# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:41:40 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 5-azanyl-6-ethyl-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=C(N)C(=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
 IHF  IHF  "5-azanyl-6-ethyl-1H-pyrimidine-2,4-dione"
  ligand  20  11  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IHF
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
 IHF  C01  C  CH3   0  -0.652  50.0228  -3.3368  11.5772
 IHF  C02  C  CH2   0  -0.530  49.4912  -2.7656  12.8924
 IHF  C03  C  CR6   0   0.350  49.0281  -1.3516  12.7385
 IHF  C04  C  CR6   0   0.033  47.7923  -1.0036  12.3138
 IHF  C06  C  CR6   0   0.535  47.4764   0.4076  12.1530
 IHF  C09  C  CR6   0   0.650  49.7758   0.9581  12.8574
 IHF  N05  N  NH2   0  -0.852  46.7956  -1.9027  11.9382
 IHF  N08  N  NR16  0  -0.712  48.5054   1.2778  12.4420
 IHF  N11  N  NR16  0  -0.708  49.9751  -0.3774  12.9896
 IHF  O07  O  O     0  -0.460  46.3872   0.8210  11.7929
 IHF  O10  O  O     0  -0.486  50.6257   1.7991  13.0845
 IHF  H1   H  HCH3  0   0.242  50.3529  -4.3657  11.7166
 IHF  H2   H  HCH3  0   0.234  49.2521  -3.3323  10.8067
 IHF  H3   H  HCH3  0   0.234  50.8716  -2.7590  11.2119
 IHF  H4   H  HCH2  0   0.261  48.6730  -3.3868  13.2604
 IHF  H5   H  HCH2  0   0.267  50.2680  -2.8153  13.6589
 IHF  H8   H  HNH2  0   0.374  46.8413  -2.7923  12.4123
 IHF  H9   H  HNH2  0   0.372  45.8707  -1.5130  12.0502
 IHF  H10  H  HNR6  0   0.422  48.3076   2.2653  12.3365
 IHF  H6   H  HNR6  0   0.426  50.8896  -0.6654  13.3073

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
 IHF  C01  C02  single  1.529  0.020  1.529
 IHF  O07  C06  double  1.219  0.020  1.219
 IHF  N05  C04  single  1.394  0.020  1.394
 IHF  C06  C04  single  1.455  0.020  1.455
 IHF  C06  N08  single  1.378  0.020  1.378
 IHF  C04  C03  double  1.352  0.020  1.352
 IHF  N08  C09  single  1.374  0.020  1.374
 IHF  C03  C02  single  1.496  0.020  1.496
 IHF  C03  N11  single  1.382  0.020  1.382
 IHF  C09  N11  single  1.357  0.020  1.357
 IHF  C09  O10  double  1.217  0.020  1.217
 IHF  C01  H1   single  0.970  0.020  1.090
 IHF  C01  H2   single  0.970  0.020  1.090
 IHF  C01  H3   single  0.970  0.020  1.090
 IHF  C02  H4   single  0.970  0.020  1.090
 IHF  C02  H5   single  0.970  0.020  1.090
 IHF  N05  H8   single  0.890  0.020  1.040
 IHF  N05  H9   single  0.890  0.020  1.040
 IHF  N08  H10  single  0.860  0.020  1.020
 IHF  N11  H6   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
 IHF  H3   C01  H2   108.15  3.000
 IHF  H3   C01  H1   107.92  3.000
 IHF  H2   C01  H1   107.97  3.000
 IHF  H3   C01  C02  111.16  3.000
 IHF  H2   C01  C02  111.14  3.000
 IHF  H1   C01  C02  110.37  3.000
 IHF  H5   C02  H4   105.70  3.000
 IHF  H5   C02  C03  109.59  3.000
 IHF  H4   C02  C03  109.92  3.000
 IHF  H5   C02  C01  109.83  3.000
 IHF  H4   C02  C01  109.76  3.000
 IHF  C03  C02  C01  111.85  3.000
 IHF  N11  C03  C04  120.13  3.000
 IHF  N11  C03  C02  115.82  3.000
 IHF  C04  C03  C02  123.95  3.000
 IHF  N05  C04  C06  116.14  3.000
 IHF  C06  C04  C03  118.86  3.000
 IHF  N05  C04  C03  124.90  3.000
 IHF  O07  C06  N08  120.98  3.000
 IHF  N08  C06  C04  115.28  3.000
 IHF  O07  C06  C04  123.74  3.000
 IHF  O10  C09  N11  124.02  3.000
 IHF  O10  C09  N08  122.76  3.000
 IHF  N11  C09  N08  113.22  3.000
 IHF  H9   N05  H8   109.25  3.000
 IHF  H9   N05  C04  112.09  3.000
 IHF  H8   N05  C04  114.18  3.000
 IHF  H10  N08  C09  116.04  3.000
 IHF  H10  N08  C06  116.61  3.000
 IHF  C09  N08  C06  127.35  3.000
 IHF  H6   N11  C09  116.38  3.000
 IHF  H6   N11  C03  118.47  3.000
 IHF  C09  N11  C03  125.15  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
 IHF  CONST_01  N08  C09  N11  C03     0.00   0.0  0
 IHF  CONST_02  C09  N08  C06  C04     0.00   0.0  0
 IHF  CONST_03  N11  C09  N08  C06     0.00   0.0  0
 IHF  CONST_04  O10  C09  N11  C03   180.00   0.0  0
 IHF  CONST_05  O10  C09  N08  C06   180.00   0.0  0
 IHF  CONST_06  O07  C06  N08  C09   180.00   0.0  0
 IHF  CONST_07  H10  N08  C06  C04   180.00   0.0  0
 IHF  CONST_08  H6   N11  C09  N08   180.00   0.0  0
 IHF  CONST_09  H10  N08  C09  N11   180.00   0.0  0
 IHF  CONST_10  H10  N08  C06  O07     0.00   0.0  0
 IHF  CONST_11  H10  N08  C09  O10     0.00   0.0  0
 IHF  CONST_12  H6   N11  C09  O10     0.00   0.0  0
 IHF  Var_01    C06  C04  C03  C02  -177.55  30.0  1
 IHF  Var_02    C09  N11  C03  C02   177.31  30.0  1
 IHF  Var_03    N08  C06  C04  N05  -175.72  30.0  1
 IHF  Var_04    N11  C03  C04  N05   175.06  30.0  1
 IHF  Var_05    C04  C03  C02  C01    85.22  30.0  2
 IHF  Var_06    N11  C03  C02  C01   -91.32  30.0  2
 IHF  Var_07    N05  C04  C03  C02    -1.34  30.0  1
 IHF  Var_08    O07  C06  C04  N05     4.45  30.0  1
 IHF  Var_09    H6   N11  C03  C02    -3.41  30.0  1
 IHF  Var_10    H8   N05  C04  C03    29.66  30.0  2
 IHF  Var_11    H9   N05  C04  C03   154.56  30.0  2
 IHF  Var_12    H4   C02  C03  C04   -36.97  30.0  3
 IHF  Var_13    H5   C02  C03  C04  -152.72  30.0  3
 IHF  Var_14    H8   N05  C04  C06  -154.04  30.0  2
 IHF  Var_15    H9   N05  C04  C06   -29.13  30.0  2
 IHF  Var_16    H4   C02  C03  N11   146.49  30.0  3
 IHF  Var_17    H5   C02  C03  N11    30.73  30.0  3
 IHF  Var_18    H1   C01  C02  C03  -180.00  30.0  3
 IHF  Var_19    H2   C01  C02  C03   -60.23  30.0  3
 IHF  Var_20    H3   C01  C02  C03    60.29  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
 IHF  plan-1  C03  0.020
 IHF  plan-1  C04  0.020
 IHF  plan-1  C06  0.020
 IHF  plan-1  C09  0.020
 IHF  plan-1  N08  0.020
 IHF  plan-1  N11  0.020
 IHF  plan-1  O07  0.020
 IHF  plan-1  O10  0.020
 IHF  plan-1  H10  0.020
 IHF  plan-1  H6   0.020

