# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:44:45 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-ethyl-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=NC(=O)NC(=O)C1
#
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
 I6R  I6R  "6-ethyl-5~{H}-pyrimidine-2,4-dione"
  ligand  18  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_I6R
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
 I6R  C01  C  CH3   0  -0.670  -16.1715  -24.7816  11.9578
 I6R  C02  C  CH2   0  -0.503  -16.3483  -25.8935  10.9198
 I6R  C03  C  C     0   0.293  -15.2978  -26.9441  11.0812
 I6R  C04  C  CH2   0  -0.678  -13.9894  -26.6910  10.4114
 I6R  C05  C  C     0   0.577  -12.9205  -27.7025  10.6932
 I6R  C08  C  C     0   0.606  -14.5897  -28.9479  11.9967
 I6R  N07  N  NH1   0  -0.694  -13.3286  -28.7609  11.4564
 I6R  N10  N  N     0  -0.439  -15.5630  -27.9750  11.7857
 I6R  O06  O  O     0  -0.423  -11.7901  -27.6115  10.2758
 I6R  O09  O  O     0  -0.420  -14.8326  -29.9359  12.6450
 I6R  H1   H  HCH3  0   0.252  -16.9495  -24.0310  11.8272
 I6R  H2   H  HCH3  0   0.240  -16.2496  -25.1761  12.9704
 I6R  H3   H  HCH3  0   0.238  -15.2083  -24.2812  11.8594
 I6R  H4   H  HCH2  0   0.261  -16.2918  -25.4696   9.9151
 I6R  H5   H  HCH2  0   0.268  -17.3288  -26.3542  11.0377
 I6R  H6   H  HCH2  0   0.332  -13.6203  -25.6943  10.6714
 I6R  H7   H  HCH2  0   0.339  -14.1579  -26.6557   9.3290
 I6R  H8   H  HNH1  0   0.422  -12.6431  -29.4806  11.6554

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
 I6R  O06  C05  double  1.208  0.020  1.208
 I6R  C04  C05  single  1.498  0.020  1.498
 I6R  C04  C03  single  1.492  0.020  1.492
 I6R  C05  N07  single  1.367  0.020  1.367
 I6R  C02  C03  single  1.494  0.020  1.494
 I6R  C02  C01  single  1.531  0.020  1.531
 I6R  C03  N10  double  1.277  0.020  1.277
 I6R  N07  C08  single  1.385  0.020  1.385
 I6R  N10  C08  single  1.392  0.020  1.392
 I6R  C08  O09  double  1.206  0.020  1.206
 I6R  C01  H1   single  0.970  0.020  1.090
 I6R  C01  H2   single  0.970  0.020  1.090
 I6R  C01  H3   single  0.970  0.020  1.090
 I6R  C02  H4   single  0.970  0.020  1.090
 I6R  C02  H5   single  0.970  0.020  1.090
 I6R  C04  H6   single  0.970  0.020  1.090
 I6R  C04  H7   single  0.970  0.020  1.090
 I6R  N07  H8   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
 I6R  H3   C01  H2   108.27  3.000
 I6R  H3   C01  H1   107.71  3.000
 I6R  H2   C01  H1   108.05  3.000
 I6R  H3   C01  C02  111.97  3.000
 I6R  H2   C01  C02  111.03  3.000
 I6R  H1   C01  C02  109.68  3.000
 I6R  H5   C02  H4   108.07  3.000
 I6R  H5   C02  C03  108.88  3.000
 I6R  H4   C02  C03  109.63  3.000
 I6R  H5   C02  C01  109.72  3.000
 I6R  H4   C02  C01  109.62  3.000
 I6R  C03  C02  C01  110.86  3.000
 I6R  N10  C03  C04  124.55  3.000
 I6R  N10  C03  C02  118.77  3.000
 I6R  C04  C03  C02  116.67  3.000
 I6R  H7   C04  H6   104.90  3.000
 I6R  H7   C04  C05  108.50  3.000
 I6R  H6   C04  C05  109.25  3.000
 I6R  H7   C04  C03  108.31  3.000
 I6R  H6   C04  C03  110.10  3.000
 I6R  C05  C04  C03  115.26  3.000
 I6R  O06  C05  N07  122.03  3.000
 I6R  N07  C05  C04  114.50  3.000
 I6R  O06  C05  C04  123.47  3.000
 I6R  O09  C08  N10  120.86  3.000
 I6R  O09  C08  N07  120.24  3.000
 I6R  N10  C08  N07  118.90  3.000
 I6R  H8   N07  C08  116.32  3.000
 I6R  H8   N07  C05  117.22  3.000
 I6R  C08  N07  C05  126.46  3.000
 I6R  C08  N10  C03  120.18  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
 I6R  CONST_01  N07  C08  N10  C03     0.00   0.0  0
 I6R  CONST_02  C08  N07  C05  C04     0.00   0.0  0
 I6R  CONST_03  N10  C08  N07  C05     0.00   0.0  0
 I6R  CONST_04  O09  C08  N10  C03   180.00   0.0  0
 I6R  CONST_05  O09  C08  N07  C05   180.00   0.0  0
 I6R  CONST_06  O06  C05  N07  C08   180.00   0.0  0
 I6R  CONST_07  H8   N07  C05  C04   180.00   0.0  0
 I6R  CONST_08  H8   N07  C08  N10   180.00   0.0  0
 I6R  CONST_09  H8   N07  C05  O06     0.00   0.0  0
 I6R  CONST_10  H8   N07  C08  O09     0.00   0.0  0
 I6R  Var_01    C05  C04  C03  C02   174.78  30.0  1
 I6R  Var_02    C08  N10  C03  C02  -177.61  30.0  1
 I6R  Var_03    H6   C04  C05  N07   128.64  30.0  1
 I6R  Var_04    H7   C04  C05  N07  -117.53  30.0  1
 I6R  Var_05    H6   C04  C03  N10  -128.33  30.0  1
 I6R  Var_06    H7   C04  C03  N10   117.50  30.0  1
 I6R  Var_07    C04  C03  C02  C01   -84.51  30.0  3
 I6R  Var_08    N10  C03  C02  C01    94.54  30.0  3
 I6R  Var_09    H6   C04  C03  C02    50.67  30.0  1
 I6R  Var_10    H7   C04  C03  C02   -63.51  30.0  1
 I6R  Var_11    H4   C02  C03  C04    36.65  30.0  2
 I6R  Var_12    H5   C02  C03  C04   154.69  30.0  2
 I6R  Var_13    H4   C02  C03  N10  -144.29  30.0  2
 I6R  Var_14    H5   C02  C03  N10   -26.25  30.0  2
 I6R  Var_15    H6   C04  C05  O06   -52.09  30.0  1
 I6R  Var_16    H7   C04  C05  O06    61.74  30.0  1
 I6R  Var_17    H1   C01  C02  C03  -179.63  30.0  3
 I6R  Var_18    H2   C01  C02  C03   -60.28  30.0  3
 I6R  Var_19    H3   C01  C02  C03    60.86  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
 I6R  plan-1  C03  0.020
 I6R  plan-1  C04  0.020
 I6R  plan-1  C05  0.020
 I6R  plan-1  C08  0.020
 I6R  plan-1  N07  0.020
 I6R  plan-1  N10  0.020
 I6R  plan-1  O06  0.020
 I6R  plan-1  O09  0.020
 I6R  plan-1  H8   0.020

