# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:56:25 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 6-[[ethyl-(4-fluorophenyl)amino]methyl]-2,3-dihydro-1~{H}-cyclopenta[3,4][1,3]thiazolo[1,4-~{a}]pyrimidin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC1=CC(=O)N2C3=C(CCC3)SC2=N1)c4ccc(F)cc4
#
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
 5YE  5YE  6-[[ethyl-(4-fluorophenyl)amino]methyl]-2,3-dihydro-1~{H}-cyclopenta[3,4][1,3]thiazolo[1,4-~{a}]pyrimidin-8-one  ligand  42  24  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5YE
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
 5YE  C4   C  CR16  0  -0.511   0.9683   2.2927   0.5740
 5YE  C14  C  CR16  0  -0.398  -5.1155  -0.9345  -0.8337
 5YE  C5   C  CR6   0   0.576   2.3316   1.9936   0.2697
 5YE  C6   C  CR55  0   0.475   3.7950   0.0069  -0.0847
 5YE  C11  C  CH2   0  -0.470   5.1381   0.5382  -0.4583
 5YE  C7   C  CR55  0  -0.277   3.7408  -1.3278  -0.0918
 5YE  C8   C  CR56  0   0.310   1.5657  -0.3006   0.3899
 5YE  C9   C  CH2   0  -0.480   5.0279  -1.9687  -0.4784
 5YE  C10  C  CH2   0  -0.473   5.9922  -0.7553  -0.4333
 5YE  C12  C  CR6   0   0.385  -3.1265   0.2181  -0.0250
 5YE  C13  C  CR16  0  -0.343  -4.2434   0.1431  -0.8740
 5YE  N1   N  N     0  -0.620   2.5715   0.6052   0.1882
 5YE  N2   N  N     0  -0.461   0.3364  -0.0110   0.6631
 5YE  C3   C  CR6   0   0.305   0.0405   1.3060   0.7523
 5YE  C15  C  CR6   0   0.480  -4.8961  -1.9527   0.0690
 5YE  C16  C  CR16  0  -0.400  -3.8089  -1.9212   0.9185
 5YE  C17  C  CR16  0  -0.317  -2.9282  -0.8530   0.8635
 5YE  N    N  NT    0  -0.504  -2.2581   1.2874  -0.0757
 5YE  C1   C  CH2   0  -0.341  -2.3287   2.2741  -1.1347
 5YE  C    C  CH3   0  -0.662  -3.2768   3.4333  -0.8481
 5YE  C2   C  CH2   0  -0.424  -1.4015   1.6360   1.0325
 5YE  O    O  O     0  -0.468   3.2418   2.7813   0.0833
 5YE  S    S  S2    0   0.259   2.1523  -1.9298   0.2390
 5YE  H1   H  HCR6  0   0.281   0.6897   3.3343   0.6575
 5YE  H2   H  HCR6  0   0.273  -5.9685  -0.9626  -1.4993
 5YE  H3   H  HCH2  0   0.262   5.1094   0.9961  -1.4498
 5YE  H4   H  HCH2  0   0.268   5.5171   1.2893   0.2321
 5YE  H5   H  HCH2  0   0.266   5.3351  -2.7649   0.2001
 5YE  H6   H  HCH2  0   0.264   4.9561  -2.4050  -1.4778
 5YE  H7   H  HCH2  0   0.253   6.7047  -0.7799  -1.2552
 5YE  H8   H  HCH2  0   0.256   6.5638  -0.7873   0.4936
 5YE  H9   H  HCR6  0   0.270  -4.4587   0.9337  -1.5781
 5YE  H11  H  HCR6  0   0.272  -3.6298  -2.7334   1.6117
 5YE  H12  H  HCR6  0   0.265  -2.0529  -0.8831   1.4955
 5YE  H13  H  HCH2  0   0.256  -1.3199   2.6629  -1.2960
 5YE  H14  H  HCH2  0   0.250  -2.6010   1.7824  -2.0698
 5YE  H15  H  HCH3  0   0.229  -4.3072   3.0959  -0.7351
 5YE  H16  H  HCH3  0   0.228  -2.9948   3.9570   0.0662
 5YE  H17  H  HCH3  0   0.234  -3.2461   4.1545  -1.6648
 5YE  H18  H  HCH2  0   0.281  -1.7226   1.1266   1.9421
 5YE  H19  H  HCH2  0   0.279  -1.4907   2.7062   1.2388
 5YE  F    F  F     0  -0.328  -5.7504  -2.9965   0.1183

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
 5YE  C10  C11  single    1.550  0.020  1.550
 5YE  C10  C9   single    1.551  0.020  1.551
 5YE  C11  C6   single    1.492  0.020  1.492
 5YE  O    C5   double    1.218  0.020  1.218
 5YE  C9   C7   single    1.489  0.020  1.489
 5YE  C6   C7   double    1.336  0.020  1.336
 5YE  C6   N1   single    1.389  0.020  1.389
 5YE  C5   N1   single    1.411  0.020  1.411
 5YE  C5   C4   single    1.428  0.020  1.428
 5YE  C7   S    single    1.731  0.020  1.731
 5YE  N1   C8   single    1.369  0.020  1.369
 5YE  C4   C3   double    1.366  0.020  1.366
 5YE  C    C1   single    1.525  0.020  1.525
 5YE  C8   S    single    1.738  0.020  1.738
 5YE  C8   N2   double    1.292  0.020  1.292
 5YE  C3   N2   single    1.353  0.020  1.353
 5YE  C3   C2   single    1.506  0.020  1.506
 5YE  C1   N    single    1.449  0.020  1.449
 5YE  C2   N    single    1.443  0.020  1.443
 5YE  N    C12  single    1.379  0.020  1.379
 5YE  C12  C13  aromatic  1.405  0.020  1.405
 5YE  C12  C17  aromatic  1.406  0.020  1.406
 5YE  C13  C14  aromatic  1.387  0.020  1.387
 5YE  C17  C16  aromatic  1.386  0.020  1.386
 5YE  C14  C15  aromatic  1.378  0.020  1.378
 5YE  C16  C15  aromatic  1.380  0.020  1.380
 5YE  C15  F    single    1.350  0.020  1.350
 5YE  C4   H1   single    0.930  0.020  1.080
 5YE  C14  H2   single    0.930  0.020  1.080
 5YE  C11  H3   single    0.970  0.020  1.090
 5YE  C11  H4   single    0.970  0.020  1.090
 5YE  C9   H5   single    0.970  0.020  1.090
 5YE  C9   H6   single    0.970  0.020  1.090
 5YE  C10  H7   single    0.970  0.020  1.090
 5YE  C10  H8   single    0.970  0.020  1.090
 5YE  C13  H9   single    0.930  0.020  1.080
 5YE  C16  H11  single    0.930  0.020  1.080
 5YE  C17  H12  single    0.930  0.020  1.080
 5YE  C1   H13  single    0.970  0.020  1.090
 5YE  C1   H14  single    0.970  0.020  1.090
 5YE  C    H15  single    0.970  0.020  1.090
 5YE  C    H16  single    0.970  0.020  1.090
 5YE  C    H17  single    0.970  0.020  1.090
 5YE  C2   H18  single    0.970  0.020  1.090
 5YE  C2   H19  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
 5YE  H1   C4   C3   120.71  3.000
 5YE  H1   C4   C5   117.64  3.000
 5YE  C3   C4   C5   121.65  3.000
 5YE  H2   C14  C15  120.60  3.000
 5YE  H2   C14  C13  119.86  3.000
 5YE  C15  C14  C13  119.53  3.000
 5YE  O    C5   N1   120.02  3.000
 5YE  N1   C5   C4   112.37  3.000
 5YE  O    C5   C4   127.62  3.000
 5YE  N1   C6   C7   113.31  3.000
 5YE  N1   C6   C11  133.53  3.000
 5YE  C7   C6   C11  113.02  3.000
 5YE  H4   C11  H3   107.20  3.000
 5YE  H4   C11  C10  111.95  3.000
 5YE  H3   C11  C10  112.26  3.000
 5YE  H4   C11  C6   113.60  3.000
 5YE  H3   C11  C6   110.66  3.000
 5YE  C10  C11  C6   101.23  3.000
 5YE  S    C7   C9   133.90  3.000
 5YE  S    C7   C6   112.57  3.000
 5YE  C9   C7   C6   113.35  3.000
 5YE  S    C8   N2   123.33  3.000
 5YE  N2   C8   N1   125.59  3.000
 5YE  S    C8   N1   111.07  3.000
 5YE  H6   C9   H5   107.22  3.000
 5YE  H6   C9   C10  112.33  3.000
 5YE  H5   C9   C10  112.21  3.000
 5YE  H6   C9   C7   110.64  3.000
 5YE  H5   C9   C7   113.35  3.000
 5YE  C10  C9   C7   101.14  3.000
 5YE  H8   C10  H7   107.36  3.000
 5YE  H8   C10  C9   109.15  3.000
 5YE  H7   C10  C9   111.57  3.000
 5YE  H8   C10  C11  109.11  3.000
 5YE  H7   C10  C11  111.56  3.000
 5YE  C9   C10  C11  108.05  3.000
 5YE  N    C12  C17  121.70  3.000
 5YE  C17  C12  C13  116.97  3.000
 5YE  N    C12  C13  121.33  3.000
 5YE  H9   C13  C12  120.88  3.000
 5YE  H9   C13  C14  117.53  3.000
 5YE  C12  C13  C14  121.59  3.000
 5YE  C8   N1   C6   113.03  3.000
 5YE  C8   N1   C5   121.18  3.000
 5YE  C6   N1   C5   125.79  3.000
 5YE  C3   N2   C8   116.12  3.000
 5YE  C2   C3   N2   115.79  3.000
 5YE  C2   C3   C4   121.09  3.000
 5YE  N2   C3   C4   123.10  3.000
 5YE  C16  C15  F    119.59  3.000
 5YE  F    C15  C14  119.63  3.000
 5YE  C16  C15  C14  120.78  3.000
 5YE  H11  C16  C17  119.91  3.000
 5YE  H11  C16  C15  120.48  3.000
 5YE  C17  C16  C15  119.60  3.000
 5YE  H12  C17  C16  118.06  3.000
 5YE  H12  C17  C12  120.36  3.000
 5YE  C16  C17  C12  121.52  3.000
 5YE  C2   N    C1   115.18  3.000
 5YE  C2   N    C12  122.21  3.000
 5YE  C1   N    C12  121.62  3.000
 5YE  H14  C1   H13  105.32  3.000
 5YE  H14  C1   C    110.40  3.000
 5YE  H13  C1   C    109.34  3.000
 5YE  H14  C1   N    109.37  3.000
 5YE  H13  C1   N    107.76  3.000
 5YE  C    C1   N    114.24  3.000
 5YE  H17  C    H16  107.65  3.000
 5YE  H17  C    H15  108.00  3.000
 5YE  H16  C    H15  107.83  3.000
 5YE  H17  C    C1   110.16  3.000
 5YE  H16  C    C1   111.21  3.000
 5YE  H15  C    C1   111.84  3.000
 5YE  H19  C2   H18  106.00  3.000
 5YE  H19  C2   N    109.44  3.000
 5YE  H18  C2   N    110.65  3.000
 5YE  H19  C2   C3   109.13  3.000
 5YE  H18  C2   C3   109.56  3.000
 5YE  N    C2   C3   111.87  3.000
 5YE  C8   S    C7    90.02  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
 5YE  CONST_01  C17  C12  C13  C14    0.00   0.0  0
 5YE  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 5YE  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 5YE  CONST_04  C15  C16  C17  C12    0.00   0.0  0
 5YE  CONST_05  C16  C17  C12  C13    0.00   0.0  0
 5YE  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 5YE  CONST_07  C6   N1   C5   C4   180.00   0.0  0
 5YE  CONST_08  C8   N1   C5   C4     0.00   0.0  0
 5YE  CONST_09  S    C8   N1   C5   180.00   0.0  0
 5YE  CONST_10  N2   C8   N1   C5     0.00   0.0  0
 5YE  CONST_11  S    C8   N1   C6     0.00   0.0  0
 5YE  CONST_12  N2   C8   N1   C6   180.00   0.0  0
 5YE  CONST_13  C3   N2   C8   N1     0.00   0.0  0
 5YE  CONST_14  S    C8   N2   C3   180.00   0.0  0
 5YE  CONST_15  N    C12  C13  C14  180.00   0.0  0
 5YE  CONST_16  F    C15  C14  C13  180.00   0.0  0
 5YE  CONST_17  C17  C16  C15  F    180.00   0.0  0
 5YE  CONST_18  N    C12  C17  C16  180.00   0.0  0
 5YE  CONST_19  O    C5   N1   C6     0.00   0.0  0
 5YE  CONST_20  O    C5   N1   C8   180.00   0.0  0
 5YE  CONST_21  H11  C16  C15  C14  180.00   0.0  0
 5YE  CONST_22  H2   C14  C13  C12  180.00   0.0  0
 5YE  CONST_23  H12  C17  C12  C13  180.00   0.0  0
 5YE  CONST_24  H9   C13  C14  C15  180.00   0.0  0
 5YE  CONST_25  C1   N    C12  C13    0.00   0.0  0
 5YE  CONST_27  C1   N    C12  C17  180.00   0.0  0
 5YE  Var_01    C9   C10  C11  C6    17.04  30.0  1
 5YE  Var_02    C10  C9   C7   C6    11.12  30.0  1
 5YE  Var_03    C7   C9   C10  C11  -17.21  30.0  1
 5YE  Var_04    C10  C11  C6   C7   -10.57  30.0  1
 5YE  Var_05    N    C2   C3   C4   111.01  30.0  3
 5YE  Var_06    C3   C2   N    C12  107.92  30.0  1
 5YE  Var_07    C    C1   N    C12   88.21  30.0  1
 5YE  Var_08    H15  C    C1   N    -62.32  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
 5YE  plan-1  C14  0.020
 5YE  plan-1  C12  0.020
 5YE  plan-1  C13  0.020
 5YE  plan-1  C15  0.020
 5YE  plan-1  C16  0.020
 5YE  plan-1  C17  0.020
 5YE  plan-1  N    0.020
 5YE  plan-1  H2   0.020
 5YE  plan-1  H9   0.020
 5YE  plan-1  H11  0.020
 5YE  plan-1  H12  0.020
 5YE  plan-1  F    0.020
 5YE  plan-2  C12  0.020
 5YE  plan-2  N    0.020
 5YE  plan-2  C1   0.020
 5YE  plan-2  C2   0.020
 5YE  plan-3  C4   0.020
 5YE  plan-3  C5   0.020
 5YE  plan-3  C6   0.020
 5YE  plan-3  C11  0.020
 5YE  plan-3  C7   0.020
 5YE  plan-3  C8   0.020
 5YE  plan-3  C9   0.020
 5YE  plan-3  N1   0.020
 5YE  plan-3  N2   0.020
 5YE  plan-3  C3   0.020
 5YE  plan-3  C2   0.020
 5YE  plan-3  O    0.020
 5YE  plan-3  S    0.020
 5YE  plan-3  H1   0.020

