# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:31:21 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)N[C@](C1)(c3cscc3)c4ccc(cc4)N5CCOCC5
#
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
 GN2  GN2  (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one  ligand  56  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GN2
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
 GN2  C4   C   CR16  0  -0.308  -0.9541  -0.7432   1.0758
 GN2  C5   C   CR6   0   0.140  -1.5804  -0.2729  -0.0685
 GN2  C6   C   CR16  0  -0.282  -1.5305  -1.0879  -1.1993
 GN2  C8   C   CT    0  -0.068  -2.3406   1.0581  -0.0885
 GN2  C9   C   CR5   0   0.259  -3.8195   0.7593   0.0099
 GN2  C10  C   CR15  0  -0.570  -4.7596   1.0691  -0.9257
 GN2  C12  C   CR15  0  -0.462  -5.7296  -0.1045   1.0084
 GN2  C13  C   CR15  0  -0.212  -4.3882   0.0733   1.1266
 GN2  C3   C   CR16  0  -0.338  -0.2651  -1.9492   1.0906
 GN2  C1   C   CR16  0  -0.316  -0.8490  -2.2884  -1.1989
 GN2  C2   C   CR6   0   0.356  -0.1823  -2.7493  -0.0525
 GN2  N7   N   NT    0  -0.520   0.4929  -3.9660  -0.0706
 GN2  S11  S   S2    0   0.234  -6.3223   0.5420  -0.4630
 GN2  N14  N   NH1   0  -0.656  -1.9680   1.8996   1.0404
 GN2  C15  C   C     0   0.547  -0.7621   2.5194   1.1286
 GN2  C16  C   C     0  -0.482  -0.0038   2.6140  -0.1298
 GN2  C17  C   C     0   0.520  -0.5935   2.3125  -1.3117
 GN2  C18  C   CH2   0  -0.571  -2.0124   1.8561  -1.3498
 GN2  O19  O   OH1   0  -0.564  -0.0220   2.4299  -2.4905
 GN2  O20  O   O     0  -0.467  -0.3478   2.9898   2.1765
 GN2  S21  S   S2    0   0.088   1.5937   3.3254  -0.1016
 GN2  C22  C   CR6   0  -0.036   2.6535   1.9449   0.2359
 GN2  C23  C   CR16  0  -0.242   2.2180   0.6245   0.2523
 GN2  C24  C   CR16  0  -0.231   3.1044  -0.4056   0.5248
 GN2  C25  C   CR16  0  -0.275   4.4423  -0.1357   0.7745
 GN2  C26  C   CR16  0  -0.200   4.8936   1.1752   0.7515
 GN2  C27  C   CR6   0  -0.066   4.0005   2.1999   0.4845
 GN2  CL   CL  CL    0  -0.117   4.5758   3.8345   0.4545
 GN2  C29  C   CH2   0  -0.324   1.3464  -4.2435  -1.2189
 GN2  C30  C   CH2   0  -0.187   1.7228  -5.7109  -1.2530
 GN2  O31  O   O2    0  -0.481   2.3393  -6.1180  -0.0538
 GN2  C32  C   CH2   0  -0.183   1.4826  -5.8916   1.0403
 GN2  C33  C   CH2   0  -0.335   1.0891  -4.4312   1.1660
 GN2  H1   H   HCR6  0   0.250  -0.9643  -0.1619   1.9891
 GN2  H2   H   HCR6  0   0.250  -2.0427  -0.8003  -2.1095
 GN2  H3   H   HCR5  0   0.298  -4.6280   1.5763  -1.8691
 GN2  H4   H   HCR5  0   0.299  -6.3973  -0.5871   1.7052
 GN2  H5   H   HCR5  0   0.273  -3.8219  -0.2812   1.9777
 GN2  H6   H   HCR6  0   0.270   0.2201  -2.2403   2.0114
 GN2  H7   H   HCR6  0   0.265  -0.8573  -2.8829  -2.1022
 GN2  H8   H   HNH1  0   0.404  -2.4610   1.7723   1.9127
 GN2  H10  H   HCH2  0   0.298  -2.1998   1.2826  -2.2557
 GN2  H11  H   HCH2  0   0.311  -2.6483   2.7464  -1.3958
 GN2  H12  H   HCR6  0   0.278   1.1792   0.3973   0.0551
 GN2  H13  H   HCR6  0   0.255   2.7414  -1.4252   0.5396
 GN2  H14  H   HCR6  0   0.270   5.1363  -0.9378   0.9853
 GN2  H15  H   HCR6  0   0.284   5.9337   1.4037   0.9410
 GN2  H16  H   HCH2  0   0.261   0.8327  -4.0082  -2.1489
 GN2  H17  H   HCH2  0   0.221   2.2560  -3.6245  -1.1853
 GN2  H18  H   HCH2  0   0.207   0.8230  -6.3113  -1.4493
 GN2  H19  H   HCH2  0   0.243   2.4300  -5.8879  -2.0643
 GN2  H20  H   HCH2  0   0.206   0.5740  -6.5034   0.9507
 GN2  H21  H   HCH2  0   0.244   2.0092  -6.2049   1.9427
 GN2  H22  H   HCH2  0   0.219   1.9691  -3.8324   1.4502
 GN2  H23  H   HCH2  0   0.259   0.3662  -4.3531   1.9794
 GN2  H9   H   HOH1  0   0.483   0.8740   2.7991  -2.3941

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
 GN2  O31  C30  single    1.409  0.020  1.409
 GN2  O31  C32  single    1.408  0.020  1.408
 GN2  C30  C29  single    1.515  0.020  1.515
 GN2  C29  N7   single    1.457  0.020  1.457
 GN2  C32  C33  single    1.518  0.020  1.518
 GN2  N7   C33  single    1.450  0.020  1.450
 GN2  N7   C2   single    1.392  0.020  1.392
 GN2  C2   C1   aromatic  1.404  0.020  1.404
 GN2  C2   C3   aromatic  1.398  0.020  1.398
 GN2  C1   C6   aromatic  1.380  0.020  1.380
 GN2  C3   C4   aromatic  1.389  0.020  1.389
 GN2  C6   C5   aromatic  1.395  0.020  1.395
 GN2  C4   C5   aromatic  1.387  0.020  1.387
 GN2  C5   C8   single    1.533  0.020  1.533
 GN2  N14  C8   single    1.456  0.020  1.456
 GN2  N14  C15  single    1.359  0.020  1.359
 GN2  C8   C18  single    1.528  0.020  1.528
 GN2  C8   C9   single    1.512  0.020  1.512
 GN2  O20  C15  double    1.221  0.020  1.221
 GN2  C15  C16  single    1.472  0.020  1.472
 GN2  C18  C17  single    1.491  0.020  1.491
 GN2  C9   C10  aromatic  1.362  0.020  1.362
 GN2  C9   C13  aromatic  1.429  0.020  1.429
 GN2  C10  S11  aromatic  1.713  0.020  1.713
 GN2  C16  C17  double    1.355  0.020  1.355
 GN2  C16  S21  single    1.749  0.020  1.749
 GN2  C17  O19  single    1.315  0.020  1.315
 GN2  C13  C12  aromatic  1.358  0.020  1.358
 GN2  S11  C12  aromatic  1.713  0.020  1.713
 GN2  S21  C22  single    1.773  0.020  1.773
 GN2  C23  C22  aromatic  1.390  0.020  1.390
 GN2  C23  C24  aromatic  1.386  0.020  1.386
 GN2  C22  C27  aromatic  1.393  0.020  1.393
 GN2  C24  C25  aromatic  1.388  0.020  1.388
 GN2  C27  CL   single    1.733  0.020  1.733
 GN2  C27  C26  aromatic  1.385  0.020  1.385
 GN2  C25  C26  aromatic  1.387  0.020  1.387
 GN2  C4   H1   single    0.930  0.020  1.080
 GN2  C6   H2   single    0.930  0.020  1.080
 GN2  C10  H3   single    0.930  0.020  1.080
 GN2  C12  H4   single    0.930  0.020  1.080
 GN2  C13  H5   single    0.930  0.020  1.080
 GN2  C3   H6   single    0.930  0.020  1.080
 GN2  C1   H7   single    0.930  0.020  1.080
 GN2  N14  H8   single    0.890  0.020  1.040
 GN2  C18  H10  single    0.970  0.020  1.090
 GN2  C18  H11  single    0.970  0.020  1.090
 GN2  C23  H12  single    0.930  0.020  1.080
 GN2  C24  H13  single    0.930  0.020  1.080
 GN2  C25  H14  single    0.930  0.020  1.080
 GN2  C26  H15  single    0.930  0.020  1.080
 GN2  C29  H16  single    0.970  0.020  1.090
 GN2  C29  H17  single    0.970  0.020  1.090
 GN2  C30  H18  single    0.970  0.020  1.090
 GN2  C30  H19  single    0.970  0.020  1.090
 GN2  C32  H20  single    0.970  0.020  1.090
 GN2  C32  H21  single    0.970  0.020  1.090
 GN2  C33  H22  single    0.970  0.020  1.090
 GN2  C33  H23  single    0.970  0.020  1.090
 GN2  O19  H9   single    0.850  0.020  0.980

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
 GN2  H1   C4   C3   117.51  3.000
 GN2  H1   C4   C5   120.65  3.000
 GN2  C3   C4   C5   121.82  3.000
 GN2  C8   C5   C6   120.97  3.000
 GN2  C8   C5   C4   121.95  3.000
 GN2  C6   C5   C4   117.04  3.000
 GN2  H2   C6   C1   117.68  3.000
 GN2  H2   C6   C5   120.61  3.000
 GN2  C1   C6   C5   121.71  3.000
 GN2  C18  C8   N14  106.44  3.000
 GN2  C18  C8   C9   111.53  3.000
 GN2  N14  C8   C9   108.29  3.000
 GN2  C9   C8   C5   108.22  3.000
 GN2  C18  C8   C5   110.96  3.000
 GN2  N14  C8   C5   111.39  3.000
 GN2  C13  C9   C10  111.80  3.000
 GN2  C13  C9   C8   122.35  3.000
 GN2  C10  C9   C8   125.83  3.000
 GN2  H3   C10  S11  119.48  3.000
 GN2  H3   C10  C9   128.55  3.000
 GN2  S11  C10  C9   111.97  3.000
 GN2  H4   C12  S11  120.63  3.000
 GN2  H4   C12  C13  127.84  3.000
 GN2  S11  C12  C13  111.53  3.000
 GN2  H5   C13  C12  122.86  3.000
 GN2  H5   C13  C9   124.32  3.000
 GN2  C12  C13  C9   112.83  3.000
 GN2  H6   C3   C2   121.06  3.000
 GN2  H6   C3   C4   117.75  3.000
 GN2  C2   C3   C4   121.18  3.000
 GN2  H7   C1   C2   120.35  3.000
 GN2  H7   C1   C6   118.29  3.000
 GN2  C2   C1   C6   121.34  3.000
 GN2  N7   C2   C1   120.45  3.000
 GN2  C1   C2   C3   116.86  3.000
 GN2  N7   C2   C3   122.67  3.000
 GN2  C33  N7   C29  111.73  3.000
 GN2  C33  N7   C2   117.98  3.000
 GN2  C29  N7   C2   117.44  3.000
 GN2  C12  S11  C10   91.86  3.000
 GN2  H8   N14  C15  115.76  3.000
 GN2  H8   N14  C8   118.14  3.000
 GN2  C15  N14  C8   122.75  3.000
 GN2  O20  C15  C16  122.28  3.000
 GN2  C16  C15  N14  115.53  3.000
 GN2  O20  C15  N14  122.18  3.000
 GN2  S21  C16  C17  120.14  3.000
 GN2  S21  C16  C15  118.87  3.000
 GN2  C17  C16  C15  120.48  3.000
 GN2  O19  C17  C18  114.70  3.000
 GN2  O19  C17  C16  124.95  3.000
 GN2  C18  C17  C16  120.30  3.000
 GN2  H11  C18  H10  107.06  3.000
 GN2  H11  C18  C17  107.75  3.000
 GN2  H10  C18  C17  110.26  3.000
 GN2  H11  C18  C8   109.54  3.000
 GN2  H10  C18  C8   112.02  3.000
 GN2  C17  C18  C8   110.07  3.000
 GN2  H9   O19  C17  110.17  3.000
 GN2  C22  S21  C16  103.43  3.000
 GN2  C27  C22  C23  118.33  3.000
 GN2  C27  C22  S21  117.99  3.000
 GN2  C23  C22  S21  123.68  3.000
 GN2  H12  C23  C24  119.61  3.000
 GN2  H12  C23  C22  119.88  3.000
 GN2  C24  C23  C22  120.51  3.000
 GN2  H13  C24  C25  120.27  3.000
 GN2  H13  C24  C23  119.23  3.000
 GN2  C25  C24  C23  120.50  3.000
 GN2  H14  C25  C26  119.71  3.000
 GN2  H14  C25  C24  120.63  3.000
 GN2  C26  C25  C24  119.65  3.000
 GN2  H15  C26  C27  119.83  3.000
 GN2  H15  C26  C25  120.65  3.000
 GN2  C27  C26  C25  119.52  3.000
 GN2  CL   C27  C26  119.14  3.000
 GN2  C26  C27  C22  121.49  3.000
 GN2  CL   C27  C22  119.37  3.000
 GN2  H17  C29  H16  107.14  3.000
 GN2  H17  C29  C30  109.88  3.000
 GN2  H16  C29  C30  107.90  3.000
 GN2  H17  C29  N7   110.66  3.000
 GN2  H16  C29  N7   110.84  3.000
 GN2  C30  C29  N7   110.34  3.000
 GN2  H19  C30  H18  108.02  3.000
 GN2  H19  C30  O31  107.61  3.000
 GN2  H18  C30  O31  110.64  3.000
 GN2  H19  C30  C29  109.57  3.000
 GN2  H18  C30  C29  109.25  3.000
 GN2  O31  C30  C29  111.68  3.000
 GN2  C32  O31  C30  110.41  3.000
 GN2  H21  C32  H20  107.86  3.000
 GN2  H21  C32  C33  109.45  3.000
 GN2  H20  C32  C33  109.15  3.000
 GN2  H21  C32  O31  107.64  3.000
 GN2  H20  C32  O31  110.50  3.000
 GN2  C33  C32  O31  112.14  3.000
 GN2  H23  C33  H22  107.35  3.000
 GN2  H23  C33  C32  107.60  3.000
 GN2  H22  C33  C32  109.71  3.000
 GN2  H23  C33  N7   109.91  3.000
 GN2  H22  C33  N7   111.97  3.000
 GN2  C32  C33  N7   110.17  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
 GN2  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 GN2  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 GN2  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 GN2  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 GN2  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 GN2  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 GN2  CONST_07  C12  S11  C10  C9      0.00   0.0  0
 GN2  CONST_08  S11  C12  C13  C9      0.00   0.0  0
 GN2  CONST_09  C12  C13  C9   C10     0.00   0.0  0
 GN2  CONST_10  C13  C12  S11  C10     0.00   0.0  0
 GN2  CONST_11  S11  C10  C9   C13     0.00   0.0  0
 GN2  CONST_12  C25  C24  C23  C22     0.00   0.0  0
 GN2  CONST_13  C25  C26  C27  C22     0.00   0.0  0
 GN2  CONST_14  C26  C27  C22  C23     0.00   0.0  0
 GN2  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 GN2  CONST_16  C27  C22  C23  C24     0.00   0.0  0
 GN2  CONST_17  C27  C26  C25  C24     0.00   0.0  0
 GN2  CONST_18  N7   C2   C3   C4    180.00   0.0  0
 GN2  CONST_19  N7   C2   C1   C6    180.00   0.0  0
 GN2  CONST_20  C1   C6   C5   C8    180.00   0.0  0
 GN2  CONST_21  C3   C4   C5   C8    180.00   0.0  0
 GN2  CONST_22  S11  C10  C9   C8    180.00   0.0  0
 GN2  CONST_23  C12  C13  C9   C8    180.00   0.0  0
 GN2  CONST_25  C24  C23  C22  S21   180.00   0.0  0
 GN2  CONST_26  C26  C27  C22  S21   180.00   0.0  0
 GN2  CONST_27  CL   C27  C22  C23   180.00   0.0  0
 GN2  CONST_28  CL   C27  C26  C25   180.00   0.0  0
 GN2  CONST_30  H2   C6   C5   C4    180.00   0.0  0
 GN2  CONST_31  H7   C1   C6   C5    180.00   0.0  0
 GN2  CONST_32  H6   C3   C4   C5    180.00   0.0  0
 GN2  CONST_33  H1   C4   C5   C6    180.00   0.0  0
 GN2  CONST_34  H3   C10  C9   C8      0.00   0.0  0
 GN2  CONST_35  H5   C13  C9   C8      0.00   0.0  0
 GN2  CONST_36  H4   C12  C13  C9    180.00   0.0  0
 GN2  CONST_37  H13  C24  C23  C22   180.00   0.0  0
 GN2  CONST_38  H15  C26  C27  C22   180.00   0.0  0
 GN2  CONST_39  H14  C25  C24  C23   180.00   0.0  0
 GN2  CONST_40  H12  C23  C24  C25   180.00   0.0  0
 GN2  CONST_41  H8   N14  C15  C16   180.00   0.0  0
 GN2  Var_01    C16  C17  C18  C8    -32.56  30.0  1
 GN2  Var_02    C29  N7   C2   C3   -136.21  30.0  3
 GN2  Var_03    C30  C29  N7   C2   -165.96  30.0  1
 GN2  Var_04    C32  C33  N7   C2    166.60  30.0  1
 GN2  Var_05    O31  C30  C29  N7    -55.95  30.0  1
 GN2  Var_06    O31  C32  C33  N7     55.61  30.0  1
 GN2  Var_07    C17  C16  C15  N14    11.15  30.0  1
 GN2  Var_08    C18  C17  C16  C15    -1.14  30.0  1
 GN2  Var_09    C33  C32  O31  C30   -58.58  30.0  1
 GN2  Var_10    C23  C22  S21  C16     8.28  30.0  2

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
 GN2  chir_01  C8  N14  C18  C9  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
 GN2  plan-1  C8   0.020
 GN2  plan-1  C9   0.020
 GN2  plan-1  C10  0.020
 GN2  plan-1  C12  0.020
 GN2  plan-1  C13  0.020
 GN2  plan-1  S11  0.020
 GN2  plan-1  H3   0.020
 GN2  plan-1  H4   0.020
 GN2  plan-1  H5   0.020
 GN2  plan-2  C4   0.020
 GN2  plan-2  C5   0.020
 GN2  plan-2  C6   0.020
 GN2  plan-2  C8   0.020
 GN2  plan-2  C3   0.020
 GN2  plan-2  C1   0.020
 GN2  plan-2  C2   0.020
 GN2  plan-2  N7   0.020
 GN2  plan-2  H1   0.020
 GN2  plan-2  H2   0.020
 GN2  plan-2  H6   0.020
 GN2  plan-2  H7   0.020
 GN2  plan-3  S21  0.020
 GN2  plan-3  C22  0.020
 GN2  plan-3  C23  0.020
 GN2  plan-3  C24  0.020
 GN2  plan-3  C25  0.020
 GN2  plan-3  C26  0.020
 GN2  plan-3  C27  0.020
 GN2  plan-3  CL   0.020
 GN2  plan-3  H12  0.020
 GN2  plan-3  H13  0.020
 GN2  plan-3  H14  0.020
 GN2  plan-3  H15  0.020
 GN2  plan-4  C8   0.020
 GN2  plan-4  N14  0.020
 GN2  plan-4  C15  0.020
 GN2  plan-4  C16  0.020
 GN2  plan-4  O20  0.020
 GN2  plan-4  H8   0.020

