# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 23:30:10 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]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=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
 DU6  DU6  1-(4-cyanophenyl)-3-[[3-(2-cyclopropylethynyl)imidazo[2,1-b][1,3]thiazol-5-yl]methyl]urea  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_DU6
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
 DU6  C10  C  CH2   0  -0.323  -1.6465  -1.6127   1.4016
 DU6  C13  C  CH2   0  -0.459   1.2256   2.4257   1.6800
 DU6  C20  C  CR16  0  -0.298   3.5833  -0.3049   0.7334
 DU6  C21  C  CR16  0  -0.233   4.8833   0.1329   0.5719
 DU6  C22  C  CR6   0  -0.021   5.4230   0.3274  -0.6989
 DU6  C24  C  CR16  0  -0.346   3.3380  -0.3645  -1.6658
 DU6  C02  C  CR5   0   0.284  -2.9597   0.7826  -0.4740
 DU6  C03  C  CR15  0  -0.617  -3.9012   1.3973  -1.2267
 DU6  C05  C  CR55  0   0.247  -4.6704  -0.7801  -0.4408
 DU6  C07  C  CR15  0  -0.248  -4.0089  -2.4095   0.7067
 DU6  C08  C  CR5   0   0.241  -2.9654  -1.5234   0.7283
 DU6  C09  C  CSP   0   0.136  -1.6812   1.2965  -0.1736
 DU6  C11  C  CSP   0   0.153  -0.6004   1.7913   0.0356
 DU6  C12  C  CH1   0  -0.470   0.6811   2.3775   0.2762
 DU6  C14  C  CH2   0  -0.479   0.7712   3.6844   1.0332
 DU6  C16  C  C     0   0.778   0.6594  -1.1545   0.7520
 DU6  C19  C  CR6   0   0.407   2.7866  -0.5599  -0.3905
 DU6  C23  C  CR16  0  -0.229   4.6339   0.0716  -1.8222
 DU6  N01  N  N     0  -0.560  -3.4120  -0.4594  -0.0293
 DU6  N06  N  N     0  -0.456  -5.0710  -1.9442  -0.0183
 DU6  N15  N  NH1   0  -0.680  -0.5637  -1.6370   0.4410
 DU6  N18  N  NH1   0  -0.794   1.4817  -1.0067  -0.3461
 DU6  N26  N  NS    0  -0.263   7.8522   1.1403  -0.9721
 DU6  O17  O  O     0  -0.504   0.9932  -0.8778   1.8919
 DU6  S04  S  S2    0   0.253  -5.3549   0.4748  -1.4131
 DU6  H1   H  HCH2  0   0.269  -1.5003  -0.7670   2.0767
 DU6  H2   H  HCH2  0   0.270  -1.6559  -2.5130   2.0219
 DU6  H3   H  HCH2  0   0.262   0.6161   1.9938   2.4611
 DU6  H4   H  HCH2  0   0.264   2.2871   2.2480   1.7871
 DU6  H5   H  HCR6  0   0.292   3.1971  -0.4427   1.7283
 DU6  H6   H  HCR6  0   0.280   5.4863   0.3240   1.4495
 DU6  H7   H  HCR6  0   0.283   2.7371  -0.5577  -2.5459
 DU6  H8   H  HCR5  0   0.326  -3.8048   2.3648  -1.6920
 DU6  H9   H  HCR5  0   0.271  -4.0375  -3.3727   1.1941
 DU6  H10  H  HCH1  0   0.291   1.4055   2.2344  -0.5181
 DU6  H11  H  HCH2  0   0.262  -0.1562   4.1302   1.3674
 DU6  H12  H  HCH2  0   0.267   1.5155   4.3893   0.6871
 DU6  H13  H  HCR6  0   0.281   5.0344   0.2163  -2.8163
 DU6  H14  H  HNH1  0   0.405  -0.7770  -1.9260  -0.4999
 DU6  H15  H  HNH1  0   0.413   1.0627  -1.1707  -1.2491
 DU6  C25  C  CSP   0   0.047   6.7640   0.7776  -0.8497

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
 DU6  N26  C25  triple    1.154  0.020  1.154
 DU6  C25  C22  single    1.423  0.020  1.423
 DU6  C21  C22  aromatic  1.394  0.020  1.394
 DU6  C21  C20  aromatic  1.381  0.020  1.381
 DU6  C22  C23  aromatic  1.396  0.020  1.396
 DU6  C20  C19  aromatic  1.401  0.020  1.401
 DU6  C23  C24  aromatic  1.376  0.020  1.376
 DU6  C19  C24  aromatic  1.403  0.020  1.403
 DU6  C19  N18  single    1.380  0.020  1.380
 DU6  N18  C16  single    1.380  0.020  1.380
 DU6  C16  O17  double    1.220  0.020  1.220
 DU6  C16  N15  single    1.351  0.020  1.351
 DU6  N15  C10  single    1.448  0.020  1.448
 DU6  C10  C08  single    1.483  0.020  1.483
 DU6  C13  C14  single    1.486  0.020  1.486
 DU6  C13  C12  single    1.506  0.020  1.506
 DU6  C07  C08  aromatic  1.369  0.020  1.369
 DU6  C07  N06  aromatic  1.368  0.020  1.368
 DU6  C08  N01  aromatic  1.380  0.020  1.380
 DU6  C14  C12  single    1.513  0.020  1.513
 DU6  C12  C11  single    1.430  0.020  1.430
 DU6  N06  C05  aromatic  1.302  0.020  1.302
 DU6  C11  C09  triple    1.207  0.020  1.207
 DU6  N01  C05  aromatic  1.362  0.020  1.362
 DU6  N01  C02  aromatic  1.395  0.020  1.395
 DU6  C09  C02  single    1.410  0.020  1.410
 DU6  C05  S04  aromatic  1.729  0.020  1.729
 DU6  C02  C03  aromatic  1.353  0.020  1.353
 DU6  S04  C03  aromatic  1.732  0.020  1.732
 DU6  C10  H1   single    0.970  0.020  1.090
 DU6  C10  H2   single    0.970  0.020  1.090
 DU6  C13  H3   single    0.970  0.020  1.090
 DU6  C13  H4   single    0.970  0.020  1.090
 DU6  C20  H5   single    0.930  0.020  1.080
 DU6  C21  H6   single    0.930  0.020  1.080
 DU6  C24  H7   single    0.930  0.020  1.080
 DU6  C03  H8   single    0.930  0.020  1.080
 DU6  C07  H9   single    0.930  0.020  1.080
 DU6  C12  H10  single    0.970  0.020  1.090
 DU6  C14  H11  single    0.970  0.020  1.090
 DU6  C14  H12  single    0.970  0.020  1.090
 DU6  C23  H13  single    0.930  0.020  1.080
 DU6  N15  H14  single    0.860  0.020  1.020
 DU6  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
 DU6  H2   C10  H1   106.75  3.000
 DU6  H2   C10  N15  111.65  3.000
 DU6  H1   C10  N15  108.85  3.000
 DU6  H2   C10  C08  107.42  3.000
 DU6  H1   C10  C08  110.67  3.000
 DU6  N15  C10  C08  111.40  3.000
 DU6  H4   C13  H3   114.59  3.000
 DU6  H4   C13  C14  118.84  3.000
 DU6  H3   C13  C14  118.72  3.000
 DU6  H4   C13  C12  116.22  3.000
 DU6  H3   C13  C12  117.18  3.000
 DU6  C14  C13  C12   60.73  3.000
 DU6  H5   C20  C19  120.95  3.000
 DU6  H5   C20  C21  119.10  3.000
 DU6  C19  C20  C21  119.95  3.000
 DU6  H6   C21  C22  119.93  3.000
 DU6  H6   C21  C20  119.07  3.000
 DU6  C22  C21  C20  121.00  3.000
 DU6  C25  C22  C23  120.36  3.000
 DU6  C23  C22  C21  119.27  3.000
 DU6  C25  C22  C21  120.37  3.000
 DU6  H7   C24  C23  119.12  3.000
 DU6  H7   C24  C19  119.72  3.000
 DU6  C23  C24  C19  121.17  3.000
 DU6  N01  C02  C09  123.41  3.000
 DU6  C09  C02  C03  125.72  3.000
 DU6  N01  C02  C03  110.87  3.000
 DU6  H8   C03  S04  120.45  3.000
 DU6  H8   C03  C02  125.85  3.000
 DU6  S04  C03  C02  113.70  3.000
 DU6  S04  C05  N06  135.23  3.000
 DU6  S04  C05  N01  111.39  3.000
 DU6  N06  C05  N01  113.38  3.000
 DU6  H9   C07  N06  121.48  3.000
 DU6  H9   C07  C08  126.18  3.000
 DU6  N06  C07  C08  112.34  3.000
 DU6  N01  C08  C07  104.10  3.000
 DU6  N01  C08  C10  125.67  3.000
 DU6  C07  C08  C10  130.23  3.000
 DU6  C11  C09  C02  180.00  3.000
 DU6  C12  C11  C09  180.00  3.000
 DU6  H10  C12  C14  116.15  3.000
 DU6  H10  C12  C11  114.92  3.000
 DU6  C14  C12  C11  119.46  3.000
 DU6  H10  C12  C13  116.44  3.000
 DU6  C11  C12  C13  119.60  3.000
 DU6  C14  C12  C13   58.98  3.000
 DU6  H12  C14  H11  114.83  3.000
 DU6  H12  C14  C12  116.34  3.000
 DU6  H11  C14  C12  117.35  3.000
 DU6  H12  C14  C13  118.73  3.000
 DU6  H11  C14  C13  118.46  3.000
 DU6  C12  C14  C13   60.29  3.000
 DU6  O17  C16  N18  123.81  3.000
 DU6  O17  C16  N15  122.95  3.000
 DU6  N18  C16  N15  113.24  3.000
 DU6  N18  C19  C24  116.48  3.000
 DU6  N18  C19  C20  124.81  3.000
 DU6  C24  C19  C20  118.70  3.000
 DU6  H13  C23  C24  119.71  3.000
 DU6  H13  C23  C22  120.37  3.000
 DU6  C24  C23  C22  119.92  3.000
 DU6  C08  N01  C05  106.45  3.000
 DU6  C05  N01  C02  114.39  3.000
 DU6  C08  N01  C02  139.16  3.000
 DU6  C07  N06  C05  103.73  3.000
 DU6  H14  N15  C16  120.61  3.000
 DU6  H14  N15  C10  117.80  3.000
 DU6  C16  N15  C10  121.22  3.000
 DU6  H15  N18  C19  114.62  3.000
 DU6  H15  N18  C16  116.57  3.000
 DU6  C19  N18  C16  128.60  3.000
 DU6  C05  S04  C03   89.64  3.000
 DU6  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
 DU6  CONST_01  C23  C22  C21  C20    0.00   0.0  0
 DU6  CONST_02  C23  C24  C19  C20    0.00   0.0  0
 DU6  CONST_03  C24  C23  C22  C21    0.00   0.0  0
 DU6  CONST_04  C24  C19  C20  C21    0.00   0.0  0
 DU6  CONST_05  C19  C20  C21  C22    0.00   0.0  0
 DU6  CONST_06  C19  C24  C23  C22    0.00   0.0  0
 DU6  CONST_07  C07  C08  N01  C02  180.00   0.0  0
 DU6  CONST_08  N06  C05  N01  C02  180.00   0.0  0
 DU6  CONST_09  S04  C05  N01  C02    0.00   0.0  0
 DU6  CONST_10  C05  S04  C03  C02    0.00   0.0  0
 DU6  CONST_11  C08  N01  C02  C03  180.00   0.0  0
 DU6  CONST_12  C05  N01  C02  C03    0.00   0.0  0
 DU6  CONST_13  N06  C05  S04  C03  180.00   0.0  0
 DU6  CONST_14  N01  C05  S04  C03    0.00   0.0  0
 DU6  CONST_15  C08  C07  N06  C05    0.00   0.0  0
 DU6  CONST_16  C07  C08  N01  C05    0.00   0.0  0
 DU6  CONST_17  N01  C05  N06  C07    0.00   0.0  0
 DU6  CONST_18  S04  C05  N06  C07  180.00   0.0  0
 DU6  CONST_19  N06  C05  N01  C08    0.00   0.0  0
 DU6  CONST_20  S04  C05  N01  C08  180.00   0.0  0
 DU6  CONST_21  N06  C07  C08  N01    0.00   0.0  0
 DU6  CONST_22  S04  C03  C02  N01    0.00   0.0  0
 DU6  CONST_23  N06  C07  C08  C10  180.00   0.0  0
 DU6  CONST_24  C05  N01  C08  C10  180.00   0.0  0
 DU6  CONST_25  C02  N01  C08  C10    0.00   0.0  0
 DU6  CONST_26  C25  C22  C21  C20  180.00   0.0  0
 DU6  CONST_27  N18  C19  C20  C21  180.00   0.0  0
 DU6  CONST_28  C25  C22  C23  C24  180.00   0.0  0
 DU6  CONST_29  C09  C02  N01  C05  180.00   0.0  0
 DU6  CONST_30  C09  C02  N01  C08    0.00   0.0  0
 DU6  CONST_31  S04  C03  C02  C09  180.00   0.0  0
 DU6  CONST_32  N18  C19  C24  C23  180.00   0.0  0
 DU6  CONST_33  H7   C24  C19  C20  180.00   0.0  0
 DU6  CONST_34  H13  C23  C22  C21  180.00   0.0  0
 DU6  CONST_35  H5   C20  C21  C22  180.00   0.0  0
 DU6  CONST_36  H9   C07  N06  C05  180.00   0.0  0
 DU6  CONST_37  H8   C03  S04  C05  180.00   0.0  0
 DU6  CONST_38  H6   C21  C20  C19  180.00   0.0  0
 DU6  CONST_39  C16  N18  C19  C20    0.00   0.0  0
 DU6  CONST_40  C16  N18  C19  C24  180.00   0.0  0
 DU6  CONST_41  H15  N18  C19  C20  180.00   0.0  0
 DU6  CONST_42  O17  C16  N18  C19    0.00   0.0  0
 DU6  CONST_43  N15  C16  N18  C19  180.00   0.0  0
 DU6  CONST_44  O17  C16  N15  C10    0.00   0.0  0
 DU6  CONST_45  N18  C16  N15  C10  180.00   0.0  0
 DU6  CONST_46  H14  N15  C16  O17  180.00   0.0  0
 DU6  Var_01    C11  C12  C14  C13  108.80  30.0  1
 DU6  Var_02    N15  C10  C08  C07  116.13  30.0  2
 DU6  Var_03    C14  C12  C11  C09  121.56  30.0  2
 DU6  Var_04    C16  N15  C10  C08  151.34  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
 DU6  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
 DU6  plan-1  C20  0.020
 DU6  plan-1  C21  0.020
 DU6  plan-1  C22  0.020
 DU6  plan-1  C24  0.020
 DU6  plan-1  C19  0.020
 DU6  plan-1  C23  0.020
 DU6  plan-1  N18  0.020
 DU6  plan-1  N26  0.020
 DU6  plan-1  H5   0.020
 DU6  plan-1  H6   0.020
 DU6  plan-1  H7   0.020
 DU6  plan-1  H13  0.020
 DU6  plan-1  C25  0.020
 DU6  plan-2  C10  0.020
 DU6  plan-2  C02  0.020
 DU6  plan-2  C03  0.020
 DU6  plan-2  C05  0.020
 DU6  plan-2  C07  0.020
 DU6  plan-2  C08  0.020
 DU6  plan-2  C09  0.020
 DU6  plan-2  C11  0.020
 DU6  plan-2  N01  0.020
 DU6  plan-2  N06  0.020
 DU6  plan-2  S04  0.020
 DU6  plan-2  H8   0.020
 DU6  plan-2  H9   0.020
 DU6  plan-3  C10  0.020
 DU6  plan-3  C16  0.020
 DU6  plan-3  C19  0.020
 DU6  plan-3  N15  0.020
 DU6  plan-3  N18  0.020
 DU6  plan-3  O17  0.020
 DU6  plan-3  H14  0.020
 DU6  plan-3  H15  0.020

