# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:22:20 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-[(4-acetylpiperazin-1-yl)sulfonyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)[S](=O)(=O)c2ccccc2C#N
#
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
 T4D  T4D  2-[(4-acetylpiperazin-1-yl)sulfonyl]benzonitrile  ligand  35  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4D
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
 T4D  N1   N  N     0  -0.569   0.4656   0.5088  -1.0292
 T4D  C4   C  CH2   0  -0.305   0.9729   1.4840  -0.0620
 T4D  C5   C  CH2   0  -0.309   2.4920   1.4700  -0.0989
 T4D  C6   C  CR6   0  -0.190  -2.0843   0.2195  -0.0816
 T4D  C7   C  CR16  0  -0.235  -2.4072   1.2186   0.8230
 T4D  C8   C  CR16  0  -0.224  -3.1131   0.9099   1.9780
 T4D  C10  C  CR16  0  -0.237  -3.1836  -1.3995   1.3298
 T4D  N    N  NT    0  -0.453   2.9931   0.1344   0.1404
 T4D  C    C  CH3   0  -0.808   4.3501   0.8724   2.0398
 T4D  O    O  O     0  -0.499   4.2500  -1.3730   1.2473
 T4D  C1   C  C     0   0.523   3.8639  -0.2197   1.1167
 T4D  C11  C  CR6   0   0.071  -2.4734  -1.1028   0.1674
 T4D  C12  C  CSP   0   0.045  -2.1977  -2.2007  -0.7058
 T4D  C2   C  CH2   0  -0.300   2.4765  -0.8382  -0.7991
 T4D  C3   C  CH2   0  -0.319   0.9575  -0.8484  -0.7802
 T4D  C9   C  CR16  0  -0.227  -3.4995  -0.3962   2.2310
 T4D  N2   N  NS    0  -0.234  -2.0190  -3.1532  -1.3274
 T4D  O1   O  OS    0  -0.634  -1.3367   2.0783  -1.7567
 T4D  O2   O  OS    0  -0.630  -1.3544  -0.3062  -2.5444
 T4D  S    S  S     0   1.376  -1.1062   0.6694  -1.5013
 T4D  H6   H  HCH2  0   0.289   0.6277   2.4816  -0.3231
 T4D  H7   H  HCH2  0   0.250   0.6264   1.2487   0.9521
 T4D  H8   H  HCH2  0   0.260   2.8339   1.8199  -1.0778
 T4D  H9   H  HCH2  0   0.290   2.8587   2.1709   0.6447
 T4D  H10  H  HCR6  0   0.304  -2.1211   2.2438   0.6335
 T4D  H11  H  HCR6  0   0.291  -3.3627   1.6979   2.6747
 T4D  H13  H  HCR6  0   0.300  -3.4885  -2.4192   1.5198
 T4D  H    H  HCH3  0   0.266   3.5308   1.3522   2.5756
 T4D  H14  H  HCH3  0   0.272   5.0265   0.4385   2.7712
 T4D  H1   H  HCH3  0   0.269   4.8856   1.6496   1.4931
 T4D  H2   H  HCH2  0   0.257   2.8278  -0.5969  -1.8072
 T4D  H3   H  HCH2  0   0.281   2.8397  -1.8289  -0.5423
 T4D  H4   H  HCH2  0   0.248   0.6058  -1.2226   0.1899
 T4D  H5   H  HCH2  0   0.289   0.6064  -1.5203  -1.5602
 T4D  H12  H  HCR6  0   0.291  -4.0517  -0.6393   3.1280

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
 T4D  C1   C    single    1.510  0.020  1.510
 T4D  C1   O    double    1.223  0.020  1.223
 T4D  N    C1   single    1.355  0.020  1.355
 T4D  C2   N    single    1.448  0.020  1.448
 T4D  C3   C2   single    1.519  0.020  1.519
 T4D  N1   C3   single    1.465  0.020  1.465
 T4D  N1   C4   single    1.464  0.020  1.464
 T4D  C4   C5   single    1.520  0.020  1.520
 T4D  C5   N    single    1.446  0.020  1.446
 T4D  S    N1   single    1.649  0.020  1.649
 T4D  S    O1   double    1.450  0.020  1.450
 T4D  S    O2   double    1.450  0.020  1.450
 T4D  C6   S    single    1.782  0.020  1.782
 T4D  C7   C6   aromatic  1.386  0.020  1.386
 T4D  C8   C7   aromatic  1.388  0.020  1.388
 T4D  C9   C8   aromatic  1.385  0.020  1.385
 T4D  C10  C9   aromatic  1.385  0.020  1.385
 T4D  C11  C10  aromatic  1.394  0.020  1.394
 T4D  C11  C6   aromatic  1.401  0.020  1.401
 T4D  C12  C11  single    1.430  0.020  1.430
 T4D  N2   C12  triple    1.151  0.020  1.151
 T4D  C4   H6   single    0.970  0.020  1.090
 T4D  C4   H7   single    0.970  0.020  1.090
 T4D  C5   H8   single    0.970  0.020  1.090
 T4D  C5   H9   single    0.970  0.020  1.090
 T4D  C7   H10  single    0.930  0.020  1.080
 T4D  C8   H11  single    0.930  0.020  1.080
 T4D  C10  H13  single    0.930  0.020  1.080
 T4D  C    H    single    0.970  0.020  1.090
 T4D  C    H14  single    0.970  0.020  1.090
 T4D  C    H1   single    0.970  0.020  1.090
 T4D  C2   H2   single    0.970  0.020  1.090
 T4D  C2   H3   single    0.970  0.020  1.090
 T4D  C3   H4   single    0.970  0.020  1.090
 T4D  C3   H5   single    0.970  0.020  1.090
 T4D  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
 T4D  S    N1   C3   117.32  3.000
 T4D  S    N1   C4   117.03  3.000
 T4D  C3   N1   C4   112.86  3.000
 T4D  H7   C4   H6   108.57  3.000
 T4D  H7   C4   C5   109.64  3.000
 T4D  H6   C4   C5   108.66  3.000
 T4D  H7   C4   N1   111.00  3.000
 T4D  H6   C4   N1   110.03  3.000
 T4D  C5   C4   N1   108.91  3.000
 T4D  H9   C5   H8   107.50  3.000
 T4D  H9   C5   N    111.45  3.000
 T4D  H8   C5   N    109.57  3.000
 T4D  H9   C5   C4   108.36  3.000
 T4D  H8   C5   C4   109.34  3.000
 T4D  N    C5   C4   110.54  3.000
 T4D  S    C6   C11  122.18  3.000
 T4D  C11  C6   C7   119.99  3.000
 T4D  S    C6   C7   117.77  3.000
 T4D  H10  C7   C8   119.42  3.000
 T4D  H10  C7   C6   120.50  3.000
 T4D  C8   C7   C6   120.07  3.000
 T4D  H11  C8   C9   120.34  3.000
 T4D  H11  C8   C7   119.43  3.000
 T4D  C9   C8   C7   120.23  3.000
 T4D  H13  C10  C9   120.30  3.000
 T4D  H13  C10  C11  119.40  3.000
 T4D  C9   C10  C11  120.30  3.000
 T4D  C2   N    C1   121.42  3.000
 T4D  C2   N    C5   112.91  3.000
 T4D  C1   N    C5   125.66  3.000
 T4D  H1   C    H14  108.44  3.000
 T4D  H1   C    H    107.56  3.000
 T4D  H14  C    H    108.23  3.000
 T4D  H1   C    C1   111.53  3.000
 T4D  H14  C    C1   108.85  3.000
 T4D  H    C    C1   112.13  3.000
 T4D  O    C1   C    120.99  3.000
 T4D  O    C1   N    121.74  3.000
 T4D  C    C1   N    117.27  3.000
 T4D  C12  C11  C10  116.37  3.000
 T4D  C12  C11  C6   124.25  3.000
 T4D  C10  C11  C6   119.38  3.000
 T4D  N2   C12  C11  180.00  3.000
 T4D  H3   C2   H2   108.16  3.000
 T4D  H3   C2   C3   108.98  3.000
 T4D  H2   C2   C3   109.51  3.000
 T4D  H3   C2   N    109.88  3.000
 T4D  H2   C2   N    109.59  3.000
 T4D  C3   C2   N    110.69  3.000
 T4D  H5   C3   H4   108.65  3.000
 T4D  H5   C3   C2   108.54  3.000
 T4D  H4   C3   C2   109.49  3.000
 T4D  H5   C3   N1   110.01  3.000
 T4D  H4   C3   N1   111.00  3.000
 T4D  C2   C3   N1   109.11  3.000
 T4D  H12  C9   C10  119.57  3.000
 T4D  H12  C9   C8   120.40  3.000
 T4D  C10  C9   C8   120.03  3.000
 T4D  O2   S    O1   119.99  3.000
 T4D  O2   S    C6   108.02  3.000
 T4D  O1   S    C6   107.36  3.000
 T4D  C6   S    N1   105.69  3.000
 T4D  O2   S    N1   107.68  3.000
 T4D  O1   S    N1   107.25  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
 T4D  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 T4D  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 T4D  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 T4D  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 T4D  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 T4D  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 T4D  CONST_07  C12  C11  C6   C7   180.00   0.0  0
 T4D  CONST_08  S    C6   C7   C8   180.00   0.0  0
 T4D  CONST_09  S    C6   C11  C10  180.00   0.0  0
 T4D  CONST_10  C9   C10  C11  C12  180.00   0.0  0
 T4D  CONST_11  H11  C8   C7   C6   180.00   0.0  0
 T4D  CONST_12  H13  C10  C11  C6   180.00   0.0  0
 T4D  CONST_13  H12  C9   C8   C7   180.00   0.0  0
 T4D  CONST_14  H10  C7   C6   C11  180.00   0.0  0
 T4D  CONST_15  C    C1   N    C5     0.00   0.0  0
 T4D  CONST_16  O    C1   N    C5   180.00   0.0  0
 T4D  CONST_17  C2   N    C1   C    180.00   0.0  0
 T4D  CONST_18  C2   N    C1   O      0.00   0.0  0
 T4D  Var_01    N    C2   C3   N1    54.92  30.0  1
 T4D  Var_02    N    C5   C4   N1   -55.69  30.0  1
 T4D  Var_03    C2   C3   N1   C4   -57.34  30.0  1
 T4D  Var_04    C2   N    C5   C4    56.88  30.0  1
 T4D  Var_05    C3   N1   C4   C5    57.69  30.0  1
 T4D  Var_06    C3   C2   N    C5   -56.50  30.0  1
 T4D  Var_07    C7   C6   S    N1    88.61  30.0  2
 T4D  Var_08    C6   S    N1   C4   -70.17  30.0  1
 T4D  Var_09    H    C    C1   N     59.61  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
 T4D  plan-1  C6   0.020
 T4D  plan-1  C7   0.020
 T4D  plan-1  C8   0.020
 T4D  plan-1  C10  0.020
 T4D  plan-1  C11  0.020
 T4D  plan-1  C12  0.020
 T4D  plan-1  C9   0.020
 T4D  plan-1  N2   0.020
 T4D  plan-1  S    0.020
 T4D  plan-1  H10  0.020
 T4D  plan-1  H11  0.020
 T4D  plan-1  H13  0.020
 T4D  plan-1  H12  0.020
 T4D  plan-2  C5   0.020
 T4D  plan-2  N    0.020
 T4D  plan-2  C    0.020
 T4D  plan-2  O    0.020
 T4D  plan-2  C1   0.020
 T4D  plan-2  C2   0.020

