# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:48:28 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 6-(methylamino)-1H-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=CC(=O)NC(=O)N1
#
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
 S76  S76  6-(methylamino)-1H-pyrimidine-2,4-dione  ligand  17  10  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S76
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
 S76  O2    O  O     0  -0.483   0.8389  -2.5469  -0.0218
 S76  C2    C  CR6   0   0.670   0.6406  -1.3481  -0.0164
 S76  N3    N  NR16  0  -0.722   1.6317  -0.4170  -0.0313
 S76  C4    C  CR6   0   0.554   1.4738   0.9750  -0.0229
 S76  O4    O  O     0  -0.508   2.4766   1.6800  -0.0375
 S76  C5    C  CR16  0  -0.606   0.1294   1.4205   0.0005
 S76  N1    N  NR16  0  -0.748  -0.6307  -0.8242   0.0055
 S76  C6    C  CR6   0   0.714  -0.9088   0.5148   0.0127
 S76  N6    N  NH1   0  -0.654  -2.1948   0.8716   0.0314
 S76  C7    C  CH3   0  -0.562  -3.3214  -0.0323   0.0392
 S76  H3    H  HNR6  0   0.418   2.5788  -0.7722  -0.0473
 S76  H1    H  HNR6  0   0.443  -1.3777  -1.5042   0.0188
 S76  H5    H  HCR6  0   0.275  -0.0759   2.4804   0.0057
 S76  H6    H  HNH1  0   0.419  -2.3845   1.8594   0.0464
 S76  H71C  H  HCH3  0   0.254  -3.3459  -0.6673  -0.8484
 S76  H72C  H  HCH3  0   0.254  -3.3375  -0.6643   0.9291
 S76  H73C  H  HCH3  0   0.281  -4.2280   0.5644   0.0417

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
 S76  O2  C2    double  1.215  0.020  1.215
 S76  C2  N3    single  1.360  0.020  1.360
 S76  C2  N1    single  1.375  0.020  1.375
 S76  N3  C4    single  1.401  0.020  1.401
 S76  C4  O4    double  1.226  0.020  1.226
 S76  C4  C5    single  1.416  0.020  1.416
 S76  C5  C6    double  1.378  0.020  1.378
 S76  N1  C6    single  1.368  0.020  1.368
 S76  C6  N6    single  1.335  0.020  1.335
 S76  N6  C7    single  1.444  0.020  1.444
 S76  N3  H3    single  0.860  0.020  1.020
 S76  N1  H1    single  0.860  0.020  1.020
 S76  C5  H5    single  0.930  0.020  1.080
 S76  N6  H6    single  0.860  0.020  1.020
 S76  C7  H71C  single  0.970  0.020  1.090
 S76  C7  H72C  single  0.970  0.020  1.090
 S76  C7  H73C  single  0.970  0.020  1.090

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
 S76  N1    C2  N3    114.40  3.000
 S76  N1    C2  O2    121.79  3.000
 S76  N3    C2  O2    123.82  3.000
 S76  H3    N3  C4    117.03  3.000
 S76  H3    N3  C2    116.23  3.000
 S76  C4    N3  C2    126.73  3.000
 S76  C5    C4  O4    126.56  3.000
 S76  C5    C4  N3    114.81  3.000
 S76  O4    C4  N3    118.63  3.000
 S76  H5    C5  C6    120.13  3.000
 S76  H5    C5  C4    119.30  3.000
 S76  C6    C5  C4    120.57  3.000
 S76  H1    N1  C6    120.57  3.000
 S76  H1    N1  C2    115.30  3.000
 S76  C6    N1  C2    124.13  3.000
 S76  N6    C6  N1    117.24  3.000
 S76  N6    C6  C5    123.39  3.000
 S76  N1    C6  C5    119.36  3.000
 S76  H6    N6  C7    117.86  3.000
 S76  H6    N6  C6    116.39  3.000
 S76  C7    N6  C6    125.75  3.000
 S76  H73C  C7  H72C  107.70  3.000
 S76  H73C  C7  H71C  107.63  3.000
 S76  H72C  C7  H71C  109.01  3.000
 S76  H73C  C7  N6    107.91  3.000
 S76  H72C  C7  N6    112.22  3.000
 S76  H71C  C7  N6    112.16  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
 S76  CONST_01  C5    C6  N1  C2    0.00   0.0  0
 S76  CONST_02  C6    N1  C2  N3    0.00   0.0  0
 S76  CONST_03  N1    C2  N3  C4    0.00   0.0  0
 S76  CONST_04  C4    N3  C2  O2  180.00   0.0  0
 S76  CONST_05  C6    N1  C2  O2  180.00   0.0  0
 S76  CONST_06  N6    C6  N1  C2  180.00   0.0  0
 S76  CONST_07  H1    N1  C2  N3  180.00   0.0  0
 S76  CONST_08  H3    N3  C2  N1  180.00   0.0  0
 S76  CONST_09  C7    N6  C6  C5  180.00   0.0  0
 S76  CONST_10  C7    N6  C6  N1    0.00   0.0  0
 S76  CONST_11  H6    N6  C6  C5    0.00   0.0  0
 S76  Var_01    H71C  C7  N6  C6  -60.89  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
 S76  plan-1  O2  0.020
 S76  plan-1  C2  0.020
 S76  plan-1  N3  0.020
 S76  plan-1  C4  0.020
 S76  plan-1  O4  0.020
 S76  plan-1  C5  0.020
 S76  plan-1  N1  0.020
 S76  plan-1  C6  0.020
 S76  plan-1  N6  0.020
 S76  plan-1  C7  0.020
 S76  plan-1  H3  0.020
 S76  plan-1  H1  0.020
 S76  plan-1  H5  0.020
 S76  plan-1  H6  0.020

