# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:26:34 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1C(=O)N=C(SC(C)C)C2=C1CCC2
#
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
 5GL  5GL  4-propan-2-ylsulfanyl-1-propyl-6,7-dihydro-5~{H}-cyclopenta[d]pyrimidin-2-one  ligand  37  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5GL
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
 5GL  C4   C  CR56  0  -0.029  -0.0245  -1.2586  -0.1283
 5GL  C5   C  CR6   0   0.080  -0.9539  -0.2047  -0.0695
 5GL  C6   C  CR6   0   0.579   0.7031   1.4044  -0.2941
 5GL  N1   N  N     0  -0.496  -0.6023   1.0506  -0.1624
 5GL  C10  C  CH2   0  -0.489  -0.1884  -2.7417   0.0093
 5GL  C11  C  CH2   0  -0.461   1.1916  -3.2691  -0.4320
 5GL  C12  C  CH2   0  -0.516   2.1817  -2.1022  -0.2613
 5GL  O    O  O     0  -0.508   1.0591   2.5719  -0.3592
 5GL  N    N  NR6   0  -0.560   1.6636   0.3828  -0.3557
 5GL  C2   C  CH2   0  -0.309   3.0743   0.7544  -0.4343
 5GL  C1   C  CH2   0  -0.436   3.6736   1.0622   0.9314
 5GL  C    C  CH3   0  -0.669   5.1478   1.4211   0.8131
 5GL  S    S  S2    0   0.066  -2.6272  -0.6449   0.1522
 5GL  C3   C  CR56  0   0.419   1.2832  -0.9061  -0.2678
 5GL  H2   H  HCH2  0   0.252  -0.4144  -3.0126   1.0447
 5GL  H3   H  HCH2  0   0.252  -0.9942  -3.1446  -0.6069
 5GL  H4   H  HCH2  0   0.252   1.5002  -4.1506   0.1268
 5GL  H5   H  HCH2  0   0.254   1.1518  -3.5484  -1.4851
 5GL  H6   H  HCH2  0   0.281   2.7230  -2.1467   0.6890
 5GL  H7   H  HCH2  0   0.281   2.9326  -2.0787  -1.0514
 5GL  H8   H  HCH2  0   0.262   3.6146  -0.0638  -0.9079
 5GL  H9   H  HCH2  0   0.268   3.1624   1.6155  -1.0938
 5GL  H10  H  HCH2  0   0.238   3.1230   1.8845   1.3923
 5GL  H11  H  HCH2  0   0.230   3.5547   0.1943   1.5853
 5GL  H12  H  HCH3  0   0.238   5.5703   1.6654   1.7872
 5GL  H13  H  HCH3  0   0.225   5.7259   0.5922   0.4007
 5GL  H14  H  HCH3  0   0.225   5.2953   2.2844   0.1622
 5GL  C7   C  CH1   0  -0.365  -3.5050   0.9596   0.1534
 5GL  C8   C  CH3   0  -0.633  -3.6805   1.4914  -1.2583
 5GL  C9   C  CH3   0  -0.649  -4.8365   0.7322   0.8546
 5GL  H1   H  HCH1  0   0.285  -2.8905   1.6452   0.7373
 5GL  H15  H  HCH3  0   0.236  -4.1905   2.4566  -1.2241
 5GL  H16  H  HCH3  0   0.246  -2.7213   1.6373  -1.7520
 5GL  H17  H  HCH3  0   0.227  -4.2842   0.8121  -1.8613
 5GL  H18  H  HCH3  0   0.246  -4.7025   0.3958   1.8823
 5GL  H19  H  HCH3  0   0.248  -5.3946   1.6689   0.8770
 5GL  H20  H  HCH3  0   0.234  -5.4481  -0.0032   0.3288

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
 5GL  C10  C11  single  1.542  0.020  1.542
 5GL  C10  C4   single  1.498  0.020  1.498
 5GL  S    C5   single  1.744  0.020  1.744
 5GL  C11  C12  single  1.540  0.020  1.540
 5GL  C4   C5   single  1.406  0.020  1.406
 5GL  C4   C3   double  1.361  0.020  1.361
 5GL  C5   N1   double  1.307  0.020  1.307
 5GL  C12  C3   single  1.496  0.020  1.496
 5GL  C3   N    single  1.347  0.020  1.347
 5GL  N1   C6   single  1.359  0.020  1.359
 5GL  N    C6   single  1.404  0.020  1.404
 5GL  N    C2   single  1.461  0.020  1.461
 5GL  C6   O    double  1.222  0.020  1.222
 5GL  C1   C2   single  1.523  0.020  1.523
 5GL  C1   C    single  1.522  0.020  1.522
 5GL  C10  H2   single  0.970  0.020  1.090
 5GL  C10  H3   single  0.970  0.020  1.090
 5GL  C11  H4   single  0.970  0.020  1.090
 5GL  C11  H5   single  0.970  0.020  1.090
 5GL  C12  H6   single  0.970  0.020  1.090
 5GL  C12  H7   single  0.970  0.020  1.090
 5GL  C2   H8   single  0.970  0.020  1.090
 5GL  C2   H9   single  0.970  0.020  1.090
 5GL  C1   H10  single  0.970  0.020  1.090
 5GL  C1   H11  single  0.970  0.020  1.090
 5GL  C    H12  single  0.970  0.020  1.090
 5GL  C    H13  single  0.970  0.020  1.090
 5GL  C    H14  single  0.970  0.020  1.090
 5GL  S    C7   single  1.829  0.020  1.829
 5GL  C7   C8   single  1.519  0.020  1.519
 5GL  C7   C9   single  1.522  0.020  1.522
 5GL  C7   H1   single  0.970  0.020  1.090
 5GL  C8   H15  single  0.970  0.020  1.090
 5GL  C8   H16  single  0.970  0.020  1.090
 5GL  C8   H17  single  0.970  0.020  1.090
 5GL  C9   H18  single  0.970  0.020  1.090
 5GL  C9   H19  single  0.970  0.020  1.090
 5GL  C9   H20  single  0.970  0.020  1.090

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
 5GL  C3   C4   C10  111.76  3.000
 5GL  C3   C4   C5   116.42  3.000
 5GL  C10  C4   C5   131.72  3.000
 5GL  S    C5   N1   120.63  3.000
 5GL  N1   C5   C4   122.62  3.000
 5GL  S    C5   C4   116.75  3.000
 5GL  N    C6   O    119.57  3.000
 5GL  O    C6   N1   122.26  3.000
 5GL  N    C6   N1   118.17  3.000
 5GL  C6   N1   C5   121.02  3.000
 5GL  H3   C10  H2   106.89  3.000
 5GL  H3   C10  C11  111.89  3.000
 5GL  H2   C10  C11  111.79  3.000
 5GL  H3   C10  C4   113.22  3.000
 5GL  H2   C10  C4   110.77  3.000
 5GL  C11  C10  C4   102.37  3.000
 5GL  H5   C11  H4   107.38  3.000
 5GL  H5   C11  C12  108.95  3.000
 5GL  H4   C11  C12  112.00  3.000
 5GL  H5   C11  C10  109.35  3.000
 5GL  H4   C11  C10  112.57  3.000
 5GL  C12  C11  C10  106.53  3.000
 5GL  H7   C12  H6   106.83  3.000
 5GL  H7   C12  C3   113.16  3.000
 5GL  H6   C12  C3   109.46  3.000
 5GL  H7   C12  C11  112.27  3.000
 5GL  H6   C12  C11  112.55  3.000
 5GL  C3   C12  C11  102.66  3.000
 5GL  C3   N    C2   121.31  3.000
 5GL  C2   N    C6   118.56  3.000
 5GL  C3   N    C6   120.02  3.000
 5GL  H9   C2   H8   106.90  3.000
 5GL  H9   C2   C1   110.59  3.000
 5GL  H8   C2   C1   110.28  3.000
 5GL  H9   C2   N    108.18  3.000
 5GL  H8   C2   N    108.14  3.000
 5GL  C1   C2   N    112.53  3.000
 5GL  H11  C1   H10  106.89  3.000
 5GL  H11  C1   C    109.82  3.000
 5GL  H10  C1   C    110.11  3.000
 5GL  H11  C1   C2   109.46  3.000
 5GL  H10  C1   C2   109.41  3.000
 5GL  C    C1   C2   111.05  3.000
 5GL  H14  C    H13  107.70  3.000
 5GL  H14  C    H12  107.66  3.000
 5GL  H13  C    H12  107.62  3.000
 5GL  H14  C    C1   111.33  3.000
 5GL  H13  C    C1   111.31  3.000
 5GL  H12  C    C1   111.04  3.000
 5GL  C7   S    C5   103.83  3.000
 5GL  N    C3   C12  126.57  3.000
 5GL  N    C3   C4   121.72  3.000
 5GL  C12  C3   C4   111.68  3.000
 5GL  H1   C7   C9   109.89  3.000
 5GL  H1   C7   C8   110.05  3.000
 5GL  C9   C7   C8   112.30  3.000
 5GL  H1   C7   S    106.35  3.000
 5GL  C9   C7   S    106.81  3.000
 5GL  C8   C7   S    111.23  3.000
 5GL  H17  C8   H16  108.69  3.000
 5GL  H17  C8   H15  108.01  3.000
 5GL  H16  C8   H15  107.89  3.000
 5GL  H17  C8   C7   111.09  3.000
 5GL  H16  C8   C7   111.51  3.000
 5GL  H15  C8   C7   109.53  3.000
 5GL  H20  C9   H19  107.57  3.000
 5GL  H20  C9   H18  108.38  3.000
 5GL  H19  C9   H18  107.99  3.000
 5GL  H20  C9   C7   111.65  3.000
 5GL  H19  C9   C7   109.20  3.000
 5GL  H18  C9   C7   111.91  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
 5GL  CONST_01  N    C6   N1   C5      0.00   0.0  0
 5GL  CONST_02  C3   N    C6   N1      0.00   0.0  0
 5GL  CONST_03  O    C6   N1   C5    180.00   0.0  0
 5GL  CONST_04  C2   N    C6   N1    180.00   0.0  0
 5GL  CONST_05  C3   N    C6   O     180.00   0.0  0
 5GL  CONST_06  C2   N    C6   O       0.00   0.0  0
 5GL  Var_01    C12  C11  C10  C4     21.51  30.0  1
 5GL  Var_02    C11  C12  C3   C4     13.01  30.0  1
 5GL  Var_03    C11  C10  C4   C5    169.63  30.0  1
 5GL  Var_04    C3   C12  C11  C10   -21.17  30.0  1
 5GL  Var_05    C1   C2   N    C6     82.90  30.0  3
 5GL  Var_06    C8   C7   S    C5     78.39  30.0  3
 5GL  Var_07    C    C1   C2   N     179.01  30.0  1
 5GL  Var_08    H12  C    C1   C2    178.59  30.0  3
 5GL  Var_09    H15  C8   C7   S    -178.99  30.0  3
 5GL  Var_10    H18  C9   C7   S      60.52  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
 5GL  plan-1  C4   0.020
 5GL  plan-1  C5   0.020
 5GL  plan-1  C6   0.020
 5GL  plan-1  N1   0.020
 5GL  plan-1  C10  0.020
 5GL  plan-1  C12  0.020
 5GL  plan-1  O    0.020
 5GL  plan-1  N    0.020
 5GL  plan-1  C2   0.020
 5GL  plan-1  S    0.020
 5GL  plan-1  C3   0.020

