# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:24:05 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(1,1-difluoroethyl)-5-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Nc2ccc(cc2)[S](F)(F)(F)(F)F)n3nc(nc3n1)C(C)(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
 D65  D65  2-(1,1-difluoroethyl)-5-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine  ligand  39  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D65
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
 D65  F7   F  F     0  -0.413  -4.1928   1.1358  -1.2920
 D65  S1   S  S     0   2.011  -4.0800   0.5533   0.2073
 D65  F4   F  F     0  -0.413  -4.1001   0.0389   1.7362
 D65  F5   F  F     0  -0.403  -5.4839   1.2869   0.5180
 D65  F3   F  F     0  -0.412  -3.3508   1.9132   0.6744
 D65  F6   F  F     0  -0.413  -4.9386  -0.7389  -0.2320
 D65  C5   C  CR6   0  -0.157  -2.5153  -0.2662  -0.1353
 D65  C4   C  CR16  0  -0.249  -1.4752  -0.1731   0.7789
 D65  C3   C  CR16  0  -0.260  -0.2767  -0.8129   0.5240
 D65  C6   C  CR16  0  -0.243  -2.3630  -0.9994  -1.3037
 D65  C1   C  CR16  0  -0.315  -1.1555  -1.6214  -1.5617
 D65  C2   C  CR6   0   0.360  -0.1024  -1.5300  -0.6564
 D65  N1   N  NH1   0  -0.766   1.0757  -2.2218  -0.9483
 D65  C7   C  CR6   0   0.689   2.3069  -2.0143  -0.4215
 D65  C8   C  CR16  0  -0.466   3.1855  -3.0228  -0.0938
 D65  C9   C  CR6   0   0.270   4.4619  -2.7145   0.4066
 D65  C10  C  CH3   0  -0.725   5.4105  -3.8150   0.7534
 D65  N2   N  N     0  -0.423   2.7785  -0.7528  -0.2490
 D65  C11  C  CR56  0   0.588   4.0382  -0.5084   0.2592
 D65  N5   N  N     0  -0.473   4.8794  -1.4752   0.5953
 D65  N3   N  N     0  -0.276   2.1687   0.3986  -0.5629
 D65  C12  C  CR5   0   0.224   3.0748   1.2804  -0.2087
 D65  N4   N  N     0  -0.501   4.2182   0.8016   0.2959
 D65  C13  C  CT    0   0.731   2.8481   2.7563  -0.3557
 D65  F1   F  F     0  -0.348   3.7803   3.2334  -1.2371
 D65  F2   F  F     0  -0.336   1.6394   2.9536  -0.9455
 D65  C14  C  CH3   0  -0.761   2.9334   3.5134   0.9407
 D65  H1   H  HCR6  0   0.291  -1.5700   0.3733   1.7060
 D65  H2   H  HCR6  0   0.289   0.5031  -0.7612   1.2703
 D65  H3   H  HCR6  0   0.292  -3.1538  -1.0979  -2.0327
 D65  H4   H  HCR6  0   0.290  -1.0350  -2.1821  -2.4795
 D65  H5   H  HNH1  0   0.432   0.9522  -3.1311  -1.3704
 D65  H6   H  HCR6  0   0.302   2.8706  -4.0505  -0.2003
 D65  H7   H  HCH3  0   0.269   6.1916  -3.8820  -0.0058
 D65  H8   H  HCH3  0   0.263   5.8977  -3.6159   1.7069
 D65  H9   H  HCH3  0   0.255   4.9106  -4.7794   0.8064
 D65  H10  H  HCH3  0   0.263   3.9140   3.3775   1.3924
 D65  H11  H  HCH3  0   0.273   2.7662   4.5772   0.7720
 D65  H12  H  HCH3  0   0.262   2.1836   3.1480   1.6411

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
 D65  C10  C9   single    1.494  0.020  1.494
 D65  N5   C9   aromatic  1.321  0.020  1.321
 D65  N5   C11  aromatic  1.325  0.020  1.325
 D65  C9   C8   aromatic  1.405  0.020  1.405
 D65  C11  N4   aromatic  1.323  0.020  1.323
 D65  C11  N2   aromatic  1.380  0.020  1.380
 D65  N4   C12  aromatic  1.338  0.020  1.338
 D65  C8   C7   aromatic  1.377  0.020  1.377
 D65  F2   C13  single    1.359  0.020  1.359
 D65  N2   C7   aromatic  1.358  0.020  1.358
 D65  N2   N3   aromatic  1.340  0.020  1.340
 D65  C12  C13  single    1.500  0.020  1.500
 D65  C12  N3   aromatic  1.313  0.020  1.313
 D65  C7   N1   single    1.355  0.020  1.355
 D65  C13  C14  single    1.504  0.020  1.504
 D65  C13  F1   single    1.369  0.020  1.369
 D65  N1   C2   single    1.397  0.020  1.397
 D65  C2   C1   aromatic  1.392  0.020  1.392
 D65  C2   C3   aromatic  1.392  0.020  1.392
 D65  C1   C6   aromatic  1.383  0.020  1.383
 D65  C3   C4   aromatic  1.382  0.020  1.382
 D65  F3   S1   single    1.612  0.020  1.612
 D65  C6   C5   aromatic  1.388  0.020  1.388
 D65  C4   C5   aromatic  1.388  0.020  1.388
 D65  C5   S1   single    1.799  0.020  1.799
 D65  F4   S1   single    1.613  0.020  1.613
 D65  S1   F7   single    1.613  0.020  1.613
 D65  S1   F5   single    1.614  0.020  1.614
 D65  S1   F6   single    1.612  0.020  1.612
 D65  C4   H1   single    0.930  0.020  1.080
 D65  C3   H2   single    0.930  0.020  1.080
 D65  C6   H3   single    0.930  0.020  1.080
 D65  C1   H4   single    0.930  0.020  1.080
 D65  N1   H5   single    0.890  0.020  1.040
 D65  C8   H6   single    0.930  0.020  1.080
 D65  C10  H7   single    0.970  0.020  1.090
 D65  C10  H8   single    0.970  0.020  1.090
 D65  C10  H9   single    0.970  0.020  1.090
 D65  C14  H10  single    0.970  0.020  1.090
 D65  C14  H11  single    0.970  0.020  1.090
 D65  C14  H12  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
 D65  C5   S1   F6    92.65  3.000
 D65  F6   S1   F3   174.72  3.000
 D65  C5   S1   F3    92.64  3.000
 D65  F6   S1   F5    87.34  3.000
 D65  C5   S1   F5   180.00  3.000
 D65  F3   S1   F5    87.38  3.000
 D65  F6   S1   F4    89.77  3.000
 D65  F5   S1   F4    87.23  3.000
 D65  C5   S1   F4    92.64  3.000
 D65  F3   S1   F4    90.00  3.000
 D65  F6   S1   F7    89.94  3.000
 D65  F5   S1   F7    87.36  3.000
 D65  F4   S1   F7   174.59  3.000
 D65  C5   S1   F7    92.77  3.000
 D65  F3   S1   F7    89.79  3.000
 D65  C6   C5   C4   120.51  3.000
 D65  C4   C5   S1   119.72  3.000
 D65  C6   C5   S1   119.76  3.000
 D65  H1   C4   C3   117.93  3.000
 D65  H1   C4   C5   122.24  3.000
 D65  C3   C4   C5   119.82  3.000
 D65  H2   C3   C2   121.32  3.000
 D65  H2   C3   C4   118.44  3.000
 D65  C2   C3   C4   120.22  3.000
 D65  H3   C6   C1   118.20  3.000
 D65  H3   C6   C5   122.42  3.000
 D65  C1   C6   C5   119.38  3.000
 D65  H4   C1   C2   120.09  3.000
 D65  H4   C1   C6   119.25  3.000
 D65  C2   C1   C6   120.66  3.000
 D65  N1   C2   C1   118.01  3.000
 D65  C1   C2   C3   119.38  3.000
 D65  N1   C2   C3   122.54  3.000
 D65  H5   N1   C7   114.29  3.000
 D65  H5   N1   C2   115.47  3.000
 D65  C7   N1   C2   127.52  3.000
 D65  N2   C7   C8   115.38  3.000
 D65  N2   C7   N1   120.48  3.000
 D65  C8   C7   N1   124.06  3.000
 D65  H6   C8   C9   120.58  3.000
 D65  H6   C8   C7   119.16  3.000
 D65  C9   C8   C7   120.24  3.000
 D65  N5   C9   C10  117.21  3.000
 D65  N5   C9   C8   122.93  3.000
 D65  C10  C9   C8   119.86  3.000
 D65  H9   C10  H8   108.97  3.000
 D65  H9   C10  H7   107.97  3.000
 D65  H8   C10  H7   107.47  3.000
 D65  H9   C10  C9   111.88  3.000
 D65  H8   C10  C9   110.65  3.000
 D65  H7   C10  C9   109.77  3.000
 D65  N3   N2   C11  110.45  3.000
 D65  N3   N2   C7   127.62  3.000
 D65  C11  N2   C7   121.90  3.000
 D65  N4   C11  N5   129.00  3.000
 D65  N4   C11  N2   108.05  3.000
 D65  N5   C11  N2   122.93  3.000
 D65  C11  N5   C9   116.59  3.000
 D65  C12  N3   N2   101.53  3.000
 D65  C13  C12  N4   121.20  3.000
 D65  C13  C12  N3   122.00  3.000
 D65  N4   C12  N3   116.80  3.000
 D65  C12  N4   C11  103.16  3.000
 D65  C14  C13  F2   110.58  3.000
 D65  C14  C13  F1   109.94  3.000
 D65  F2   C13  F1   106.00  3.000
 D65  F1   C13  C12  107.64  3.000
 D65  C14  C13  C12  113.72  3.000
 D65  F2   C13  C12  108.64  3.000
 D65  H12  C14  H11  108.75  3.000
 D65  H12  C14  H10  108.15  3.000
 D65  H11  C14  H10  108.93  3.000
 D65  H12  C14  C13  110.27  3.000
 D65  H11  C14  C13  110.44  3.000
 D65  H10  C14  C13  110.25  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
 D65  CONST_01  C2   C1   C6   C5     0.00   0.0  0
 D65  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 D65  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 D65  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 D65  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 D65  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 D65  CONST_07  N5   C9   C8   C7     0.00   0.0  0
 D65  CONST_08  N5   C11  N2   C7     0.00   0.0  0
 D65  CONST_09  N4   C11  N2   C7   180.00   0.0  0
 D65  CONST_10  C12  N3   N2   C7   180.00   0.0  0
 D65  CONST_11  C11  N5   C9   C8     0.00   0.0  0
 D65  CONST_12  C11  N2   C7   C8     0.00   0.0  0
 D65  CONST_13  N3   N2   C7   C8   180.00   0.0  0
 D65  CONST_14  N4   C11  N5   C9   180.00   0.0  0
 D65  CONST_15  N2   C11  N5   C9     0.00   0.0  0
 D65  CONST_16  N2   C7   C8   C9     0.00   0.0  0
 D65  CONST_17  C12  N4   C11  N2     0.00   0.0  0
 D65  CONST_18  N4   C12  N3   N2     0.00   0.0  0
 D65  CONST_19  N3   C12  N4   C11    0.00   0.0  0
 D65  CONST_20  C12  N3   N2   C11    0.00   0.0  0
 D65  CONST_21  C12  N4   C11  N5   180.00   0.0  0
 D65  CONST_22  N3   N2   C11  N5   180.00   0.0  0
 D65  CONST_23  N4   C11  N2   N3     0.00   0.0  0
 D65  CONST_24  C1   C6   C5   S1   180.00   0.0  0
 D65  CONST_25  C3   C4   C5   S1   180.00   0.0  0
 D65  CONST_26  N1   C2   C3   C4   180.00   0.0  0
 D65  CONST_27  N1   C2   C1   C6   180.00   0.0  0
 D65  CONST_28  C9   C8   C7   N1   180.00   0.0  0
 D65  CONST_29  C11  N2   C7   N1   180.00   0.0  0
 D65  CONST_30  N3   N2   C7   N1     0.00   0.0  0
 D65  CONST_31  C10  C9   C8   C7   180.00   0.0  0
 D65  CONST_32  C11  N5   C9   C10  180.00   0.0  0
 D65  CONST_33  C13  C12  N3   N2   180.00   0.0  0
 D65  CONST_34  C13  C12  N4   C11  180.00   0.0  0
 D65  CONST_35  H4   C1   C6   C5   180.00   0.0  0
 D65  CONST_36  H2   C3   C4   C5   180.00   0.0  0
 D65  CONST_37  H3   C6   C5   C4   180.00   0.0  0
 D65  CONST_38  H1   C4   C5   C6   180.00   0.0  0
 D65  CONST_39  H6   C8   C7   N2   180.00   0.0  0
 D65  Var_01    C7   N1   C2   C3   -21.45  30.0  3
 D65  Var_02    C8   C7   N1   C2   140.89  30.0  3
 D65  Var_03    C6   C5   S1   F7   -45.45  30.0  2
 D65  Var_04    F2   C13  C12  N3    -2.87  30.0  2
 D65  Var_05    H7   C10  C9   C8   105.67  30.0  2
 D65  Var_06    H10  C14  C13  C12   59.27  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
 D65  plan-1  S1   0.020
 D65  plan-1  C5   0.020
 D65  plan-1  C4   0.020
 D65  plan-1  C3   0.020
 D65  plan-1  C6   0.020
 D65  plan-1  C1   0.020
 D65  plan-1  C2   0.020
 D65  plan-1  N1   0.020
 D65  plan-1  H1   0.020
 D65  plan-1  H2   0.020
 D65  plan-1  H3   0.020
 D65  plan-1  H4   0.020
 D65  plan-2  N1   0.020
 D65  plan-2  C7   0.020
 D65  plan-2  C8   0.020
 D65  plan-2  C9   0.020
 D65  plan-2  C10  0.020
 D65  plan-2  N2   0.020
 D65  plan-2  C11  0.020
 D65  plan-2  N5   0.020
 D65  plan-2  N3   0.020
 D65  plan-2  C12  0.020
 D65  plan-2  N4   0.020
 D65  plan-2  C13  0.020
 D65  plan-2  H6   0.020

