# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 16:28:08 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: ethyl ({4-oxo-3-[3-(pyrrolidin-1-yl)propyl]-3,4-dihydro[1]benzothieno[3,2-d]pyrimidin-2-yl}sulfanyl)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CSC1=Nc2c(sc3ccccc23)C(=O)N1CCCN4CCCC4
#
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
 3XG  3XG  'ethyl ({4-oxo-3-[3-(pyrrolidin-1-yl)propyl]-3,4-dihydro[1]benzothieno[3,2-d]pyrimidin-2-yl}sulfanyl)acetate'  ligand  54  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XG
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
 3XG  C4   C  CR16  0  -0.299   4.4154  -0.5311  -0.8042
 3XG  C5   C  CR16  0  -0.255   5.7170  -0.3655  -1.2299
 3XG  C6   C  CR16  0  -0.253   6.2964   0.9095  -1.2710
 3XG  C8   C  CR56  0  -0.420   1.9535   1.9539   0.3435
 3XG  C13  C  CR6   0   0.600   0.6401   2.2559   0.8096
 3XG  C17  C  CH2   0  -0.259  -3.9262   1.6762   0.7005
 3XG  C1   C  CR16  0  -0.282   5.5881   2.0328  -0.8875
 3XG  C2   C  CR56  0  -0.230   4.2752   1.8646  -0.4564
 3XG  C3   C  CR56  0   0.189   3.6839   0.5922  -0.4139
 3XG  C16  C  CH2   0  -0.451  -2.4866   1.5801   0.2141
 3XG  C11  C  CR6   0   0.364   0.2966  -0.1325   0.6103
 3XG  C9   C  CR56  0   0.317   2.3269   0.6682   0.0530
 3XG  O29  O  O     0  -0.439  -1.7968  -4.0888   0.6888
 3XG  C25  C  C     0   0.621  -0.6315  -4.0810   0.3836
 3XG  O26  O  O2    0  -0.448   0.0822  -5.1464   0.0893
 3XG  C27  C  CH2   0  -0.184  -0.5723  -6.4309   0.1202
 3XG  C28  C  CH3   0  -0.689   0.4444  -7.4752  -0.2670
 3XG  C24  C  CH2   0  -0.675   0.2050  -2.8306   0.2847
 3XG  S23  S  S2    0   0.081  -0.8527  -1.4504   0.7757
 3XG  N10  N  N     0  -0.457   1.4903  -0.3860   0.1866
 3XG  N12  N  NR6   0  -0.558  -0.1632   1.1126   0.9423
 3XG  O14  O  O     0  -0.461   0.2208   3.3682   1.0750
 3XG  S7   S  S2    0   0.247   3.1949   3.1267   0.0697
 3XG  N18  N  NT    0  -0.427  -4.8323   2.1167  -0.3322
 3XG  C22  C  CH2   0  -0.273  -6.1864   2.3333   0.1447
 3XG  C21  C  CH2   0  -0.463  -6.9896   2.5266  -1.1383
 3XG  C20  C  CH2   0  -0.467  -6.2246   1.6907  -2.1857
 3XG  C19  C  CH2   0  -0.282  -4.9786   1.1920  -1.4448
 3XG  H1   H  HCR6  0   0.261   3.9603  -1.5123  -0.7673
 3XG  H2   H  HCR6  0   0.266   6.2978  -1.2257  -1.5344
 3XG  H3   H  HCR6  0   0.270   7.3183   1.0202  -1.6090
 3XG  H4   H  HCH2  0   0.294  -1.5445   2.1693   2.0669
 3XG  H5   H  HCH2  0   0.280  -1.8601   0.4601   1.9686
 3XG  H6   H  HCH2  0   0.190  -4.2334   0.6997   1.1186
 3XG  H7   H  HCH2  0   0.233  -3.9752   2.3956   1.5243
 3XG  H8   H  HCR6  0   0.275   6.0432   3.0137  -0.9248
 3XG  H9   H  HCH2  0   0.245  -2.2076   2.5130  -0.2799
 3XG  H10  H  HCH2  0   0.242  -2.3835   0.7774  -0.5198
 3XG  H11  H  HCH2  0   0.243  -0.9608  -6.6143   1.1233
 3XG  H12  H  HCH2  0   0.243  -1.4135  -6.4237  -0.5749
 3XG  H13  H  HCH3  0   0.243  -0.0364  -8.4530  -0.2615
 3XG  H14  H  HCH3  0   0.239   0.8384  -7.3023  -1.2682
 3XG  H15  H  HCH3  0   0.239   1.2764  -7.5081   0.4362
 3XG  H16  H  HCH2  0   0.330   1.0752  -2.8960   0.9378
 3XG  H17  H  HCH2  0   0.331   0.5657  -2.6951  -0.7355
 3XG  H19  H  HCH2  0   0.188  -6.5657   1.4588   0.7011
 3XG  H20  H  HCH2  0   0.232  -6.2312   3.1919   0.8181
 3XG  H21  H  HCH2  0   0.233  -8.0247   2.2083  -1.0182
 3XG  H22  H  HCH2  0   0.233  -7.0057   3.5789  -1.4236
 3XG  H23  H  HCH2  0   0.234  -6.8150   0.8556  -2.5619
 3XG  H24  H  HCH2  0   0.235  -5.9513   2.3005  -3.0471
 3XG  H25  H  HCH2  0   0.233  -4.0890   1.1836  -2.0769
 3XG  H26  H  HCH2  0   0.191  -5.1347   0.1599  -1.0858
 3XG  C15  C  CH2   0  -0.350  -1.5441   1.3242   1.3826

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
 3XG  S7   C2   aromatic  1.743  0.020  1.743
 3XG  S7   C8   aromatic  1.730  0.020  1.730
 3XG  C1   C2   aromatic  1.392  0.020  1.392
 3XG  C1   C6   aromatic  1.382  0.020  1.382
 3XG  O14  C13  double    1.218  0.020  1.218
 3XG  C2   C3   aromatic  1.404  0.020  1.404
 3XG  C6   C5   aromatic  1.401  0.020  1.401
 3XG  C8   C13  single    1.426  0.020  1.426
 3XG  C8   C9   aromatic  1.370  0.020  1.370
 3XG  C13  N12  single    1.404  0.020  1.404
 3XG  C3   C9   aromatic  1.437  0.020  1.437
 3XG  C3   C4   aromatic  1.396  0.020  1.396
 3XG  C9   N10  single    1.352  0.020  1.352
 3XG  C5   C4   aromatic  1.379  0.020  1.379
 3XG  N12  C15  single    1.465  0.020  1.465
 3XG  N12  C11  single    1.368  0.020  1.368
 3XG  C15  C16  single    1.523  0.020  1.523
 3XG  N10  C11  double    1.292  0.020  1.292
 3XG  C11  S23  single    1.756  0.020  1.756
 3XG  C16  C17  single    1.523  0.020  1.523
 3XG  S23  C24  single    1.807  0.020  1.807
 3XG  C17  N18  single    1.443  0.020  1.443
 3XG  C24  C25  single    1.508  0.020  1.508
 3XG  N18  C22  single    1.452  0.020  1.452
 3XG  N18  C19  single    1.454  0.020  1.454
 3XG  C22  C21  single    1.526  0.020  1.526
 3XG  C25  O26  single    1.316  0.020  1.316
 3XG  C25  O29  double    1.205  0.020  1.205
 3XG  O26  C27  single    1.442  0.020  1.442
 3XG  C27  C28  single    1.508  0.020  1.508
 3XG  C21  C20  single    1.543  0.020  1.543
 3XG  C19  C20  single    1.533  0.020  1.533
 3XG  C4   H1   single    0.930  0.020  1.080
 3XG  C5   H2   single    0.930  0.020  1.080
 3XG  C6   H3   single    0.930  0.020  1.080
 3XG  C15  H4   single    0.970  0.020  1.090
 3XG  C15  H5   single    0.970  0.020  1.090
 3XG  C17  H6   single    0.970  0.020  1.090
 3XG  C17  H7   single    0.970  0.020  1.090
 3XG  C1   H8   single    0.930  0.020  1.080
 3XG  C16  H9   single    0.970  0.020  1.090
 3XG  C16  H10  single    0.970  0.020  1.090
 3XG  C27  H11  single    0.970  0.020  1.090
 3XG  C27  H12  single    0.970  0.020  1.090
 3XG  C28  H13  single    0.970  0.020  1.090
 3XG  C28  H14  single    0.970  0.020  1.090
 3XG  C28  H15  single    0.970  0.020  1.090
 3XG  C24  H16  single    0.970  0.020  1.090
 3XG  C24  H17  single    0.970  0.020  1.090
 3XG  C22  H19  single    0.970  0.020  1.090
 3XG  C22  H20  single    0.970  0.020  1.090
 3XG  C21  H21  single    0.970  0.020  1.090
 3XG  C21  H22  single    0.970  0.020  1.090
 3XG  C20  H23  single    0.970  0.020  1.090
 3XG  C20  H24  single    0.970  0.020  1.090
 3XG  C19  H25  single    0.970  0.020  1.090
 3XG  C19  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
 3XG  H1   C4   C3   119.98  3.000
 3XG  H1   C4   C5   121.07  3.000
 3XG  C3   C4   C5   118.95  3.000
 3XG  H2   C5   C6   119.57  3.000
 3XG  H2   C5   C4   119.87  3.000
 3XG  C6   C5   C4   120.56  3.000
 3XG  H3   C6   C1   119.18  3.000
 3XG  H3   C6   C5   119.52  3.000
 3XG  C1   C6   C5   121.30  3.000
 3XG  S7   C8   C9   114.03  3.000
 3XG  C9   C8   C13  121.27  3.000
 3XG  S7   C8   C13  124.70  3.000
 3XG  O14  C13  N12  121.75  3.000
 3XG  N12  C13  C8   112.68  3.000
 3XG  O14  C13  C8   125.57  3.000
 3XG  H7   C17  H6   106.46  3.000
 3XG  H7   C17  N18  108.05  3.000
 3XG  H6   C17  N18  111.46  3.000
 3XG  H7   C17  C16  108.92  3.000
 3XG  H6   C17  C16  109.13  3.000
 3XG  N18  C17  C16  112.61  3.000
 3XG  H8   C1   C2   121.13  3.000
 3XG  H8   C1   C6   120.77  3.000
 3XG  C2   C1   C6   118.10  3.000
 3XG  S7   C2   C3   112.72  3.000
 3XG  C3   C2   C1   121.08  3.000
 3XG  S7   C2   C1   126.21  3.000
 3XG  C9   C3   C2   111.08  3.000
 3XG  C9   C3   C4   128.91  3.000
 3XG  C2   C3   C4   120.01  3.000
 3XG  H10  C16  H9   107.44  3.000
 3XG  H10  C16  C17  110.50  3.000
 3XG  H9   C16  C17  109.40  3.000
 3XG  H10  C16  C15  109.49  3.000
 3XG  H9   C16  C15  109.43  3.000
 3XG  C17  C16  C15  110.53  3.000
 3XG  N12  C11  N10  124.66  3.000
 3XG  N10  C11  S23  119.23  3.000
 3XG  N12  C11  S23  116.11  3.000
 3XG  N10  C9   C3   125.10  3.000
 3XG  N10  C9   C8   122.82  3.000
 3XG  C3   C9   C8   112.08  3.000
 3XG  C24  C25  O26  110.85  3.000
 3XG  O26  C25  O29  125.19  3.000
 3XG  C24  C25  O29  123.96  3.000
 3XG  C27  O26  C25  118.05  3.000
 3XG  H12  C27  H11  108.19  3.000
 3XG  H12  C27  C28  111.15  3.000
 3XG  H11  C27  C28  111.08  3.000
 3XG  H12  C27  O26  109.29  3.000
 3XG  H11  C27  O26  109.33  3.000
 3XG  C28  C27  O26  107.78  3.000
 3XG  H15  C28  H14  108.76  3.000
 3XG  H15  C28  H13  107.85  3.000
 3XG  H14  C28  H13  107.85  3.000
 3XG  H15  C28  C27  111.72  3.000
 3XG  H14  C28  C27  111.70  3.000
 3XG  H13  C28  C27  108.82  3.000
 3XG  H17  C24  H16  107.69  3.000
 3XG  H17  C24  S23  110.67  3.000
 3XG  H16  C24  S23  110.51  3.000
 3XG  H17  C24  C25  110.35  3.000
 3XG  H16  C24  C25  110.72  3.000
 3XG  S23  C24  C25  106.91  3.000
 3XG  C24  S23  C11   99.47  3.000
 3XG  C9   N10  C11  116.81  3.000
 3XG  C11  N12  C15  121.41  3.000
 3XG  C11  N12  C13  121.74  3.000
 3XG  C15  N12  C13  116.76  3.000
 3XG  C2   S7   C8    90.10  3.000
 3XG  C19  N18  C22  104.62  3.000
 3XG  C19  N18  C17  114.63  3.000
 3XG  C22  N18  C17  113.34  3.000
 3XG  H20  C22  H19  107.33  3.000
 3XG  H20  C22  C21  113.41  3.000
 3XG  H19  C22  C21  110.08  3.000
 3XG  H20  C22  N18  110.98  3.000
 3XG  H19  C22  N18  111.59  3.000
 3XG  C21  C22  N18  103.51  3.000
 3XG  H22  C21  H21  107.27  3.000
 3XG  H22  C21  C20  110.64  3.000
 3XG  H21  C21  C20  112.80  3.000
 3XG  H22  C21  C22  110.49  3.000
 3XG  H21  C21  C22  111.74  3.000
 3XG  C20  C21  C22  103.95  3.000
 3XG  H24  C20  H23  106.96  3.000
 3XG  H24  C20  C19  111.10  3.000
 3XG  H23  C20  C19  110.97  3.000
 3XG  H24  C20  C21  110.95  3.000
 3XG  H23  C20  C21  112.39  3.000
 3XG  C19  C20  C21  104.54  3.000
 3XG  H26  C19  H25  107.24  3.000
 3XG  H26  C19  C20  110.27  3.000
 3XG  H25  C19  C20  112.66  3.000
 3XG  H26  C19  N18  111.10  3.000
 3XG  H25  C19  N18  111.47  3.000
 3XG  C20  C19  N18  104.16  3.000
 3XG  H5   C15  H4   106.11  3.000
 3XG  H5   C15  N12  108.67  3.000
 3XG  H4   C15  N12  107.56  3.000
 3XG  H5   C15  C16  111.47  3.000
 3XG  H4   C15  C16  110.61  3.000
 3XG  N12  C15  C16  112.15  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
 3XG  CONST_01  S7   C2   C3   C4    180.00   0.0  0
 3XG  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 3XG  CONST_03  C8   C9   C3   C4    180.00   0.0  0
 3XG  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 3XG  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 3XG  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 3XG  CONST_07  C9   C3   C4   C5    180.00   0.0  0
 3XG  CONST_08  S7   C2   C1   C6    180.00   0.0  0
 3XG  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 3XG  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 3XG  CONST_11  C1   C2   S7   C8    180.00   0.0  0
 3XG  CONST_12  C3   C2   S7   C8      0.00   0.0  0
 3XG  CONST_13  C2   C3   C9   C8      0.00   0.0  0
 3XG  CONST_14  C9   C3   C2   C1    180.00   0.0  0
 3XG  CONST_15  C9   C8   S7   C2      0.00   0.0  0
 3XG  CONST_16  S7   C8   C9   C3      0.00   0.0  0
 3XG  CONST_17  S7   C2   C3   C9      0.00   0.0  0
 3XG  CONST_18  C11  N12  C13  C8      0.00   0.0  0
 3XG  CONST_19  N10  C11  N12  C13     0.00   0.0  0
 3XG  CONST_20  N12  C11  N10  C9      0.00   0.0  0
 3XG  CONST_21  C15  N12  C13  C8    180.00   0.0  0
 3XG  CONST_22  S23  C11  N12  C13   180.00   0.0  0
 3XG  CONST_23  N10  C11  N12  C15   180.00   0.0  0
 3XG  CONST_24  O14  C13  N12  C11   180.00   0.0  0
 3XG  CONST_25  S23  C11  N10  C9    180.00   0.0  0
 3XG  CONST_26  H3   C6   C5   C4    180.00   0.0  0
 3XG  CONST_27  H8   C1   C6   C5    180.00   0.0  0
 3XG  CONST_28  H1   C4   C5   C6    180.00   0.0  0
 3XG  CONST_29  H2   C5   C6   C1    180.00   0.0  0
 3XG  CONST_30  O14  C13  N12  C15     0.00   0.0  0
 3XG  CONST_31  S23  C11  N12  C15     0.00   0.0  0
 3XG  Var_01    C20  C21  C22  N18    29.35  30.0  1
 3XG  Var_02    C21  C20  C19  N18   -21.13  30.0  1
 3XG  Var_03    C20  C19  N18  C22    40.86  30.0  1
 3XG  Var_04    C19  C20  C21  C22    -4.93  30.0  1
 3XG  Var_05    C19  N18  C22  C21   -44.18  30.0  1
 3XG  Var_06    C16  C15  N12  C13    88.27  30.0  3
 3XG  Var_07    C22  N18  C17  C16  -174.61  30.0  3
 3XG  Var_08    N12  C11  S23  C24  -178.47  30.0  1
 3XG  Var_09    N18  C17  C16  C15   171.22  30.0  3
 3XG  Var_10    N12  C15  C16  C17   175.16  30.0  2
 3XG  Var_11    C25  C24  S23  C11   179.38  30.0  3
 3XG  Var_12    S23  C24  C25  O29     2.55  30.0  1
 3XG  Var_13    C28  C27  O26  C25   179.31  30.0  3
 3XG  Var_14    C24  C25  O26  C27  -179.29  30.0  2
 3XG  Var_15    H13  C28  C27  O26  -179.28  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
 3XG  plan-1  C4   0.020
 3XG  plan-1  C5   0.020
 3XG  plan-1  C6   0.020
 3XG  plan-1  C8   0.020
 3XG  plan-1  C13  0.020
 3XG  plan-1  C1   0.020
 3XG  plan-1  C2   0.020
 3XG  plan-1  C3   0.020
 3XG  plan-1  C11  0.020
 3XG  plan-1  C9   0.020
 3XG  plan-1  S23  0.020
 3XG  plan-1  N10  0.020
 3XG  plan-1  N12  0.020
 3XG  plan-1  O14  0.020
 3XG  plan-1  S7   0.020
 3XG  plan-1  H1   0.020
 3XG  plan-1  H2   0.020
 3XG  plan-1  H3   0.020
 3XG  plan-1  H8   0.020
 3XG  plan-1  C15  0.020
 3XG  plan-2  O29  0.020
 3XG  plan-2  C25  0.020
 3XG  plan-2  O26  0.020
 3XG  plan-2  C24  0.020

