# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 00:25:34 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)C(=O)c2sccc2
#
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
 T8J  T8J  1-[4-(thiophene-2-carbonyl)piperazin-1-yl]ethan-1-one  ligand  30  16  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T8J
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
 T8J  N1   N  NT    0  -0.467   0.0621   0.6400   0.3723
 T8J  C4   C  CH2   0  -0.314   1.2170   1.4743   0.6575
 T8J  C5   C  CH2   0  -0.313   2.3201   1.2624  -0.3697
 T8J  C6   C  C     0   0.539  -1.0634   1.2013  -0.1314
 T8J  C7   C  CR5   0  -0.329  -2.2877   0.3676  -0.2002
 T8J  C8   C  CR15  0  -0.182  -3.2411   0.4466  -1.1753
 T8J  C10  C  CR15  0  -0.451  -4.2659  -1.0307   0.2759
 T8J  N    N  NT    0  -0.448   2.6604  -0.1452  -0.4422
 T8J  C    C  CH3   0  -0.808   5.0122   0.2971   0.0672
 T8J  O    O  O     0  -0.504   4.0989  -1.8746  -0.2885
 T8J  C1   C  C     0   0.521   3.8909  -0.6692  -0.2348
 T8J  C2   C  CH2   0  -0.298   1.5182  -0.9893  -0.7294
 T8J  C3   C  CH2   0  -0.323   0.4011  -0.7721   0.2868
 T8J  C9   C  CR15  0  -0.183  -4.3694  -0.3685  -0.9109
 T8J  O1   O  O     0  -0.471  -1.1225   2.3697  -0.4868
 T8J  S    S  S2    0   0.245  -2.7939  -0.6836   1.0702
 T8J  H7   H  HCH2  0   0.275   0.9222   2.5197   0.6817
 T8J  H8   H  HCH2  0   0.259   1.5919   1.2044   1.6492
 T8J  H9   H  HCH2  0   0.255   1.9811   1.6048  -1.3528
 T8J  H10  H  HCH2  0   0.283   3.1833   1.8613  -0.0946
 T8J  H11  H  HCR5  0   0.273  -3.1354   1.0646  -2.0556
 T8J  H13  H  HCR5  0   0.305  -4.9803  -1.7008   0.7293
 T8J  H    H  HCH3  0   0.265   4.8279   0.8570   0.9849
 T8J  H2   H  HCH3  0   0.270   5.9359  -0.2623   0.1890
 T8J  H1   H  HCH3  0   0.267   5.1523   1.0207  -0.7363
 T8J  H3   H  HCH2  0   0.249   1.1425  -0.7559  -1.7317
 T8J  H4   H  HCH2  0   0.275   1.8186  -2.0333  -0.7178
 T8J  H5   H  HCH2  0   0.257   0.7145  -1.1307   1.2706
 T8J  H6   H  HCH2  0   0.276  -0.4522  -1.3658  -0.0290
 T8J  H12  H  HCR5  0   0.275  -5.2222  -0.4524  -1.5683

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
 T8J  C1   C    single    1.511  0.020  1.511
 T8J  C1   O    double    1.224  0.020  1.224
 T8J  N    C1   single    1.353  0.020  1.353
 T8J  C2   N    single    1.449  0.020  1.449
 T8J  C3   C2   single    1.526  0.020  1.526
 T8J  N1   C3   single    1.455  0.020  1.455
 T8J  N1   C4   single    1.453  0.020  1.453
 T8J  C4   C5   single    1.522  0.020  1.522
 T8J  C5   N    single    1.450  0.020  1.450
 T8J  C6   N1   single    1.355  0.020  1.355
 T8J  O1   C6   double    1.223  0.020  1.223
 T8J  C6   C7   single    1.483  0.020  1.483
 T8J  C7   C8   aromatic  1.366  0.020  1.366
 T8J  C9   C8   aromatic  1.417  0.020  1.417
 T8J  C10  C9   aromatic  1.363  0.020  1.363
 T8J  S    C10  aromatic  1.708  0.020  1.708
 T8J  C7   S    aromatic  1.725  0.020  1.725
 T8J  C4   H7   single    0.970  0.020  1.090
 T8J  C4   H8   single    0.970  0.020  1.090
 T8J  C5   H9   single    0.970  0.020  1.090
 T8J  C5   H10  single    0.970  0.020  1.090
 T8J  C8   H11  single    0.930  0.020  1.080
 T8J  C10  H13  single    0.930  0.020  1.080
 T8J  C    H    single    0.970  0.020  1.090
 T8J  C    H2   single    0.970  0.020  1.090
 T8J  C    H1   single    0.970  0.020  1.090
 T8J  C2   H3   single    0.970  0.020  1.090
 T8J  C2   H4   single    0.970  0.020  1.090
 T8J  C3   H5   single    0.970  0.020  1.090
 T8J  C3   H6   single    0.970  0.020  1.090
 T8J  C9   H12  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
 T8J  C3   N1   C6   125.02  3.000
 T8J  C6   N1   C4   119.69  3.000
 T8J  C3   N1   C4   112.56  3.000
 T8J  H8   C4   H7   108.07  3.000
 T8J  H8   C4   C5   109.21  3.000
 T8J  H7   C4   C5   110.22  3.000
 T8J  H8   C4   N1   107.98  3.000
 T8J  H7   C4   N1   109.96  3.000
 T8J  C5   C4   N1   111.32  3.000
 T8J  H10  C5   H9   107.52  3.000
 T8J  H10  C5   N    111.19  3.000
 T8J  H9   C5   N    109.36  3.000
 T8J  H10  C5   C4   109.16  3.000
 T8J  H9   C5   C4   109.76  3.000
 T8J  N    C5   C4   109.82  3.000
 T8J  O1   C6   C7   118.94  3.000
 T8J  C7   C6   N1   118.04  3.000
 T8J  O1   C6   N1   122.97  3.000
 T8J  S    C7   C8   110.86  3.000
 T8J  S    C7   C6   123.43  3.000
 T8J  C8   C7   C6   125.23  3.000
 T8J  H11  C8   C9   123.98  3.000
 T8J  H11  C8   C7   123.11  3.000
 T8J  C9   C8   C7   112.91  3.000
 T8J  H13  C10  S    120.08  3.000
 T8J  H13  C10  C9   128.11  3.000
 T8J  S    C10  C9   111.81  3.000
 T8J  C2   N    C1   121.44  3.000
 T8J  C2   N    C5   112.98  3.000
 T8J  C1   N    C5   125.56  3.000
 T8J  H1   C    H2   108.36  3.000
 T8J  H1   C    H    107.52  3.000
 T8J  H2   C    H    108.28  3.000
 T8J  H1   C    C1   111.87  3.000
 T8J  H2   C    C1   108.90  3.000
 T8J  H    C    C1   111.79  3.000
 T8J  O    C1   C    120.82  3.000
 T8J  O    C1   N    121.93  3.000
 T8J  C    C1   N    117.25  3.000
 T8J  H4   C2   H3   108.02  3.000
 T8J  H4   C2   C3   109.39  3.000
 T8J  H3   C2   C3   109.14  3.000
 T8J  H4   C2   N    109.86  3.000
 T8J  H3   C2   N    109.13  3.000
 T8J  C3   C2   N    111.24  3.000
 T8J  H6   C3   H5   107.91  3.000
 T8J  H6   C3   C2   107.68  3.000
 T8J  H5   C3   C2   110.05  3.000
 T8J  H6   C3   N1   111.38  3.000
 T8J  H5   C3   N1   109.41  3.000
 T8J  C2   C3   N1   110.36  3.000
 T8J  H12  C9   C10  123.52  3.000
 T8J  H12  C9   C8   124.05  3.000
 T8J  C10  C9   C8   112.43  3.000
 T8J  C10  S    C7    91.96  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
 T8J  CONST_01  C10  C9   C8  C7      0.00   0.0  0
 T8J  CONST_02  C9   C10  S   C7      0.00   0.0  0
 T8J  CONST_03  C10  S    C7  C8      0.00   0.0  0
 T8J  CONST_04  S    C10  C9  C8      0.00   0.0  0
 T8J  CONST_05  S    C7   C8  C9      0.00   0.0  0
 T8J  CONST_06  C9   C8   C7  C6    180.00   0.0  0
 T8J  CONST_07  C10  S    C7  C6    180.00   0.0  0
 T8J  CONST_08  C7   C6   N1  C4    180.00   0.0  0
 T8J  CONST_10  H12  C9   C8  C7    180.00   0.0  0
 T8J  CONST_11  H13  C10  S   C7    180.00   0.0  0
 T8J  CONST_12  H11  C8   C9  C10   180.00   0.0  0
 T8J  CONST_13  O1   C6   N1  C4      0.00   0.0  0
 T8J  CONST_14  C    C1   N   C5      0.00   0.0  0
 T8J  CONST_15  O    C1   N   C5    180.00   0.0  0
 T8J  CONST_16  C2   N    C1  C     180.00   0.0  0
 T8J  CONST_17  C2   N    C1  O       0.00   0.0  0
 T8J  Var_01    N    C2   C3  N1     53.53  30.0  1
 T8J  Var_02    N    C5   C4  N1    -54.90  30.0  1
 T8J  Var_03    C2   C3   N1  C4    -54.48  30.0  1
 T8J  Var_04    C2   N    C5  C4     55.65  30.0  1
 T8J  Var_05    C3   N1   C4  C5     55.82  30.0  1
 T8J  Var_06    C3   C2   N   C5    -55.61  30.0  1
 T8J  Var_07    C8   C7   C6  N1   -146.04  30.0  2
 T8J  Var_08    H    C    C1  N      61.54  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
 T8J  plan-1  C6   0.020
 T8J  plan-1  C7   0.020
 T8J  plan-1  C8   0.020
 T8J  plan-1  C10  0.020
 T8J  plan-1  C9   0.020
 T8J  plan-1  S    0.020
 T8J  plan-1  H11  0.020
 T8J  plan-1  H13  0.020
 T8J  plan-1  H12  0.020
 T8J  plan-2  N1   0.020
 T8J  plan-2  C4   0.020
 T8J  plan-2  C6   0.020
 T8J  plan-2  C7   0.020
 T8J  plan-2  C3   0.020
 T8J  plan-2  O1   0.020
 T8J  plan-3  C5   0.020
 T8J  plan-3  N    0.020
 T8J  plan-3  C    0.020
 T8J  plan-3  O    0.020
 T8J  plan-3  C1   0.020
 T8J  plan-3  C2   0.020

