# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:49:34 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CNC(=O)NC1=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
 TDR  TDR  5-methylpyrimidine-2,4(1H,3H)-dione  ligand  15  9  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TDR
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
 TDR  N1    N  NR16  0  -0.671  -1.2264   0.1401  -1.0686
 TDR  C2    C  CR6   0   0.679   0.0335  -0.0065  -1.5737
 TDR  O2    O  O     0  -0.483   0.2835  -0.0084  -2.7623
 TDR  N3    N  NR16  0  -0.717   0.9950  -0.1527  -0.6058
 TDR  C4    C  CR6   0   0.567   0.8166  -0.1617   0.7688
 TDR  O4    O  O     0  -0.458   1.7719  -0.3020   1.5113
 TDR  C5    C  CR6   0  -0.174  -0.5561   0.0046   1.2105
 TDR  CM5   C  CH3   0  -0.705  -0.8459   0.0121   2.6753
 TDR  C6    C  CR16  0   0.049  -1.5041   0.1463   0.2665
 TDR  HN1   H  HNR6  0   0.436  -1.9796   0.2533  -1.7303
 TDR  HN3   H  HNR6  0   0.425   1.9433  -0.2685  -0.9418
 TDR  H5M1  H  HCH3  0   0.246  -0.3030   0.8098   3.1842
 TDR  H5M2  H  HCH3  0   0.247  -1.9085   0.1619   2.8594
 TDR  H5M3  H  HCH3  0   0.246  -0.5526  -0.9276   3.1457
 TDR  H6    H  HCR6  0   0.314  -2.5491   0.2733   0.5116

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
 TDR  N1   C2    single  1.365  0.020  1.365
 TDR  N1   C6    single  1.364  0.020  1.364
 TDR  N1   HN1   single  0.860  0.020  1.020
 TDR  C2   O2    double  1.215  0.020  1.215
 TDR  C2   N3    single  1.372  0.020  1.372
 TDR  N3   C4    single  1.386  0.020  1.386
 TDR  N3   HN3   single  0.860  0.020  1.020
 TDR  C4   O4    double  1.218  0.020  1.218
 TDR  C4   C5    single  1.452  0.020  1.452
 TDR  C5   CM5   single  1.493  0.020  1.493
 TDR  C5   C6    double  1.345  0.020  1.345
 TDR  CM5  H5M1  single  0.970  0.020  1.090
 TDR  CM5  H5M2  single  0.970  0.020  1.090
 TDR  CM5  H5M3  single  0.970  0.020  1.090
 TDR  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
 TDR  HN1   N1   C6    119.31  3.000
 TDR  HN1   N1   C2    117.28  3.000
 TDR  C6    N1   C2    123.41  3.000
 TDR  N3    C2   O2    123.09  3.000
 TDR  N3    C2   N1    113.40  3.000
 TDR  O2    C2   N1    123.52  3.000
 TDR  HN3   N3   C4    116.66  3.000
 TDR  HN3   N3   C2    115.74  3.000
 TDR  C4    N3   C2    127.59  3.000
 TDR  C5    C4   O4    124.70  3.000
 TDR  C5    C4   N3    115.01  3.000
 TDR  O4    C4   N3    120.29  3.000
 TDR  C6    C5   CM5   123.44  3.000
 TDR  C6    C5   C4    117.70  3.000
 TDR  CM5   C5   C4    118.86  3.000
 TDR  H5M3  CM5  H5M2  107.94  3.000
 TDR  H5M3  CM5  H5M1  107.15  3.000
 TDR  H5M2  CM5  H5M1  107.84  3.000
 TDR  H5M3  CM5  C5    111.49  3.000
 TDR  H5M2  CM5  C5    110.85  3.000
 TDR  H5M1  CM5  C5    111.39  3.000
 TDR  H6    C6   C5    122.31  3.000
 TDR  H6    C6   N1    114.80  3.000
 TDR  C5    C6   N1    122.89  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
 TDR  CONST_01  C4    N3   C2  N1    0.00   0.0  0
 TDR  CONST_02  C5    C4   N3  C2    0.00   0.0  0
 TDR  CONST_03  C6    N1   C2  N3    0.00   0.0  0
 TDR  CONST_04  O4    C4   N3  C2  180.00   0.0  0
 TDR  CONST_05  C6    N1   C2  O2  180.00   0.0  0
 TDR  CONST_06  C4    N3   C2  O2  180.00   0.0  0
 TDR  CONST_07  HN3   N3   C2  N1  180.00   0.0  0
 TDR  CONST_08  HN1   N1   C2  N3  180.00   0.0  0
 TDR  Var_01    H5M1  CM5  C5  C4   58.92  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
 TDR  plan-1  N1   0.020
 TDR  plan-1  C2   0.020
 TDR  plan-1  O2   0.020
 TDR  plan-1  N3   0.020
 TDR  plan-1  C4   0.020
 TDR  plan-1  O4   0.020
 TDR  plan-1  C5   0.020
 TDR  plan-1  CM5  0.020
 TDR  plan-1  C6   0.020
 TDR  plan-1  HN1  0.020
 TDR  plan-1  HN3  0.020
 TDR  plan-1  H6   0.020

