# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:21:02 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-{4-[(thiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2sccc2
#
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
 T8M  T8M  1-{4-[(thiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one  ligand  31  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T8M
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
 T8M  N1   N  NT    0  -0.428  -0.0040   0.5363  -0.3368
 T8M  C4   C  CH2   0  -0.318   1.1532   0.7072  -1.1885
 T8M  C5   C  CR5   0  -0.157   2.3391  -0.0132  -0.6349
 T8M  C6   C  CR15  0  -0.243   3.3335  -0.6753  -1.2880
 T8M  C7   C  CR15  0  -0.185   4.3351  -1.1803  -0.4099
 T8M  C8   C  CR15  0  -0.475   4.0744  -0.8953   0.8943
 T8M  C10  C  CH2   0  -0.311  -1.6643  -0.9786   0.6075
 T8M  N    N  NT    0  -0.447  -2.6851   0.0338   0.4207
 T8M  C    C  CH3   0  -0.807  -4.4543  -1.6474   0.2723
 T8M  O    O  O     0  -0.510  -4.8195   0.7029   0.1323
 T8M  C1   C  C     0   0.516  -4.0064  -0.2040   0.2682
 T8M  C2   C  CH2   0  -0.306  -2.1533   1.3836   0.4344
 T8M  C3   C  CH2   0  -0.284  -1.0372   1.5229  -0.5859
 T8M  C9   C  CH2   0  -0.273  -0.5523  -0.8034  -0.4112
 T8M  S    S  S2    0   0.205   2.6104  -0.0147   1.0674
 T8M  H7   H  HCH2  0   0.226   0.9832   0.3716  -2.2242
 T8M  H8   H  HCH2  0   0.263   1.3731   1.7777  -1.2448
 T8M  H9   H  HCR5  0   0.258   3.3524  -0.7994  -2.3622
 T8M  H10  H  HCR5  0   0.263   5.2008  -1.7378  -0.7382
 T8M  H11  H  HCR5  0   0.289   4.6542  -1.1690   1.7624
 T8M  H15  H  HCH2  0   0.242  -1.2469  -0.8903   1.6162
 T8M  H14  H  HCH2  0   0.274  -2.0830  -1.9762   0.5134
 T8M  H    H  HCH3  0   0.268  -5.5357  -1.6824   0.1712
 T8M  H2   H  HCH3  0   0.265  -4.0152  -2.2090  -0.5535
 T8M  H1   H  HCH3  0   0.265  -4.1777  -2.1553   1.1967
 T8M  H4   H  HCH2  0   0.264  -2.9476   2.0926   0.2189
 T8M  H3   H  HCH2  0   0.239  -1.7630   1.6063   1.4331
 T8M  H6   H  HCH2  0   0.247  -0.6045   2.5222  -0.5011
 T8M  H5   H  HCH2  0   0.204  -1.4589   1.4336  -1.6009
 T8M  H13  H  HCH2  0   0.206  -0.9412  -1.0254  -1.4198
 T8M  H12  H  HCH2  0   0.250   0.2323  -1.5322  -0.1989

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
 T8M  C1   C    single    1.511  0.020  1.511
 T8M  O    C1   double    1.226  0.020  1.226
 T8M  C1   N    single    1.351  0.020  1.351
 T8M  N    C2   single    1.451  0.020  1.451
 T8M  C3   C2   single    1.519  0.020  1.519
 T8M  N1   C3   single    1.450  0.020  1.450
 T8M  N1   C4   single    1.447  0.020  1.447
 T8M  C4   C5   single    1.494  0.020  1.494
 T8M  C5   C6   aromatic  1.361  0.020  1.361
 T8M  C7   C6   aromatic  1.425  0.020  1.425
 T8M  C8   C7   aromatic  1.360  0.020  1.360
 T8M  S    C8   aromatic  1.717  0.020  1.717
 T8M  C5   S    aromatic  1.724  0.020  1.724
 T8M  C9   N1   single    1.450  0.020  1.450
 T8M  C10  C9   single    1.518  0.020  1.518
 T8M  N    C10  single    1.450  0.020  1.450
 T8M  C4   H7   single    0.970  0.020  1.090
 T8M  C4   H8   single    0.970  0.020  1.090
 T8M  C6   H9   single    0.930  0.020  1.080
 T8M  C7   H10  single    0.930  0.020  1.080
 T8M  C8   H11  single    0.930  0.020  1.080
 T8M  C10  H15  single    0.970  0.020  1.090
 T8M  C10  H14  single    0.970  0.020  1.090
 T8M  C    H    single    0.970  0.020  1.090
 T8M  C    H2   single    0.970  0.020  1.090
 T8M  C    H1   single    0.970  0.020  1.090
 T8M  C2   H4   single    0.970  0.020  1.090
 T8M  C2   H3   single    0.970  0.020  1.090
 T8M  C3   H6   single    0.970  0.020  1.090
 T8M  C3   H5   single    0.970  0.020  1.090
 T8M  C9   H13  single    0.970  0.020  1.090
 T8M  C9   H12  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
 T8M  C9   N1   C3   110.52  3.000
 T8M  C9   N1   C4   112.42  3.000
 T8M  C3   N1   C4   112.85  3.000
 T8M  H8   C4   H7   106.29  3.000
 T8M  H8   C4   C5   109.34  3.000
 T8M  H7   C4   C5   108.90  3.000
 T8M  H8   C4   N1   107.86  3.000
 T8M  H7   C4   N1   113.20  3.000
 T8M  C5   C4   N1   111.09  3.000
 T8M  S    C5   C6   111.00  3.000
 T8M  S    C5   C4   119.42  3.000
 T8M  C6   C5   C4   129.53  3.000
 T8M  H9   C6   C7   124.00  3.000
 T8M  H9   C6   C5   123.03  3.000
 T8M  C7   C6   C5   112.97  3.000
 T8M  H10  C7   C8   123.56  3.000
 T8M  H10  C7   C6   123.98  3.000
 T8M  C8   C7   C6   112.46  3.000
 T8M  H11  C8   S    120.46  3.000
 T8M  H11  C8   C7   127.97  3.000
 T8M  S    C8   C7   111.57  3.000
 T8M  H14  C10  H15  107.51  3.000
 T8M  H14  C10  C9   109.28  3.000
 T8M  H15  C10  C9   109.24  3.000
 T8M  H14  C10  N    111.03  3.000
 T8M  H15  C10  N    109.31  3.000
 T8M  C9   C10  N    110.41  3.000
 T8M  C2   N    C1   121.55  3.000
 T8M  C2   N    C10  112.98  3.000
 T8M  C1   N    C10  125.46  3.000
 T8M  H1   C    H2   107.45  3.000
 T8M  H1   C    H    108.44  3.000
 T8M  H2   C    H    108.27  3.000
 T8M  H1   C    C1   111.84  3.000
 T8M  H2   C    C1   111.73  3.000
 T8M  H    C    C1   108.99  3.000
 T8M  O    C1   C    120.69  3.000
 T8M  O    C1   N    122.08  3.000
 T8M  C    C1   N    117.23  3.000
 T8M  H3   C2   H4   107.99  3.000
 T8M  H3   C2   C3   109.40  3.000
 T8M  H4   C2   C3   110.14  3.000
 T8M  H3   C2   N    109.17  3.000
 T8M  H4   C2   N    109.71  3.000
 T8M  C3   C2   N    110.39  3.000
 T8M  H5   C3   H6   107.28  3.000
 T8M  H5   C3   C2   109.26  3.000
 T8M  H6   C3   C2   108.84  3.000
 T8M  H5   C3   N1   112.05  3.000
 T8M  H6   C3   N1   109.08  3.000
 T8M  C2   C3   N1   110.23  3.000
 T8M  H12  C9   H13  107.27  3.000
 T8M  H12  C9   C10  108.59  3.000
 T8M  H13  C9   C10  109.38  3.000
 T8M  H12  C9   N1   109.58  3.000
 T8M  H13  C9   N1   111.48  3.000
 T8M  C10  C9   N1   110.44  3.000
 T8M  C8   S    C5    92.01  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
 T8M  CONST_01  C8   C7   C6  C5     0.00   0.0  0
 T8M  CONST_02  C7   C8   S   C5     0.00   0.0  0
 T8M  CONST_03  C8   S    C5  C6     0.00   0.0  0
 T8M  CONST_04  S    C8   C7  C6     0.00   0.0  0
 T8M  CONST_05  S    C5   C6  C7     0.00   0.0  0
 T8M  CONST_06  C7   C6   C5  C4   180.00   0.0  0
 T8M  CONST_07  C8   S    C5  C4   180.00   0.0  0
 T8M  CONST_08  H10  C7   C6  C5   180.00   0.0  0
 T8M  CONST_09  H11  C8   S   C5   180.00   0.0  0
 T8M  CONST_10  H9   C6   C7  C8   180.00   0.0  0
 T8M  CONST_11  C    C1   N   C10    0.00   0.0  0
 T8M  CONST_12  O    C1   N   C10  180.00   0.0  0
 T8M  CONST_13  C2   N    C1  C    180.00   0.0  0
 T8M  CONST_14  C2   N    C1  O      0.00   0.0  0
 T8M  Var_01    N    C2   C3  N1   -56.09  30.0  1
 T8M  Var_02    N    C10  C9  N1    55.75  30.0  1
 T8M  Var_03    C3   N1   C9  C10  -59.11  30.0  1
 T8M  Var_04    C3   C2   N   C10   54.35  30.0  1
 T8M  Var_05    C9   C10  N   C2   -54.13  30.0  1
 T8M  Var_06    C9   N1   C3  C2    59.24  30.0  1
 T8M  Var_07    C6   C5   C4  N1   143.70  30.0  2
 T8M  Var_08    H    C    C1  N    178.33  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
 T8M  plan-1  C4   0.020
 T8M  plan-1  C5   0.020
 T8M  plan-1  C6   0.020
 T8M  plan-1  C7   0.020
 T8M  plan-1  C8   0.020
 T8M  plan-1  S    0.020
 T8M  plan-1  H9   0.020
 T8M  plan-1  H10  0.020
 T8M  plan-1  H11  0.020
 T8M  plan-2  C10  0.020
 T8M  plan-2  N    0.020
 T8M  plan-2  C    0.020
 T8M  plan-2  O    0.020
 T8M  plan-2  C1   0.020
 T8M  plan-2  C2   0.020

