# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:26:05 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-(4,4-dimethylpent-2-ynyl)-4~{H}-pyrrolo[2,3-d][1,3]thiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C#CCc1c[nH]c2ncsc12
#
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
 PXK  PXK  6-(4,4-dimethylpent-2-ynyl)-4~{H}-pyrrolo[2,3-d][1,3]thiazole  ligand  29  15  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PXK
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
 PXK  S1   S  S2    0   0.183   0.9038   1.3836  -0.2762
 PXK  C2   C  CR55  0  -0.268   1.3252  -0.2417   0.0843
 PXK  C3   C  CR55  0   0.515   2.5716  -0.4914  -0.4614
 PXK  N4   N  N     0  -0.370   3.1949   0.5102  -1.1254
 PXK  C5   C  CR15  0  -0.233   2.4297   1.5551  -1.1009
 PXK  N6   N  NR15  0  -0.659   2.9027  -1.7796  -0.1986
 PXK  C7   C  CR15  0  -0.077   1.8751  -2.3473   0.5036
 PXK  C8   C  CR5   0  -0.038   0.8706  -1.4277   0.7079
 PXK  C9   C  CH2   0  -0.672  -0.4067  -1.6323   1.4640
 PXK  C10  C  CSP   0  -0.063  -1.5266  -0.9318   0.8402
 PXK  C11  C  CSP   0   0.236  -2.4160  -0.3157   0.3111
 PXK  C12  C  CT    0  -0.296  -3.5120   0.4276  -0.3220
 PXK  C13  C  CH3   0  -0.632  -3.9532  -0.3001  -1.5979
 PXK  C14  C  CH3   0  -0.632  -4.6893   0.5167   0.6571
 PXK  C15  C  CH3   0  -0.629  -3.0270   1.8389  -0.6760
 PXK  H1   H  HCR5  0   0.296   2.6880   2.4987  -1.5606
 PXK  H2   H  HCR5  0   0.286   1.9260  -3.3779   0.8161
 PXK  H3   H  HCH2  0   0.278  -0.6276  -2.6997   1.5394
 PXK  H4   H  HCH2  0   0.278  -0.2987  -1.2756   2.4937
 PXK  H5   H  HCH3  0   0.232  -4.2917  -1.3137  -1.3799
 PXK  H6   H  HCH3  0   0.231  -4.7789   0.2393  -2.0662
 PXK  H7   H  HCH3  0   0.232  -3.1378  -0.3621  -2.3197
 PXK  H8   H  HCH3  0   0.232  -4.4027   1.0387   1.5707
 PXK  H9   H  HCH3  0   0.231  -5.5147   1.0650   0.1993
 PXK  H10  H  HCH3  0   0.232  -5.0518  -0.4744   0.9321
 PXK  H11  H  HCH3  0   0.231  -2.1885   1.8059  -1.3723
 PXK  H12  H  HCH3  0   0.231  -3.8358   2.4048  -1.1422
 PXK  H13  H  HCH3  0   0.231  -2.7033   2.3810   0.2133
 PXK  H14  H  HNR5  0   0.415   3.7432  -2.2530  -0.4865

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
 PXK  N6   C7   aromatic  1.368  0.020  1.368
 PXK  N6   C3   aromatic  1.356  0.020  1.356
 PXK  C7   C8   aromatic  1.377  0.020  1.377
 PXK  C3   N4   aromatic  1.354  0.020  1.354
 PXK  C3   C2   aromatic  1.383  0.020  1.383
 PXK  N4   C5   aromatic  1.295  0.020  1.295
 PXK  C8   C2   aromatic  1.415  0.020  1.415
 PXK  C8   C9   single    1.498  0.020  1.498
 PXK  C5   S1   aromatic  1.743  0.020  1.743
 PXK  C2   S1   aromatic  1.717  0.020  1.717
 PXK  C9   C10  single    1.461  0.020  1.461
 PXK  C10  C11  triple    1.204  0.020  1.204
 PXK  C11  C12  single    1.468  0.020  1.468
 PXK  C15  C12  single    1.534  0.020  1.534
 PXK  C12  C14  single    1.534  0.020  1.534
 PXK  C12  C13  single    1.534  0.020  1.534
 PXK  C5   H1   single    0.930  0.020  1.080
 PXK  C7   H2   single    0.930  0.020  1.080
 PXK  C9   H3   single    0.970  0.020  1.090
 PXK  C9   H4   single    0.970  0.020  1.090
 PXK  C13  H5   single    0.970  0.020  1.090
 PXK  C13  H6   single    0.970  0.020  1.090
 PXK  C13  H7   single    0.970  0.020  1.090
 PXK  C14  H8   single    0.970  0.020  1.090
 PXK  C14  H9   single    0.970  0.020  1.090
 PXK  C14  H10  single    0.970  0.020  1.090
 PXK  C15  H11  single    0.970  0.020  1.090
 PXK  C15  H12  single    0.970  0.020  1.090
 PXK  C15  H13  single    0.970  0.020  1.090
 PXK  N6   H14  single    0.860  0.020  1.020

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
 PXK  C5   S1   C2    88.72  3.000
 PXK  C8   C2   C3   108.18  3.000
 PXK  C8   C2   S1   143.80  3.000
 PXK  C3   C2   S1   108.01  3.000
 PXK  N6   C3   N4   133.28  3.000
 PXK  N4   C3   C2   118.35  3.000
 PXK  N6   C3   C2   108.36  3.000
 PXK  C5   N4   C3   108.39  3.000
 PXK  H1   C5   N4   123.71  3.000
 PXK  H1   C5   S1   119.75  3.000
 PXK  N4   C5   S1   116.54  3.000
 PXK  H14  N6   C7   125.37  3.000
 PXK  H14  N6   C3   126.53  3.000
 PXK  C7   N6   C3   108.08  3.000
 PXK  H2   C7   C8   129.04  3.000
 PXK  H2   C7   N6   120.66  3.000
 PXK  C8   C7   N6   110.30  3.000
 PXK  C9   C8   C7   127.26  3.000
 PXK  C9   C8   C2   127.64  3.000
 PXK  C7   C8   C2   105.07  3.000
 PXK  H4   C9   H3   105.86  3.000
 PXK  H4   C9   C10  108.72  3.000
 PXK  H3   C9   C10  110.06  3.000
 PXK  H4   C9   C8   110.23  3.000
 PXK  H3   C9   C8   109.91  3.000
 PXK  C10  C9   C8   111.87  3.000
 PXK  C11  C10  C9   180.00  3.000
 PXK  C12  C11  C10  180.00  3.000
 PXK  C15  C12  C14  109.67  3.000
 PXK  C14  C12  C13  109.74  3.000
 PXK  C15  C12  C13  109.61  3.000
 PXK  C13  C12  C11  109.47  3.000
 PXK  C14  C12  C11  109.10  3.000
 PXK  C15  C12  C11  109.23  3.000
 PXK  H7   C13  H6   108.03  3.000
 PXK  H7   C13  H5   108.15  3.000
 PXK  H6   C13  H5   108.06  3.000
 PXK  H7   C13  C12  111.25  3.000
 PXK  H6   C13  C12  109.87  3.000
 PXK  H5   C13  C12  111.34  3.000
 PXK  H10  C14  H9   108.12  3.000
 PXK  H10  C14  H8   108.13  3.000
 PXK  H9   C14  H8   108.03  3.000
 PXK  H10  C14  C12  111.31  3.000
 PXK  H9   C14  C12  109.99  3.000
 PXK  H8   C14  C12  111.15  3.000
 PXK  H13  C15  H12  108.09  3.000
 PXK  H13  C15  H11  107.91  3.000
 PXK  H12  C15  H11  108.23  3.000
 PXK  H13  C15  C12  111.28  3.000
 PXK  H12  C15  C12  109.95  3.000
 PXK  H11  C15  C12  111.27  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
 PXK  CONST_01  C3   N4   C5   S1     0.00   0.0  0
 PXK  CONST_02  N6   C3   C2   S1   180.00   0.0  0
 PXK  CONST_03  N4   C3   C2   S1     0.00   0.0  0
 PXK  CONST_04  C7   C8   C2   S1   180.00   0.0  0
 PXK  CONST_05  C7   N6   C3   C2     0.00   0.0  0
 PXK  CONST_06  C5   N4   C3   C2     0.00   0.0  0
 PXK  CONST_07  N6   C7   C8   C2     0.00   0.0  0
 PXK  CONST_08  N4   C5   S1   C2     0.00   0.0  0
 PXK  CONST_09  C8   C7   N6   C3     0.00   0.0  0
 PXK  CONST_10  C7   C8   C2   C3     0.00   0.0  0
 PXK  CONST_11  C5   S1   C2   C3     0.00   0.0  0
 PXK  CONST_12  C7   N6   C3   N4   180.00   0.0  0
 PXK  CONST_13  C8   C2   C3   N4   180.00   0.0  0
 PXK  CONST_14  N6   C3   N4   C5   180.00   0.0  0
 PXK  CONST_15  C8   C2   S1   C5   180.00   0.0  0
 PXK  CONST_16  C8   C2   C3   N6     0.00   0.0  0
 PXK  CONST_17  C9   C8   C2   S1     0.00   0.0  0
 PXK  CONST_18  C9   C8   C2   C3   180.00   0.0  0
 PXK  CONST_19  C9   C8   C7   N6   180.00   0.0  0
 PXK  CONST_20  H14  N6   C3   C2   180.00   0.0  0
 PXK  CONST_21  H2   C7   C8   C2   180.00   0.0  0
 PXK  CONST_22  H1   C5   S1   C2   180.00   0.0  0
 PXK  Var_01    C10  C9   C8   C2    38.96  30.0  2
 PXK  Var_02    C15  C12  C11  C10  140.66  30.0  3
 PXK  Var_03    H11  C15  C12  C11   60.48  30.0  3
 PXK  Var_04    H8   C14  C12  C11   60.56  30.0  3
 PXK  Var_05    H5   C13  C12  C11   59.45  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
 PXK  plan-1  S1   0.020
 PXK  plan-1  C2   0.020
 PXK  plan-1  C3   0.020
 PXK  plan-1  N4   0.020
 PXK  plan-1  C5   0.020
 PXK  plan-1  N6   0.020
 PXK  plan-1  C7   0.020
 PXK  plan-1  C8   0.020
 PXK  plan-1  C9   0.020
 PXK  plan-1  H1   0.020
 PXK  plan-1  H2   0.020
 PXK  plan-1  H14  0.020

