# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:35:35 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCCCN2CCCCC2)nc3sc4CCCc4c13
#
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
 RMS  RMS  2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-amine  ligand  47  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RMS
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
 RMS  C10  C  CH2   0  -0.297  20.8688  -11.2499  42.7643
 RMS  C11  C  CH2   0  -0.433  20.2859  -12.4148  43.5726
 RMS  C12  C  CH2   0  -0.430  19.7490  -11.9254  44.9220
 RMS  C13  C  CH2   0  -0.480  20.5885  -10.7545  45.4152
 RMS  C19  C  CR55  0   0.192  21.2558  -12.7199  35.2930
 RMS  C20  C  CR55  0  -0.228  20.4196  -12.8658  34.2430
 RMS  C21  C  CH2   0  -0.478  20.7790  -13.9920  33.3336
 RMS  C23  C  CH2   0  -0.528  22.3470  -13.7472  35.2574
 RMS  C02  C  CR6   0   0.475  21.3786  -11.1579  37.3813
 RMS  N03  N  N     0  -0.450  20.7626  -10.1506  38.0009
 RMS  C04  C  CR6   0   0.212  19.6491   -9.6698  37.4727
 RMS  S05  S  S2    0   0.045  18.8252   -8.3437  38.2831
 RMS  C06  C  CH2   0  -0.576  19.7812   -8.1353  39.8084
 RMS  C07  C  CH2   0  -0.419  19.5187   -9.2165  40.8430
 RMS  N09  N  NT    0  -0.427  20.1563  -10.0276  43.0919
 RMS  C14  C  CH2   0  -0.268  20.5196   -9.5798  44.4291
 RMS  N15  N  N     0  -0.458  19.0470  -10.0616  36.3628
 RMS  C16  C  CR56  0  -0.030  19.6684  -11.0616  35.7455
 RMS  S17  S  S2    0   0.203  19.0858  -11.7623  34.2629
 RMS  C18  C  CR56  0  -0.039  20.8421  -11.6796  36.1801
 RMS  C22  C  CH2   0  -0.463  22.2028  -14.3387  33.8338
 RMS  H1   H  HCH2  0   0.235  20.7762  -11.4593  41.6979
 RMS  H2   H  HCH2  0   0.195  21.9505  -11.1420  42.9569
 RMS  H3   H  HCH2  0   0.223  19.4858  -12.8973  43.0073
 RMS  H4   H  HCH2  0   0.218  21.0608  -13.1702  43.7224
 RMS  H5   H  HCH2  0   0.217  18.7082  -11.6091  44.8202
 RMS  H6   H  HCH2  0   0.228  19.7563  -12.7367  45.6524
 RMS  H7   H  HCH2  0   0.222  21.6237  -11.0866  45.5336
 RMS  H8   H  HCH2  0   0.239  20.2623  -10.4247  46.4031
 RMS  H9   H  HCH2  0   0.256  20.7695  -13.7197  32.2772
 RMS  H10  H  HCH2  0   0.254  20.0845  -14.8281  33.4538
 RMS  H11  H  HCH2  0   0.254  22.1900  -14.5050  36.0307
 RMS  H12  H  HCH2  0   0.250  23.3444  -13.3315  35.4176
 RMS  H13  H  HNH2  0   0.404  22.8313  -11.2475  38.7973
 RMS  H14  H  HNH2  0   0.421  23.0012  -12.4080  37.5366
 RMS  H15  H  HCH2  0   0.276  20.8384   -8.0769  39.5498
 RMS  H16  H  HCH2  0   0.281  19.4796   -7.1537  40.1808
 RMS  H17  H  HCH2  0   0.228  18.4552   -9.2433  41.0902
 RMS  H18  H  HCH2  0   0.241  19.7749  -10.1846  40.4112
 RMS  H19  H  HCH2  0   0.188  21.3861   -8.8099  41.8666
 RMS  H20  H  HCH2  0   0.227  19.9746   -8.0366  42.5676
 RMS  H22  H  HCH2  0   0.192  21.4881   -9.0513  44.4259
 RMS  H23  H  HCH2  0   0.223  19.7715   -8.8525  44.7580
 RMS  H24  H  HCH2  0   0.246  22.3906  -15.4112  33.8153
 RMS  H25  H  HCH2  0   0.249  22.9357  -13.8704  33.1763
 RMS  C08  C  CH2   0  -0.257  20.3221   -8.9710  42.1154
 RMS  N01  N  NH2   0  -0.830  22.4976  -11.6339  37.9308

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
 RMS  C21  C22  single    1.548  0.020  1.548
 RMS  C21  C20  single    1.491  0.020  1.491
 RMS  C22  C23  single    1.548  0.020  1.548
 RMS  C20  S17  aromatic  1.731  0.020  1.731
 RMS  C20  C19  aromatic  1.350  0.020  1.350
 RMS  S17  C16  aromatic  1.740  0.020  1.740
 RMS  C23  C19  single    1.499  0.020  1.499
 RMS  C19  C18  aromatic  1.428  0.020  1.428
 RMS  C16  C18  aromatic  1.396  0.020  1.396
 RMS  C16  N15  aromatic  1.329  0.020  1.329
 RMS  C18  C02  aromatic  1.415  0.020  1.415
 RMS  N15  C04  aromatic  1.322  0.020  1.322
 RMS  C02  N01  single    1.334  0.020  1.334
 RMS  C02  N03  aromatic  1.333  0.020  1.333
 RMS  C04  N03  aromatic  1.323  0.020  1.323
 RMS  C04  S05  single    1.759  0.020  1.759
 RMS  S05  C06  single    1.812  0.020  1.812
 RMS  C06  C07  single    1.519  0.020  1.519
 RMS  C07  C08  single    1.525  0.020  1.525
 RMS  C08  N09  single    1.448  0.020  1.448
 RMS  C10  N09  single    1.452  0.020  1.452
 RMS  C10  C11  single    1.533  0.020  1.533
 RMS  N09  C14  single    1.456  0.020  1.456
 RMS  C11  C12  single    1.533  0.020  1.533
 RMS  C14  C13  single    1.535  0.020  1.535
 RMS  C12  C13  single    1.523  0.020  1.523
 RMS  C10  H1   single    0.970  0.020  1.090
 RMS  C10  H2   single    0.970  0.020  1.090
 RMS  C11  H3   single    0.970  0.020  1.090
 RMS  C11  H4   single    0.970  0.020  1.090
 RMS  C12  H5   single    0.970  0.020  1.090
 RMS  C12  H6   single    0.970  0.020  1.090
 RMS  C13  H7   single    0.970  0.020  1.090
 RMS  C13  H8   single    0.970  0.020  1.090
 RMS  C21  H9   single    0.970  0.020  1.090
 RMS  C21  H10  single    0.970  0.020  1.090
 RMS  C23  H11  single    0.970  0.020  1.090
 RMS  C23  H12  single    0.970  0.020  1.090
 RMS  N01  H13  single    0.860  0.020  1.020
 RMS  N01  H14  single    0.860  0.020  1.020
 RMS  C06  H15  single    0.970  0.020  1.090
 RMS  C06  H16  single    0.970  0.020  1.090
 RMS  C07  H17  single    0.970  0.020  1.090
 RMS  C07  H18  single    0.970  0.020  1.090
 RMS  C08  H19  single    0.970  0.020  1.090
 RMS  C08  H20  single    0.970  0.020  1.090
 RMS  C14  H22  single    0.970  0.020  1.090
 RMS  C14  H23  single    0.970  0.020  1.090
 RMS  C22  H24  single    0.970  0.020  1.090
 RMS  C22  H25  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
 RMS  H2   C10  H1   105.82  3.000
 RMS  H2   C10  N09  111.04  3.000
 RMS  H1   C10  N09  109.90  3.000
 RMS  H2   C10  C11  110.79  3.000
 RMS  H1   C10  C11  109.71  3.000
 RMS  N09  C10  C11  109.52  3.000
 RMS  H4   C11  H3   106.57  3.000
 RMS  H4   C11  C12  110.40  3.000
 RMS  H3   C11  C12  109.89  3.000
 RMS  H4   C11  C10  109.15  3.000
 RMS  H3   C11  C10  109.96  3.000
 RMS  C12  C11  C10  110.78  3.000
 RMS  H6   C12  H5   106.49  3.000
 RMS  H6   C12  C13  110.56  3.000
 RMS  H5   C12  C13  109.44  3.000
 RMS  H6   C12  C11  110.45  3.000
 RMS  H5   C12  C11  110.13  3.000
 RMS  C13  C12  C11  109.73  3.000
 RMS  H8   C13  H7   106.06  3.000
 RMS  H8   C13  C14  109.68  3.000
 RMS  H7   C13  C14  110.14  3.000
 RMS  H8   C13  C12  111.14  3.000
 RMS  H7   C13  C12  108.87  3.000
 RMS  C14  C13  C12  110.83  3.000
 RMS  C18  C19  C23  136.44  3.000
 RMS  C18  C19  C20  112.48  3.000
 RMS  C23  C19  C20  111.00  3.000
 RMS  S17  C20  C21  132.37  3.000
 RMS  S17  C20  C19  113.54  3.000
 RMS  C21  C20  C19  113.99  3.000
 RMS  H10  C21  H9   106.96  3.000
 RMS  H10  C21  C22  112.16  3.000
 RMS  H9   C21  C22  112.13  3.000
 RMS  H10  C21  C20  110.93  3.000
 RMS  H9   C21  C20  113.57  3.000
 RMS  C22  C21  C20  101.17  3.000
 RMS  H12  C23  H11  106.92  3.000
 RMS  H12  C23  C22  111.42  3.000
 RMS  H11  C23  C22  111.83  3.000
 RMS  H12  C23  C19  113.60  3.000
 RMS  H11  C23  C19  110.70  3.000
 RMS  C22  C23  C19  102.47  3.000
 RMS  C18  C02  N03  119.85  3.000
 RMS  N03  C02  N01  117.74  3.000
 RMS  C18  C02  N01  122.41  3.000
 RMS  C04  N03  C02  118.55  3.000
 RMS  N15  C04  S05  113.38  3.000
 RMS  S05  C04  N03  118.97  3.000
 RMS  N15  C04  N03  127.65  3.000
 RMS  C06  S05  C04  103.15  3.000
 RMS  H16  C06  H15  107.49  3.000
 RMS  H16  C06  C07  111.08  3.000
 RMS  H15  C06  C07  111.55  3.000
 RMS  H16  C06  S05  104.16  3.000
 RMS  H15  C06  S05  108.55  3.000
 RMS  C07  C06  S05  113.59  3.000
 RMS  H18  C07  H17  107.25  3.000
 RMS  H18  C07  C08  110.47  3.000
 RMS  H17  C07  C08  109.16  3.000
 RMS  H18  C07  C06  108.76  3.000
 RMS  H17  C07  C06  109.86  3.000
 RMS  C08  C07  C06  111.26  3.000
 RMS  C14  N09  C08  111.48  3.000
 RMS  C14  N09  C10  110.09  3.000
 RMS  C08  N09  C10  113.94  3.000
 RMS  H23  C14  H22  106.42  3.000
 RMS  H23  C14  N09  108.05  3.000
 RMS  H22  C14  N09  111.32  3.000
 RMS  H23  C14  C13  110.26  3.000
 RMS  H22  C14  C13  109.21  3.000
 RMS  N09  C14  C13  111.45  3.000
 RMS  C16  N15  C04  113.57  3.000
 RMS  C18  C16  S17  111.62  3.000
 RMS  C18  C16  N15  125.56  3.000
 RMS  S17  C16  N15  122.82  3.000
 RMS  C16  S17  C20   90.49  3.000
 RMS  C16  C18  C02  114.82  3.000
 RMS  C02  C18  C19  133.30  3.000
 RMS  C16  C18  C19  111.88  3.000
 RMS  H25  C22  H24  107.27  3.000
 RMS  H25  C22  C23  109.14  3.000
 RMS  H24  C22  C23  112.07  3.000
 RMS  H25  C22  C21  109.09  3.000
 RMS  H24  C22  C21  111.94  3.000
 RMS  C23  C22  C21  107.28  3.000
 RMS  H20  C08  H19  105.92  3.000
 RMS  H20  C08  N09  107.94  3.000
 RMS  H19  C08  N09  111.63  3.000
 RMS  H20  C08  C07  108.36  3.000
 RMS  H19  C08  C07  110.06  3.000
 RMS  N09  C08  C07  112.63  3.000
 RMS  H14  N01  H13  117.91  3.000
 RMS  H14  N01  C02  122.27  3.000
 RMS  H13  N01  C02  119.74  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
 RMS  CONST_01  C16  S17  C20  C19     0.00   0.0  0
 RMS  CONST_02  S17  C16  C18  C19     0.00   0.0  0
 RMS  CONST_03  N15  C16  C18  C19   180.00   0.0  0
 RMS  CONST_04  N03  C02  C18  C19   180.00   0.0  0
 RMS  CONST_05  C18  C16  S17  C20     0.00   0.0  0
 RMS  CONST_06  N15  C16  S17  C20   180.00   0.0  0
 RMS  CONST_07  C16  C18  C19  C20     0.00   0.0  0
 RMS  CONST_08  C02  C18  C19  C20   180.00   0.0  0
 RMS  CONST_09  S17  C16  C18  C02   180.00   0.0  0
 RMS  CONST_10  N15  C16  C18  C02     0.00   0.0  0
 RMS  CONST_11  N15  C04  N03  C02     0.00   0.0  0
 RMS  CONST_12  C16  C18  C02  N03     0.00   0.0  0
 RMS  CONST_13  C16  N15  C04  N03     0.00   0.0  0
 RMS  CONST_14  S17  C16  N15  C04   180.00   0.0  0
 RMS  CONST_15  C18  C16  N15  C04     0.00   0.0  0
 RMS  CONST_16  C18  C02  N03  C04     0.00   0.0  0
 RMS  CONST_17  C18  C19  C20  S17     0.00   0.0  0
 RMS  CONST_18  N01  C02  C18  C19     0.00   0.0  0
 RMS  CONST_19  C16  C18  C02  N01   180.00   0.0  0
 RMS  CONST_20  C04  N03  C02  N01   180.00   0.0  0
 RMS  CONST_21  S05  C04  N03  C02   180.00   0.0  0
 RMS  CONST_22  C16  N15  C04  S05   180.00   0.0  0
 RMS  CONST_23  H13  N01  C02  N03     0.00   0.0  0
 RMS  CONST_24  H14  N01  C02  N03   180.00   0.0  0
 RMS  Var_01    C13  C14  N09  C10   -42.27  30.0  1
 RMS  Var_02    C13  C12  C11  C10   -32.42  30.0  1
 RMS  Var_03    C14  N09  C10  C11    72.21  30.0  1
 RMS  Var_04    C14  C13  C12  C11    61.07  30.0  1
 RMS  Var_05    N09  C10  C11  C12   -30.69  30.0  1
 RMS  Var_06    N09  C14  C13  C12   -22.89  30.0  1
 RMS  Var_07    C22  C21  C20  C19   -12.46  30.0  1
 RMS  Var_08    C21  C22  C23  C19   -19.44  30.0  1
 RMS  Var_09    C23  C22  C21  C20    19.29  30.0  1
 RMS  Var_10    C22  C23  C19  C20    12.12  30.0  1
 RMS  Var_11    C07  C08  N09  C10    74.78  30.0  1
 RMS  Var_12    N15  C04  S05  C06   175.21  30.0  2
 RMS  Var_13    C07  C06  S05  C04   -74.87  30.0  3
 RMS  Var_14    N09  C08  C07  C06  -176.51  30.0  3
 RMS  Var_15    C08  C07  C06  S05  -178.59  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
 RMS  plan-1  C19  0.020
 RMS  plan-1  C20  0.020
 RMS  plan-1  C21  0.020
 RMS  plan-1  C23  0.020
 RMS  plan-1  C02  0.020
 RMS  plan-1  N03  0.020
 RMS  plan-1  C04  0.020
 RMS  plan-1  S05  0.020
 RMS  plan-1  N15  0.020
 RMS  plan-1  C16  0.020
 RMS  plan-1  S17  0.020
 RMS  plan-1  C18  0.020
 RMS  plan-1  N01  0.020
 RMS  plan-2  C02  0.020
 RMS  plan-2  H13  0.020
 RMS  plan-2  H14  0.020
 RMS  plan-2  N01  0.020

