# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:56:36 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-(5-{2-[(6-amino-5-bromopyrimidin-4-yl)amino]ethyl}-1,3-thiazol-2-yl)-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(NCCc2sc(NC(=O)Nc3cccc(c3)C(F)(F)F)nc2)c1Br
#
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
 AK7  AK7  1-(5-{2-[(6-amino-5-bromopyrimidin-4-yl)amino]ethyl}-1,3-thiazol-2-yl)-3-[3-(trifluoromethyl)phenyl]urea  ligand  45  30  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AK7
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
 AK7  N29   N   NH2   0  -0.826    8.9997   2.1163   0.2585
 AK7  C24   C   CR16  0  -0.301   -6.3576  -0.9866  -1.5252
 AK7  C23   C   CR16  0  -0.232   -7.6602  -0.8041  -1.9601
 AK7  C22   C   CR16  0  -0.305   -8.5773  -0.0681  -1.2252
 AK7  C16   C   C     0   0.743   -3.5305  -0.9629  -0.4088
 AK7  O18   O   O     0  -0.467   -3.4736  -1.3262  -1.5625
 AK7  C20   C   CR16  0  -0.379   -6.8624   0.3313   0.4210
 AK7  C12   C   CR5   0   0.301   -1.1573  -1.2915   0.0829
 AK7  C14   C   CR15  0  -0.040    0.5333  -2.2643  -0.9001
 AK7  C10   C   CR5   0  -0.201    1.2646  -1.5454  -0.0148
 AK7  C9    C   CH2   0  -0.546    2.7407  -1.5072   0.1752
 AK7  C8    C   CH2   0  -0.233    3.3396  -0.1520  -0.1933
 AK7  C4    C   CR16  0   0.066    5.6932   3.1615   0.0715
 AK7  C6    C   CR6   0   0.594    5.5477   0.8994   0.0336
 AK7  C2    C   CR6   0   0.520    7.6602   2.0452   0.1916
 AK7  C1    C   CR6   0  -0.348    6.9477   0.8442   0.1279
 AK7  BR30  BR  BR    0  -0.041    7.8527  -0.8103   0.1759
 AK7  N5    N   N     0  -0.490    4.9288   2.0901   0.0050
 AK7  N3    N   N     0  -0.476    7.0039   3.2197   0.1598
 AK7  N13   N   N     0  -0.391   -0.8265  -2.1292  -0.8377
 AK7  S11   S   S2    0   0.200    0.1811  -0.5964   0.9502
 AK7  N17   N   NH1   0  -0.795   -4.6688  -0.5480   0.2237
 AK7  C19   C   CR6   0   0.407   -5.9448  -0.4111  -0.3209
 AK7  C21   C   CR6   0  -0.176   -8.1647   0.4969  -0.0272
 AK7  C25   C   CT    0   1.052   -9.1116   1.2802   0.8282
 AK7  F26   F   F     0  -0.302  -10.2728   1.5272   0.2170
 AK7  F27   F   F     0  -0.315   -9.3992   0.6314   1.9669
 AK7  F28   F   F     0  -0.313   -8.5975   2.4650   1.1869
 AK7  HN29  H   HNH2  0   0.400    9.4044   3.0166   0.4529
 AK7  HN2A  H   HNH2  0   0.405    9.5627   1.3171   0.4917
 AK7  H23   H   HCR6  0   0.271   -7.9665  -1.2544  -2.8945
 AK7  H22   H   HCR6  0   0.271   -9.5875   0.0498  -1.5902
 AK7  H20   H   HCR6  0   0.288   -6.5442   0.7798   1.3551
 AK7  H14   H   HCR5  0   0.271    0.9653  -2.9409  -1.6254
 AK7  H9    H   HCH2  0   0.272    2.9988  -1.7497   1.2094
 AK7  H9A   H   HCH2  0   0.271    3.1769  -2.2892  -0.4518
 AK7  H8    H   HCH2  0   0.242    3.0734   0.1025  -1.2243
 AK7  H8A   H   HCH2  0   0.245    2.9243   0.6275   0.4454
 AK7  H4    H   HCR6  0   0.255    5.1754   4.1158   0.0488
 AK7  HN17  H   HNH1  0   0.421   -4.5811  -0.2186   1.1735
 AK7  N7    N   NH1   0  -0.681    4.7740  -0.1972  -0.0141
 AK7  N15   N   NH1   0  -0.760   -2.4345  -0.9195   0.4324
 AK7  H24   H   HCR6  0   0.288   -5.6813  -1.5773  -2.1199
 AK7  HN7   H   HNH1  0   0.401    5.2158  -1.0909  -0.1577
 AK7  HN15  H   HNH1  0   0.429   -2.5463  -0.5083   1.3471

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
 AK7  N29   C2    single    1.343  0.020  1.343
 AK7  N29   HN29  single    0.890  0.020  1.040
 AK7  N29   HN2A  single    0.890  0.020  1.040
 AK7  C23   C24   aromatic  1.385  0.020  1.385
 AK7  C24   C19   aromatic  1.397  0.020  1.397
 AK7  C24   H24   single    0.930  0.020  1.080
 AK7  C23   C22   aromatic  1.387  0.020  1.387
 AK7  C23   H23   single    0.930  0.020  1.080
 AK7  C22   C21   aromatic  1.387  0.020  1.387
 AK7  C22   H22   single    0.930  0.020  1.080
 AK7  O18   C16   double    1.211  0.020  1.211
 AK7  C16   N17   single    1.367  0.020  1.367
 AK7  C16   N15   single    1.382  0.020  1.382
 AK7  C21   C20   aromatic  1.387  0.020  1.387
 AK7  C19   C20   aromatic  1.394  0.020  1.394
 AK7  C20   H20   single    0.930  0.020  1.080
 AK7  S11   C12   aromatic  1.740  0.020  1.740
 AK7  C12   N15   single    1.375  0.020  1.375
 AK7  C12   N13   aromatic  1.288  0.020  1.288
 AK7  C10   C14   aromatic  1.355  0.020  1.355
 AK7  C14   N13   aromatic  1.368  0.020  1.368
 AK7  C14   H14   single    0.930  0.020  1.080
 AK7  C9    C10   single    1.489  0.020  1.489
 AK7  S11   C10   aromatic  1.734  0.020  1.734
 AK7  C8    C9    single    1.527  0.020  1.527
 AK7  C9    H9    single    0.970  0.020  1.090
 AK7  C9    H9A   single    0.970  0.020  1.090
 AK7  N7    C8    single    1.446  0.020  1.446
 AK7  C8    H8    single    0.970  0.020  1.090
 AK7  C8    H8A   single    0.970  0.020  1.090
 AK7  N3    C4    aromatic  1.315  0.020  1.315
 AK7  N5    C4    aromatic  1.318  0.020  1.318
 AK7  C4    H4    single    0.930  0.020  1.080
 AK7  C1    C6    aromatic  1.404  0.020  1.404
 AK7  N7    C6    single    1.343  0.020  1.343
 AK7  C6    N5    aromatic  1.342  0.020  1.342
 AK7  C1    C2    aromatic  1.398  0.020  1.398
 AK7  C2    N3    aromatic  1.346  0.020  1.346
 AK7  BR30  C1    single    1.886  0.020  1.886
 AK7  N7    HN7   single    0.860  0.020  1.020
 AK7  N15   HN15  single    0.860  0.020  1.020
 AK7  C19   N17   single    1.394  0.020  1.394
 AK7  N17   HN17  single    0.860  0.020  1.020
 AK7  C21   C25   single    1.497  0.020  1.497
 AK7  F27   C25   single    1.342  0.020  1.342
 AK7  C25   F26   single    1.335  0.020  1.335
 AK7  C25   F28   single    1.340  0.020  1.340

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
 AK7  HN2A  N29  HN29  116.20  3.000
 AK7  HN2A  N29  C2    121.88  3.000
 AK7  HN29  N29  C2    117.27  3.000
 AK7  H24   C24  C19   121.09  3.000
 AK7  H24   C24  C23   119.30  3.000
 AK7  C19   C24  C23   119.61  3.000
 AK7  H23   C23  C22   119.44  3.000
 AK7  H23   C23  C24   118.86  3.000
 AK7  C22   C23  C24   121.70  3.000
 AK7  H22   C22  C21   121.69  3.000
 AK7  H22   C22  C23   119.81  3.000
 AK7  C21   C22  C23   118.49  3.000
 AK7  N17   C16  N15   111.67  3.000
 AK7  N15   C16  O18   123.51  3.000
 AK7  N17   C16  O18   124.83  3.000
 AK7  H20   C20  C21   120.31  3.000
 AK7  H20   C20  C19   119.06  3.000
 AK7  C21   C20  C19   120.63  3.000
 AK7  N15   C12  S11   118.66  3.000
 AK7  N15   C12  N13   126.59  3.000
 AK7  S11   C12  N13   114.75  3.000
 AK7  H14   C14  N13   119.29  3.000
 AK7  H14   C14  C10   123.67  3.000
 AK7  N13   C14  C10   117.03  3.000
 AK7  S11   C10  C9    122.31  3.000
 AK7  S11   C10  C14   108.47  3.000
 AK7  C9    C10  C14   129.21  3.000
 AK7  H9A   C9   H9    106.84  3.000
 AK7  H9A   C9   C8    109.88  3.000
 AK7  H9    C9   C8    109.43  3.000
 AK7  H9A   C9   C10   107.70  3.000
 AK7  H9    C9   C10   110.43  3.000
 AK7  C8    C9   C10   112.39  3.000
 AK7  H8A   C8   H8    107.03  3.000
 AK7  H8A   C8   N7    109.13  3.000
 AK7  H8    C8   N7    111.41  3.000
 AK7  H8A   C8   C9    110.11  3.000
 AK7  H8    C8   C9    109.77  3.000
 AK7  N7    C8   C9    109.35  3.000
 AK7  H4    C4   N3    115.96  3.000
 AK7  H4    C4   N5    115.90  3.000
 AK7  N3    C4   N5    128.14  3.000
 AK7  N7    C6   N5    117.25  3.000
 AK7  N5    C6   C1    119.74  3.000
 AK7  N7    C6   C1    123.00  3.000
 AK7  N3    C2   C1    120.01  3.000
 AK7  N3    C2   N29   116.19  3.000
 AK7  C1    C2   N29   123.79  3.000
 AK7  BR30  C1   C2    120.52  3.000
 AK7  BR30  C1   C6    120.97  3.000
 AK7  C2    C1   C6    118.52  3.000
 AK7  C6    N5   C4    116.91  3.000
 AK7  C2    N3   C4    116.68  3.000
 AK7  C14   N13  C12   110.62  3.000
 AK7  C10   S11  C12    89.12  3.000
 AK7  HN17  N17  C19   114.53  3.000
 AK7  HN17  N17  C16   117.53  3.000
 AK7  C19   N17  C16   127.69  3.000
 AK7  N17   C19  C20   116.54  3.000
 AK7  N17   C19  C24   124.52  3.000
 AK7  C20   C19  C24   118.92  3.000
 AK7  C25   C21  C20   118.13  3.000
 AK7  C25   C21  C22   121.22  3.000
 AK7  C20   C21  C22   120.64  3.000
 AK7  F28   C25  F27   106.42  3.000
 AK7  F28   C25  F26   107.01  3.000
 AK7  F27   C25  F26   106.95  3.000
 AK7  F28   C25  C21   111.89  3.000
 AK7  F26   C25  C21   112.65  3.000
 AK7  F27   C25  C21   111.56  3.000
 AK7  HN7   N7   C6    118.48  3.000
 AK7  HN7   N7   C8    116.43  3.000
 AK7  C6    N7   C8    123.39  3.000
 AK7  HN15  N15  C12   116.32  3.000
 AK7  HN15  N15  C16   118.46  3.000
 AK7  C12   N15  C16   124.97  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
 AK7  CONST_01  C21   C22  C23  C24      0.00   0.0  0
 AK7  CONST_02  C21   C20  C19  C24      0.00   0.0  0
 AK7  CONST_03  C20   C19  C24  C23      0.00   0.0  0
 AK7  CONST_04  C20   C21  C22  C23      0.00   0.0  0
 AK7  CONST_05  C19   C24  C23  C22      0.00   0.0  0
 AK7  CONST_06  C19   C20  C21  C22      0.00   0.0  0
 AK7  CONST_07  C14   C10  S11  C12      0.00   0.0  0
 AK7  CONST_08  C10   C14  N13  C12      0.00   0.0  0
 AK7  CONST_09  S11   C12  N13  C14      0.00   0.0  0
 AK7  CONST_10  N13   C12  S11  C10      0.00   0.0  0
 AK7  CONST_11  C1    C2   N3   C4       0.00   0.0  0
 AK7  CONST_12  C1    C6   N5   C4       0.00   0.0  0
 AK7  CONST_13  N3    C2   C1   C6       0.00   0.0  0
 AK7  CONST_14  N3    C4   N5   C6       0.00   0.0  0
 AK7  CONST_15  N5    C6   C1   C2       0.00   0.0  0
 AK7  CONST_16  N5    C4   N3   C2       0.00   0.0  0
 AK7  CONST_17  S11   C10  C14  N13      0.00   0.0  0
 AK7  CONST_18  C6    C1   C2   N29    180.00   0.0  0
 AK7  CONST_19  C4    N3   C2   N29    180.00   0.0  0
 AK7  CONST_20  N17   C19  C24  C23    180.00   0.0  0
 AK7  CONST_21  C25   C21  C22  C23    180.00   0.0  0
 AK7  CONST_22  C9    C10  S11  C12    180.00   0.0  0
 AK7  CONST_23  N15   C12  N13  C14    180.00   0.0  0
 AK7  CONST_24  N15   C12  S11  C10    180.00   0.0  0
 AK7  CONST_25  N13   C14  C10  C9     180.00   0.0  0
 AK7  CONST_26  N7    C6   N5   C4     180.00   0.0  0
 AK7  CONST_27  N7    C6   C1   C2     180.00   0.0  0
 AK7  CONST_28  N5    C6   C1   BR30   180.00   0.0  0
 AK7  CONST_29  N3    C2   C1   BR30   180.00   0.0  0
 AK7  CONST_30  C21   C20  C19  N17    180.00   0.0  0
 AK7  CONST_31  C25   C21  C20  C19    180.00   0.0  0
 AK7  CONST_32  H22   C22  C23  C24    180.00   0.0  0
 AK7  CONST_33  H20   C20  C19  C24    180.00   0.0  0
 AK7  CONST_34  H24   C24  C23  C22    180.00   0.0  0
 AK7  CONST_35  H14   C14  N13  C12    180.00   0.0  0
 AK7  CONST_36  H4    C4   N5   C6     180.00   0.0  0
 AK7  CONST_37  H23   C23  C24  C19    180.00   0.0  0
 AK7  CONST_42  C1    C6   N7   C8     180.00   0.0  0
 AK7  CONST_43  N5    C6   N7   C8       0.00   0.0  0
 AK7  CONST_44  HN17  N17  C19  C24    180.00   0.0  0
 AK7  CONST_45  HN7   N7   C6   C1       0.00   0.0  0
 AK7  CONST_46  HN29  N29  C2   C1     180.00   0.0  0
 AK7  CONST_49  C19   N17  C16  O18      0.00   0.0  0
 AK7  CONST_50  C12   N15  C16  O18      0.00   0.0  0
 AK7  CONST_51  N17   C16  N15  C12    180.00   0.0  0
 AK7  CONST_52  C19   N17  C16  N15    180.00   0.0  0
 AK7  Var_01    F27   C25  C21  C22    110.74  30.0  2
 AK7  Var_02    C8    C9   C10  C14    113.37  30.0  2
 AK7  Var_03    N7    C8   C9   C10   -178.71  30.0  1
 AK7  Var_04    C6    N7   C8   C9    -164.71  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
 AK7  plan-1  C12   0.020
 AK7  plan-1  C14   0.020
 AK7  plan-1  C10   0.020
 AK7  plan-1  C9    0.020
 AK7  plan-1  N13   0.020
 AK7  plan-1  S11   0.020
 AK7  plan-1  H14   0.020
 AK7  plan-1  N15   0.020
 AK7  plan-2  C8    0.020
 AK7  plan-2  C6    0.020
 AK7  plan-2  N7    0.020
 AK7  plan-2  HN7   0.020
 AK7  plan-3  C24   0.020
 AK7  plan-3  C23   0.020
 AK7  plan-3  C22   0.020
 AK7  plan-3  C20   0.020
 AK7  plan-3  N17   0.020
 AK7  plan-3  C19   0.020
 AK7  plan-3  C21   0.020
 AK7  plan-3  C25   0.020
 AK7  plan-3  H23   0.020
 AK7  plan-3  H22   0.020
 AK7  plan-3  H20   0.020
 AK7  plan-3  H24   0.020
 AK7  plan-4  N29   0.020
 AK7  plan-4  C4    0.020
 AK7  plan-4  C6    0.020
 AK7  plan-4  C2    0.020
 AK7  plan-4  C1    0.020
 AK7  plan-4  BR30  0.020
 AK7  plan-4  N5    0.020
 AK7  plan-4  N3    0.020
 AK7  plan-4  H4    0.020
 AK7  plan-4  N7    0.020
 AK7  plan-5  C16   0.020
 AK7  plan-5  O18   0.020
 AK7  plan-5  C12   0.020
 AK7  plan-5  N17   0.020
 AK7  plan-5  C19   0.020
 AK7  plan-5  HN17  0.020
 AK7  plan-5  N15   0.020
 AK7  plan-5  HN15  0.020
 AK7  plan-6  N29   0.020
 AK7  plan-6  C2    0.020
 AK7  plan-6  HN29  0.020
 AK7  plan-6  HN2A  0.020

