# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:31:15 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: 6-methoxy-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=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
 IGX  IGX  "6-methoxy-1H-pyrimidine-2,4-dione"
  ligand  16  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 OK
;

data_comp_IGX
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
 IGX  C01  C  CH3   0  -0.438  18.1317  24.0039  2.7569
 IGX  C03  C  CR6   0   0.684  17.5228  26.1867  3.3942
 IGX  C04  C  CR16  0  -0.614  16.2027  26.0294  3.1192
 IGX  C05  C  CR6   0   0.565  15.3003  27.1224  3.3442
 IGX  C08  C  CR6   0   0.674  17.2191  28.4662  4.1298
 IGX  N07  N  NR16  0  -0.722  15.8954  28.2780  3.8458
 IGX  N10  N  NR16  0  -0.720  18.0039  27.3676  3.8797
 IGX  O02  O  O2    0  -0.429  18.4785  25.2949  3.2492
 IGX  O06  O  O     0  -0.467  14.0999  27.1036  3.1344
 IGX  O09  O  O     0  -0.465  17.6711  29.5031  4.5646
 IGX  H1   H  HCH3  0   0.275  19.0569  23.4372  2.7234
 IGX  H2   H  HCH3  0   0.249  17.4253  23.5070  3.4230
 IGX  H3   H  HCH3  0   0.249  17.7075  24.0675  1.7541
 IGX  H6   H  HNR6  0   0.422  15.2879  29.0690  4.0180
 IGX  H4   H  HCR6  0   0.300  15.8026  25.1054  2.7329
 IGX  H5   H  HNR6  0   0.435  18.9926  27.4533  4.0783

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
 IGX  C01  O02  single  1.425  0.020  1.425
 IGX  O06  C05  double  1.219  0.020  1.219
 IGX  C04  C05  single  1.435  0.020  1.435
 IGX  C04  C03  double  1.358  0.020  1.358
 IGX  O02  C03  single  1.315  0.020  1.315
 IGX  C05  N07  single  1.393  0.020  1.393
 IGX  C03  N10  single  1.364  0.020  1.364
 IGX  N07  C08  single  1.367  0.020  1.367
 IGX  N10  C08  single  1.373  0.020  1.373
 IGX  C08  O09  double  1.212  0.020  1.212
 IGX  C01  H1   single  0.970  0.020  1.090
 IGX  C01  H2   single  0.970  0.020  1.090
 IGX  C01  H3   single  0.970  0.020  1.090
 IGX  N07  H6   single  0.860  0.020  1.020
 IGX  C04  H4   single  0.930  0.020  1.080
 IGX  N10  H5   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
 IGX  H3   C01  H2   109.65  3.000
 IGX  H3   C01  H1   109.49  3.000
 IGX  H2   C01  H1   109.45  3.000
 IGX  H3   C01  O02  111.07  3.000
 IGX  H2   C01  O02  111.07  3.000
 IGX  H1   C01  O02  106.03  3.000
 IGX  O02  C03  N10  111.71  3.000
 IGX  N10  C03  C04  121.01  3.000
 IGX  O02  C03  C04  127.28  3.000
 IGX  H4   C04  C05  118.39  3.000
 IGX  H4   C04  C03  122.18  3.000
 IGX  C05  C04  C03  119.43  3.000
 IGX  O06  C05  N07  119.70  3.000
 IGX  N07  C05  C04  114.80  3.000
 IGX  O06  C05  C04  125.49  3.000
 IGX  O09  C08  N10  122.46  3.000
 IGX  O09  C08  N07  123.61  3.000
 IGX  N10  C08  N07  113.92  3.000
 IGX  H6   N07  C08  116.00  3.000
 IGX  H6   N07  C05  116.94  3.000
 IGX  C08  N07  C05  127.06  3.000
 IGX  H5   N10  C08  117.06  3.000
 IGX  H5   N10  C03  119.18  3.000
 IGX  C08  N10  C03  123.76  3.000
 IGX  C03  O02  C01  118.41  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
 IGX  CONST_01  N07  C08  N10  C03     0.00   0.0  0
 IGX  CONST_02  C08  N07  C05  C04     0.00   0.0  0
 IGX  CONST_03  N10  C08  N07  C05     0.00   0.0  0
 IGX  CONST_04  O09  C08  N10  C03   180.00   0.0  0
 IGX  CONST_05  O09  C08  N07  C05   180.00   0.0  0
 IGX  CONST_06  O06  C05  N07  C08   180.00   0.0  0
 IGX  CONST_07  H6   N07  C05  C04   180.00   0.0  0
 IGX  CONST_08  H5   N10  C08  N07   180.00   0.0  0
 IGX  CONST_09  H6   N07  C08  N10   180.00   0.0  0
 IGX  CONST_10  H6   N07  C05  O06     0.00   0.0  0
 IGX  CONST_11  H6   N07  C08  O09     0.00   0.0  0
 IGX  CONST_12  H5   N10  C08  O09     0.00   0.0  0
 IGX  Var_01    O02  C03  C04  C05   179.91  30.0  1
 IGX  Var_02    O02  C03  N10  C08  -179.74  30.0  1
 IGX  Var_03    H4   C04  C05  N07   179.89  30.0  1
 IGX  Var_04    H4   C04  C03  N10   179.86  30.0  1
 IGX  Var_05    C04  C03  O02  C01    -0.32  30.0  3
 IGX  Var_06    N10  C03  O02  C01   179.64  30.0  3
 IGX  Var_07    H4   C04  C03  O02    -0.18  30.0  1
 IGX  Var_08    H5   N10  C03  O02    -0.19  30.0  1
 IGX  Var_09    H4   C04  C05  O06    -0.04  30.0  1
 IGX  Var_10    H1   C01  O02  C03  -179.65  30.0  3
 IGX  Var_11    H2   C01  O02  C03   -60.83  30.0  3
 IGX  Var_12    H3   C01  O02  C03    61.48  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
 IGX  plan-1  C03  0.020
 IGX  plan-1  C04  0.020
 IGX  plan-1  C05  0.020
 IGX  plan-1  C08  0.020
 IGX  plan-1  N07  0.020
 IGX  plan-1  N10  0.020
 IGX  plan-1  O06  0.020
 IGX  plan-1  O09  0.020
 IGX  plan-1  H6   0.020
 IGX  plan-1  H5   0.020

