# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 13:07:47 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(NC(=O)NCc2ccccc2C(F)(F)F)c(n1)c3ccccc3
#
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
 6UK  6UK  1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea  ligand  45  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6UK
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
 6UK  C2   C  CR16  0  -0.050  -2.9683   2.5374   0.0036
 6UK  C3   C  CR6   0   0.335  -4.9093   1.5839  -0.6681
 6UK  C5   C  C     0   0.722  -0.0468   1.7303   0.3710
 6UK  C7   C  CR6   0   0.118   3.3911   0.7082   0.6752
 6UK  C9   C  CR16  0  -0.230   5.0405  -0.4523   2.0255
 6UK  C10  C  CR16  0  -0.249   5.2136  -1.3925   1.0254
 6UK  C11  C  CR16  0  -0.279   4.4859  -1.2864  -0.1511
 6UK  C12  C  CR6   0  -0.253   3.5771  -0.2502  -0.3321
 6UK  C13  C  CT    0   1.062   2.8304  -0.1664  -1.6317
 6UK  C15  C  CR16  0  -0.281  -3.7588  -2.0292   1.1003
 6UK  C18  C  CR16  0  -0.236  -1.2916  -3.0178   0.3035
 6UK  F2   F  F     0  -0.311   1.5005  -0.1953  -1.4615
 6UK  F    F  F     0  -0.314   3.1085   0.9648  -2.2987
 6UK  F1   F  F     0  -0.299   3.1256  -1.1738  -2.4581
 6UK  C8   C  CR16  0  -0.286   4.1373   0.5850   1.8418
 6UK  C6   C  CH2   0  -0.379   2.3985   1.8475   0.6070
 6UK  N3   N  NH1   0  -0.667   1.0880   1.4140   1.0317
 6UK  O    O  O     0  -0.516  -0.0886   2.4444  -0.6182
 6UK  N2   N  NH1   0  -0.783  -1.1793   1.1705   0.9223
 6UK  C1   C  CR6   0   0.223  -2.4388   1.2940   0.3378
 6UK  C    C  CR6   0   0.216  -3.2704   0.1952   0.1155
 6UK  N1   N  N     0  -0.422  -4.5031   0.3630  -0.3608
 6UK  C4   C  CH3   0  -0.731  -6.2881   1.7547  -1.2205
 6UK  N    N  N     0  -0.406  -4.1748   2.6841  -0.5104
 6UK  C14  C  CR6   0   0.032  -2.8681  -1.1938   0.4271
 6UK  C19  C  CR16  0  -0.294  -1.6319  -1.7016   0.0270
 6UK  C17  C  CR16  0  -0.257  -2.1755  -3.8373   0.9925
 6UK  C16  C  CR16  0  -0.241  -3.4102  -3.3395   1.3895
 6UK  H1   H  HCR6  0   0.282  -2.3936   3.4399   0.1732
 6UK  H2   H  HCR6  0   0.269   5.6052  -0.5198   2.9459
 6UK  H3   H  HCR6  0   0.271   5.9149  -2.2063   1.1491
 6UK  H4   H  HCR6  0   0.274   4.6425  -2.0251  -0.9238
 6UK  H5   H  HCR6  0   0.258  -4.7241  -1.6470   1.4063
 6UK  H6   H  HCR6  0   0.262  -0.3354  -3.4033  -0.0248
 6UK  H7   H  HCR6  0   0.267   4.0059   1.3214   2.6252
 6UK  H8   H  HCH2  0   0.269   2.7588   2.6527   1.2525
 6UK  H9   H  HCH2  0   0.273   2.3154   2.2730  -0.3889
 6UK  H10  H  HNH1  0   0.402   1.0340   0.8979   1.8953
 6UK  H11  H  HNH1  0   0.408  -1.0707   0.4441   1.6148
 6UK  H12  H  HCH3  0   0.257  -6.9059   2.3324  -0.5310
 6UK  H13  H  HCH3  0   0.255  -6.2598   2.3038  -2.1620
 6UK  H14  H  HCH3  0   0.249  -6.7655   0.7926  -1.3883
 6UK  H15  H  HCR6  0   0.257  -0.9414  -1.0823  -0.5295
 6UK  H16  H  HCR6  0   0.263  -1.9065  -4.8614   1.2155
 6UK  H17  H  HCR6  0   0.263  -4.1049  -3.9736   1.9245

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
 6UK  O    C5   double    1.221  0.020  1.221
 6UK  C4   C3   single    1.495  0.020  1.495
 6UK  F    C13  single    1.342  0.020  1.342
 6UK  N    C3   aromatic  1.332  0.020  1.332
 6UK  N    C2   aromatic  1.320  0.020  1.320
 6UK  C3   N1   aromatic  1.323  0.020  1.323
 6UK  C2   C1   aromatic  1.392  0.020  1.392
 6UK  N1   C    aromatic  1.332  0.020  1.332
 6UK  C15  C16  aromatic  1.386  0.020  1.386
 6UK  C15  C14  aromatic  1.394  0.020  1.394
 6UK  C5   N2   single    1.378  0.020  1.378
 6UK  C5   N3   single    1.351  0.020  1.351
 6UK  C1   C    aromatic  1.396  0.020  1.396
 6UK  C1   N2   single    1.394  0.020  1.394
 6UK  C    C14  single    1.479  0.020  1.479
 6UK  C6   N3   single    1.444  0.020  1.444
 6UK  C6   C7   single    1.513  0.020  1.513
 6UK  C13  F1   single    1.336  0.020  1.336
 6UK  C13  F2   single    1.341  0.020  1.341
 6UK  C13  C12  single    1.501  0.020  1.501
 6UK  C16  C17  aromatic  1.389  0.020  1.389
 6UK  C14  C19  aromatic  1.395  0.020  1.395
 6UK  C7   C12  aromatic  1.403  0.020  1.403
 6UK  C7   C8   aromatic  1.390  0.020  1.390
 6UK  C12  C11  aromatic  1.390  0.020  1.390
 6UK  C17  C18  aromatic  1.388  0.020  1.388
 6UK  C19  C18  aromatic  1.387  0.020  1.387
 6UK  C8   C9   aromatic  1.388  0.020  1.388
 6UK  C11  C10  aromatic  1.387  0.020  1.387
 6UK  C9   C10  aromatic  1.384  0.020  1.384
 6UK  C2   H1   single    0.930  0.020  1.080
 6UK  C9   H2   single    0.930  0.020  1.080
 6UK  C10  H3   single    0.930  0.020  1.080
 6UK  C11  H4   single    0.930  0.020  1.080
 6UK  C15  H5   single    0.930  0.020  1.080
 6UK  C18  H6   single    0.930  0.020  1.080
 6UK  C8   H7   single    0.930  0.020  1.080
 6UK  C6   H8   single    0.970  0.020  1.090
 6UK  C6   H9   single    0.970  0.020  1.090
 6UK  N3   H10  single    0.860  0.020  1.020
 6UK  N2   H11  single    0.860  0.020  1.020
 6UK  C4   H12  single    0.970  0.020  1.090
 6UK  C4   H13  single    0.970  0.020  1.090
 6UK  C4   H14  single    0.970  0.020  1.090
 6UK  C19  H15  single    0.930  0.020  1.080
 6UK  C17  H16  single    0.930  0.020  1.080
 6UK  C16  H17  single    0.930  0.020  1.080

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
 6UK  H1   C2   N    116.96  3.000
 6UK  H1   C2   C1   120.31  3.000
 6UK  N    C2   C1   122.72  3.000
 6UK  N    C3   C4   117.25  3.000
 6UK  N    C3   N1   124.43  3.000
 6UK  C4   C3   N1   118.32  3.000
 6UK  N2   C5   O    122.25  3.000
 6UK  N2   C5   N3   113.55  3.000
 6UK  O    C5   N3   124.20  3.000
 6UK  C6   C7   C8   117.18  3.000
 6UK  C8   C7   C12  118.09  3.000
 6UK  C6   C7   C12  124.69  3.000
 6UK  H2   C9   C8   119.93  3.000
 6UK  H2   C9   C10  120.48  3.000
 6UK  C8   C9   C10  119.58  3.000
 6UK  H3   C10  C11  119.65  3.000
 6UK  H3   C10  C9   120.65  3.000
 6UK  C11  C10  C9   119.69  3.000
 6UK  H4   C11  C12  120.75  3.000
 6UK  H4   C11  C10  118.56  3.000
 6UK  C12  C11  C10  120.69  3.000
 6UK  C13  C12  C11  118.65  3.000
 6UK  C11  C12  C7   120.16  3.000
 6UK  C13  C12  C7   121.17  3.000
 6UK  F1   C13  F    106.39  3.000
 6UK  F1   C13  F2   106.34  3.000
 6UK  F    C13  F2   106.66  3.000
 6UK  F2   C13  C12  112.47  3.000
 6UK  F1   C13  C12  112.55  3.000
 6UK  F    C13  C12  111.97  3.000
 6UK  H5   C15  C16  119.93  3.000
 6UK  H5   C15  C14  119.65  3.000
 6UK  C16  C15  C14  120.42  3.000
 6UK  H6   C18  C17  120.20  3.000
 6UK  H6   C18  C19  119.63  3.000
 6UK  C17  C18  C19  120.18  3.000
 6UK  H7   C8   C9   119.43  3.000
 6UK  H7   C8   C7   118.79  3.000
 6UK  C9   C8   C7   121.78  3.000
 6UK  H9   C6   H8   106.15  3.000
 6UK  H9   C6   N3   108.53  3.000
 6UK  H8   C6   N3   110.28  3.000
 6UK  H9   C6   C7   112.74  3.000
 6UK  H8   C6   C7   108.17  3.000
 6UK  N3   C6   C7   110.86  3.000
 6UK  H10  N3   C6   117.03  3.000
 6UK  H10  N3   C5   119.61  3.000
 6UK  C6   N3   C5   123.25  3.000
 6UK  H11  N2   C1   116.65  3.000
 6UK  H11  N2   C5   118.57  3.000
 6UK  C1   N2   C5   122.59  3.000
 6UK  C    C1   N2   122.37  3.000
 6UK  N2   C1   C2   121.56  3.000
 6UK  C    C1   C2   115.99  3.000
 6UK  C14  C    N1   116.44  3.000
 6UK  C14  C    C1   122.92  3.000
 6UK  N1   C    C1   120.61  3.000
 6UK  C    N1   C3   118.91  3.000
 6UK  H14  C4   H13  108.89  3.000
 6UK  H14  C4   H12  108.51  3.000
 6UK  H13  C4   H12  107.08  3.000
 6UK  H14  C4   C3   111.16  3.000
 6UK  H13  C4   C3   110.64  3.000
 6UK  H12  C4   C3   110.44  3.000
 6UK  C3   N    C2   117.28  3.000
 6UK  C19  C14  C    121.49  3.000
 6UK  C19  C14  C15  119.11  3.000
 6UK  C    C14  C15  119.37  3.000
 6UK  H15  C19  C14  120.32  3.000
 6UK  H15  C19  C18  119.28  3.000
 6UK  C14  C19  C18  120.37  3.000
 6UK  H16  C17  C16  120.08  3.000
 6UK  H16  C17  C18  120.17  3.000
 6UK  C16  C17  C18  119.75  3.000
 6UK  H17  C16  C17  120.13  3.000
 6UK  H17  C16  C15  119.70  3.000
 6UK  C17  C16  C15  120.17  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
 6UK  CONST_01  N1   C3   N    C2      0.00   0.0  0
 6UK  CONST_02  N1   C    C1   C2      0.00   0.0  0
 6UK  CONST_03  C14  C    C1   C2    180.00   0.0  0
 6UK  CONST_04  C1   C2   N    C3      0.00   0.0  0
 6UK  CONST_05  C1   C    N1   C3      0.00   0.0  0
 6UK  CONST_06  C14  C    N1   C3    180.00   0.0  0
 6UK  CONST_07  C10  C11  C12  C7      0.00   0.0  0
 6UK  CONST_08  C10  C9   C8   C7      0.00   0.0  0
 6UK  CONST_09  C12  C7   C8   C9      0.00   0.0  0
 6UK  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 6UK  CONST_11  C8   C7   C12  C11     0.00   0.0  0
 6UK  CONST_12  C8   C9   C10  C11     0.00   0.0  0
 6UK  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 6UK  CONST_16  C18  C19  C14  C15     0.00   0.0  0
 6UK  CONST_17  C    C14  C19  C18   180.00   0.0  0
 6UK  CONST_19  N    C3   N1   C       0.00   0.0  0
 6UK  CONST_20  N    C2   C1   C       0.00   0.0  0
 6UK  CONST_21  C16  C15  C14  C     180.00   0.0  0
 6UK  CONST_23  C17  C16  C15  C14     0.00   0.0  0
 6UK  CONST_24  C17  C18  C19  C14     0.00   0.0  0
 6UK  CONST_25  C16  C15  C14  C19     0.00   0.0  0
 6UK  CONST_26  C16  C17  C18  C19     0.00   0.0  0
 6UK  CONST_27  C4   C3   N    C2    180.00   0.0  0
 6UK  CONST_28  C6   C7   C8   C9    180.00   0.0  0
 6UK  CONST_29  C13  C12  C11  C10   180.00   0.0  0
 6UK  CONST_30  C6   C7   C12  C11   180.00   0.0  0
 6UK  CONST_31  C8   C7   C12  C13   180.00   0.0  0
 6UK  CONST_32  N    C2   C1   N2    180.00   0.0  0
 6UK  CONST_33  N1   C    C1   N2    180.00   0.0  0
 6UK  CONST_34  C14  C    C1   N2      0.00   0.0  0
 6UK  CONST_35  C4   C3   N1   C     180.00   0.0  0
 6UK  CONST_36  H1   C2   N    C3    180.00   0.0  0
 6UK  CONST_37  H4   C11  C12  C7    180.00   0.0  0
 6UK  CONST_38  H2   C9   C8   C7    180.00   0.0  0
 6UK  CONST_39  H7   C8   C9   C10   180.00   0.0  0
 6UK  CONST_40  H3   C10  C11  C12   180.00   0.0  0
 6UK  CONST_41  H16  C17  C16  C15   180.00   0.0  0
 6UK  CONST_42  H15  C19  C14  C15   180.00   0.0  0
 6UK  CONST_43  H17  C16  C17  C18   180.00   0.0  0
 6UK  CONST_44  H5   C15  C14  C       0.00   0.0  0
 6UK  CONST_45  H6   C18  C19  C14   180.00   0.0  0
 6UK  CONST_49  C1   N2   C5   O       0.00   0.0  0
 6UK  CONST_50  C1   N2   C5   N3    180.00   0.0  0
 6UK  CONST_51  O    C5   N3   C6      0.00   0.0  0
 6UK  CONST_52  N2   C5   N3   C6    180.00   0.0  0
 6UK  CONST_53  H10  N3   C5   O     180.00   0.0  0
 6UK  Var_01    F    C13  C12  C7     60.96  30.0  3
 6UK  Var_02    N3   C6   C7   C12    84.29  30.0  2
 6UK  Var_03    H12  C4   C3   N1    115.11  30.0  2
 6UK  Var_04    C7   C6   N3   C5   -135.21  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
 6UK  plan-1  C7   0.020
 6UK  plan-1  C9   0.020
 6UK  plan-1  C10  0.020
 6UK  plan-1  C11  0.020
 6UK  plan-1  C12  0.020
 6UK  plan-1  C13  0.020
 6UK  plan-1  C8   0.020
 6UK  plan-1  C6   0.020
 6UK  plan-1  H2   0.020
 6UK  plan-1  H3   0.020
 6UK  plan-1  H4   0.020
 6UK  plan-1  H7   0.020
 6UK  plan-2  C15  0.020
 6UK  plan-2  C18  0.020
 6UK  plan-2  C    0.020
 6UK  plan-2  C14  0.020
 6UK  plan-2  C19  0.020
 6UK  plan-2  C17  0.020
 6UK  plan-2  C16  0.020
 6UK  plan-2  H5   0.020
 6UK  plan-2  H6   0.020
 6UK  plan-2  H15  0.020
 6UK  plan-2  H16  0.020
 6UK  plan-2  H17  0.020
 6UK  plan-3  C2   0.020
 6UK  plan-3  C3   0.020
 6UK  plan-3  N2   0.020
 6UK  plan-3  C1   0.020
 6UK  plan-3  C    0.020
 6UK  plan-3  N1   0.020
 6UK  plan-3  C4   0.020
 6UK  plan-3  N    0.020
 6UK  plan-3  C14  0.020
 6UK  plan-3  H1   0.020
 6UK  plan-4  C5   0.020
 6UK  plan-4  C6   0.020
 6UK  plan-4  N3   0.020
 6UK  plan-4  O    0.020
 6UK  plan-4  N2   0.020
 6UK  plan-4  C1   0.020
 6UK  plan-4  H10  0.020
 6UK  plan-4  H11  0.020

