# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:28:53 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 6-[(2,5-dimethoxyphenyl)sulfanyl]-3-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(Sc2ccc3nnc(n3n2)c4cnn(C)c4)c1
#
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
 2YK  2YK  6-[(2,5-dimethoxyphenyl)sulfanyl]-3-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazine  ligand  42  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2YK
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
 2YK  N3   N  N     0  -0.320  -3.4785  -1.9697  -0.6007
 2YK  C4   C  CR15  0  -0.077  -3.7329   1.7620  -1.2167
 2YK  N2   N  N     0  -0.273  -4.7201   2.3772  -1.8353
 2YK  C7   C  CR6   0   0.096  -0.1652   0.4339   0.8543
 2YK  C6   C  CR56  0   0.461  -1.5922  -1.8139   0.3907
 2YK  C9   C  CR16  0  -0.273  -0.3642  -1.9506   1.0768
 2YK  C13  C  CR16  0  -0.362   5.0344   0.8315   1.4889
 2YK  C8   C  CR16  0  -0.227   0.3462  -0.8238   1.3141
 2YK  N5   N  N     0  -0.419  -1.9711  -0.5486   0.0199
 2YK  C16  C  CH3   0  -0.436   2.8338   0.0568  -2.0158
 2YK  C17  C  CH3   0  -0.438   6.3536   1.3725   3.9137
 2YK  C12  C  CR6   0   0.369   4.3938   1.4001   2.5818
 2YK  C11  C  CR16  0  -0.299   3.0342   1.6975   2.4836
 2YK  C14  C  CR16  0  -0.367   4.3356   0.5716   0.3129
 2YK  C15  C  CR6   0   0.446   2.9892   0.8838   0.1991
 2YK  O1   O  O2    0  -0.459   2.2357   0.6728  -0.8914
 2YK  C10  C  CR6   0  -0.296   2.3434   1.4462   1.3114
 2YK  S    S  S2    0   0.145   0.6567   1.9527   1.1952
 2YK  N4   N  N     0  -0.330  -2.5100  -2.6695   0.0116
 2YK  N6   N  N     0  -0.250  -1.2845   0.5780   0.2204
 2YK  C5   C  CR5   0   0.405  -3.1680  -0.6920  -0.6042
 2YK  C3   C  CR5   0  -0.197  -3.9561   0.3701  -1.1711
 2YK  C2   C  CR15  0   0.068  -5.1677   0.2039  -1.8189
 2YK  N1   N  NR5   0  -0.265  -5.5746   1.4212  -2.1906
 2YK  C1   C  CH3   0  -0.506  -6.7843   1.7600  -2.9031
 2YK  H1   H  HCR5  0   0.268  -2.8989   2.3206  -0.8244
 2YK  H2   H  HCR6  0   0.309  -0.0301  -2.9257   1.4014
 2YK  H3   H  HCR6  0   0.289   6.0845   0.5754   1.5216
 2YK  H4   H  HCR6  0   0.303   1.2839  -0.8589   1.8494
 2YK  H5   H  HCH3  0   0.232   3.2185  -0.9377  -1.7767
 2YK  H6   H  HCH3  0   0.263   2.0523  -0.0392  -2.7647
 2YK  H7   H  HCH3  0   0.232   3.6456   0.6621  -2.4268
 2YK  H8   H  HCH3  0   0.228   6.5413   0.3009   3.8040
 2YK  H9   H  HCH3  0   0.228   6.9810   1.9141   3.2005
 2YK  H10  H  HCH3  0   0.261   6.6297   1.6737   4.9208
 2YK  H11  H  HCR6  0   0.283   2.5165   2.1256   3.3329
 2YK  H12  H  HCR6  0   0.291   4.8751   0.1267  -0.5121
 2YK  H13  H  HCR5  0   0.300  -5.7407  -0.6849  -2.0262
 2YK  H14  H  HCH3  0   0.265  -7.4000   2.4263  -2.3027
 2YK  H15  H  HCH3  0   0.265  -6.5408   2.2462  -3.8453
 2YK  H16  H  HCH3  0   0.262  -7.3400   0.8495  -3.1058
 2YK  O2   O  O2    0  -0.474   4.9845   1.6868   3.7600

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
 2YK  C17  O2   single    1.413  0.020  1.413
 2YK  S    C10  single    1.765  0.020  1.765
 2YK  S    C7   single    1.760  0.020  1.760
 2YK  C11  C10  aromatic  1.384  0.020  1.384
 2YK  C11  C12  aromatic  1.395  0.020  1.395
 2YK  C8   C7   aromatic  1.433  0.020  1.433
 2YK  C8   C9   aromatic  1.353  0.020  1.353
 2YK  O2   C12  single    1.349  0.020  1.349
 2YK  C10  C15  aromatic  1.404  0.020  1.404
 2YK  C7   N6   aromatic  1.294  0.020  1.294
 2YK  C12  C13  aromatic  1.389  0.020  1.389
 2YK  C9   C6   aromatic  1.413  0.020  1.413
 2YK  N6   N5   aromatic  1.335  0.020  1.335
 2YK  C15  O1   single    1.342  0.020  1.342
 2YK  C15  C14  aromatic  1.387  0.020  1.387
 2YK  C13  C14  aromatic  1.392  0.020  1.392
 2YK  C6   N5   aromatic  1.372  0.020  1.372
 2YK  C6   N4   aromatic  1.311  0.020  1.311
 2YK  N5   C5   aromatic  1.357  0.020  1.357
 2YK  O1   C16  single    1.415  0.020  1.415
 2YK  N4   N3   aromatic  1.343  0.020  1.343
 2YK  C5   N3   aromatic  1.315  0.020  1.315
 2YK  C5   C3   single    1.439  0.020  1.439
 2YK  C2   C3   aromatic  1.384  0.020  1.384
 2YK  C2   N1   aromatic  1.336  0.020  1.336
 2YK  C3   C4   aromatic  1.410  0.020  1.410
 2YK  N1   C1   single    1.444  0.020  1.444
 2YK  N1   N2   aromatic  1.331  0.020  1.331
 2YK  C4   N2   aromatic  1.317  0.020  1.317
 2YK  C4   H1   single    0.930  0.020  1.080
 2YK  C9   H2   single    0.930  0.020  1.080
 2YK  C13  H3   single    0.930  0.020  1.080
 2YK  C8   H4   single    0.930  0.020  1.080
 2YK  C16  H5   single    0.970  0.020  1.090
 2YK  C16  H6   single    0.970  0.020  1.090
 2YK  C16  H7   single    0.970  0.020  1.090
 2YK  C17  H8   single    0.970  0.020  1.090
 2YK  C17  H9   single    0.970  0.020  1.090
 2YK  C17  H10  single    0.970  0.020  1.090
 2YK  C11  H11  single    0.930  0.020  1.080
 2YK  C14  H12  single    0.930  0.020  1.080
 2YK  C2   H13  single    0.930  0.020  1.080
 2YK  C1   H14  single    0.970  0.020  1.090
 2YK  C1   H15  single    0.970  0.020  1.090
 2YK  C1   H16  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
 2YK  C5   N3   N4   109.72  3.000
 2YK  H1   C4   C3   128.47  3.000
 2YK  H1   C4   N2   120.58  3.000
 2YK  C3   C4   N2   110.94  3.000
 2YK  N1   N2   C4   105.73  3.000
 2YK  N6   C7   S    113.74  3.000
 2YK  N6   C7   C8   124.28  3.000
 2YK  S    C7   C8   121.89  3.000
 2YK  N4   C6   N5   109.30  3.000
 2YK  N4   C6   C9   133.29  3.000
 2YK  N5   C6   C9   117.42  3.000
 2YK  H2   C9   C8   122.44  3.000
 2YK  H2   C9   C6   120.12  3.000
 2YK  C8   C9   C6   117.44  3.000
 2YK  H3   C13  C14  117.95  3.000
 2YK  H3   C13  C12  121.41  3.000
 2YK  C14  C13  C12  120.64  3.000
 2YK  H4   C8   C9   121.04  3.000
 2YK  H4   C8   C7   119.81  3.000
 2YK  C9   C8   C7   119.15  3.000
 2YK  C5   N5   N6   127.73  3.000
 2YK  C5   N5   C6   105.69  3.000
 2YK  N6   N5   C6   126.58  3.000
 2YK  H7   C16  H6   108.90  3.000
 2YK  H7   C16  H5   108.96  3.000
 2YK  H6   C16  H5   108.88  3.000
 2YK  H7   C16  O1   111.83  3.000
 2YK  H6   C16  O1   106.39  3.000
 2YK  H5   C16  O1   111.79  3.000
 2YK  H10  C17  H9   108.75  3.000
 2YK  H10  C17  H8   108.72  3.000
 2YK  H9   C17  H8   108.75  3.000
 2YK  H10  C17  O2   106.57  3.000
 2YK  H9   C17  O2   112.01  3.000
 2YK  H8   C17  O2   111.93  3.000
 2YK  C11  C12  O2   116.30  3.000
 2YK  O2   C12  C13  124.92  3.000
 2YK  C11  C12  C13  118.78  3.000
 2YK  H11  C11  C10  119.84  3.000
 2YK  H11  C11  C12  119.67  3.000
 2YK  C10  C11  C12  120.50  3.000
 2YK  H12  C14  C15  120.96  3.000
 2YK  H12  C14  C13  118.08  3.000
 2YK  C15  C14  C13  120.96  3.000
 2YK  C10  C15  O1   116.64  3.000
 2YK  O1   C15  C14  125.19  3.000
 2YK  C10  C15  C14  118.16  3.000
 2YK  C15  O1   C16  118.48  3.000
 2YK  S    C10  C15  120.17  3.000
 2YK  C15  C10  C11  120.95  3.000
 2YK  S    C10  C11  118.74  3.000
 2YK  C10  S    C7   102.20  3.000
 2YK  C6   N4   N3   107.26  3.000
 2YK  N5   N6   C7   115.12  3.000
 2YK  C3   C5   N5   125.88  3.000
 2YK  C3   C5   N3   126.09  3.000
 2YK  N5   C5   N3   108.03  3.000
 2YK  C2   C3   C5   125.12  3.000
 2YK  C2   C3   C4   104.00  3.000
 2YK  C5   C3   C4   130.88  3.000
 2YK  H13  C2   N1   122.41  3.000
 2YK  H13  C2   C3   130.89  3.000
 2YK  N1   C2   C3   106.70  3.000
 2YK  C1   N1   C2   127.30  3.000
 2YK  C1   N1   N2   120.08  3.000
 2YK  C2   N1   N2   112.62  3.000
 2YK  H16  C1   H15  109.13  3.000
 2YK  H16  C1   H14  109.09  3.000
 2YK  H15  C1   H14  109.33  3.000
 2YK  H16  C1   N1   108.91  3.000
 2YK  H15  C1   N1   110.16  3.000
 2YK  H14  C1   N1   110.20  3.000
 2YK  C12  O2   C17  118.17  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
 2YK  CONST_01  C9   C6   N4   N3    180.00   0.0  0
 2YK  CONST_02  N5   C6   N4   N3      0.00   0.0  0
 2YK  CONST_03  N6   N5   C5   N3    180.00   0.0  0
 2YK  CONST_04  C6   N5   C5   N3      0.00   0.0  0
 2YK  CONST_05  C2   C3   C5   N3      0.00   0.0  0
 2YK  CONST_06  C4   C3   C5   N3    180.00   0.0  0
 2YK  CONST_07  N5   C5   C3   C4      0.00   0.0  0
 2YK  CONST_08  N1   C2   C3   C4      0.00   0.0  0
 2YK  CONST_09  C2   N1   N2   C4      0.00   0.0  0
 2YK  CONST_10  C3   C2   N1   N2      0.00   0.0  0
 2YK  CONST_11  C5   C3   C4   N2    180.00   0.0  0
 2YK  CONST_12  C2   C3   C4   N2      0.00   0.0  0
 2YK  CONST_13  C6   C9   C8   C7      0.00   0.0  0
 2YK  CONST_14  C6   N5   N6   C7      0.00   0.0  0
 2YK  CONST_15  C5   N5   N6   C7    180.00   0.0  0
 2YK  CONST_16  C3   C5   N5   C6    180.00   0.0  0
 2YK  CONST_17  C5   N3   N4   C6      0.00   0.0  0
 2YK  CONST_18  N6   C7   C8   C9      0.00   0.0  0
 2YK  CONST_19  N6   N5   C6   C9      0.00   0.0  0
 2YK  CONST_20  C5   N5   C6   C9    180.00   0.0  0
 2YK  CONST_21  C10  C11  C12  C13     0.00   0.0  0
 2YK  CONST_22  C10  C15  C14  C13     0.00   0.0  0
 2YK  CONST_23  N5   N6   C7   C8      0.00   0.0  0
 2YK  CONST_24  N5   C6   C9   C8      0.00   0.0  0
 2YK  CONST_25  N4   C6   C9   C8    180.00   0.0  0
 2YK  CONST_26  N4   N3   C5   N5      0.00   0.0  0
 2YK  CONST_27  C2   C3   C5   N5    180.00   0.0  0
 2YK  CONST_28  C15  C10  C11  C12     0.00   0.0  0
 2YK  CONST_29  C15  C14  C13  C12     0.00   0.0  0
 2YK  CONST_30  C14  C15  C10  C11     0.00   0.0  0
 2YK  CONST_31  C14  C13  C12  C11     0.00   0.0  0
 2YK  CONST_32  N6   N5   C6   N4    180.00   0.0  0
 2YK  CONST_33  C5   N5   C6   N4      0.00   0.0  0
 2YK  CONST_34  C3   C5   N3   N4    180.00   0.0  0
 2YK  CONST_35  C3   C5   N5   N6      0.00   0.0  0
 2YK  CONST_36  N1   C2   C3   C5    180.00   0.0  0
 2YK  CONST_37  N1   N2   C4   C3      0.00   0.0  0
 2YK  CONST_38  C1   N1   N2   C4    180.00   0.0  0
 2YK  CONST_39  S    C7   C8   C9    180.00   0.0  0
 2YK  CONST_40  O1   C15  C14  C13   180.00   0.0  0
 2YK  CONST_41  S    C7   N6   N5    180.00   0.0  0
 2YK  CONST_42  C10  C11  C12  O2    180.00   0.0  0
 2YK  CONST_43  C14  C13  C12  O2    180.00   0.0  0
 2YK  CONST_44  S    C10  C11  C12   180.00   0.0  0
 2YK  CONST_45  O1   C15  C10  C11   180.00   0.0  0
 2YK  CONST_46  S    C10  C15  C14   180.00   0.0  0
 2YK  CONST_47  C1   N1   C2   C3    180.00   0.0  0
 2YK  CONST_48  H13  C2   C3   C4    180.00   0.0  0
 2YK  CONST_49  H2   C9   C8   C7    180.00   0.0  0
 2YK  CONST_50  H4   C8   C9   C6    180.00   0.0  0
 2YK  CONST_51  H11  C11  C12  C13   180.00   0.0  0
 2YK  CONST_52  H12  C14  C13  C12   180.00   0.0  0
 2YK  CONST_53  H3   C13  C12  C11   180.00   0.0  0
 2YK  CONST_54  H1   C4   C3   C5      0.00   0.0  0
 2YK  Var_01    C11  C10  S    C7   -121.85  30.0  2
 2YK  Var_02    N6   C7   S    C10  -154.20  30.0  2
 2YK  Var_03    C10  C15  O1   C16  -177.43  30.0  2
 2YK  Var_04    C11  C12  O2   C17   178.53  30.0  2
 2YK  Var_05    H14  C1   N1   N2    -60.73  30.0  2
 2YK  Var_06    H8   C17  O2   C12   -60.96  30.0  3
 2YK  Var_07    H5   C16  O1   C15    59.90  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
 2YK  plan-1  C4   0.020
 2YK  plan-1  N2   0.020
 2YK  plan-1  C5   0.020
 2YK  plan-1  C3   0.020
 2YK  plan-1  C2   0.020
 2YK  plan-1  N1   0.020
 2YK  plan-1  C1   0.020
 2YK  plan-1  H1   0.020
 2YK  plan-1  H13  0.020
 2YK  plan-2  C13  0.020
 2YK  plan-2  C12  0.020
 2YK  plan-2  C11  0.020
 2YK  plan-2  C14  0.020
 2YK  plan-2  C15  0.020
 2YK  plan-2  O1   0.020
 2YK  plan-2  C10  0.020
 2YK  plan-2  S    0.020
 2YK  plan-2  H3   0.020
 2YK  plan-2  H11  0.020
 2YK  plan-2  H12  0.020
 2YK  plan-2  O2   0.020
 2YK  plan-3  N3   0.020
 2YK  plan-3  C7   0.020
 2YK  plan-3  C6   0.020
 2YK  plan-3  C9   0.020
 2YK  plan-3  C8   0.020
 2YK  plan-3  N5   0.020
 2YK  plan-3  S    0.020
 2YK  plan-3  N4   0.020
 2YK  plan-3  N6   0.020
 2YK  plan-3  C5   0.020
 2YK  plan-3  C3   0.020
 2YK  plan-3  H2   0.020
 2YK  plan-3  H4   0.020

