# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:09:13 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-[(2S)-1-azabicyclo[2.2.2]octan-2-yl]-6-(5-methyl-1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]ncc1c2sc3C(=O)NC(=Nc3c2)[C@@H]4CC5CCN4CC5
#
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
 O1V  O1V  2-[(2S)-1-azabicyclo[2.2.2]octan-2-yl]-6-(5-methyl-1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-4(3H)-one  ligand  43  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O1V
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
 O1V  N3   N  NR15  0  -0.477   6.2837   0.9267  -0.1050
 O1V  C6   C  CR15  0  -0.105   4.5899   1.7564  -1.0145
 O1V  C7   C  CR5   0  -0.105   4.1316   0.6684  -0.2370
 O1V  C8   C  CR5   0  -0.214   2.7611   0.2385  -0.0957
 O1V  C10  C  CR56  0   0.366   0.4465   0.2009  -0.2506
 O1V  C15  C  CR6   0   0.539  -0.3869  -1.7989   0.9052
 O1V  C17  C  CR56  0  -0.413   0.6809  -0.9694   0.4493
 O1V  C21  C  CH2   0  -0.437  -3.4633   1.6835  -0.8845
 O1V  C22  C  CH1   0  -0.265  -4.8248   2.0565  -0.2919
 O1V  C24  C  CH2   0  -0.330  -5.4656  -0.3337  -0.0420
 O1V  C2   C  CR5   0   0.405   5.2858   0.1532   0.3437
 O1V  N5   N  N     0  -0.254   5.8918   1.8992  -0.9246
 O1V  C9   C  CR15  0  -0.311   1.6484   0.8861  -0.5623
 O1V  N11  N  N     0  -0.475  -0.8077   0.6271  -0.5766
 O1V  C12  C  CR6   0   0.481  -1.7812  -0.1172  -0.1712
 O1V  N13  N  NR16  0  -0.688  -1.6095  -1.2597   0.5399
 O1V  O16  O  O     0  -0.468  -0.2949  -2.8399   1.5363
 O1V  S18  S  S2    0   0.237   2.3520  -1.2363   0.7261
 O1V  C19  C  CH1   0  -0.195  -3.2093   0.2046  -0.5332
 O1V  C23  C  CH2   0  -0.458  -5.8610   1.0072  -0.7037
 O1V  N25  N  NT    0  -0.423  -4.1146  -0.2621   0.5136
 O1V  C27  C  CH2   0  -0.450  -4.7024   2.0416   1.2320
 O1V  H1   H  HNR5  0   0.423   7.2611   0.8338   0.1258
 O1V  H2   H  HCR5  0   0.263   4.0069   2.4234  -1.6317
 O1V  H4   H  HCH2  0   0.240  -2.6843   2.3298  -0.4744
 O1V  H5   H  HCH1  0   0.242  -5.1255   3.0457  -0.6411
 O1V  H6   H  HCH2  0   0.244  -6.1458  -0.5844   0.7746
 O1V  H7   H  HCH2  0   0.248  -5.5122  -1.1589  -0.7554
 O1V  H8   H  HCH2  0   0.250  -4.6610   0.2274   2.4618
 O1V  H9   H  HCH2  0   0.244  -3.0753   0.7884   1.9874
 O1V  H10  H  HCH3  0   0.265   4.8985  -0.9003   2.1635
 O1V  H11  H  HCH3  0   0.267   5.2847  -1.9386   0.7941
 O1V  H12  H  HCH3  0   0.278   6.5570  -1.0224   1.5921
 O1V  H13  H  HCR5  0   0.266   1.6742   1.8240  -1.0989
 O1V  H14  H  HNR6  0   0.424  -2.4601  -1.7176   0.8575
 O1V  H15  H  HCH1  0   0.299  -3.4204  -0.4125  -1.4158
 O1V  H16  H  HCH2  0   0.240  -6.8605   1.3139  -0.3880
 O1V  H17  H  HCH2  0   0.234  -5.8869   0.9135  -1.7926
 O1V  H19  H  HCH2  0   0.238  -4.0662   2.8604   1.5754
 O1V  H20  H  HCH2  0   0.234  -5.6850   2.1934   1.6864
 O1V  C1   C  CH3   0  -0.767   5.5173  -0.9849   1.2697
 O1V  H3   H  HCH2  0   0.247  -3.4542   1.8204  -1.9670
 O1V  C26  C  CH2   0  -0.337  -4.1049   0.6765   1.6375

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
 O1V  N5   C6   aromatic  1.313  0.020  1.313
 O1V  N5   N3   aromatic  1.331  0.020  1.331
 O1V  C6   C7   aromatic  1.414  0.020  1.414
 O1V  N3   C2   aromatic  1.340  0.020  1.340
 O1V  C7   C2   aromatic  1.391  0.020  1.391
 O1V  C7   C8   single    1.443  0.020  1.443
 O1V  C9   C8   aromatic  1.369  0.020  1.369
 O1V  C9   C10  aromatic  1.418  0.020  1.418
 O1V  C24  C23  single    1.547  0.020  1.547
 O1V  C24  N25  single    1.463  0.020  1.463
 O1V  C2   C1   single    1.485  0.020  1.485
 O1V  C8   S18  aromatic  1.737  0.020  1.737
 O1V  N11  C10  single    1.364  0.020  1.364
 O1V  N11  C12  double    1.291  0.020  1.291
 O1V  C23  C22  single    1.531  0.020  1.531
 O1V  C10  C17  aromatic  1.384  0.020  1.384
 O1V  C19  N25  single    1.460  0.020  1.460
 O1V  C19  C12  single    1.508  0.020  1.508
 O1V  C19  C21  single    1.541  0.020  1.541
 O1V  N25  C26  single    1.464  0.020  1.464
 O1V  C12  N13  single    1.357  0.020  1.357
 O1V  C21  C22  single    1.531  0.020  1.531
 O1V  C22  C27  single    1.529  0.020  1.529
 O1V  C17  S18  aromatic  1.715  0.020  1.715
 O1V  C17  C15  single    1.427  0.020  1.427
 O1V  C26  C27  single    1.544  0.020  1.544
 O1V  N13  C15  single    1.385  0.020  1.385
 O1V  C15  O16  double    1.221  0.020  1.221
 O1V  N3   H1   single    0.860  0.020  1.020
 O1V  C6   H2   single    0.930  0.020  1.080
 O1V  C21  H3   single    0.970  0.020  1.090
 O1V  C21  H4   single    0.970  0.020  1.090
 O1V  C22  H5   single    0.970  0.020  1.090
 O1V  C24  H6   single    0.970  0.020  1.090
 O1V  C24  H7   single    0.970  0.020  1.090
 O1V  C26  H8   single    0.970  0.020  1.090
 O1V  C26  H9   single    0.970  0.020  1.090
 O1V  C1   H10  single    0.970  0.020  1.090
 O1V  C1   H11  single    0.970  0.020  1.090
 O1V  C1   H12  single    0.970  0.020  1.090
 O1V  C9   H13  single    0.930  0.020  1.080
 O1V  N13  H14  single    0.860  0.020  1.020
 O1V  C19  H15  single    0.970  0.020  1.090
 O1V  C23  H16  single    0.970  0.020  1.090
 O1V  C23  H17  single    0.970  0.020  1.090
 O1V  C27  H19  single    0.970  0.020  1.090
 O1V  C27  H20  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
 O1V  H1   N3   N5   119.58  3.000
 O1V  H1   N3   C2   126.29  3.000
 O1V  N5   N3   C2   114.13  3.000
 O1V  H2   C6   N5   120.49  3.000
 O1V  H2   C6   C7   127.94  3.000
 O1V  N5   C6   C7   111.56  3.000
 O1V  C2   C7   C8   129.55  3.000
 O1V  C8   C7   C6   126.22  3.000
 O1V  C2   C7   C6   104.23  3.000
 O1V  S18  C8   C9   111.79  3.000
 O1V  S18  C8   C7   121.52  3.000
 O1V  C9   C8   C7   126.69  3.000
 O1V  N11  C10  C9   125.15  3.000
 O1V  N11  C10  C17  122.74  3.000
 O1V  C9   C10  C17  112.11  3.000
 O1V  O16  C15  N13  122.33  3.000
 O1V  O16  C15  C17  127.19  3.000
 O1V  N13  C15  C17  110.48  3.000
 O1V  S18  C17  C15  125.96  3.000
 O1V  C15  C17  C10  121.77  3.000
 O1V  S18  C17  C10  112.23  3.000
 O1V  H4   C21  H3   106.99  3.000
 O1V  H4   C21  C19  111.39  3.000
 O1V  H3   C21  C19  110.19  3.000
 O1V  H4   C21  C22  110.17  3.000
 O1V  H3   C21  C22  111.15  3.000
 O1V  C19  C21  C22  106.99  3.000
 O1V  H5   C22  C27  110.48  3.000
 O1V  H5   C22  C23  110.40  3.000
 O1V  C27  C22  C23  108.39  3.000
 O1V  H5   C22  C21  110.00  3.000
 O1V  C27  C22  C21  108.19  3.000
 O1V  C23  C22  C21  109.32  3.000
 O1V  H7   C24  H6   106.77  3.000
 O1V  H7   C24  N25  108.94  3.000
 O1V  H6   C24  N25  107.61  3.000
 O1V  H7   C24  C23  111.40  3.000
 O1V  H6   C24  C23  111.09  3.000
 O1V  N25  C24  C23  110.87  3.000
 O1V  C1   C2   C7   132.33  3.000
 O1V  C1   C2   N3   122.34  3.000
 O1V  C7   C2   N3   105.33  3.000
 O1V  C6   N5   N3   104.76  3.000
 O1V  H13  C9   C10  123.28  3.000
 O1V  H13  C9   C8   124.06  3.000
 O1V  C10  C9   C8   112.66  3.000
 O1V  C12  N11  C10  115.99  3.000
 O1V  C19  C12  N13  115.17  3.000
 O1V  N13  C12  N11  123.70  3.000
 O1V  C19  C12  N11  121.05  3.000
 O1V  H14  N13  C12  115.91  3.000
 O1V  H14  N13  C15  118.73  3.000
 O1V  C12  N13  C15  125.29  3.000
 O1V  C17  S18  C8    91.20  3.000
 O1V  H15  C19  N25  106.11  3.000
 O1V  H15  C19  C12  104.79  3.000
 O1V  N25  C19  C12  110.29  3.000
 O1V  H15  C19  C21  108.94  3.000
 O1V  C12  C19  C21  114.56  3.000
 O1V  N25  C19  C21  111.58  3.000
 O1V  H17  C23  H16  106.88  3.000
 O1V  H17  C23  C24  110.97  3.000
 O1V  H16  C23  C24  110.72  3.000
 O1V  H17  C23  C22  110.04  3.000
 O1V  H16  C23  C22  110.44  3.000
 O1V  C24  C23  C22  107.82  3.000
 O1V  C19  N25  C26  109.95  3.000
 O1V  C26  N25  C24  109.21  3.000
 O1V  C19  N25  C24  108.42  3.000
 O1V  H20  C27  H19  106.78  3.000
 O1V  H20  C27  C26  111.18  3.000
 O1V  H19  C27  C26  110.78  3.000
 O1V  H20  C27  C22  109.94  3.000
 O1V  H19  C27  C22  110.65  3.000
 O1V  C26  C27  C22  107.54  3.000
 O1V  H12  C1   H11  107.61  3.000
 O1V  H12  C1   H10  107.56  3.000
 O1V  H11  C1   H10  107.71  3.000
 O1V  H12  C1   C2   111.08  3.000
 O1V  H11  C1   C2   111.39  3.000
 O1V  H10  C1   C2   111.29  3.000
 O1V  H9   C26  H8   106.28  3.000
 O1V  H9   C26  C27  110.97  3.000
 O1V  H8   C26  C27  111.41  3.000
 O1V  H9   C26  N25  108.51  3.000
 O1V  H8   C26  N25  108.22  3.000
 O1V  C27  C26  N25  111.25  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
 O1V  CONST_01  C7   C6   N5   N3     0.00   0.0  0
 O1V  CONST_02  C6   C7   C2   N3     0.00   0.0  0
 O1V  CONST_03  C8   C7   C2   N3   180.00   0.0  0
 O1V  CONST_04  C2   N3   N5   C6     0.00   0.0  0
 O1V  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 O1V  CONST_06  S18  C8   C7   C6   180.00   0.0  0
 O1V  CONST_07  N5   N3   C2   C7     0.00   0.0  0
 O1V  CONST_08  C10  C9   C8   C7   180.00   0.0  0
 O1V  CONST_09  C17  S18  C8   C7   180.00   0.0  0
 O1V  CONST_10  N5   C6   C7   C8   180.00   0.0  0
 O1V  CONST_11  C17  C10  C9   C8     0.00   0.0  0
 O1V  CONST_12  C10  C17  S18  C8     0.00   0.0  0
 O1V  CONST_13  S18  C8   C9   C10    0.00   0.0  0
 O1V  CONST_14  C9   C8   S18  C17    0.00   0.0  0
 O1V  CONST_15  N5   C6   C7   C2     0.00   0.0  0
 O1V  CONST_16  C9   C8   C7   C2   180.00   0.0  0
 O1V  CONST_17  S18  C8   C7   C2     0.00   0.0  0
 O1V  CONST_18  S18  C17  C10  C9     0.00   0.0  0
 O1V  CONST_19  C19  C12  N11  C10  180.00   0.0  0
 O1V  CONST_20  N13  C12  N11  C10    0.00   0.0  0
 O1V  CONST_21  N11  C12  N13  C15    0.00   0.0  0
 O1V  CONST_22  C19  C12  N13  C15  180.00   0.0  0
 O1V  CONST_23  C12  N13  C15  C17    0.00   0.0  0
 O1V  CONST_24  C1   C2   C7   C6   180.00   0.0  0
 O1V  CONST_25  C1   C2   C7   C8     0.00   0.0  0
 O1V  CONST_26  N5   N3   C2   C1   180.00   0.0  0
 O1V  CONST_27  O16  C15  N13  C12  180.00   0.0  0
 O1V  CONST_28  H2   C6   N5   N3   180.00   0.0  0
 O1V  CONST_29  H1   N3   N5   C6   180.00   0.0  0
 O1V  CONST_30  H13  C9   C8   C7     0.00   0.0  0
 O1V  CONST_31  H14  N13  C15  C17  180.00   0.0  0
 O1V  Var_01    N25  C24  C23  C22  -12.07  30.0  1
 O1V  Var_02    N25  C26  C27  C22  -12.22  30.0  3
 O1V  Var_03    C27  C26  N25  C24  -52.72  30.0  3
 O1V  Var_04    C23  C24  N25  C26   67.14  30.0  1
 O1V  Var_05    H10  C1   C2   N3   125.59  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
 O1V  chir_01  C22  C23  C21  C27  positiv
 O1V  chir_02  C19  N25  C12  C21  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
 O1V  plan-1  N3   0.020
 O1V  plan-1  C6   0.020
 O1V  plan-1  C7   0.020
 O1V  plan-1  C8   0.020
 O1V  plan-1  C2   0.020
 O1V  plan-1  N5   0.020
 O1V  plan-1  H1   0.020
 O1V  plan-1  H2   0.020
 O1V  plan-1  C1   0.020
 O1V  plan-2  C7   0.020
 O1V  plan-2  C8   0.020
 O1V  plan-2  C10  0.020
 O1V  plan-2  C15  0.020
 O1V  plan-2  C17  0.020
 O1V  plan-2  C9   0.020
 O1V  plan-2  N11  0.020
 O1V  plan-2  C12  0.020
 O1V  plan-2  N13  0.020
 O1V  plan-2  O16  0.020
 O1V  plan-2  S18  0.020
 O1V  plan-2  C19  0.020
 O1V  plan-2  H13  0.020
 O1V  plan-2  H14  0.020

