# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 09:45:05 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(NC(=O)Nc2ccccn2)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
 6UM  6UM  1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea  ligand  38  23  .  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_6UM
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
 6UM  C2   C  CR16  0  -0.046  -1.0751   2.4553   0.5992
 6UM  C3   C  CR6   0   0.338  -3.2672   2.6027   0.0557
 6UM  N4   N  N     0  -0.424   3.9122   0.1168  -0.9661
 6UM  C5   C  C     0   0.710   1.2612   0.5476   0.1558
 6UM  C7   C  CR16  0  -0.065   5.1925   0.0204  -1.3144
 6UM  C9   C  CR16  0  -0.144   5.7399  -1.2311   0.6247
 6UM  C10  C  CR16  0  -0.400   4.4197  -1.1276   1.0101
 6UM  C11  C  CR6   0   0.033  -2.5145  -0.9255  -0.1921
 6UM  C12  C  CR16  0  -0.281  -3.6576  -1.5442   0.3137
 6UM  C13  C  CR16  0  -0.241  -3.8793  -2.8950   0.0950
 6UM  C15  C  CR16  0  -0.237  -1.8432  -3.0258  -1.1740
 6UM  O    O  O     0  -0.473   1.4697   1.4874  -0.5811
 6UM  N3   N  NH1   0  -0.770   2.2024  -0.3667   0.5603
 6UM  C6   C  CR6   0   0.518   3.5365  -0.4346   0.1740
 6UM  C8   C  CR16  0  -0.344   6.1490  -0.6393  -0.5657
 6UM  C1   C  CR6   0   0.220  -1.0955   1.0750   0.4246
 6UM  C    C  CR6   0   0.226  -2.3158   0.5225   0.0333
 6UM  N1   N  N     0  -0.423  -3.3888   1.2968  -0.1186
 6UM  C4   C  CH3   0  -0.732  -4.4724   3.4594  -0.1618
 6UM  N    N  N     0  -0.406  -2.1354   3.2151   0.4002
 6UM  C16  C  CR16  0  -0.294  -1.6103  -1.6781  -0.9418
 6UM  C14  C  CR16  0  -0.256  -2.9731  -3.6393  -0.6497
 6UM  H1   H  HCR6  0   0.284  -0.1693   2.9524   0.9262
 6UM  H3   H  HCR6  0   0.277   6.4451  -1.7619   1.2503
 6UM  H4   H  HCR6  0   0.280   4.0747  -1.5650   1.9380
 6UM  H5   H  HCR6  0   0.258  -4.3706  -0.9657   0.8865
 6UM  H6   H  HCR6  0   0.262  -4.7629  -3.3666   0.5042
 6UM  H7   H  HCR6  0   0.264  -1.1414  -3.5948  -1.7692
 6UM  H8   H  HNH1  0   0.419   1.9522  -0.9736   1.3261
 6UM  H9   H  HCR6  0   0.269   7.1747  -0.6903  -0.9020
 6UM  H11  H  HCH3  0   0.260  -4.3784   4.0121  -1.0986
 6UM  H12  H  HCH3  0   0.250  -5.3774   2.8591  -0.2115
 6UM  H13  H  HCH3  0   0.254  -4.5742   4.1944   0.6360
 6UM  H14  H  HCR6  0   0.265  -0.7364  -1.2106  -1.3757
 6UM  H15  H  HCR6  0   0.263  -3.1501  -4.6922  -0.8260
 6UM  N2   N  NH1   0  -0.790   0.0265   0.2894   0.6985
 6UM  H2   H  HCR6  0   0.263   5.4635   0.4917  -2.2526
 6UM  H10  H  HNH1  0   0.413  -0.1370  -0.5952   1.1567

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
 6UM  C8   C9   aromatic  1.391  0.020  1.391
 6UM  C8   C7   aromatic  1.382  0.020  1.382
 6UM  C9   C10  aromatic  1.379  0.020  1.379
 6UM  C7   N4   aromatic  1.330  0.020  1.330
 6UM  C10  C6   aromatic  1.400  0.020  1.400
 6UM  C14  C13  aromatic  1.389  0.020  1.389
 6UM  C14  C15  aromatic  1.388  0.020  1.388
 6UM  C13  C12  aromatic  1.386  0.020  1.386
 6UM  N4   C6   aromatic  1.321  0.020  1.321
 6UM  C6   N3   single    1.391  0.020  1.391
 6UM  C15  C16  aromatic  1.387  0.020  1.387
 6UM  C12  C11  aromatic  1.395  0.020  1.395
 6UM  N3   C5   single    1.373  0.020  1.373
 6UM  C16  C11  aromatic  1.395  0.020  1.395
 6UM  C11  C    single    1.479  0.020  1.479
 6UM  N2   C5   single    1.373  0.020  1.373
 6UM  N2   C1   single    1.397  0.020  1.397
 6UM  C5   O    double    1.212  0.020  1.212
 6UM  C    C1   aromatic  1.396  0.020  1.396
 6UM  C    N1   aromatic  1.332  0.020  1.332
 6UM  C1   C2   aromatic  1.391  0.020  1.391
 6UM  N1   C3   aromatic  1.323  0.020  1.323
 6UM  C2   N    aromatic  1.320  0.020  1.320
 6UM  C3   N    aromatic  1.332  0.020  1.332
 6UM  C3   C4   single    1.495  0.020  1.495
 6UM  C2   H1   single    0.930  0.020  1.080
 6UM  C7   H2   single    0.930  0.020  1.080
 6UM  C9   H3   single    0.930  0.020  1.080
 6UM  C10  H4   single    0.930  0.020  1.080
 6UM  C12  H5   single    0.930  0.020  1.080
 6UM  C13  H6   single    0.930  0.020  1.080
 6UM  C15  H7   single    0.930  0.020  1.080
 6UM  N3   H8   single    0.860  0.020  1.020
 6UM  C8   H9   single    0.930  0.020  1.080
 6UM  N2   H10  single    0.860  0.020  1.020
 6UM  C4   H11  single    0.970  0.020  1.090
 6UM  C4   H12  single    0.970  0.020  1.090
 6UM  C4   H13  single    0.970  0.020  1.090
 6UM  C16  H14  single    0.930  0.020  1.080
 6UM  C14  H15  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
 6UM  H1   C2   N    116.93  3.000
 6UM  H1   C2   C1   120.34  3.000
 6UM  N    C2   C1   122.72  3.000
 6UM  N    C3   C4   117.34  3.000
 6UM  C4   C3   N1   118.19  3.000
 6UM  N    C3   N1   124.46  3.000
 6UM  C6   N4   C7   118.00  3.000
 6UM  N2   C5   N3   112.00  3.000
 6UM  N2   C5   O    122.72  3.000
 6UM  N3   C5   O    125.27  3.000
 6UM  H2   C7   C8   120.21  3.000
 6UM  H2   C7   N4   115.82  3.000
 6UM  C8   C7   N4   123.97  3.000
 6UM  H3   C9   C8   120.79  3.000
 6UM  H3   C9   C10  119.94  3.000
 6UM  C8   C9   C10  119.26  3.000
 6UM  H4   C10  C6   120.74  3.000
 6UM  H4   C10  C9   120.96  3.000
 6UM  C6   C10  C9   118.30  3.000
 6UM  C16  C11  C    121.54  3.000
 6UM  C    C11  C12  119.29  3.000
 6UM  C16  C11  C12  119.13  3.000
 6UM  H5   C12  C13  119.93  3.000
 6UM  H5   C12  C11  119.66  3.000
 6UM  C13  C12  C11  120.41  3.000
 6UM  H6   C13  C14  120.13  3.000
 6UM  H6   C13  C12  119.72  3.000
 6UM  C14  C13  C12  120.16  3.000
 6UM  H7   C15  C14  120.21  3.000
 6UM  H7   C15  C16  119.61  3.000
 6UM  C14  C15  C16  120.18  3.000
 6UM  H8   N3   C6   114.80  3.000
 6UM  H8   N3   C5   117.02  3.000
 6UM  C6   N3   C5   127.46  3.000
 6UM  N3   C6   C10  117.61  3.000
 6UM  N3   C6   N4   119.49  3.000
 6UM  C10  C6   N4   122.87  3.000
 6UM  H9   C8   C9   121.70  3.000
 6UM  H9   C8   C7   120.71  3.000
 6UM  C9   C8   C7   117.59  3.000
 6UM  C    C1   N2   122.32  3.000
 6UM  C    C1   C2   116.15  3.000
 6UM  N2   C1   C2   121.44  3.000
 6UM  N1   C    C1   120.41  3.000
 6UM  N1   C    C11  116.33  3.000
 6UM  C1   C    C11  123.23  3.000
 6UM  C    N1   C3   119.00  3.000
 6UM  H13  C4   H12  109.17  3.000
 6UM  H13  C4   H11  107.14  3.000
 6UM  H12  C4   H11  108.18  3.000
 6UM  H13  C4   C3   110.82  3.000
 6UM  H12  C4   C3   111.19  3.000
 6UM  H11  C4   C3   110.21  3.000
 6UM  C3   N    C2   117.19  3.000
 6UM  H14  C16  C15  119.23  3.000
 6UM  H14  C16  C11  120.39  3.000
 6UM  C15  C16  C11  120.35  3.000
 6UM  H15  C14  C15  120.10  3.000
 6UM  H15  C14  C13  120.13  3.000
 6UM  C15  C14  C13  119.77  3.000
 6UM  H10  N2   C1   116.86  3.000
 6UM  H10  N2   C5   119.32  3.000
 6UM  C1   N2   C5   122.62  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
 6UM  CONST_01  C11  C    C1   C2    180.00   0.0  0
 6UM  CONST_02  N1   C    C1   C2      0.00   0.0  0
 6UM  CONST_03  N1   C3   N    C2      0.00   0.0  0
 6UM  CONST_04  C11  C    N1   C3    180.00   0.0  0
 6UM  CONST_05  C1   C    N1   C3      0.00   0.0  0
 6UM  CONST_06  C1   C2   N    C3      0.00   0.0  0
 6UM  CONST_07  C9   C8   C7   N4      0.00   0.0  0
 6UM  CONST_08  C9   C10  C6   N4      0.00   0.0  0
 6UM  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 6UM  CONST_10  C10  C6   N4   C7      0.00   0.0  0
 6UM  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 6UM  CONST_12  C14  C15  C16  C11     0.00   0.0  0
 6UM  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 6UM  CONST_14  C15  C16  C11  C12     0.00   0.0  0
 6UM  CONST_17  C16  C15  C14  C13     0.00   0.0  0
 6UM  CONST_18  C16  C11  C12  C13     0.00   0.0  0
 6UM  CONST_19  C    C11  C12  C13   180.00   0.0  0
 6UM  CONST_20  C    C11  C16  C15   180.00   0.0  0
 6UM  CONST_21  C8   C9   C10  C6      0.00   0.0  0
 6UM  CONST_22  C8   C7   N4   C6      0.00   0.0  0
 6UM  CONST_24  N    C2   C1   C       0.00   0.0  0
 6UM  CONST_25  N    C3   N1   C       0.00   0.0  0
 6UM  CONST_27  C4   C3   N    C2    180.00   0.0  0
 6UM  CONST_28  N3   C6   N4   C7    180.00   0.0  0
 6UM  CONST_29  N3   C6   C10  C9    180.00   0.0  0
 6UM  CONST_30  N2   C1   C    C11     0.00   0.0  0
 6UM  CONST_31  N1   C    C1   N2    180.00   0.0  0
 6UM  CONST_32  N    C2   C1   N2    180.00   0.0  0
 6UM  CONST_33  C4   C3   N1   C     180.00   0.0  0
 6UM  CONST_34  H1   C2   N    C3    180.00   0.0  0
 6UM  CONST_35  H9   C8   C7   N4    180.00   0.0  0
 6UM  CONST_36  H4   C10  C6   N4    180.00   0.0  0
 6UM  CONST_37  H3   C9   C8   C7    180.00   0.0  0
 6UM  CONST_38  H2   C7   C8   C9    180.00   0.0  0
 6UM  CONST_39  H6   C13  C12  C11   180.00   0.0  0
 6UM  CONST_40  H7   C15  C16  C11   180.00   0.0  0
 6UM  CONST_41  H15  C14  C13  C12   180.00   0.0  0
 6UM  CONST_42  H14  C16  C11  C12   180.00   0.0  0
 6UM  CONST_43  H5   C12  C11  C       0.00   0.0  0
 6UM  CONST_49  H8   N3   C6   N4    180.00   0.0  0
 6UM  CONST_50  C6   N3   C5   O       0.00   0.0  0
 6UM  CONST_51  C1   N2   C5   O       0.00   0.0  0
 6UM  CONST_52  C1   N2   C5   N3    180.00   0.0  0
 6UM  CONST_53  N2   C5   N3   C6    180.00   0.0  0
 6UM  Var_01    H11  C4   C3   N1   -106.24  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
 6UM  plan-1  N4   0.020
 6UM  plan-1  C7   0.020
 6UM  plan-1  C9   0.020
 6UM  plan-1  C10  0.020
 6UM  plan-1  N3   0.020
 6UM  plan-1  C6   0.020
 6UM  plan-1  C8   0.020
 6UM  plan-1  H3   0.020
 6UM  plan-1  H4   0.020
 6UM  plan-1  H9   0.020
 6UM  plan-1  H2   0.020
 6UM  plan-2  C2   0.020
 6UM  plan-2  C3   0.020
 6UM  plan-2  C11  0.020
 6UM  plan-2  C1   0.020
 6UM  plan-2  C    0.020
 6UM  plan-2  N1   0.020
 6UM  plan-2  C4   0.020
 6UM  plan-2  N    0.020
 6UM  plan-2  H1   0.020
 6UM  plan-2  N2   0.020
 6UM  plan-3  C11  0.020
 6UM  plan-3  C12  0.020
 6UM  plan-3  C13  0.020
 6UM  plan-3  C15  0.020
 6UM  plan-3  C    0.020
 6UM  plan-3  C16  0.020
 6UM  plan-3  C14  0.020
 6UM  plan-3  H5   0.020
 6UM  plan-3  H6   0.020
 6UM  plan-3  H7   0.020
 6UM  plan-3  H14  0.020
 6UM  plan-3  H15  0.020
 6UM  plan-4  C5   0.020
 6UM  plan-4  O    0.020
 6UM  plan-4  N3   0.020
 6UM  plan-4  C6   0.020
 6UM  plan-4  C1   0.020
 6UM  plan-4  H8   0.020
 6UM  plan-4  N2   0.020
 6UM  plan-4  H10  0.020

