# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:03:28 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-[(4-amino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(morpholin-4-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCC(=O)NCCN2CCOCC2)nc3sc4CCCCc4c13
#
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
 RN7  RN7  2-[(4-amino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(morpholin-4-yl)ethyl]acetamide  ligand  52  27  .  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_RN7
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
 RN7  C26  C  CH2   0  -0.444  22.0909  -14.4769  34.1061
 RN7  C25  C  CH2   0  -0.449  20.7166  -14.8879  33.5942
 RN7  C22  C  CR5   0   0.240  20.9388  -12.4585  35.0517
 RN7  C23  C  CR5   0  -0.268  20.0528  -12.5517  34.0295
 RN7  C24  C  CH2   0  -0.479  19.9610  -13.6773  33.0520
 RN7  N18  N  N     0  -0.450  19.2839   -9.3138  35.8438
 RN7  C15  C  C     0  -0.218  20.2070  -13.8681  39.4228
 RN7  C13  C  C     0  -0.143  18.6042  -13.1456  37.8774
 RN7  C12  C  C     0  -0.345  18.0009  -12.5150  39.1299
 RN7  C16  C  C     0  -0.285  20.0815  -12.6287  40.3091
 RN7  C06  C  CH2   0  -0.709  20.4942   -7.1411  39.0008
 RN7  C02  C  CR6   0   0.507  21.3388  -10.7674  37.0063
 RN7  C04  C  CR6   0   0.231  19.9509   -8.9500  36.9187
 RN7  N01  N  NH2   0  -0.832  22.3455  -11.3876  37.6335
 RN7  N03  N  N     0  -0.508  20.9298   -9.6046  37.5203
 RN7  S05  S  S2    0   0.069  19.4160   -7.4002  37.5667
 RN7  C07  C  C     0   0.531  19.9260   -7.7555  40.2704
 RN7  N08  N  NH1   0  -0.621  20.0604   -9.0850  40.3451
 RN7  C09  C  CH2   0  -0.323  19.5006   -9.9065  41.3905
 RN7  C10  C  CH2   0  -0.269  18.4781  -10.8949  40.8498
 RN7  N11  N  NR6   0  -0.412  19.0199  -11.7560  39.8224
 RN7  O14  O  O     0  -0.475  19.9408  -13.5619  38.0782
 RN7  O17  O  O     0  -0.496  19.4005   -7.0600  41.1285
 RN7  C19  C  CR56  0  -0.029  19.6957  -10.4736  35.3341
 RN7  S20  S  S2    0   0.195  18.9599  -11.1974  33.9500
 RN7  C21  C  CR56  0  -0.011  20.7321  -11.2641  35.8274
 RN7  C27  C  CH2   0  -0.550  21.9865  -13.5079  35.2825
 RN7  H1   H  HCH2  0   0.242  22.6640  -15.3532  34.4137
 RN7  H2   H  HCH2  0   0.228  22.6516  -14.0060  33.2931
 RN7  H3   H  HCH2  0   0.229  20.1412  -15.3418  34.4062
 RN7  H4   H  HCH2  0   0.243  20.8097  -15.6414  32.8106
 RN7  H5   H  HCH2  0   0.252  20.3814  -13.3726  32.0881
 RN7  H6   H  HCH2  0   0.256  18.9165  -13.9351  32.8616
 RN7  H8   H  H     0   0.246  21.2237  -14.2596  39.4760
 RN7  H9   H  H     0   0.224  18.6259  -12.4165  37.0658
 RN7  H10  H  H     0   0.202  17.9780  -13.9878  37.5551
 RN7  H11  H  H     0   0.251  17.1927  -11.8467  38.8252
 RN7  H12  H  H     0   0.205  17.5381  -13.2808  39.7745
 RN7  H13  H  H     0   0.205  19.8986  -12.9697  41.3413
 RN7  H14  H  H     0   0.222  21.0287  -12.0823  40.3205
 RN7  H15  H  HCH2  0   0.313  21.4883   -7.5229  38.7690
 RN7  H16  H  HCH2  0   0.318  20.5588   -6.0614  39.1242
 RN7  H17  H  HNH2  0   0.402  22.6325  -11.0331  38.5311
 RN7  H18  H  HNH2  0   0.422  22.5194  -12.3631  37.4689
 RN7  H19  H  HNH1  0   0.427  20.4483   -9.5560  39.5357
 RN7  H20  H  HCH2  0   0.246  20.3026  -10.4299  41.9179
 RN7  H21  H  HCH2  0   0.261  19.0152   -9.2642  42.1230
 RN7  H22  H  HCH2  0   0.235  17.6444  -10.3326  40.4216
 RN7  H23  H  HCH2  0   0.200  18.0775  -11.4674  41.7038
 RN7  H25  H  HCH2  0   0.253  21.7446  -14.0581  36.1968
 RN7  H26  H  HCH2  0   0.249  22.9607  -13.0393  35.4469
 RN7  H7   H  H     0   0.210  19.5421  -14.6638  39.7836

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
 RN7  C24  C25  single    1.527  0.020  1.527
 RN7  C24  C23  single    1.494  0.020  1.494
 RN7  C25  C26  single    1.523  0.020  1.523
 RN7  C26  C27  single    1.528  0.020  1.528
 RN7  C23  S20  aromatic  1.742  0.020  1.742
 RN7  C23  C22  aromatic  1.356  0.020  1.356
 RN7  S20  C19  aromatic  1.727  0.020  1.727
 RN7  C22  C27  single    1.501  0.020  1.501
 RN7  C22  C21  aromatic  1.439  0.020  1.439
 RN7  C19  C21  aromatic  1.394  0.020  1.394
 RN7  C19  N18  aromatic  1.332  0.020  1.332
 RN7  C21  C02  aromatic  1.416  0.020  1.416
 RN7  N18  C04  aromatic  1.316  0.020  1.316
 RN7  C02  N01  single    1.339  0.020  1.339
 RN7  C02  N03  aromatic  1.335  0.020  1.335
 RN7  C04  N03  aromatic  1.322  0.020  1.322
 RN7  C04  S05  single    1.763  0.020  1.763
 RN7  S05  C06  single    1.813  0.020  1.813
 RN7  C06  C07  single    1.521  0.020  1.521
 RN7  C13  O14  single    1.414  0.020  1.414
 RN7  C13  C12  single    1.527  0.020  1.527
 RN7  O14  C15  single    1.405  0.020  1.405
 RN7  C12  N11  single    1.447  0.020  1.447
 RN7  C07  N08  single    1.338  0.020  1.338
 RN7  C07  O17  double    1.223  0.020  1.223
 RN7  C15  C16  single    1.529  0.020  1.529
 RN7  N08  C09  single    1.443  0.020  1.443
 RN7  N11  C16  single    1.458  0.020  1.458
 RN7  N11  C10  single    1.446  0.020  1.446
 RN7  C09  C10  single    1.521  0.020  1.521
 RN7  C26  H1   single    0.970  0.020  1.090
 RN7  C26  H2   single    0.970  0.020  1.090
 RN7  C25  H3   single    0.970  0.020  1.090
 RN7  C25  H4   single    0.970  0.020  1.090
 RN7  C24  H5   single    0.970  0.020  1.090
 RN7  C24  H6   single    0.970  0.020  1.090
 RN7  C15  H7   single    0.970  0.020  1.090
 RN7  C15  H8   single    0.970  0.020  1.090
 RN7  C13  H9   single    0.970  0.020  1.090
 RN7  C13  H10  single    0.970  0.020  1.090
 RN7  C12  H11  single    0.970  0.020  1.090
 RN7  C12  H12  single    0.970  0.020  1.090
 RN7  C16  H13  single    0.970  0.020  1.090
 RN7  C16  H14  single    0.970  0.020  1.090
 RN7  C06  H15  single    0.970  0.020  1.090
 RN7  C06  H16  single    0.970  0.020  1.090
 RN7  N01  H17  single    0.890  0.020  1.040
 RN7  N01  H18  single    0.890  0.020  1.040
 RN7  N08  H19  single    0.860  0.020  1.020
 RN7  C09  H20  single    0.970  0.020  1.090
 RN7  C09  H21  single    0.970  0.020  1.090
 RN7  C10  H22  single    0.970  0.020  1.090
 RN7  C10  H23  single    0.970  0.020  1.090
 RN7  C27  H25  single    0.970  0.020  1.090
 RN7  C27  H26  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
 RN7  H2   C26  H1   106.62  3.000
 RN7  H2   C26  C27  109.52  3.000
 RN7  H1   C26  C27  109.16  3.000
 RN7  H2   C26  C25  109.19  3.000
 RN7  H1   C26  C25  110.60  3.000
 RN7  C27  C26  C25  111.61  3.000
 RN7  H4   C25  H3   106.95  3.000
 RN7  H4   C25  C24  109.56  3.000
 RN7  H3   C25  C24  109.41  3.000
 RN7  H4   C25  C26  110.54  3.000
 RN7  H3   C25  C26  109.70  3.000
 RN7  C24  C25  C26  110.61  3.000
 RN7  C27  C22  C21  126.71  3.000
 RN7  C21  C22  C23  111.69  3.000
 RN7  C27  C22  C23  121.60  3.000
 RN7  S20  C23  C24  121.16  3.000
 RN7  S20  C23  C22  113.01  3.000
 RN7  C24  C23  C22  125.82  3.000
 RN7  H6   C24  H5   106.22  3.000
 RN7  H6   C24  C23  110.52  3.000
 RN7  H5   C24  C23  110.05  3.000
 RN7  H6   C24  C25  110.36  3.000
 RN7  H5   C24  C25  110.08  3.000
 RN7  C23  C24  C25  109.56  3.000
 RN7  C19  N18  C04  113.36  3.000
 RN7  H8   C15  H7   106.76  3.000
 RN7  H8   C15  O14  107.55  3.000
 RN7  H7   C15  O14  110.96  3.000
 RN7  H8   C15  C16  109.83  3.000
 RN7  H7   C15  C16  110.32  3.000
 RN7  O14  C15  C16  111.27  3.000
 RN7  H10  C13  H9   107.79  3.000
 RN7  H10  C13  O14  110.79  3.000
 RN7  H9   C13  O14  106.47  3.000
 RN7  H10  C13  C12  109.41  3.000
 RN7  H9   C13  C12  110.00  3.000
 RN7  O14  C13  C12  112.25  3.000
 RN7  H12  C12  H11  106.11  3.000
 RN7  H12  C12  N11  112.34  3.000
 RN7  H11  C12  N11  109.50  3.000
 RN7  H12  C12  C13  111.01  3.000
 RN7  H11  C12  C13  108.44  3.000
 RN7  N11  C12  C13  109.33  3.000
 RN7  H14  C16  H13  106.77  3.000
 RN7  H14  C16  N11  109.58  3.000
 RN7  H13  C16  N11  112.14  3.000
 RN7  H14  C16  C15  109.88  3.000
 RN7  H13  C16  C15  107.80  3.000
 RN7  N11  C16  C15  110.58  3.000
 RN7  H16  C06  H15  108.51  3.000
 RN7  H16  C06  C07  109.16  3.000
 RN7  H15  C06  C07  112.14  3.000
 RN7  H16  C06  S05  105.47  3.000
 RN7  H15  C06  S05  108.92  3.000
 RN7  C07  C06  S05  112.37  3.000
 RN7  C21  C02  N03  119.65  3.000
 RN7  N03  C02  N01  116.97  3.000
 RN7  C21  C02  N01  123.36  3.000
 RN7  S05  C04  N03  119.51  3.000
 RN7  S05  C04  N18  112.92  3.000
 RN7  N03  C04  N18  127.57  3.000
 RN7  H18  N01  H17  116.02  3.000
 RN7  H18  N01  C02  120.23  3.000
 RN7  H17  N01  C02  117.97  3.000
 RN7  C04  N03  C02  118.86  3.000
 RN7  C04  S05  C06  103.64  3.000
 RN7  O17  C07  N08  124.67  3.000
 RN7  O17  C07  C06  121.10  3.000
 RN7  N08  C07  C06  114.23  3.000
 RN7  H19  N08  C09  117.55  3.000
 RN7  H19  N08  C07  117.09  3.000
 RN7  C09  N08  C07  124.55  3.000
 RN7  H21  C09  H20  106.56  3.000
 RN7  H21  C09  C10  108.84  3.000
 RN7  H20  C09  C10  110.70  3.000
 RN7  H21  C09  N08  108.94  3.000
 RN7  H20  C09  N08  109.72  3.000
 RN7  C10  C09  N08  111.91  3.000
 RN7  H23  C10  H22  107.05  3.000
 RN7  H23  C10  N11  112.14  3.000
 RN7  H22  C10  N11  108.29  3.000
 RN7  H23  C10  C09  107.82  3.000
 RN7  H22  C10  C09  108.52  3.000
 RN7  N11  C10  C09  112.81  3.000
 RN7  C10  N11  C16  113.09  3.000
 RN7  C10  N11  C12  112.86  3.000
 RN7  C16  N11  C12  111.01  3.000
 RN7  C13  O14  C15  112.29  3.000
 RN7  C21  C19  S20  111.28  3.000
 RN7  C21  C19  N18  126.03  3.000
 RN7  S20  C19  N18  122.68  3.000
 RN7  C19  S20  C23   91.26  3.000
 RN7  C19  C21  C02  114.48  3.000
 RN7  C02  C21  C22  132.72  3.000
 RN7  C19  C21  C22  112.75  3.000
 RN7  H26  C27  H25  106.66  3.000
 RN7  H26  C27  C22  110.21  3.000
 RN7  H25  C27  C22  109.01  3.000
 RN7  H26  C27  C26  109.07  3.000
 RN7  H25  C27  C26  109.86  3.000
 RN7  C22  C27  C26  111.89  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
 RN7  CONST_01  C19  S20  C23  C22     0.00   0.0  0
 RN7  CONST_02  S20  C19  C21  C22     0.00   0.0  0
 RN7  CONST_03  N18  C19  C21  C22   180.00   0.0  0
 RN7  CONST_04  N03  C02  C21  C22   180.00   0.0  0
 RN7  CONST_05  C21  C19  S20  C23     0.00   0.0  0
 RN7  CONST_06  N18  C19  S20  C23   180.00   0.0  0
 RN7  CONST_07  C19  C21  C22  C23     0.00   0.0  0
 RN7  CONST_08  C02  C21  C22  C23   180.00   0.0  0
 RN7  CONST_09  C02  C21  C19  N18     0.00   0.0  0
 RN7  CONST_10  C02  N03  C04  N18     0.00   0.0  0
 RN7  CONST_11  S20  C19  C21  C02   180.00   0.0  0
 RN7  CONST_12  S20  C19  N18  C04   180.00   0.0  0
 RN7  CONST_13  C21  C19  N18  C04     0.00   0.0  0
 RN7  CONST_14  C21  C02  N03  C04     0.00   0.0  0
 RN7  CONST_15  C19  C21  C02  N03     0.00   0.0  0
 RN7  CONST_16  C19  N18  C04  N03     0.00   0.0  0
 RN7  CONST_17  C21  C22  C23  S20     0.00   0.0  0
 RN7  CONST_18  N01  C02  C21  C22     0.00   0.0  0
 RN7  CONST_19  S05  C04  N03  C02   180.00   0.0  0
 RN7  CONST_20  N01  C02  N03  C04   180.00   0.0  0
 RN7  CONST_21  C19  C21  C02  N01   180.00   0.0  0
 RN7  CONST_22  C19  N18  C04  S05   180.00   0.0  0
 RN7  CONST_23  H17  N01  C02  N03     0.00   0.0  0
 RN7  CONST_25  C09  N08  C07  C06   180.00   0.0  0
 RN7  CONST_26  O17  C07  N08  C09     0.00   0.0  0
 RN7  CONST_27  H19  N08  C07  C06     0.00   0.0  0
 RN7  Var_01    C23  C24  C25  C26   -47.43  30.0  1
 RN7  Var_02    C23  C22  C27  C26    11.35  30.0  1
 RN7  Var_03    S20  C23  C24  C25  -162.73  30.0  1
 RN7  Var_04    C22  C27  C26  C25   -43.06  30.0  1
 RN7  Var_05    C27  C26  C25  C24    63.15  30.0  1
 RN7  Var_06    C12  C13  O14  C15    26.84  30.0  1
 RN7  Var_07    C12  N11  C16  C15    28.11  30.0  1
 RN7  Var_08    C16  C15  O14  C13   -64.48  30.0  1
 RN7  Var_09    C16  N11  C12  C13   -64.46  30.0  1
 RN7  Var_10    O14  C13  C12  N11    36.24  30.0  1
 RN7  Var_11    O14  C15  C16  N11    34.89  30.0  1
 RN7  Var_12    C09  C10  N11  C12  -168.89  30.0  3
 RN7  Var_13    N03  C04  S05  C06     0.59  30.0  1
 RN7  Var_14    C07  C06  S05  C04   -88.42  30.0  3
 RN7  Var_15    N11  C10  C09  N08    57.00  30.0  3
 RN7  Var_16    N08  C07  C06  S05    76.68  30.0  3
 RN7  Var_17    C10  C09  N08  C07   116.95  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
 RN7  plan-1  C06  0.020
 RN7  plan-1  C07  0.020
 RN7  plan-1  N08  0.020
 RN7  plan-1  C09  0.020
 RN7  plan-1  O17  0.020
 RN7  plan-1  H19  0.020
 RN7  plan-2  C22  0.020
 RN7  plan-2  C23  0.020
 RN7  plan-2  C24  0.020
 RN7  plan-2  N18  0.020
 RN7  plan-2  C02  0.020
 RN7  plan-2  C04  0.020
 RN7  plan-2  N01  0.020
 RN7  plan-2  N03  0.020
 RN7  plan-2  S05  0.020
 RN7  plan-2  C19  0.020
 RN7  plan-2  S20  0.020
 RN7  plan-2  C21  0.020
 RN7  plan-2  C27  0.020
 RN7  plan-3  C02  0.020
 RN7  plan-3  N01  0.020
 RN7  plan-3  H17  0.020
 RN7  plan-3  H18  0.020

