# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:42:29 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C(NCc1cnc2scc(C#CC3CC3)n12)Nc4ccc(cc4)C#N
#
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
 DO9  DO9  1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]thiourea  ligand  41  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DO9
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
 DO9  C10  C  CH2   0  -0.310  -1.5544  -1.5076   1.2706
 DO9  C13  C  CH2   0  -0.478   1.0392   2.5363   1.0397
 DO9  C20  C  CR16  0  -0.251   3.8344  -1.2125   0.2182
 DO9  C21  C  CR16  0  -0.243   5.1771  -0.9008   0.1375
 DO9  C22  C  CR6   0  -0.006   5.6047   0.1725  -0.6458
 DO9  C24  C  CR16  0  -0.310   3.3312   0.6195  -1.2677
 DO9  C02  C  CR5   0   0.295  -3.3665   0.6421  -0.4835
 DO9  C03  C  CR15  0  -0.612  -4.4502   1.0985  -1.1528
 DO9  C05  C  CR55  0   0.251  -4.7600  -1.2075  -0.4186
 DO9  C07  C  CR15  0  -0.245  -3.7454  -2.7195   0.6274
 DO9  C08  C  CR5   0   0.225  -2.8823  -1.6561   0.6298
 DO9  C09  C  CSP   0   0.132  -2.1698   1.3548  -0.2632
 DO9  C11  C  CSP   0   0.148  -1.1680   2.0151  -0.1318
 DO9  C12  C  CH1   0  -0.496   0.0132   2.8151  -0.0306
 DO9  C14  C  CH2   0  -0.472   0.1937   3.7543   1.1409
 DO9  C16  C  C     0   0.421   0.7613  -1.0679   0.6059
 DO9  C19  C  CR6   0   0.396   2.8987  -0.4433  -0.4743
 DO9  C23  C  CR16  0  -0.226   4.6741   0.9279  -1.3576
 DO9  N01  N  N     0  -0.560  -3.5600  -0.6721  -0.0618
 DO9  N06  N  N     0  -0.454  -4.9139  -2.4383  -0.0225
 DO9  N15  N  NH1   0  -0.602  -0.4983  -1.3670   0.2862
 DO9  N18  N  NH1   0  -0.733   1.5358  -0.7336  -0.4633
 DO9  N26  N  NS    0  -0.251   8.1136   0.7456  -0.7922
 DO9  S04  S  S2    0   0.257  -5.7205  -0.0703  -1.2962
 DO9  S17  S  S1    0  -0.356   1.2962  -1.0726   2.1919
 DO9  H1   H  HCH2  0   0.275  -1.5342  -0.6439   1.9397
 DO9  H2   H  HCH2  0   0.284  -1.3817  -2.3885   1.8921
 DO9  H3   H  HCH2  0   0.264   0.8513   1.7119   1.7148
 DO9  H4   H  HCH2  0   0.262   2.0749   2.6488   0.7475
 DO9  H5   H  HCR6  0   0.285   3.5197  -2.0606   0.8064
 DO9  H6   H  HCR6  0   0.285   5.8982  -1.5028   0.6734
 DO9  H7   H  HCR6  0   0.283   2.6095   1.2140  -1.8137
 DO9  H8   H  HCR5  0   0.327  -4.5586   2.0794  -1.5867
 DO9  H9   H  HCR5  0   0.278  -3.5707  -3.6837   1.0813
 DO9  H10  H  HCH1  0   0.317   0.3977   3.1600  -0.9845
 DO9  H11  H  HCH2  0   0.280  -0.5897   3.7746   1.8866
 DO9  H12  H  HCH2  0   0.259   0.6380   4.7160   0.9216
 DO9  H13  H  HCR6  0   0.273   4.9967   1.7591  -1.9694
 DO9  H14  H  HNH1  0   0.381  -0.7538  -1.4522  -0.6868
 DO9  H15  H  HNH1  0   0.381   1.0426  -0.4719  -1.3060
 DO9  C25  C  CSP   0   0.049   6.9917   0.4885  -0.7271

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
 DO9  N26  C25  triple    1.153  0.020  1.153
 DO9  C25  C22  single    1.425  0.020  1.425
 DO9  C21  C22  aromatic  1.396  0.020  1.396
 DO9  C21  C20  aromatic  1.381  0.020  1.381
 DO9  C22  C23  aromatic  1.394  0.020  1.394
 DO9  C20  C19  aromatic  1.395  0.020  1.395
 DO9  C23  C24  aromatic  1.381  0.020  1.381
 DO9  C19  C24  aromatic  1.395  0.020  1.395
 DO9  C19  N18  single    1.394  0.020  1.394
 DO9  N18  C16  single    1.362  0.020  1.362
 DO9  C16  S17  double    1.674  0.020  1.674
 DO9  C16  N15  single    1.334  0.020  1.334
 DO9  N15  C10  single    1.450  0.020  1.450
 DO9  C10  C08  single    1.482  0.020  1.482
 DO9  C13  C14  single    1.486  0.020  1.486
 DO9  C13  C12  single    1.509  0.020  1.509
 DO9  C07  C08  aromatic  1.370  0.020  1.370
 DO9  C07  N06  aromatic  1.366  0.020  1.366
 DO9  C08  N01  aromatic  1.381  0.020  1.381
 DO9  C14  C12  single    1.512  0.020  1.512
 DO9  C12  C11  single    1.430  0.020  1.430
 DO9  N06  C05  aromatic  1.302  0.020  1.302
 DO9  N01  C05  aromatic  1.362  0.020  1.362
 DO9  N01  C02  aromatic  1.394  0.020  1.394
 DO9  C11  C09  triple    1.207  0.020  1.207
 DO9  C05  S04  aromatic  1.728  0.020  1.728
 DO9  C09  C02  single    1.410  0.020  1.410
 DO9  C02  C03  aromatic  1.353  0.020  1.353
 DO9  S04  C03  aromatic  1.732  0.020  1.732
 DO9  C10  H1   single    0.970  0.020  1.090
 DO9  C10  H2   single    0.970  0.020  1.090
 DO9  C13  H3   single    0.970  0.020  1.090
 DO9  C13  H4   single    0.970  0.020  1.090
 DO9  C20  H5   single    0.930  0.020  1.080
 DO9  C21  H6   single    0.930  0.020  1.080
 DO9  C24  H7   single    0.930  0.020  1.080
 DO9  C03  H8   single    0.930  0.020  1.080
 DO9  C07  H9   single    0.930  0.020  1.080
 DO9  C12  H10  single    0.970  0.020  1.090
 DO9  C14  H11  single    0.970  0.020  1.090
 DO9  C14  H12  single    0.970  0.020  1.090
 DO9  C23  H13  single    0.930  0.020  1.080
 DO9  N15  H14  single    0.860  0.020  1.020
 DO9  N18  H15  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
 DO9  H2   C10  H1   106.63  3.000
 DO9  H2   C10  N15  110.45  3.000
 DO9  H1   C10  N15  108.99  3.000
 DO9  H2   C10  C08  107.88  3.000
 DO9  H1   C10  C08  111.13  3.000
 DO9  N15  C10  C08  111.63  3.000
 DO9  H4   C13  H3   114.46  3.000
 DO9  H4   C13  C14  118.54  3.000
 DO9  H3   C13  C14  118.89  3.000
 DO9  H4   C13  C12  116.11  3.000
 DO9  H3   C13  C12  117.73  3.000
 DO9  C14  C13  C12   60.65  3.000
 DO9  H5   C20  C19  120.55  3.000
 DO9  H5   C20  C21  119.53  3.000
 DO9  C19  C20  C21  119.92  3.000
 DO9  H6   C21  C22  120.12  3.000
 DO9  H6   C21  C20  119.59  3.000
 DO9  C22  C21  C20  120.28  3.000
 DO9  C25  C22  C23  120.04  3.000
 DO9  C23  C22  C21  119.91  3.000
 DO9  C25  C22  C21  120.05  3.000
 DO9  H7   C24  C23  119.52  3.000
 DO9  H7   C24  C19  119.90  3.000
 DO9  C23  C24  C19  120.58  3.000
 DO9  N01  C02  C09  123.17  3.000
 DO9  C09  C02  C03  125.91  3.000
 DO9  N01  C02  C03  110.89  3.000
 DO9  H8   C03  S04  120.46  3.000
 DO9  H8   C03  C02  125.91  3.000
 DO9  S04  C03  C02  113.62  3.000
 DO9  S04  C05  N06  135.31  3.000
 DO9  S04  C05  N01  111.35  3.000
 DO9  N06  C05  N01  113.34  3.000
 DO9  H9   C07  N06  121.47  3.000
 DO9  H9   C07  C08  126.20  3.000
 DO9  N06  C07  C08  112.33  3.000
 DO9  N01  C08  C07  104.08  3.000
 DO9  N01  C08  C10  125.81  3.000
 DO9  C07  C08  C10  130.03  3.000
 DO9  C11  C09  C02  180.00  3.000
 DO9  C12  C11  C09  180.00  3.000
 DO9  H10  C12  C14  116.20  3.000
 DO9  H10  C12  C11  114.11  3.000
 DO9  C14  C12  C11  120.05  3.000
 DO9  H10  C12  C13  116.20  3.000
 DO9  C11  C12  C13  120.56  3.000
 DO9  C14  C12  C13   58.93  3.000
 DO9  H12  C14  H11  114.86  3.000
 DO9  H12  C14  C12  116.36  3.000
 DO9  H11  C14  C12  117.34  3.000
 DO9  H12  C14  C13  118.76  3.000
 DO9  H11  C14  C13  118.32  3.000
 DO9  C12  C14  C13   60.41  3.000
 DO9  S17  C16  N18  124.25  3.000
 DO9  S17  C16  N15  121.90  3.000
 DO9  N18  C16  N15  113.83  3.000
 DO9  N18  C19  C24  117.80  3.000
 DO9  N18  C19  C20  122.49  3.000
 DO9  C24  C19  C20  119.63  3.000
 DO9  H13  C23  C24  119.91  3.000
 DO9  H13  C23  C22  120.41  3.000
 DO9  C24  C23  C22  119.67  3.000
 DO9  C08  N01  C05  106.47  3.000
 DO9  C05  N01  C02  114.45  3.000
 DO9  C08  N01  C02  139.07  3.000
 DO9  C07  N06  C05  103.78  3.000
 DO9  H14  N15  C16  119.27  3.000
 DO9  H14  N15  C10  117.49  3.000
 DO9  C16  N15  C10  123.15  3.000
 DO9  H15  N18  C19  114.62  3.000
 DO9  H15  N18  C16  116.14  3.000
 DO9  C19  N18  C16  127.85  3.000
 DO9  C05  S04  C03   89.68  3.000
 DO9  N26  C25  C22  180.00  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
 DO9  CONST_01  C23  C22  C21  C20    0.00   0.0  0
 DO9  CONST_02  C23  C24  C19  C20    0.00   0.0  0
 DO9  CONST_03  C24  C23  C22  C21    0.00   0.0  0
 DO9  CONST_04  C24  C19  C20  C21    0.00   0.0  0
 DO9  CONST_05  C19  C20  C21  C22    0.00   0.0  0
 DO9  CONST_06  C19  C24  C23  C22    0.00   0.0  0
 DO9  CONST_07  C07  C08  N01  C02  180.00   0.0  0
 DO9  CONST_08  N06  C05  N01  C02  180.00   0.0  0
 DO9  CONST_09  S04  C05  N01  C02    0.00   0.0  0
 DO9  CONST_10  C05  S04  C03  C02    0.00   0.0  0
 DO9  CONST_11  C08  N01  C02  C03  180.00   0.0  0
 DO9  CONST_12  C05  N01  C02  C03    0.00   0.0  0
 DO9  CONST_13  N06  C05  S04  C03  180.00   0.0  0
 DO9  CONST_14  N01  C05  S04  C03    0.00   0.0  0
 DO9  CONST_15  C08  C07  N06  C05    0.00   0.0  0
 DO9  CONST_16  C07  C08  N01  C05    0.00   0.0  0
 DO9  CONST_17  N01  C05  N06  C07    0.00   0.0  0
 DO9  CONST_18  S04  C05  N06  C07  180.00   0.0  0
 DO9  CONST_19  N06  C05  N01  C08    0.00   0.0  0
 DO9  CONST_20  S04  C05  N01  C08  180.00   0.0  0
 DO9  CONST_21  N06  C07  C08  N01    0.00   0.0  0
 DO9  CONST_22  S04  C03  C02  N01    0.00   0.0  0
 DO9  CONST_23  N06  C07  C08  C10  180.00   0.0  0
 DO9  CONST_24  C05  N01  C08  C10  180.00   0.0  0
 DO9  CONST_25  C02  N01  C08  C10    0.00   0.0  0
 DO9  CONST_26  C25  C22  C21  C20  180.00   0.0  0
 DO9  CONST_27  N18  C19  C20  C21  180.00   0.0  0
 DO9  CONST_28  C25  C22  C23  C24  180.00   0.0  0
 DO9  CONST_29  C09  C02  N01  C05  180.00   0.0  0
 DO9  CONST_30  C09  C02  N01  C08    0.00   0.0  0
 DO9  CONST_31  S04  C03  C02  C09  180.00   0.0  0
 DO9  CONST_32  N18  C19  C24  C23  180.00   0.0  0
 DO9  CONST_33  H7   C24  C19  C20  180.00   0.0  0
 DO9  CONST_34  H13  C23  C22  C21  180.00   0.0  0
 DO9  CONST_35  H5   C20  C21  C22  180.00   0.0  0
 DO9  CONST_36  H9   C07  N06  C05  180.00   0.0  0
 DO9  CONST_37  H8   C03  S04  C05  180.00   0.0  0
 DO9  CONST_38  H6   C21  C20  C19  180.00   0.0  0
 DO9  CONST_42  S17  C16  N18  C19    0.00   0.0  0
 DO9  CONST_43  N15  C16  N18  C19  180.00   0.0  0
 DO9  CONST_44  N18  C16  N15  C10  180.00   0.0  0
 DO9  CONST_45  S17  C16  N15  C10    0.00   0.0  0
 DO9  CONST_46  H14  N15  C16  N18    0.00   0.0  0
 DO9  Var_01    C11  C12  C14  C13  109.71  30.0  1
 DO9  Var_02    N15  C10  C08  C07  114.55  30.0  1
 DO9  Var_03    C14  C12  C11  C09  130.85  30.0  1
 DO9  Var_04    C16  N15  C10  C08  172.13  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DO9  chir_01  C12  C13  C14  C11  both

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
 DO9  plan-1  C20  0.020
 DO9  plan-1  C21  0.020
 DO9  plan-1  C22  0.020
 DO9  plan-1  C24  0.020
 DO9  plan-1  C19  0.020
 DO9  plan-1  C23  0.020
 DO9  plan-1  N18  0.020
 DO9  plan-1  N26  0.020
 DO9  plan-1  H5   0.020
 DO9  plan-1  H6   0.020
 DO9  plan-1  H7   0.020
 DO9  plan-1  H13  0.020
 DO9  plan-1  C25  0.020
 DO9  plan-2  C10  0.020
 DO9  plan-2  C02  0.020
 DO9  plan-2  C03  0.020
 DO9  plan-2  C05  0.020
 DO9  plan-2  C07  0.020
 DO9  plan-2  C08  0.020
 DO9  plan-2  C09  0.020
 DO9  plan-2  C11  0.020
 DO9  plan-2  N01  0.020
 DO9  plan-2  N06  0.020
 DO9  plan-2  S04  0.020
 DO9  plan-2  H8   0.020
 DO9  plan-2  H9   0.020
 DO9  plan-3  C10  0.020
 DO9  plan-3  C16  0.020
 DO9  plan-3  C19  0.020
 DO9  plan-3  N15  0.020
 DO9  plan-3  N18  0.020
 DO9  plan-3  S17  0.020
 DO9  plan-3  H14  0.020
 DO9  plan-3  H15  0.020

