# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:30:39 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 4-methoxy-N-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nccc(OC)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
 K2J  K2J  4-methoxy-N-methylpyrimidin-2-amine  ligand  19  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K2J
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
 K2J  N1  N  N     0  -0.484  -1.3530  -1.0965  -0.0167
 K2J  C4  C  CR6   0   0.558   1.2261  -0.2447  -0.0034
 K2J  C5  C  CH3   0  -0.394   2.7605   1.5464  -0.0055
 K2J  N   N  NH1   0  -0.635  -1.9649   1.1116  -0.0404
 K2J  C   C  CH3   0  -0.481  -3.3683   0.7973  -0.0420
 K2J  O   O  O2    0  -0.461   2.4923   0.1509   0.0014
 K2J  C1  C  CR6   0   0.597  -0.9926   0.1856  -0.0250
 K2J  C2  C  CR16  0   0.001  -0.3523  -1.9743   0.0004
 K2J  C3  C  CR16  0  -0.433   0.9762  -1.6253   0.0086
 K2J  N2  N  N     0  -0.504   0.2679   0.6479  -0.0195
 K2J  H1  H  HCH3  0   0.225   2.3556   2.0321  -0.8935
 K2J  H2  H  HCH3  0   0.226   2.3558   2.0410   0.8777
 K2J  H3  H  HCH3  0   0.233   3.8430   1.6395  -0.0063
 K2J  H4  H  HNH1  0   0.376  -1.6779   2.0732  -0.0381
 K2J  H5  H  HCH3  0   0.226  -3.6612   0.2314  -0.9274
 K2J  H6  H  HCH3  0   0.226  -3.6604   0.2209   0.8368
 K2J  H7  H  HCH3  0   0.233  -3.9250   1.7303  -0.0366
 K2J  H8  H  HCR6  0   0.245  -0.6356  -3.0213   0.0091
 K2J  H9  H  HCR6  0   0.246   1.7685  -2.3572   0.0249

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
 K2J  O   C5  single    1.421  0.020  1.421
 K2J  O   C4  single    1.327  0.020  1.327
 K2J  N2  C4  aromatic  1.310  0.020  1.310
 K2J  N2  C1  aromatic  1.343  0.020  1.343
 K2J  N   C1  single    1.343  0.020  1.343
 K2J  N   C   single    1.438  0.020  1.438
 K2J  C4  C3  aromatic  1.403  0.020  1.403
 K2J  C1  N1  aromatic  1.332  0.020  1.332
 K2J  C3  C2  aromatic  1.374  0.020  1.374
 K2J  N1  C2  aromatic  1.331  0.020  1.331
 K2J  C5  H1  single    0.970  0.020  1.090
 K2J  C5  H2  single    0.970  0.020  1.090
 K2J  C5  H3  single    0.970  0.020  1.090
 K2J  N   H4  single    0.860  0.020  1.020
 K2J  C   H5  single    0.970  0.020  1.090
 K2J  C   H6  single    0.970  0.020  1.090
 K2J  C   H7  single    0.970  0.020  1.090
 K2J  C2  H8  single    0.930  0.020  1.080
 K2J  C3  H9  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
 K2J  C2  N1  C1  115.56  3.000
 K2J  N2  C4  C3  122.72  3.000
 K2J  C3  C4  O   117.60  3.000
 K2J  N2  C4  O   119.68  3.000
 K2J  H3  C5  H2  109.37  3.000
 K2J  H3  C5  H1  109.35  3.000
 K2J  H2  C5  H1  108.66  3.000
 K2J  H3  C5  O   105.79  3.000
 K2J  H2  C5  O   111.81  3.000
 K2J  H1  C5  O   111.80  3.000
 K2J  H4  N   C1  116.99  3.000
 K2J  H4  N   C   119.24  3.000
 K2J  C1  N   C   123.77  3.000
 K2J  H7  C   H6  108.21  3.000
 K2J  H7  C   H5  108.18  3.000
 K2J  H6  C   H5  107.93  3.000
 K2J  H7  C   N   108.20  3.000
 K2J  H6  C   N   112.08  3.000
 K2J  H5  C   N   112.11  3.000
 K2J  C5  O   C4  118.23  3.000
 K2J  N2  C1  N   116.26  3.000
 K2J  N   C1  N1  117.91  3.000
 K2J  N2  C1  N1  125.83  3.000
 K2J  H8  C2  C3  119.86  3.000
 K2J  H8  C2  N1  116.12  3.000
 K2J  C3  C2  N1  124.02  3.000
 K2J  H9  C3  C2  122.55  3.000
 K2J  H9  C3  C4  122.48  3.000
 K2J  C2  C3  C4  114.97  3.000
 K2J  C1  N2  C4  116.89  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
 K2J  CONST_01  C4  N2  C1  N1    0.00   0.0  0
 K2J  CONST_02  C4  C3  C2  N1    0.00   0.0  0
 K2J  CONST_03  C3  C4  N2  C1    0.00   0.0  0
 K2J  CONST_04  C3  C2  N1  C1    0.00   0.0  0
 K2J  CONST_05  N2  C4  C3  C2    0.00   0.0  0
 K2J  CONST_06  N2  C1  N1  C2    0.00   0.0  0
 K2J  CONST_07  N   C1  N2  C4  180.00   0.0  0
 K2J  CONST_08  C2  N1  C1  N   180.00   0.0  0
 K2J  CONST_09  C1  N2  C4  O   180.00   0.0  0
 K2J  CONST_10  C2  C3  C4  O   180.00   0.0  0
 K2J  CONST_11  H9  C3  C2  N1  180.00   0.0  0
 K2J  CONST_12  H8  C2  C3  C4  180.00   0.0  0
 K2J  CONST_13  C   N   C1  N1    0.00   0.0  0
 K2J  CONST_14  N2  C1  N   C   180.00   0.0  0
 K2J  CONST_15  H4  N   C1  N1  180.00   0.0  0
 K2J  Var_01    N2  C4  O   C5    0.26  30.0  2
 K2J  Var_02    H1  C5  O   C4  -60.70  30.0  3
 K2J  Var_03    H5  C   N   C1  -61.86  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
 K2J  plan-1  N1  0.020
 K2J  plan-1  C4  0.020
 K2J  plan-1  N   0.020
 K2J  plan-1  O   0.020
 K2J  plan-1  C1  0.020
 K2J  plan-1  C2  0.020
 K2J  plan-1  C3  0.020
 K2J  plan-1  N2  0.020
 K2J  plan-1  H8  0.020
 K2J  plan-1  H9  0.020
 K2J  plan-2  N   0.020
 K2J  plan-2  C   0.020
 K2J  plan-2  C1  0.020
 K2J  plan-2  H4  0.020

