.0903
 9LM  H15  H  HCH3  0   0.236  -4.0094   3.2852   0.1546
 9LM  H16  H  HCH3  0   0.235  -3.2759   4.8713   0.3877
 9LM  H17  H  HNH1  0   0.410  -1.2097   1.7745  -0.7179
 9LM  H18  H  HCH2  0   0.255   0.8267   0.7305  -0.4053
 9LM  H19  H  HCH2  0   0.296   0.5076   0.4676   1.3144
 9LM  H20  H  HCR5  0   0.256  -2.2707  -3.5139  -0.8673
 9LM  H21  H  HCR6  0   0.248  -4.1263   0.5868  -1.3290
 9LM  H22  H  HCR6  0   0.259  -6.5542   0.7353  -1.5711
 9LM  H23  H  HCR6  0   0.258  -6.9849  -3.1301   0.2194
 9LM  C24  C  C     0   0.673  -2.2985   0.8020   0.6819

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
 9LM  C13  C14  aromatic  1.389  0.020  1.389
 9LM  C13  C12  aromatic  1.389  0.020  1.389
 9LM  C14  C15  aromatic  1.387  0.020  1.387
 9LM  C12  C11  aromatic  1.386  0.020  1.386
 9LM  C15  C10  aromatic  1.396  0.020  1.396
 9LM  C11  C10  aromatic  1.397  0.020  1.397
 9LM  C10  C4   single    1.462  0.020  1.462
 9LM  C29  C27  single    1.524  0.020  1.524
 9LM  C28  C27  single    1.521  0.020  1.521
 9LM  C27  N26  single    1.457  0.020  1.457
 9LM  C4   C3   aromatic  1.370  0.020  1.370
 9LM  C4   N5   aromatic  1.383  0.020  1.383
 9LM  N26  C24  single    1.337  0.020  1.337
 9LM  C3   C2   aromatic  1.420  0.020  1.420
 9LM  C24  N5   single    1.425  0.020  1.425
 9LM  C24  O25  double    1.211  0.020  1.211
 9LM  N5   C1   aromatic  1.379  0.020  1.379
 9LM  C2   C1   aromatic  1.362  0.020  1.362
 9LM  C2   C8   single    1.490  0.020  1.490
 9LM  C1   C9   single    1.492  0.020  1.492
 9LM  C8   C7   single    1.522  0.020  1.522
 9LM  C9   N6   single    1.465  0.020  1.465
 9LM  C7   N6   single    1.470  0.020  1.470
 9LM  N6   S16  single    1.653  0.020  1.653
 9LM  O17  S16  double    1.451  0.020  1.451
 9LM  S16  O18  double    1.451  0.020  1.451
 9LM  S16  C19  single    1.747  0.020  1.747
 9LM  C19  C20  aromatic  1.366  0.020  1.366
 9LM  C19  S23  aromatic  1.717  0.020  1.717
 9LM  C20  C21  aromatic  1.416  0.020  1.416
 9LM  S23  C22  aromatic  1.707  0.020  1.707
 9LM  C21  C22  aromatic  1.364  0.020  1.364
 9LM  C7   H1   single    0.970  0.020  1.090
 9LM  C7   H2   single    0.970  0.020  1.090
 9LM  C8   H3   single    0.970  0.020  1.090
 9LM  C8   H4   single    0.970  0.020  1.090
 9LM  C13  H5   single    0.930  0.020  1.080
 9LM  C15  H6   single    0.930  0.020  1.080
 9LM  C20  H7   single    0.930  0.020  1.080
 9LM  C21  H8   single    0.930  0.020  1.080
 9LM  C22  H9   single    0.930  0.020  1.080
 9LM  C28  H10  single    0.970  0.020  1.090
 9LM  C28  H11  single    0.970  0.020  1.090
 9LM  C28  H12  single    0.970  0.020  1.090
 9LM  C27  H13  single    0.970  0.020  1.090
 9LM  C29  H14  single    0.970  0.020  1.090
 9LM  C29  H15  single    0.970  0.020  1.090
 9LM  C29  H16  single    0.970  0.020  1.090
 9LM  N26  H17  single    0.860  0.020  1.020
 9LM  C9   H18  single    0.970  0.020  1.090
 9LM  C9   H19  single    0.970  0.020  1.090
 9LM  C3   H20  single    0.930  0.020  1.080
 9LM  C11  H21  single    0.930  0.020  1.080
 9LM  C12  H22  single    0.930  0.020  1.080
 9LM  C14  H23  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
 9LM  C3   C4   N5   107.54  3.000
 9LM  N5   C4   C10  123.50  3.000
 9LM  C3   C4   C10  128.62  3.000
 9LM  H2   C7   H1   107.93  3.000
 9LM  H2   C7   N6   110.23  3.000
 9LM  H1   C7   N6   109.67  3.000
 9LM  H2   C7   C8   110.18  3.000
 9LM  H1   C7   C8   109.60  3.000
 9LM  N6   C7   C8   109.21  3.000
 9LM  H4   C8   H3   106.84  3.000
 9LM  H4   C8   C2   110.99  3.000
 9LM  H3   C8   C2   111.31  3.000
 9LM  H4   C8   C7   109.89  3.000
 9LM  H3   C8   C7   108.66  3.000
 9LM  C2   C8   C7   109.11  3.000
 9LM  C11  C10  C15  118.61  3.000
 9LM  C11  C10  C4   121.70  3.000
 9LM  C15  C10  C4   119.64  3.000
 9LM  H5   C13  C14  120.29  3.000
 9LM  H5   C13  C12  120.22  3.000
 9LM  C14  C13  C12  119.49  3.000
 9LM  H6   C15  C14  119.76  3.000
 9LM  H6   C15  C10  119.53  3.000
 9LM  C14  C15  C10  120.70  3.000
 9LM  H7   C20  C19  124.10  3.000
 9LM  H7   C20  C21  124.24  3.000
 9LM  C19  C20  C21  111.65  3.000
 9LM  H8   C21  C22  123.54  3.000
 9LM  H8   C21  C20  123.96  3.000
 9LM  C22  C21  C20  112.50  3.000
 9LM  H9   C22  S23  119.80  3.000
 9LM  H9   C22  C21  127.81  3.000
 9LM  S23  C22  C21  112.39  3.000
 9LM  H12  C28  H11  108.01  3.000
 9LM  H12  C28  H10  108.37  3.000
 9LM  H11  C28  H10  107.65  3.000
 9LM  H12  C28  C27  111.28  3.000
 9LM  H11  C28  C27  110.15  3.000
 9LM  H10  C28  C27  111.25  3.000
 9LM  H13  C27  N26  106.97  3.000
 9LM  H13  C27  C29  109.03  3.000
 9LM  N26  C27  C29  111.03  3.000
 9LM  H13  C27  C28  108.75  3.000
 9LM  N26  C27  C28  108.77  3.000
 9LM  C29  C27  C28  112.14  3.000
 9LM  H16  C29  H15  107.89  3.000
 9LM  H16  C29  H14  107.97  3.000
 9LM  H15  C29  H14  108.30  3.000
 9LM  H16  C29  C27  110.39  3.000
 9LM  H15  C29  C27  111.22  3.000
 9LM  H14  C29  C27  110.95  3.000
 9LM  H17  N26  C27  117.03  3.000
 9LM  H17  N26  C24  118.43  3.000
 9LM  C27  N26  C24  123.31  3.000
 9LM  C1   N5   C24  124.88  3.000
 9LM  C1   N5   C4   108.79  3.000
 9LM  C24  N5   C4   124.78  3.000
 9LM  C2   C1   C9   125.74  3.000
 9LM  C9   C1   N5   125.72  3.000
 9LM  C2   C1   N5   108.47  3.000
 9LM  H19  C9   H18  107.77  3.000
 9LM  H19  C9   N6   108.94  3.000
 9LM  H18  C9   N6   110.89  3.000
 9LM  H19  C9   C1   111.10  3.000
 9LM  H18  C9   C1   110.89  3.000
 9LM  N6   C9   C1   107.25  3.000
 9LM  S16  N6   C9   115.05  3.000
 9LM  S16  N6   C7   117.40  3.000
 9LM  C9   N6   C7   114.42  3.000
 9LM  C3   C2   C1   107.25  3.000
 9LM  C1   C2   C8   121.62  3.000
 9LM  C3   C2   C8   131.13  3.000
 9LM  H20  C3   C2   126.67  3.000
 9LM  H20  C3   C4   125.27  3.000
 9LM  C2   C3   C4   107.94  3.000
 9LM  H21  C11  C12  118.98  3.000
 9LM  H21  C11  C10  120.38  3.000
 9LM  C12  C11  C10  120.62  3.000
 9LM  H22  C12  C11  119.53  3.000
 9LM  H22  C12  C13  120.13  3.000
 9LM  C11  C12  C13  120.33  3.000
 9LM  H23  C14  C15  119.59  3.000
 9LM  H23  C14  C13  120.16  3.000
 9LM  C15  C14  C13  120.24  3.000
 9LM  C19  S16  O18  107.08  3.000
 9LM  C19  S16  O17  107.32  3.000
 9LM  O18  S16  O17  120.68  3.000
 9LM  C19  S16  N6   106.90  3.000
 9LM  O18  S16  N6   107.15  3.000
 9LM  O17  S16  N6   107.01  3.000
 9LM  S23  C19  S16  120.61  3.000
 9LM  S23  C19  C20  112.48  3.000
 9LM  S16  C19  C20  126.84  3.000
 9LM  C19  S23  C22   90.98  3.000
 9LM  N5   C24  O25  121.11  3.000
 9LM  O25  C24  N26  126.14  3.000
 9LM  N5   C24  N26  112.74  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
 9LM  CONST_01  C14  C15  C10  C4   180.00   0.0  0
 9LM  CONST_02  C12  C11  C10  C4   180.00   0.0  0
 9LM  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 9LM  CONST_04  C2   C1   N5   C4     0.00   0.0  0
 9LM  CONST_05  C13  C14  C15  C10    0.00   0.0  0
 9LM  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 9LM  CONST_07  C2   C3   C4   C10  180.00   0.0  0
 9LM  CONST_08  C1   N5   C4   C10  180.00   0.0  0
 9LM  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 9LM  CONST_10  C12  C11  C10  C15    0.00   0.0  0
 9LM  CONST_13  C22  S23  C19  C20    0.00   0.0  0
 9LM  CONST_14  S23  C22  C21  C20    0.00   0.0  0
 9LM  CONST_15  S23  C19  C20  C21    0.00   0.0  0
 9LM  CONST_16  C19  S23  C22  C21    0.00   0.0  0
 9LM  CONST_17  C19  C20  C21  C22    0.00   0.0  0
 9LM  CONST_19  C2   C3   C4   N5     0.00   0.0  0
 9LM  CONST_20  C3   C2   C1   N5     0.00   0.0  0
 9LM  CONST_21  C3   C4   N5   C1     0.00   0.0  0
 9LM  CONST_23  C14  C13  C12  C11    0.00   0.0  0
 9LM  CONST_24  C14  C15  C10  C11    0.00   0.0  0
 9LM  CONST_26  S16  C19  C20  C21  180.00   0.0  0
 9LM  CONST_27  S16  C19  S23  C22  180.00   0.0  0
 9LM  CONST_28  C3   C4   N5   C24  180.00   0.0  0
 9LM  CONST_29  C2   C1   N5   C24  180.00   0.0  0
 9LM  CONST_30  C9   C1   N5   C24    0.00   0.0  0
 9LM  CONST_31  H6   C15  C10  C4     0.00   0.0  0
 9LM  CONST_32  H21  C11  C10  C4     0.00   0.0  0
 9LM  CONST_33  H20  C3   C2   C8     0.00   0.0  0
 9LM  CONST_34  H23  C14  C15  C10  180.00   0.0  0
 9LM  CONST_35  H22  C12  C11  C10  180.00   0.0  0
 9LM  CONST_36  H5   C13  C14  C15  180.00   0.0  0
 9LM  CONST_37  H9   C22  C21  C20  180.00   0.0  0
 9LM  CONST_38  H7   C20  C21  C22  180.00   0.0  0
 9LM  CONST_39  H8   C21  C20  C19  180.00   0.0  0
 9LM  CONST_44  N5   C24  N26  C27  180.00   0.0  0
 9LM  CONST_46  O25  C24  N26  C27    0.00   0.0  0
 9LM  Var_01    C3   C2   C8   C7   163.78  30.0  1
 9LM  Var_02    C1   C9   N6   C7    46.18  30.0  1
 9LM  Var_03    C9   N6   C7   C8   -68.83  30.0  1
 9LM  Var_04    N6   C9   C1   N5   166.32  30.0  1
 9LM  Var_05    C2   C8   C7   N6    48.61  30.0  1
 9LM  Var_06    C19  S16  N6   C7    71.07  30.0  3
 9LM  Var_07    N6   S16  C19  C20   90.84  30.0  2
 9LM  Var_08    C29  C27  N26  C24  -86.24  30.0  3
 9LM  Var_09    H14  C29  C27  C28   59.48  30.0  3
 9LM  Var_10    H10  C28  C27  C29  -61.18  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
 9LM  plan-1  C20  0.020
 9LM  plan-1  C21  0.020
 9LM  plan-1  C22  0.020
 9LM  plan-1  S16  0.020
 9LM  plan-1  C19  0.020
 9LM  plan-1  S23  0.020
 9LM  plan-1  H7   0.020
 9LM  plan-1  H8   0.020
 9LM  plan-1  H9   0.020
 9LM  plan-2  C4   0.020
 9LM  plan-2  C10  0.020
 9LM  plan-2  C13  0.020
 9LM  plan-2  C15  0.020
 9LM  plan-2  C11  0.020
 9LM  plan-2  C12  0.020
 9LM  plan-2  C14  0.020
 9LM  plan-2  H5   0.020
 9LM  plan-2  H6   0.020
 9LM  plan-2  H21  0.020
 9LM  plan-2  H22  0.020
 9LM  plan-2  H23  0.020
 9LM  plan-3  C4   0.020
 9LM  plan-3  C8   0.020
 9LM  plan-3  C10  0.020
 9LM  plan-3  C27  0.020
 9LM  plan-3  N26  0.020
 9LM  plan-3  O25  0.020
 9LM  plan-3  N5   0.020
 9LM  plan-3  C1   0.020
 9LM  plan-3  C9   0.020
 9LM  plan-3  C2   0.020
 9LM  plan-3  C3   0.020
 9LM  plan-3  H17  0.020
 9LM  plan-3  H20  0.020
 9LM  plan-3  C24  0.020

