# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:54:31 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: (3~{a}~{R},4~{S},9~{b}~{S})-4-(2-chloranyl-4-oxidanyl-phenyl)-2,3,3~{a},4,5,9~{b}-hexahydro-1~{H}-cyclopenta[c]quinoline-8-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1ccc2N[C@@H]([C@@H]3CCC[C@@H]3c2c1)c4ccc(O)cc4Cl
#
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
 LYQ  LYQ  (3~{a}~{R},4~{S},9~{b}~{S})-4-(2-chloranyl-4-oxidanyl-phenyl)-2,3,3~{a},4,5,9~{b}-hexahydro-1~{H}-cyclopenta[c]quinoline-8-sulfonamide  ligand  44  25  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LYQ
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
 LYQ  C4   C   CR16  0  -0.308  -2.4185   8.1665  11.4393
 LYQ  C5   C   CR6   0   0.183  -2.2822   7.4827  12.6507
 LYQ  C6   C   CH1   0  -0.068  -3.1952   6.2885  12.8484
 LYQ  N1   N   NC2   0  -0.887  -5.3393  -0.1163  15.9195
 LYQ  C7   C   CH1   0  -0.279  -4.5390   6.6862  13.4546
 LYQ  C8   C   CH1   0  -0.280  -5.4532   5.4800  13.6865
 LYQ  C9   C   CH2   0  -0.461  -6.6005   6.1158  14.4749
 LYQ  C10  C   CH2   0  -0.436  -5.9282   7.1464  15.4021
 LYQ  C11  C   CH2   0  -0.443  -4.5182   7.3779  14.8210
 LYQ  C12  C   CR6   0   0.073  -4.7051   4.4027  14.4400
 LYQ  C13  C   CR6   0   0.402  -3.2988   4.3265  14.3332
 LYQ  C14  C   CR16  0  -0.359  -2.6094   3.2942  15.0004
 LYQ  C15  C   CR16  0  -0.227  -3.2829   2.3630  15.7523
 LYQ  O2   O   OS    0  -0.663  -6.9213   1.6777  16.9291
 LYQ  O1   O   OS    0  -0.679  -4.8011   1.0044  18.0622
 LYQ  C16  C   CR6   0  -0.243  -4.6707   2.4403  15.8540
 LYQ  N    N   NH1   0  -0.717  -2.5952   5.2267  13.6116
 LYQ  C17  C   CR16  0  -0.316  -5.3631   3.4542  15.2017
 LYQ  C    C   CR6   0  -0.129  -1.3550   8.0126  13.5444
 LYQ  CL   CL  CL    0  -0.125  -1.0330   7.3052  15.1003
 LYQ  C3   C   CR16  0  -0.315  -1.7031   9.3028  11.1217
 LYQ  C2   C   CR6   0   0.347  -0.7818   9.8038  12.0375
 LYQ  O    O   OH1   0  -0.627  -0.0880  10.9059  11.7056
 LYQ  C1   C   CR16  0  -0.325  -0.6098   9.1485  13.2494
 LYQ  H1   H   HCR6  0   0.262  -3.1210   7.7797  10.7104
 LYQ  H2   H   HCH1  0   0.260  -3.4169   5.9203  11.8370
 LYQ  H3   H   HNC2  0   0.412  -5.5880  -0.9440  16.4539
 LYQ  H4   H   HNC2  0   0.410  -5.8770  -0.0878  15.0590
 LYQ  H5   H   HCH1  0   0.259  -5.0280   7.3456  12.7306
 LYQ  H6   H   HCH1  0   0.267  -5.8086   5.0686  12.7361
 LYQ  H7   H   HCH2  0   0.241  -7.2632   6.6180  13.7663
 LYQ  H8   H   HCH2  0   0.242  -7.2148   5.3980  15.0180
 LYQ  H9   H   HCH2  0   0.232  -6.5072   8.0695  15.4421
 LYQ  H10  H   HCH2  0   0.231  -5.8668   6.7746  16.4253
 LYQ  H11  H   HCH2  0   0.236  -3.7678   6.9217  15.4665
 LYQ  H12  H   HCH2  0   0.239  -4.2623   8.4345  14.7370
 LYQ  H13  H   HCR6  0   0.266  -1.5305   3.2395  14.9190
 LYQ  H14  H   HCR6  0   0.275  -2.7279   1.5809  16.2537
 LYQ  H15  H   HNH1  0   0.389  -1.6220   5.0285  13.4492
 LYQ  H16  H   HCR6  0   0.267  -6.4416   3.4997  15.2811
 LYQ  H17  H   HCR6  0   0.271  -1.8459   9.7912  10.1667
 LYQ  H18  H   HOH1  0   0.478   0.5339  11.1406  12.4038
 LYQ  H19  H   HCR6  0   0.291   0.1040   9.5221  13.9736
 LYQ  S    S   S     0   1.353  -5.5261   1.2613  16.8229

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
 LYQ  C3   C4   aromatic  1.380  0.020  1.380
 LYQ  C3   C2   aromatic  1.392  0.020  1.392
 LYQ  O    C2   single    1.344  0.020  1.344
 LYQ  C4   C5   aromatic  1.398  0.020  1.398
 LYQ  C2   C1   aromatic  1.388  0.020  1.388
 LYQ  C5   C6   single    1.516  0.020  1.516
 LYQ  C5   C    aromatic  1.393  0.020  1.393
 LYQ  C6   C7   single    1.527  0.020  1.527
 LYQ  C6   N    single    1.439  0.020  1.439
 LYQ  C1   C    aromatic  1.390  0.020  1.390
 LYQ  C    CL   single    1.739  0.020  1.739
 LYQ  C7   C8   single    1.531  0.020  1.531
 LYQ  C7   C11  single    1.532  0.020  1.532
 LYQ  N    C13  single    1.351  0.020  1.351
 LYQ  C8   C12  single    1.513  0.020  1.513
 LYQ  C8   C9   single    1.530  0.020  1.530
 LYQ  C13  C12  aromatic  1.412  0.020  1.412
 LYQ  C13  C14  aromatic  1.409  0.020  1.409
 LYQ  C12  C17  aromatic  1.383  0.020  1.383
 LYQ  C14  C15  aromatic  1.373  0.020  1.373
 LYQ  C9   C10  single    1.541  0.020  1.541
 LYQ  C11  C10  single    1.542  0.020  1.542
 LYQ  C17  C16  aromatic  1.390  0.020  1.390
 LYQ  C15  C16  aromatic  1.394  0.020  1.394
 LYQ  C16  S    single    1.749  0.020  1.749
 LYQ  N1   S    single    1.658  0.020  1.658
 LYQ  O2   S    double    1.460  0.020  1.460
 LYQ  S    O1   double    1.459  0.020  1.459
 LYQ  C4   H1   single    0.930  0.020  1.080
 LYQ  C6   H2   single    0.970  0.020  1.090
 LYQ  N1   H3   single    0.890  0.020  1.040
 LYQ  N1   H4   single    0.890  0.020  1.040
 LYQ  C7   H5   single    0.970  0.020  1.090
 LYQ  C8   H6   single    0.970  0.020  1.090
 LYQ  C9   H7   single    0.970  0.020  1.090
 LYQ  C9   H8   single    0.970  0.020  1.090
 LYQ  C10  H9   single    0.970  0.020  1.090
 LYQ  C10  H10  single    0.970  0.020  1.090
 LYQ  C11  H11  single    0.970  0.020  1.090
 LYQ  C11  H12  single    0.970  0.020  1.090
 LYQ  C14  H13  single    0.930  0.020  1.080
 LYQ  C15  H14  single    0.930  0.020  1.080
 LYQ  N    H15  single    0.860  0.020  1.020
 LYQ  C17  H16  single    0.930  0.020  1.080
 LYQ  C3   H17  single    0.930  0.020  1.080
 LYQ  O    H18  single    0.850  0.020  0.980
 LYQ  C1   H19  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
 LYQ  H1   C4   C3   118.38  3.000
 LYQ  H1   C4   C5   118.13  3.000
 LYQ  C3   C4   C5   123.49  3.000
 LYQ  C    C5   C6   128.10  3.000
 LYQ  C    C5   C4   115.78  3.000
 LYQ  C6   C5   C4   116.08  3.000
 LYQ  H2   C6   N    108.97  3.000
 LYQ  H2   C6   C7   105.97  3.000
 LYQ  N    C6   C7   110.40  3.000
 LYQ  H2   C6   C5   105.39  3.000
 LYQ  N    C6   C5   113.54  3.000
 LYQ  C7   C6   C5   112.12  3.000
 LYQ  H4   N1   H3   109.81  3.000
 LYQ  H4   N1   S    112.27  3.000
 LYQ  H3   N1   S    111.27  3.000
 LYQ  H5   C7   C11  108.91  3.000
 LYQ  H5   C7   C8   107.94  3.000
 LYQ  C11  C7   C8   103.22  3.000
 LYQ  H5   C7   C6   106.71  3.000
 LYQ  C11  C7   C6   117.38  3.000
 LYQ  C8   C7   C6   112.36  3.000
 LYQ  H6   C8   C12  108.98  3.000
 LYQ  H6   C8   C9   111.10  3.000
 LYQ  C12  C8   C9   114.21  3.000
 LYQ  H6   C8   C7   111.00  3.000
 LYQ  C9   C8   C7   101.44  3.000
 LYQ  C12  C8   C7   109.95  3.000
 LYQ  H8   C9   H7   106.50  3.000
 LYQ  H8   C9   C10  112.75  3.000
 LYQ  H7   C9   C10  110.34  3.000
 LYQ  H8   C9   C8   113.94  3.000
 LYQ  H7   C9   C8   108.16  3.000
 LYQ  C10  C9   C8   105.12  3.000
 LYQ  H10  C10  H9   106.51  3.000
 LYQ  H10  C10  C11  110.69  3.000
 LYQ  H9   C10  C11  111.85  3.000
 LYQ  H10  C10  C9   111.17  3.000
 LYQ  H9   C10  C9   110.89  3.000
 LYQ  C11  C10  C9   105.81  3.000
 LYQ  H12  C11  H11  106.83  3.000
 LYQ  H12  C11  C10  112.89  3.000
 LYQ  H11  C11  C10  110.09  3.000
 LYQ  H12  C11  C7   111.85  3.000
 LYQ  H11  C11  C7   110.40  3.000
 LYQ  C10  C11  C7   104.83  3.000
 LYQ  C17  C12  C13  118.58  3.000
 LYQ  C17  C12  C8   121.83  3.000
 LYQ  C13  C12  C8   119.55  3.000
 LYQ  N    C13  C14  119.08  3.000
 LYQ  C14  C13  C12  119.39  3.000
 LYQ  N    C13  C12  121.53  3.000
 LYQ  H13  C14  C15  119.69  3.000
 LYQ  H13  C14  C13  119.25  3.000
 LYQ  C15  C14  C13  121.06  3.000
 LYQ  H14  C15  C16  121.13  3.000
 LYQ  H14  C15  C14  119.49  3.000
 LYQ  C16  C15  C14  119.39  3.000
 LYQ  C17  C16  S    120.52  3.000
 LYQ  S    C16  C15  119.34  3.000
 LYQ  C17  C16  C15  120.14  3.000
 LYQ  H15  N    C13  117.29  3.000
 LYQ  H15  N    C6   117.58  3.000
 LYQ  C13  N    C6   123.90  3.000
 LYQ  H16  C17  C16  119.51  3.000
 LYQ  H16  C17  C12  119.05  3.000
 LYQ  C16  C17  C12  121.44  3.000
 LYQ  C1   C    CL   115.02  3.000
 LYQ  CL   C    C5   122.86  3.000
 LYQ  C1   C    C5   122.12  3.000
 LYQ  H17  C3   C2   120.36  3.000
 LYQ  H17  C3   C4   120.42  3.000
 LYQ  C2   C3   C4   119.21  3.000
 LYQ  C1   C2   O    122.59  3.000
 LYQ  C1   C2   C3   119.09  3.000
 LYQ  O    C2   C3   118.31  3.000
 LYQ  H18  O    C2   110.72  3.000
 LYQ  H19  C1   C2   120.16  3.000
 LYQ  H19  C1   C    119.55  3.000
 LYQ  C2   C1   C    120.30  3.000
 LYQ  C16  S    O1   110.25  3.000
 LYQ  O1   S    O2   117.61  3.000
 LYQ  C16  S    O2   108.38  3.000
 LYQ  O1   S    N1   105.11  3.000
 LYQ  O2   S    N1   112.60  3.000
 LYQ  C16  S    N1   101.72  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
 LYQ  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 LYQ  CONST_02  C1   C    C5   C4     0.00   0.0  0
 LYQ  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 LYQ  CONST_04  C2   C1   C    C5     0.00   0.0  0
 LYQ  CONST_05  C15  C14  C13  C12    0.00   0.0  0
 LYQ  CONST_06  C15  C16  C17  C12    0.00   0.0  0
 LYQ  CONST_07  C16  C17  C12  C13    0.00   0.0  0
 LYQ  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 LYQ  CONST_09  C17  C12  C13  C14    0.00   0.0  0
 LYQ  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 LYQ  CONST_11  C3   C4   C5   C      0.00   0.0  0
 LYQ  CONST_12  C3   C2   C1   C      0.00   0.0  0
 LYQ  CONST_13  C3   C4   C5   C6   180.00   0.0  0
 LYQ  CONST_14  C1   C    C5   C6   180.00   0.0  0
 LYQ  CONST_15  O    C2   C3   C4   180.00   0.0  0
 LYQ  CONST_16  CL   C    C5   C4   180.00   0.0  0
 LYQ  CONST_17  CL   C    C5   C6     0.00   0.0  0
 LYQ  CONST_18  S    C16  C17  C12  180.00   0.0  0
 LYQ  CONST_19  S    C16  C15  C14  180.00   0.0  0
 LYQ  CONST_20  O    C2   C1   C    180.00   0.0  0
 LYQ  CONST_21  C2   C1   C    CL   180.00   0.0  0
 LYQ  CONST_22  H17  C3   C4   C5   180.00   0.0  0
 LYQ  CONST_23  H19  C1   C    C5   180.00   0.0  0
 LYQ  CONST_24  H1   C4   C5   C6     0.00   0.0  0
 LYQ  CONST_25  H16  C17  C12  C8     0.00   0.0  0
 LYQ  CONST_26  H13  C14  C13  C12  180.00   0.0  0
 LYQ  CONST_27  H14  C15  C14  C13  180.00   0.0  0
 LYQ  Var_01    C12  C13  N    C6    -2.95  30.0  1
 LYQ  Var_02    C9   C10  C11  C7    10.47  30.0  1
 LYQ  Var_03    C11  C10  C9   C8    17.04  30.0  1
 LYQ  Var_04    C17  C16  S    N1   111.07  30.0  1
 LYQ  Var_05    H3   N1   S    C16  166.23  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
 LYQ  chir_01  C6  C5  C7   N    positiv
 LYQ  chir_02  C7  C6  C8   C11  negativ
 LYQ  chir_03  C8  C7  C12  C9   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
 LYQ  plan-1  C4   0.020
 LYQ  plan-1  C5   0.020
 LYQ  plan-1  C6   0.020
 LYQ  plan-1  C    0.020
 LYQ  plan-1  CL   0.020
 LYQ  plan-1  C3   0.020
 LYQ  plan-1  C2   0.020
 LYQ  plan-1  O    0.020
 LYQ  plan-1  C1   0.020
 LYQ  plan-1  H1   0.020
 LYQ  plan-1  H17  0.020
 LYQ  plan-1  H19  0.020
 LYQ  plan-2  C8   0.020
 LYQ  plan-2  C12  0.020
 LYQ  plan-2  C13  0.020
 LYQ  plan-2  C14  0.020
 LYQ  plan-2  C15  0.020
 LYQ  plan-2  C16  0.020
 LYQ  plan-2  N    0.020
 LYQ  plan-2  C17  0.020
 LYQ  plan-2  H13  0.020
 LYQ  plan-2  H14  0.020
 LYQ  plan-2  H16  0.020
 LYQ  plan-2  S    0.020

