# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 11:44:47 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)CNC2=Nc3sc4CCCCc4c3C(=O)N2
#
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
 91J  91J  2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one  ligand  47  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_91J
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
 91J  C4   C  CH2   0  -0.425  -4.9189   1.1724  -1.0643
 91J  C5   C  CH1   0  -0.284  -3.9234   0.0382  -0.8440
 91J  C6   C  CH2   0  -0.246  -2.5364   0.4356  -1.3308
 91J  C8   C  CR6   0   0.758  -0.3291  -0.5940  -0.9481
 91J  C10  C  CR56  0  -0.016   1.5077   0.4992  -0.2898
 91J  C13  C  CH2   0  -0.476   5.1237   1.6399   0.8368
 91J  C15  C  CH2   0  -0.449   6.1657  -0.5762   0.2727
 91J  C17  C  CR5   0   0.202   3.6867  -0.3159   0.0879
 91J  C24  C  CH2   0  -0.275  -5.3443  -0.6788   1.0952
 91J  N2   N  NT    0  -0.407  -6.2437   0.4361   0.8656
 91J  C3   C  CH2   0  -0.276  -6.2948   0.7937  -0.5393
 91J  N7   N  NH1   0  -0.683  -1.6231  -0.6858  -1.2697
 91J  N9   N  N     0  -0.510   0.2058   0.5522  -0.6085
 91J  S11  S  S2    0   0.188   2.3783   1.9092   0.1994
 91J  C12  C  CR5   0  -0.277   3.8515   0.9961   0.3905
 91J  C14  C  CH2   0  -0.447   6.1132   0.5647   1.2820
 91J  C16  C  CH2   0  -0.490   4.8219  -1.2935   0.1598
 91J  C18  C  CR56  0  -0.106   2.3350  -0.6107  -0.2958
 91J  C19  C  CR6   0   0.524   1.7481  -1.8645  -0.6692
 91J  O20  O  O     0  -0.471   2.2959  -2.9547  -0.7296
 91J  N21  N  NR16  0  -0.735   0.3962  -1.7505  -0.9805
 91J  C23  C  CH2   0  -0.416  -3.9334  -0.3565   0.6295
 91J  H1   H  HCH2  0   0.218  -4.5703   2.0726  -0.5470
 91J  H2   H  HCH2  0   0.234  -4.9925   1.4197  -2.1262
 91J  H3   H  HCH1  0   0.225  -4.2627  -0.8240  -1.4358
 91J  H4   H  HCH2  0   0.245  -2.5962   0.8156  -2.3562
 91J  H5   H  HCH2  0   0.249  -2.1399   1.2398  -0.7114
 91J  H6   H  HCH2  0   0.246   5.5548   2.2263   0.0187
 91J  H7   H  HCH2  0   0.252   4.9374   2.3445   1.6512
 91J  H8   H  HCH2  0   0.223   6.4463  -0.1750  -0.7063
 91J  H9   H  HCH2  0   0.237   6.9392  -1.2953   0.5483
 91J  H10  H  HCH2  0   0.233  -5.3382  -0.9076   2.1640
 91J  H11  H  HCH2  0   0.182  -5.6953  -1.5925   0.5808
 91J  H12  H  HCH3  0   0.230  -7.5058  -0.0472   2.4570
 91J  H13  H  HCH3  0   0.230  -8.2057   1.0373   1.2554
 91J  H14  H  HCH3  0   0.188  -8.0572  -0.6914   0.9037
 91J  H16  H  HCH2  0   0.233  -6.9821   1.6350  -0.6593
 91J  H17  H  HCH2  0   0.183  -6.7006  -0.0338  -1.1506
 91J  H18  H  HNH1  0   0.406  -1.9683  -1.5692  -1.6109
 91J  H19  H  HCH2  0   0.239   7.1014   1.0105   1.4080
 91J  H20  H  HCH2  0   0.226   5.8142   0.1764   2.2601
 91J  H21  H  HCH2  0   0.246   4.8147  -1.9394  -0.7193
 91J  H22  H  HCH2  0   0.238   4.6764  -1.9577   1.0176
 91J  H23  H  HNR6  0   0.422  -0.0673  -2.6118  -1.2408
 91J  H24  H  HCH2  0   0.235  -3.2884  -1.2199   0.8065
 91J  H25  H  HCH2  0   0.215  -3.5328   0.4697   1.2270
 91J  C1   C  CH3   0  -0.517  -7.5624   0.1659   1.3882

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
 91J  C15  C16  single    1.527  0.020  1.527
 91J  C15  C14  single    1.524  0.020  1.524
 91J  C16  C17  single    1.500  0.020  1.500
 91J  C14  C13  single    1.528  0.020  1.528
 91J  O20  C19  double    1.222  0.020  1.222
 91J  C17  C18  aromatic  1.436  0.020  1.436
 91J  C17  C12  aromatic  1.356  0.020  1.356
 91J  C13  C12  single    1.494  0.020  1.494
 91J  C19  C18  single    1.434  0.020  1.434
 91J  C19  N21  single    1.392  0.020  1.392
 91J  C18  C10  aromatic  1.384  0.020  1.384
 91J  C12  S11  aromatic  1.744  0.020  1.744
 91J  N21  C8   single    1.366  0.020  1.366
 91J  C10  S11  aromatic  1.728  0.020  1.728
 91J  C10  N9   single    1.341  0.020  1.341
 91J  C8   N9   double    1.310  0.020  1.310
 91J  C8   N7   single    1.337  0.020  1.337
 91J  N7   C6   single    1.447  0.020  1.447
 91J  C23  C24  single    1.520  0.020  1.520
 91J  C23  C5   single    1.525  0.020  1.525
 91J  C6   C5   single    1.523  0.020  1.523
 91J  C24  N2   single    1.451  0.020  1.451
 91J  C5   C4   single    1.525  0.020  1.525
 91J  N2   C3   single    1.451  0.020  1.451
 91J  N2   C1   single    1.444  0.020  1.444
 91J  C4   C3   single    1.521  0.020  1.521
 91J  C4   H1   single    0.970  0.020  1.090
 91J  C4   H2   single    0.970  0.020  1.090
 91J  C5   H3   single    0.970  0.020  1.090
 91J  C6   H4   single    0.970  0.020  1.090
 91J  C6   H5   single    0.970  0.020  1.090
 91J  C13  H6   single    0.970  0.020  1.090
 91J  C13  H7   single    0.970  0.020  1.090
 91J  C15  H8   single    0.970  0.020  1.090
 91J  C15  H9   single    0.970  0.020  1.090
 91J  C24  H10  single    0.970  0.020  1.090
 91J  C24  H11  single    0.970  0.020  1.090
 91J  C1   H12  single    0.970  0.020  1.090
 91J  C1   H13  single    0.970  0.020  1.090
 91J  C1   H14  single    0.970  0.020  1.090
 91J  C3   H16  single    0.970  0.020  1.090
 91J  C3   H17  single    0.970  0.020  1.090
 91J  N7   H18  single    0.860  0.020  1.020
 91J  C14  H19  single    0.970  0.020  1.090
 91J  C14  H20  single    0.970  0.020  1.090
 91J  C16  H21  single    0.970  0.020  1.090
 91J  C16  H22  single    0.970  0.020  1.090
 91J  N21  H23  single    0.860  0.020  1.020
 91J  C23  H24  single    0.970  0.020  1.090
 91J  C23  H25  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
 91J  H2   C4   H1   107.12  3.000
 91J  H2   C4   C3   109.32  3.000
 91J  H1   C4   C3   109.25  3.000
 91J  H2   C4   C5   110.65  3.000
 91J  H1   C4   C5   109.59  3.000
 91J  C3   C4   C5   110.83  3.000
 91J  H3   C5   C23  108.36  3.000
 91J  H3   C5   C6   108.28  3.000
 91J  C23  C5   C6   112.48  3.000
 91J  H3   C5   C4   107.70  3.000
 91J  C6   C5   C4   110.75  3.000
 91J  C23  C5   C4   109.13  3.000
 91J  H5   C6   H4   107.21  3.000
 91J  H5   C6   N7   108.55  3.000
 91J  H4   C6   N7   110.04  3.000
 91J  H5   C6   C5   110.01  3.000
 91J  H4   C6   C5   109.89  3.000
 91J  N7   C6   C5   111.04  3.000
 91J  N21  C8   N9   122.04  3.000
 91J  N9   C8   N7   121.19  3.000
 91J  N21  C8   N7   116.77  3.000
 91J  C18  C10  S11  110.76  3.000
 91J  S11  C10  N9   121.60  3.000
 91J  C18  C10  N9   127.64  3.000
 91J  H7   C13  H6   106.18  3.000
 91J  H7   C13  C14  110.31  3.000
 91J  H6   C13  C14  109.86  3.000
 91J  H7   C13  C12  110.81  3.000
 91J  H6   C13  C12  110.05  3.000
 91J  C14  C13  C12  109.59  3.000
 91J  H9   C15  H8   106.60  3.000
 91J  H9   C15  C16  109.43  3.000
 91J  H8   C15  C16  109.36  3.000
 91J  H9   C15  C14  110.51  3.000
 91J  H8   C15  C14  109.07  3.000
 91J  C16  C15  C14  111.73  3.000
 91J  C18  C17  C16  126.27  3.000
 91J  C18  C17  C12  111.88  3.000
 91J  C16  C17  C12  121.85  3.000
 91J  H11  C24  H10  106.48  3.000
 91J  H11  C24  C23  109.10  3.000
 91J  H10  C24  C23  109.80  3.000
 91J  H11  C24  N2   111.38  3.000
 91J  H10  C24  N2   108.61  3.000
 91J  C23  C24  N2   111.34  3.000
 91J  C3   N2   C1   111.38  3.000
 91J  C1   N2   C24  111.41  3.000
 91J  C3   N2   C24  111.38  3.000
 91J  H17  C3   H16  106.53  3.000
 91J  H17  C3   N2   111.34  3.000
 91J  H16  C3   N2   108.56  3.000
 91J  H17  C3   C4   109.11  3.000
 91J  H16  C3   C4   109.83  3.000
 91J  N2   C3   C4   111.34  3.000
 91J  H18  N7   C8   118.24  3.000
 91J  H18  N7   C6   116.66  3.000
 91J  C8   N7   C6   124.60  3.000
 91J  C10  N9   C8   115.05  3.000
 91J  C12  S11  C10   91.68  3.000
 91J  S11  C12  C17  112.29  3.000
 91J  S11  C12  C13  121.77  3.000
 91J  C17  C12  C13  125.94  3.000
 91J  H20  C14  H19  106.81  3.000
 91J  H20  C14  C15  109.62  3.000
 91J  H19  C14  C15  110.55  3.000
 91J  H20  C14  C13  109.47  3.000
 91J  H19  C14  C13  109.43  3.000
 91J  C15  C14  C13  110.87  3.000
 91J  H22  C16  H21  105.74  3.000
 91J  H22  C16  C17  109.41  3.000
 91J  H21  C16  C17  110.02  3.000
 91J  H22  C16  C15  110.12  3.000
 91J  H21  C16  C15  110.09  3.000
 91J  C17  C16  C15  111.31  3.000
 91J  C19  C18  C17  129.39  3.000
 91J  C19  C18  C10  117.23  3.000
 91J  C17  C18  C10  113.38  3.000
 91J  N21  C19  O20  119.84  3.000
 91J  N21  C19  C18  112.59  3.000
 91J  O20  C19  C18  127.56  3.000
 91J  H23  N21  C19  115.63  3.000
 91J  H23  N21  C8   118.92  3.000
 91J  C19  N21  C8   125.44  3.000
 91J  H25  C23  H24  106.97  3.000
 91J  H25  C23  C24  109.40  3.000
 91J  H24  C23  C24  109.32  3.000
 91J  H25  C23  C5   109.22  3.000
 91J  H24  C23  C5   110.93  3.000
 91J  C24  C23  C5   110.91  3.000
 91J  H14  C1   H13  107.64  3.000
 91J  H14  C1   H12  107.58  3.000
 91J  H13  C1   H12  107.80  3.000
 91J  H14  C1   N2   113.36  3.000
 91J  H13  C1   N2   110.17  3.000
 91J  H12  C1   N2   110.10  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
 91J  CONST_01  C12  C17  C18  C10     0.00   0.0  0
 91J  CONST_02  C17  C12  S11  C10     0.00   0.0  0
 91J  CONST_03  S11  C10  C18  C17     0.00   0.0  0
 91J  CONST_04  C18  C17  C12  S11     0.00   0.0  0
 91J  CONST_05  C18  C10  S11  C12     0.00   0.0  0
 91J  CONST_06  C18  C19  N21  C8      0.00   0.0  0
 91J  CONST_07  N21  C8   N9   C10     0.00   0.0  0
 91J  CONST_08  C19  N21  C8   N9      0.00   0.0  0
 91J  CONST_09  O20  C19  N21  C8    180.00   0.0  0
 91J  CONST_10  N7   C8   N9   C10   180.00   0.0  0
 91J  CONST_11  C19  N21  C8   N7    180.00   0.0  0
 91J  CONST_12  H23  N21  C8   N9    180.00   0.0  0
 91J  CONST_13  N21  C8   N7   C6    180.00   0.0  0
 91J  CONST_14  N9   C8   N7   C6      0.00   0.0  0
 91J  CONST_15  H18  N7   C8   N9    180.00   0.0  0
 91J  Var_01    C24  N2   C3   C4    -58.93  30.0  1
 91J  Var_02    N2   C24  C23  C5    -56.71  30.0  1
 91J  Var_03    N2   C3   C4   C5     56.89  30.0  1
 91J  Var_04    C16  C15  C14  C13   -63.10  30.0  1
 91J  Var_05    C18  C17  C16  C15   166.22  30.0  1
 91J  Var_06    C12  C13  C14  C15    46.09  30.0  1
 91J  Var_07    C14  C15  C16  C17    44.56  30.0  1
 91J  Var_08    C14  C13  C12  C17   -15.83  30.0  1
 91J  Var_09    C23  C24  N2   C3     58.83  30.0  1
 91J  Var_10    C8   N7   C6   C5   -143.68  30.0  1
 91J  Var_11    H12  C1   N2   C24    58.05  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
 91J  chir_01  C5  C23  C6  C4  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
 91J  plan-1  C6   0.020
 91J  plan-1  C8   0.020
 91J  plan-1  C10  0.020
 91J  plan-1  C13  0.020
 91J  plan-1  C17  0.020
 91J  plan-1  N7   0.020
 91J  plan-1  N9   0.020
 91J  plan-1  S11  0.020
 91J  plan-1  C12  0.020
 91J  plan-1  C16  0.020
 91J  plan-1  C18  0.020
 91J  plan-1  C19  0.020
 91J  plan-1  O20  0.020
 91J  plan-1  N21  0.020
 91J  plan-1  H18  0.020
 91J  plan-1  H23  0.020

