# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:16:47 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 1-(3-chlorophenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(NC(=O)Nc2sc(CCNc3ncnc4ccsc34)cn2)c1
#
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
 AK2  AK2  1-(3-chlorophenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}urea  ligand  43  28  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AK2
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
 AK2  C27   C   CR16  0  -0.309    6.6937   0.6524  -1.1889
 AK2  C26   C   CR16  0  -0.253    8.0680   0.6164  -1.3770
 AK2  C24   C   CR6   0  -0.023    8.3619  -0.4876   0.7008
 AK2  C23   C   CR16  0  -0.320    6.9985  -0.4679   0.9222
 AK2  C22   C   CR6   0   0.382    6.1463   0.1064  -0.0262
 AK2  C17   C   CR15  0  -0.038   -0.3165   1.4621  -1.5501
 AK2  C15   C   CR5   0   0.302    1.3102   0.8112  -0.2467
 AK2  C13   C   CR5   0  -0.206   -1.0672   1.3185  -0.4325
 AK2  C11   C   CH2   0  -0.241   -3.2536   0.1886   0.0003
 AK2  C9    C   CR15  0  -0.209   -9.2035  -0.9904   0.3564
 AK2  C8    C   CR15  0  -0.449   -9.3083   0.3337   0.6153
 AK2  C4    C   CR16  0   0.023   -6.1244  -2.7477  -0.2991
 AK2  C6    C   CR6   0   0.573   -5.5898  -0.5532   0.0637
 AK2  C2    C   CR56  0   0.287   -7.8453  -1.3878   0.1414
 AK2  C1    C   CR56  0  -0.338   -6.9678  -0.3124   0.2534
 AK2  CL28  CL  CL    0  -0.130    9.3897  -1.2065   1.8974
 AK2  C25   C   CR16  0  -0.256    8.9241   0.0511  -0.4454
 AK2  N20   N   NH1   0  -0.808    4.7876   0.0797   0.2815
 AK2  C19   C   C     0   0.734    3.7486   0.6131  -0.4285
 AK2  O21   O   O     0  -0.470    3.8540   1.1754  -1.4954
 AK2  N18   N   NH1   0  -0.771    2.5436   0.4339   0.2266
 AK2  N16   N   N     0  -0.399    1.0175   1.1748  -1.4469
 AK2  S14   S   S2    0   0.186   -0.0337   0.7996   0.8605
 AK2  N10   N   NH1   0  -0.683   -4.6741   0.4219   0.1360
 AK2  N5    N   N     0  -0.484   -5.1971  -1.7942  -0.2102
 AK2  N3    N   N     0  -0.462   -7.4223  -2.6354  -0.1407
 AK2  S7    S   S2    0   0.220   -7.7942   1.1591   0.6100
 AK2  H27   H   HCR6  0   0.284    6.0706   1.0997  -1.9442
 AK2  H26   H   HCR6  0   0.268    8.4806   1.0433  -2.2814
 AK2  H23   H   HCR6  0   0.289    6.5922  -0.8955   1.8303
 AK2  H17   H   HCR5  0   0.267   -0.7165   1.7801  -2.5034
 AK2  H12   H   HCH2  0   0.267   -2.7328   2.2102   0.5568
 AK2  H12A  H   HCH2  0   0.268   -2.9243   1.9636  -1.1723
 AK2  H11   H   HCH2  0   0.252   -3.0801  -0.4925  -0.8321
 AK2  H11A  H   HCH2  0   0.234   -2.8522  -0.2928   0.8988
 AK2  H8    H   HCR5  0   0.309  -10.2094   0.8934   0.8150
 AK2  H4    H   HCR6  0   0.268   -5.7479  -3.7396  -0.5271
 AK2  H25   H   HCR6  0   0.301    9.9925   0.0301  -0.6078
 AK2  HN20  H   HNH1  0   0.459    4.5657  -0.3890   1.1468
 AK2  HN18  H   HNH1  0   0.474    2.5596   0.0308   1.1513
 AK2  HN10  H   HNH1  0   0.423   -4.9616   1.3244   0.4797
 AK2  C12   C   CH2   0  -0.520   -2.5337   1.5090  -0.2592
 AK2  H9    H   HCR5  0   0.299  -10.0419  -1.6699   0.3141

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
 AK2  C26  C27   aromatic  1.388  0.020  1.388
 AK2  C27  C22   aromatic  1.396  0.020  1.396
 AK2  C27  H27   single    0.930  0.020  1.080
 AK2  C26  C25   aromatic  1.386  0.020  1.386
 AK2  C26  H26   single    0.930  0.020  1.080
 AK2  C25  C24   aromatic  1.386  0.020  1.386
 AK2  C24  CL28  single    1.734  0.020  1.734
 AK2  C24  C23   aromatic  1.381  0.020  1.381
 AK2  C22  C23   aromatic  1.398  0.020  1.398
 AK2  C23  H23   single    0.930  0.020  1.080
 AK2  C22  N20   single    1.393  0.020  1.393
 AK2  C13  C17   aromatic  1.354  0.020  1.354
 AK2  C17  N16   aromatic  1.368  0.020  1.368
 AK2  C17  H17   single    0.930  0.020  1.080
 AK2  S14  C15   aromatic  1.741  0.020  1.741
 AK2  C15  N18   single    1.374  0.020  1.374
 AK2  C15  N16   aromatic  1.288  0.020  1.288
 AK2  C11  C12   single    1.526  0.020  1.526
 AK2  C12  C13   single    1.489  0.020  1.489
 AK2  C12  H12   single    0.970  0.020  1.090
 AK2  C12  H12A  single    0.970  0.020  1.090
 AK2  S14  C13   aromatic  1.735  0.020  1.735
 AK2  N10  C11   single    1.446  0.020  1.446
 AK2  C11  H11   single    0.970  0.020  1.090
 AK2  C11  H11A  single    0.970  0.020  1.090
 AK2  C8   C9    aromatic  1.353  0.020  1.353
 AK2  C9   C2    aromatic  1.431  0.020  1.431
 AK2  C9   H9    single    0.930  0.020  1.080
 AK2  S7   C8    aromatic  1.725  0.020  1.725
 AK2  C8   H8    single    0.930  0.020  1.080
 AK2  N3   C4    aromatic  1.312  0.020  1.312
 AK2  N5   C4    aromatic  1.333  0.020  1.333
 AK2  C4   H4    single    0.930  0.020  1.080
 AK2  C1   C6    aromatic  1.412  0.020  1.412
 AK2  N10  C6    single    1.340  0.020  1.340
 AK2  C6   N5    aromatic  1.330  0.020  1.330
 AK2  C1   C2    aromatic  1.393  0.020  1.393
 AK2  C2   N3    aromatic  1.347  0.020  1.347
 AK2  S7   C1    aromatic  1.725  0.020  1.725
 AK2  C25  H25   single    0.930  0.020  1.080
 AK2  C19  N20   single    1.367  0.020  1.367
 AK2  N20  HN20  single    0.860  0.020  1.020
 AK2  O21  C19   double    1.211  0.020  1.211
 AK2  C19  N18   single    1.383  0.020  1.383
 AK2  N18  HN18  single    0.860  0.020  1.020
 AK2  N10  HN10  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
 AK2  H27   C27  C22   121.32  3.000
 AK2  H27   C27  C26   119.27  3.000
 AK2  C22   C27  C26   119.41  3.000
 AK2  H26   C26  C25   119.17  3.000
 AK2  H26   C26  C27   118.74  3.000
 AK2  C25   C26  C27   122.09  3.000
 AK2  C25   C24  CL28  119.45  3.000
 AK2  CL28  C24  C23   118.71  3.000
 AK2  C25   C24  C23   121.83  3.000
 AK2  H23   C23  C22   120.15  3.000
 AK2  H23   C23  C24   119.94  3.000
 AK2  C22   C23  C24   119.91  3.000
 AK2  N20   C22  C23   115.89  3.000
 AK2  N20   C22  C27   125.00  3.000
 AK2  C23   C22  C27   119.11  3.000
 AK2  H17   C17  N16   119.25  3.000
 AK2  H17   C17  C13   123.62  3.000
 AK2  N16   C17  C13   117.13  3.000
 AK2  S14   C15  N16   114.78  3.000
 AK2  N16   C15  N18   127.05  3.000
 AK2  S14   C15  N18   118.17  3.000
 AK2  S14   C13  C12   122.56  3.000
 AK2  S14   C13  C17   108.47  3.000
 AK2  C12   C13  C17   128.95  3.000
 AK2  H11A  C11  H11   107.08  3.000
 AK2  H11A  C11  N10   110.73  3.000
 AK2  H11   C11  N10   109.21  3.000
 AK2  H11A  C11  C12   110.29  3.000
 AK2  H11   C11  C12   109.62  3.000
 AK2  N10   C11  C12   109.86  3.000
 AK2  H9    C9   C2    123.78  3.000
 AK2  H9    C9   C8    124.26  3.000
 AK2  C2    C9   C8    111.96  3.000
 AK2  H8    C8   S7    119.04  3.000
 AK2  H8    C8   C9    127.40  3.000
 AK2  S7    C8   C9    113.56  3.000
 AK2  H4    C4   N3    116.53  3.000
 AK2  H4    C4   N5    115.25  3.000
 AK2  N3    C4   N5    128.22  3.000
 AK2  N5    C6   N10   119.24  3.000
 AK2  N5    C6   C1    118.36  3.000
 AK2  N10   C6   C1    122.40  3.000
 AK2  N3    C2   C1    122.29  3.000
 AK2  N3    C2   C9    125.91  3.000
 AK2  C1    C2   C9    111.80  3.000
 AK2  S7    C1   C2    111.94  3.000
 AK2  S7    C1   C6    129.87  3.000
 AK2  C2    C1   C6    118.20  3.000
 AK2  H25   C25  C24   121.18  3.000
 AK2  H25   C25  C26   121.17  3.000
 AK2  C24   C25  C26   117.65  3.000
 AK2  HN20  N20  C19   117.36  3.000
 AK2  HN20  N20  C22   114.38  3.000
 AK2  C19   N20  C22   128.25  3.000
 AK2  N18   C19  O21   123.60  3.000
 AK2  N18   C19  N20   111.45  3.000
 AK2  O21   C19  N20   124.95  3.000
 AK2  HN18  N18  C19   118.17  3.000
 AK2  HN18  N18  C15   116.08  3.000
 AK2  C19   N18  C15   125.69  3.000
 AK2  C15   N16  C17   110.55  3.000
 AK2  C13   S14  C15    89.07  3.000
 AK2  HN10  N10  C6    118.38  3.000
 AK2  HN10  N10  C11   117.18  3.000
 AK2  C6    N10  C11   123.30  3.000
 AK2  C6    N5   C4    118.41  3.000
 AK2  C2    N3   C4    114.52  3.000
 AK2  C1    S7   C8     90.74  3.000
 AK2  H12A  C12  H12   106.96  3.000
 AK2  H12A  C12  C11   109.48  3.000
 AK2  H12   C12  C11   109.99  3.000
 AK2  H12A  C12  C13   107.95  3.000
 AK2  H12   C12  C13   110.36  3.000
 AK2  C11   C12  C13   111.94  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
 AK2  CONST_01  C24   C25  C26  C27     0.00   0.0  0
 AK2  CONST_02  C24   C23  C22  C27     0.00   0.0  0
 AK2  CONST_03  C23   C22  C27  C26     0.00   0.0  0
 AK2  CONST_04  C23   C24  C25  C26     0.00   0.0  0
 AK2  CONST_05  C25   C26  C27  C22     0.00   0.0  0
 AK2  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 AK2  CONST_07  C15   S14  C13  C17     0.00   0.0  0
 AK2  CONST_08  S14   C15  N16  C17     0.00   0.0  0
 AK2  CONST_09  C13   C17  N16  C15     0.00   0.0  0
 AK2  CONST_10  N16   C15  S14  C13     0.00   0.0  0
 AK2  CONST_11  C1    S7   C8   C9      0.00   0.0  0
 AK2  CONST_12  C6    C1   C2   C9    180.00   0.0  0
 AK2  CONST_13  S7    C1   C2   C9      0.00   0.0  0
 AK2  CONST_14  C4    N3   C2   C9    180.00   0.0  0
 AK2  CONST_15  C1    C2   C9   C8      0.00   0.0  0
 AK2  CONST_16  N3    C2   C9   C8    180.00   0.0  0
 AK2  CONST_17  C6    C1   S7   C8    180.00   0.0  0
 AK2  CONST_18  C2    C1   S7   C8      0.00   0.0  0
 AK2  CONST_19  C1    C2   N3   C4      0.00   0.0  0
 AK2  CONST_20  C1    C6   N5   C4      0.00   0.0  0
 AK2  CONST_21  N3    C2   C1   C6      0.00   0.0  0
 AK2  CONST_22  N3    C4   N5   C6      0.00   0.0  0
 AK2  CONST_23  S7    C8   C9   C2      0.00   0.0  0
 AK2  CONST_24  N5    C6   C1   C2      0.00   0.0  0
 AK2  CONST_25  N5    C4   N3   C2      0.00   0.0  0
 AK2  CONST_26  S14   C13  C17  N16     0.00   0.0  0
 AK2  CONST_27  S7    C1   C6   N5    180.00   0.0  0
 AK2  CONST_28  S7    C1   C2   N3    180.00   0.0  0
 AK2  CONST_29  N20   C22  C27  C26   180.00   0.0  0
 AK2  CONST_30  CL28  C24  C25  C26   180.00   0.0  0
 AK2  CONST_31  N20   C22  C23  C24   180.00   0.0  0
 AK2  CONST_32  CL28  C24  C23  C22   180.00   0.0  0
 AK2  CONST_33  N18   C15  N16  C17   180.00   0.0  0
 AK2  CONST_34  C12   C13  S14  C15   180.00   0.0  0
 AK2  CONST_35  N16   C17  C13  C12   180.00   0.0  0
 AK2  CONST_36  N18   C15  S14  C13   180.00   0.0  0
 AK2  CONST_37  N10   C6   N5   C4    180.00   0.0  0
 AK2  CONST_38  N10   C6   C1   C2    180.00   0.0  0
 AK2  CONST_39  S7    C1   C6   N10     0.00   0.0  0
 AK2  CONST_40  H25   C25  C26  C27   180.00   0.0  0
 AK2  CONST_41  H23   C23  C22  C27   180.00   0.0  0
 AK2  CONST_42  H26   C26  C25  C24   180.00   0.0  0
 AK2  CONST_43  H27   C27  C22  C23   180.00   0.0  0
 AK2  CONST_44  H17   C17  N16  C15   180.00   0.0  0
 AK2  CONST_45  H4    C4   N5   C6    180.00   0.0  0
 AK2  CONST_46  H8    C8   C9   C2    180.00   0.0  0
 AK2  CONST_47  H9    C9   C2   C1    180.00   0.0  0
 AK2  CONST_48  C19   N20  C22  C27     0.00   0.0  0
 AK2  CONST_49  C19   N20  C22  C23   180.00   0.0  0
 AK2  CONST_50  C1    C6   N10  C11   180.00   0.0  0
 AK2  CONST_51  N5    C6   N10  C11     0.00   0.0  0
 AK2  CONST_52  S14   C15  N18  C19   180.00   0.0  0
 AK2  CONST_53  N16   C15  N18  C19     0.00   0.0  0
 AK2  CONST_54  HN20  N20  C22  C27   180.00   0.0  0
 AK2  CONST_55  HN10  N10  C6   C1      0.00   0.0  0
 AK2  CONST_56  HN18  N18  C15  N16   180.00   0.0  0
 AK2  CONST_57  O21   C19  N20  C22     0.00   0.0  0
 AK2  CONST_58  O21   C19  N18  C15     0.00   0.0  0
 AK2  CONST_59  N18   C19  N20  C22   180.00   0.0  0
 AK2  CONST_60  N20   C19  N18  C15   180.00   0.0  0
 AK2  Var_01    C11   C12  C13  C17   111.02  30.0  1
 AK2  Var_02    C6    N10  C11  C12   164.23  30.0  1
 AK2  Var_03    N10   C11  C12  C13  -178.91  30.0  1

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
 AK2  plan-1  C17   0.020
 AK2  plan-1  C15   0.020
 AK2  plan-1  C13   0.020
 AK2  plan-1  N18   0.020
 AK2  plan-1  N16   0.020
 AK2  plan-1  S14   0.020
 AK2  plan-1  H17   0.020
 AK2  plan-1  C12   0.020
 AK2  plan-2  C27   0.020
 AK2  plan-2  C26   0.020
 AK2  plan-2  C24   0.020
 AK2  plan-2  C23   0.020
 AK2  plan-2  C22   0.020
 AK2  plan-2  CL28  0.020
 AK2  plan-2  C25   0.020
 AK2  plan-2  N20   0.020
 AK2  plan-2  H27   0.020
 AK2  plan-2  H26   0.020
 AK2  plan-2  H23   0.020
 AK2  plan-2  H25   0.020
 AK2  plan-3  C9    0.020
 AK2  plan-3  C8    0.020
 AK2  plan-3  C4    0.020
 AK2  plan-3  C6    0.020
 AK2  plan-3  C2    0.020
 AK2  plan-3  C1    0.020
 AK2  plan-3  N10   0.020
 AK2  plan-3  N5    0.020
 AK2  plan-3  N3    0.020
 AK2  plan-3  S7    0.020
 AK2  plan-3  H8    0.020
 AK2  plan-3  H4    0.020
 AK2  plan-3  H9    0.020
 AK2  plan-4  C22   0.020
 AK2  plan-4  C15   0.020
 AK2  plan-4  N20   0.020
 AK2  plan-4  C19   0.020
 AK2  plan-4  O21   0.020
 AK2  plan-4  N18   0.020
 AK2  plan-4  HN20  0.020
 AK2  plan-4  HN18  0.020
 AK2  plan-5  C11   0.020
 AK2  plan-5  C6    0.020
 AK2  plan-5  N10   0.020
 AK2  plan-5  HN10  0.020

