# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 21:51:20 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CSC2=NC3=C(CCC3)C(=O)N2)cc1
#
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
 1UA  1UA  2-[(4-methylbenzyl)sulfanyl]-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one  ligand  35  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1UA
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
 1UA  O17  O  O     0  -0.472   4.1737   2.3750   0.0502
 1UA  C6   C  CR6   0   0.521   3.4642   1.3814   0.0278
 1UA  C5   C  CR56  0  -0.148   3.8743   0.0157  -0.0344
 1UA  C4   C  CR56  0   0.249   2.9386  -0.9698  -0.0674
 1UA  C2   C  CH2   0  -0.501   3.5788  -2.3191  -0.1735
 1UA  C3   C  CH2   0  -0.477   5.2657  -0.5272  -0.1120
 1UA  C1   C  CH2   0  -0.465   5.0498  -2.0291   0.1722
 1UA  N19  N  NR16  0  -0.688   2.0714   1.5030   0.0701
 1UA  C7   C  CR6   0   0.344   1.2144   0.4566   0.0282
 1UA  N18  N  N     0  -0.454   1.5966  -0.7784  -0.0425
 1UA  S16  S  S2    0   0.079  -0.4817   0.8806   0.0749
 1UA  C8   C  CH2   0  -0.621  -1.2666  -0.7660   0.0192
 1UA  C9   C  CR6   0   0.075  -2.7486  -0.5430   0.0261
 1UA  C11  C  CR16  0  -0.268  -3.4491  -0.4550   1.2246
 1UA  C13  C  CR16  0  -0.285  -4.8190  -0.2352   1.2273
 1UA  C14  C  CR6   0   0.088  -5.5260  -0.0916   0.0355
 1UA  C15  C  CH3   0  -0.720  -7.0032   0.1733   0.0374
 1UA  C12  C  CR16  0  -0.282  -4.8178  -0.1803  -1.1618
 1UA  C10  C  CR16  0  -0.269  -3.4488  -0.3991  -1.1680
 1UA  H1   H  HCH2  0   0.260   3.1156  -3.0527   0.4880
 1UA  H2   H  HCH2  0   0.248   5.6914  -0.3592  -1.1060
 1UA  H3   H  HCH2  0   0.249   5.9464  -0.0642   0.6041
 1UA  H4   H  HCH2  0   0.245   5.2136  -2.2205   1.2336
 1UA  H5   H  HNR6  0   0.429   1.7050   2.4465   0.1279
 1UA  H6   H  HCH2  0   0.305  -0.9358  -1.2747  -0.8843
 1UA  H7   H  HCH2  0   0.305  -0.9349  -1.3356   0.8852
 1UA  H8   H  HCR6  0   0.255  -2.9223  -0.5699   2.1647
 1UA  H9   H  HCR6  0   0.250  -5.3467  -0.1782   2.1720
 1UA  H10  H  HCH3  0   0.250  -7.2063   1.2435  -0.0413
 1UA  H11  H  HCH3  0   0.244  -7.4965  -0.3105  -0.8055
 1UA  H12  H  HCH3  0   0.244  -7.4732  -0.1810   0.9541
 1UA  H13  H  HCR6  0   0.250  -5.3444  -0.0788  -2.1034
 1UA  H14  H  HCR6  0   0.255  -2.9204  -0.4684  -2.1117
 1UA  H15  H  HCH2  0   0.262   3.4613  -2.6947  -1.1950
 1UA  H16  H  HCH2  0   0.243   5.7417  -2.6611  -0.3822

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
 1UA  C2   C1   single    1.539  0.020  1.539
 1UA  C2   C4   single    1.497  0.020  1.497
 1UA  C1   C3   single    1.544  0.020  1.544
 1UA  C4   N18  single    1.356  0.020  1.356
 1UA  C4   C5   double    1.359  0.020  1.359
 1UA  C3   C5   single    1.496  0.020  1.496
 1UA  N18  C7   double    1.295  0.020  1.295
 1UA  C5   C6   single    1.427  0.020  1.427
 1UA  C8   C9   single    1.499  0.020  1.499
 1UA  C8   S16  single    1.825  0.020  1.825
 1UA  C11  C9   aromatic  1.391  0.020  1.391
 1UA  C11  C13  aromatic  1.387  0.020  1.387
 1UA  C7   S16  single    1.749  0.020  1.749
 1UA  C7   N19  single    1.353  0.020  1.353
 1UA  C6   N19  single    1.399  0.020  1.399
 1UA  C6   O17  double    1.221  0.020  1.221
 1UA  C9   C10  aromatic  1.392  0.020  1.392
 1UA  C13  C14  aromatic  1.393  0.020  1.393
 1UA  C10  C12  aromatic  1.386  0.020  1.386
 1UA  C14  C12  aromatic  1.394  0.020  1.394
 1UA  C14  C15  single    1.501  0.020  1.501
 1UA  C2   H1   single    0.970  0.020  1.090
 1UA  C3   H2   single    0.970  0.020  1.090
 1UA  C3   H3   single    0.970  0.020  1.090
 1UA  C1   H4   single    0.970  0.020  1.090
 1UA  N19  H5   single    0.860  0.020  1.020
 1UA  C8   H6   single    0.970  0.020  1.090
 1UA  C8   H7   single    0.970  0.020  1.090
 1UA  C11  H8   single    0.930  0.020  1.080
 1UA  C13  H9   single    0.930  0.020  1.080
 1UA  C15  H10  single    0.970  0.020  1.090
 1UA  C15  H11  single    0.970  0.020  1.090
 1UA  C15  H12  single    0.970  0.020  1.090
 1UA  C12  H13  single    0.930  0.020  1.080
 1UA  C10  H14  single    0.930  0.020  1.080
 1UA  C2   H15  single    0.970  0.020  1.090
 1UA  C1   H16  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
 1UA  N19  C6   C5   111.75  3.000
 1UA  N19  C6   O17  120.48  3.000
 1UA  C5   C6   O17  127.76  3.000
 1UA  C3   C5   C4   112.08  3.000
 1UA  C3   C5   C6   128.09  3.000
 1UA  C4   C5   C6   119.80  3.000
 1UA  N18  C4   C2   123.48  3.000
 1UA  N18  C4   C5   125.35  3.000
 1UA  C2   C4   C5   111.15  3.000
 1UA  H15  C2   H1   106.83  3.000
 1UA  H15  C2   C1   112.14  3.000
 1UA  H1   C2   C1   113.36  3.000
 1UA  H15  C2   C4   109.23  3.000
 1UA  H1   C2   C4   112.43  3.000
 1UA  C1   C2   C4   102.89  3.000
 1UA  H3   C3   H2   106.75  3.000
 1UA  H3   C3   C1   112.29  3.000
 1UA  H2   C3   C1   111.77  3.000
 1UA  H3   C3   C5   113.11  3.000
 1UA  H2   C3   C5   110.69  3.000
 1UA  C1   C3   C5   102.33  3.000
 1UA  H16  C1   H4   107.35  3.000
 1UA  H16  C1   C3   112.47  3.000
 1UA  H4   C1   C3   109.19  3.000
 1UA  H16  C1   C2   112.57  3.000
 1UA  H4   C1   C2   109.21  3.000
 1UA  C3   C1   C2   106.00  3.000
 1UA  H5   N19  C7   119.51  3.000
 1UA  H5   N19  C6   116.26  3.000
 1UA  C7   N19  C6   124.23  3.000
 1UA  S16  C7   N18  121.26  3.000
 1UA  S16  C7   N19  115.21  3.000
 1UA  N18  C7   N19  123.53  3.000
 1UA  C7   N18  C4   115.33  3.000
 1UA  C8   S16  C7   101.39  3.000
 1UA  H7   C8   H6   108.86  3.000
 1UA  H7   C8   C9   112.06  3.000
 1UA  H6   C8   C9   111.97  3.000
 1UA  H7   C8   S16  108.47  3.000
 1UA  H6   C8   S16  108.44  3.000
 1UA  C9   C8   S16  106.91  3.000
 1UA  C10  C9   C11  118.64  3.000
 1UA  C10  C9   C8   120.59  3.000
 1UA  C11  C9   C8   120.76  3.000
 1UA  H8   C11  C13  119.68  3.000
 1UA  H8   C11  C9   119.73  3.000
 1UA  C13  C11  C9   120.59  3.000
 1UA  H9   C13  C14  119.55  3.000
 1UA  H9   C13  C11  119.39  3.000
 1UA  C14  C13  C11  121.05  3.000
 1UA  C12  C14  C15  120.83  3.000
 1UA  C15  C14  C13  121.11  3.000
 1UA  C12  C14  C13  118.06  3.000
 1UA  H12  C15  H11  108.13  3.000
 1UA  H12  C15  H10  107.41  3.000
 1UA  H11  C15  H10  107.16  3.000
 1UA  H12  C15  C14  111.60  3.000
 1UA  H11  C15  C14  111.48  3.000
 1UA  H10  C15  C14  110.85  3.000
 1UA  H13  C12  C10  119.39  3.000
 1UA  H13  C12  C14  119.57  3.000
 1UA  C10  C12  C14  121.04  3.000
 1UA  H14  C10  C12  119.70  3.000
 1UA  H14  C10  C9   119.68  3.000
 1UA  C12  C10  C9   120.62  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
 1UA  CONST_01  C14  C13  C11  C9      0.00   0.0  0
 1UA  CONST_02  C14  C12  C10  C9      0.00   0.0  0
 1UA  CONST_03  C12  C10  C9   C11     0.00   0.0  0
 1UA  CONST_04  C12  C14  C13  C11     0.00   0.0  0
 1UA  CONST_05  C10  C9   C11  C13     0.00   0.0  0
 1UA  CONST_06  C10  C12  C14  C13     0.00   0.0  0
 1UA  CONST_07  N18  C7   N19  C6      0.00   0.0  0
 1UA  CONST_08  C7   N19  C6   C5      0.00   0.0  0
 1UA  CONST_09  N19  C7   N18  C4      0.00   0.0  0
 1UA  CONST_10  C13  C11  C9   C8    180.00   0.0  0
 1UA  CONST_11  C12  C10  C9   C8    180.00   0.0  0
 1UA  CONST_12  C15  C14  C13  C11   180.00   0.0  0
 1UA  CONST_13  C10  C12  C14  C15   180.00   0.0  0
 1UA  CONST_14  C7   N19  C6   O17   180.00   0.0  0
 1UA  CONST_15  S16  C7   N19  C6    180.00   0.0  0
 1UA  CONST_16  S16  C7   N18  C4    180.00   0.0  0
 1UA  CONST_17  H9   C13  C11  C9    180.00   0.0  0
 1UA  CONST_18  H13  C12  C10  C9    180.00   0.0  0
 1UA  CONST_19  H14  C10  C9   C11   180.00   0.0  0
 1UA  CONST_20  H8   C11  C13  C14   180.00   0.0  0
 1UA  CONST_21  H5   N19  C6   C5    180.00   0.0  0
 1UA  Var_01    C1   C3   C5   C6    167.62  30.0  1
 1UA  Var_02    C1   C2   C4   C5     14.39  30.0  1
 1UA  Var_03    C2   C1   C3   C5     22.39  30.0  1
 1UA  Var_04    C3   C1   C2   C4    -22.54  30.0  1
 1UA  Var_05    C9   C8   S16  C7   -178.90  30.0  1
 1UA  Var_06    C11  C9   C8   S16   -88.92  30.0  2
 1UA  Var_07    H10  C15  C14  C13    95.24  30.0  2

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
 1UA  plan-1  C8   0.020
 1UA  plan-1  C9   0.020
 1UA  plan-1  C11  0.020
 1UA  plan-1  C13  0.020
 1UA  plan-1  C14  0.020
 1UA  plan-1  C15  0.020
 1UA  plan-1  C12  0.020
 1UA  plan-1  C10  0.020
 1UA  plan-1  H8   0.020
 1UA  plan-1  H9   0.020
 1UA  plan-1  H13  0.020
 1UA  plan-1  H14  0.020
 1UA  plan-2  O17  0.020
 1UA  plan-2  C6   0.020
 1UA  plan-2  C5   0.020
 1UA  plan-2  C4   0.020
 1UA  plan-2  C2   0.020
 1UA  plan-2  C3   0.020
 1UA  plan-2  N19  0.020
 1UA  plan-2  C7   0.020
 1UA  plan-2  N18  0.020
 1UA  plan-2  S16  0.020
 1UA  plan-2  H5   0.020

