# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 09:54:23 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 5-azanyl-6-methyl-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=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
 I3V  I3V  "5-azanyl-6-methyl-1~{H}-pyrimidine-2,4-dione"
  ligand  17  10  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I3V
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
 I3V  C01  C  CH3   0  -0.728  22.1215  43.8932  -12.0097
 I3V  C02  C  CR6   0   0.348  23.1814  42.8532  -11.9090
 I3V  C03  C  CR6   0   0.017  22.9256  41.5646  -11.5845
 I3V  C04  C  CR6   0   0.539  24.0294  40.6210  -11.5304
 I3V  C07  C  CR6   0   0.655  25.5693  42.4648  -12.0954
 I3V  N06  N  NR16  0  -0.714  25.2718  41.1553  -11.8094
 I3V  N09  N  NR16  0  -0.708  24.4745  43.2722  -12.1284
 I3V  N10  N  NH2   0  -0.855  21.6291  41.0939  -11.3362
 I3V  O05  O  O     0  -0.463  23.9048  39.4351  -11.2736
 I3V  O08  O  O     0  -0.481  26.7025  42.8550  -12.3002
 I3V  H1   H  HCH3  0   0.265  21.1702  43.4399  -12.2805
 I3V  H2   H  HCH3  0   0.272  21.9839  44.4050  -11.0547
 I3V  H3   H  HCH3  0   0.263  22.3733  44.6476  -12.7552
 I3V  H4   H  HNR6  0   0.422  26.0586  40.5190  -11.7745
 I3V  H5   H  HNR6  0   0.427  24.6408  44.2461  -12.3393
 I3V  H6   H  HNH2  0   0.368  21.6289  40.0939  -11.1933
 I3V  H7   H  HNH2  0   0.373  21.2018  41.5277  -10.5296

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
 I3V  O08  C07  double  1.216  0.020  1.216
 I3V  N09  C07  single  1.361  0.020  1.361
 I3V  N09  C02  single  1.377  0.020  1.377
 I3V  C07  N06  single  1.373  0.020  1.373
 I3V  C01  C02  single  1.488  0.020  1.488
 I3V  C02  C03  double  1.353  0.020  1.353
 I3V  N06  C04  single  1.381  0.020  1.381
 I3V  C03  C04  single  1.453  0.020  1.453
 I3V  C03  N10  single  1.401  0.020  1.401
 I3V  C04  O05  double  1.220  0.020  1.220
 I3V  C01  H1   single  0.970  0.020  1.090
 I3V  C01  H2   single  0.970  0.020  1.090
 I3V  C01  H3   single  0.970  0.020  1.090
 I3V  N06  H4   single  0.860  0.020  1.020
 I3V  N09  H5   single  0.860  0.020  1.020
 I3V  N10  H6   single  0.890  0.020  1.040
 I3V  N10  H7   single  0.890  0.020  1.040

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
 I3V  H3   C01  H2   107.62  3.000
 I3V  H3   C01  H1   108.66  3.000
 I3V  H2   C01  H1   107.62  3.000
 I3V  H3   C01  C02  111.43  3.000
 I3V  H2   C01  C02  110.98  3.000
 I3V  H1   C01  C02  110.39  3.000
 I3V  N09  C02  C03  120.36  3.000
 I3V  C03  C02  C01  123.16  3.000
 I3V  N09  C02  C01  116.45  3.000
 I3V  N10  C03  C04  118.55  3.000
 I3V  N10  C03  C02  122.49  3.000
 I3V  C04  C03  C02  118.93  3.000
 I3V  O05  C04  N06  120.70  3.000
 I3V  O05  C04  C03  124.17  3.000
 I3V  N06  C04  C03  115.13  3.000
 I3V  O08  C07  N09  123.73  3.000
 I3V  N09  C07  N06  113.37  3.000
 I3V  O08  C07  N06  122.90  3.000
 I3V  H4   N06  C07  115.98  3.000
 I3V  H4   N06  C04  116.68  3.000
 I3V  C07  N06  C04  127.31  3.000
 I3V  H5   N09  C07  116.40  3.000
 I3V  H5   N09  C02  118.76  3.000
 I3V  C07  N09  C02  124.83  3.000
 I3V  H7   N10  H6   108.17  3.000
 I3V  H7   N10  C03  112.86  3.000
 I3V  H6   N10  C03  110.96  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
 I3V  CONST_01  N06  C07  N09  C02     0.00   0.0  0
 I3V  CONST_02  C07  N06  C04  C03     0.00   0.0  0
 I3V  CONST_03  N09  C07  N06  C04     0.00   0.0  0
 I3V  CONST_04  O08  C07  N09  C02   180.00   0.0  0
 I3V  CONST_05  O08  C07  N06  C04   180.00   0.0  0
 I3V  CONST_06  O05  C04  N06  C07   180.00   0.0  0
 I3V  CONST_07  H4   N06  C04  C03   180.00   0.0  0
 I3V  CONST_08  H5   N09  C07  N06   180.00   0.0  0
 I3V  CONST_09  H4   N06  C07  N09   180.00   0.0  0
 I3V  CONST_10  H4   N06  C04  O05     0.00   0.0  0
 I3V  CONST_11  H5   N09  C07  O08     0.00   0.0  0
 I3V  CONST_12  H4   N06  C07  O08     0.00   0.0  0
 I3V  Var_01    C07  N09  C02  C01  -179.15  30.0  1
 I3V  Var_02    C04  C03  C02  C01   179.17  30.0  1
 I3V  Var_03    N10  C03  C04  N06   178.90  30.0  1
 I3V  Var_04    N10  C03  C02  N09   179.22  30.0  1
 I3V  Var_05    N10  C03  C02  C01     1.09  30.0  1
 I3V  Var_06    O05  C04  C03  N10    -0.42  30.0  1
 I3V  Var_07    H5   N09  C02  C01     0.24  30.0  1
 I3V  Var_08    H6   N10  C03  C02   174.85  30.0  2
 I3V  Var_09    H7   N10  C03  C02   -63.56  30.0  2
 I3V  Var_10    H1   C01  C02  C03   -27.99  30.0  3
 I3V  Var_11    H2   C01  C02  C03    91.24  30.0  3
 I3V  Var_12    H3   C01  C02  C03  -148.84  30.0  3
 I3V  Var_13    H6   N10  C03  C04    -3.23  30.0  2
 I3V  Var_14    H7   N10  C03  C04   118.36  30.0  2
 I3V  Var_15    H1   C01  C02  N09   153.81  30.0  3
 I3V  Var_16    H2   C01  C02  N09   -86.95  30.0  3
 I3V  Var_17    H3   C01  C02  N09    32.97  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
 I3V  plan-1  C02  0.020
 I3V  plan-1  C03  0.020
 I3V  plan-1  C04  0.020
 I3V  plan-1  C07  0.020
 I3V  plan-1  N06  0.020
 I3V  plan-1  N09  0.020
 I3V  plan-1  O05  0.020
 I3V  plan-1  O08  0.020
 I3V  plan-1  H4   0.020
 I3V  plan-1  H5   0.020

