# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:24:59 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-{4-[(5-bromothiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2sc(Br)cc2
#
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
 T81  T81  1-{4-[(5-bromothiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one  ligand  31  16  .  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_T81
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
 T81  N1   N   NT    0  -0.431  -1.7203  -0.7634   0.2553
 T81  C4   C   CH2   0  -0.317  -0.7610  -1.3919   1.1381
 T81  C5   C   CR5   0  -0.161   0.5806  -0.7506   1.0085
 T81  C6   C   CR15  0  -0.230   1.5288  -0.5131   1.9539
 T81  C7   C   CR15  0  -0.148   2.7205   0.0628   1.4284
 T81  C8   C   CR5   0  -0.351   2.6322   0.2476   0.0857
 T81  C10  C   CH2   0  -0.308  -3.0170   1.2316  -0.2943
 T81  N    N   NT    0  -0.444  -4.1748   0.3970  -0.5523
 T81  C    C   CH3   0  -0.806  -6.5646  -0.1200  -0.6068
 T81  O    O   O     0  -0.509  -5.6600   1.9866   0.0412
 T81  C1   C   C     0   0.515  -5.4320   0.8453  -0.3427
 T81  C2   C   CH2   0  -0.318  -3.8161  -0.9407  -0.9796
 T81  C3   C   CH2   0  -0.274  -2.8926  -1.5898   0.0377
 T81  C9   C   CH2   0  -0.282  -2.1004   0.5615   0.7131
 T81  S    S   S2    0   0.269   1.1180  -0.2592  -0.5563
 T81  BR   BR  BR    0   0.005   3.9225   0.9921  -1.0300
 T81  H8   H   HCH2  0   0.232  -1.0654  -1.3720   2.1963
 T81  H7   H   HCH2  0   0.269  -0.6819  -2.4463   0.8565
 T81  H9   H   HCR5  0   0.269   1.3881  -0.7406   3.0016
 T81  H10  H   HCR5  0   0.284   3.5815   0.3294   2.0242
 T81  H14  H   HCH2  0   0.241  -2.4744   1.3919  -1.2317
 T81  H13  H   HCH2  0   0.265  -3.3382   2.1999   0.0782
 T81  H    H   HCH3  0   0.264  -6.5054  -0.9985   0.0372
 T81  H2   H   HCH3  0   0.268  -7.5088   0.3821  -0.4133
 T81  H1   H   HCH3  0   0.266  -6.5677  -0.4711  -1.6390
 T81  H4   H   HCH2  0   0.276  -4.6986  -1.5595  -1.1116
 T81  H3   H   HCH2  0   0.245  -3.3069  -0.8828  -1.9470
 T81  H6   H   HCH2  0   0.250  -2.5772  -2.5625  -0.3452
 T81  H5   H   HCH2  0   0.205  -3.4515  -1.7689   0.9713
 T81  H12  H   HCH2  0   0.209  -2.6026   0.5187   1.6942
 T81  H11  H   HCH2  0   0.250  -1.2061   1.1755   0.8328

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
 T81  C1   C    single    1.511  0.020  1.511
 T81  C1   O    double    1.225  0.020  1.225
 T81  N    C1   single    1.351  0.020  1.351
 T81  C2   N    single    1.449  0.020  1.449
 T81  C3   C2   single    1.520  0.020  1.520
 T81  N1   C3   single    1.451  0.020  1.451
 T81  C4   N1   single    1.447  0.020  1.447
 T81  C5   C4   single    1.493  0.020  1.493
 T81  C6   C5   aromatic  1.360  0.020  1.360
 T81  C7   C6   aromatic  1.424  0.020  1.424
 T81  C8   C7   aromatic  1.358  0.020  1.358
 T81  BR   C8   single    1.861  0.020  1.861
 T81  C8   S    aromatic  1.721  0.020  1.721
 T81  S    C5   aromatic  1.726  0.020  1.726
 T81  N1   C9   single    1.452  0.020  1.452
 T81  C9   C10  single    1.518  0.020  1.518
 T81  C10  N    single    1.450  0.020  1.450
 T81  C4   H8   single    0.970  0.020  1.090
 T81  C4   H7   single    0.970  0.020  1.090
 T81  C6   H9   single    0.930  0.020  1.080
 T81  C7   H10  single    0.930  0.020  1.080
 T81  C10  H14  single    0.970  0.020  1.090
 T81  C10  H13  single    0.970  0.020  1.090
 T81  C    H    single    0.970  0.020  1.090
 T81  C    H2   single    0.970  0.020  1.090
 T81  C    H1   single    0.970  0.020  1.090
 T81  C2   H4   single    0.970  0.020  1.090
 T81  C2   H3   single    0.970  0.020  1.090
 T81  C3   H6   single    0.970  0.020  1.090
 T81  C3   H5   single    0.970  0.020  1.090
 T81  C9   H12  single    0.970  0.020  1.090
 T81  C9   H11  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
 T81  C9   N1   C3   110.82  3.000
 T81  C9   N1   C4   112.17  3.000
 T81  C3   N1   C4   112.32  3.000
 T81  H7   C4   H8   106.54  3.000
 T81  H7   C4   C5   109.07  3.000
 T81  H8   C4   C5   108.91  3.000
 T81  H7   C4   N1   108.03  3.000
 T81  H8   C4   N1   113.27  3.000
 T81  C5   C4   N1   110.87  3.000
 T81  S    C5   C6   111.32  3.000
 T81  S    C5   C4   118.74  3.000
 T81  C6   C5   C4   129.89  3.000
 T81  H9   C6   C7   123.47  3.000
 T81  H9   C6   C5   123.10  3.000
 T81  C7   C6   C5   113.43  3.000
 T81  H10  C7   C8   124.29  3.000
 T81  H10  C7   C6   124.28  3.000
 T81  C8   C7   C6   111.43  3.000
 T81  BR   C8   S    120.28  3.000
 T81  S    C8   C7   112.70  3.000
 T81  BR   C8   C7   127.01  3.000
 T81  H13  C10  H14  108.04  3.000
 T81  H13  C10  C9   110.15  3.000
 T81  H14  C10  C9   109.49  3.000
 T81  H13  C10  N    109.75  3.000
 T81  H14  C10  N    109.12  3.000
 T81  C9   C10  N    110.25  3.000
 T81  C2   N    C1   125.61  3.000
 T81  C2   N    C10  112.71  3.000
 T81  C1   N    C10  121.62  3.000
 T81  H1   C    H2   108.35  3.000
 T81  H1   C    H    107.44  3.000
 T81  H2   C    H    108.31  3.000
 T81  H1   C    C1   111.92  3.000
 T81  H2   C    C1   108.96  3.000
 T81  H    C    C1   111.75  3.000
 T81  O    C1   C    120.67  3.000
 T81  O    C1   N    122.05  3.000
 T81  C    C1   N    117.28  3.000
 T81  H3   C2   H4   107.50  3.000
 T81  H3   C2   C3   109.36  3.000
 T81  H4   C2   C3   109.38  3.000
 T81  H3   C2   N    109.07  3.000
 T81  H4   C2   N    111.15  3.000
 T81  C3   C2   N    110.32  3.000
 T81  H5   C3   H6   107.37  3.000
 T81  H5   C3   C2   109.15  3.000
 T81  H6   C3   C2   108.75  3.000
 T81  H5   C3   N1   112.03  3.000
 T81  H6   C3   N1   109.06  3.000
 T81  C2   C3   N1   110.38  3.000
 T81  H11  C9   H12  107.30  3.000
 T81  H11  C9   C10  108.61  3.000
 T81  H12  C9   C10  109.42  3.000
 T81  H11  C9   N1   109.47  3.000
 T81  H12  C9   N1   111.36  3.000
 T81  C10  C9   N1   110.58  3.000
 T81  C8   S    C5    91.12  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
 T81  CONST_01  C8   C7   C6  C5     0.00   0.0  0
 T81  CONST_02  C7   C8   S   C5     0.00   0.0  0
 T81  CONST_03  C8   S    C5  C6     0.00   0.0  0
 T81  CONST_04  S    C8   C7  C6     0.00   0.0  0
 T81  CONST_05  S    C5   C6  C7     0.00   0.0  0
 T81  CONST_06  C7   C6   C5  C4   180.00   0.0  0
 T81  CONST_07  C8   S    C5  C4   180.00   0.0  0
 T81  CONST_08  BR   C8   S   C5   180.00   0.0  0
 T81  CONST_09  BR   C8   C7  C6   180.00   0.0  0
 T81  CONST_10  H10  C7   C6  C5   180.00   0.0  0
 T81  CONST_11  H9   C6   C7  C8   180.00   0.0  0
 T81  CONST_12  C    C1   N   C10  180.00   0.0  0
 T81  CONST_13  O    C1   N   C10    0.00   0.0  0
 T81  CONST_14  C2   N    C1  C      0.00   0.0  0
 T81  CONST_15  C2   N    C1  O    180.00   0.0  0
 T81  Var_01    N    C2   C3  N1   -56.05  30.0  1
 T81  Var_02    N    C10  C9  N1    55.80  30.0  1
 T81  Var_03    C3   N1   C9  C10  -58.21  30.0  1
 T81  Var_04    C3   C2   N   C10   55.30  30.0  1
 T81  Var_05    C9   C10  N   C2   -55.13  30.0  1
 T81  Var_06    C9   N1   C3  C2    58.22  30.0  1
 T81  Var_07    C6   C5   C4  N1   144.27  30.0  2
 T81  Var_08    H    C    C1  N     61.34  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
 T81  plan-1  C4   0.020
 T81  plan-1  C5   0.020
 T81  plan-1  C6   0.020
 T81  plan-1  C7   0.020
 T81  plan-1  C8   0.020
 T81  plan-1  S    0.020
 T81  plan-1  BR   0.020
 T81  plan-1  H9   0.020
 T81  plan-1  H10  0.020
 T81  plan-2  C10  0.020
 T81  plan-2  N    0.020
 T81  plan-2  C    0.020
 T81  plan-2  O    0.020
 T81  plan-2  C1   0.020
 T81  plan-2  C2   0.020

