# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 06:58:33 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 4-amino-5-methylpyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CNC(=O)N=C1N
#
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
 17E  17E  4-amino-5-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 PERFECT
;

data_comp_17E
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
 17E  N1   N  NR16  0  -0.660   1.1719   1.1702  -0.0677
 17E  C2   C  CR6   0   0.548   1.5900  -0.1510  -0.0193
 17E  O2   O  O     0  -0.529   2.7895  -0.4060  -0.0198
 17E  N3   N  N     0  -0.536   0.6277  -1.0961   0.0266
 17E  C4   C  CR6   0   0.485  -0.6492  -0.7623   0.0279
 17E  N4   N  NH2   0  -0.812  -1.5449  -1.7505   0.0847
 17E  C5   C  CR6   0  -0.102  -1.1134   0.5988  -0.0202
 17E  C6   C  CR16  0   0.046  -0.1310   1.5252  -0.0674
 17E  CM5  C  CH3   0  -0.745  -2.5672   0.9503  -0.0171
 17E  H1   H  HNH2  0   0.402  -1.2334  -2.7069   0.0753
 17E  H2   H  HNH2  0   0.419  -2.5334  -1.5823   0.0308
 17E  H4   H  HCR6  0   0.306  -0.3327   2.5869  -0.1068
 17E  H5   H  HCH3  0   0.249  -3.0718   0.5882   0.8816
 17E  H6   H  HCH3  0   0.261  -2.6997   2.0306  -0.0522
 17E  H7   H  HCH3  0   0.249  -3.0920   0.5288  -0.8777
 17E  H8   H  HNR6  0   0.419   1.8793   1.8887  -0.1034

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
 17E  O2   C2   double  1.226  0.020  1.226
 17E  C2   N3   single  1.350  0.020  1.350
 17E  C2   N1   single  1.387  0.020  1.387
 17E  N3   C4   double  1.320  0.020  1.320
 17E  N1   C6   single  1.350  0.020  1.350
 17E  C4   N4   single  1.335  0.020  1.335
 17E  C4   C5   single  1.439  0.020  1.439
 17E  C6   C5   double  1.351  0.020  1.351
 17E  C5   CM5  single  1.496  0.020  1.496
 17E  N4   H1   single  0.860  0.020  1.020
 17E  N4   H2   single  0.860  0.020  1.020
 17E  C6   H4   single  0.930  0.020  1.080
 17E  CM5  H5   single  0.970  0.020  1.090
 17E  CM5  H6   single  0.970  0.020  1.090
 17E  CM5  H7   single  0.970  0.020  1.090
 17E  N1   H8   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
 17E  H8   N1   C6  119.29  3.000
 17E  H8   N1   C2  117.93  3.000
 17E  C6   N1   C2  122.78  3.000
 17E  N3   C2   O2  123.49  3.000
 17E  N3   C2   N1  116.97  3.000
 17E  O2   C2   N1  119.54  3.000
 17E  C4   N3   C2  120.85  3.000
 17E  C5   C4   N4  119.03  3.000
 17E  C5   C4   N3  123.46  3.000
 17E  N4   C4   N3  117.52  3.000
 17E  H2   N4   H1  117.63  3.000
 17E  H2   N4   C4  122.29  3.000
 17E  H1   N4   C4  119.71  3.000
 17E  CM5  C5   C6  123.07  3.000
 17E  CM5  C5   C4  122.40  3.000
 17E  C6   C5   C4  114.54  3.000
 17E  H4   C6   C5  122.61  3.000
 17E  H4   C6   N1  115.98  3.000
 17E  C5   C6   N1  121.41  3.000
 17E  H7   CM5  H6  107.39  3.000
 17E  H7   CM5  H5  107.35  3.000
 17E  H6   CM5  H5  107.40  3.000
 17E  H7   CM5  C5  112.00  3.000
 17E  H6   CM5  C5  110.57  3.000
 17E  H5   CM5  C5  111.88  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
 17E  CONST_01  C4  N3   C2  N1    0.00   0.0  0
 17E  CONST_02  C5  C4   N3  C2    0.00   0.0  0
 17E  CONST_03  C6  N1   C2  N3    0.00   0.0  0
 17E  CONST_04  N4  C4   N3  C2  180.00   0.0  0
 17E  CONST_05  C4  N3   C2  O2  180.00   0.0  0
 17E  CONST_06  C6  N1   C2  O2  180.00   0.0  0
 17E  CONST_07  H8  N1   C2  N3  180.00   0.0  0
 17E  CONST_08  H1  N4   C4  N3    0.00   0.0  0
 17E  CONST_09  H2  N4   C4  N3  180.00   0.0  0
 17E  Var_01    H5  CM5  C5  C4   60.00  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
 17E  plan-1  N1   0.020
 17E  plan-1  C2   0.020
 17E  plan-1  O2   0.020
 17E  plan-1  N3   0.020
 17E  plan-1  C4   0.020
 17E  plan-1  N4   0.020
 17E  plan-1  C5   0.020
 17E  plan-1  C6   0.020
 17E  plan-1  CM5  0.020
 17E  plan-1  H1   0.020
 17E  plan-1  H2   0.020
 17E  plan-1  H4   0.020
 17E  plan-1  H8   0.020

