# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:18:16 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: ~{N}-propan-2-yl-5-(2-pyridin-4-ylethynyl)pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)c1ccc(cn1)C#Cc2ccncc2
#
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
 S8B  S8B  ~{N}-propan-2-yl-5-(2-pyridin-4-ylethynyl)pyridine-2-carboxamide  ligand  35  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S8B
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
 S8B  N1   N  NH1   0  -0.637  6.8832   2.0154  28.7856
 S8B  N3   N  N     0  -0.400  6.7122  -0.4304  17.2636
 S8B  C4   C  C     0   0.518  5.7828   1.8597  28.0397
 S8B  C5   C  CR6   0   0.125  6.0309   1.6156  26.5750
 S8B  C6   C  CR16  0  -0.100  5.2942   0.5616  24.6956
 S8B  C7   C  CR6   0  -0.189  6.3162   1.1123  23.9117
 S8B  C8   C  CR16  0  -0.181  7.2196   1.9700  24.5357
 S8B  C10  C  CSP   0   0.160  6.4097   0.8005  22.5313
 S8B  C13  C  CR16  0  -0.359  7.5981   0.6940  19.1805
 S8B  C15  C  CR16  0  -0.061  5.7280  -0.8943  18.0255
 S8B  C1   C  CH3   0  -0.647  6.6712   3.8137  30.4493
 S8B  C11  C  CSP   0   0.172  6.4818   0.5283  21.3582
 S8B  C12  C  CR6   0  -0.039  6.5614   0.2054  19.9768
 S8B  C14  C  CR16  0  -0.062  7.6228   0.3463  17.8403
 S8B  C16  C  CR16  0  -0.359  5.6032  -0.6119  19.3754
 S8B  C2   C  CH1   0  -0.084  6.8553   2.3193  30.2101
 S8B  C3   C  CH3   0  -0.679  8.1304   1.7951  30.8515
 S8B  C9   C  CR16  0  -0.303  7.0762   2.2217  25.8882
 S8B  N2   N  N     0  -0.397  5.1530   0.8127  25.9814
 S8B  O1   O  O     0  -0.482  4.6441   1.8949  28.4787
 S8B  H8   H  HNH1  0   0.407  7.7874   1.9153  28.3514
 S8B  H9   H  HCR6  0   0.277  4.5704  -0.1061  24.2418
 S8B  H10  H  HCR6  0   0.284  8.0173   2.4318  23.9703
 S8B  H14  H  HCR6  0   0.272  4.9945  -1.5273  17.5394
 S8B  H1   H  HCH3  0   0.231  6.6021   4.0206  31.5179
 S8B  H2   H  HCH3  0   0.222  7.5154   4.3779  30.0491
 S8B  H3   H  HCH3  0   0.236  5.7595   4.1791  29.9772
 S8B  H13  H  HCR6  0   0.272  8.4195   0.7155  17.2045
 S8B  H15  H  HCR6  0   0.279  4.7804  -1.0188  19.9462
 S8B  H4   H  HCH1  0   0.246  6.0035   1.7873  30.6387
 S8B  H5   H  HCH3  0   0.243  8.1190   1.9903  31.9232
 S8B  H6   H  HCH3  0   0.243  8.2357   0.7197  30.7063
 S8B  H7   H  HCH3  0   0.229  9.0125   2.2860  30.4346
 S8B  H11  H  HCR6  0   0.287  7.7601   2.8970  26.3843
 S8B  H12  H  HCR6  0   0.278  8.3677   1.3293  19.5961

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
 S8B  N3   C15  aromatic  1.328  0.020  1.328
 S8B  N3   C14  aromatic  1.329  0.020  1.329
 S8B  C15  C16  aromatic  1.385  0.020  1.385
 S8B  C14  C13  aromatic  1.385  0.020  1.385
 S8B  C16  C12  aromatic  1.396  0.020  1.396
 S8B  C13  C12  aromatic  1.396  0.020  1.396
 S8B  C12  C11  single    1.421  0.020  1.421
 S8B  C11  C10  triple    1.206  0.020  1.206
 S8B  C10  C7   single    1.418  0.020  1.418
 S8B  C7   C6   aromatic  1.401  0.020  1.401
 S8B  C7   C8   aromatic  1.393  0.020  1.393
 S8B  C6   N2   aromatic  1.318  0.020  1.318
 S8B  C8   C9   aromatic  1.383  0.020  1.383
 S8B  N2   C5   aromatic  1.330  0.020  1.330
 S8B  C9   C5   aromatic  1.390  0.020  1.390
 S8B  C5   C4   single    1.505  0.020  1.505
 S8B  C4   O1   double    1.221  0.020  1.221
 S8B  C4   N1   single    1.338  0.020  1.338
 S8B  N1   C2   single    1.457  0.020  1.457
 S8B  C2   C3   single    1.521  0.020  1.521
 S8B  C2   C1   single    1.525  0.020  1.525
 S8B  N1   H8   single    0.860  0.020  1.020
 S8B  C6   H9   single    0.930  0.020  1.080
 S8B  C8   H10  single    0.930  0.020  1.080
 S8B  C13  H12  single    0.930  0.020  1.080
 S8B  C15  H14  single    0.930  0.020  1.080
 S8B  C1   H1   single    0.970  0.020  1.090
 S8B  C1   H2   single    0.970  0.020  1.090
 S8B  C1   H3   single    0.970  0.020  1.090
 S8B  C14  H13  single    0.930  0.020  1.080
 S8B  C16  H15  single    0.930  0.020  1.080
 S8B  C2   H4   single    0.970  0.020  1.090
 S8B  C3   H5   single    0.970  0.020  1.090
 S8B  C3   H6   single    0.970  0.020  1.090
 S8B  C3   H7   single    0.970  0.020  1.090
 S8B  C9   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
 S8B  H8   N1   C2   117.33  3.000
 S8B  H8   N1   C4   119.07  3.000
 S8B  C2   N1   C4   123.61  3.000
 S8B  C14  N3   C15  117.59  3.000
 S8B  O1   C4   C5   120.55  3.000
 S8B  O1   C4   N1   124.26  3.000
 S8B  C5   C4   N1   115.19  3.000
 S8B  N2   C5   C9   122.64  3.000
 S8B  C9   C5   C4   122.28  3.000
 S8B  N2   C5   C4   115.05  3.000
 S8B  H9   C6   N2   117.01  3.000
 S8B  H9   C6   C7   119.66  3.000
 S8B  N2   C6   C7   123.32  3.000
 S8B  C10  C7   C8   121.90  3.000
 S8B  C8   C7   C6   117.67  3.000
 S8B  C10  C7   C6   120.42  3.000
 S8B  H10  C8   C9   120.67  3.000
 S8B  H10  C8   C7   120.47  3.000
 S8B  C9   C8   C7   118.86  3.000
 S8B  C11  C10  C7   180.00  3.000
 S8B  H12  C13  C14  120.46  3.000
 S8B  H12  C13  C12  121.01  3.000
 S8B  C14  C13  C12  118.53  3.000
 S8B  H14  C15  C16  119.69  3.000
 S8B  H14  C15  N3   116.63  3.000
 S8B  C16  C15  N3   123.69  3.000
 S8B  H3   C1   H2   108.35  3.000
 S8B  H3   C1   H1   107.93  3.000
 S8B  H2   C1   H1   108.07  3.000
 S8B  H3   C1   C2   111.21  3.000
 S8B  H2   C1   C2   110.84  3.000
 S8B  H1   C1   C2   110.33  3.000
 S8B  C12  C11  C10  180.00  3.000
 S8B  C16  C12  C11  120.90  3.000
 S8B  C11  C12  C13  121.12  3.000
 S8B  C16  C12  C13  117.98  3.000
 S8B  H13  C14  C13  119.68  3.000
 S8B  H13  C14  N3   116.63  3.000
 S8B  C13  C14  N3   123.68  3.000
 S8B  H15  C16  C12  121.04  3.000
 S8B  H15  C16  C15  120.43  3.000
 S8B  C12  C16  C15  118.53  3.000
 S8B  H4   C2   C3   108.70  3.000
 S8B  H4   C2   C1   108.77  3.000
 S8B  C3   C2   C1   111.90  3.000
 S8B  H4   C2   N1   107.28  3.000
 S8B  C1   C2   N1   111.12  3.000
 S8B  C3   C2   N1   108.94  3.000
 S8B  H7   C3   H6   108.33  3.000
 S8B  H7   C3   H5   107.66  3.000
 S8B  H6   C3   H5   107.98  3.000
 S8B  H7   C3   C2   111.18  3.000
 S8B  H6   C3   C2   111.40  3.000
 S8B  H5   C3   C2   110.15  3.000
 S8B  H11  C9   C8   119.77  3.000
 S8B  H11  C9   C5   121.41  3.000
 S8B  C8   C9   C5   118.80  3.000
 S8B  C6   N2   C5   118.68  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
 S8B  CONST_01  C12  C16  C15  N3      0.00   0.0  0
 S8B  CONST_02  C12  C13  C14  N3      0.00   0.0  0
 S8B  CONST_03  C7   C6   N2   C5      0.00   0.0  0
 S8B  CONST_04  C7   C8   C9   C5      0.00   0.0  0
 S8B  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 S8B  CONST_06  C9   C5   N2   C6      0.00   0.0  0
 S8B  CONST_07  N2   C6   C7   C8      0.00   0.0  0
 S8B  CONST_08  N2   C5   C9   C8      0.00   0.0  0
 S8B  CONST_09  C15  N3   C14  C13     0.00   0.0  0
 S8B  CONST_10  C15  C16  C12  C13     0.00   0.0  0
 S8B  CONST_11  C16  C15  N3   C14     0.00   0.0  0
 S8B  CONST_12  C16  C12  C13  C14     0.00   0.0  0
 S8B  CONST_13  C6   N2   C5   C4    180.00   0.0  0
 S8B  CONST_14  C8   C9   C5   C4    180.00   0.0  0
 S8B  CONST_15  N2   C6   C7   C10   180.00   0.0  0
 S8B  CONST_16  C9   C8   C7   C10   180.00   0.0  0
 S8B  CONST_17  C11  C12  C16  C15   180.00   0.0  0
 S8B  CONST_18  C14  C13  C12  C11   180.00   0.0  0
 S8B  CONST_19  H15  C16  C15  N3    180.00   0.0  0
 S8B  CONST_20  H12  C13  C14  N3    180.00   0.0  0
 S8B  CONST_21  H9   C6   N2   C5    180.00   0.0  0
 S8B  CONST_22  H10  C8   C9   C5    180.00   0.0  0
 S8B  CONST_23  H11  C9   C8   C7    180.00   0.0  0
 S8B  CONST_24  H13  C14  N3   C15   180.00   0.0  0
 S8B  CONST_25  H14  C15  C16  C12   180.00   0.0  0
 S8B  CONST_26  C2   N1   C4   C5    180.00   0.0  0
 S8B  CONST_27  H8   N1   C4   C5      0.00   0.0  0
 S8B  CONST_28  O1   C4   N1   C2      0.00   0.0  0
 S8B  Var_01    N2   C5   C4   N1    146.26  30.0  2
 S8B  Var_02    C3   C2   N1   C4    153.46  30.0  3
 S8B  Var_03    H5   C3   C2   N1   -178.60  30.0  3
 S8B  Var_04    H1   C1   C2   N1    177.17  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
 S8B  plan-1  N3   0.020
 S8B  plan-1  C10  0.020
 S8B  plan-1  C13  0.020
 S8B  plan-1  C15  0.020
 S8B  plan-1  C11  0.020
 S8B  plan-1  C12  0.020
 S8B  plan-1  C14  0.020
 S8B  plan-1  C16  0.020
 S8B  plan-1  H14  0.020
 S8B  plan-1  H13  0.020
 S8B  plan-1  H15  0.020
 S8B  plan-1  H12  0.020
 S8B  plan-2  C4   0.020
 S8B  plan-2  C5   0.020
 S8B  plan-2  C6   0.020
 S8B  plan-2  C7   0.020
 S8B  plan-2  C8   0.020
 S8B  plan-2  C10  0.020
 S8B  plan-2  C11  0.020
 S8B  plan-2  C9   0.020
 S8B  plan-2  N2   0.020
 S8B  plan-2  H9   0.020
 S8B  plan-2  H10  0.020
 S8B  plan-2  H11  0.020
 S8B  plan-3  N1   0.020
 S8B  plan-3  C4   0.020
 S8B  plan-3  C5   0.020
 S8B  plan-3  C2   0.020
 S8B  plan-3  O1   0.020
 S8B  plan-3  H8   0.020

