# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:42:26 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-({4-[(6-chloro-1-benzothiophen-2-yl)sulfonyl]-2-oxopiperazin-1-yl}methyl)benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CN2CCN(CC2=O)[S](=O)(=O)c3sc4cc(Cl)ccc4c3)cc1
#
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
 RTR  RTR  4-({4-[(6-chloro-1-benzothiophen-2-yl)sulfonyl]-2-oxopiperazin-1-yl}methyl)benzenecarboximidamide  ligand  49  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RTR
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
 RTR  N29   N   N      0  -0.640   1.7776  -0.7783   -8.4176
 RTR  C28   C   C      0   0.330   0.9106   0.1333   -8.1930
 RTR  N30   N   NH2    0  -0.804   0.6517   1.0884   -9.1301
 RTR  C27   C   CR6    0  -0.004   0.1530   0.2826   -6.9184
 RTR  C26   C   CR16   0  -0.276  -0.2209  -0.8506   -6.1956
 RTR  C24   C   CR16   0  -0.282  -0.9112  -0.7304   -5.0029
 RTR  C22   C   CR6    0   0.130  -1.2373   0.5257   -4.4942
 RTR  C23   C   CR16   0  -0.293  -0.8604   1.6535   -5.2118
 RTR  C25   C   CR16   0  -0.267  -0.1797   1.5371   -6.4163
 RTR  C21   C   CH2    0  -0.420  -1.9751   0.6518   -3.1862
 RTR  N19   N   NT     0  -0.456  -1.1593   0.2427   -2.0542
 RTR  C16   C   C      0   0.556  -1.3727  -0.9417   -1.4561
 RTR  O20   O   O      0  -0.499  -2.2733  -1.7070   -1.7668
 RTR  C12   C   CH2    0  -0.398  -0.4826  -1.3411   -0.2920
 RTR  N7    N   N     -1  -0.574   0.7130  -0.5236   -0.1587
 RTR  C13   C   CH2    0  -0.352   0.4310   0.8978   -0.3119
 RTR  C17   C   CH2    0  -0.252  -0.0432   1.1122   -1.7279
 RTR  S4    S   S      0   1.391   1.7938  -0.9863    1.0009
 RTR  O8    O   OS     0  -0.632   1.9396  -2.4234    0.8889
 RTR  O9    O   OS     0  -0.636   2.9381  -0.1028    0.8939
 RTR  C1    C   CR5    0  -0.444   1.0375  -0.6418    2.5427
 RTR  C3    C   CR15   0  -0.168   0.2190  -1.4671    3.2368
 RTR  C6    C   CR56   0   0.216  -0.2845  -0.8354    4.4149
 RTR  C5    C   CR56   0  -0.223   0.1950   0.4788    4.5555
 RTR  S2    S   S2     0   0.310   1.2533   0.9216    3.2609
 RTR  C10   C   CR16   0  -0.226  -0.1583   1.2818    5.6364
 RTR  C14   C   CR6    0  -0.048  -1.0097   0.7347    6.5720
 RTR  CL    CL  CL     0  -0.108  -1.4820   1.6893    7.9343
 RTR  C15   C   CR16   0  -0.207  -1.5083  -0.5704    6.4618
 RTR  C11   C   CR16   0  -0.308  -1.1466  -1.3525    5.3894
 RTR  H29   H   H      0   0.333   1.9286  -1.3421   -7.5894
 RTR  H301  H   HNH2   0   0.385   1.0551   0.9361  -10.0409
 RTR  H302  H   HNH2   0   0.393  -0.2651   1.5030   -9.1488
 RTR  H26   H   HCR6   0   0.263   0.0067  -1.8384   -6.5773
 RTR  H24   H   HCR6   0   0.258  -1.2095  -1.6250   -4.4703
 RTR  H23   H   HCR6   0   0.261  -1.0973   2.6389   -4.8290
 RTR  H25   H   HCR6   0   0.264   0.1076   2.4342   -6.9496
 RTR  H211  H   HCH2   0   0.278  -2.2798   1.6884   -3.0270
 RTR  H212  H   HCH2   0   0.289  -2.8777   0.0442   -3.1983
 RTR  H121  H   HCH2   0   0.312  -0.2069  -2.3812   -0.4526
 RTR  H122  H   HCH2   0   0.283  -1.1149  -1.2931    0.6059
 RTR  H131  H   HCH2   0   0.264  -0.3305   1.2303    0.4028
 RTR  H132  H   HCH2   0   0.298   1.3304   1.4886   -0.1562
 RTR  H171  H   HCH2   0   0.262   0.7821   0.9578   -2.4279
 RTR  H172  H   HCH2   0   0.267  -0.3735   2.1471   -1.8299
 RTR  H3    H   HCR5   0   0.308  -0.0196  -2.4806    2.9467
 RTR  H10   H   HCR6   0   0.300   0.2179   2.2902    5.7390
 RTR  H15   H   HCR6   0   0.290  -2.1742  -0.9595    7.2193
 RTR  H11   H   HCR6   0   0.279  -1.5271  -2.3612    5.2994

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
 RTR  N29  C28   double    1.278  0.020  1.278
 RTR  N29  H29   single    0.890  0.020  1.040
 RTR  C28  N30   single    1.363  0.020  1.363
 RTR  C28  C27   single    1.490  0.020  1.490
 RTR  N30  H301  single    0.890  0.020  1.040
 RTR  N30  H302  single    0.890  0.020  1.040
 RTR  C27  C26   aromatic  1.395  0.020  1.395
 RTR  C27  C25   aromatic  1.392  0.020  1.392
 RTR  C26  C24   aromatic  1.383  0.020  1.383
 RTR  C26  H26   single    0.930  0.020  1.080
 RTR  C24  C22   aromatic  1.394  0.020  1.394
 RTR  C24  H24   single    0.930  0.020  1.080
 RTR  C22  C23   aromatic  1.389  0.020  1.389
 RTR  C22  C21   single    1.507  0.020  1.507
 RTR  C23  C25   aromatic  1.388  0.020  1.388
 RTR  C23  H23   single    0.930  0.020  1.080
 RTR  C25  H25   single    0.930  0.020  1.080
 RTR  C21  N19   single    1.454  0.020  1.454
 RTR  C21  H211  single    0.970  0.020  1.090
 RTR  C21  H212  single    0.970  0.020  1.090
 RTR  N19  C16   single    1.344  0.020  1.344
 RTR  N19  C17   single    1.452  0.020  1.452
 RTR  C16  O20   double    1.222  0.020  1.222
 RTR  C16  C12   single    1.519  0.020  1.519
 RTR  C12  N7    single    1.454  0.020  1.454
 RTR  C12  H121  single    0.970  0.020  1.090
 RTR  C12  H122  single    0.970  0.020  1.090
 RTR  N7   C13   single    1.457  0.020  1.457
 RTR  N7   S4    single    1.651  0.020  1.651
 RTR  C13  C17   single    1.509  0.020  1.509
 RTR  C13  H131  single    0.970  0.020  1.090
 RTR  C13  H132  single    0.970  0.020  1.090
 RTR  C17  H171  single    0.970  0.020  1.090
 RTR  C17  H172  single    0.970  0.020  1.090
 RTR  S4   O8    double    1.449  0.020  1.449
 RTR  S4   O9    double    1.450  0.020  1.450
 RTR  S4   C1    single    1.752  0.020  1.752
 RTR  C1   C3    aromatic  1.354  0.020  1.354
 RTR  C1   S2    aromatic  1.734  0.020  1.734
 RTR  C3   C6    aromatic  1.428  0.020  1.428
 RTR  C3   H3    single    0.930  0.020  1.080
 RTR  C6   C5    aromatic  1.406  0.020  1.406
 RTR  C6   C11   aromatic  1.400  0.020  1.400
 RTR  C5   S2    aromatic  1.730  0.020  1.730
 RTR  C5   C10   aromatic  1.392  0.020  1.392
 RTR  C10  C14   aromatic  1.378  0.020  1.378
 RTR  C10  H10   single    0.930  0.020  1.080
 RTR  C14  CL    single    1.729  0.020  1.729
 RTR  C14  C15   aromatic  1.401  0.020  1.401
 RTR  C15  C11   aromatic  1.376  0.020  1.376
 RTR  C15  H15   single    0.930  0.020  1.080
 RTR  C11  H11   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
 RTR  H29   N29  C28   110.75  3.000
 RTR  C27   C28  N30   114.92  3.000
 RTR  C27   C28  N29   124.52  3.000
 RTR  N30   C28  N29   120.52  3.000
 RTR  H302  N30  H301  114.22  3.000
 RTR  H302  N30  C28   118.33  3.000
 RTR  H301  N30  C28   116.07  3.000
 RTR  C25   C27  C26   118.76  3.000
 RTR  C25   C27  C28   121.36  3.000
 RTR  C26   C27  C28   119.87  3.000
 RTR  H26   C26  C24   119.21  3.000
 RTR  H26   C26  C27   120.12  3.000
 RTR  C24   C26  C27   120.66  3.000
 RTR  H24   C24  C22   120.03  3.000
 RTR  H24   C24  C26   119.32  3.000
 RTR  C22   C24  C26   120.64  3.000
 RTR  C21   C22  C23   120.89  3.000
 RTR  C21   C22  C24   120.44  3.000
 RTR  C23   C22  C24   118.67  3.000
 RTR  H23   C23  C25   119.34  3.000
 RTR  H23   C23  C22   119.78  3.000
 RTR  C25   C23  C22   120.88  3.000
 RTR  H25   C25  C23   119.21  3.000
 RTR  H25   C25  C27   120.39  3.000
 RTR  C23   C25  C27   120.39  3.000
 RTR  H212  C21  H211  107.47  3.000
 RTR  H212  C21  N19   108.48  3.000
 RTR  H211  C21  N19   108.06  3.000
 RTR  H212  C21  C22   110.47  3.000
 RTR  H211  C21  C22   110.03  3.000
 RTR  N19   C21  C22   112.18  3.000
 RTR  C17   N19  C16   123.36  3.000
 RTR  C17   N19  C21   115.96  3.000
 RTR  C16   N19  C21   120.35  3.000
 RTR  C12   C16  O20   117.52  3.000
 RTR  C12   C16  N19   118.67  3.000
 RTR  O20   C16  N19   123.77  3.000
 RTR  H122  C12  H121  107.94  3.000
 RTR  H122  C12  N7    111.93  3.000
 RTR  H121  C12  N7    110.03  3.000
 RTR  H122  C12  C16   106.11  3.000
 RTR  H121  C12  C16   106.66  3.000
 RTR  N7    C12  C16   113.84  3.000
 RTR  S4    N7   C13   118.28  3.000
 RTR  S4    N7   C12   116.41  3.000
 RTR  C13   N7   C12   112.31  3.000
 RTR  H132  C13  H131  108.45  3.000
 RTR  H132  C13  C17   108.49  3.000
 RTR  H131  C13  C17   110.52  3.000
 RTR  H132  C13  N7    110.79  3.000
 RTR  H131  C13  N7    111.21  3.000
 RTR  C17   C13  N7    107.35  3.000
 RTR  H172  C17  H171  107.62  3.000
 RTR  H172  C17  C13   108.53  3.000
 RTR  H171  C17  C13   110.10  3.000
 RTR  H172  C17  N19   108.32  3.000
 RTR  H171  C17  N19   110.60  3.000
 RTR  C13   C17  N19   111.56  3.000
 RTR  C1    S4   O9    106.62  3.000
 RTR  C1    S4   O8    107.85  3.000
 RTR  O9    S4   O8    121.29  3.000
 RTR  C1    S4   N7    106.28  3.000
 RTR  O9    S4   N7    107.10  3.000
 RTR  O8    S4   N7    106.83  3.000
 RTR  S2    C1   C3    114.36  3.000
 RTR  S2    C1   S4    119.22  3.000
 RTR  C3    C1   S4    126.33  3.000
 RTR  H3    C3   C6    123.93  3.000
 RTR  H3    C3   C1    124.57  3.000
 RTR  C6    C3   C1    111.49  3.000
 RTR  C11   C6   C5    119.05  3.000
 RTR  C11   C6   C3    128.88  3.000
 RTR  C5    C6   C3    112.06  3.000
 RTR  C10   C5   S2    126.07  3.000
 RTR  C10   C5   C6    122.02  3.000
 RTR  S2    C5   C6    111.90  3.000
 RTR  C5    S2   C1     90.17  3.000
 RTR  H10   C10  C14   121.38  3.000
 RTR  H10   C10  C5    121.56  3.000
 RTR  C14   C10  C5    117.06  3.000
 RTR  C15   C14  CL    118.62  3.000
 RTR  C15   C14  C10   122.41  3.000
 RTR  CL    C14  C10   118.97  3.000
 RTR  H15   C15  C11   120.24  3.000
 RTR  H15   C15  C14   119.95  3.000
 RTR  C11   C15  C14   119.82  3.000
 RTR  H11   C11  C15   120.16  3.000
 RTR  H11   C11  C6    120.20  3.000
 RTR  C15   C11  C6    119.64  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
 RTR  CONST_01  C22   C24  C26  C27     0.00   0.0  0
 RTR  CONST_02  C22   C23  C25  C27     0.00   0.0  0
 RTR  CONST_03  C23   C25  C27  C26     0.00   0.0  0
 RTR  CONST_04  C23   C22  C24  C26     0.00   0.0  0
 RTR  CONST_05  C25   C27  C26  C24     0.00   0.0  0
 RTR  CONST_06  C25   C23  C22  C24     0.00   0.0  0
 RTR  CONST_07  C5    C6   C3   C1      0.00   0.0  0
 RTR  CONST_08  C11   C6   C3   C1    180.00   0.0  0
 RTR  CONST_09  C6    C5   S2   C1      0.00   0.0  0
 RTR  CONST_10  C10   C5   S2   C1    180.00   0.0  0
 RTR  CONST_11  C5    S2   C1   C3      0.00   0.0  0
 RTR  CONST_12  S2    C5   C6   C3      0.00   0.0  0
 RTR  CONST_13  C10   C5   C6   C3    180.00   0.0  0
 RTR  CONST_14  C15   C11  C6   C3    180.00   0.0  0
 RTR  CONST_15  S2    C1   C3   C6      0.00   0.0  0
 RTR  CONST_16  C14   C10  C5   C6      0.00   0.0  0
 RTR  CONST_17  C14   C15  C11  C6      0.00   0.0  0
 RTR  CONST_18  C15   C11  C6   C5      0.00   0.0  0
 RTR  CONST_19  C15   C14  C10  C5      0.00   0.0  0
 RTR  CONST_20  C11   C6   C5   S2    180.00   0.0  0
 RTR  CONST_21  C14   C10  C5   S2    180.00   0.0  0
 RTR  CONST_22  C11   C6   C5   C10     0.00   0.0  0
 RTR  CONST_23  C11   C15  C14  C10     0.00   0.0  0
 RTR  CONST_24  C17   N19  C16  C12     0.00   0.0  0
 RTR  CONST_25  C24   C26  C27  C28   180.00   0.0  0
 RTR  CONST_26  C23   C25  C27  C28   180.00   0.0  0
 RTR  CONST_27  C21   C22  C24  C26   180.00   0.0  0
 RTR  CONST_28  C21   C22  C23  C25   180.00   0.0  0
 RTR  CONST_29  C6    C3   C1   S4    180.00   0.0  0
 RTR  CONST_30  C5    S2   C1   S4    180.00   0.0  0
 RTR  CONST_31  CL    C14  C10  C5    180.00   0.0  0
 RTR  CONST_32  C11   C15  C14  CL    180.00   0.0  0
 RTR  CONST_33  C12   C16  N19  C21   180.00   0.0  0
 RTR  CONST_34  C17   N19  C16  O20   180.00   0.0  0
 RTR  CONST_35  H24   C24  C26  C27   180.00   0.0  0
 RTR  CONST_36  H23   C23  C25  C27   180.00   0.0  0
 RTR  CONST_37  H25   C25  C27  C26   180.00   0.0  0
 RTR  CONST_38  H26   C26  C24  C22   180.00   0.0  0
 RTR  CONST_39  H11   C11  C6   C3      0.00   0.0  0
 RTR  CONST_40  H10   C10  C5   C6    180.00   0.0  0
 RTR  CONST_41  H15   C15  C11  C6    180.00   0.0  0
 RTR  CONST_42  H3    C3   C6   C5    180.00   0.0  0
 RTR  CONST_43  O20   C16  N19  C21     0.00   0.0  0
 RTR  CONST_44  H29   N29  C28  C27     0.00   0.0  0
 RTR  CONST_45  H301  N30  C28  C27   180.00   0.0  0
 RTR  Var_01    N7    C12  C16  N19   -13.91  30.0  1
 RTR  Var_02    N7    C13  C17  N19    54.03  30.0  1
 RTR  Var_03    C13   C17  N19  C16   -26.52  30.0  1
 RTR  Var_04    N19   C21  C22  C24    68.55  30.0  2
 RTR  Var_05    C16   N19  C21  C22  -104.46  30.0  3
 RTR  Var_06    C3    C1   S4   N7     87.70  30.0  2
 RTR  Var_07    C26   C27  C28  N29   -34.52  30.0  2

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
 RTR  chir_01  N7  S4  C13  C12  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
 RTR  plan-1  C28   0.020
 RTR  plan-1  C27   0.020
 RTR  plan-1  C26   0.020
 RTR  plan-1  C24   0.020
 RTR  plan-1  C22   0.020
 RTR  plan-1  C23   0.020
 RTR  plan-1  C25   0.020
 RTR  plan-1  C21   0.020
 RTR  plan-1  H26   0.020
 RTR  plan-1  H24   0.020
 RTR  plan-1  H23   0.020
 RTR  plan-1  H25   0.020
 RTR  plan-2  S4    0.020
 RTR  plan-2  C1    0.020
 RTR  plan-2  C3    0.020
 RTR  plan-2  C6    0.020
 RTR  plan-2  C5    0.020
 RTR  plan-2  S2    0.020
 RTR  plan-2  C10   0.020
 RTR  plan-2  C14   0.020
 RTR  plan-2  CL    0.020
 RTR  plan-2  C15   0.020
 RTR  plan-2  C11   0.020
 RTR  plan-2  H3    0.020
 RTR  plan-2  H10   0.020
 RTR  plan-2  H15   0.020
 RTR  plan-2  H11   0.020
 RTR  plan-3  C21   0.020
 RTR  plan-3  N19   0.020
 RTR  plan-3  C16   0.020
 RTR  plan-3  O20   0.020
 RTR  plan-3  C12   0.020
 RTR  plan-3  C17   0.020
 RTR  plan-4  N29   0.020
 RTR  plan-4  C28   0.020
 RTR  plan-4  N30   0.020
 RTR  plan-4  C27   0.020
 RTR  plan-4  H29   0.020
 RTR  plan-4  H301  0.020
 RTR  plan-4  H302  0.020

