# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 00:58:54 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(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
 AK1  AK1  1-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}-3-[3-(trifluoromethyl)phenyl]urea  ligand  46  31  .  2022-03-11  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AK1
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
 AK1  C31   C  CR15  0  -0.035   1.0496   0.1331  -2.0986
 AK1  C27   C  CR5   0  -0.202   1.7567  -0.5111  -1.1393
 AK1  C23   C  CT    0   1.054  -8.7025  -0.2974   1.4752
 AK1  C17   C  CR16  0  -0.382  -6.3419   0.0456   0.7274
 AK1  C20   C  CR16  0  -0.238  -7.2052   1.1931  -1.6310
 AK1  C15   C  CR6   0   0.403  -5.4029   0.5105  -0.1942
 AK1  C12   C  CH2   0  -0.551   3.1956  -0.8942  -1.1426
 AK1  C14   C  C     0   0.734  -3.0038   0.2710  -0.7054
 AK1  C11   C  CH2   0  -0.234   4.0097  -0.0765  -0.1437
 AK1  C9    C  CR6   0   0.577   6.3888   0.2458   0.3505
 AK1  C7    C  CR16  0   0.035   7.0887   2.0688   1.5421
 AK1  C4    C  CR56  0  -0.337   7.7388  -0.1646   0.3011
 AK1  C3    C  CR56  0   0.288   8.6928   0.6377   0.9220
 AK1  C2    C  CR15  0  -0.195  10.0110   0.0964   0.7883
 AK1  C1    C  CR15  0  -0.446  10.0136  -1.0633   0.0909
 AK1  F26   F  F     0  -0.310  -9.7466  -0.9067   0.8999
 AK1  N30   N  N     0  -0.390  -0.2579   0.4203  -1.8202
 AK1  C29   C  CR5   0   0.300  -0.5772  -0.0092  -0.6484
 AK1  S28   S  S2    0   0.202   0.7079  -0.8113   0.2076
 AK1  N6    N  N     0  -0.459   8.3690   1.7803   1.5579
 AK1  N10   N  NH1   0  -0.678   5.4038  -0.4525  -0.2281
 AK1  N8    N  N     0  -0.482   6.0943   1.3762   0.9867
 AK1  S5    S  S2    0   0.224   8.4467  -1.5544  -0.4361
 AK1  F24   F  F     0  -0.314  -9.2004   0.7350   2.1735
 AK1  F25   F  F     0  -0.303  -8.1901  -1.1538   2.3643
 AK1  C18   C  CR6   0  -0.182  -7.6972   0.1593   0.4643
 AK1  C19   C  CR16  0  -0.290  -8.1419   0.7307  -0.7222
 AK1  C21   C  CR16  0  -0.290  -5.8447   1.0964  -1.3797
 AK1  N22   N  NH1   0  -0.791  -4.0564   0.3963   0.1577
 AK1  N13   N  NH1   0  -0.758  -1.8040   0.1135  -0.0380
 AK1  O16   O  O     0  -0.467  -3.1006   0.2958  -1.9119
 AK1  H31   H  HCR5  0   0.272   1.4664   0.4379  -3.0487
 AK1  H17   H  HCR6  0   0.286  -5.9947  -0.4081   1.6471
 AK1  H20   H  HCR6  0   0.272  -7.5373   1.6477  -2.5544
 AK1  H12   H  HCH2  0   0.272   3.3089  -1.9612  -0.9292
 AK1  H12A  H  HCH2  0   0.275   3.5819  -0.7278  -2.1504
 AK1  H11   H  HCH2  0   0.254   3.9052   0.9851  -0.3680
 AK1  H11A  H  HCH2  0   0.238   3.6292  -0.2298   0.8717
 AK1  H7    H  HCR6  0   0.252   6.7916   2.9837   2.0447
 AK1  H2    H  HCR5  0   0.278  10.8967   0.5619   1.1949
 AK1  H1    H  HCR5  0   0.311  10.8657  -1.6785  -0.1552
 AK1  HN10  H  HNH1  0   0.406   5.6171  -1.3629  -0.6032
 AK1  H19   H  HCR6  0   0.275  -9.1966   0.8215  -0.9443
 AK1  H21   H  HCR6  0   0.283  -5.1457   1.4857  -2.1025
 AK1  HN22  H  HNH1  0   0.419  -3.8830   0.2457   1.1397
 AK1  HN13  H  HNH1  0   0.429  -1.8192   0.0173   0.9665

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
 AK1  N30  C31   aromatic  1.367  0.020  1.367
 AK1  C31  C27   aromatic  1.355  0.020  1.355
 AK1  C31  H31   single    0.930  0.020  1.080
 AK1  C27  S28   aromatic  1.733  0.020  1.733
 AK1  C27  C12   single    1.489  0.020  1.489
 AK1  F26  C23   single    1.339  0.020  1.339
 AK1  C23  F24   single    1.342  0.020  1.342
 AK1  C23  C18   single    1.497  0.020  1.497
 AK1  C23  F25   single    1.337  0.020  1.337
 AK1  C17  C15   aromatic  1.395  0.020  1.395
 AK1  C17  C18   aromatic  1.385  0.020  1.385
 AK1  C17  H17   single    0.930  0.020  1.080
 AK1  C21  C20   aromatic  1.387  0.020  1.387
 AK1  C19  C20   aromatic  1.385  0.020  1.385
 AK1  C20  H20   single    0.930  0.020  1.080
 AK1  N22  C15   single    1.396  0.020  1.396
 AK1  C15  C21   aromatic  1.394  0.020  1.394
 AK1  C12  C11   single    1.526  0.020  1.526
 AK1  C12  H12   single    0.970  0.020  1.090
 AK1  C12  H12A  single    0.970  0.020  1.090
 AK1  N13  C14   single    1.382  0.020  1.382
 AK1  N22  C14   single    1.367  0.020  1.367
 AK1  C14  O16   double    1.211  0.020  1.211
 AK1  C11  N10   single    1.446  0.020  1.446
 AK1  C11  H11   single    0.970  0.020  1.090
 AK1  C11  H11A  single    0.970  0.020  1.090
 AK1  N8   C9    aromatic  1.330  0.020  1.330
 AK1  C9   N10   single    1.339  0.020  1.339
 AK1  C9   C4    aromatic  1.412  0.020  1.412
 AK1  C7   N8    aromatic  1.333  0.020  1.333
 AK1  C7   N6    aromatic  1.312  0.020  1.312
 AK1  C7   H7    single    0.930  0.020  1.080
 AK1  C3   C4    aromatic  1.393  0.020  1.393
 AK1  C4   S5    aromatic  1.725  0.020  1.725
 AK1  N6   C3    aromatic  1.347  0.020  1.347
 AK1  C3   C2    aromatic  1.431  0.020  1.431
 AK1  C2   C1    aromatic  1.353  0.020  1.353
 AK1  C2   H2    single    0.930  0.020  1.080
 AK1  C1   S5    aromatic  1.725  0.020  1.725
 AK1  C1   H1    single    0.930  0.020  1.080
 AK1  N30  C29   aromatic  1.288  0.020  1.288
 AK1  N13  C29   single    1.376  0.020  1.376
 AK1  C29  S28   aromatic  1.740  0.020  1.740
 AK1  N10  HN10  single    0.860  0.020  1.020
 AK1  C18  C19   aromatic  1.390  0.020  1.390
 AK1  C19  H19   single    0.930  0.020  1.080
 AK1  C21  H21   single    0.930  0.020  1.080
 AK1  N22  HN22  single    0.860  0.020  1.020
 AK1  N13  HN13  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
 AK1  H31   C31  N30  119.23  3.000
 AK1  H31   C31  C27  123.71  3.000
 AK1  N30   C31  C27  117.05  3.000
 AK1  S28   C27  C12  122.81  3.000
 AK1  C12   C27  C31  128.69  3.000
 AK1  S28   C27  C31  108.47  3.000
 AK1  C18   C23  F25  112.78  3.000
 AK1  F25   C23  F24  106.80  3.000
 AK1  C18   C23  F24  111.46  3.000
 AK1  F25   C23  F26  107.05  3.000
 AK1  C18   C23  F26  111.86  3.000
 AK1  F24   C23  F26  106.51  3.000
 AK1  H17   C17  C18  120.63  3.000
 AK1  H17   C17  C15  119.00  3.000
 AK1  C18   C17  C15  120.37  3.000
 AK1  H20   C20  C21  119.03  3.000
 AK1  H20   C20  C19  119.54  3.000
 AK1  C21   C20  C19  121.43  3.000
 AK1  N22   C15  C21  123.65  3.000
 AK1  C21   C15  C17  119.23  3.000
 AK1  N22   C15  C17  117.08  3.000
 AK1  H12A  C12  H12  106.98  3.000
 AK1  H12A  C12  C11  109.49  3.000
 AK1  H12   C12  C11  109.86  3.000
 AK1  H12A  C12  C27  107.74  3.000
 AK1  H12   C12  C27  110.52  3.000
 AK1  C11   C12  C27  112.10  3.000
 AK1  O16   C14  N13  123.58  3.000
 AK1  O16   C14  N22  124.46  3.000
 AK1  N13   C14  N22  111.96  3.000
 AK1  H11A  C11  H11  107.08  3.000
 AK1  H11A  C11  N10  110.65  3.000
 AK1  H11   C11  N10  109.49  3.000
 AK1  H11A  C11  C12  110.27  3.000
 AK1  H11   C11  C12  109.63  3.000
 AK1  N10   C11  C12  109.67  3.000
 AK1  N8    C9   N10  119.14  3.000
 AK1  N10   C9   C4   122.46  3.000
 AK1  N8    C9   C4   118.39  3.000
 AK1  H7    C7   N8   115.26  3.000
 AK1  H7    C7   N6   116.54  3.000
 AK1  N8    C7   N6   128.20  3.000
 AK1  S5    C4   C3   111.94  3.000
 AK1  S5    C4   C9   129.90  3.000
 AK1  C3    C4   C9   118.16  3.000
 AK1  N6    C3   C2   125.89  3.000
 AK1  C2    C3   C4   111.80  3.000
 AK1  N6    C3   C4   122.31  3.000
 AK1  H2    C2   C1   124.18  3.000
 AK1  H2    C2   C3   123.85  3.000
 AK1  C1    C2   C3   111.97  3.000
 AK1  H1    C1   S5   119.03  3.000
 AK1  H1    C1   C2   127.40  3.000
 AK1  S5    C1   C2   113.56  3.000
 AK1  C29   N30  C31  110.62  3.000
 AK1  N13   C29  S28  118.78  3.000
 AK1  S28   C29  N30  114.71  3.000
 AK1  N13   C29  N30  126.51  3.000
 AK1  C29   S28  C27   89.13  3.000
 AK1  C3    N6   C7   114.53  3.000
 AK1  HN10  N10  C9   118.45  3.000
 AK1  HN10  N10  C11  117.43  3.000
 AK1  C9    N10  C11  123.25  3.000
 AK1  C7    N8   C9   118.40  3.000
 AK1  C1    S5   C4    90.73  3.000
 AK1  C19   C18  C17  120.59  3.000
 AK1  C19   C18  C23  119.14  3.000
 AK1  C17   C18  C23  120.24  3.000
 AK1  H19   C19  C18  121.45  3.000
 AK1  H19   C19  C20  119.79  3.000
 AK1  C18   C19  C20  118.76  3.000
 AK1  H21   C21  C15  121.09  3.000
 AK1  H21   C21  C20  119.29  3.000
 AK1  C15   C21  C20  119.62  3.000
 AK1  HN22  N22  C14  117.95  3.000
 AK1  HN22  N22  C15  115.05  3.000
 AK1  C14   N22  C15  126.22  3.000
 AK1  HN13  N13  C29  116.52  3.000
 AK1  HN13  N13  C14  118.59  3.000
 AK1  C29   N13  C14  124.76  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
 AK1  CONST_01  S28   C29  N30  C31     0.00   0.0  0
 AK1  CONST_02  C29   S28  C27  C31     0.00   0.0  0
 AK1  CONST_03  C29   N30  C31  C27     0.00   0.0  0
 AK1  CONST_04  N30   C29  S28  C27     0.00   0.0  0
 AK1  CONST_05  C20   C21  C15  C17     0.00   0.0  0
 AK1  CONST_06  C20   C19  C18  C17     0.00   0.0  0
 AK1  CONST_07  C19   C18  C17  C15     0.00   0.0  0
 AK1  CONST_08  C19   C20  C21  C15     0.00   0.0  0
 AK1  CONST_09  N6    C7   N8   C9      0.00   0.0  0
 AK1  CONST_10  N6    C3   C4   C9      0.00   0.0  0
 AK1  CONST_11  C2    C3   C4   C9    180.00   0.0  0
 AK1  CONST_12  C1    S5   C4   C9    180.00   0.0  0
 AK1  CONST_13  C4    C9   N8   C7      0.00   0.0  0
 AK1  CONST_14  C4    C3   N6   C7      0.00   0.0  0
 AK1  CONST_15  C2    C3   N6   C7    180.00   0.0  0
 AK1  CONST_16  C1    C2   C3   C4      0.00   0.0  0
 AK1  CONST_17  C2    C1   S5   C4      0.00   0.0  0
 AK1  CONST_18  N8    C9   C4   C3      0.00   0.0  0
 AK1  CONST_19  C1    S5   C4   C3      0.00   0.0  0
 AK1  CONST_20  N8    C7   N6   C3      0.00   0.0  0
 AK1  CONST_21  S5    C1   C2   C3      0.00   0.0  0
 AK1  CONST_22  S5    C4   C3   C2      0.00   0.0  0
 AK1  CONST_23  N6    C3   C2   C1    180.00   0.0  0
 AK1  CONST_24  S28   C27  C31  N30     0.00   0.0  0
 AK1  CONST_25  S5    C4   C3   N6    180.00   0.0  0
 AK1  CONST_26  S5    C4   C9   N8    180.00   0.0  0
 AK1  CONST_27  C21   C15  C17  C18     0.00   0.0  0
 AK1  CONST_28  C21   C20  C19  C18     0.00   0.0  0
 AK1  CONST_29  N13   C29  N30  C31   180.00   0.0  0
 AK1  CONST_30  N13   C29  S28  C27   180.00   0.0  0
 AK1  CONST_31  C15   C17  C18  C23   180.00   0.0  0
 AK1  CONST_32  C20   C19  C18  C23   180.00   0.0  0
 AK1  CONST_33  N22   C15  C21  C20   180.00   0.0  0
 AK1  CONST_34  N30   C31  C27  C12   180.00   0.0  0
 AK1  CONST_35  C29   S28  C27  C12   180.00   0.0  0
 AK1  CONST_36  N10   C9   N8   C7    180.00   0.0  0
 AK1  CONST_37  N10   C9   C4   C3    180.00   0.0  0
 AK1  CONST_38  S5    C4   C9   N10     0.00   0.0  0
 AK1  CONST_39  N22   C15  C17  C18   180.00   0.0  0
 AK1  CONST_40  H21   C21  C15  C17   180.00   0.0  0
 AK1  CONST_41  H19   C19  C18  C17   180.00   0.0  0
 AK1  CONST_42  H20   C20  C21  C15   180.00   0.0  0
 AK1  CONST_43  H7    C7   N8   C9    180.00   0.0  0
 AK1  CONST_44  H2    C2   C3   C4    180.00   0.0  0
 AK1  CONST_45  H1    C1   S5   C4    180.00   0.0  0
 AK1  CONST_46  H31   C31  N30  C29   180.00   0.0  0
 AK1  CONST_47  H17   C17  C18  C19   180.00   0.0  0
 AK1  CONST_52  N8    C9   N10  C11     0.00   0.0  0
 AK1  CONST_53  C4    C9   N10  C11   180.00   0.0  0
 AK1  CONST_55  HN10  N10  C9   C4      0.00   0.0  0
 AK1  CONST_57  O16   C14  N22  C15     0.00   0.0  0
 AK1  CONST_58  O16   C14  N13  C29     0.00   0.0  0
 AK1  CONST_59  N13   C14  N22  C15   180.00   0.0  0
 AK1  CONST_60  N22   C14  N13  C29   180.00   0.0  0
 AK1  Var_01    C11   C12  C27  C31   110.39  30.0  2
 AK1  Var_02    F26   C23  C18  C17  -140.62  30.0  3
 AK1  Var_03    N10   C11  C12  C27  -177.72  30.0  3
 AK1  Var_04    C9    N10  C11  C12   167.96  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
 AK1  plan-1  C31   0.020
 AK1  plan-1  C27   0.020
 AK1  plan-1  C12   0.020
 AK1  plan-1  N30   0.020
 AK1  plan-1  C29   0.020
 AK1  plan-1  S28   0.020
 AK1  plan-1  N13   0.020
 AK1  plan-1  H31   0.020
 AK1  plan-2  C23   0.020
 AK1  plan-2  C17   0.020
 AK1  plan-2  C20   0.020
 AK1  plan-2  C15   0.020
 AK1  plan-2  C18   0.020
 AK1  plan-2  C19   0.020
 AK1  plan-2  C21   0.020
 AK1  plan-2  N22   0.020
 AK1  plan-2  H17   0.020
 AK1  plan-2  H20   0.020
 AK1  plan-2  H19   0.020
 AK1  plan-2  H21   0.020
 AK1  plan-3  C9    0.020
 AK1  plan-3  C7    0.020
 AK1  plan-3  C4    0.020
 AK1  plan-3  C3    0.020
 AK1  plan-3  C2    0.020
 AK1  plan-3  C1    0.020
 AK1  plan-3  N6    0.020
 AK1  plan-3  N10   0.020
 AK1  plan-3  N8    0.020
 AK1  plan-3  S5    0.020
 AK1  plan-3  H7    0.020
 AK1  plan-3  H2    0.020
 AK1  plan-3  H1    0.020
 AK1  plan-4  C15   0.020
 AK1  plan-4  C14   0.020
 AK1  plan-4  C29   0.020
 AK1  plan-4  N22   0.020
 AK1  plan-4  N13   0.020
 AK1  plan-4  O16   0.020
 AK1  plan-4  HN22  0.020
 AK1  plan-4  HN13  0.020
 AK1  plan-5  C11   0.020
 AK1  plan-5  C9    0.020
 AK1  plan-5  N10   0.020
 AK1  plan-5  HN10  0.020

