# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:04:51 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-{[(7S)-4-amino-7-ethyl-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl]sulfanyl}-N-[2-(piperidin-1-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]1CCc2c(C1)sc3nc(SCC(=O)NCCN4CCCCC4)nc(N)c23
#
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
 H66  H66  2-{[(7S)-4-amino-7-ethyl-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl]sulfanyl}-N-[2-(piperidin-1-yl)ethyl]acetamide  ligand  60  29  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H66
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
 H66  N01  N  NH2   0  -0.838  22.4750  -10.8446  38.1187
 H66  C02  C  CR6   0   0.499  21.4233  -10.2454  37.5561
 H66  N03  N  N     0  -0.492  20.9457   -9.1595  38.1719
 H66  C04  C  CR6   0   0.210  19.9049   -8.5371  37.6449
 H66  S05  S  S2    0   0.071  19.2694   -7.0906  38.4259
 H66  C06  C  CH2   0  -0.707  20.3699   -6.8600  39.8463
 H66  C07  C  C     0   0.541  19.8667   -7.5984  41.0746
 H66  N08  N  NH1   0  -0.617  20.2404   -8.8823  41.1535
 H66  C09  C  CH2   0  -0.287  19.8089   -9.7658  42.2144
 H66  C10  C  CH2   0  -0.281  18.4994  -10.4829  41.9102
 H66  N11  N  NT    0  -0.419  18.6274  -11.3892  40.7827
 H66  C12  C  CH2   0  -0.290  18.4369  -12.7917  41.0970
 H66  C13  C  CH2   0  -0.431  19.0912  -13.6698  40.0201
 H66  C14  C  CH2   0  -0.432  19.1446  -12.9359  38.6788
 H66  C15  C  CH2   0  -0.484  17.9130  -12.0569  38.5186
 H66  C16  C  CH2   0  -0.269  17.8541  -10.9891  39.6205
 H66  O17  O  O     0  -0.495  19.1794   -7.0323  41.9130
 H66  N18  N  N     0  -0.444  19.2320   -8.8673  36.5622
 H66  C19  C  CR56  0  -0.023  19.6998   -9.9600  35.9627
 H66  C20  C  CR56  0  -0.005  20.8017  -10.7094  36.3699
 H66  C21  C  CR5   0   0.230  21.0506  -11.8399  35.5153
 H66  C22  C  CR5   0  -0.261  20.1343  -11.9308  34.5213
 H66  C23  C  CH2   0  -0.477  20.0708  -12.9953  33.4774
 H66  C24  C  CH1   0  -0.236  20.9502  -14.1871  33.8661
 H66  C25  C  CH2   0  -0.416  21.1321  -15.1598  32.7036
 H66  C26  C  CH3   0  -0.676  19.8323  -15.7320  32.1542
 H66  C27  C  CH2   0  -0.425  22.2972  -13.6848  34.3777
 H66  C28  C  CH2   0  -0.560  22.1637  -12.8364  35.6392
 H66  S29  S  S2    0   0.202  18.9601  -10.6446  34.5607
 H66  H1   H  HNH2  0   0.408  22.8320  -10.4986  38.9935
 H66  H2   H  HNH2  0   0.428  22.8303  -11.7247  37.7924
 H66  H3   H  HCH2  0   0.312  21.3810   -7.1503  39.5640
 H66  H4   H  HCH2  0   0.320  20.3600   -5.7900  40.0487
 H66  H5   H  HNH1  0   0.411  20.7130   -9.2791  40.3525
 H66  H6   H  HCH2  0   0.242  20.5958  -10.5041  42.3743
 H66  H7   H  HCH2  0   0.236  19.7143   -9.1879  43.1339
 H66  H8   H  HCH2  0   0.223  17.7145   -9.7397  41.7302
 H66  H9   H  HCH2  0   0.228  18.1931  -11.0247  42.8112
 H66  H11  H  HCH2  0   0.189  17.3674  -13.0448  41.1980
 H66  H12  H  HCH2  0   0.234  18.8883  -13.0024  42.0679
 H66  H13  H  HCH2  0   0.216  18.5255  -14.5999  39.9233
 H66  H14  H  HCH2  0   0.221  20.1011  -13.9495  40.3275
 H66  H15  H  HCH2  0   0.223  19.2210  -13.6447  37.8517
 H66  H16  H  HCH2  0   0.226  20.0405  -12.3158  38.6389
 H66  H17  H  HCH2  0   0.238  17.8997  -11.5781  37.5374
 H66  H18  H  HCH2  0   0.223  17.0200  -12.6876  38.5582
 H66  H19  H  HCH2  0   0.223  18.2547  -10.0418  39.2507
 H66  H20  H  HCH2  0   0.191  16.8000  -10.7927  39.8811
 H66  H21  H  HCH2  0   0.249  20.3953  -12.5916  32.5103
 H66  H22  H  HCH2  0   0.261  19.0364  -13.3183  33.3372
 H66  H23  H  HCH1  0   0.226  20.4492  -14.7202  34.6846
 H66  H24  H  HCH2  0   0.225  21.7725  -15.9810  33.0392
 H66  H25  H  HCH2  0   0.213  21.6812  -14.6559  31.9012
 H66  H26  H  HCH3  0   0.232  20.0303  -16.4837  31.3893
 H66  H27  H  HCH3  0   0.219  19.2455  -16.2099  32.9410
 H66  H28  H  HCH3  0   0.225  19.2077  -14.9639  31.6966
 H66  H29  H  HCH2  0   0.241  22.9627  -14.5265  34.5821
 H66  H30  H  HCH2  0   0.227  22.7771  -13.0908  33.5926
 H66  H31  H  HCH2  0   0.251  21.9897  -13.4839  36.5064
 H66  H32  H  HCH2  0   0.252  23.1137  -12.3250  35.8194

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
 H66  C26  C25  single    1.523  0.020  1.523
 H66  C25  C24  single    1.527  0.020  1.527
 H66  C23  C24  single    1.531  0.020  1.531
 H66  C23  C22  single    1.492  0.020  1.492
 H66  C24  C27  single    1.526  0.020  1.526
 H66  C27  C28  single    1.526  0.020  1.526
 H66  C22  S29  aromatic  1.742  0.020  1.742
 H66  C22  C21  aromatic  1.355  0.020  1.355
 H66  S29  C19  aromatic  1.727  0.020  1.727
 H66  C21  C28  single    1.499  0.020  1.499
 H66  C21  C20  aromatic  1.439  0.020  1.439
 H66  C19  C20  aromatic  1.393  0.020  1.393
 H66  C19  N18  aromatic  1.331  0.020  1.331
 H66  C20  C02  aromatic  1.417  0.020  1.417
 H66  N18  C04  aromatic  1.317  0.020  1.317
 H66  C02  N01  single    1.335  0.020  1.335
 H66  C02  N03  aromatic  1.337  0.020  1.337
 H66  C04  N03  aromatic  1.322  0.020  1.322
 H66  C04  S05  single    1.762  0.020  1.762
 H66  S05  C06  single    1.812  0.020  1.812
 H66  C14  C15  single    1.522  0.020  1.522
 H66  C14  C13  single    1.530  0.020  1.530
 H66  C15  C16  single    1.536  0.020  1.536
 H66  C06  C07  single    1.519  0.020  1.519
 H66  C13  C12  single    1.536  0.020  1.536
 H66  C16  N11  single    1.452  0.020  1.452
 H66  C07  N08  single    1.339  0.020  1.339
 H66  C07  O17  double    1.223  0.020  1.223
 H66  N11  C12  single    1.450  0.020  1.450
 H66  N11  C10  single    1.452  0.020  1.452
 H66  N08  C09  single    1.446  0.020  1.446
 H66  C10  C09  single    1.524  0.020  1.524
 H66  N01  H1   single    0.860  0.020  1.020
 H66  N01  H2   single    0.860  0.020  1.020
 H66  C06  H3   single    0.970  0.020  1.090
 H66  C06  H4   single    0.970  0.020  1.090
 H66  N08  H5   single    0.860  0.020  1.020
 H66  C09  H6   single    0.970  0.020  1.090
 H66  C09  H7   single    0.970  0.020  1.090
 H66  C10  H8   single    0.970  0.020  1.090
 H66  C10  H9   single    0.970  0.020  1.090
 H66  C12  H11  single    0.970  0.020  1.090
 H66  C12  H12  single    0.970  0.020  1.090
 H66  C13  H13  single    0.970  0.020  1.090
 H66  C13  H14  single    0.970  0.020  1.090
 H66  C14  H15  single    0.970  0.020  1.090
 H66  C14  H16  single    0.970  0.020  1.090
 H66  C15  H17  single    0.970  0.020  1.090
 H66  C15  H18  single    0.970  0.020  1.090
 H66  C16  H19  single    0.970  0.020  1.090
 H66  C16  H20  single    0.970  0.020  1.090
 H66  C23  H21  single    0.970  0.020  1.090
 H66  C23  H22  single    0.970  0.020  1.090
 H66  C24  H23  single    0.970  0.020  1.090
 H66  C25  H24  single    0.970  0.020  1.090
 H66  C25  H25  single    0.970  0.020  1.090
 H66  C26  H26  single    0.970  0.020  1.090
 H66  C26  H27  single    0.970  0.020  1.090
 H66  C26  H28  single    0.970  0.020  1.090
 H66  C27  H29  single    0.970  0.020  1.090
 H66  C27  H30  single    0.970  0.020  1.090
 H66  C28  H31  single    0.970  0.020  1.090
 H66  C28  H32  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
 H66  H2   N01  H1   117.30  3.000
 H66  H2   N01  C02  122.38  3.000
 H66  H1   N01  C02  119.45  3.000
 H66  C20  C02  N03  119.66  3.000
 H66  N03  C02  N01  116.87  3.000
 H66  C20  C02  N01  123.46  3.000
 H66  C04  N03  C02  118.68  3.000
 H66  N18  C04  S05  112.70  3.000
 H66  S05  C04  N03  119.57  3.000
 H66  N18  C04  N03  127.73  3.000
 H66  C06  S05  C04  103.47  3.000
 H66  H4   C06  H3   108.56  3.000
 H66  H4   C06  C07  108.93  3.000
 H66  H3   C06  C07  112.80  3.000
 H66  H4   C06  S05  105.39  3.000
 H66  H3   C06  S05  109.08  3.000
 H66  C07  C06  S05  111.77  3.000
 H66  O17  C07  N08  124.06  3.000
 H66  O17  C07  C06  121.03  3.000
 H66  N08  C07  C06  114.91  3.000
 H66  H5   N08  C09  118.73  3.000
 H66  H5   N08  C07  117.38  3.000
 H66  C09  N08  C07  123.05  3.000
 H66  H7   C09  H6   107.32  3.000
 H66  H7   C09  C10  110.08  3.000
 H66  H6   C09  C10  109.31  3.000
 H66  H7   C09  N08  108.70  3.000
 H66  H6   C09  N08  107.80  3.000
 H66  C10  C09  N08  113.42  3.000
 H66  H9   C10  H8   105.68  3.000
 H66  H9   C10  N11  110.78  3.000
 H66  H8   C10  N11  111.03  3.000
 H66  H9   C10  C09  108.00  3.000
 H66  H8   C10  C09  109.22  3.000
 H66  N11  C10  C09  111.90  3.000
 H66  C16  N11  C12  111.72  3.000
 H66  C12  N11  C10  115.07  3.000
 H66  C16  N11  C10  113.74  3.000
 H66  H12  C12  H11  105.97  3.000
 H66  H12  C12  C13  109.71  3.000
 H66  H11  C12  C13  110.24  3.000
 H66  H12  C12  N11  108.98  3.000
 H66  H11  C12  N11  111.65  3.000
 H66  C13  C12  N11  110.19  3.000
 H66  H14  C13  H13  106.60  3.000
 H66  H14  C13  C14  109.72  3.000
 H66  H13  C13  C14  110.40  3.000
 H66  H14  C13  C12  110.06  3.000
 H66  H13  C13  C12  109.15  3.000
 H66  C14  C13  C12  110.81  3.000
 H66  H16  C14  H15  106.50  3.000
 H66  H16  C14  C15  109.43  3.000
 H66  H15  C14  C15  110.60  3.000
 H66  H16  C14  C13  109.49  3.000
 H66  H15  C14  C13  110.80  3.000
 H66  C15  C14  C13  109.95  3.000
 H66  H18  C15  H17  105.99  3.000
 H66  H18  C15  C16  110.09  3.000
 H66  H17  C15  C16  109.84  3.000
 H66  H18  C15  C14  108.90  3.000
 H66  H17  C15  C14  110.97  3.000
 H66  C16  C15  C14  110.93  3.000
 H66  H20  C16  H19  106.01  3.000
 H66  H20  C16  C15  109.26  3.000
 H66  H19  C16  C15  110.23  3.000
 H66  H20  C16  N11  111.64  3.000
 H66  H19  C16  N11  108.32  3.000
 H66  C15  C16  N11  111.24  3.000
 H66  C19  N18  C04  113.36  3.000
 H66  S29  C19  C20  111.27  3.000
 H66  C20  C19  N18  125.99  3.000
 H66  S29  C19  N18  122.72  3.000
 H66  C21  C20  C19  112.69  3.000
 H66  C19  C20  C02  114.55  3.000
 H66  C21  C20  C02  132.72  3.000
 H66  C28  C21  C22  121.21  3.000
 H66  C28  C21  C20  126.98  3.000
 H66  C22  C21  C20  111.81  3.000
 H66  S29  C22  C23  120.92  3.000
 H66  S29  C22  C21  112.93  3.000
 H66  C23  C22  C21  126.15  3.000
 H66  H22  C23  H21  106.00  3.000
 H66  H22  C23  C24  110.25  3.000
 H66  H21  C23  C24  109.89  3.000
 H66  H22  C23  C22  109.93  3.000
 H66  H21  C23  C22  109.98  3.000
 H66  C24  C23  C22  110.68  3.000
 H66  H23  C24  C27  108.22  3.000
 H66  H23  C24  C25  108.23  3.000
 H66  C27  C24  C25  111.09  3.000
 H66  H23  C24  C23  107.77  3.000
 H66  C27  C24  C23  109.62  3.000
 H66  C25  C24  C23  111.78  3.000
 H66  H25  C25  H24  106.06  3.000
 H66  H25  C25  C26  109.67  3.000
 H66  H24  C25  C26  109.16  3.000
 H66  H25  C25  C24  108.93  3.000
 H66  H24  C25  C24  108.33  3.000
 H66  C26  C25  C24  114.36  3.000
 H66  H28  C26  H27  107.63  3.000
 H66  H28  C26  H26  107.16  3.000
 H66  H27  C26  H26  107.54  3.000
 H66  H28  C26  C25  112.06  3.000
 H66  H27  C26  C25  111.30  3.000
 H66  H26  C26  C25  110.92  3.000
 H66  H30  C27  H29  106.57  3.000
 H66  H30  C27  C28  109.23  3.000
 H66  H29  C27  C28  109.09  3.000
 H66  H30  C27  C24  108.96  3.000
 H66  H29  C27  C24  110.30  3.000
 H66  C28  C27  C24  112.51  3.000
 H66  H32  C28  H31  106.48  3.000
 H66  H32  C28  C27  108.67  3.000
 H66  H31  C28  C27  109.84  3.000
 H66  H32  C28  C21  110.35  3.000
 H66  H31  C28  C21  109.88  3.000
 H66  C27  C28  C21  111.48  3.000
 H66  C22  S29  C19   91.28  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
 H66  CONST_01  C22  C21  C20  C02   180.00   0.0  0
 H66  CONST_02  S29  C19  C20  C02   180.00   0.0  0
 H66  CONST_03  N18  C19  C20  C02     0.00   0.0  0
 H66  CONST_04  N18  C04  N03  C02     0.00   0.0  0
 H66  CONST_05  C21  C20  C02  N03   180.00   0.0  0
 H66  CONST_06  C19  C20  C02  N03     0.00   0.0  0
 H66  CONST_07  C19  N18  C04  N03     0.00   0.0  0
 H66  CONST_08  S29  C19  N18  C04   180.00   0.0  0
 H66  CONST_09  C20  C19  N18  C04     0.00   0.0  0
 H66  CONST_10  C20  C02  N03  C04     0.00   0.0  0
 H66  CONST_11  C22  S29  C19  N18   180.00   0.0  0
 H66  CONST_12  C21  C20  C19  N18   180.00   0.0  0
 H66  CONST_13  C21  C22  S29  C19     0.00   0.0  0
 H66  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 H66  CONST_15  S29  C22  C21  C20     0.00   0.0  0
 H66  CONST_16  C22  S29  C19  C20     0.00   0.0  0
 H66  CONST_17  S29  C19  C20  C21     0.00   0.0  0
 H66  CONST_18  C21  C20  C02  N01     0.00   0.0  0
 H66  CONST_19  C19  C20  C02  N01   180.00   0.0  0
 H66  CONST_20  C04  N03  C02  N01   180.00   0.0  0
 H66  CONST_21  S05  C04  N03  C02   180.00   0.0  0
 H66  CONST_22  C19  N18  C04  S05   180.00   0.0  0
 H66  CONST_23  H1   N01  C02  N03     0.00   0.0  0
 H66  CONST_24  H2   N01  C02  N03   180.00   0.0  0
 H66  CONST_25  C09  N08  C07  C06   180.00   0.0  0
 H66  CONST_26  O17  C07  N08  C09     0.00   0.0  0
 H66  CONST_27  H5   N08  C07  C06     0.00   0.0  0
 H66  Var_01    C14  C15  C16  N11   -22.57  30.0  1
 H66  Var_02    C14  C13  C12  N11   -27.06  30.0  1
 H66  Var_03    C15  C14  C13  C12   -34.68  30.0  1
 H66  Var_04    C15  C16  N11  C12   -41.74  30.0  1
 H66  Var_05    C16  C15  C14  C13    61.51  30.0  1
 H66  Var_06    C16  N11  C12  C13    69.57  30.0  1
 H66  Var_07    C27  C28  C21  C20  -166.44  30.0  1
 H66  Var_08    C24  C23  C22  C21    14.73  30.0  1
 H66  Var_09    C24  C27  C28  C21   -45.31  30.0  1
 H66  Var_10    N18  C04  S05  C06  -179.41  30.0  2
 H66  Var_11    C07  C06  S05  C04   -89.52  30.0  3
 H66  Var_12    N11  C10  C09  N08    64.78  30.0  2
 H66  Var_13    H26  C26  C25  C24  -174.94  30.0  3
 H66  Var_14    N08  C07  C06  S05    85.74  30.0  3
 H66  Var_15    C10  C09  N08  C07    88.71  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
 H66  chir_01  C24  C25  C23  C27  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
 H66  plan-1  C06  0.020
 H66  plan-1  C07  0.020
 H66  plan-1  N08  0.020
 H66  plan-1  C09  0.020
 H66  plan-1  O17  0.020
 H66  plan-1  H5   0.020
 H66  plan-2  N01  0.020
 H66  plan-2  C02  0.020
 H66  plan-2  N03  0.020
 H66  plan-2  C04  0.020
 H66  plan-2  S05  0.020
 H66  plan-2  N18  0.020
 H66  plan-2  C19  0.020
 H66  plan-2  C20  0.020
 H66  plan-2  C21  0.020
 H66  plan-2  C22  0.020
 H66  plan-2  C23  0.020
 H66  plan-2  C28  0.020
 H66  plan-2  S29  0.020
 H66  plan-3  N01  0.020
 H66  plan-3  C02  0.020
 H66  plan-3  H1   0.020
 H66  plan-3  H2   0.020

