# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 03:42:05 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 1-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nccc(n1)c2cccnc2Oc3ccc(NC(=O)Nc4cccc(c4)C(F)(F)F)cc3C
#
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
 AK8  AK8  1-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)phenyl]-3-[3-(trifluoromethyl)phenyl]urea  ligand  57  36  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AK8
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
 AK8  N1    N  N     0  -0.462  -6.0543   0.8563  -0.1980
 AK8  N3    N  N     0  -0.435  -3.5673  -2.6068  -0.2264
 AK8  C4    C  CR16  0  -0.010  -8.1658   0.8976   1.4859
 AK8  C5    C  CR6   0  -0.109  -5.6609  -1.4880   0.1006
 AK8  C6    C  CR16  0  -0.169  -6.3233  -2.6535  -0.2501
 AK8  C7    C  CR16  0  -0.340  -5.6033  -3.7874  -0.6057
 AK8  C8    C  CR16  0  -0.055  -4.2253  -3.7047  -0.5919
 AK8  C10   C  CH3   0  -0.509  -7.0559   4.3519  -0.4037
 AK8  C13   C  CR16  0  -0.322   0.0068  -0.3296   1.1101
 AK8  C15   C  CR16  0  -0.406  -0.4721   0.2179  -1.1804
 AK8  C17   C  CH3   0  -0.750  -2.8094   0.2448  -2.1032
 AK8  C20   C  CR16  0  -0.298   5.6645  -1.4793   0.5335
 AK8  C21   C  CR16  0  -0.234   6.9831  -1.7915   0.8182
 AK8  C22   C  CR16  0  -0.307   8.0202  -0.9249   0.5050
 AK8  C24   C  CR16  0  -0.377   6.3964   0.6162  -0.3899
 AK8  C1    C  CR6   0   0.585  -6.7709   1.9587   0.0624
 AK8  N2    N  N     0  -0.462  -7.8229   2.0263   0.8873
 AK8  C3    C  CR16  0  -0.399  -7.4966  -0.2979   1.2944
 AK8  C2    C  CR6   0   0.269  -6.4166  -0.2577   0.4143
 AK8  C9    C  CR6   0   0.496  -4.2590  -1.5462   0.1155
 AK8  O1    O  O2    0  -0.504  -3.6011  -0.4588   0.5559
 AK8  C11   C  CR6   0   0.308  -2.2550  -0.3386   0.2896
 AK8  C16   C  CR6   0   0.071  -1.8347   0.0430  -0.9822
 AK8  C12   C  CR16  0  -0.310  -1.3509  -0.5216   1.3183
 AK8  C14   C  CR6   0   0.390   0.4581   0.0333  -0.1567
 AK8  N5    N  NH1   0  -0.790   1.8008   0.2830  -0.4600
 AK8  C18   C  C     0   0.728   2.8898  -0.3068   0.1183
 AK8  O2    O  O     0  -0.491   2.8240  -1.1277   1.0140
 AK8  N6    N  NH1   0  -0.794   4.0695   0.1350  -0.4270
 AK8  C19   C  CR6   0   0.406   5.3579  -0.2577  -0.0727
 AK8  C23   C  CR6   0  -0.176   7.7133   0.2814  -0.1070
 AK8  C25   C  CT    0   1.051   8.7841   1.2542  -0.4907
 AK8  F2    F  F     0  -0.302   9.9976   0.8721  -0.0853
 AK8  F3    F  F     0  -0.315   8.8499   1.4175  -1.8209
 AK8  F1    F  F     0  -0.314   8.5617   2.4702   0.0289
 AK8  H4    H  HCR6  0   0.269  -9.0154   0.9474   2.1587
 AK8  H6    H  HCR6  0   0.277  -7.4058  -2.6670  -0.2731
 AK8  H7    H  HCR6  0   0.274  -6.1002  -4.7006  -0.8991
 AK8  H8    H  HCR6  0   0.273  -3.6171  -4.5542  -0.8796
 AK8  H10   H  HCH3  0   0.250  -6.5666   5.0740  -1.0515
 AK8  H10A  H  HCH3  0   0.233  -8.1094   4.3029  -0.6824
 AK8  H10B  H  HCH3  0   0.232  -6.9961   4.7171   0.6233
 AK8  H13   H  HCR6  0   0.273   0.6890  -0.4545   1.9353
 AK8  H15   H  HCR6  0   0.267  -0.1244   0.5118  -2.1648
 AK8  H17   H  HCH3  0   0.250  -3.1425  -0.7122  -2.5111
 AK8  H17A  H  HCH3  0   0.260  -3.7013   0.7791  -1.7749
 AK8  H17B  H  HCH3  0   0.255  -2.3533   0.8052  -2.9175
 AK8  H20   H  HCR6  0   0.283   4.8897  -2.1878   0.7766
 AK8  H21   H  HCR6  0   0.270   7.2077  -2.7391   1.2891
 AK8  H22   H  HCR6  0   0.271   9.0387  -1.2025   0.7346
 AK8  H24   H  HCR6  0   0.286   6.1592   1.5636  -0.8605
 AK8  HN4   H  HNH1  0   0.395  -5.5954   3.0206  -1.1708
 AK8  H3    H  HCR6  0   0.271  -7.7893  -1.2009   1.8091
 AK8  H12   H  HCR6  0   0.268  -1.7068  -0.8031   2.3011
 AK8  HN5   H  HNH1  0   0.413   1.9536   0.8178  -1.3010
 AK8  HN6   H  HNH1  0   0.416   4.0237   0.9308  -1.0455
 AK8  N4    N  NH1   0  -0.649  -6.3977   3.0824  -0.5684

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
 AK8  N1   C1    aromatic  1.340  0.020  1.340
 AK8  N1   C2    aromatic  1.322  0.020  1.322
 AK8  N3   C8    aromatic  1.331  0.020  1.331
 AK8  N3   C9    aromatic  1.312  0.020  1.312
 AK8  C4   N2    aromatic  1.323  0.020  1.323
 AK8  C4   C3    aromatic  1.383  0.020  1.383
 AK8  C5   C6    aromatic  1.386  0.020  1.386
 AK8  C5   C2    single    1.477  0.020  1.477
 AK8  C5   C9    aromatic  1.403  0.020  1.403
 AK8  C6   C7    aromatic  1.390  0.020  1.390
 AK8  C7   C8    aromatic  1.381  0.020  1.381
 AK8  C10  N4    single    1.439  0.020  1.439
 AK8  C13  C12   aromatic  1.387  0.020  1.387
 AK8  C13  C14   aromatic  1.393  0.020  1.393
 AK8  C15  C16   aromatic  1.388  0.020  1.388
 AK8  C15  C14   aromatic  1.395  0.020  1.395
 AK8  C17  C16   single    1.499  0.020  1.499
 AK8  C20  C21   aromatic  1.385  0.020  1.385
 AK8  C20  C19   aromatic  1.398  0.020  1.398
 AK8  C21  C22   aromatic  1.387  0.020  1.387
 AK8  C22  C23   aromatic  1.387  0.020  1.387
 AK8  C24  C19   aromatic  1.394  0.020  1.394
 AK8  C24  C23   aromatic  1.388  0.020  1.388
 AK8  N4   C1    single    1.342  0.020  1.342
 AK8  C1   N2    aromatic  1.339  0.020  1.339
 AK8  C3   C2    aromatic  1.394  0.020  1.394
 AK8  C9   O1    single    1.345  0.020  1.345
 AK8  O1   C11   single    1.377  0.020  1.377
 AK8  C11  C16   aromatic  1.393  0.020  1.393
 AK8  C11  C12   aromatic  1.382  0.020  1.382
 AK8  C14  N5    single    1.399  0.020  1.399
 AK8  N5   C18   single    1.367  0.020  1.367
 AK8  C18  O2    double    1.217  0.020  1.217
 AK8  C18  N6    single    1.373  0.020  1.373
 AK8  N6   C19   single    1.393  0.020  1.393
 AK8  C23  C25   single    1.497  0.020  1.497
 AK8  C25  F2    single    1.335  0.020  1.335
 AK8  C25  F3    single    1.342  0.020  1.342
 AK8  C25  F1    single    1.341  0.020  1.341
 AK8  C4   H4    single    0.930  0.020  1.080
 AK8  C6   H6    single    0.930  0.020  1.080
 AK8  C7   H7    single    0.930  0.020  1.080
 AK8  C8   H8    single    0.930  0.020  1.080
 AK8  C10  H10   single    0.970  0.020  1.090
 AK8  C10  H10A  single    0.970  0.020  1.090
 AK8  C10  H10B  single    0.970  0.020  1.090
 AK8  C13  H13   single    0.930  0.020  1.080
 AK8  C15  H15   single    0.930  0.020  1.080
 AK8  C17  H17   single    0.970  0.020  1.090
 AK8  C17  H17A  single    0.970  0.020  1.090
 AK8  C17  H17B  single    0.970  0.020  1.090
 AK8  C20  H20   single    0.930  0.020  1.080
 AK8  C21  H21   single    0.930  0.020  1.080
 AK8  C22  H22   single    0.930  0.020  1.080
 AK8  C24  H24   single    0.930  0.020  1.080
 AK8  N4   HN4   single    0.860  0.020  1.020
 AK8  C3   H3    single    0.930  0.020  1.080
 AK8  C12  H12   single    0.930  0.020  1.080
 AK8  N5   HN5   single    0.860  0.020  1.020
 AK8  N6   HN6   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
 AK8  C2    N1   C1    117.17  3.000
 AK8  C9    N3   C8    118.54  3.000
 AK8  H4    C4   C3    120.29  3.000
 AK8  H4    C4   N2    116.39  3.000
 AK8  C3    C4   N2    123.32  3.000
 AK8  C9    C5   C2    122.91  3.000
 AK8  C9    C5   C6    116.45  3.000
 AK8  C2    C5   C6    120.64  3.000
 AK8  H6    C6   C7    120.16  3.000
 AK8  H6    C6   C5    119.59  3.000
 AK8  C7    C6   C5    120.23  3.000
 AK8  H7    C7   C8    120.83  3.000
 AK8  H7    C7   C6    121.40  3.000
 AK8  C8    C7   C6    117.76  3.000
 AK8  H8    C8   C7    120.70  3.000
 AK8  H8    C8   N3    116.24  3.000
 AK8  C7    C8   N3    123.06  3.000
 AK8  H10B  C10  H10A  107.96  3.000
 AK8  H10B  C10  H10   108.30  3.000
 AK8  H10A  C10  H10   108.21  3.000
 AK8  H10B  C10  N4    112.19  3.000
 AK8  H10A  C10  N4    111.88  3.000
 AK8  H10   C10  N4    108.18  3.000
 AK8  H13   C13  C14   121.43  3.000
 AK8  H13   C13  C12   119.25  3.000
 AK8  C14   C13  C12   119.32  3.000
 AK8  H15   C15  C14   119.21  3.000
 AK8  H15   C15  C16   118.59  3.000
 AK8  C14   C15  C16   122.20  3.000
 AK8  H17B  C17  H17A  108.40  3.000
 AK8  H17B  C17  H17   107.42  3.000
 AK8  H17A  C17  H17   107.00  3.000
 AK8  H17B  C17  C16   110.87  3.000
 AK8  H17A  C17  C16   111.88  3.000
 AK8  H17   C17  C16   111.07  3.000
 AK8  H20   C20  C19   120.98  3.000
 AK8  H20   C20  C21   119.34  3.000
 AK8  C19   C20  C21   119.68  3.000
 AK8  H21   C21  C22   119.36  3.000
 AK8  H21   C21  C20   119.00  3.000
 AK8  C22   C21  C20   121.64  3.000
 AK8  H22   C22  C23   121.72  3.000
 AK8  H22   C22  C21   119.75  3.000
 AK8  C23   C22  C21   118.52  3.000
 AK8  H24   C24  C23   120.45  3.000
 AK8  H24   C24  C19   118.93  3.000
 AK8  C23   C24  C19   120.62  3.000
 AK8  N2    C1   N4    117.77  3.000
 AK8  N2    C1   N1    125.56  3.000
 AK8  N4    C1   N1    116.67  3.000
 AK8  C1    N2   C4    116.07  3.000
 AK8  H3    C3   C2    122.35  3.000
 AK8  H3    C3   C4    121.71  3.000
 AK8  C2    C3   C4    115.94  3.000
 AK8  C3    C2   C5    120.42  3.000
 AK8  C3    C2   N1    121.95  3.000
 AK8  C5    C2   N1    117.60  3.000
 AK8  O1    C9   C5    117.29  3.000
 AK8  O1    C9   N3    118.76  3.000
 AK8  C5    C9   N3    123.90  3.000
 AK8  C11   O1   C9    119.03  3.000
 AK8  C12   C11  C16   121.24  3.000
 AK8  C12   C11  O1    118.94  3.000
 AK8  C16   C11  O1    119.69  3.000
 AK8  C11   C16  C17   121.57  3.000
 AK8  C11   C16  C15   117.46  3.000
 AK8  C17   C16  C15   120.96  3.000
 AK8  H12   C12  C11   119.68  3.000
 AK8  H12   C12  C13   119.61  3.000
 AK8  C11   C12  C13   120.69  3.000
 AK8  N5    C14  C15   117.20  3.000
 AK8  N5    C14  C13   123.69  3.000
 AK8  C15   C14  C13   119.06  3.000
 AK8  HN5   N5   C18   117.45  3.000
 AK8  HN5   N5   C14   114.90  3.000
 AK8  C18   N5   C14   126.58  3.000
 AK8  N6    C18  O2    123.78  3.000
 AK8  N6    C18  N5    112.19  3.000
 AK8  O2    C18  N5    124.02  3.000
 AK8  HN6   N6   C19   114.85  3.000
 AK8  HN6   N6   C18   117.29  3.000
 AK8  C19   N6   C18   127.10  3.000
 AK8  N6    C19  C24   117.04  3.000
 AK8  N6    C19  C20   124.03  3.000
 AK8  C24   C19  C20   118.90  3.000
 AK8  C25   C23  C24   118.02  3.000
 AK8  C25   C23  C22   121.34  3.000
 AK8  C24   C23  C22   120.64  3.000
 AK8  F1    C25  F3    106.38  3.000
 AK8  F1    C25  F2    107.02  3.000
 AK8  F3    C25  F2    106.93  3.000
 AK8  F1    C25  C23   111.80  3.000
 AK8  F3    C25  C23   111.61  3.000
 AK8  F2    C25  C23   112.72  3.000
 AK8  HN4   N4   C1    116.89  3.000
 AK8  HN4   N4   C10   119.19  3.000
 AK8  C1    N4   C10   123.90  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
 AK8  CONST_01  C4   N2   C1   N1      0.00   0.0  0
 AK8  CONST_04  C4   C3   C2   N1      0.00   0.0  0
 AK8  CONST_05  C6   C7   C8   N3      0.00   0.0  0
 AK8  CONST_06  C6   C5   C9   N3      0.00   0.0  0
 AK8  CONST_07  C2   C5   C9   N3    180.00   0.0  0
 AK8  CONST_08  C5   C2   C3   C4    180.00   0.0  0
 AK8  CONST_09  C8   C7   C6   C5      0.00   0.0  0
 AK8  CONST_10  C1   N1   C2   C5    180.00   0.0  0
 AK8  CONST_11  C8   N3   C9   C5      0.00   0.0  0
 AK8  CONST_13  C2   C5   C6   C7    180.00   0.0  0
 AK8  CONST_14  C9   C5   C6   C7      0.00   0.0  0
 AK8  CONST_15  C9   N3   C8   C7      0.00   0.0  0
 AK8  CONST_16  C16  C11  C12  C13     0.00   0.0  0
 AK8  CONST_17  C16  C15  C14  C13     0.00   0.0  0
 AK8  CONST_18  C12  C11  C16  C15     0.00   0.0  0
 AK8  CONST_19  C12  C13  C14  C15     0.00   0.0  0
 AK8  CONST_20  C23  C22  C21  C20     0.00   0.0  0
 AK8  CONST_21  C23  C24  C19  C20     0.00   0.0  0
 AK8  CONST_22  C24  C19  C20  C21     0.00   0.0  0
 AK8  CONST_23  C24  C23  C22  C21     0.00   0.0  0
 AK8  CONST_24  C19  C20  C21  C22     0.00   0.0  0
 AK8  CONST_25  C19  C24  C23  C22     0.00   0.0  0
 AK8  CONST_26  C3   C2   N1   C1      0.00   0.0  0
 AK8  CONST_27  C3   C4   N2   C1      0.00   0.0  0
 AK8  CONST_28  C2   C3   C4   N2      0.00   0.0  0
 AK8  CONST_29  C2   N1   C1   N2      0.00   0.0  0
 AK8  CONST_31  C14  C15  C16  C11     0.00   0.0  0
 AK8  CONST_32  C14  C13  C12  C11     0.00   0.0  0
 AK8  CONST_33  N4   C1   N2   C4    180.00   0.0  0
 AK8  CONST_34  O1   C9   C5   C6    180.00   0.0  0
 AK8  CONST_35  O1   C9   N3   C8    180.00   0.0  0
 AK8  CONST_36  O1   C11  C12  C13   180.00   0.0  0
 AK8  CONST_37  O1   C11  C16  C15   180.00   0.0  0
 AK8  CONST_38  C14  C15  C16  C17   180.00   0.0  0
 AK8  CONST_39  C12  C11  C16  C17   180.00   0.0  0
 AK8  CONST_40  N6   C19  C20  C21   180.00   0.0  0
 AK8  CONST_41  C25  C23  C22  C21   180.00   0.0  0
 AK8  CONST_42  C2   N1   C1   N4    180.00   0.0  0
 AK8  CONST_43  O1   C9   C5   C2      0.00   0.0  0
 AK8  CONST_44  N5   C14  C15  C16   180.00   0.0  0
 AK8  CONST_45  N5   C14  C13  C12   180.00   0.0  0
 AK8  CONST_46  C23  C24  C19  N6    180.00   0.0  0
 AK8  CONST_47  C25  C23  C24  C19   180.00   0.0  0
 AK8  CONST_48  H3   C3   C2   N1    180.00   0.0  0
 AK8  CONST_49  H7   C7   C8   N3    180.00   0.0  0
 AK8  CONST_50  H8   C8   C7   C6    180.00   0.0  0
 AK8  CONST_51  H6   C6   C7   C8    180.00   0.0  0
 AK8  CONST_52  H15  C15  C14  C13   180.00   0.0  0
 AK8  CONST_53  H13  C13  C14  C15   180.00   0.0  0
 AK8  CONST_54  H22  C22  C21  C20   180.00   0.0  0
 AK8  CONST_55  H24  C24  C19  C20   180.00   0.0  0
 AK8  CONST_56  H20  C20  C21  C22   180.00   0.0  0
 AK8  CONST_57  H4   C4   N2   C1    180.00   0.0  0
 AK8  CONST_58  H12  C12  C11  C16   180.00   0.0  0
 AK8  CONST_59  H21  C21  C20  C19   180.00   0.0  0
 AK8  CONST_60  C10  N4   C1   N1    180.00   0.0  0
 AK8  CONST_61  N2   C1   N4   C10     0.00   0.0  0
 AK8  CONST_66  HN4  N4   C1   N1      0.00   0.0  0
 AK8  CONST_68  HN6  N6   C19  C20   180.00   0.0  0
 AK8  CONST_69  O2   C18  N5   C14     0.00   0.0  0
 AK8  CONST_70  C19  N6   C18  O2      0.00   0.0  0
 AK8  CONST_71  N6   C18  N5   C14   180.00   0.0  0
 AK8  CONST_72  C19  N6   C18  N5    180.00   0.0  0
 AK8  Var_01    C16  C11  O1   C9     77.04  30.0  2
 AK8  Var_02    F2   C25  C23  C22    -4.95  30.0  2
 AK8  Var_03    H17  C17  C16  C15   102.38  30.0  2
 AK8  Var_04    H10  C10  N4   C1   -178.33  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
 AK8  plan-1  N1   0.020
 AK8  plan-1  C4   0.020
 AK8  plan-1  C5   0.020
 AK8  plan-1  C1   0.020
 AK8  plan-1  N2   0.020
 AK8  plan-1  C3   0.020
 AK8  plan-1  C2   0.020
 AK8  plan-1  H4   0.020
 AK8  plan-1  H3   0.020
 AK8  plan-1  N4   0.020
 AK8  plan-2  N3   0.020
 AK8  plan-2  C5   0.020
 AK8  plan-2  C6   0.020
 AK8  plan-2  C7   0.020
 AK8  plan-2  C8   0.020
 AK8  plan-2  C2   0.020
 AK8  plan-2  C9   0.020
 AK8  plan-2  O1   0.020
 AK8  plan-2  H6   0.020
 AK8  plan-2  H7   0.020
 AK8  plan-2  H8   0.020
 AK8  plan-3  C13  0.020
 AK8  plan-3  C15  0.020
 AK8  plan-3  C17  0.020
 AK8  plan-3  O1   0.020
 AK8  plan-3  C11  0.020
 AK8  plan-3  C16  0.020
 AK8  plan-3  C12  0.020
 AK8  plan-3  C14  0.020
 AK8  plan-3  N5   0.020
 AK8  plan-3  H13  0.020
 AK8  plan-3  H15  0.020
 AK8  plan-3  H12  0.020
 AK8  plan-4  C20  0.020
 AK8  plan-4  C21  0.020
 AK8  plan-4  C22  0.020
 AK8  plan-4  C24  0.020
 AK8  plan-4  N6   0.020
 AK8  plan-4  C19  0.020
 AK8  plan-4  C23  0.020
 AK8  plan-4  C25  0.020
 AK8  plan-4  H20  0.020
 AK8  plan-4  H21  0.020
 AK8  plan-4  H22  0.020
 AK8  plan-4  H24  0.020
 AK8  plan-5  C14  0.020
 AK8  plan-5  N5   0.020
 AK8  plan-5  C18  0.020
 AK8  plan-5  O2   0.020
 AK8  plan-5  N6   0.020
 AK8  plan-5  C19  0.020
 AK8  plan-5  HN5  0.020
 AK8  plan-5  HN6  0.020
 AK8  plan-6  C10  0.020
 AK8  plan-6  C1   0.020
 AK8  plan-6  HN4  0.020
 AK8  plan-6  N4   0.020

