# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:51:12 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN(C1)CC2=Nc3c(sc4ccc(Cl)cc34)C(=O)N2
#
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
 LYG  LYG  8-chloro-2-{[(3S)-3-hydroxypyrrolidin-1-yl]methyl}[1]benzothieno[3,2-d]pyrimidin-4(3H)-one  ligand  36  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LYG
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
 LYG  C1    C   CH1   0   0.036   4.8856   1.6099   0.2027
 LYG  N1    N   NT    0  -0.426   3.2117  -0.0251   0.2581
 LYG  O1    O   OH1   0  -0.676   6.2633   1.6976  -0.0779
 LYG  S1    S   S2    0   0.262  -3.0491  -2.1107  -0.3003
 LYG  CL1   CL  CL    0  -0.120  -2.8017   4.0423   0.5235
 LYG  C2    C   CH2   0  -0.496   3.9562   1.7794  -1.0217
 LYG  N2    N   N     0  -0.437   0.4840  -0.5221   0.2967
 LYG  O2    O   O     0  -0.455  -0.7834  -4.3467  -0.3650
 LYG  C3    C   CH2   0  -0.284   3.1872   0.4628  -1.1118
 LYG  N3    N   NR16  0  -0.703   0.8590  -2.8016   0.0002
 LYG  C4    C   CH2   0  -0.367   2.7687  -1.3747   0.4280
 LYG  C5    C   CR6   0   0.494   1.2863  -1.5313   0.2274
 LYG  C6    C   CR56  0   0.299  -0.8328  -0.7947   0.1194
 LYG  C7    C   CR56  0   0.177  -1.8770   0.1937   0.1348
 LYG  C8    C   CR16  0  -0.263  -1.7576   1.5704   0.3258
 LYG  C9    C   CR6   0  -0.039  -2.9061   2.3287   0.2939
 LYG  C10   C   CR16  0  -0.209  -4.1649   1.7553   0.0789
 LYG  C11   C   CR16  0  -0.284  -4.2863   0.3939  -0.1107
 LYG  C12   C   CR56  0  -0.226  -3.1344  -0.3871  -0.0822
 LYG  C13   C   CR56  0  -0.406  -1.3332  -2.0543  -0.1038
 LYG  C14   C   CR6   0   0.554  -0.4616  -3.1876  -0.1735
 LYG  C15   C   CH2   0  -0.298   4.5711   0.2022   0.7070
 LYG  H1    H   HCH1  0   0.217   4.6080   2.3421   0.9696
 LYG  HO1   H   HOH1  0   0.451   6.4692   2.6138  -0.2855
 LYG  H2    H   HCH2  0   0.240   3.2733   2.6166  -0.8741
 LYG  H2A   H   HCH2  0   0.241   4.5263   1.9765  -1.9300
 LYG  H3    H   HCH2  0   0.201   3.6966  -0.2378  -1.7945
 LYG  H3A   H   HCH2  0   0.243   2.1646   0.5884  -1.4676
 LYG  HN3   H   HNR6  0   0.434   1.5523  -3.5391  -0.0507
 LYG  H4    H   HCH2  0   0.237   3.2924  -2.0847  -0.2359
 LYG  H4A   H   HCH2  0   0.295   2.9886  -1.7019   1.4504
 LYG  H8    H   HCR6  0   0.282  -0.7862   2.0166   0.4929
 LYG  H10   H   HCR6  0   0.290  -5.0470   2.3804   0.0600
 LYG  H11   H   HCR6  0   0.286  -5.2598  -0.0458  -0.2801
 LYG  H15   H   HCH2  0   0.200   5.2846  -0.5049   0.2491
 LYG  H15A  H   HCH2  0   0.246   4.6515   0.1025   1.7917

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
 LYG  C15  C1    single    1.528  0.020  1.528
 LYG  O1   C1    single    1.409  0.020  1.409
 LYG  C1   C2    single    1.546  0.020  1.546
 LYG  C1   H1    single    0.970  0.020  1.090
 LYG  C4   N1    single    1.430  0.020  1.430
 LYG  C15  N1    single    1.449  0.020  1.449
 LYG  N1   C3    single    1.454  0.020  1.454
 LYG  O1   HO1   single    0.850  0.020  0.980
 LYG  S1   C12   aromatic  1.739  0.020  1.739
 LYG  S1   C13   aromatic  1.728  0.020  1.728
 LYG  C9   CL1   single    1.732  0.020  1.732
 LYG  C3   C2    single    1.527  0.020  1.527
 LYG  C2   H2    single    0.970  0.020  1.090
 LYG  C2   H2A   single    0.970  0.020  1.090
 LYG  C6   N2    single    1.356  0.020  1.356
 LYG  C5   N2    double    1.291  0.020  1.291
 LYG  O2   C14   double    1.218  0.020  1.218
 LYG  C3   H3    single    0.970  0.020  1.090
 LYG  C3   H3A   single    0.970  0.020  1.090
 LYG  C14  N3    single    1.387  0.020  1.387
 LYG  N3   C5    single    1.359  0.020  1.359
 LYG  N3   HN3   single    0.860  0.020  1.020
 LYG  C5   C4    single    1.504  0.020  1.504
 LYG  C4   H4    single    0.970  0.020  1.090
 LYG  C4   H4A   single    0.970  0.020  1.090
 LYG  C13  C6    aromatic  1.374  0.020  1.374
 LYG  C7   C6    aromatic  1.438  0.020  1.438
 LYG  C12  C7    aromatic  1.402  0.020  1.402
 LYG  C7   C8    aromatic  1.395  0.020  1.395
 LYG  C9   C8    aromatic  1.377  0.020  1.377
 LYG  C8   H8    single    0.930  0.020  1.080
 LYG  C10  C9    aromatic  1.400  0.020  1.400
 LYG  C11  C10   aromatic  1.380  0.020  1.380
 LYG  C10  H10   single    0.930  0.020  1.080
 LYG  C11  C12   aromatic  1.392  0.020  1.392
 LYG  C11  H11   single    0.930  0.020  1.080
 LYG  C14  C13   single    1.431  0.020  1.431
 LYG  C15  H15   single    0.970  0.020  1.090
 LYG  C15  H15A  single    0.970  0.020  1.090

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
 LYG  H1    C1   C15  109.41  3.000
 LYG  H1    C1   C2   109.18  3.000
 LYG  C15   C1   C2   103.80  3.000
 LYG  H1    C1   O1   110.21  3.000
 LYG  C2    C1   O1   115.04  3.000
 LYG  C15   C1   O1   108.93  3.000
 LYG  C15   N1   C4   113.68  3.000
 LYG  C15   N1   C3   104.77  3.000
 LYG  C4    N1   C3   115.03  3.000
 LYG  HO1   O1   C1   108.16  3.000
 LYG  C13   S1   C12   90.12  3.000
 LYG  H2A   C2   H2   107.55  3.000
 LYG  H2A   C2   C3   111.71  3.000
 LYG  H2    C2   C3   110.76  3.000
 LYG  H2A   C2   C1   111.41  3.000
 LYG  H2    C2   C1   110.69  3.000
 LYG  C3    C2   C1   104.76  3.000
 LYG  C6    N2   C5   116.06  3.000
 LYG  H3A   C3   H3   107.73  3.000
 LYG  H3A   C3   C2   113.09  3.000
 LYG  H3    C3   C2   110.58  3.000
 LYG  H3A   C3   N1   111.22  3.000
 LYG  H3    C3   N1   111.23  3.000
 LYG  C2    C3   N1   103.01  3.000
 LYG  HN3   N3   C14  116.27  3.000
 LYG  HN3   N3   C5   118.26  3.000
 LYG  C14   N3   C5   125.47  3.000
 LYG  H4A   C4   H4   105.89  3.000
 LYG  H4A   C4   C5   106.93  3.000
 LYG  H4    C4   C5   108.69  3.000
 LYG  H4A   C4   N1   109.29  3.000
 LYG  H4    C4   N1   112.85  3.000
 LYG  C5    C4   N1   112.81  3.000
 LYG  C4    C5   N3   115.43  3.000
 LYG  C4    C5   N2   121.60  3.000
 LYG  N3    C5   N2   122.96  3.000
 LYG  C13   C6   C7   111.56  3.000
 LYG  C7    C6   N2   124.44  3.000
 LYG  C13   C6   N2   124.00  3.000
 LYG  C12   C7   C8   120.45  3.000
 LYG  C8    C7   C6   128.15  3.000
 LYG  C12   C7   C6   111.40  3.000
 LYG  H8    C8   C9   121.70  3.000
 LYG  H8    C8   C7   120.33  3.000
 LYG  C9    C8   C7   117.97  3.000
 LYG  C10   C9   C8   121.89  3.000
 LYG  C10   C9   CL1  118.67  3.000
 LYG  C8    C9   CL1  119.44  3.000
 LYG  H10   C10  C11  119.75  3.000
 LYG  H10   C10  C9   119.97  3.000
 LYG  C11   C10  C9   120.28  3.000
 LYG  H11   C11  C12  121.33  3.000
 LYG  H11   C11  C10  120.12  3.000
 LYG  C12   C11  C10  118.55  3.000
 LYG  C11   C12  C7   120.86  3.000
 LYG  C11   C12  S1   126.44  3.000
 LYG  C7    C12  S1   112.70  3.000
 LYG  C14   C13  C6   120.80  3.000
 LYG  C14   C13  S1   124.98  3.000
 LYG  C6    C13  S1   114.21  3.000
 LYG  C13   C14  N3   110.70  3.000
 LYG  C13   C14  O2   126.88  3.000
 LYG  N3    C14  O2   122.42  3.000
 LYG  H15A  C15  H15  107.81  3.000
 LYG  H15A  C15  N1   111.24  3.000
 LYG  H15   C15  N1   112.17  3.000
 LYG  H15A  C15  C1   113.37  3.000
 LYG  H15   C15  C1   108.67  3.000
 LYG  N1    C15  C1   103.61  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
 LYG  CONST_01  C6   C7   C12  S1     0.00   0.0  0
 LYG  CONST_02  C8   C7   C12  S1   180.00   0.0  0
 LYG  CONST_03  C10  C11  C12  S1   180.00   0.0  0
 LYG  CONST_04  C7   C6   C13  S1     0.00   0.0  0
 LYG  CONST_05  C12  S1   C13  C6     0.00   0.0  0
 LYG  CONST_06  C11  C12  C7   C6   180.00   0.0  0
 LYG  CONST_07  C9   C8   C7   C6   180.00   0.0  0
 LYG  CONST_08  C13  S1   C12  C7     0.00   0.0  0
 LYG  CONST_09  C10  C11  C12  C7     0.00   0.0  0
 LYG  CONST_10  C10  C9   C8   C7     0.00   0.0  0
 LYG  CONST_11  C13  C6   C7   C8   180.00   0.0  0
 LYG  CONST_12  C11  C12  C7   C8     0.00   0.0  0
 LYG  CONST_13  C11  C10  C9   C8     0.00   0.0  0
 LYG  CONST_14  C12  C7   C8   C9     0.00   0.0  0
 LYG  CONST_15  C12  C11  C10  C9     0.00   0.0  0
 LYG  CONST_16  C13  S1   C12  C11  180.00   0.0  0
 LYG  CONST_17  C13  C6   C7   C12    0.00   0.0  0
 LYG  CONST_18  C14  N3   C5   N2     0.00   0.0  0
 LYG  CONST_19  C6   N2   C5   N3     0.00   0.0  0
 LYG  CONST_20  C13  C14  N3   C5     0.00   0.0  0
 LYG  CONST_21  C7   C8   C9   CL1  180.00   0.0  0
 LYG  CONST_22  C11  C10  C9   CL1  180.00   0.0  0
 LYG  CONST_23  C5   N3   C14  O2   180.00   0.0  0
 LYG  CONST_24  C6   N2   C5   C4   180.00   0.0  0
 LYG  CONST_25  C14  N3   C5   C4   180.00   0.0  0
 LYG  CONST_26  H11  C11  C12  S1     0.00   0.0  0
 LYG  CONST_27  H8   C8   C7   C6     0.00   0.0  0
 LYG  CONST_28  H10  C10  C9   C8   180.00   0.0  0
 LYG  CONST_29  HN3  N3   C5   N2   180.00   0.0  0
 LYG  Var_01    C3   N1   C15  C1    43.97  30.0  1
 LYG  Var_02    N1   C3   C2   C1    25.56  30.0  1
 LYG  Var_03    C15  N1   C3   C2   -43.54  30.0  1
 LYG  Var_04    N2   C5   C4   N1   -19.17  30.0  3
 LYG  Var_05    C5   C4   N1   C3   -71.04  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
 LYG  chir_01  C1  C15  O1  C2  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
 LYG  plan-1  S1   0.020
 LYG  plan-1  CL1  0.020
 LYG  plan-1  N2   0.020
 LYG  plan-1  O2   0.020
 LYG  plan-1  N3   0.020
 LYG  plan-1  C4   0.020
 LYG  plan-1  C5   0.020
 LYG  plan-1  C6   0.020
 LYG  plan-1  C7   0.020
 LYG  plan-1  C8   0.020
 LYG  plan-1  C9   0.020
 LYG  plan-1  C10  0.020
 LYG  plan-1  C11  0.020
 LYG  plan-1  C12  0.020
 LYG  plan-1  C13  0.020
 LYG  plan-1  C14  0.020
 LYG  plan-1  HN3  0.020
 LYG  plan-1  H8   0.020
 LYG  plan-1  H10  0.020
 LYG  plan-1  H11  0.020

