# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:13:28 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 4,6-dimethyl-~{N}-phenyl-pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(Nc2ccccc2)n1
#
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
 MUK  MUK  4,6-dimethyl-~{N}-phenyl-pyrimidin-2-amine  ligand  28  15  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MUK
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
 MUK  N1   N  N     0  -0.489  -13.8947  -13.5703  91.2041
 MUK  N3   N  NH1   0  -0.771  -11.6825  -13.5866  91.6810
 MUK  C4   C  CR6   0   0.295  -14.9850  -12.9262  90.8259
 MUK  C5   C  CR6   0   0.582  -12.7645  -12.8554  91.2885
 MUK  C6   C  CR6   0   0.361  -10.3503  -13.2407  91.8730
 MUK  C7   C  CR16  0  -0.319   -9.8125  -11.9658  91.6746
 MUK  C8   C  CR16  0  -0.245   -8.4584  -11.7459  91.8958
 MUK  C10  C  CR16  0  -0.245   -8.1507  -14.0331  92.5096
 MUK  C1   C  CH3   0  -0.721  -13.5903   -9.4533  90.3680
 MUK  C2   C  CR6   0   0.319  -13.7400  -10.9125  90.6512
 MUK  C3   C  CR16  0  -0.421  -14.9544  -11.5620  90.5317
 MUK  N2   N  N     0  -0.487  -12.6390  -11.5640  91.0320
 MUK  C9   C  CR16  0  -0.279   -7.6161  -12.7655  92.3120
 MUK  C11  C  CR16  0  -0.354   -9.4964  -14.2694  92.2943
 MUK  C12  C  CH3   0  -0.736  -16.2551  -13.7063  90.7113
 MUK  H1   H  HNH1  0   0.405  -11.9059  -14.5551  91.8547
 MUK  H2   H  HCR6  0   0.285  -10.4433  -11.1540  91.3521
 MUK  H3   H  HCR6  0   0.254   -8.0633  -10.7505  91.7352
 MUK  H4   H  HCR6  0   0.256   -7.5174  -14.8492  92.8335
 MUK  H5   H  HCH3  0   0.258  -13.2477   -8.9273  91.2602
 MUK  H6   H  HCH3  0   0.257  -12.8411   -9.2914  89.5921
 MUK  H7   H  HCH3  0   0.248  -14.5278   -9.0064  90.0439
 MUK  H8   H  HCR6  0   0.262  -15.8473  -11.0366  90.2226
 MUK  H9   H  HCR6  0   0.251   -6.5637  -12.5790  92.4794
 MUK  H10  H  HCR6  0   0.265   -9.8957  -15.2647  92.4535
 MUK  H11  H  HCH3  0   0.253  -16.1261  -14.7220  91.0777
 MUK  H12  H  HCH3  0   0.257  -17.0576  -13.2272  91.2725
 MUK  H13  H  HCH3  0   0.260  -16.5779  -13.7522  89.6698

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
 MUK  C1   C2   single    1.494  0.020  1.494
 MUK  C2   C3   aromatic  1.382  0.020  1.382
 MUK  C2   N2   aromatic  1.335  0.020  1.335
 MUK  C3   C4   aromatic  1.396  0.020  1.396
 MUK  N2   C5   aromatic  1.323  0.020  1.323
 MUK  C4   C12  single    1.495  0.020  1.495
 MUK  C4   N1   aromatic  1.322  0.020  1.322
 MUK  C5   N1   aromatic  1.340  0.020  1.340
 MUK  C5   N3   single    1.364  0.020  1.364
 MUK  N3   C6   single    1.390  0.020  1.390
 MUK  C6   C11  aromatic  1.402  0.020  1.402
 MUK  C6   C7   aromatic  1.398  0.020  1.398
 MUK  C11  C10  aromatic  1.383  0.020  1.383
 MUK  C7   C8   aromatic  1.390  0.020  1.390
 MUK  C10  C9   aromatic  1.390  0.020  1.390
 MUK  C8   C9   aromatic  1.386  0.020  1.386
 MUK  N3   H1   single    0.860  0.020  1.020
 MUK  C7   H2   single    0.930  0.020  1.080
 MUK  C8   H3   single    0.930  0.020  1.080
 MUK  C10  H4   single    0.930  0.020  1.080
 MUK  C1   H5   single    0.970  0.020  1.090
 MUK  C1   H6   single    0.970  0.020  1.090
 MUK  C1   H7   single    0.970  0.020  1.090
 MUK  C3   H8   single    0.930  0.020  1.080
 MUK  C9   H9   single    0.930  0.020  1.080
 MUK  C11  H10  single    0.930  0.020  1.080
 MUK  C12  H11  single    0.970  0.020  1.090
 MUK  C12  H12  single    0.970  0.020  1.090
 MUK  C12  H13  single    0.970  0.020  1.090

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
 MUK  C5   N1   C4   116.99  3.000
 MUK  H1   N3   C6   115.30  3.000
 MUK  H1   N3   C5   112.87  3.000
 MUK  C6   N3   C5   131.83  3.000
 MUK  C12  C4   C3   120.83  3.000
 MUK  C12  C4   N1   117.94  3.000
 MUK  C3   C4   N1   121.23  3.000
 MUK  N2   C5   N3   120.27  3.000
 MUK  N3   C5   N1   113.66  3.000
 MUK  N2   C5   N1   126.07  3.000
 MUK  C11  C6   C7   118.53  3.000
 MUK  C7   C6   N3   125.18  3.000
 MUK  C11  C6   N3   116.29  3.000
 MUK  H2   C7   C8   119.93  3.000
 MUK  H2   C7   C6   120.29  3.000
 MUK  C8   C7   C6   119.78  3.000
 MUK  H3   C8   C9   119.92  3.000
 MUK  H3   C8   C7   118.52  3.000
 MUK  C9   C8   C7   121.56  3.000
 MUK  H4   C10  C11  119.14  3.000
 MUK  H4   C10  C9   120.33  3.000
 MUK  C11  C10  C9   120.53  3.000
 MUK  H7   C1   H6   108.61  3.000
 MUK  H7   C1   H5   108.43  3.000
 MUK  H6   C1   H5   107.13  3.000
 MUK  H7   C1   C2   111.80  3.000
 MUK  H6   C1   C2   110.40  3.000
 MUK  H5   C1   C2   110.33  3.000
 MUK  N2   C2   C3   121.33  3.000
 MUK  N2   C2   C1   116.63  3.000
 MUK  C3   C2   C1   122.04  3.000
 MUK  H8   C3   C2   121.46  3.000
 MUK  H8   C3   C4   121.13  3.000
 MUK  C2   C3   C4   117.40  3.000
 MUK  C2   N2   C5   116.98  3.000
 MUK  H9   C9   C10  120.62  3.000
 MUK  H9   C9   C8   120.71  3.000
 MUK  C10  C9   C8   118.66  3.000
 MUK  H10  C11  C10  119.49  3.000
 MUK  H10  C11  C6   119.57  3.000
 MUK  C10  C11  C6   120.94  3.000
 MUK  H13  C12  H12  106.98  3.000
 MUK  H13  C12  H11  108.51  3.000
 MUK  H12  C12  H11  108.93  3.000
 MUK  H13  C12  C4   110.27  3.000
 MUK  H12  C12  C4   110.89  3.000
 MUK  H11  C12  C4   111.15  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
 MUK  CONST_01  C2   C3   C4   N1    0.00   0.0  0
 MUK  CONST_02  C2   N2   C5   N1    0.00   0.0  0
 MUK  CONST_03  N2   C2   C3   C4    0.00   0.0  0
 MUK  CONST_04  N2   C5   N1   C4    0.00   0.0  0
 MUK  CONST_05  C3   C2   N2   C5    0.00   0.0  0
 MUK  CONST_06  C3   C4   N1   C5    0.00   0.0  0
 MUK  CONST_07  C9   C10  C11  C6    0.00   0.0  0
 MUK  CONST_08  C9   C8   C7   C6    0.00   0.0  0
 MUK  CONST_09  C10  C11  C6   C7    0.00   0.0  0
 MUK  CONST_10  C10  C9   C8   C7    0.00   0.0  0
 MUK  CONST_11  C11  C6   C7   C8    0.00   0.0  0
 MUK  CONST_12  C11  C10  C9   C8    0.00   0.0  0
 MUK  CONST_13  C2   N2   C5   N3  180.00   0.0  0
 MUK  CONST_14  C4   N1   C5   N3  180.00   0.0  0
 MUK  CONST_15  C10  C11  C6   N3  180.00   0.0  0
 MUK  CONST_16  C8   C7   C6   N3  180.00   0.0  0
 MUK  CONST_17  C1   C2   C3   C4  180.00   0.0  0
 MUK  CONST_18  C1   C2   N2   C5  180.00   0.0  0
 MUK  CONST_19  C12  C4   N1   C5  180.00   0.0  0
 MUK  CONST_20  C12  C4   C3   C2  180.00   0.0  0
 MUK  CONST_21  H8   C3   C4   N1  180.00   0.0  0
 MUK  CONST_22  H4   C10  C11  C6  180.00   0.0  0
 MUK  CONST_23  H3   C8   C7   C6  180.00   0.0  0
 MUK  CONST_24  H10  C11  C6   C7  180.00   0.0  0
 MUK  CONST_25  H9   C9   C8   C7  180.00   0.0  0
 MUK  CONST_26  H2   C7   C8   C9  180.00   0.0  0
 MUK  Var_01    C6   N3   C5   N1  179.11  30.0  2
 MUK  Var_02    C11  C6   N3   C5  179.74  30.0  2
 MUK  Var_03    H11  C12  C4   N1    6.58  30.0  2
 MUK  Var_04    H5   C1   C2   C3  119.29  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
 MUK  plan-1  N3   0.020
 MUK  plan-1  C6   0.020
 MUK  plan-1  C7   0.020
 MUK  plan-1  C8   0.020
 MUK  plan-1  C10  0.020
 MUK  plan-1  C9   0.020
 MUK  plan-1  C11  0.020
 MUK  plan-1  H2   0.020
 MUK  plan-1  H3   0.020
 MUK  plan-1  H4   0.020
 MUK  plan-1  H9   0.020
 MUK  plan-1  H10  0.020
 MUK  plan-2  N1   0.020
 MUK  plan-2  N3   0.020
 MUK  plan-2  C4   0.020
 MUK  plan-2  C5   0.020
 MUK  plan-2  C1   0.020
 MUK  plan-2  C2   0.020
 MUK  plan-2  C3   0.020
 MUK  plan-2  N2   0.020
 MUK  plan-2  C12  0.020
 MUK  plan-2  H8   0.020

