# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:15:41 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1nc(nc2CCSCc12)c3ccc(cc3)C(F)(F)F
#
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
 XAV  XAV  2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol  ligand  32  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XAV
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
 XAV  N1    N  N     0  -0.486   1.1383   1.5148   0.0132
 XAV  C2    C  CR6   0   0.391   0.6263   0.2880  -0.0099
 XAV  N3    N  N     0  -0.463   1.3325  -0.8216  -0.0624
 XAV  C4    C  CR6   0   0.295   2.6670  -0.7234  -0.0783
 XAV  C5    C  CR6   0  -0.086   3.3084   0.5045  -0.0265
 XAV  C6    C  CR6   0   0.506   2.4492   1.6148  -0.0015
 XAV  O6    O  OH1   0  -0.592   2.9892   2.8243   0.0076
 XAV  FAB   F  F     0  -0.314  -5.5946  -0.2456  -1.1809
 XAV  FAC   F  F     0  -0.306  -5.7220   0.8245   0.6791
 XAV  FAD   F  F     0  -0.307  -5.5324  -1.3190   0.6808
 XAV  CAE   C  CR16  0  -0.265  -1.6551   1.3013   0.0647
 XAV  CAF   C  CR16  0  -0.267  -1.4523  -1.0898   0.0041
 XAV  CAG   C  CR16  0  -0.259  -3.0344   1.1855   0.0966
 XAV  CAH   C  CR16  0  -0.258  -2.8302  -1.2110   0.0368
 XAV  CAI   C  CH2   0  -0.587   4.8541  -1.9405  -0.5341
 XAV  CAJ   C  CH2   0  -0.487   3.3930  -2.0360  -0.1436
 XAV  CAK   C  CH2   0  -0.636   4.7956   0.7079  -0.0258
 XAV  SAN   S  S2    0  -0.006   5.7190  -0.7479   0.5157
 XAV  CAP   C  CR6   0  -0.000  -0.8484   0.1663   0.0193
 XAV  CAQ   C  CR6   0  -0.202  -3.6261  -0.0720   0.0862
 XAV  CAU   C  CT    0   1.053  -5.1166  -0.2022   0.0728
 XAV  HO6   H  HOH1  0   0.483   2.2874   3.4899   0.0401
 XAV  HAE   H  HCR6  0   0.265  -1.2041   2.2837   0.0770
 XAV  HAF   H  HCR6  0   0.266  -0.8378  -1.9782  -0.0320
 XAV  HAG   H  HCR6  0   0.276  -3.6356   2.0839   0.1331
 XAV  HAH   H  HCR6  0   0.275  -3.2696  -2.1995   0.0258
 XAV  HAI   H  HCH2  0   0.296   5.3458  -2.9036  -0.4028
 XAV  HAIA  H  HCH2  0   0.278   4.9720  -1.6484  -1.5794
 XAV  HAJ   H  HCH2  0   0.274   3.3058  -2.5205   0.8328
 XAV  HAJA  H  HCH2  0   0.272   2.8628  -2.6778  -0.8514
 XAV  HAK   H  HCH2  0   0.293   5.1380   1.0083  -1.0198
 XAV  HAKA  H  HCH2  0   0.298   5.0714   1.5109   0.6590

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
 XAV  N1   C2    aromatic  1.330  0.020  1.330
 XAV  N1   C6    aromatic  1.315  0.020  1.315
 XAV  C2   N3    aromatic  1.316  0.020  1.316
 XAV  C2   CAP   single    1.480  0.020  1.480
 XAV  N3   C4    aromatic  1.338  0.020  1.338
 XAV  C4   C5    aromatic  1.386  0.020  1.386
 XAV  C4   CAJ   single    1.501  0.020  1.501
 XAV  C5   C6    aromatic  1.404  0.020  1.404
 XAV  C5   CAK   single    1.501  0.020  1.501
 XAV  C6   O6    single    1.325  0.020  1.325
 XAV  FAB  CAU   single    1.342  0.020  1.342
 XAV  FAC  CAU   single    1.337  0.020  1.337
 XAV  FAD  CAU   single    1.338  0.020  1.338
 XAV  CAE  CAG   aromatic  1.385  0.020  1.385
 XAV  CAE  CAP   aromatic  1.393  0.020  1.393
 XAV  CAF  CAH   aromatic  1.384  0.020  1.384
 XAV  CAF  CAP   aromatic  1.394  0.020  1.394
 XAV  CAG  CAQ   aromatic  1.390  0.020  1.390
 XAV  CAH  CAQ   aromatic  1.390  0.020  1.390
 XAV  CAI  CAJ   single    1.515  0.020  1.515
 XAV  CAI  SAN   single    1.809  0.020  1.809
 XAV  CAK  SAN   single    1.807  0.020  1.807
 XAV  CAQ  CAU   single    1.496  0.020  1.496
 XAV  O6   HO6   single    0.850  0.020  0.980
 XAV  CAE  HAE   single    0.930  0.020  1.080
 XAV  CAF  HAF   single    0.930  0.020  1.080
 XAV  CAG  HAG   single    0.930  0.020  1.080
 XAV  CAH  HAH   single    0.930  0.020  1.080
 XAV  CAI  HAI   single    0.970  0.020  1.090
 XAV  CAI  HAIA  single    0.970  0.020  1.090
 XAV  CAJ  HAJ   single    0.970  0.020  1.090
 XAV  CAJ  HAJA  single    0.970  0.020  1.090
 XAV  CAK  HAK   single    0.970  0.020  1.090
 XAV  CAK  HAKA  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
 XAV  C6    N1   C2   116.99  3.000
 XAV  CAP   C2   N3   117.78  3.000
 XAV  CAP   C2   N1   117.34  3.000
 XAV  N3    C2   N1   124.88  3.000
 XAV  C4    N3   C2   118.27  3.000
 XAV  CAJ   C4   C5   123.52  3.000
 XAV  CAJ   C4   N3   114.74  3.000
 XAV  C5    C4   N3   121.73  3.000
 XAV  CAK   C5   C6   119.95  3.000
 XAV  CAK   C5   C4   125.34  3.000
 XAV  C6    C5   C4   114.70  3.000
 XAV  O6    C6   C5   118.21  3.000
 XAV  O6    C6   N1   118.41  3.000
 XAV  C5    C6   N1   123.38  3.000
 XAV  HO6   O6   C6   109.43  3.000
 XAV  HAE   CAE  CAP  119.94  3.000
 XAV  HAE   CAE  CAG  119.43  3.000
 XAV  CAP   CAE  CAG  120.62  3.000
 XAV  HAF   CAF  CAP  119.66  3.000
 XAV  HAF   CAF  CAH  119.67  3.000
 XAV  CAP   CAF  CAH  120.67  3.000
 XAV  HAG   CAG  CAQ  121.01  3.000
 XAV  HAG   CAG  CAE  119.01  3.000
 XAV  CAQ   CAG  CAE  119.98  3.000
 XAV  HAH   CAH  CAQ  121.09  3.000
 XAV  HAH   CAH  CAF  118.97  3.000
 XAV  CAQ   CAH  CAF  119.94  3.000
 XAV  HAIA  CAI  HAI  107.65  3.000
 XAV  HAIA  CAI  SAN  109.13  3.000
 XAV  HAI   CAI  SAN  107.28  3.000
 XAV  HAIA  CAI  CAJ  111.58  3.000
 XAV  HAI   CAI  CAJ  110.39  3.000
 XAV  SAN   CAI  CAJ  110.67  3.000
 XAV  HAJA  CAJ  HAJ  106.23  3.000
 XAV  HAJA  CAJ  CAI  109.75  3.000
 XAV  HAJ   CAJ  CAI  109.57  3.000
 XAV  HAJA  CAJ  C4   107.88  3.000
 XAV  HAJ   CAJ  C4   108.06  3.000
 XAV  CAI   CAJ  C4   114.98  3.000
 XAV  HAKA  CAK  HAK  106.82  3.000
 XAV  HAKA  CAK  SAN  106.01  3.000
 XAV  HAK   CAK  SAN  109.50  3.000
 XAV  HAKA  CAK  C5   110.52  3.000
 XAV  HAK   CAK  C5   110.30  3.000
 XAV  SAN   CAK  C5   113.41  3.000
 XAV  CAK   SAN  CAI   96.48  3.000
 XAV  CAF   CAP  CAE  118.93  3.000
 XAV  CAF   CAP  C2   120.37  3.000
 XAV  CAE   CAP  C2   120.70  3.000
 XAV  CAU   CAQ  CAH  119.91  3.000
 XAV  CAU   CAQ  CAG  120.19  3.000
 XAV  CAH   CAQ  CAG  119.85  3.000
 XAV  CAQ   CAU  FAD  112.22  3.000
 XAV  CAQ   CAU  FAC  112.34  3.000
 XAV  FAD   CAU  FAC  107.11  3.000
 XAV  CAQ   CAU  FAB  111.46  3.000
 XAV  FAD   CAU  FAB  106.66  3.000
 XAV  FAC   CAU  FAB  106.68  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
 XAV  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 XAV  CONST_02  CAE  CAP  C2   N1     0.00   0.0  0
 XAV  CONST_03  CAF  CAP  C2   N1   180.00   0.0  0
 XAV  CONST_04  C4   C5   C6   N1     0.00   0.0  0
 XAV  CONST_05  C5   C6   N1   C2     0.00   0.0  0
 XAV  CONST_06  C5   C4   N3   C2     0.00   0.0  0
 XAV  CONST_07  CAG  CAE  CAP  C2   180.00   0.0  0
 XAV  CONST_08  CAH  CAF  CAP  C2   180.00   0.0  0
 XAV  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 XAV  CONST_10  CAE  CAP  C2   N3   180.00   0.0  0
 XAV  CONST_11  CAF  CAP  C2   N3     0.00   0.0  0
 XAV  CONST_12  C6   C5   C4   N3     0.00   0.0  0
 XAV  CONST_13  CAP  C2   N3   C4   180.00   0.0  0
 XAV  CONST_14  CAP  C2   N1   C6   180.00   0.0  0
 XAV  CONST_15  CAH  CAQ  CAG  CAE    0.00   0.0  0
 XAV  CONST_16  CAH  CAF  CAP  CAE    0.00   0.0  0
 XAV  CONST_17  CAG  CAQ  CAH  CAF    0.00   0.0  0
 XAV  CONST_18  CAG  CAE  CAP  CAF    0.00   0.0  0
 XAV  CONST_19  CAQ  CAG  CAE  CAP    0.00   0.0  0
 XAV  CONST_20  CAQ  CAH  CAF  CAP    0.00   0.0  0
 XAV  CONST_21  O6   C6   N1   C2   180.00   0.0  0
 XAV  CONST_22  O6   C6   C5   C4   180.00   0.0  0
 XAV  CONST_23  CAK  C5   C6   O6     0.00   0.0  0
 XAV  CONST_24  CAU  CAQ  CAG  CAE  180.00   0.0  0
 XAV  CONST_25  CAU  CAQ  CAH  CAF  180.00   0.0  0
 XAV  CONST_26  HAE  CAE  CAP  C2     0.00   0.0  0
 XAV  CONST_27  HAF  CAF  CAP  C2     0.00   0.0  0
 XAV  CONST_28  HAH  CAH  CAQ  CAG  180.00   0.0  0
 XAV  CONST_29  HAG  CAG  CAQ  CAH  180.00   0.0  0
 XAV  Var_01    CAI  CAJ  C4   N3   164.28  30.0  1
 XAV  Var_02    SAN  CAK  C5   C4   -21.66  30.0  1
 XAV  Var_03    SAN  CAI  CAJ  C4    52.23  30.0  1
 XAV  Var_04    CAG  CAQ  CAU  FAB   90.27  30.0  3

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
 XAV  plan-1  C2   0.020
 XAV  plan-1  CAE  0.020
 XAV  plan-1  CAF  0.020
 XAV  plan-1  CAG  0.020
 XAV  plan-1  CAH  0.020
 XAV  plan-1  CAP  0.020
 XAV  plan-1  CAQ  0.020
 XAV  plan-1  CAU  0.020
 XAV  plan-1  HAE  0.020
 XAV  plan-1  HAF  0.020
 XAV  plan-1  HAG  0.020
 XAV  plan-1  HAH  0.020
 XAV  plan-2  N1   0.020
 XAV  plan-2  C2   0.020
 XAV  plan-2  N3   0.020
 XAV  plan-2  C4   0.020
 XAV  plan-2  C5   0.020
 XAV  plan-2  C6   0.020
 XAV  plan-2  O6   0.020
 XAV  plan-2  CAJ  0.020
 XAV  plan-2  CAK  0.020
 XAV  plan-2  CAP  0.020

