# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:12:47 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: (7S)-7-phenyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCCCN2CCCCC2)nc3sc4C[C@H](CCc4c13)c5ccccc5
#
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
 RN4  RN4  (7S)-7-phenyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine  ligand  60  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RN4
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
 RN4  C10  C  CH2   0  -0.297  18.9593  -11.5109  40.2128
 RN4  C11  C  CH2   0  -0.454  18.8478  -12.6979  41.1638
 RN4  C12  C  CH2   0  -0.430  20.2508  -13.1442  41.6057
 RN4  C14  C  CH2   0  -0.258  20.5612  -10.6587  41.8403
 RN4  C16  C  CR56  0  -0.031  19.5945  -10.5271  36.5100
 RN4  C18  C  CR5   0   0.225  21.0989  -12.2298  35.8784
 RN4  C19  C  CR5   0  -0.274  20.0230  -12.5307  35.1105
 RN4  C20  C  CH2   0  -0.458  19.9195  -13.6735  34.1564
 RN4  C21  C  CH1   0  -0.356  21.0144  -14.7053  34.4523
 RN4  C23  C  CR16  0  -0.319  21.3202  -15.4730  32.0609
 RN4  C25  C  CR16  0  -0.274  21.2031  -17.8017  31.4592
 RN4  C26  C  CR16  0  -0.237  20.9519  -18.1215  32.7859
 RN4  C29  C  CH2   0  -0.560  22.3537  -13.0504  35.8205
 RN4  C02  C  CR6   0   0.472  21.6474  -10.3956  37.6703
 RN4  N03  N  N     0  -0.433  21.1700   -9.3048  38.2630
 RN4  C04  C  CR6   0   0.217  19.9348   -8.9202  37.9981
 RN4  S05  S  S2    0   0.007  19.3066   -7.4763  38.7982
 RN4  C06  C  CH2   0  -0.562  20.1464   -7.5049  40.4109
 RN4  C07  C  CH2   0  -0.446  19.2495   -7.9895  41.5425
 RN4  N09  N  NT    0  -0.393  19.5542  -10.3402  40.8424
 RN4  C13  C  CH2   0  -0.477  21.2461  -11.9791  41.5258
 RN4  N15  N  N     0  -0.451  19.0931   -9.4683  37.1411
 RN4  C17  C  CR56  0  -0.007  20.8598  -11.0762  36.7056
 RN4  C22  C  CR6   0   0.193  21.0690  -15.7811  33.3982
 RN4  C24  C  CR16  0  -0.238  21.3865  -16.4719  31.1000
 RN4  C27  C  CR16  0  -0.340  20.8851  -17.1171  33.7440
 RN4  C28  C  CH2   0  -0.417  22.3604  -13.9968  34.6227
 RN4  S30  S  S2    0   0.200  18.6952  -11.4277  35.3388
 RN4  H1   H  HCH2  0   0.227  17.9797  -11.2345  39.8194
 RN4  H2   H  HCH2  0   0.216  19.5538  -11.8065  39.3395
 RN4  H3   H  HCH2  0   0.221  18.2527  -12.3990  42.0317
 RN4  H4   H  HCH2  0   0.228  18.3084  -13.5193  40.6876
 RN4  H5   H  HCH2  0   0.221  20.2128  -13.5310  42.6270
 RN4  H6   H  HCH2  0   0.223  20.6023  -13.9677  40.9799
 RN4  H7   H  HCH2  0   0.220  21.3038   -9.8552  41.8846
 RN4  H8   H  HCH2  0   0.179  20.1209  -10.7236  42.8520
 RN4  H9   H  HCH2  0   0.258  20.0082  -13.3085  33.1281
 RN4  H10  H  HCH2  0   0.265  18.9370  -14.1476  34.2260
 RN4  H11  H  HCH1  0   0.257  20.7661  -15.1823  35.4067
 RN4  H12  H  HCR6  0   0.247  21.4675  -14.4427  31.7579
 RN4  H13  H  HCR6  0   0.254  21.2553  -18.5809  30.7100
 RN4  H14  H  HCR6  0   0.254  20.8057  -19.1536  33.0780
 RN4  H15  H  HCH2  0   0.255  22.4570  -13.6276  36.7460
 RN4  H16  H  HCH2  0   0.256  23.2308  -12.4016  35.7551
 RN4  H17  H  HNH2  0   0.402  23.3474  -10.2987  38.7655
 RN4  H18  H  HNH2  0   0.421  23.2860  -11.6433  37.7017
 RN4  H19  H  HCH2  0   0.295  21.0278   -8.1337  40.2972
 RN4  H20  H  HCH2  0   0.273  20.4861   -6.4880  40.6077
 RN4  H21  H  HCH2  0   0.237  19.8569   -8.0029  42.4531
 RN4  H22  H  HCH2  0   0.240  18.4523   -7.2649  41.7267
 RN4  H26  H  HCH2  0   0.226  21.6876  -11.9194  40.5272
 RN4  H27  H  HCH2  0   0.235  22.0748  -12.1333  42.2190
 RN4  H28  H  HCR6  0   0.254  21.5813  -16.2109  30.0676
 RN4  H29  H  HCR6  0   0.248  20.6861  -17.3759  34.7776
 RN4  H30  H  HCH2  0   0.251  23.1570  -14.7317  34.7498
 RN4  H31  H  HCH2  0   0.234  22.5947  -13.4349  33.7137
 RN4  C08  C  CH2   0  -0.274  18.6090   -9.3516  41.2997
 RN4  N01  N  NH2   0  -0.843  22.8834  -10.7789  38.0132
 RN4  H23  H  HCH2  0   0.193  18.0890   -9.6530  42.2274
 RN4  H24  H  HCH2  0   0.225  17.8394   -9.2378  40.5337

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
 RN4  C24  C25  aromatic  1.390  0.020  1.390
 RN4  C24  C23  aromatic  1.388  0.020  1.388
 RN4  C25  C26  aromatic  1.388  0.020  1.388
 RN4  C23  C22  aromatic  1.395  0.020  1.395
 RN4  C26  C27  aromatic  1.390  0.020  1.390
 RN4  C22  C27  aromatic  1.392  0.020  1.392
 RN4  C22  C21  single    1.507  0.020  1.507
 RN4  C20  C21  single    1.533  0.020  1.533
 RN4  C20  C19  single    1.492  0.020  1.492
 RN4  C21  C28  single    1.531  0.020  1.531
 RN4  C28  C29  single    1.527  0.020  1.527
 RN4  C19  S30  aromatic  1.741  0.020  1.741
 RN4  C19  C18  aromatic  1.356  0.020  1.356
 RN4  S30  C16  aromatic  1.730  0.020  1.730
 RN4  C18  C29  single    1.500  0.020  1.500
 RN4  C18  C17  aromatic  1.439  0.020  1.439
 RN4  C16  C17  aromatic  1.393  0.020  1.393
 RN4  C16  N15  aromatic  1.331  0.020  1.331
 RN4  C17  C02  aromatic  1.419  0.020  1.419
 RN4  N15  C04  aromatic  1.320  0.020  1.320
 RN4  C02  N01  single    1.339  0.020  1.339
 RN4  C02  N03  aromatic  1.330  0.020  1.330
 RN4  C04  N03  aromatic  1.321  0.020  1.321
 RN4  C04  S05  single    1.766  0.020  1.766
 RN4  S05  C06  single    1.819  0.020  1.819
 RN4  C06  C07  single    1.523  0.020  1.523
 RN4  C07  C08  single    1.525  0.020  1.525
 RN4  C08  N09  single    1.442  0.020  1.442
 RN4  N09  C10  single    1.456  0.020  1.456
 RN4  N09  C14  single    1.453  0.020  1.453
 RN4  C10  C11  single    1.525  0.020  1.525
 RN4  C14  C13  single    1.520  0.020  1.520
 RN4  C11  C12  single    1.537  0.020  1.537
 RN4  C13  C12  single    1.534  0.020  1.534
 RN4  C10  H1   single    0.970  0.020  1.090
 RN4  C10  H2   single    0.970  0.020  1.090
 RN4  C11  H3   single    0.970  0.020  1.090
 RN4  C11  H4   single    0.970  0.020  1.090
 RN4  C12  H5   single    0.970  0.020  1.090
 RN4  C12  H6   single    0.970  0.020  1.090
 RN4  C14  H7   single    0.970  0.020  1.090
 RN4  C14  H8   single    0.970  0.020  1.090
 RN4  C20  H9   single    0.970  0.020  1.090
 RN4  C20  H10  single    0.970  0.020  1.090
 RN4  C21  H11  single    0.970  0.020  1.090
 RN4  C23  H12  single    0.930  0.020  1.080
 RN4  C25  H13  single    0.930  0.020  1.080
 RN4  C26  H14  single    0.930  0.020  1.080
 RN4  C29  H15  single    0.970  0.020  1.090
 RN4  C29  H16  single    0.970  0.020  1.090
 RN4  N01  H17  single    0.860  0.020  1.020
 RN4  N01  H18  single    0.860  0.020  1.020
 RN4  C06  H19  single    0.970  0.020  1.090
 RN4  C06  H20  single    0.970  0.020  1.090
 RN4  C07  H21  single    0.970  0.020  1.090
 RN4  C07  H22  single    0.970  0.020  1.090
 RN4  C08  H23  single    0.970  0.020  1.090
 RN4  C08  H24  single    0.970  0.020  1.090
 RN4  C13  H26  single    0.970  0.020  1.090
 RN4  C13  H27  single    0.970  0.020  1.090
 RN4  C24  H28  single    0.930  0.020  1.080
 RN4  C27  H29  single    0.930  0.020  1.080
 RN4  C28  H30  single    0.970  0.020  1.090
 RN4  C28  H31  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
 RN4  H2   C10  H1   105.53  3.000
 RN4  H2   C10  N09  109.84  3.000
 RN4  H1   C10  N09  108.60  3.000
 RN4  H2   C10  C11  109.04  3.000
 RN4  H1   C10  C11  110.87  3.000
 RN4  N09  C10  C11  112.70  3.000
 RN4  H4   C11  H3   106.43  3.000
 RN4  H4   C11  C12  110.96  3.000
 RN4  H3   C11  C12  110.35  3.000
 RN4  H4   C11  C10  110.47  3.000
 RN4  H3   C11  C10  108.78  3.000
 RN4  C12  C11  C10  109.79  3.000
 RN4  H6   C12  H5   106.25  3.000
 RN4  H6   C12  C13  109.50  3.000
 RN4  H5   C12  C13  109.88  3.000
 RN4  H6   C12  C11  110.35  3.000
 RN4  H5   C12  C11  109.86  3.000
 RN4  C13  C12  C11  110.89  3.000
 RN4  H8   C14  H7   106.03  3.000
 RN4  H8   C14  C13  108.53  3.000
 RN4  H7   C14  C13  109.89  3.000
 RN4  H8   C14  N09  111.43  3.000
 RN4  H7   C14  N09  109.69  3.000
 RN4  C13  C14  N09  111.13  3.000
 RN4  S30  C16  C17  111.23  3.000
 RN4  C17  C16  N15  126.11  3.000
 RN4  S30  C16  N15  122.65  3.000
 RN4  C17  C18  C29  126.83  3.000
 RN4  C17  C18  C19  111.81  3.000
 RN4  C29  C18  C19  121.36  3.000
 RN4  S30  C19  C20  121.06  3.000
 RN4  S30  C19  C18  112.98  3.000
 RN4  C20  C19  C18  125.96  3.000
 RN4  H10  C20  H9   106.10  3.000
 RN4  H10  C20  C21  109.74  3.000
 RN4  H9   C20  C21  110.35  3.000
 RN4  H10  C20  C19  110.72  3.000
 RN4  H9   C20  C19  109.85  3.000
 RN4  C21  C20  C19  110.02  3.000
 RN4  H11  C21  C28  107.69  3.000
 RN4  H11  C21  C22  107.87  3.000
 RN4  C28  C21  C22  112.11  3.000
 RN4  H11  C21  C20  107.42  3.000
 RN4  C28  C21  C20  109.75  3.000
 RN4  C22  C21  C20  111.79  3.000
 RN4  H12  C23  C24  118.96  3.000
 RN4  H12  C23  C22  120.15  3.000
 RN4  C24  C23  C22  120.89  3.000
 RN4  H13  C25  C24  120.24  3.000
 RN4  H13  C25  C26  120.32  3.000
 RN4  C24  C25  C26  119.44  3.000
 RN4  H14  C26  C27  119.78  3.000
 RN4  H14  C26  C25  120.13  3.000
 RN4  C27  C26  C25  120.09  3.000
 RN4  H16  C29  H15  106.72  3.000
 RN4  H16  C29  C28  108.52  3.000
 RN4  H15  C29  C28  109.61  3.000
 RN4  H16  C29  C18  110.41  3.000
 RN4  H15  C29  C18  109.54  3.000
 RN4  C28  C29  C18  111.90  3.000
 RN4  C17  C02  N03  119.81  3.000
 RN4  N03  C02  N01  116.87  3.000
 RN4  C17  C02  N01  123.31  3.000
 RN4  C04  N03  C02  119.02  3.000
 RN4  N15  C04  S05  113.99  3.000
 RN4  S05  C04  N03  118.68  3.000
 RN4  N15  C04  N03  127.28  3.000
 RN4  C06  S05  C04  102.98  3.000
 RN4  H20  C06  H19  107.78  3.000
 RN4  H20  C06  C07  110.25  3.000
 RN4  H19  C06  C07  111.75  3.000
 RN4  H20  C06  S05  106.82  3.000
 RN4  H19  C06  S05  106.88  3.000
 RN4  C07  C06  S05  113.07  3.000
 RN4  H22  C07  H21  105.82  3.000
 RN4  H22  C07  C08  108.23  3.000
 RN4  H21  C07  C08  110.77  3.000
 RN4  H22  C07  C06  110.11  3.000
 RN4  H21  C07  C06  107.17  3.000
 RN4  C08  C07  C06  114.41  3.000
 RN4  C08  N09  C14  112.75  3.000
 RN4  C14  N09  C10  113.82  3.000
 RN4  C08  N09  C10  114.86  3.000
 RN4  H27  C13  H26  106.33  3.000
 RN4  H27  C13  C14  109.47  3.000
 RN4  H26  C13  C14  108.87  3.000
 RN4  H27  C13  C12  110.62  3.000
 RN4  H26  C13  C12  110.54  3.000
 RN4  C14  C13  C12  110.88  3.000
 RN4  C04  N15  C16  113.45  3.000
 RN4  C02  C17  C18  133.06  3.000
 RN4  C02  C17  C16  114.23  3.000
 RN4  C18  C17  C16  112.71  3.000
 RN4  C27  C22  C23  118.28  3.000
 RN4  C27  C22  C21  120.43  3.000
 RN4  C23  C22  C21  121.29  3.000
 RN4  H28  C24  C25  120.07  3.000
 RN4  H28  C24  C23  119.70  3.000
 RN4  C25  C24  C23  120.23  3.000
 RN4  H29  C27  C22  119.35  3.000
 RN4  H29  C27  C26  119.59  3.000
 RN4  C22  C27  C26  121.06  3.000
 RN4  H31  C28  H30  106.64  3.000
 RN4  H31  C28  C29  109.54  3.000
 RN4  H30  C28  C29  109.23  3.000
 RN4  H31  C28  C21  109.48  3.000
 RN4  H30  C28  C21  110.07  3.000
 RN4  C29  C28  C21  111.75  3.000
 RN4  C19  S30  C16   91.27  3.000
 RN4  H24  C08  H23  106.60  3.000
 RN4  H24  C08  N09  108.12  3.000
 RN4  H23  C08  N09  112.80  3.000
 RN4  H24  C08  C07  108.34  3.000
 RN4  H23  C08  C07  107.92  3.000
 RN4  N09  C08  C07  112.80  3.000
 RN4  H18  N01  H17  117.29  3.000
 RN4  H18  N01  C02  122.53  3.000
 RN4  H17  N01  C02  118.74  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
 RN4  CONST_01  C18  C19  S30  C16     0.00   0.0  0
 RN4  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 RN4  CONST_03  N03  C02  C17  C16     0.00   0.0  0
 RN4  CONST_04  N03  C04  N15  C16     0.00   0.0  0
 RN4  CONST_05  S30  C16  C17  C18     0.00   0.0  0
 RN4  CONST_06  N15  C16  C17  C18   180.00   0.0  0
 RN4  CONST_07  N03  C02  C17  C18   180.00   0.0  0
 RN4  CONST_08  C17  C16  S30  C19     0.00   0.0  0
 RN4  CONST_09  N15  C16  S30  C19   180.00   0.0  0
 RN4  CONST_10  C02  C17  C18  C19   180.00   0.0  0
 RN4  CONST_11  C26  C25  C24  C23     0.00   0.0  0
 RN4  CONST_12  C26  C27  C22  C23     0.00   0.0  0
 RN4  CONST_13  C22  C23  C24  C25     0.00   0.0  0
 RN4  CONST_14  C22  C27  C26  C25     0.00   0.0  0
 RN4  CONST_15  S30  C16  C17  C02   180.00   0.0  0
 RN4  CONST_16  N15  C16  C17  C02     0.00   0.0  0
 RN4  CONST_17  N15  C04  N03  C02     0.00   0.0  0
 RN4  CONST_18  S30  C16  N15  C04   180.00   0.0  0
 RN4  CONST_19  C17  C16  N15  C04     0.00   0.0  0
 RN4  CONST_20  C17  C02  N03  C04     0.00   0.0  0
 RN4  CONST_21  S30  C19  C18  C17     0.00   0.0  0
 RN4  CONST_22  C27  C26  C25  C24     0.00   0.0  0
 RN4  CONST_23  C27  C22  C23  C24     0.00   0.0  0
 RN4  CONST_24  C24  C23  C22  C21   180.00   0.0  0
 RN4  CONST_25  C26  C27  C22  C21   180.00   0.0  0
 RN4  CONST_26  N01  C02  C17  C16   180.00   0.0  0
 RN4  CONST_27  S05  C04  N15  C16   180.00   0.0  0
 RN4  CONST_28  N01  C02  C17  C18     0.00   0.0  0
 RN4  CONST_29  C04  N03  C02  N01   180.00   0.0  0
 RN4  CONST_30  S05  C04  N03  C02   180.00   0.0  0
 RN4  CONST_31  H12  C23  C22  C21     0.00   0.0  0
 RN4  CONST_32  H29  C27  C22  C21     0.00   0.0  0
 RN4  CONST_33  H13  C25  C24  C23   180.00   0.0  0
 RN4  CONST_34  H28  C24  C25  C26   180.00   0.0  0
 RN4  CONST_35  H14  C26  C27  C22   180.00   0.0  0
 RN4  CONST_36  H17  N01  C02  N03     0.00   0.0  0
 RN4  CONST_37  H18  N01  C02  N03   180.00   0.0  0
 RN4  Var_01    C13  C14  N09  C10    28.61  30.0  1
 RN4  Var_02    C13  C12  C11  C10    25.78  30.0  1
 RN4  Var_03    C14  N09  C10  C11    33.47  30.0  1
 RN4  Var_04    C14  C13  C12  C11    33.13  30.0  1
 RN4  Var_05    N09  C10  C11  C12   -62.98  30.0  1
 RN4  Var_06    N09  C14  C13  C12   -64.45  30.0  1
 RN4  Var_07    C21  C20  C19  C18    16.89  30.0  1
 RN4  Var_08    C21  C28  C29  C18   -44.35  30.0  1
 RN4  Var_09    C28  C29  C18  C19    12.75  30.0  1
 RN4  Var_10    C07  C08  N09  C10  -162.05  30.0  3
 RN4  Var_11    N15  C04  S05  C06   150.15  30.0  1
 RN4  Var_12    C07  C06  S05  C04  -102.75  30.0  3
 RN4  Var_13    N09  C08  C07  C06    47.82  30.0  3
 RN4  Var_14    C08  C07  C06  S05    54.78  30.0  3

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
 RN4  chir_01  C21  C22  C20  C28  positiv

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
 RN4  plan-1  C21  0.020
 RN4  plan-1  C23  0.020
 RN4  plan-1  C25  0.020
 RN4  plan-1  C26  0.020
 RN4  plan-1  C22  0.020
 RN4  plan-1  C24  0.020
 RN4  plan-1  C27  0.020
 RN4  plan-1  H12  0.020
 RN4  plan-1  H13  0.020
 RN4  plan-1  H14  0.020
 RN4  plan-1  H28  0.020
 RN4  plan-1  H29  0.020
 RN4  plan-2  C16  0.020
 RN4  plan-2  C18  0.020
 RN4  plan-2  C19  0.020
 RN4  plan-2  C20  0.020
 RN4  plan-2  C29  0.020
 RN4  plan-2  C02  0.020
 RN4  plan-2  N03  0.020
 RN4  plan-2  C04  0.020
 RN4  plan-2  S05  0.020
 RN4  plan-2  N15  0.020
 RN4  plan-2  C17  0.020
 RN4  plan-2  S30  0.020
 RN4  plan-2  N01  0.020
 RN4  plan-3  C02  0.020
 RN4  plan-3  H17  0.020
 RN4  plan-3  H18  0.020
 RN4  plan-3  N01  0.020

