# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 03:36:21 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(pyridin-2-yl)-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1nc(nc2CCSCc12)c3ccccn3
#
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
 P4L  P4L  2-(pyridin-2-yl)-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol  ligand  28  17  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P4L
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
 P4L  N1    N  N     0  -0.487  -0.5407   1.4042   0.0147
 P4L  C2    C  CR6   0   0.358  -0.9695   0.1455   0.0069
 P4L  N3    N  N     0  -0.439  -0.1951  -0.9163  -0.0322
 P4L  C4    C  CR6   0   0.277   1.1301  -0.7267  -0.0488
 P4L  C5    C  CR6   0  -0.079   1.6900   0.5410  -0.0122
 P4L  C6    C  CR6   0   0.503   0.7600   1.5925  -0.0018
 P4L  O6    O  OH1   0  -0.593   1.2188   2.8357  -0.0085
 P4L  CAB   C  CR16  0  -0.312  -5.1268  -0.5109   0.1000
 P4L  CAC   C  CR16  0  -0.152  -4.6728   0.7975   0.0768
 P4L  CAD   C  CR16  0  -0.083  -4.1828  -1.5297   0.0906
 P4L  CAE   C  CR16  0  -0.295  -3.3074   1.0325   0.0460
 P4L  CAF   C  CH2   0  -0.587   3.3965  -1.8052  -0.4794
 P4L  CAG   C  CH2   0  -0.487   1.9419  -1.9898  -0.0968
 P4L  CAH   C  CH2   0  -0.636   3.1606   0.8409  -0.0140
 P4L  NAI   N  N     0  -0.406  -2.8769  -1.3151   0.0605
 P4L  SAL   S  S2    0  -0.007   4.1748  -0.5419   0.5555
 P4L  CAN   C  CR6   0   0.147  -2.4418  -0.0584   0.0387
 P4L  HO6   H  HOH1  0   0.483   0.4743   3.4533   0.0167
 P4L  HAC   H  HCR6  0   0.277  -5.3695   1.6249   0.0825
 P4L  HAD   H  HCR6  0   0.264  -4.5004  -2.5664   0.1088
 P4L  HAE   H  HCR6  0   0.272  -2.9179   2.0399   0.0268
 P4L  HAF   H  HCH2  0   0.295   3.9499  -2.7315  -0.3300
 P4L  HAFA  H  HCH2  0   0.278   3.5031  -1.5231  -1.5287
 P4L  HAG   H  HCH2  0   0.273   1.8794  -2.4691   0.8843
 P4L  HAGA  H  HCH2  0   0.271   1.4584  -2.6724  -0.7998
 P4L  HAH   H  HCH2  0   0.293   3.4855   1.1435  -1.0132
 P4L  HAHA  H  HCH2  0   0.297   3.3828   1.6727   0.6556
 P4L  HAB   H  HCR6  0   0.275  -6.1826  -0.7422   0.1247

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
 P4L  N1   C2    aromatic  1.330  0.020  1.330
 P4L  N1   C6    aromatic  1.314  0.020  1.314
 P4L  C2   N3    aromatic  1.315  0.020  1.315
 P4L  C2   CAN   single    1.487  0.020  1.487
 P4L  N3   C4    aromatic  1.339  0.020  1.339
 P4L  C4   C5    aromatic  1.386  0.020  1.386
 P4L  C4   CAG   single    1.502  0.020  1.502
 P4L  C5   C6    aromatic  1.404  0.020  1.404
 P4L  C5   CAH   single    1.501  0.020  1.501
 P4L  C6   O6    single    1.325  0.020  1.325
 P4L  CAB  CAC   aromatic  1.385  0.020  1.385
 P4L  CAB  CAD   aromatic  1.389  0.020  1.389
 P4L  CAC  CAE   aromatic  1.386  0.020  1.386
 P4L  CAD  NAI   aromatic  1.324  0.020  1.324
 P4L  CAE  CAN   aromatic  1.393  0.020  1.393
 P4L  CAF  CAG   single    1.515  0.020  1.515
 P4L  CAF  SAL   single    1.809  0.020  1.809
 P4L  CAH  SAL   single    1.807  0.020  1.807
 P4L  NAI  CAN   aromatic  1.330  0.020  1.330
 P4L  O6   HO6   single    0.850  0.020  0.980
 P4L  CAB  HAB   single    0.930  0.020  1.080
 P4L  CAC  HAC   single    0.930  0.020  1.080
 P4L  CAD  HAD   single    0.930  0.020  1.080
 P4L  CAE  HAE   single    0.930  0.020  1.080
 P4L  CAF  HAF   single    0.970  0.020  1.090
 P4L  CAF  HAFA  single    0.970  0.020  1.090
 P4L  CAG  HAG   single    0.970  0.020  1.090
 P4L  CAG  HAGA  single    0.970  0.020  1.090
 P4L  CAH  HAH   single    0.970  0.020  1.090
 P4L  CAH  HAHA  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
 P4L  C6    N1   C2   117.04  3.000
 P4L  CAN   C2   N3   118.24  3.000
 P4L  CAN   C2   N1   116.68  3.000
 P4L  N3    C2   N1   125.08  3.000
 P4L  C4    N3   C2   117.97  3.000
 P4L  CAG   C4   C5   123.46  3.000
 P4L  CAG   C4   N3   114.60  3.000
 P4L  C5    C4   N3   121.94  3.000
 P4L  CAH   C5   C6   119.96  3.000
 P4L  CAH   C5   C4   125.34  3.000
 P4L  C6    C5   C4   114.68  3.000
 P4L  O6    C6   C5   118.25  3.000
 P4L  O6    C6   N1   118.50  3.000
 P4L  C5    C6   N1   123.25  3.000
 P4L  HO6   O6   C6   109.40  3.000
 P4L  HAB   CAB  CAD  120.46  3.000
 P4L  HAB   CAB  CAC  121.50  3.000
 P4L  CAD   CAB  CAC  118.03  3.000
 P4L  HAC   CAC  CAE  120.33  3.000
 P4L  HAC   CAC  CAB  120.76  3.000
 P4L  CAE   CAC  CAB  118.91  3.000
 P4L  HAD   CAD  NAI  116.38  3.000
 P4L  HAD   CAD  CAB  120.14  3.000
 P4L  NAI   CAD  CAB  123.48  3.000
 P4L  HAE   CAE  CAN  120.42  3.000
 P4L  HAE   CAE  CAC  120.91  3.000
 P4L  CAN   CAE  CAC  118.66  3.000
 P4L  HAFA  CAF  HAF  107.57  3.000
 P4L  HAFA  CAF  SAL  109.11  3.000
 P4L  HAF   CAF  SAL  107.27  3.000
 P4L  HAFA  CAF  CAG  111.59  3.000
 P4L  HAF   CAF  CAG  110.45  3.000
 P4L  SAL   CAF  CAG  110.71  3.000
 P4L  HAGA  CAG  HAG  106.14  3.000
 P4L  HAGA  CAG  CAF  109.78  3.000
 P4L  HAG   CAG  CAF  109.56  3.000
 P4L  HAGA  CAG  C4   107.86  3.000
 P4L  HAG   CAG  C4   107.99  3.000
 P4L  CAF   CAG  C4   115.11  3.000
 P4L  HAHA  CAH  HAH  106.83  3.000
 P4L  HAHA  CAH  SAL  106.01  3.000
 P4L  HAH   CAH  SAL  109.45  3.000
 P4L  HAHA  CAH  C5   110.56  3.000
 P4L  HAH   CAH  C5   110.34  3.000
 P4L  SAL   CAH  C5   113.37  3.000
 P4L  CAN   NAI  CAD  118.44  3.000
 P4L  CAH   SAL  CAF   96.47  3.000
 P4L  NAI   CAN  CAE  122.46  3.000
 P4L  NAI   CAN  C2   117.00  3.000
 P4L  CAE   CAN  C2   120.54  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
 P4L  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 P4L  CONST_02  CAE  CAN  C2   N1     0.00   0.0  0
 P4L  CONST_03  NAI  CAN  C2   N1   180.00   0.0  0
 P4L  CONST_04  C4   C5   C6   N1     0.00   0.0  0
 P4L  CONST_05  C5   C6   N1   C2     0.00   0.0  0
 P4L  CONST_06  C5   C4   N3   C2     0.00   0.0  0
 P4L  CONST_07  CAC  CAE  CAN  C2   180.00   0.0  0
 P4L  CONST_08  CAD  NAI  CAN  C2   180.00   0.0  0
 P4L  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 P4L  CONST_10  CAE  CAN  C2   N3   180.00   0.0  0
 P4L  CONST_11  NAI  CAN  C2   N3     0.00   0.0  0
 P4L  CONST_12  C6   C5   C4   N3     0.00   0.0  0
 P4L  CONST_13  CAN  C2   N3   C4   180.00   0.0  0
 P4L  CONST_14  CAN  C2   N1   C6   180.00   0.0  0
 P4L  CONST_15  CAN  CAE  CAC  CAB    0.00   0.0  0
 P4L  CONST_16  CAN  NAI  CAD  CAB    0.00   0.0  0
 P4L  CONST_17  NAI  CAD  CAB  CAC    0.00   0.0  0
 P4L  CONST_18  NAI  CAN  CAE  CAC    0.00   0.0  0
 P4L  CONST_19  CAE  CAC  CAB  CAD    0.00   0.0  0
 P4L  CONST_20  CAE  CAN  NAI  CAD    0.00   0.0  0
 P4L  CONST_21  O6   C6   N1   C2   180.00   0.0  0
 P4L  CONST_22  O6   C6   C5   C4   180.00   0.0  0
 P4L  CONST_23  CAH  C5   C6   O6     0.00   0.0  0
 P4L  CONST_24  HAE  CAE  CAN  C2     0.00   0.0  0
 P4L  CONST_25  HAD  CAD  CAB  CAC  180.00   0.0  0
 P4L  CONST_26  HAC  CAC  CAB  CAD  180.00   0.0  0
 P4L  CONST_27  HAB  CAB  CAC  CAE  180.00   0.0  0
 P4L  Var_01    CAF  CAG  C4   N3   164.64  30.0  1
 P4L  Var_02    SAL  CAH  C5   C4   -22.01  30.0  1
 P4L  Var_03    SAL  CAF  CAG  C4    51.87  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
 P4L  plan-1  C2   0.020
 P4L  plan-1  CAB  0.020
 P4L  plan-1  CAC  0.020
 P4L  plan-1  CAD  0.020
 P4L  plan-1  CAE  0.020
 P4L  plan-1  NAI  0.020
 P4L  plan-1  CAN  0.020
 P4L  plan-1  HAC  0.020
 P4L  plan-1  HAD  0.020
 P4L  plan-1  HAE  0.020
 P4L  plan-1  HAB  0.020
 P4L  plan-2  N1   0.020
 P4L  plan-2  C2   0.020
 P4L  plan-2  N3   0.020
 P4L  plan-2  C4   0.020
 P4L  plan-2  C5   0.020
 P4L  plan-2  C6   0.020
 P4L  plan-2  O6   0.020
 P4L  plan-2  CAG  0.020
 P4L  plan-2  CAH  0.020
 P4L  plan-2  CAN  0.020

