# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 19:07:16 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 6-cyclopropyl-3-methyl-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NC(=CC1=O)C2CC2
#
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
 FIQ  FIQ  "6-cyclopropyl-3-methyl-1H-pyrimidine-2,4-dione"
  ligand  22  12  .  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_FIQ
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
 FIQ  C10  C  CH1   0  -0.378  14.4528  27.2183  -8.2725
 FIQ  C01  C  CH3   0  -0.526  19.7842  25.3251  -8.5906
 FIQ  C03  C  CR6   0   0.689  17.4368  24.9724  -8.0313
 FIQ  C06  C  CR6   0   0.529  15.8495  26.7747  -8.3793
 FIQ  C07  C  CR16  0  -0.550  16.8225  27.5803  -8.8586
 FIQ  C08  C  CR6   0   0.607  18.1813  27.1210  -8.9499
 FIQ  C11  C  CH2   0  -0.474  13.2938  26.2854  -8.5203
 FIQ  C12  C  CH2   0  -0.474  13.5560  26.7778  -7.1422
 FIQ  N02  N  NR6   0  -0.576  18.4147  25.8137  -8.5117
 FIQ  N05  N  NR16  0  -0.755  16.1754  25.5112  -7.9836
 FIQ  O09  O  O     0  -0.473  19.1087  27.7892  -9.3740
 FIQ  H1   H  HCH1  0   0.288  14.3189  28.2378  -8.6110
 FIQ  H2   H  HCH3  0   0.266  19.8321  24.3233  -8.1825
 FIQ  H3   H  HCH3  0   0.254  20.1218  25.3015  -9.6250
 FIQ  H4   H  HCH3  0   0.254  20.4481  25.9702  -8.0196
 FIQ  H5   H  HCR6  0   0.279  16.5978  28.5855  -9.1821
 FIQ  H7   H  HCH2  0   0.278  12.4579  26.6962  -9.0702
 FIQ  H8   H  HCH2  0   0.267  13.5036  25.2477  -8.7490
 FIQ  H9   H  HCH2  0   0.278  12.9046  27.5334  -6.7245
 FIQ  H10  H  HCH2  0   0.266  13.9514  26.0841  -6.4105
 FIQ  H6   H  HNR6  0   0.429  15.4675  24.8832  -7.6295
 FIQ  O04  O  O     0  -0.475  17.6446  23.8326  -7.6676

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
 FIQ  O09  C08  double  1.219  0.020  1.219
 FIQ  C08  C07  single  1.437  0.020  1.437
 FIQ  C08  N02  single  1.398  0.020  1.398
 FIQ  C07  C06  double  1.351  0.020  1.351
 FIQ  C01  N02  single  1.456  0.020  1.456
 FIQ  N02  C03  single  1.376  0.020  1.376
 FIQ  C11  C10  single  1.508  0.020  1.508
 FIQ  C11  C12  single  1.487  0.020  1.487
 FIQ  C06  C10  single  1.469  0.020  1.469
 FIQ  C06  N05  single  1.364  0.020  1.364
 FIQ  C10  C12  single  1.509  0.020  1.509
 FIQ  C03  N05  single  1.372  0.020  1.372
 FIQ  C03  O04  double  1.214  0.020  1.214
 FIQ  C10  H1   single  0.970  0.020  1.090
 FIQ  C01  H2   single  0.970  0.020  1.090
 FIQ  C01  H3   single  0.970  0.020  1.090
 FIQ  C01  H4   single  0.970  0.020  1.090
 FIQ  C07  H5   single  0.930  0.020  1.080
 FIQ  C11  H7   single  0.970  0.020  1.090
 FIQ  C11  H8   single  0.970  0.020  1.090
 FIQ  C12  H9   single  0.970  0.020  1.090
 FIQ  C12  H10  single  0.970  0.020  1.090
 FIQ  N05  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
 FIQ  H1   C10  C12  115.83  3.000
 FIQ  H1   C10  C11  115.86  3.000
 FIQ  C12  C10  C11   59.05  3.000
 FIQ  H1   C10  C06  112.28  3.000
 FIQ  C12  C10  C06  122.10  3.000
 FIQ  C11  C10  C06  122.12  3.000
 FIQ  H4   C01  H3   108.82  3.000
 FIQ  H4   C01  H2   108.90  3.000
 FIQ  H3   C01  H2   108.93  3.000
 FIQ  H4   C01  N02  110.28  3.000
 FIQ  H3   C01  N02  110.52  3.000
 FIQ  H2   C01  N02  109.36  3.000
 FIQ  O04  C03  N05  121.02  3.000
 FIQ  O04  C03  N02  123.82  3.000
 FIQ  N05  C03  N02  115.16  3.000
 FIQ  N05  C06  C07  118.90  3.000
 FIQ  N05  C06  C10  119.07  3.000
 FIQ  C07  C06  C10  122.03  3.000
 FIQ  H5   C07  C08  118.37  3.000
 FIQ  H5   C07  C06  120.77  3.000
 FIQ  C08  C07  C06  120.86  3.000
 FIQ  O09  C08  N02  119.63  3.000
 FIQ  N02  C08  C07  115.89  3.000
 FIQ  O09  C08  C07  124.48  3.000
 FIQ  H8   C11  H7   113.97  3.000
 FIQ  H8   C11  C12  118.61  3.000
 FIQ  H7   C11  C12  118.80  3.000
 FIQ  H8   C11  C10  118.59  3.000
 FIQ  H7   C11  C10  116.26  3.000
 FIQ  C12  C11  C10   60.49  3.000
 FIQ  H10  C12  H9   113.98  3.000
 FIQ  H10  C12  C11  118.59  3.000
 FIQ  H9   C12  C11  118.89  3.000
 FIQ  H10  C12  C10  118.44  3.000
 FIQ  H9   C12  C10  116.32  3.000
 FIQ  C11  C12  C10   60.47  3.000
 FIQ  C08  N02  C03  124.20  3.000
 FIQ  C03  N02  C01  118.82  3.000
 FIQ  C08  N02  C01  116.98  3.000
 FIQ  H6   N05  C06  120.67  3.000
 FIQ  H6   N05  C03  114.34  3.000
 FIQ  C06  N05  C03  124.98  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
 FIQ  CONST_01  N02  C03  N05  C06     0.00   0.0  0
 FIQ  CONST_02  N05  C03  N02  C08     0.00   0.0  0
 FIQ  CONST_03  N05  C03  N02  C01   180.00   0.0  0
 FIQ  CONST_04  O04  C03  N05  C06   180.00   0.0  0
 FIQ  CONST_05  O04  C03  N02  C08   180.00   0.0  0
 FIQ  CONST_06  H6   N05  C03  N02   180.00   0.0  0
 FIQ  CONST_07  O04  C03  N02  C01     0.00   0.0  0
 FIQ  CONST_08  H6   N05  C03  O04     0.00   0.0  0
 FIQ  Var_01    C08  C07  C06  C10   179.89  30.0  1
 FIQ  Var_02    C03  N05  C06  C10   179.93  30.0  1
 FIQ  Var_03    C07  C08  N02  C03     0.85  30.0  1
 FIQ  Var_04    C07  C06  N05  C03    -0.04  30.0  1
 FIQ  Var_05    N02  C08  C07  C06    -0.24  30.0  1
 FIQ  Var_06    C12  C11  C10  C06   110.80  30.0  1
 FIQ  Var_07    C11  C10  C06  C07   144.14  30.0  3
 FIQ  Var_08    C12  C10  C06  C07  -144.71  30.0  3
 FIQ  Var_09    N05  C06  C07  C08    -0.14  30.0  1
 FIQ  Var_10    N05  C06  C10  C11   -35.83  30.0  2
 FIQ  Var_11    N05  C06  C10  C12    35.32  30.0  2
 FIQ  Var_12    C07  C08  N02  C01  -179.85  30.0  1
 FIQ  Var_13    O09  C08  N02  C03  -179.20  30.0  1
 FIQ  Var_14    O09  C08  C07  C06   179.81  30.0  1
 FIQ  Var_15    H9   C12  C11  C10   105.63  30.0  1
 FIQ  Var_16    H10  C12  C11  C10  -108.34  30.0  1
 FIQ  Var_17    H5   C07  C06  C10    -0.09  30.0  1
 FIQ  Var_18    H6   N05  C06  C10     0.57  30.0  1
 FIQ  Var_19    H7   C11  C12  C10  -105.60  30.0  1
 FIQ  Var_20    H8   C11  C12  C10   108.51  30.0  1
 FIQ  Var_21    H7   C11  C10  C06  -139.45  30.0  1
 FIQ  Var_22    H8   C11  C10  C06     2.24  30.0  1
 FIQ  Var_23    H9   C12  C10  C06   139.33  30.0  1
 FIQ  Var_24    H10  C12  C10  C06    -2.26  30.0  1
 FIQ  Var_25    H1   C10  C06  C07    -0.33  30.0  3
 FIQ  Var_26    H6   N05  C06  C07  -179.40  30.0  1
 FIQ  Var_27    H1   C10  C12  C11   105.94  30.0  1
 FIQ  Var_28    H5   C07  C08  N02   179.74  30.0  1
 FIQ  Var_29    H5   C07  C06  N05   179.88  30.0  1
 FIQ  Var_30    H1   C10  C06  N05   179.70  30.0  3
 FIQ  Var_31    O09  C08  N02  C01     0.10  30.0  1
 FIQ  Var_32    H2   C01  N02  C03    -3.12  30.0  3
 FIQ  Var_33    H3   C01  N02  C03   116.79  30.0  3
 FIQ  Var_34    H4   C01  N02  C03  -122.85  30.0  3
 FIQ  Var_35    H2   C01  N02  C08   177.54  30.0  3
 FIQ  Var_36    H3   C01  N02  C08   -62.55  30.0  3
 FIQ  Var_37    H4   C01  N02  C08    57.81  30.0  3
 FIQ  Var_38    H5   C07  C08  O09    -0.21  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 FIQ  chir_01  C10  C11  C06  C12  both

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
 FIQ  plan-1  C07  0.020
 FIQ  plan-1  C08  0.020
 FIQ  plan-1  N02  0.020
 FIQ  plan-1  O09  0.020
 FIQ  plan-2  C01  0.020
 FIQ  plan-2  C03  0.020
 FIQ  plan-2  C06  0.020
 FIQ  plan-2  C08  0.020
 FIQ  plan-2  N02  0.020
 FIQ  plan-2  N05  0.020
 FIQ  plan-2  H6   0.020
 FIQ  plan-2  O04  0.020

