# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:02:04 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 6-methyl-5-[(1E)-3-oxobut-1-en-1-yl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)/C=C/C1=C(C)NC(=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
 OYG  OYG  6-methyl-5-[(1E)-3-oxobut-1-en-1-yl]pyrimidine-2,4(1H,3H)-dione  ligand  24  14  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYG
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
 OYG  N    N  NR16  0  -0.709  -2.5510   0.9898  -0.0098
 OYG  C    C  CH3   0  -0.781   4.5806  -0.9573  -0.0287
 OYG  C1   C  C     0   0.363   3.5159   0.1058  -0.0204
 OYG  C2   C  C1    0  -0.391   2.1313  -0.3971  -0.0194
 OYG  C3   C  C1    0  -0.224   1.0925   0.4571  -0.0110
 OYG  C4   C  CR6   0  -0.182  -0.3246   0.1810  -0.0098
 OYG  C5   C  CR6   0   0.444  -1.2192   1.2246  -0.0104
 OYG  C6   C  CH3   0  -0.770  -0.8252   2.6648  -0.0123
 OYG  C7   C  CR6   0   0.679  -3.1356  -0.2549  -0.0071
 OYG  C8   C  CR6   0   0.570  -0.8491  -1.1766  -0.0083
 OYG  N1   N  NR16  0  -0.715  -2.2319  -1.2755  -0.0052
 OYG  O1   O  O     0  -0.462  -4.3361  -0.4126  -0.0064
 OYG  O2   O  O     0  -0.447  -0.1852  -2.1956  -0.0097
 OYG  H1   H  HNR6  0   0.439  -3.1884   1.7740  -0.0137
 OYG  H2   H  HCH3  0   0.256   5.5790  -0.5257  -0.0227
 OYG  H3   H  HCH3  0   0.263   4.4660  -1.6095   0.8396
 OYG  H4   H  HCH3  0   0.264   4.4692  -1.5920  -0.9104
 OYG  H7   H  H     0   0.269   1.9984  -1.4680  -0.0262
 OYG  H8   H  H     0   0.267   1.3517   1.5109  -0.0041
 OYG  H9   H  HCH3  0   0.285  -1.6952   3.3173  -0.0200
 OYG  H10  H  HCH3  0   0.289  -0.2349   2.9037   0.8717
 OYG  H11  H  HCH3  0   0.289  -0.2212   2.8996  -0.8878
 OYG  H12  H  HNR6  0   0.430  -2.6161  -2.2127  -0.0015
 OYG  O3   O  O     0  -0.428   3.7921   1.2924  -0.0152

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
 OYG  O1  C7   double  1.211  0.020  1.211
 OYG  C6  C5   single  1.493  0.020  1.493
 OYG  N   C7   single  1.375  0.020  1.375
 OYG  N   C5   single  1.352  0.020  1.352
 OYG  C7  N1   single  1.363  0.020  1.363
 OYG  C5  C4   double  1.375  0.020  1.375
 OYG  N1  C8   single  1.386  0.020  1.386
 OYG  C4  C3   single  1.444  0.020  1.444
 OYG  C4  C8   single  1.455  0.020  1.455
 OYG  C3  C2   double  1.345  0.020  1.345
 OYG  C8  O2   double  1.216  0.020  1.216
 OYG  C   C1   single  1.505  0.020  1.505
 OYG  C2  C1   single  1.473  0.020  1.473
 OYG  N   H1   single  0.860  0.020  1.020
 OYG  C   H2   single  0.970  0.020  1.090
 OYG  C   H3   single  0.970  0.020  1.090
 OYG  C   H4   single  0.970  0.020  1.090
 OYG  C2  H7   single  0.930  0.020  1.080
 OYG  C3  H8   single  0.930  0.020  1.080
 OYG  C6  H9   single  0.970  0.020  1.090
 OYG  C6  H10  single  0.970  0.020  1.090
 OYG  C6  H11  single  0.970  0.020  1.090
 OYG  N1  H12  single  0.860  0.020  1.020
 OYG  C1  O3   double  1.218  0.020  1.218

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
 OYG  H1   N   C7   115.74  3.000
 OYG  H1   N   C5   119.11  3.000
 OYG  C7   N   C5   125.15  3.000
 OYG  H4   C   H3   106.51  3.000
 OYG  H4   C   H2   109.19  3.000
 OYG  H3   C   H2   109.20  3.000
 OYG  H4   C   C1   110.06  3.000
 OYG  H3   C   C1   110.08  3.000
 OYG  H2   C   C1   111.66  3.000
 OYG  O3   C1  C2   123.07  3.000
 OYG  O3   C1  C    121.85  3.000
 OYG  C2   C1  C    115.08  3.000
 OYG  H7   C2  C3   122.36  3.000
 OYG  H7   C2  C1   117.04  3.000
 OYG  C3   C2  C1   120.60  3.000
 OYG  H8   C3  C4   114.84  3.000
 OYG  H8   C3  C2   115.62  3.000
 OYG  C4   C3  C2   129.54  3.000
 OYG  C8   C4  C5   118.28  3.000
 OYG  C8   C4  C3   122.15  3.000
 OYG  C5   C4  C3   119.58  3.000
 OYG  C6   C5  C4   124.10  3.000
 OYG  C4   C5  N    120.60  3.000
 OYG  C6   C5  N    115.30  3.000
 OYG  H11  C6  H10  107.73  3.000
 OYG  H11  C6  H9   107.97  3.000
 OYG  H10  C6  H9   107.91  3.000
 OYG  H11  C6  C5   110.81  3.000
 OYG  H10  C6  C5   110.70  3.000
 OYG  H9   C6  C5   111.57  3.000
 OYG  O1   C7  N1   124.04  3.000
 OYG  N1   C7  N    113.32  3.000
 OYG  O1   C7  N    122.64  3.000
 OYG  O2   C8  N1   119.00  3.000
 OYG  O2   C8  C4   125.79  3.000
 OYG  N1   C8  C4   115.21  3.000
 OYG  H12  N1  C8   116.38  3.000
 OYG  H12  N1  C7   116.19  3.000
 OYG  C8   N1  C7   127.43  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
 OYG  CONST_01  C8   N1  C7  N      0.00   0.0  0
 OYG  CONST_02  C7   N1  C8  C4     0.00   0.0  0
 OYG  CONST_03  N1   C7  N   C5     0.00   0.0  0
 OYG  CONST_04  O1   C7  N   C5   180.00   0.0  0
 OYG  CONST_05  O2   C8  N1  C7   180.00   0.0  0
 OYG  CONST_06  O1   C7  N1  C8   180.00   0.0  0
 OYG  CONST_07  H12  N1  C7  N    180.00   0.0  0
 OYG  CONST_08  H1   N   C7  N1   180.00   0.0  0
 OYG  CONST_09  C4   C3  C2  C1   180.00   0.0  0
 OYG  CONST_10  H7   C2  C3  C4     0.00   0.0  0
 OYG  CONST_11  H8   C3  C2  C1     0.00   0.0  0
 OYG  Var_01    C5   C4  C3  C2  -179.51  30.0  2
 OYG  Var_02    H9   C6  C5  N     -0.40  30.0  3
 OYG  Var_03    C3   C2  C1  C    179.93  30.0  1
 OYG  Var_04    H2   C   C1  C2  -179.64  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
 OYG  plan-1  N    0.020
 OYG  plan-1  C3   0.020
 OYG  plan-1  C4   0.020
 OYG  plan-1  C5   0.020
 OYG  plan-1  C6   0.020
 OYG  plan-1  C7   0.020
 OYG  plan-1  C8   0.020
 OYG  plan-1  N1   0.020
 OYG  plan-1  O1   0.020
 OYG  plan-1  O2   0.020
 OYG  plan-1  H1   0.020
 OYG  plan-1  H12  0.020
 OYG  plan-2  C    0.020
 OYG  plan-2  C1   0.020
 OYG  plan-2  C2   0.020
 OYG  plan-2  O3   0.020
 OYG  plan-3  C1   0.020
 OYG  plan-3  C2   0.020
 OYG  plan-3  C3   0.020
 OYG  plan-3  C4   0.020
 OYG  plan-3  H7   0.020
 OYG  plan-3  H8   0.020

