# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:13:20 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[2-amino-5-(quinolin-3-yl)pyridin-3-yl]-1,3,4-oxadiazole-2(3H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(cc1C2=NNC(=S)O2)c3cnc4ccccc4c3
#
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
 49B  49B  5-[2-amino-5-(quinolin-3-yl)pyridin-3-yl]-1,3,4-oxadiazole-2(3H)-thione  ligand  34  23  .  2022-07-23  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_49B
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
 49B  C1   C  CR16  0  -0.082   0.5117   2.3715   0.4668
 49B  C2   C  CR6   0  -0.011   0.5717   0.9908   0.2635
 49B  C3   C  CR16  0  -0.227  -0.6429   0.3505   0.0668
 49B  C11  C  CR16  0  -0.260   6.5311  -1.4555  -0.1095
 49B  C12  C  CR16  0  -0.253   6.5535  -0.1747  -0.7019
 49B  C13  C  CR16  0  -0.313   5.4137   0.5795  -0.7618
 49B  C14  C  CR66  0   0.099   4.2023   0.0822  -0.2294
 49B  C15  C  CR16  0  -0.256   2.9963   0.8104  -0.2691
 49B  C6   C  CR5   0   0.396  -4.3879  -1.3120  -0.5453
 49B  N3   N  NR15  0  -0.442  -5.0690  -0.1758  -0.4220
 49B  N2   N  N     0  -0.284  -4.2724   0.8878  -0.1773
 49B  O    O  O     0  -0.417  -3.0985  -0.9433  -0.3689
 49B  C5   C  CR5   0   0.554  -3.0867   0.3918  -0.1509
 49B  C4   C  CR6   0  -0.170  -1.8336   1.0665   0.0701
 49B  C    C  CR6   0   0.483  -1.7729   2.4718   0.2798
 49B  N    N  NH2   0  -0.839  -2.8567   3.2540   0.2954
 49B  N1   N  N     0  -0.443  -0.5965   3.0800   0.4744
 49B  C7   C  CR6   0   0.009   1.8514   0.2724   0.2627
 49B  C9   C  CR66  0   0.201   4.1792  -1.2053   0.3604
 49B  N4   N  N     0  -0.422   3.0441  -1.7307   0.8818
 49B  C8   C  CR16  0  -0.124   1.9510  -1.0244   0.8340
 49B  C10  C  CR16  0  -0.290   5.3705  -1.9621   0.4105
 49B  H1   H  HCR6  0   0.271   1.4258   2.9275   0.6517
 49B  H2   H  HCR6  0   0.278  -0.6617  -0.7173  -0.1101
 49B  H3   H  HCR6  0   0.265   7.4417  -2.0386  -0.0660
 49B  H4   H  HCR6  0   0.265   7.4801   0.2091  -1.1077
 49B  H5   H  HCR6  0   0.262   5.4263   1.5630  -1.2161
 49B  H6   H  HCR6  0   0.267   2.9867   1.7861  -0.7416
 49B  H7   H  HNR5  0   0.454  -6.0701  -0.0674  -0.4916
 49B  H8   H  HNH2  0   0.425  -3.7867   2.8896   0.1755
 49B  H9   H  HNH2  0   0.403  -2.7381   4.2419   0.4409
 49B  H10  H  HCR6  0   0.263   1.0687  -1.4729   1.2820
 49B  H11  H  HCR6  0   0.263   5.3427  -2.9430   0.8679
 49B  S    S  S1    0  -0.322  -4.8857  -2.8477  -0.8420

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
 49B  C11  C12  aromatic  1.411  0.020  1.411
 49B  C11  C10  aromatic  1.369  0.020  1.369
 49B  C12  C13  aromatic  1.368  0.020  1.368
 49B  C10  C9   aromatic  1.412  0.020  1.412
 49B  C13  C14  aromatic  1.414  0.020  1.414
 49B  C9   C14  aromatic  1.416  0.020  1.416
 49B  C9   N4   aromatic  1.355  0.020  1.355
 49B  C14  C15  aromatic  1.409  0.020  1.409
 49B  N4   C8   aromatic  1.302  0.020  1.302
 49B  C8   C7   aromatic  1.421  0.020  1.421
 49B  C15  C7   aromatic  1.372  0.020  1.372
 49B  C7   C2   single    1.468  0.020  1.468
 49B  C2   C1   aromatic  1.397  0.020  1.397
 49B  C2   C3   aromatic  1.387  0.020  1.387
 49B  C1   N1   aromatic  1.315  0.020  1.315
 49B  C3   C4   aromatic  1.389  0.020  1.389
 49B  N1   C    aromatic  1.338  0.020  1.338
 49B  C4   C    aromatic  1.422  0.020  1.422
 49B  C4   C5   single    1.440  0.020  1.440
 49B  O    C5   single    1.353  0.020  1.353
 49B  O    C6   single    1.353  0.020  1.353
 49B  C    N    single    1.337  0.020  1.337
 49B  C5   N2   double    1.285  0.020  1.285
 49B  S    C6   double    1.641  0.020  1.641
 49B  C6   N3   single    1.330  0.020  1.330
 49B  N2   N3   single    1.351  0.020  1.351
 49B  C1   H1   single    0.930  0.020  1.080
 49B  C3   H2   single    0.930  0.020  1.080
 49B  C11  H3   single    0.930  0.020  1.080
 49B  C12  H4   single    0.930  0.020  1.080
 49B  C13  H5   single    0.930  0.020  1.080
 49B  C15  H6   single    0.930  0.020  1.080
 49B  N3   H7   single    0.860  0.020  1.020
 49B  N    H8   single    0.860  0.020  1.020
 49B  N    H9   single    0.860  0.020  1.020
 49B  C8   H10  single    0.930  0.020  1.080
 49B  C10  H11  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
 49B  H1   C1   N1   115.62  3.000
 49B  H1   C1   C2   119.66  3.000
 49B  N1   C1   C2   124.71  3.000
 49B  C7   C2   C3   122.51  3.000
 49B  C3   C2   C1   116.06  3.000
 49B  C7   C2   C1   121.42  3.000
 49B  H2   C3   C4   119.59  3.000
 49B  H2   C3   C2   119.59  3.000
 49B  C4   C3   C2   120.81  3.000
 49B  H3   C11  C10  119.91  3.000
 49B  H3   C11  C12  119.51  3.000
 49B  C10  C11  C12  120.58  3.000
 49B  H4   C12  C13  120.10  3.000
 49B  H4   C12  C11  119.54  3.000
 49B  C13  C12  C11  120.36  3.000
 49B  H5   C13  C14  119.16  3.000
 49B  H5   C13  C12  120.60  3.000
 49B  C14  C13  C12  120.23  3.000
 49B  C9   C14  C15  117.87  3.000
 49B  C15  C14  C13  122.75  3.000
 49B  C9   C14  C13  119.38  3.000
 49B  H6   C15  C7   120.96  3.000
 49B  H6   C15  C14  119.00  3.000
 49B  C7   C15  C14  120.03  3.000
 49B  O    C6   N3   104.08  3.000
 49B  N3   C6   S    131.34  3.000
 49B  O    C6   S    124.59  3.000
 49B  H7   N3   N2   120.85  3.000
 49B  H7   N3   C6   126.37  3.000
 49B  N2   N3   C6   112.78  3.000
 49B  C5   N2   N3   104.11  3.000
 49B  C5   O    C6   107.35  3.000
 49B  C4   C5   O    119.64  3.000
 49B  O    C5   N2   111.68  3.000
 49B  C4   C5   N2   128.68  3.000
 49B  C    C4   C5   121.51  3.000
 49B  C5   C4   C3   120.25  3.000
 49B  C    C4   C3   118.23  3.000
 49B  N1   C    N    116.42  3.000
 49B  N    C    C4   123.05  3.000
 49B  N1   C    C4   120.53  3.000
 49B  H9   N    H8   118.82  3.000
 49B  H9   N    C    118.75  3.000
 49B  H8   N    C    122.43  3.000
 49B  C    N1   C1   119.66  3.000
 49B  C8   C7   C15  117.08  3.000
 49B  C15  C7   C2   122.40  3.000
 49B  C8   C7   C2   120.52  3.000
 49B  C10  C9   N4   119.02  3.000
 49B  N4   C9   C14  121.76  3.000
 49B  C10  C9   C14  119.22  3.000
 49B  C8   N4   C9   118.60  3.000
 49B  H10  C8   N4   116.27  3.000
 49B  H10  C8   C7   119.06  3.000
 49B  N4   C8   C7   124.66  3.000
 49B  H11  C10  C9   118.61  3.000
 49B  H11  C10  C11  121.17  3.000
 49B  C9   C10  C11  120.22  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
 49B  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 49B  CONST_04  C4   C    N1   C1     0.00   0.0  0
 49B  CONST_05  N4   C8   C7   C2   180.00   0.0  0
 49B  CONST_06  C14  C15  C7   C2   180.00   0.0  0
 49B  CONST_07  C    N1   C1   C2     0.00   0.0  0
 49B  CONST_08  C    C4   C3   C2     0.00   0.0  0
 49B  CONST_11  N1   C1   C2   C3     0.00   0.0  0
 49B  CONST_12  N1   C    C4   C3     0.00   0.0  0
 49B  CONST_13  C14  C13  C12  C11    0.00   0.0  0
 49B  CONST_14  C14  C9   C10  C11    0.00   0.0  0
 49B  CONST_15  N4   C9   C10  C11  180.00   0.0  0
 49B  CONST_16  C9   C10  C11  C12    0.00   0.0  0
 49B  CONST_17  C9   C14  C13  C12    0.00   0.0  0
 49B  CONST_18  C15  C14  C13  C12  180.00   0.0  0
 49B  CONST_19  C10  C11  C12  C13    0.00   0.0  0
 49B  CONST_20  C10  C9   C14  C13    0.00   0.0  0
 49B  CONST_21  N4   C9   C14  C13  180.00   0.0  0
 49B  CONST_22  C7   C15  C14  C13  180.00   0.0  0
 49B  CONST_23  C8   N4   C9   C14    0.00   0.0  0
 49B  CONST_24  C8   C7   C15  C14    0.00   0.0  0
 49B  CONST_25  C10  C9   C14  C15  180.00   0.0  0
 49B  CONST_26  N4   C9   C14  C15    0.00   0.0  0
 49B  CONST_27  N4   C8   C7   C15    0.00   0.0  0
 49B  CONST_28  C7   C2   C3   C4   180.00   0.0  0
 49B  CONST_29  C7   C2   C1   N1   180.00   0.0  0
 49B  CONST_30  C9   N4   C8   C7     0.00   0.0  0
 49B  CONST_31  C9   C14  C15  C7     0.00   0.0  0
 49B  CONST_32  C10  C9   N4   C8   180.00   0.0  0
 49B  CONST_33  C5   C4   C3   C2   180.00   0.0  0
 49B  CONST_34  N1   C    C4   C5   180.00   0.0  0
 49B  CONST_35  N    C    N1   C1   180.00   0.0  0
 49B  CONST_36  N    C    C4   C3   180.00   0.0  0
 49B  CONST_37  N    C    C4   C5     0.00   0.0  0
 49B  CONST_38  H2   C3   C2   C1   180.00   0.0  0
 49B  CONST_39  H10  C8   C7   C2     0.00   0.0  0
 49B  CONST_40  H6   C15  C7   C2     0.00   0.0  0
 49B  CONST_41  H1   C1   C2   C3   180.00   0.0  0
 49B  CONST_42  H5   C13  C12  C11  180.00   0.0  0
 49B  CONST_43  H11  C10  C11  C12  180.00   0.0  0
 49B  CONST_44  H3   C11  C12  C13  180.00   0.0  0
 49B  CONST_45  H4   C12  C13  C14  180.00   0.0  0
 49B  CONST_46  H8   N    C    C4     0.00   0.0  0
 49B  CONST_47  H9   N    C    C4   180.00   0.0  0
 49B  Var_01    O    C5   C4   C3    -0.33  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
 49B  plan-1  C6   0.020
 49B  plan-1  N3   0.020
 49B  plan-1  N2   0.020
 49B  plan-1  O    0.020
 49B  plan-1  C5   0.020
 49B  plan-1  C4   0.020
 49B  plan-1  H7   0.020
 49B  plan-1  S    0.020
 49B  plan-2  C1   0.020
 49B  plan-2  C2   0.020
 49B  plan-2  C3   0.020
 49B  plan-2  C5   0.020
 49B  plan-2  C4   0.020
 49B  plan-2  C    0.020
 49B  plan-2  N    0.020
 49B  plan-2  N1   0.020
 49B  plan-2  C7   0.020
 49B  plan-2  H1   0.020
 49B  plan-2  H2   0.020
 49B  plan-3  C2   0.020
 49B  plan-3  C11  0.020
 49B  plan-3  C12  0.020
 49B  plan-3  C13  0.020
 49B  plan-3  C14  0.020
 49B  plan-3  C15  0.020
 49B  plan-3  C7   0.020
 49B  plan-3  C9   0.020
 49B  plan-3  N4   0.020
 49B  plan-3  C8   0.020
 49B  plan-3  C10  0.020
 49B  plan-3  H3   0.020
 49B  plan-3  H4   0.020
 49B  plan-3  H5   0.020
 49B  plan-3  H6   0.020
 49B  plan-3  H10  0.020
 49B  plan-3  H11  0.020
 49B  plan-4  C    0.020
 49B  plan-4  N    0.020
 49B  plan-4  H8   0.020
 49B  plan-4  H9   0.020

