# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 19:43:40 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2sc3CCCCc3c12
#
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
 ZYR  ZYR  5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one  ligand  24  14  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZYR
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
 ZYR  OAA   O  O     0  -0.462  -1.4964  -2.5927   0.0523
 ZYR  CAL   C  CR6   0   0.538  -1.6765  -1.3868   0.0312
 ZYR  CAN   C  CR56  0  -0.080  -0.6733  -0.3524   0.0154
 ZYR  CAK   C  CR5   0   0.201   0.7531  -0.4824   0.0096
 ZYR  CAF   C  CH2   0  -0.490   1.5338  -1.7632   0.0097
 ZYR  CAD   C  CH2   0  -0.450   2.9984  -1.5192  -0.3460
 ZYR  CAC   C  CH2   0  -0.449   3.5665  -0.3195   0.4023
 ZYR  CAE   C  CH2   0  -0.477   2.8416   0.9651   0.0065
 ZYR  CAJ   C  CR5   0  -0.267   1.3658   0.7322   0.0052
 ZYR  SAI   S  S2    0   0.226   0.2358   2.0500  -0.0058
 ZYR  CAM   C  CR56  0  -0.039  -1.0986   0.9640   0.0033
 ZYR  NAG   N  N     0  -0.428  -2.3796   1.3995  -0.0017
 ZYR  CAB   C  CR16  0   0.152  -3.2613   0.4575   0.0066
 ZYR  NAH   N  NR16  0  -0.652  -2.9633  -0.8589   0.0216
 ZYR  HAH   H  HNR6  0   0.435  -3.7309  -1.5186   0.0279
 ZYR  HAF1  H  HCH2  0   0.241   1.4617  -2.2304   0.9971
 ZYR  HAF2  H  HCH2  0   0.250   1.0891  -2.4737  -0.6879
 ZYR  HAD1  H  HCH2  0   0.240   3.5803  -2.4151  -0.1225
 ZYR  HAD2  H  HCH2  0   0.226   3.0898  -1.3479  -1.4231
 ZYR  HAC1  H  HCH2  0   0.229   3.4641  -0.4774   1.4798
 ZYR  HAC2  H  HCH2  0   0.243   4.6331  -0.2111   0.1986
 ZYR  HAE1  H  HCH2  0   0.257   3.1028   1.7753   0.6913
 ZYR  HAE2  H  HCH2  0   0.253   3.1663   1.2890  -0.9876
 ZYR  HAB   H  HCR6  0   0.306  -4.3157   0.7003   0.0026

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
 ZYR  OAA  CAL   double    1.220  0.020  1.220
 ZYR  CAL  CAN   single    1.441  0.020  1.441
 ZYR  CAL  NAH   single    1.391  0.020  1.391
 ZYR  CAN  CAK   aromatic  1.432  0.020  1.432
 ZYR  CAN  CAM   aromatic  1.383  0.020  1.383
 ZYR  CAK  CAF   single    1.500  0.020  1.500
 ZYR  CAK  CAJ   aromatic  1.360  0.020  1.360
 ZYR  CAF  CAD   single    1.527  0.020  1.527
 ZYR  CAD  CAC   single    1.524  0.020  1.524
 ZYR  CAC  CAE   single    1.527  0.020  1.527
 ZYR  CAE  CAJ   single    1.494  0.020  1.494
 ZYR  CAJ  SAI   aromatic  1.736  0.020  1.736
 ZYR  SAI  CAM   aromatic  1.721  0.020  1.721
 ZYR  CAM  NAG   single    1.353  0.020  1.353
 ZYR  NAG  CAB   double    1.290  0.020  1.290
 ZYR  CAB  NAH   single    1.350  0.020  1.350
 ZYR  NAH  HAH   single    0.860  0.020  1.020
 ZYR  CAF  HAF1  single    0.970  0.020  1.090
 ZYR  CAF  HAF2  single    0.970  0.020  1.090
 ZYR  CAD  HAD1  single    0.970  0.020  1.090
 ZYR  CAD  HAD2  single    0.970  0.020  1.090
 ZYR  CAC  HAC1  single    0.970  0.020  1.090
 ZYR  CAC  HAC2  single    0.970  0.020  1.090
 ZYR  CAE  HAE1  single    0.970  0.020  1.090
 ZYR  CAE  HAE2  single    0.970  0.020  1.090
 ZYR  CAB  HAB   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
 ZYR  NAH   CAL  CAN   111.81  3.000
 ZYR  NAH   CAL  OAA   120.80  3.000
 ZYR  CAN   CAL  OAA   127.39  3.000
 ZYR  CAM   CAN  CAK   113.11  3.000
 ZYR  CAM   CAN  CAL   117.98  3.000
 ZYR  CAK   CAN  CAL   128.92  3.000
 ZYR  CAJ   CAK  CAF   121.87  3.000
 ZYR  CAJ   CAK  CAN   111.56  3.000
 ZYR  CAF   CAK  CAN   126.57  3.000
 ZYR  HAF2  CAF  HAF1  105.79  3.000
 ZYR  HAF2  CAF  CAD   110.26  3.000
 ZYR  HAF1  CAF  CAD   109.97  3.000
 ZYR  HAF2  CAF  CAK   110.12  3.000
 ZYR  HAF1  CAF  CAK   109.28  3.000
 ZYR  CAD   CAF  CAK   111.27  3.000
 ZYR  HAD2  CAD  HAD1  106.59  3.000
 ZYR  HAD2  CAD  CAC   109.21  3.000
 ZYR  HAD1  CAD  CAC   110.30  3.000
 ZYR  HAD2  CAD  CAF   109.53  3.000
 ZYR  HAD1  CAD  CAF   109.42  3.000
 ZYR  CAC   CAD  CAF   111.65  3.000
 ZYR  HAC2  CAC  HAC1  106.84  3.000
 ZYR  HAC2  CAC  CAE   109.39  3.000
 ZYR  HAC1  CAC  CAE   109.41  3.000
 ZYR  HAC2  CAC  CAD   110.54  3.000
 ZYR  HAC1  CAC  CAD   109.59  3.000
 ZYR  CAE   CAC  CAD   110.98  3.000
 ZYR  HAE2  CAE  HAE1  106.19  3.000
 ZYR  HAE2  CAE  CAJ   109.77  3.000
 ZYR  HAE1  CAE  CAJ   110.63  3.000
 ZYR  HAE2  CAE  CAC   110.09  3.000
 ZYR  HAE1  CAE  CAC   110.36  3.000
 ZYR  CAJ   CAE  CAC   109.75  3.000
 ZYR  SAI   CAJ  CAE   121.65  3.000
 ZYR  SAI   CAJ  CAK   112.62  3.000
 ZYR  CAE   CAJ  CAK   125.73  3.000
 ZYR  CAM   SAI  CAJ    91.47  3.000
 ZYR  NAG   CAM  SAI   122.08  3.000
 ZYR  NAG   CAM  CAN   126.68  3.000
 ZYR  SAI   CAM  CAN   111.24  3.000
 ZYR  CAB   NAG  CAM   114.33  3.000
 ZYR  HAB   CAB  NAH   115.72  3.000
 ZYR  HAB   CAB  NAG   120.14  3.000
 ZYR  NAH   CAB  NAG   124.14  3.000
 ZYR  HAH   NAH  CAB   117.92  3.000
 ZYR  HAH   NAH  CAL   117.01  3.000
 ZYR  CAB   NAH  CAL   125.06  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
 ZYR  CONST_01  SAI  CAJ  CAK  CAN    0.00   0.0  0
 ZYR  CONST_02  CAJ  SAI  CAM  CAN    0.00   0.0  0
 ZYR  CONST_03  SAI  CAM  CAN  CAK    0.00   0.0  0
 ZYR  CONST_04  CAM  SAI  CAJ  CAK    0.00   0.0  0
 ZYR  CONST_05  CAM  CAN  CAK  CAJ    0.00   0.0  0
 ZYR  CONST_06  NAG  CAB  NAH  CAL    0.00   0.0  0
 ZYR  CONST_07  CAB  NAH  CAL  CAN    0.00   0.0  0
 ZYR  CONST_08  NAH  CAB  NAG  CAM    0.00   0.0  0
 ZYR  CONST_09  CAB  NAH  CAL  OAA  180.00   0.0  0
 ZYR  CONST_10  HAB  CAB  NAH  CAL  180.00   0.0  0
 ZYR  CONST_11  HAH  NAH  CAL  CAN  180.00   0.0  0
 ZYR  Var_01    CAD  CAF  CAK  CAN  165.81  30.0  1
 ZYR  Var_02    CAC  CAD  CAF  CAK   45.03  30.0  1
 ZYR  Var_03    CAC  CAE  CAJ  CAK  -15.71  30.0  1
 ZYR  Var_04    CAE  CAC  CAD  CAF  -63.10  30.0  1
 ZYR  Var_05    CAJ  CAE  CAC  CAD   45.83  30.0  1

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
 ZYR  plan-1  OAA  0.020
 ZYR  plan-1  CAL  0.020
 ZYR  plan-1  CAN  0.020
 ZYR  plan-1  CAK  0.020
 ZYR  plan-1  CAF  0.020
 ZYR  plan-1  CAE  0.020
 ZYR  plan-1  CAJ  0.020
 ZYR  plan-1  SAI  0.020
 ZYR  plan-1  CAM  0.020
 ZYR  plan-1  NAG  0.020
 ZYR  plan-1  CAB  0.020
 ZYR  plan-1  NAH  0.020
 ZYR  plan-1  HAH  0.020
 ZYR  plan-1  HAB  0.020

