# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:45:53 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-{4-[6-(1-benzothiophen-2-yl)pyrimidin-4-yl]piperazin-1-yl}-1-(pyrrolidin-1-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN1CCN(CC1)c2cc(ncn2)c3sc4ccccc4c3)N5CCCC5
#
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
 B87  B87  2-{4-[6-(1-benzothiophen-2-yl)pyrimidin-4-yl]piperazin-1-yl}-1-(pyrrolidin-1-yl)ethanone  ligand  54  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B87
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
 B87  C1    C  CH2   0  -0.482   8.7435   1.9978   0.1397
 B87  C2    C  CH2   0  -0.259   7.4780   2.0360  -0.7082
 B87  N3    N  NR5   0  -0.474   6.5683   1.1406   0.0008
 B87  C4    C  CH2   0  -0.273   7.0616   0.7844   1.3286
 B87  C5    C  CH2   0  -0.476   8.2144   1.7572   1.5495
 B87  C6    C  C     0   0.540   5.4684   0.6463  -0.5889
 B87  O7    O  O     0  -0.501   5.1365   0.9698  -1.7220
 B87  C8    C  CH2   0  -0.404   4.6804  -0.3584   0.2400
 B87  N9    N  NT    0  -0.421   3.4810  -0.8093  -0.4172
 B87  C10   C  CH2   0  -0.287   3.0108  -2.0662   0.1342
 B87  C11   C  CH2   0  -0.318   1.8065  -2.5765  -0.6366
 B87  N12   N  NT    0  -0.501   0.7537  -1.5767  -0.6468
 B87  C13   C  CH2   0  -0.321   1.2044  -0.2910  -1.1408
 B87  C14   C  CH2   0  -0.282   2.4234   0.1821  -0.3694
 B87  C15   C  CR6   0   0.591  -0.5222  -1.8687  -0.3342
 B87  C16   C  CR16  0  -0.459  -1.5619  -0.9109  -0.3517
 B87  C17   C  CR6   0   0.303  -2.8255  -1.3312   0.0016
 B87  N18   N  N     0  -0.468  -3.0899  -2.6028   0.3459
 B87  C19   C  CR16  0   0.057  -2.0541  -3.4160   0.3295
 B87  N20   N  N     0  -0.481  -0.8047  -3.1319   0.0151
 B87  C21   C  CR5   0  -0.240  -3.9662  -0.4172   0.0314
 B87  S22   S  S2    0   0.215  -3.7940   1.2695  -0.3775
 B87  C23   C  CR56  0  -0.214  -5.4758   1.5563  -0.0840
 B87  C24   C  CR56  0   0.241  -6.1329   0.3781   0.3132
 B87  C25   C  CR15  0  -0.244  -5.2415  -0.7364   0.3704
 B87  C26   C  CR16  0  -0.279  -6.1517   2.7675  -0.2038
 B87  C27   C  CR16  0  -0.265  -7.5040   2.7872   0.0793
 B87  C28   C  CR16  0  -0.255  -8.1773   1.6229   0.4746
 B87  C29   C  CR16  0  -0.319  -7.5047   0.4250   0.5928
 B87  H1    H  HCH2  0   0.238   9.3785   1.1653  -0.1712
 B87  H1A   H  HCH2  0   0.252   9.3284   2.9125   0.0516
 B87  H2    H  HCH2  0   0.235   7.0601   3.0456  -0.7594
 B87  H2A   H  HCH2  0   0.246   7.6449   1.6952  -1.7299
 B87  H4    H  HCH2  0   0.252   6.2882   0.8904   2.0902
 B87  H4A   H  HCH2  0   0.243   7.4107  -0.2524   1.3501
 B87  H5    H  HCH2  0   0.253   8.9639   1.3542   2.2293
 B87  H5A   H  HCH2  0   0.241   7.8411   2.6896   1.9787
 B87  H8    H  HCH2  0   0.279   5.3325  -1.2208   0.4172
 B87  H8A   H  HCH2  0   0.235   4.4735   0.0637   1.2377
 B87  H10   H  HCH2  0   0.250   3.8065  -2.8106   0.0606
 B87  H10A  H  HCH2  0   0.202   2.7428  -1.9787   1.2007
 B87  H11   H  HCH2  0   0.239   2.0996  -2.8036  -1.6676
 B87  H11A  H  HCH2  0   0.277   1.4392  -3.4915  -0.1834
 B87  H13   H  HCH2  0   0.247   1.4543  -0.3803  -2.2035
 B87  H13A  H  HCH2  0   0.271   0.4266   0.4611  -1.0538
 B87  H14   H  HCH2  0   0.202   2.1262   0.4064   0.6693
 B87  H14A  H  HCH2  0   0.255   2.7667   1.1130  -0.8193
 B87  H16   H  HCR6  0   0.279  -1.3808   0.1188  -0.6206
 B87  H19   H  HCR6  0   0.253  -2.2489  -4.4480   0.6058
 B87  H25   H  HCR5  0   0.270  -5.5429  -1.7342   0.6542
 B87  H26   H  HCR6  0   0.272  -5.6361   3.6686  -0.5087
 B87  H27   H  HCR6  0   0.265  -8.0508   3.7170  -0.0055
 B87  H28   H  HCR6  0   0.262  -9.2371   1.6689   0.6874
 B87  H29   H  HCR6  0   0.260  -8.0245  -0.4745   0.8977

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
 B87  C1   C2    single    1.524  0.020  1.524
 B87  C1   C5    single    1.525  0.020  1.525
 B87  C2   N3    single    1.460  0.020  1.460
 B87  N3   C4    single    1.461  0.020  1.461
 B87  N3   C6    single    1.342  0.020  1.342
 B87  C4   C5    single    1.524  0.020  1.524
 B87  C6   O7    double    1.224  0.020  1.224
 B87  C6   C8    single    1.522  0.020  1.522
 B87  C8   N9    single    1.440  0.020  1.440
 B87  N9   C10   single    1.451  0.020  1.451
 B87  N9   C14   single    1.450  0.020  1.450
 B87  C10  C11   single    1.518  0.020  1.518
 B87  C11  N12   single    1.452  0.020  1.452
 B87  N12  C13   single    1.449  0.020  1.449
 B87  N12  C15   single    1.346  0.020  1.346
 B87  C13  C14   single    1.518  0.020  1.518
 B87  C15  C16   aromatic  1.414  0.020  1.414
 B87  C15  N20   aromatic  1.341  0.020  1.341
 B87  C16  C17   aromatic  1.378  0.020  1.378
 B87  C17  N18   aromatic  1.344  0.020  1.344
 B87  C17  C21   single    1.462  0.020  1.462
 B87  N18  C19   aromatic  1.317  0.020  1.317
 B87  C19  N20   aromatic  1.319  0.020  1.319
 B87  C21  S22   aromatic  1.744  0.020  1.744
 B87  C21  C25   aromatic  1.358  0.020  1.358
 B87  S22  C23   aromatic  1.731  0.020  1.731
 B87  C23  C24   aromatic  1.406  0.020  1.406
 B87  C23  C26   aromatic  1.392  0.020  1.392
 B87  C24  C25   aromatic  1.428  0.020  1.428
 B87  C24  C29   aromatic  1.401  0.020  1.401
 B87  C26  C27   aromatic  1.382  0.020  1.382
 B87  C27  C28   aromatic  1.402  0.020  1.402
 B87  C28  C29   aromatic  1.379  0.020  1.379
 B87  C1   H1    single    0.970  0.020  1.090
 B87  C1   H1A   single    0.970  0.020  1.090
 B87  C2   H2    single    0.970  0.020  1.090
 B87  C2   H2A   single    0.970  0.020  1.090
 B87  C4   H4    single    0.970  0.020  1.090
 B87  C4   H4A   single    0.970  0.020  1.090
 B87  C5   H5    single    0.970  0.020  1.090
 B87  C5   H5A   single    0.970  0.020  1.090
 B87  C8   H8    single    0.970  0.020  1.090
 B87  C8   H8A   single    0.970  0.020  1.090
 B87  C10  H10   single    0.970  0.020  1.090
 B87  C10  H10A  single    0.970  0.020  1.090
 B87  C11  H11   single    0.970  0.020  1.090
 B87  C11  H11A  single    0.970  0.020  1.090
 B87  C13  H13   single    0.970  0.020  1.090
 B87  C13  H13A  single    0.970  0.020  1.090
 B87  C14  H14   single    0.970  0.020  1.090
 B87  C14  H14A  single    0.970  0.020  1.090
 B87  C16  H16   single    0.930  0.020  1.080
 B87  C19  H19   single    0.930  0.020  1.080
 B87  C25  H25   single    0.930  0.020  1.080
 B87  C26  H26   single    0.930  0.020  1.080
 B87  C27  H27   single    0.930  0.020  1.080
 B87  C28  H28   single    0.930  0.020  1.080
 B87  C29  H29   single    0.930  0.020  1.080

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
 B87  H1A   C1   H1   107.75  3.000
 B87  H1A   C1   C5   113.18  3.000
 B87  H1    C1   C5   110.16  3.000
 B87  H1A   C1   C2   112.33  3.000
 B87  H1    C1   C2   110.09  3.000
 B87  C5    C1   C2   103.31  3.000
 B87  H2A   C2   H2   107.65  3.000
 B87  H2A   C2   N3   111.03  3.000
 B87  H2    C2   N3   110.53  3.000
 B87  H2A   C2   C1   112.74  3.000
 B87  H2    C2   C1   111.50  3.000
 B87  N3    C2   C1   103.41  3.000
 B87  C6    N3   C4   125.90  3.000
 B87  C6    N3   C2   121.53  3.000
 B87  C4    N3   C2   112.36  3.000
 B87  H4A   C4   H4   107.73  3.000
 B87  H4A   C4   C5   111.13  3.000
 B87  H4    C4   C5   111.91  3.000
 B87  H4A   C4   N3   110.89  3.000
 B87  H4    C4   N3   111.82  3.000
 B87  C5    C4   N3   103.39  3.000
 B87  H5A   C5   H5   107.80  3.000
 B87  H5A   C5   C4   110.08  3.000
 B87  H5    C5   C4   112.00  3.000
 B87  H5A   C5   C1   110.32  3.000
 B87  H5    C5   C1   113.37  3.000
 B87  C4    C5   C1   103.25  3.000
 B87  C8    C6   O7   122.55  3.000
 B87  C8    C6   N3   115.34  3.000
 B87  O7    C6   N3   122.11  3.000
 B87  H8A   C8   H8   105.47  3.000
 B87  H8A   C8   N9   112.11  3.000
 B87  H8    C8   N9   108.85  3.000
 B87  H8A   C8   C6   109.70  3.000
 B87  H8    C8   C6   107.43  3.000
 B87  N9    C8   C6   112.91  3.000
 B87  C14   N9   C10  110.08  3.000
 B87  C14   N9   C8   112.22  3.000
 B87  C10   N9   C8   111.57  3.000
 B87  H10A  C10  H10  107.23  3.000
 B87  H10A  C10  C11  108.96  3.000
 B87  H10   C10  C11  108.34  3.000
 B87  H10A  C10  N9   112.17  3.000
 B87  H10   C10  N9   109.19  3.000
 B87  C11   C10  N9   110.81  3.000
 B87  H11A  C11  H11  107.98  3.000
 B87  H11A  C11  N12  109.76  3.000
 B87  H11   C11  N12  109.27  3.000
 B87  H11A  C11  C10  109.87  3.000
 B87  H11   C11  C10  109.59  3.000
 B87  N12   C11  C10  110.33  3.000
 B87  C15   N12  C13  124.51  3.000
 B87  C15   N12  C11  122.44  3.000
 B87  C13   N12  C11  112.82  3.000
 B87  H13A  C13  H13  107.33  3.000
 B87  H13A  C13  C14  108.59  3.000
 B87  H13   C13  C14  109.58  3.000
 B87  H13A  C13  N12  111.38  3.000
 B87  H13   C13  N12  109.23  3.000
 B87  C14   C13  N12  110.67  3.000
 B87  H14A  C14  H14  107.46  3.000
 B87  H14A  C14  C13  108.02  3.000
 B87  H14   C14  C13  108.99  3.000
 B87  H14A  C14  N9   109.92  3.000
 B87  H14   C14  N9   111.50  3.000
 B87  C13   C14  N9   110.84  3.000
 B87  N20   C15  C16  119.11  3.000
 B87  N20   C15  N12  117.70  3.000
 B87  C16   C15  N12  123.19  3.000
 B87  H16   C16  C17  120.58  3.000
 B87  H16   C16  C15  121.73  3.000
 B87  C17   C16  C15  117.69  3.000
 B87  C21   C17  N18  115.65  3.000
 B87  C21   C17  C16  122.01  3.000
 B87  N18   C17  C16  122.34  3.000
 B87  C19   N18  C17  115.24  3.000
 B87  H19   C19  N20  115.79  3.000
 B87  H19   C19  N18  116.27  3.000
 B87  N20   C19  N18  127.94  3.000
 B87  C19   N20  C15  117.68  3.000
 B87  C25   C21  S22  112.25  3.000
 B87  C25   C21  C17  126.22  3.000
 B87  S22   C21  C17  121.52  3.000
 B87  C23   S22  C21   91.40  3.000
 B87  C26   C23  C24  121.76  3.000
 B87  C26   C23  S22  126.95  3.000
 B87  C24   C23  S22  111.29  3.000
 B87  C29   C24  C25  129.00  3.000
 B87  C29   C24  C23  119.07  3.000
 B87  C25   C24  C23  111.93  3.000
 B87  H25   C25  C24  123.86  3.000
 B87  H25   C25  C21  123.02  3.000
 B87  C24   C25  C21  113.13  3.000
 B87  H26   C26  C27  120.81  3.000
 B87  H26   C26  C23  121.17  3.000
 B87  C27   C26  C23  118.02  3.000
 B87  H27   C27  C28  119.54  3.000
 B87  H27   C27  C26  119.39  3.000
 B87  C28   C27  C26  121.07  3.000
 B87  H28   C28  C29  119.86  3.000
 B87  H28   C28  C27  119.39  3.000
 B87  C29   C28  C27  120.75  3.000
 B87  H29   C29  C28  120.77  3.000
 B87  H29   C29  C24  119.91  3.000
 B87  C28   C29  C24  119.32  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
 B87  CONST_01  N18  C17  C16  C15     0.00   0.0  0
 B87  CONST_02  C21  C17  C16  C15   180.00   0.0  0
 B87  CONST_03  N18  C19  N20  C15     0.00   0.0  0
 B87  CONST_04  C19  N20  C15  C16     0.00   0.0  0
 B87  CONST_05  C19  N18  C17  C16     0.00   0.0  0
 B87  CONST_06  S22  C21  C17  C16     0.00   0.0  0
 B87  CONST_07  C25  C21  C17  C16   180.00   0.0  0
 B87  CONST_08  N20  C15  C16  C17     0.00   0.0  0
 B87  CONST_09  N20  C19  N18  C17     0.00   0.0  0
 B87  CONST_10  C23  S22  C21  C17   180.00   0.0  0
 B87  CONST_11  C24  C25  C21  C17   180.00   0.0  0
 B87  CONST_12  S22  C21  C17  N18   180.00   0.0  0
 B87  CONST_13  C25  C21  C17  N18     0.00   0.0  0
 B87  CONST_14  C21  C17  N18  C19   180.00   0.0  0
 B87  CONST_15  C24  C23  S22  C21     0.00   0.0  0
 B87  CONST_16  C26  C23  S22  C21   180.00   0.0  0
 B87  CONST_17  C23  C24  C25  C21     0.00   0.0  0
 B87  CONST_18  C29  C24  C25  C21   180.00   0.0  0
 B87  CONST_19  C24  C25  C21  S22     0.00   0.0  0
 B87  CONST_20  C25  C24  C23  S22     0.00   0.0  0
 B87  CONST_21  C29  C24  C23  S22   180.00   0.0  0
 B87  CONST_22  C27  C26  C23  S22   180.00   0.0  0
 B87  CONST_23  C25  C21  S22  C23     0.00   0.0  0
 B87  CONST_24  C28  C29  C24  C23     0.00   0.0  0
 B87  CONST_25  C28  C27  C26  C23     0.00   0.0  0
 B87  CONST_26  C27  C26  C23  C24     0.00   0.0  0
 B87  CONST_27  C27  C28  C29  C24     0.00   0.0  0
 B87  CONST_28  C26  C23  C24  C25   180.00   0.0  0
 B87  CONST_29  C28  C29  C24  C25   180.00   0.0  0
 B87  CONST_30  C29  C24  C23  C26     0.00   0.0  0
 B87  CONST_31  C29  C28  C27  C26     0.00   0.0  0
 B87  CONST_32  C17  C16  C15  N12   180.00   0.0  0
 B87  CONST_33  C19  N20  C15  N12   180.00   0.0  0
 B87  CONST_34  H16  C16  C15  N12     0.00   0.0  0
 B87  CONST_35  H19  C19  N20  C15   180.00   0.0  0
 B87  CONST_36  H25  C25  C21  C17     0.00   0.0  0
 B87  CONST_37  H26  C26  C23  S22     0.00   0.0  0
 B87  CONST_38  H29  C29  C24  C23   180.00   0.0  0
 B87  CONST_39  H27  C27  C26  C23   180.00   0.0  0
 B87  CONST_40  H28  C28  C29  C24   180.00   0.0  0
 B87  CONST_41  O7   C6   N3   C2      0.00   0.0  0
 B87  CONST_42  C8   C6   N3   C2    180.00   0.0  0
 B87  CONST_43  O7   C6   N3   C4    180.00   0.0  0
 B87  CONST_44  C8   C6   N3   C4      0.00   0.0  0
 B87  Var_01    C4   N3   C2   C1     11.75  30.0  1
 B87  Var_02    N3   C4   C5   C1    -30.64  30.0  1
 B87  Var_03    C4   C5   C1   C2     38.10  30.0  1
 B87  Var_04    C5   C4   N3   C2     11.93  30.0  1
 B87  Var_05    C5   C1   C2   N3    -30.55  30.0  1
 B87  Var_06    N12  C11  C10  N9    -56.20  30.0  1
 B87  Var_07    N12  C13  C14  N9     55.61  30.0  1
 B87  Var_08    C13  C14  N9   C10   -58.46  30.0  1
 B87  Var_09    C13  N12  C11  C10    54.13  30.0  1
 B87  Var_10    C14  N9   C10  C11    58.87  30.0  1
 B87  Var_11    C14  C13  N12  C11   -53.90  30.0  1
 B87  Var_12    C16  C15  N12  C11  -179.36  30.0  2
 B87  Var_13    N9   C8   C6   N3    177.40  30.0  3
 B87  Var_14    C10  N9   C8   C6    159.69  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
 B87  plan-1  N12  0.020
 B87  plan-1  C15  0.020
 B87  plan-1  C16  0.020
 B87  plan-1  C17  0.020
 B87  plan-1  N18  0.020
 B87  plan-1  C19  0.020
 B87  plan-1  N20  0.020
 B87  plan-1  C21  0.020
 B87  plan-1  H16  0.020
 B87  plan-1  H19  0.020
 B87  plan-2  C17  0.020
 B87  plan-2  C21  0.020
 B87  plan-2  S22  0.020
 B87  plan-2  C23  0.020
 B87  plan-2  C24  0.020
 B87  plan-2  C25  0.020
 B87  plan-2  C26  0.020
 B87  plan-2  C27  0.020
 B87  plan-2  C28  0.020
 B87  plan-2  C29  0.020
 B87  plan-2  H25  0.020
 B87  plan-2  H26  0.020
 B87  plan-2  H27  0.020
 B87  plan-2  H28  0.020
 B87  plan-2  H29  0.020
 B87  plan-3  C2   0.020
 B87  plan-3  N3   0.020
 B87  plan-3  C4   0.020
 B87  plan-3  C6   0.020
 B87  plan-3  O7   0.020
 B87  plan-3  C8   0.020

