# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:25:35 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ncc(Cl)c(n1)C(N)=O
#
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
 K2G  K2G  5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide  ligand  23  13  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K2G
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
 K2G  N1   N   N     0  -0.451   0.5229  -0.8646   0.0038
 K2G  C4   C   CR16  0   0.011   0.1349   1.7800   0.0204
 K2G  C5   C   CR6   0  -0.112  -0.9805   0.9427   0.0147
 K2G  C6   C   CR6   0   0.223  -0.7313  -0.4214   0.0077
 K2G  C7   C   C     0   0.485  -1.8085  -1.4844   0.0042
 K2G  N    N   N     0  -0.385   1.3652   1.3185   0.0171
 K2G  C    C   CH3   0  -0.652   3.6710  -0.0844  -1.2560
 K2G  O    O   O     0  -0.453  -2.9922  -1.1962   0.0045
 K2G  C2   C   CH3   0  -0.652   3.6706  -0.1122   1.2687
 K2G  C3   C   CR6   0   0.408   1.5250  -0.0051   0.0075
 K2G  N2   N   NH2   0  -0.800  -1.3270  -2.7284   0.0010
 K2G  CL   CL  CL    0  -0.077  -2.5275   1.6812   0.0177
 K2G  H1   H   HCR6  0   0.303   0.0013   2.8561   0.0276
 K2G  H2   H   HCH3  0   0.237   4.6812  -0.4945  -1.2633
 K2G  H3   H   HCH3  0   0.236   3.1674  -0.4232  -2.1622
 K2G  H4   H   HCH3  0   0.228   3.7491   1.0025  -1.2966
 K2G  H5   H   HCH1  0   0.256   2.8561  -1.6277  -0.0105
 K2G  H6   H   HCH3  0   0.228   3.7467   0.9735   1.3341
 K2G  H7   H   HCH3  0   0.236   3.1672  -0.4720   2.1669
 K2G  H8   H   HCH3  0   0.237   4.6813  -0.5212   1.2671
 K2G  H9   H   HNH2  0   0.417  -0.3342  -2.8948  -0.0030
 K2G  H10  H   HNH2  0   0.411  -1.9549  -3.5151  -0.0059
 K2G  C1   C   CH1   0  -0.337   2.9303  -0.5383   0.0014

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
 K2G  C   C1   single    1.528  0.020  1.528
 K2G  C1  C2   single    1.528  0.020  1.528
 K2G  C1  C3   single    1.503  0.020  1.503
 K2G  N   C3   aromatic  1.333  0.020  1.333
 K2G  N   C4   aromatic  1.314  0.020  1.314
 K2G  C3  N1   aromatic  1.320  0.020  1.320
 K2G  C4  C5   aromatic  1.395  0.020  1.395
 K2G  N1  C6   aromatic  1.330  0.020  1.330
 K2G  C5  C6   aromatic  1.387  0.020  1.387
 K2G  C5  CL   single    1.714  0.020  1.714
 K2G  C6  C7   single    1.513  0.020  1.513
 K2G  N2  C7   single    1.334  0.020  1.334
 K2G  C7  O    double    1.218  0.020  1.218
 K2G  C4  H1   single    0.930  0.020  1.080
 K2G  C   H2   single    0.970  0.020  1.090
 K2G  C   H3   single    0.970  0.020  1.090
 K2G  C   H4   single    0.970  0.020  1.090
 K2G  C1  H5   single    0.970  0.020  1.090
 K2G  C2  H6   single    0.970  0.020  1.090
 K2G  C2  H7   single    0.970  0.020  1.090
 K2G  C2  H8   single    0.970  0.020  1.090
 K2G  N2  H9   single    0.860  0.020  1.020
 K2G  N2  H10  single    0.860  0.020  1.020

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
 K2G  C3   N1  C6  119.92  3.000
 K2G  H1   C4  N   117.64  3.000
 K2G  H1   C4  C5  119.82  3.000
 K2G  N    C4  C5  122.54  3.000
 K2G  CL   C5  C6  125.87  3.000
 K2G  CL   C5  C4  117.58  3.000
 K2G  C6   C5  C4  116.55  3.000
 K2G  C7   C6  C5  124.27  3.000
 K2G  C7   C6  N1  115.92  3.000
 K2G  C5   C6  N1  119.81  3.000
 K2G  N2   C7  O   124.85  3.000
 K2G  O    C7  C6  121.69  3.000
 K2G  N2   C7  C6  113.46  3.000
 K2G  C3   N   C4  117.44  3.000
 K2G  H4   C   H3  108.16  3.000
 K2G  H4   C   H2  107.96  3.000
 K2G  H3   C   H2  107.78  3.000
 K2G  H4   C   C1  111.18  3.000
 K2G  H3   C   C1  111.56  3.000
 K2G  H2   C   C1  110.05  3.000
 K2G  H8   C2  H7  107.78  3.000
 K2G  H8   C2  H6  107.99  3.000
 K2G  H7   C2  H6  108.14  3.000
 K2G  H8   C2  C1  110.07  3.000
 K2G  H7   C2  C1  111.55  3.000
 K2G  H6   C2  C1  111.17  3.000
 K2G  C1   C3  N   117.66  3.000
 K2G  N    C3  N1  123.74  3.000
 K2G  C1   C3  N1  118.60  3.000
 K2G  H10  N2  H9  119.07  3.000
 K2G  H10  N2  C7  120.25  3.000
 K2G  H9   N2  C7  120.68  3.000
 K2G  H5   C1  C3  106.89  3.000
 K2G  H5   C1  C2  108.67  3.000
 K2G  C3   C1  C2  110.52  3.000
 K2G  H5   C1  C   108.68  3.000
 K2G  C3   C1  C   110.56  3.000
 K2G  C2   C1  C   111.38  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
 K2G  CONST_01  C4   N   C3  N1     0.00   0.0  0
 K2G  CONST_02  C4   C5  C6  N1     0.00   0.0  0
 K2G  CONST_03  C3   N   C4  C5     0.00   0.0  0
 K2G  CONST_04  C3   N1  C6  C5     0.00   0.0  0
 K2G  CONST_05  N    C3  N1  C6     0.00   0.0  0
 K2G  CONST_06  N    C4  C5  C6     0.00   0.0  0
 K2G  CONST_07  CL   C5  C6  N1   180.00   0.0  0
 K2G  CONST_08  C1   C3  N   C4   180.00   0.0  0
 K2G  CONST_09  C7   C6  C5  C4   180.00   0.0  0
 K2G  CONST_10  C1   C3  N1  C6   180.00   0.0  0
 K2G  CONST_11  C3   N1  C6  C7   180.00   0.0  0
 K2G  CONST_12  CL   C5  C4  N    180.00   0.0  0
 K2G  CONST_13  H1   C4  C5  C6   180.00   0.0  0
 K2G  CONST_14  H9   N2  C7  C6     0.00   0.0  0
 K2G  CONST_15  H10  N2  C7  C6   180.00   0.0  0
 K2G  Var_01    C    C1  C3  N1   118.38  30.0  3
 K2G  Var_02    N2   C7  C6  N1     0.16  30.0  2
 K2G  Var_03    H2   C   C1  C3  -178.69  30.0  3
 K2G  Var_04    H6   C2  C1  C3   -61.64  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
 K2G  plan-1  N1   0.020
 K2G  plan-1  C4   0.020
 K2G  plan-1  C5   0.020
 K2G  plan-1  C6   0.020
 K2G  plan-1  C7   0.020
 K2G  plan-1  N    0.020
 K2G  plan-1  C3   0.020
 K2G  plan-1  CL   0.020
 K2G  plan-1  H1   0.020
 K2G  plan-1  C1   0.020
 K2G  plan-2  C6   0.020
 K2G  plan-2  C7   0.020
 K2G  plan-2  O    0.020
 K2G  plan-2  N2   0.020
 K2G  plan-2  H9   0.020
 K2G  plan-2  H10  0.020

