# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 13:31:45 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: (2~{R})-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
 GN0  GN0  (2~{R})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one  ligand  56  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GN0
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
 GN0  C4   C   CR16  0  -0.302  -2.6535  -0.1994  -1.0601
 GN0  C5   C   CR6   0   0.175  -2.0074  -0.4464   0.1474
 GN0  C6   C   CR16  0  -0.320  -2.8127  -0.6746   1.2582
 GN0  C8   C   CT    0  -0.079  -0.4863  -0.4195   0.2153
 GN0  C9   C   CR5   0   0.232  -0.0071   0.9936  -0.1082
 GN0  C10  C   CR15  0  -0.539   0.1478   1.9939   0.8068
 GN0  C12  C   CR15  0  -0.456   0.6777   2.7443  -1.4753
 GN0  C13  C   CR15  0  -0.221   0.3026   1.4378  -1.4289
 GN0  C3   C   CR16  0  -0.343  -4.0341  -0.1845  -1.1640
 GN0  C1   C   CR16  0  -0.317  -4.1940  -0.6641   1.1687
 GN0  C2   C   CR6   0   0.367  -4.8471  -0.4220  -0.0472
 GN0  N7   N   NT    0  -0.523  -6.2339  -0.4481  -0.1282
 GN0  S11  S   S2    0   0.225   0.6641   3.4560   0.0807
 GN0  N14  N   NH1   0  -0.649   0.0456  -1.3662  -0.7578
 GN0  C15  C   C     0   0.548   1.3627  -1.6904  -0.8202
 GN0  C16  C   C     0  -0.485   2.1456  -1.3745   0.3847
 GN0  C17  C   C     0   0.530   1.5247  -1.0034   1.5307
 GN0  C18  C   CH2   0  -0.586   0.0418  -0.8537   1.5802
 GN0  O19  O   OH1   0  -0.564   2.1333  -0.7861   2.6764
 GN0  O20  O   O     0  -0.469   1.8533  -2.2409  -1.7937
 GN0  S21  S   S2    0   0.086   3.8661  -1.6924   0.3850
 GN0  C22  C   CR6   0  -0.037   4.5635  -0.1595  -0.1701
 GN0  C23  C   CR16  0  -0.241   3.8152   0.9883  -0.4068
 GN0  C24  C   CR16  0  -0.233   4.4314   2.1546  -0.8332
 GN0  C25  C   CR16  0  -0.275   5.8052   2.1962  -1.0228
 GN0  C26  C   CR16  0  -0.200   6.5658   1.0613  -0.7854
 GN0  C27  C   CR6   0  -0.065   5.9421  -0.1016  -0.3643
 GN0  CL   CL  CL    0  -0.117   6.9009  -1.5148  -0.0676
 GN0  C29  C   CH2   0  -0.330  -6.8494  -0.2520  -1.4269
 GN0  C30  C   CH2   0  -0.184  -8.3125  -0.6534  -1.3801
 GN0  O31  O   O2    0  -0.481  -9.0188   0.0341  -0.3745
 GN0  C32  C   CH2   0  -0.188  -8.4429  -0.2192   0.8857
 GN0  C33  C   CH2   0  -0.323  -6.9884   0.2030   0.9348
 GN0  H1   H   HCR6  0   0.252  -2.0853   0.0140  -1.9583
 GN0  H2   H   HCR6  0   0.261  -2.3813  -0.8744   2.2297
 GN0  H3   H   HCR5  0   0.294  -0.0226   1.9641   1.8723
 GN0  H4   H   HCR5  0   0.299   0.9687   3.3190  -2.3411
 GN0  H5   H   HCR5  0   0.269   0.2690   0.8100  -2.3081
 GN0  H6   H   HCR6  0   0.272  -4.4654   0.0370  -2.1299
 GN0  H7   H   HCR6  0   0.265  -4.7621  -0.8717   2.0653
 GN0  H8   H   HNH1  0   0.404  -0.4951  -1.5541  -1.5894
 GN0  H10  H   HCH2  0   0.295  -0.2316  -0.1476   2.3632
 GN0  H11  H   HCH2  0   0.317  -0.3868  -1.8218   1.8588
 GN0  H12  H   HCR6  0   0.277   2.7434   0.9726  -0.2599
 GN0  H13  H   HCR6  0   0.259   3.8279   3.0339  -1.0150
 GN0  H14  H   HCR6  0   0.270   6.2880   3.1054  -1.3538
 GN0  H15  H   HCR6  0   0.284   7.6381   1.0768  -0.9260
 GN0  H16  H   HCH2  0   0.222  -6.7569   0.7901  -1.7684
 GN0  H17  H   HCH2  0   0.258  -6.3597  -0.8840  -2.1692
 GN0  H18  H   HCH2  0   0.243  -8.7830  -0.4172  -2.3355
 GN0  H19  H   HCH2  0   0.206  -8.3849  -1.7394  -1.2261
 GN0  H20  H   HCH2  0   0.243  -9.0108   0.3430   1.6282
 GN0  H21  H   HCH2  0   0.206  -8.5205  -1.2865   1.1363
 GN0  H22  H   HCH2  0   0.260  -6.5968  -0.0740   1.9115
 GN0  H23  H   HCH2  0   0.225  -6.9117   1.2967   0.8499
 GN0  H9   H   HOH1  0   0.483   3.0853  -0.9722   2.5890

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
 GN0  O31  C30  single    1.408  0.020  1.408
 GN0  O31  C32  single    1.409  0.020  1.409
 GN0  C30  C29  single    1.518  0.020  1.518
 GN0  C32  C33  single    1.515  0.020  1.515
 GN0  C29  N7   single    1.450  0.020  1.450
 GN0  C33  N7   single    1.457  0.020  1.457
 GN0  N7   C2   single    1.389  0.020  1.389
 GN0  C2   C1   aromatic  1.401  0.020  1.401
 GN0  C2   C3   aromatic  1.402  0.020  1.402
 GN0  C1   C6   aromatic  1.384  0.020  1.384
 GN0  C3   C4   aromatic  1.385  0.020  1.385
 GN0  C6   C5   aromatic  1.391  0.020  1.391
 GN0  C4   C5   aromatic  1.392  0.020  1.392
 GN0  C5   C8   single    1.523  0.020  1.523
 GN0  C18  C8   single    1.527  0.020  1.527
 GN0  C18  C17  single    1.491  0.020  1.491
 GN0  C8   N14  single    1.458  0.020  1.458
 GN0  C8   C9   single    1.527  0.020  1.527
 GN0  O19  C17  single    1.315  0.020  1.315
 GN0  C17  C16  double    1.355  0.020  1.355
 GN0  N14  C15  single    1.358  0.020  1.358
 GN0  C9   C10  aromatic  1.364  0.020  1.364
 GN0  C9   C13  aromatic  1.427  0.020  1.427
 GN0  C10  S11  aromatic  1.712  0.020  1.712
 GN0  C16  C15  single    1.471  0.020  1.471
 GN0  C16  S21  single    1.750  0.020  1.750
 GN0  C15  O20  double    1.221  0.020  1.221
 GN0  C13  C12  aromatic  1.360  0.020  1.360
 GN0  S11  C12  aromatic  1.711  0.020  1.711
 GN0  S21  C22  single    1.773  0.020  1.773
 GN0  C23  C22  aromatic  1.390  0.020  1.390
 GN0  C23  C24  aromatic  1.386  0.020  1.386
 GN0  C22  C27  aromatic  1.393  0.020  1.393
 GN0  C24  C25  aromatic  1.387  0.020  1.387
 GN0  C27  CL   single    1.733  0.020  1.733
 GN0  C27  C26  aromatic  1.385  0.020  1.385
 GN0  C25  C26  aromatic  1.387  0.020  1.387
 GN0  C4   H1   single    0.930  0.020  1.080
 GN0  C6   H2   single    0.930  0.020  1.080
 GN0  C10  H3   single    0.930  0.020  1.080
 GN0  C12  H4   single    0.930  0.020  1.080
 GN0  C13  H5   single    0.930  0.020  1.080
 GN0  C3   H6   single    0.930  0.020  1.080
 GN0  C1   H7   single    0.930  0.020  1.080
 GN0  N14  H8   single    0.890  0.020  1.040
 GN0  C18  H10  single    0.970  0.020  1.090
 GN0  C18  H11  single    0.970  0.020  1.090
 GN0  C23  H12  single    0.930  0.020  1.080
 GN0  C24  H13  single    0.930  0.020  1.080
 GN0  C25  H14  single    0.930  0.020  1.080
 GN0  C26  H15  single    0.930  0.020  1.080
 GN0  C29  H16  single    0.970  0.020  1.090
 GN0  C29  H17  single    0.970  0.020  1.090
 GN0  C30  H18  single    0.970  0.020  1.090
 GN0  C30  H19  single    0.970  0.020  1.090
 GN0  C32  H20  single    0.970  0.020  1.090
 GN0  C32  H21  single    0.970  0.020  1.090
 GN0  C33  H22  single    0.970  0.020  1.090
 GN0  C33  H23  single    0.970  0.020  1.090
 GN0  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
 GN0  H1   C4   C3   117.28  3.000
 GN0  H1   C4   C5   120.70  3.000
 GN0  C3   C4   C5   122.01  3.000
 GN0  C8   C5   C6   123.07  3.000
 GN0  C8   C5   C4   119.95  3.000
 GN0  C6   C5   C4   116.95  3.000
 GN0  H2   C6   C1   117.22  3.000
 GN0  H2   C6   C5   121.11  3.000
 GN0  C1   C6   C5   121.66  3.000
 GN0  C18  C8   N14  106.61  3.000
 GN0  N14  C8   C9   110.19  3.000
 GN0  C18  C8   C9   110.13  3.000
 GN0  C9   C8   C5   108.69  3.000
 GN0  N14  C8   C5   108.85  3.000
 GN0  C18  C8   C5   112.35  3.000
 GN0  C13  C9   C10  111.58  3.000
 GN0  C13  C9   C8   123.51  3.000
 GN0  C10  C9   C8   124.89  3.000
 GN0  H3   C10  S11  119.33  3.000
 GN0  H3   C10  C9   128.59  3.000
 GN0  S11  C10  C9   112.07  3.000
 GN0  H4   C12  S11  120.68  3.000
 GN0  H4   C12  C13  127.83  3.000
 GN0  S11  C12  C13  111.49  3.000
 GN0  H5   C13  C12  122.60  3.000
 GN0  H5   C13  C9   124.41  3.000
 GN0  C12  C13  C9   112.98  3.000
 GN0  H6   C3   C2   121.02  3.000
 GN0  H6   C3   C4   117.86  3.000
 GN0  C2   C3   C4   121.11  3.000
 GN0  H7   C1   C2   120.51  3.000
 GN0  H7   C1   C6   117.97  3.000
 GN0  C2   C1   C6   121.50  3.000
 GN0  N7   C2   C1   120.83  3.000
 GN0  C1   C2   C3   116.77  3.000
 GN0  N7   C2   C3   122.39  3.000
 GN0  C33  N7   C29  111.91  3.000
 GN0  C33  N7   C2   117.77  3.000
 GN0  C29  N7   C2   118.24  3.000
 GN0  C12  S11  C10   91.89  3.000
 GN0  H8   N14  C15  115.92  3.000
 GN0  H8   N14  C8   118.37  3.000
 GN0  C15  N14  C8   122.65  3.000
 GN0  O20  C15  C16  122.40  3.000
 GN0  O20  C15  N14  122.27  3.000
 GN0  C16  C15  N14  115.29  3.000
 GN0  S21  C16  C17  120.01  3.000
 GN0  S21  C16  C15  118.97  3.000
 GN0  C17  C16  C15  120.50  3.000
 GN0  O19  C17  C18  114.49  3.000
 GN0  O19  C17  C16  124.74  3.000
 GN0  C18  C17  C16  120.74  3.000
 GN0  H11  C18  H10  106.98  3.000
 GN0  H11  C18  C17  107.99  3.000
 GN0  H10  C18  C17  109.79  3.000
 GN0  H11  C18  C8   110.10  3.000
 GN0  H10  C18  C8   111.81  3.000
 GN0  C17  C18  C8   110.05  3.000
 GN0  H9   O19  C17  110.03  3.000
 GN0  C22  S21  C16  103.27  3.000
 GN0  C27  C22  C23  118.32  3.000
 GN0  C27  C22  S21  117.95  3.000
 GN0  C23  C22  S21  123.73  3.000
 GN0  H12  C23  C24  119.62  3.000
 GN0  H12  C23  C22  119.87  3.000
 GN0  C24  C23  C22  120.50  3.000
 GN0  H13  C24  C25  120.33  3.000
 GN0  H13  C24  C23  119.18  3.000
 GN0  C25  C24  C23  120.49  3.000
 GN0  H14  C25  C26  119.71  3.000
 GN0  H14  C25  C24  120.60  3.000
 GN0  C26  C25  C24  119.68  3.000
 GN0  H15  C26  C27  119.86  3.000
 GN0  H15  C26  C25  120.65  3.000
 GN0  C27  C26  C25  119.48  3.000
 GN0  CL   C27  C26  119.17  3.000
 GN0  C26  C27  C22  121.52  3.000
 GN0  CL   C27  C22  119.31  3.000
 GN0  H17  C29  H16  107.44  3.000
 GN0  H17  C29  C30  107.48  3.000
 GN0  H16  C29  C30  109.93  3.000
 GN0  H17  C29  N7   109.91  3.000
 GN0  H16  C29  N7   111.73  3.000
 GN0  C30  C29  N7   110.22  3.000
 GN0  H19  C30  H18  107.95  3.000
 GN0  H19  C30  O31  110.44  3.000
 GN0  H18  C30  O31  107.66  3.000
 GN0  H19  C30  C29  109.21  3.000
 GN0  H18  C30  C29  109.36  3.000
 GN0  O31  C30  C29  112.11  3.000
 GN0  C32  O31  C30  110.25  3.000
 GN0  H21  C32  H20  107.97  3.000
 GN0  H21  C32  C33  109.32  3.000
 GN0  H20  C32  C33  109.52  3.000
 GN0  H21  C32  O31  110.47  3.000
 GN0  H20  C32  O31  107.67  3.000
 GN0  C33  C32  O31  111.80  3.000
 GN0  H23  C33  H22  107.31  3.000
 GN0  H23  C33  C32  109.97  3.000
 GN0  H22  C33  C32  107.67  3.000
 GN0  H23  C33  N7   110.60  3.000
 GN0  H22  C33  N7   110.78  3.000
 GN0  C32  C33  N7   110.42  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
 GN0  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 GN0  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 GN0  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 GN0  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 GN0  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 GN0  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 GN0  CONST_07  C12  S11  C10  C9      0.00   0.0  0
 GN0  CONST_08  S11  C12  C13  C9      0.00   0.0  0
 GN0  CONST_09  C12  C13  C9   C10     0.00   0.0  0
 GN0  CONST_10  C13  C12  S11  C10     0.00   0.0  0
 GN0  CONST_11  S11  C10  C9   C13     0.00   0.0  0
 GN0  CONST_12  C25  C24  C23  C22     0.00   0.0  0
 GN0  CONST_13  C25  C26  C27  C22     0.00   0.0  0
 GN0  CONST_14  C26  C27  C22  C23     0.00   0.0  0
 GN0  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 GN0  CONST_16  C27  C22  C23  C24     0.00   0.0  0
 GN0  CONST_17  C27  C26  C25  C24     0.00   0.0  0
 GN0  CONST_18  N7   C2   C3   C4    180.00   0.0  0
 GN0  CONST_19  N7   C2   C1   C6    180.00   0.0  0
 GN0  CONST_20  C1   C6   C5   C8    180.00   0.0  0
 GN0  CONST_21  C3   C4   C5   C8    180.00   0.0  0
 GN0  CONST_22  S11  C10  C9   C8    180.00   0.0  0
 GN0  CONST_23  C12  C13  C9   C8    180.00   0.0  0
 GN0  CONST_25  C24  C23  C22  S21   180.00   0.0  0
 GN0  CONST_26  C26  C27  C22  S21   180.00   0.0  0
 GN0  CONST_27  CL   C27  C22  C23   180.00   0.0  0
 GN0  CONST_28  CL   C27  C26  C25   180.00   0.0  0
 GN0  CONST_30  H2   C6   C5   C4    180.00   0.0  0
 GN0  CONST_31  H7   C1   C6   C5    180.00   0.0  0
 GN0  CONST_32  H6   C3   C4   C5    180.00   0.0  0
 GN0  CONST_33  H1   C4   C5   C6    180.00   0.0  0
 GN0  CONST_34  H3   C10  C9   C8      0.00   0.0  0
 GN0  CONST_35  H5   C13  C9   C8      0.00   0.0  0
 GN0  CONST_36  H4   C12  C13  C9    180.00   0.0  0
 GN0  CONST_37  H13  C24  C23  C22   180.00   0.0  0
 GN0  CONST_38  H15  C26  C27  C22   180.00   0.0  0
 GN0  CONST_39  H14  C25  C24  C23   180.00   0.0  0
 GN0  CONST_40  H12  C23  C24  C25   180.00   0.0  0
 GN0  CONST_41  H8   N14  C15  C16   180.00   0.0  0
 GN0  Var_01    C16  C17  C18  C8    -30.60  30.0  1
 GN0  Var_02    C29  N7   C2   C3      1.47  30.0  3
 GN0  Var_03    C30  C29  N7   C2    165.89  30.0  1
 GN0  Var_04    C32  C33  N7   C2   -165.45  30.0  1
 GN0  Var_05    O31  C30  C29  N7     55.64  30.0  1
 GN0  Var_06    O31  C32  C33  N7    -55.71  30.0  1
 GN0  Var_07    C17  C16  C15  N14    10.68  30.0  1
 GN0  Var_08    C18  C17  C16  C15    -2.50  30.0  1
 GN0  Var_09    C33  C32  O31  C30    58.83  30.0  1
 GN0  Var_10    C23  C22  S21  C16     4.73  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
 GN0  chir_01  C8  C18  N14  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
 GN0  plan-1  C8   0.020
 GN0  plan-1  C9   0.020
 GN0  plan-1  C10  0.020
 GN0  plan-1  C12  0.020
 GN0  plan-1  C13  0.020
 GN0  plan-1  S11  0.020
 GN0  plan-1  H3   0.020
 GN0  plan-1  H4   0.020
 GN0  plan-1  H5   0.020
 GN0  plan-2  C4   0.020
 GN0  plan-2  C5   0.020
 GN0  plan-2  C6   0.020
 GN0  plan-2  C8   0.020
 GN0  plan-2  C3   0.020
 GN0  plan-2  C1   0.020
 GN0  plan-2  C2   0.020
 GN0  plan-2  N7   0.020
 GN0  plan-2  H1   0.020
 GN0  plan-2  H2   0.020
 GN0  plan-2  H6   0.020
 GN0  plan-2  H7   0.020
 GN0  plan-3  S21  0.020
 GN0  plan-3  C22  0.020
 GN0  plan-3  C23  0.020
 GN0  plan-3  C24  0.020
 GN0  plan-3  C25  0.020
 GN0  plan-3  C26  0.020
 GN0  plan-3  C27  0.020
 GN0  plan-3  CL   0.020
 GN0  plan-3  H12  0.020
 GN0  plan-3  H13  0.020
 GN0  plan-3  H14  0.020
 GN0  plan-3  H15  0.020
 GN0  plan-4  C8   0.020
 GN0  plan-4  N14  0.020
 GN0  plan-4  C15  0.020
 GN0  plan-4  C16  0.020
 GN0  plan-4  O20  0.020
 GN0  plan-4  H8   0.020

