# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:06:24 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 6-cyclopropyl-5~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC(=NC(=O)N1)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
 I5Z  I5Z  "6-cyclopropyl-5~{H}-pyrimidine-2,4-dione"
  ligand  19  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 GRAND
;

data_comp_I5Z
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
 I5Z  C10  C  CH2   0  -0.451  13.4276  26.9697  -5.0127
 I5Z  C02  C  C     0   0.597  17.3499  25.4048  -5.7380
 I5Z  C04  C  C     0   0.575  18.1027  27.5186  -6.7428
 I5Z  C06  C  CH2   0  -0.679  16.6654  27.9409  -6.7776
 I5Z  C07  C  C     0   0.348  15.7007  26.9587  -6.2018
 I5Z  C09  C  CH1   0  -0.366  14.2982  27.3769  -6.1853
 I5Z  C11  C  CH2   0  -0.450  13.2122  26.3322  -6.3268
 I5Z  N03  N  NH1   0  -0.697  18.3165  26.2726  -6.2268
 I5Z  N08  N  N     0  -0.478  16.0273  25.8107  -5.7380
 I5Z  O05  O  O     0  -0.426  19.0071  28.2156  -7.1402
 I5Z  H1   H  HCH2  0   0.272  12.7190  27.7110  -4.6688
 I5Z  H2   H  HCH2  0   0.266  13.9088  26.3934  -4.2338
 I5Z  H3   H  HCH2  0   0.335  16.5615  28.8989  -6.2588
 I5Z  H4   H  HCH2  0   0.337  16.3829  28.1478  -7.8156
 I5Z  H5   H  HCH1  0   0.286  14.1018  28.3490  -6.6202
 I5Z  H6   H  HCH2  0   0.272  12.3488  26.6212  -6.9107
 I5Z  H7   H  HCH2  0   0.265  13.5415  25.3107  -6.4626
 I5Z  H8   H  HNH1  0   0.421  19.2739  25.9419  -6.1923
 I5Z  O01  O  O     0  -0.427  17.6731  24.3187  -5.3198

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
 I5Z  O05  C04  double  1.209  0.020  1.209
 I5Z  C04  C06  single  1.498  0.020  1.498
 I5Z  C04  N03  single  1.366  0.020  1.366
 I5Z  C06  C07  single  1.492  0.020  1.492
 I5Z  C11  C09  single  1.513  0.020  1.513
 I5Z  C11  C10  single  1.476  0.020  1.476
 I5Z  N03  C02  single  1.388  0.020  1.388
 I5Z  C07  C09  single  1.464  0.020  1.464
 I5Z  C07  N08  double  1.280  0.020  1.280
 I5Z  C09  C10  single  1.516  0.020  1.516
 I5Z  C02  N08  single  1.383  0.020  1.383
 I5Z  C02  O01  double  1.208  0.020  1.208
 I5Z  C10  H1   single  0.970  0.020  1.090
 I5Z  C10  H2   single  0.970  0.020  1.090
 I5Z  C06  H3   single  0.970  0.020  1.090
 I5Z  C06  H4   single  0.970  0.020  1.090
 I5Z  C09  H5   single  0.970  0.020  1.090
 I5Z  C11  H6   single  0.970  0.020  1.090
 I5Z  C11  H7   single  0.970  0.020  1.090
 I5Z  N03  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
 I5Z  H2   C10  H1   115.31  3.000
 I5Z  H2   C10  C11  118.41  3.000
 I5Z  H1   C10  C11  118.90  3.000
 I5Z  H2   C10  C09  116.40  3.000
 I5Z  H1   C10  C09  115.98  3.000
 I5Z  C11  C10  C09   60.75  3.000
 I5Z  O01  C02  N08  121.30  3.000
 I5Z  O01  C02  N03  119.85  3.000
 I5Z  N08  C02  N03  118.84  3.000
 I5Z  O05  C04  N03  122.22  3.000
 I5Z  N03  C04  C06  114.59  3.000
 I5Z  O05  C04  C06  123.19  3.000
 I5Z  H4   C06  H3   105.03  3.000
 I5Z  H4   C06  C07  108.86  3.000
 I5Z  H3   C06  C07  109.38  3.000
 I5Z  H4   C06  C04  108.82  3.000
 I5Z  H3   C06  C04  109.07  3.000
 I5Z  C07  C06  C04  115.19  3.000
 I5Z  N08  C07  C09  119.77  3.000
 I5Z  N08  C07  C06  124.40  3.000
 I5Z  C09  C07  C06  115.83  3.000
 I5Z  H5   C09  C11  116.87  3.000
 I5Z  H5   C09  C07  115.20  3.000
 I5Z  C11  C09  C07  119.29  3.000
 I5Z  H5   C09  C10  116.59  3.000
 I5Z  C07  C09  C10  118.83  3.000
 I5Z  C11  C09  C10   58.33  3.000
 I5Z  H7   C11  H6   115.31  3.000
 I5Z  H7   C11  C09  116.43  3.000
 I5Z  H6   C11  C09  116.03  3.000
 I5Z  H7   C11  C10  118.36  3.000
 I5Z  H6   C11  C10  118.80  3.000
 I5Z  C09  C11  C10   60.93  3.000
 I5Z  H8   N03  C04  117.29  3.000
 I5Z  H8   N03  C02  116.23  3.000
 I5Z  C04  N03  C02  126.48  3.000
 I5Z  C07  N08  C02  120.46  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
 I5Z  CONST_01  N08  C02  N03  C04     0.00   0.0  0
 I5Z  CONST_02  N03  C02  N08  C07     0.00   0.0  0
 I5Z  CONST_03  O01  C02  N03  C04   180.00   0.0  0
 I5Z  CONST_04  O01  C02  N08  C07   180.00   0.0  0
 I5Z  CONST_05  H8   N03  C02  N08   180.00   0.0  0
 I5Z  CONST_06  H8   N03  C02  O01     0.00   0.0  0
 I5Z  Var_01    C07  C09  C11  C10   107.67  30.0  1
 I5Z  Var_02    C06  C07  C09  C10  -143.80  30.0  1
 I5Z  Var_03    N08  C07  C09  C10    36.17  30.0  1
 I5Z  Var_04    C06  C04  N03  C02    -0.70  30.0  1
 I5Z  Var_05    C06  C07  N08  C02     0.43  30.0  1
 I5Z  Var_06    C09  C07  N08  C02  -179.55  30.0  1
 I5Z  Var_07    C09  C07  C06  C04   177.91  30.0  1
 I5Z  Var_08    N08  C07  C06  C04    -2.06  30.0  1
 I5Z  Var_09    C11  C09  C07  C06   148.44  30.0  3
 I5Z  Var_10    N03  C04  C06  C07     2.05  30.0  1
 I5Z  Var_11    N08  C07  C09  C11   -31.59  30.0  1
 I5Z  Var_12    O05  C04  N03  C02   179.49  30.0  1
 I5Z  Var_13    O05  C04  C06  C07  -178.14  30.0  1
 I5Z  Var_14    H5   C09  C11  C10  -106.08  30.0  1
 I5Z  Var_15    H6   C11  C09  C10   109.99  30.0  1
 I5Z  Var_16    H7   C11  C09  C10  -109.31  30.0  1
 I5Z  Var_17    H8   N03  C04  C06   179.41  30.0  1
 I5Z  Var_18    H5   C09  C07  C06     1.65  30.0  3
 I5Z  Var_19    H6   C11  C09  C07  -142.35  30.0  1
 I5Z  Var_20    H7   C11  C09  C07    -1.64  30.0  1
 I5Z  Var_21    H1   C10  C09  C07   141.46  30.0  1
 I5Z  Var_22    H2   C10  C09  C07     0.86  30.0  1
 I5Z  Var_23    H1   C10  C11  C09   105.32  30.0  1
 I5Z  Var_24    H2   C10  C11  C09  -106.04  30.0  1
 I5Z  Var_25    H3   C06  C07  C09    54.67  30.0  1
 I5Z  Var_26    H4   C06  C07  C09   -59.58  30.0  1
 I5Z  Var_27    H3   C06  C04  N03   125.45  30.0  1
 I5Z  Var_28    H4   C06  C04  N03  -120.48  30.0  1
 I5Z  Var_29    H3   C06  C07  N08  -125.30  30.0  1
 I5Z  Var_30    H4   C06  C07  N08   120.45  30.0  1
 I5Z  Var_31    H5   C09  C07  N08  -178.38  30.0  3
 I5Z  Var_32    H3   C06  C04  O05   -54.73  30.0  1
 I5Z  Var_33    H4   C06  C04  O05    59.33  30.0  1
 I5Z  Var_34    H8   N03  C04  O05    -0.40  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
 I5Z  chir_01  C09  C11  C07  C10  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
 I5Z  plan-1  C04  0.020
 I5Z  plan-1  C06  0.020
 I5Z  plan-1  N03  0.020
 I5Z  plan-1  O05  0.020
 I5Z  plan-2  C02  0.020
 I5Z  plan-2  C04  0.020
 I5Z  plan-2  C07  0.020
 I5Z  plan-2  N03  0.020
 I5Z  plan-2  N08  0.020
 I5Z  plan-2  H8   0.020
 I5Z  plan-2  O01  0.020

