# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:42:58 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5,6-dimethyl-3-(4-methylpyridin-2-yl)-2-sulfanylthieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(c1)N2C(=Nc3sc(C)c(C)c3C2=O)S
#
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
 3QI  3QI  5,6-dimethyl-3-(4-methylpyridin-2-yl)-2-sulfanylthieno[2,3-d]pyrimidin-4(3H)-one  ligand  33  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3QI
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
 3QI  CAA   C  CH3   0  -0.722   4.9428   1.1288  -1.9206
 3QI  CAC   C  CH3   0  -0.727  -2.8934   2.8108   0.1264
 3QI  OAD   O  O     0  -0.448   0.0969   2.0925   0.2288
 3QI  SAE   S  S2    0  -0.106   1.5351  -2.5927  -0.0330
 3QI  CAF   C  CR16  0  -0.057   3.7390   0.5293   1.6185
 3QI  CAG   C  CR16  0  -0.360   4.5773   0.8366   0.5583
 3QI  CAH   C  CR16  0  -0.335   2.7292   0.5114  -0.8942
 3QI  NAI   N  N     0  -0.373   2.4563   0.2255   1.4670
 3QI  NAJ   N  N     0  -0.432  -0.9980  -1.8142  -0.0988
 3QI  SAK   S  S2    0   0.235  -3.6049  -1.1520  -0.1786
 3QI  CAL   C  CR6   0   0.188   4.0757   0.8306  -0.7392
 3QI  CAM   C  CR5   0  -0.257  -3.9872   0.5432  -0.0886
 3QI  CAN   C  CR5   0   0.183  -2.8733   1.3199   0.0170
 3QI  CAO   C  CR6   0   0.374   1.9883   0.2229   0.2356
 3QI  CAP   C  CR6   0   0.299   0.2275  -1.4241  -0.0102
 3QI  CAQ   C  CR6   0   0.566  -0.3143   0.9542   0.1249
 3QI  CAR   C  CR56  0  -0.047  -1.9225  -0.8308  -0.0773
 3QI  CAS   C  CR56  0  -0.047  -1.6802   0.5238   0.0217
 3QI  NAT   N  NR6   0  -0.615   0.6031  -0.1164   0.0972
 3QI  HAA   H  HCH3  0   0.265   5.3035   0.2001  -2.3666
 3QI  HAAA  H  HCH3  0   0.257   4.3943   1.6691  -2.6906
 3QI  HAAB  H  HCH3  0   0.256   5.8133   1.7173  -1.6362
 3QI  HAB   H  HCH3  0   0.256  -6.0600   0.1981  -0.5414
 3QI  HABA  H  HCH3  0   0.261  -5.7889   1.1589   0.9051
 3QI  HABB  H  HCH3  0   0.258  -5.5551   1.8722  -0.6882
 3QI  HAC   H  HCH3  0   0.248  -2.4615   3.1415   1.0710
 3QI  HACA  H  HCH3  0   0.248  -2.3152   3.2759  -0.6717
 3QI  HACB  H  HCH3  0   0.243  -3.9098   3.1955   0.0736
 3QI  HSAE  H  HSH1  0   0.274   0.7238  -3.6466  -0.1762
 3QI  HAF   H  HCR6  0   0.275   4.1185   0.5311   2.6334
 3QI  HAG   H  HCR6  0   0.274   5.6141   1.0805   0.7486
 3QI  HAH   H  HCR6  0   0.285   2.2670   0.4868  -1.8728
 3QI  CAB   C  CH3   0  -0.721  -5.4205   0.9631  -0.1034

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
 3QI  CAA  CAL   single    1.495  0.020  1.495
 3QI  CAB  CAM   single    1.494  0.020  1.494
 3QI  CAC  CAN   single    1.495  0.020  1.495
 3QI  OAD  CAQ   double    1.215  0.020  1.215
 3QI  SAE  CAP   single    1.754  0.020  1.754
 3QI  CAF  CAG   aromatic  1.386  0.020  1.386
 3QI  CAF  NAI   aromatic  1.327  0.020  1.327
 3QI  CAG  CAL   aromatic  1.391  0.020  1.391
 3QI  CAH  CAL   aromatic  1.392  0.020  1.392
 3QI  CAH  CAO   aromatic  1.381  0.020  1.381
 3QI  NAI  CAO   aromatic  1.317  0.020  1.317
 3QI  NAJ  CAP   double    1.289  0.020  1.289
 3QI  NAJ  CAR   single    1.350  0.020  1.350
 3QI  SAK  CAM   aromatic  1.740  0.020  1.740
 3QI  SAK  CAR   aromatic  1.716  0.020  1.716
 3QI  CAM  CAN   aromatic  1.362  0.020  1.362
 3QI  CAN  CAS   aromatic  1.434  0.020  1.434
 3QI  CAO  NAT   single    1.433  0.020  1.433
 3QI  CAP  NAT   single    1.365  0.020  1.365
 3QI  CAQ  CAS   single    1.436  0.020  1.436
 3QI  CAQ  NAT   single    1.410  0.020  1.410
 3QI  CAR  CAS   aromatic  1.380  0.020  1.380
 3QI  CAA  HAA   single    0.970  0.020  1.090
 3QI  CAA  HAAA  single    0.970  0.020  1.090
 3QI  CAA  HAAB  single    0.970  0.020  1.090
 3QI  CAB  HAB   single    0.970  0.020  1.090
 3QI  CAB  HABA  single    0.970  0.020  1.090
 3QI  CAB  HABB  single    0.970  0.020  1.090
 3QI  CAC  HAC   single    0.970  0.020  1.090
 3QI  CAC  HACA  single    0.970  0.020  1.090
 3QI  CAC  HACB  single    0.970  0.020  1.090
 3QI  SAE  HSAE  single    1.200  0.020  1.300
 3QI  CAF  HAF   single    0.930  0.020  1.080
 3QI  CAG  HAG   single    0.930  0.020  1.080
 3QI  CAH  HAH   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
 3QI  HAAB  CAA  HAAA  108.62  3.000
 3QI  HAAB  CAA  HAA   107.61  3.000
 3QI  HAAA  CAA  HAA   107.43  3.000
 3QI  HAAB  CAA  CAL   111.42  3.000
 3QI  HAAA  CAA  CAL   111.44  3.000
 3QI  HAA   CAA  CAL   110.17  3.000
 3QI  HACB  CAC  HACA  108.01  3.000
 3QI  HACB  CAC  HAC   107.76  3.000
 3QI  HACA  CAC  HAC   107.16  3.000
 3QI  HACB  CAC  CAN   111.19  3.000
 3QI  HACA  CAC  CAN   111.40  3.000
 3QI  HAC   CAC  CAN   111.14  3.000
 3QI  HSAE  SAE  CAP    94.26  3.000
 3QI  HAF   CAF  NAI   116.48  3.000
 3QI  HAF   CAF  CAG   120.29  3.000
 3QI  NAI   CAF  CAG   123.23  3.000
 3QI  HAG   CAG  CAL   120.71  3.000
 3QI  HAG   CAG  CAF   119.66  3.000
 3QI  CAL   CAG  CAF   119.63  3.000
 3QI  HAH   CAH  CAO   120.36  3.000
 3QI  HAH   CAH  CAL   121.25  3.000
 3QI  CAO   CAH  CAL   118.39  3.000
 3QI  CAO   NAI  CAF   116.78  3.000
 3QI  CAR   NAJ  CAP   115.43  3.000
 3QI  CAR   SAK  CAM    91.72  3.000
 3QI  CAH   CAL  CAG   116.97  3.000
 3QI  CAH   CAL  CAA   121.23  3.000
 3QI  CAG   CAL  CAA   121.79  3.000
 3QI  CAN   CAM  SAK   112.32  3.000
 3QI  CAN   CAM  CAB   128.70  3.000
 3QI  SAK   CAM  CAB   118.96  3.000
 3QI  CAS   CAN  CAM   111.35  3.000
 3QI  CAS   CAN  CAC   124.36  3.000
 3QI  CAM   CAN  CAC   124.29  3.000
 3QI  NAT   CAO  NAI   115.73  3.000
 3QI  NAT   CAO  CAH   119.27  3.000
 3QI  NAI   CAO  CAH   125.00  3.000
 3QI  NAT   CAP  NAJ   123.85  3.000
 3QI  NAT   CAP  SAE   115.74  3.000
 3QI  NAJ   CAP  SAE   120.41  3.000
 3QI  NAT   CAQ  CAS   112.95  3.000
 3QI  NAT   CAQ  OAD   119.53  3.000
 3QI  CAS   CAQ  OAD   127.52  3.000
 3QI  CAS   CAR  SAK   111.12  3.000
 3QI  CAS   CAR  NAJ   126.60  3.000
 3QI  SAK   CAR  NAJ   122.29  3.000
 3QI  CAR   CAS  CAQ   117.81  3.000
 3QI  CAR   CAS  CAN   113.49  3.000
 3QI  CAQ   CAS  CAN   128.70  3.000
 3QI  CAQ   NAT  CAP   123.36  3.000
 3QI  CAQ   NAT  CAO   116.57  3.000
 3QI  CAP   NAT  CAO   120.04  3.000
 3QI  HABB  CAB  HABA  107.73  3.000
 3QI  HABB  CAB  HAB   107.32  3.000
 3QI  HABA  CAB  HAB   107.42  3.000
 3QI  HABB  CAB  CAM   111.01  3.000
 3QI  HABA  CAB  CAM   111.42  3.000
 3QI  HAB   CAB  CAM   111.72  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
 3QI  CONST_01  CAH  CAL  CAG  CAF    0.00   0.0  0
 3QI  CONST_02  CAH  CAO  NAI  CAF    0.00   0.0  0
 3QI  CONST_03  CAO  NAI  CAF  CAG    0.00   0.0  0
 3QI  CONST_04  CAO  CAH  CAL  CAG    0.00   0.0  0
 3QI  CONST_05  CAL  CAG  CAF  NAI    0.00   0.0  0
 3QI  CONST_06  CAL  CAH  CAO  NAI    0.00   0.0  0
 3QI  CONST_07  CAS  CAN  CAM  SAK    0.00   0.0  0
 3QI  CONST_08  CAN  CAS  CAR  SAK    0.00   0.0  0
 3QI  CONST_09  CAS  CAR  SAK  CAM    0.00   0.0  0
 3QI  CONST_10  CAR  CAS  CAN  CAM    0.00   0.0  0
 3QI  CONST_11  CAR  SAK  CAM  CAN    0.00   0.0  0
 3QI  CONST_12  NAT  CAO  NAI  CAF  180.00   0.0  0
 3QI  CONST_13  NAT  CAO  CAH  CAL  180.00   0.0  0
 3QI  CONST_14  CAO  NAT  CAP  NAJ  180.00   0.0  0
 3QI  CONST_15  CAQ  NAT  CAP  NAJ    0.00   0.0  0
 3QI  CONST_16  CAS  CAQ  NAT  CAO  180.00   0.0  0
 3QI  CONST_17  CAS  CAQ  NAT  CAP    0.00   0.0  0
 3QI  CONST_18  NAT  CAP  NAJ  CAR    0.00   0.0  0
 3QI  CONST_19  CAF  CAG  CAL  CAA  180.00   0.0  0
 3QI  CONST_20  CAO  CAH  CAL  CAA  180.00   0.0  0
 3QI  CONST_21  CAR  SAK  CAM  CAB  180.00   0.0  0
 3QI  CONST_22  CAS  CAN  CAM  CAB  180.00   0.0  0
 3QI  CONST_23  SAK  CAM  CAN  CAC  180.00   0.0  0
 3QI  CONST_24  CAQ  CAS  CAN  CAC    0.00   0.0  0
 3QI  CONST_25  CAR  CAS  CAN  CAC  180.00   0.0  0
 3QI  CONST_26  CAO  NAT  CAQ  OAD    0.00   0.0  0
 3QI  CONST_27  CAP  NAT  CAQ  OAD  180.00   0.0  0
 3QI  CONST_28  CAR  NAJ  CAP  SAE  180.00   0.0  0
 3QI  CONST_29  CAO  NAT  CAP  SAE    0.00   0.0  0
 3QI  CONST_30  CAQ  NAT  CAP  SAE  180.00   0.0  0
 3QI  CONST_31  HAH  CAH  CAL  CAG  180.00   0.0  0
 3QI  CONST_32  HAG  CAG  CAL  CAH  180.00   0.0  0
 3QI  CONST_33  HAF  CAF  CAG  CAL  180.00   0.0  0
 3QI  Var_01    CAP  NAT  CAO  CAH   92.93  30.0  2
 3QI  Var_02    HAA  CAA  CAL  CAG   96.04  30.0  2
 3QI  Var_03    HAB  CAB  CAM  SAK  -21.69  30.0  2
 3QI  Var_04    HAC  CAC  CAN  CAM  117.94  30.0  2

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
 3QI  plan-1  CAA  0.020
 3QI  plan-1  CAF  0.020
 3QI  plan-1  CAG  0.020
 3QI  plan-1  CAH  0.020
 3QI  plan-1  NAI  0.020
 3QI  plan-1  CAL  0.020
 3QI  plan-1  CAO  0.020
 3QI  plan-1  NAT  0.020
 3QI  plan-1  HAF  0.020
 3QI  plan-1  HAG  0.020
 3QI  plan-1  HAH  0.020
 3QI  plan-2  CAC  0.020
 3QI  plan-2  OAD  0.020
 3QI  plan-2  SAE  0.020
 3QI  plan-2  NAJ  0.020
 3QI  plan-2  SAK  0.020
 3QI  plan-2  CAM  0.020
 3QI  plan-2  CAN  0.020
 3QI  plan-2  CAO  0.020
 3QI  plan-2  CAP  0.020
 3QI  plan-2  CAQ  0.020
 3QI  plan-2  CAR  0.020
 3QI  plan-2  CAS  0.020
 3QI  plan-2  NAT  0.020
 3QI  plan-2  CAB  0.020

