# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:47:37 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1=C(N)C=CNC1=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
 3MC  3MC  6-amino-1-methyl-2-oxo-2,3-dihydropyrimidin-1-ium  ligand  17  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3MC
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
 3MC  N3    N  NR6   1  -0.572   0.1463   0.6719   0.0385
 3MC  CN3   C  CH3   0  -0.589   0.4781   2.0947   0.0362
 3MC  N1    N  NR16  0  -0.670  -1.4362  -1.0352   0.0936
 3MC  C2    C  CR6   0   0.741  -1.2030   0.3132   0.0931
 3MC  O2    O  O     0  -0.442  -2.0919   1.1269   0.1361
 3MC  C4    C  CR6   0   0.751   1.1474  -0.2402  -0.0140
 3MC  N4    N  NH2   0  -0.804   2.3944   0.1615  -0.0671
 3MC  C5    C  CR16  0  -0.452   0.8315  -1.6217  -0.0103
 3MC  C6    C  CR16  0   0.120  -0.4684  -1.9705   0.0437
 3MC  H31   H  HCH3  0   0.286   1.0832   2.3396   0.9078
 3MC  H32   H  HCH3  0   0.286   1.0123   2.3535  -0.8767
 3MC  H33   H  HCH3  0   0.307  -0.4342   2.6750   0.0773
 3MC  HN1   H  HNR6  0   0.455  -2.4053  -1.3221   0.1321
 3MC  HN41  H  HNH2  0   0.457   2.6740   1.1295  -0.0777
 3MC  HN42  H  HNH2  0   0.449   3.1358  -0.5202  -0.1103
 3MC  H5    H  HCR6  0   0.327   1.6158  -2.3599  -0.0509
 3MC  H6    H  HCR6  0   0.349  -0.7979  -2.9985   0.0506

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
 3MC  N3   CN3   single  1.461  0.020  1.461
 3MC  N3   C2    single  1.397  0.020  1.397
 3MC  N3   C4    double  1.355  0.020  1.355
 3MC  CN3  H31   single  0.970  0.020  1.090
 3MC  CN3  H32   single  0.970  0.020  1.090
 3MC  CN3  H33   single  0.970  0.020  1.090
 3MC  N1   C2    single  1.368  0.020  1.368
 3MC  N1   C6    single  1.347  0.020  1.347
 3MC  N1   HN1   single  0.860  0.020  1.020
 3MC  C2   O2    double  1.206  0.020  1.206
 3MC  C4   N4    single  1.311  0.020  1.311
 3MC  C4   C5    single  1.417  0.020  1.417
 3MC  N4   HN41  single  0.860  0.020  1.020
 3MC  N4   HN42  single  0.860  0.020  1.020
 3MC  C5   C6    double  1.347  0.020  1.347
 3MC  C5   H5    single  0.930  0.020  1.080
 3MC  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
 3MC  C4    N3   C2    122.82  3.000
 3MC  C4    N3   CN3   119.18  3.000
 3MC  C2    N3   CN3   118.00  3.000
 3MC  H33   CN3  H32   108.54  3.000
 3MC  H33   CN3  H31   108.51  3.000
 3MC  H32   CN3  H31   110.18  3.000
 3MC  H33   CN3  N3    109.31  3.000
 3MC  H32   CN3  N3    110.13  3.000
 3MC  H31   CN3  N3    110.12  3.000
 3MC  HN1   N1   C6    119.54  3.000
 3MC  HN1   N1   C2    116.28  3.000
 3MC  C6    N1   C2    124.18  3.000
 3MC  O2    C2   N1    122.63  3.000
 3MC  O2    C2   N3    122.69  3.000
 3MC  N1    C2   N3    114.68  3.000
 3MC  C5    C4   N4    120.71  3.000
 3MC  C5    C4   N3    119.43  3.000
 3MC  N4    C4   N3    119.86  3.000
 3MC  HN42  N4   HN41  116.43  3.000
 3MC  HN42  N4   C4    119.61  3.000
 3MC  HN41  N4   C4    123.96  3.000
 3MC  H5    C5   C6    121.76  3.000
 3MC  H5    C5   C4    120.36  3.000
 3MC  C6    C5   C4    117.88  3.000
 3MC  H6    C6   C5    122.78  3.000
 3MC  H6    C6   N1    116.21  3.000
 3MC  C5    C6   N1    121.01  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
 3MC  CONST_01  C6    N1   C2  N3     0.00   0.0  0
 3MC  CONST_02  C4    N3   C2  N1     0.00   0.0  0
 3MC  CONST_03  C5    C4   N3  C2     0.00   0.0  0
 3MC  CONST_04  N1    C2   N3  CN3  180.00   0.0  0
 3MC  CONST_05  C5    C4   N3  CN3  180.00   0.0  0
 3MC  CONST_06  N4    C4   N3  C2   180.00   0.0  0
 3MC  CONST_07  C4    N3   C2  O2   180.00   0.0  0
 3MC  CONST_08  C6    N1   C2  O2   180.00   0.0  0
 3MC  CONST_09  HN1   N1   C2  N3   180.00   0.0  0
 3MC  CONST_10  O2    C2   N3  CN3    0.00   0.0  0
 3MC  CONST_11  N4    C4   N3  CN3    0.00   0.0  0
 3MC  CONST_12  HN41  N4   C4  N3     0.00   0.0  0
 3MC  CONST_13  HN42  N4   C4  N3   180.00   0.0  0
 3MC  Var_01    H31   CN3  N3  C2   118.98  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
 3MC  plan-1  N3    0.020
 3MC  plan-1  CN3   0.020
 3MC  plan-1  N1    0.020
 3MC  plan-1  C2    0.020
 3MC  plan-1  O2    0.020
 3MC  plan-1  C4    0.020
 3MC  plan-1  N4    0.020
 3MC  plan-1  C5    0.020
 3MC  plan-1  C6    0.020
 3MC  plan-1  HN1   0.020
 3MC  plan-1  HN41  0.020
 3MC  plan-1  HN42  0.020
 3MC  plan-1  H5    0.020
 3MC  plan-1  H6    0.020

