# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 18:39:39 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 4-amino-1-methylpyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=CC(=NC1=O)N
#
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
 1MC  1MC  4-amino-1-methylpyrimidin-2(1H)-one  ligand  16  9  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1MC
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
 1MC  N3    N  N     0  -0.306   1.0412  -0.0927  -0.7162
 1MC  C4    C  CR6   0   0.398   0.0254   0.0047  -1.5526
 1MC  N1    N  NR6   0  -0.476  -0.4698   0.0055   1.0962
 1MC  CN1   C  CH3   0  -0.502  -0.6934  -0.0119   2.5332
 1MC  C2    C  CR6   0   0.557   0.8421  -0.1086   0.6180
 1MC  O2    O  O     0  -0.664   1.7555  -0.2223   1.4265
 1MC  N4    N  NH2   0  -0.789   0.2889   0.0292  -2.8619
 1MC  C5    C  CR16  0  -0.403  -1.3235   0.1051  -1.1002
 1MC  C6    C  CR16  0   0.047  -1.5065   0.0956   0.2379
 1MC  H11   H  HCH3  0   0.292  -0.0349   0.6995   3.0231
 1MC  H12   H  HCH3  0   0.261  -1.7253   0.2636   2.7298
 1MC  H13   H  HCH3  0   0.256  -0.5126  -1.0045   2.9437
 1MC  HN41  H  HNH2  0   0.374   1.2281  -0.1402  -3.1799
 1MC  HN42  H  HNH2  0   0.347  -0.4480   0.0109  -3.5442
 1MC  H5    H  HCR6  0   0.292  -2.1563   0.1777  -1.7824
 1MC  H6    H  HCR6  0   0.318  -2.4942   0.1619   0.6732

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
 1MC  N3   C4    double  1.319  0.020  1.319
 1MC  N3   C2    single  1.349  0.020  1.349
 1MC  C4   N4    single  1.336  0.020  1.336
 1MC  C4   C5    single  1.426  0.020  1.426
 1MC  N1   CN1   single  1.454  0.020  1.454
 1MC  N1   C2    single  1.401  0.020  1.401
 1MC  N1   C6    single  1.349  0.020  1.349
 1MC  CN1  H11   single  0.970  0.020  1.090
 1MC  CN1  H12   single  0.970  0.020  1.090
 1MC  CN1  H13   single  0.970  0.020  1.090
 1MC  C2   O2    double  1.225  0.020  1.225
 1MC  N4   HN41  single  0.860  0.020  1.020
 1MC  N4   HN42  single  0.860  0.020  1.020
 1MC  C5   C6    double  1.351  0.020  1.351
 1MC  C5   H5    single  0.930  0.020  1.080
 1MC  C6   H6    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
 1MC  C2    N3   C4    120.94  3.000
 1MC  C5    C4   N4    119.75  3.000
 1MC  C5    C4   N3    122.16  3.000
 1MC  N4    C4   N3    118.09  3.000
 1MC  C6    N1   C2    120.52  3.000
 1MC  C6    N1   CN1   120.75  3.000
 1MC  C2    N1   CN1   118.70  3.000
 1MC  H13   CN1  H12   108.71  3.000
 1MC  H13   CN1  H11   109.04  3.000
 1MC  H12   CN1  H11   109.17  3.000
 1MC  H13   CN1  N1    110.96  3.000
 1MC  H12   CN1  N1    108.78  3.000
 1MC  H11   CN1  N1    110.15  3.000
 1MC  O2    C2   N1    118.71  3.000
 1MC  O2    C2   N3    122.94  3.000
 1MC  N1    C2   N3    118.35  3.000
 1MC  HN42  N4   HN41  117.84  3.000
 1MC  HN42  N4   C4    121.39  3.000
 1MC  HN41  N4   C4    119.40  3.000
 1MC  H5    C5   C6    121.48  3.000
 1MC  H5    C5   C4    122.29  3.000
 1MC  C6    C5   C4    116.22  3.000
 1MC  H6    C6   C5    121.48  3.000
 1MC  H6    C6   N1    116.73  3.000
 1MC  C5    C6   N1    121.79  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
 1MC  CONST_01  C6    N1   C2  N3     0.00   0.0  0
 1MC  CONST_02  N1    C2   N3  C4     0.00   0.0  0
 1MC  CONST_03  C5    C4   N3  C2     0.00   0.0  0
 1MC  CONST_04  CN1   N1   C2  N3   180.00   0.0  0
 1MC  CONST_05  O2    C2   N3  C4   180.00   0.0  0
 1MC  CONST_06  N4    C4   N3  C2   180.00   0.0  0
 1MC  CONST_07  C6    N1   C2  O2   180.00   0.0  0
 1MC  CONST_08  O2    C2   N1  CN1    0.00   0.0  0
 1MC  CONST_09  HN41  N4   C4  N3     0.00   0.0  0
 1MC  CONST_10  HN42  N4   C4  N3   180.00   0.0  0
 1MC  Var_01    H11   CN1  N1  C2    50.30  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
 1MC  plan-1  N3    0.020
 1MC  plan-1  C4    0.020
 1MC  plan-1  N1    0.020
 1MC  plan-1  CN1   0.020
 1MC  plan-1  C2    0.020
 1MC  plan-1  O2    0.020
 1MC  plan-1  N4    0.020
 1MC  plan-1  C5    0.020
 1MC  plan-1  C6    0.020
 1MC  plan-1  HN41  0.020
 1MC  plan-1  HN42  0.020
 1MC  plan-1  H5    0.020
 1MC  plan-1  H6    0.020

