# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 11:24:05 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(NC(=O)Nc2cccc3ccccc23)c(n1)c4ccccc4
#
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
 6UJ  6UJ  1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea  ligand  45  27  .  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_6UJ
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
 6UJ  C2   C  CR16  0  -0.046  -2.0802   2.1105   1.1021
 6UJ  C3   C  CR6   0   0.222  -1.9798   0.8249   0.5794
 6UJ  C5   C  CR6   0   0.313   2.6854   0.1198  -0.5842
 6UJ  C7   C  CR16  0  -0.264   4.1154   0.9363  -2.3489
 6UJ  C9   C  CR66  0   0.098   5.1178   0.1023  -0.3207
 6UJ  C10  C  CR16  0  -0.311   6.2621  -0.1917   0.4581
 6UJ  C11  C  CR16  0  -0.256   6.1407  -0.7019   1.7209
 6UJ  C12  C  CR16  0  -0.250   4.8621  -0.9317   2.2671
 6UJ  C13  C  CR16  0  -0.306   3.7358  -0.6621   1.5376
 6UJ  C15  C  CR6   0   0.222  -3.1768   0.2307   0.1757
 6UJ  C18  C  CR16  0  -0.235  -2.4974  -2.8270  -1.9368
 6UJ  C20  C  CR16  0  -0.241  -4.3420  -3.2848  -0.4672
 6UJ  C21  C  CR16  0  -0.280  -4.2390  -2.0076   0.0620
 6UJ  O    O  O     0  -0.490   0.4239   1.8256  -0.4464
 6UJ  C4   C  C     0   0.700   0.3696   0.6825  -0.0337
 6UJ  N2   N  NH1   0  -0.792   1.4135  -0.1951  -0.0765
 6UJ  C14  C  CR66  0   0.073   3.8291  -0.1522   0.2203
 6UJ  C8   C  CR16  0  -0.323   5.2343   0.6585  -1.6148
 6UJ  C6   C  CR16  0  -0.294   2.8348   0.6505  -1.8399
 6UJ  N1   N  NH1   0  -0.785  -0.7615   0.1456   0.5287
 6UJ  N    N  N     0  -0.406  -3.2303   2.7505   1.2028
 6UJ  N3   N  N     0  -0.422  -4.3341   0.8715   0.3257
 6UJ  C1   C  CR6   0   0.337  -4.3265   2.1005   0.8163
 6UJ  C    C  CH3   0  -0.732  -5.6307   2.8210   0.9365
 6UJ  C16  C  CR6   0   0.030  -3.2502  -1.1339  -0.3897
 6UJ  C19  C  CR16  0  -0.257  -3.4716  -3.6979  -1.4679
 6UJ  C17  C  CR16  0  -0.296  -2.3819  -1.5539  -1.3976
 6UJ  H1   H  HCR6  0   0.283  -1.1984   2.6264   1.4623
 6UJ  H2   H  HCR6  0   0.262   4.2048   1.3622  -3.3396
 6UJ  H3   H  HCR6  0   0.259   7.2413  -0.0010   0.0361
 6UJ  H4   H  HCR6  0   0.260   7.0236  -0.9217   2.3066
 6UJ  H5   H  HCR6  0   0.261   4.7703  -1.3188   3.2735
 6UJ  H6   H  HCR6  0   0.246   2.7666  -0.8327   1.9870
 6UJ  H7   H  HCR6  0   0.263  -1.8258  -3.1360  -2.7269
 6UJ  H8   H  HCR6  0   0.262  -5.1044  -3.9579  -0.0978
 6UJ  H9   H  HCR6  0   0.258  -4.9236  -1.6876   0.8368
 6UJ  H10  H  HNH1  0   0.410   1.3089  -1.0939   0.3691
 6UJ  H11  H  HCR6  0   0.258   6.2203   0.8607  -2.0144
 6UJ  H12  H  HCR6  0   0.267   1.9662   0.8354  -2.4563
 6UJ  H13  H  HNH1  0   0.412  -0.7881  -0.8452   0.7198
 6UJ  H14  H  HCH3  0   0.260  -5.7133   3.5849   0.1606
 6UJ  H15  H  HCH3  0   0.250  -6.4687   2.1369   0.8283
 6UJ  H16  H  HCH3  0   0.254  -5.7046   3.3297   1.8970
 6UJ  H17  H  HCR6  0   0.263  -3.5554  -4.6937  -1.8831
 6UJ  H18  H  HCR6  0   0.265  -1.6316  -0.8809  -1.7919

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
 6UJ  C7   C6   aromatic  1.407  0.020  1.407
 6UJ  C7   C8   aromatic  1.367  0.020  1.367
 6UJ  O    C4   double    1.217  0.020  1.217
 6UJ  C6   C5   aromatic  1.371  0.020  1.371
 6UJ  C    C1   single    1.495  0.020  1.495
 6UJ  N    C1   aromatic  1.332  0.020  1.332
 6UJ  N    C2   aromatic  1.320  0.020  1.320
 6UJ  C1   N3   aromatic  1.323  0.020  1.323
 6UJ  C4   N2   single    1.365  0.020  1.365
 6UJ  C4   N1   single    1.373  0.020  1.373
 6UJ  C8   C9   aromatic  1.413  0.020  1.413
 6UJ  N2   C5   single    1.405  0.020  1.405
 6UJ  C2   C3   aromatic  1.391  0.020  1.391
 6UJ  N3   C15  aromatic  1.331  0.020  1.331
 6UJ  C5   C14  aromatic  1.425  0.020  1.425
 6UJ  C17  C18  aromatic  1.387  0.020  1.387
 6UJ  C17  C16  aromatic  1.395  0.020  1.395
 6UJ  C3   C15  aromatic  1.396  0.020  1.396
 6UJ  C3   N1   single    1.396  0.020  1.396
 6UJ  C15  C16  single    1.479  0.020  1.479
 6UJ  C18  C19  aromatic  1.388  0.020  1.388
 6UJ  C9   C14  aromatic  1.421  0.020  1.421
 6UJ  C9   C10  aromatic  1.415  0.020  1.415
 6UJ  C16  C21  aromatic  1.395  0.020  1.395
 6UJ  C14  C13  aromatic  1.416  0.020  1.416
 6UJ  C10  C11  aromatic  1.367  0.020  1.367
 6UJ  C19  C20  aromatic  1.389  0.020  1.389
 6UJ  C21  C20  aromatic  1.386  0.020  1.386
 6UJ  C13  C12  aromatic  1.369  0.020  1.369
 6UJ  C11  C12  aromatic  1.409  0.020  1.409
 6UJ  C2   H1   single    0.930  0.020  1.080
 6UJ  C7   H2   single    0.930  0.020  1.080
 6UJ  C10  H3   single    0.930  0.020  1.080
 6UJ  C11  H4   single    0.930  0.020  1.080
 6UJ  C12  H5   single    0.930  0.020  1.080
 6UJ  C13  H6   single    0.930  0.020  1.080
 6UJ  C18  H7   single    0.930  0.020  1.080
 6UJ  C20  H8   single    0.930  0.020  1.080
 6UJ  C21  H9   single    0.930  0.020  1.080
 6UJ  N2   H10  single    0.860  0.020  1.020
 6UJ  C8   H11  single    0.930  0.020  1.080
 6UJ  C6   H12  single    0.930  0.020  1.080
 6UJ  N1   H13  single    0.860  0.020  1.020
 6UJ  C    H14  single    0.970  0.020  1.090
 6UJ  C    H15  single    0.970  0.020  1.090
 6UJ  C    H16  single    0.970  0.020  1.090
 6UJ  C19  H17  single    0.930  0.020  1.080
 6UJ  C17  H18  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
 6UJ  H1   C2   N    116.94  3.000
 6UJ  H1   C2   C3   120.41  3.000
 6UJ  N    C2   C3   122.64  3.000
 6UJ  N1   C3   C15  122.06  3.000
 6UJ  N1   C3   C2   121.75  3.000
 6UJ  C15  C3   C2   116.11  3.000
 6UJ  C6   C5   C14  120.24  3.000
 6UJ  C14  C5   N2   118.67  3.000
 6UJ  C6   C5   N2   121.07  3.000
 6UJ  H2   C7   C6   119.10  3.000
 6UJ  H2   C7   C8   120.27  3.000
 6UJ  C6   C7   C8   120.62  3.000
 6UJ  C8   C9   C14  119.60  3.000
 6UJ  C14  C9   C10  119.12  3.000
 6UJ  C8   C9   C10  121.27  3.000
 6UJ  H3   C10  C11  120.38  3.000
 6UJ  H3   C10  C9   118.68  3.000
 6UJ  C11  C10  C9   120.94  3.000
 6UJ  H4   C11  C12  119.83  3.000
 6UJ  H4   C11  C10  120.21  3.000
 6UJ  C12  C11  C10  119.95  3.000
 6UJ  H5   C12  C13  119.76  3.000
 6UJ  H5   C12  C11  119.71  3.000
 6UJ  C13  C12  C11  120.53  3.000
 6UJ  H6   C13  C14  120.16  3.000
 6UJ  H6   C13  C12  118.99  3.000
 6UJ  C14  C13  C12  120.84  3.000
 6UJ  C16  C15  N3   116.36  3.000
 6UJ  C16  C15  C3   123.08  3.000
 6UJ  N3   C15  C3   120.52  3.000
 6UJ  H7   C18  C17  119.61  3.000
 6UJ  H7   C18  C19  120.20  3.000
 6UJ  C17  C18  C19  120.19  3.000
 6UJ  H8   C20  C19  120.16  3.000
 6UJ  H8   C20  C21  119.68  3.000
 6UJ  C19  C20  C21  120.16  3.000
 6UJ  H9   C21  C16  119.68  3.000
 6UJ  H9   C21  C20  119.91  3.000
 6UJ  C16  C21  C20  120.41  3.000
 6UJ  N1   C4   N2   113.06  3.000
 6UJ  N1   C4   O    122.91  3.000
 6UJ  N2   C4   O    124.03  3.000
 6UJ  H10  N2   C4   118.68  3.000
 6UJ  H10  N2   C5   116.95  3.000
 6UJ  C4   N2   C5   124.03  3.000
 6UJ  C13  C14  C9   118.60  3.000
 6UJ  C13  C14  C5   122.78  3.000
 6UJ  C9   C14  C5   118.62  3.000
 6UJ  H11  C8   C9   119.10  3.000
 6UJ  H11  C8   C7   120.61  3.000
 6UJ  C9   C8   C7   120.29  3.000
 6UJ  H12  C6   C7   119.35  3.000
 6UJ  H12  C6   C5   120.05  3.000
 6UJ  C7   C6   C5   120.59  3.000
 6UJ  H13  N1   C4   118.90  3.000
 6UJ  H13  N1   C3   116.60  3.000
 6UJ  C4   N1   C3   122.94  3.000
 6UJ  C1   N    C2   117.29  3.000
 6UJ  C1   N3   C15  118.93  3.000
 6UJ  C    C1   N3   118.19  3.000
 6UJ  N3   C1   N    124.45  3.000
 6UJ  C    C1   N    117.36  3.000
 6UJ  H16  C    H15  109.23  3.000
 6UJ  H16  C    H14  107.14  3.000
 6UJ  H15  C    H14  108.13  3.000
 6UJ  H16  C    C1   110.80  3.000
 6UJ  H15  C    C1   111.17  3.000
 6UJ  H14  C    C1   110.25  3.000
 6UJ  C17  C16  C21  119.13  3.000
 6UJ  C21  C16  C15  119.30  3.000
 6UJ  C17  C16  C15  121.53  3.000
 6UJ  H17  C19  C20  120.10  3.000
 6UJ  H17  C19  C18  120.14  3.000
 6UJ  C20  C19  C18  119.76  3.000
 6UJ  H18  C17  C16  120.50  3.000
 6UJ  H18  C17  C18  119.12  3.000
 6UJ  C16  C17  C18  120.34  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
 6UJ  CONST_01  N3   C1   N    C2     0.00   0.0  0
 6UJ  CONST_02  N3   C15  C3   C2     0.00   0.0  0
 6UJ  CONST_03  C16  C15  C3   C2   180.00   0.0  0
 6UJ  CONST_04  C1   N    C2   C3     0.00   0.0  0
 6UJ  CONST_05  C1   N3   C15  C3     0.00   0.0  0
 6UJ  CONST_08  C8   C7   C6   C5     0.00   0.0  0
 6UJ  CONST_09  C8   C9   C14  C5     0.00   0.0  0
 6UJ  CONST_10  C10  C9   C14  C5   180.00   0.0  0
 6UJ  CONST_11  C12  C13  C14  C5   180.00   0.0  0
 6UJ  CONST_12  C14  C5   C6   C7     0.00   0.0  0
 6UJ  CONST_13  C14  C9   C8   C7     0.00   0.0  0
 6UJ  CONST_14  C10  C9   C8   C7   180.00   0.0  0
 6UJ  CONST_15  C6   C7   C8   C9     0.00   0.0  0
 6UJ  CONST_16  C6   C5   C14  C9     0.00   0.0  0
 6UJ  CONST_17  C12  C13  C14  C9     0.00   0.0  0
 6UJ  CONST_18  C12  C11  C10  C9     0.00   0.0  0
 6UJ  CONST_19  C13  C14  C9   C10    0.00   0.0  0
 6UJ  CONST_20  C13  C12  C11  C10    0.00   0.0  0
 6UJ  CONST_21  C8   C9   C10  C11  180.00   0.0  0
 6UJ  CONST_22  C14  C9   C10  C11    0.00   0.0  0
 6UJ  CONST_23  C14  C13  C12  C11    0.00   0.0  0
 6UJ  CONST_24  C6   C5   C14  C13  180.00   0.0  0
 6UJ  CONST_25  C8   C9   C14  C13  180.00   0.0  0
 6UJ  CONST_26  N    C1   N3   C15    0.00   0.0  0
 6UJ  CONST_27  N    C2   C3   C15    0.00   0.0  0
 6UJ  CONST_28  C18  C17  C16  C15  180.00   0.0  0
 6UJ  CONST_29  C20  C21  C16  C15  180.00   0.0  0
 6UJ  CONST_30  C21  C16  C17  C18    0.00   0.0  0
 6UJ  CONST_31  C21  C20  C19  C18    0.00   0.0  0
 6UJ  CONST_32  C17  C18  C19  C20    0.00   0.0  0
 6UJ  CONST_33  C17  C16  C21  C20    0.00   0.0  0
 6UJ  CONST_36  C16  C15  N3   C1   180.00   0.0  0
 6UJ  CONST_37  C19  C18  C17  C16    0.00   0.0  0
 6UJ  CONST_38  C19  C20  C21  C16    0.00   0.0  0
 6UJ  CONST_39  C    C1   N    C2   180.00   0.0  0
 6UJ  CONST_40  N2   C5   C6   C7   180.00   0.0  0
 6UJ  CONST_41  N2   C5   C14  C9   180.00   0.0  0
 6UJ  CONST_42  N2   C5   C14  C13    0.00   0.0  0
 6UJ  CONST_43  C    C1   N3   C15  180.00   0.0  0
 6UJ  CONST_44  N    C2   C3   N1   180.00   0.0  0
 6UJ  CONST_45  N3   C15  C3   N1   180.00   0.0  0
 6UJ  CONST_46  C16  C15  C3   N1     0.00   0.0  0
 6UJ  CONST_47  H2   C7   C6   C5   180.00   0.0  0
 6UJ  CONST_48  H6   C13  C14  C5     0.00   0.0  0
 6UJ  CONST_49  H4   C11  C10  C9   180.00   0.0  0
 6UJ  CONST_50  H11  C8   C9   C10    0.00   0.0  0
 6UJ  CONST_51  H5   C12  C11  C10  180.00   0.0  0
 6UJ  CONST_52  H3   C10  C11  C12  180.00   0.0  0
 6UJ  CONST_53  H1   C2   C3   C15  180.00   0.0  0
 6UJ  CONST_54  H18  C17  C16  C15    0.00   0.0  0
 6UJ  CONST_55  H9   C21  C16  C15    0.00   0.0  0
 6UJ  CONST_56  H8   C20  C19  C18  180.00   0.0  0
 6UJ  CONST_57  H7   C18  C19  C20  180.00   0.0  0
 6UJ  CONST_58  H17  C19  C20  C21  180.00   0.0  0
 6UJ  CONST_59  H12  C6   C5   C14  180.00   0.0  0
 6UJ  CONST_66  O    C4   N1   C3     0.00   0.0  0
 6UJ  CONST_67  O    C4   N2   C5     0.00   0.0  0
 6UJ  CONST_68  N2   C4   N1   C3   180.00   0.0  0
 6UJ  CONST_69  N1   C4   N2   C5   180.00   0.0  0
 6UJ  Var_01    H14  C    C1   N     73.83  30.0  2

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
 6UJ  plan-1  C2   0.020
 6UJ  plan-1  C3   0.020
 6UJ  plan-1  C15  0.020
 6UJ  plan-1  N1   0.020
 6UJ  plan-1  N    0.020
 6UJ  plan-1  N3   0.020
 6UJ  plan-1  C1   0.020
 6UJ  plan-1  C    0.020
 6UJ  plan-1  C16  0.020
 6UJ  plan-1  H1   0.020
 6UJ  plan-2  C15  0.020
 6UJ  plan-2  C18  0.020
 6UJ  plan-2  C20  0.020
 6UJ  plan-2  C21  0.020
 6UJ  plan-2  C16  0.020
 6UJ  plan-2  C19  0.020
 6UJ  plan-2  C17  0.020
 6UJ  plan-2  H7   0.020
 6UJ  plan-2  H8   0.020
 6UJ  plan-2  H9   0.020
 6UJ  plan-2  H17  0.020
 6UJ  plan-2  H18  0.020
 6UJ  plan-3  C5   0.020
 6UJ  plan-3  C7   0.020
 6UJ  plan-3  C9   0.020
 6UJ  plan-3  C10  0.020
 6UJ  plan-3  C11  0.020
 6UJ  plan-3  C12  0.020
 6UJ  plan-3  C13  0.020
 6UJ  plan-3  N2   0.020
 6UJ  plan-3  C14  0.020
 6UJ  plan-3  C8   0.020
 6UJ  plan-3  C6   0.020
 6UJ  plan-3  H2   0.020
 6UJ  plan-3  H3   0.020
 6UJ  plan-3  H4   0.020
 6UJ  plan-3  H5   0.020
 6UJ  plan-3  H6   0.020
 6UJ  plan-3  H11  0.020
 6UJ  plan-3  H12  0.020
 6UJ  plan-4  C3   0.020
 6UJ  plan-4  C5   0.020
 6UJ  plan-4  O    0.020
 6UJ  plan-4  C4   0.020
 6UJ  plan-4  N2   0.020
 6UJ  plan-4  N1   0.020
 6UJ  plan-4  H10  0.020
 6UJ  plan-4  H13  0.020

