# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:00:16 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 3-({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)c1cccc(CN2CCN(CC2=O)[S](=O)(=O)c3sc4cc(Cl)ccc4c3)c1
#
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
 RRP  RRP  3-({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_RRP
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
 RRP  N29   N   N      0  -0.641   1.8619  -2.2077   7.6676
 RRP  C28   C   C      0   0.330   1.5075  -0.9910   7.5014
 RRP  N30   N   NH2    0  -0.803   2.1322   0.0120   8.1791
 RRP  C27   C   CR6    0   0.026   0.3879  -0.5479   6.6223
 RRP  C26   C   CR16   0  -0.353   0.1439  -1.2199   5.4256
 RRP  C24   C   CR6    0   0.152  -0.8952  -0.8418   4.5875
 RRP  C22   C   CR16   0  -0.297  -1.7126   0.2234   4.9619
 RRP  C23   C   CR16   0  -0.225  -1.4815   0.8956   6.1511
 RRP  C25   C   CR16   0  -0.294  -0.4310   0.5194   6.9780
 RRP  C21   C   CH2    0  -0.424  -1.1188  -1.5580   3.2796
 RRP  N2    N   NT     0  -0.455  -0.7848  -0.7265   2.1342
 RRP  C8    C   C      0   0.557  -1.7547  -0.1072   1.4404
 RRP  O1    O   O      0  -0.499  -2.9474  -0.2514   1.6631
 RRP  C4    C   CH2    0  -0.396  -1.3604   0.7839   0.2751
 RRP  N1    N   N     -1  -0.575   0.0566   1.1098   0.2304
 RRP  C7    C   CH2    0  -0.350   0.9046  -0.0449   0.4990
 RRP  C2    C   CH2    0  -0.255   0.6292  -0.4773   1.9177
 RRP  S4    S   S      0   1.390   0.5227   2.1703  -0.9479
 RRP  O8    O   OS     0  -0.632  -0.3996   3.2866  -0.9000
 RRP  O9    O   OS     0  -0.635   1.9516   2.3666  -0.8027
 RRP  C1    C   CR5    0  -0.444   0.2679   1.3421  -2.4701
 RRP  C3    C   CR15   0  -0.166  -0.8622   1.3785  -3.2143
 RRP  C6    C   CR56   0   0.217  -0.7762   0.5056  -4.3413
 RRP  C5    C   CR56   0  -0.221   0.4542  -0.1728  -4.3914
 RRP  S2    S   S2     0   0.309   1.4897   0.2710  -3.0776
 RRP  C10   C   CR16   0  -0.226   0.7571  -1.0771  -5.4054
 RRP  C14   C   CR6    0  -0.047  -0.2092  -1.2895  -6.3655
 RRP  CL    CL  CL     0  -0.108   0.1082  -2.4124  -7.6418
 RRP  C15   C   CR16   0  -0.208  -1.4454  -0.6298  -6.3457
 RRP  C11   C   CR16   0  -0.308  -1.7271   0.2654  -5.3400
 RRP  H29   H   H      0   0.333   1.2342  -2.8355   7.1793
 RRP  H301  H   HNH2   0   0.385   2.9720  -0.2392   8.6762
 RRP  H302  H   HNH2   0   0.393   2.1542   0.9286   7.7646
 RRP  H26   H   HCR6   0   0.261   0.7858  -2.0422   5.1301
 RRP  H22   H   HCR6   0   0.260  -2.5345   0.5279   4.3254
 RRP  H23   H   HCR6   0   0.263  -2.1250   1.7156   6.4417
 RRP  H25   H   HCR6   0   0.265  -0.2679   1.0469   7.9090
 RRP  H211  H   HCH2   0   0.276  -0.4973  -2.4549   3.2369
 RRP  H212  H   HCH2   0   0.288  -2.1547  -1.8778   3.1884
 RRP  H41   H   HCH2   0   0.311  -1.9493   1.6948   0.3636
 RRP  H42   H   HCH2   0   0.283  -1.6897   0.2609  -0.6343
 RRP  H71   H   HCH2   0   0.263   0.7024  -0.8610  -0.2045
 RRP  H72   H   HCH2   0   0.298   1.9543   0.2267   0.4185
 RRP  H21   H   HCH2   0   0.261   0.9991   0.2801   2.6138
 RRP  H22A  H   HCH2   0   0.267   1.1751  -1.4007   2.1153
 RRP  H3    H   HCR5   0   0.307  -1.7222   1.9930  -2.9885
 RRP  H10   H   HCR6   0   0.299   1.7059  -1.5950  -5.4367
 RRP  H15   H   HCR6   0   0.289  -2.1742  -0.8268  -7.1194
 RRP  H11   H   HCR6   0   0.279  -2.6793   0.7787  -5.3199

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
 RRP  N29  C28   double    1.278  0.020  1.278
 RRP  N29  H29   single    0.890  0.020  1.040
 RRP  C28  N30   single    1.362  0.020  1.362
 RRP  C28  C27   single    1.491  0.020  1.491
 RRP  N30  H301  single    0.890  0.020  1.040
 RRP  N30  H302  single    0.890  0.020  1.040
 RRP  C27  C26   aromatic  1.394  0.020  1.394
 RRP  C27  C25   aromatic  1.392  0.020  1.392
 RRP  C26  C24   aromatic  1.387  0.020  1.387
 RRP  C26  H26   single    0.930  0.020  1.080
 RRP  C24  C22   aromatic  1.394  0.020  1.394
 RRP  C24  C21   single    1.508  0.020  1.508
 RRP  C22  C23   aromatic  1.385  0.020  1.385
 RRP  C22  H22   single    0.930  0.020  1.080
 RRP  C23  C25   aromatic  1.389  0.020  1.389
 RRP  C23  H23   single    0.930  0.020  1.080
 RRP  C25  H25   single    0.930  0.020  1.080
 RRP  C21  N2    single    1.454  0.020  1.454
 RRP  C21  H211  single    0.970  0.020  1.090
 RRP  C21  H212  single    0.970  0.020  1.090
 RRP  N2   C8    single    1.344  0.020  1.344
 RRP  N2   C2    single    1.452  0.020  1.452
 RRP  C8   O1    double    1.222  0.020  1.222
 RRP  C8   C4    single    1.519  0.020  1.519
 RRP  C4   N1    single    1.455  0.020  1.455
 RRP  C4   H41   single    0.970  0.020  1.090
 RRP  C4   H42   single    0.970  0.020  1.090
 RRP  N1   C7    single    1.458  0.020  1.458
 RRP  N1   S4    single    1.652  0.020  1.652
 RRP  C7   C2    single    1.508  0.020  1.508
 RRP  C7   H71   single    0.970  0.020  1.090
 RRP  C7   H72   single    0.970  0.020  1.090
 RRP  C2   H21   single    0.970  0.020  1.090
 RRP  C2   H22A  single    0.970  0.020  1.090
 RRP  S4   O8    double    1.449  0.020  1.449
 RRP  S4   O9    double    1.450  0.020  1.450
 RRP  S4   C1    single    1.752  0.020  1.752
 RRP  C1   C3    aromatic  1.354  0.020  1.354
 RRP  C1   S2    aromatic  1.735  0.020  1.735
 RRP  C3   C6    aromatic  1.428  0.020  1.428
 RRP  C3   H3    single    0.930  0.020  1.080
 RRP  C6   C5    aromatic  1.406  0.020  1.406
 RRP  C6   C11   aromatic  1.400  0.020  1.400
 RRP  C5   S2    aromatic  1.731  0.020  1.731
 RRP  C5   C10   aromatic  1.392  0.020  1.392
 RRP  C10  C14   aromatic  1.379  0.020  1.379
 RRP  C10  H10   single    0.930  0.020  1.080
 RRP  C14  CL    single    1.729  0.020  1.729
 RRP  C14  C15   aromatic  1.401  0.020  1.401
 RRP  C15  C11   aromatic  1.376  0.020  1.376
 RRP  C15  H15   single    0.930  0.020  1.080
 RRP  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
 RRP  H29   N29  C28   110.82  3.000
 RRP  C27   C28  N30   114.77  3.000
 RRP  C27   C28  N29   124.60  3.000
 RRP  N30   C28  N29   120.60  3.000
 RRP  H302  N30  H301  114.33  3.000
 RRP  H302  N30  C28   118.41  3.000
 RRP  H301  N30  C28   116.37  3.000
 RRP  C25   C27  C26   119.09  3.000
 RRP  C25   C27  C28   121.28  3.000
 RRP  C26   C27  C28   119.63  3.000
 RRP  H26   C26  C24   119.04  3.000
 RRP  H26   C26  C27   119.73  3.000
 RRP  C24   C26  C27   121.22  3.000
 RRP  C21   C24  C22   120.60  3.000
 RRP  C21   C24  C26   120.37  3.000
 RRP  C22   C24  C26   119.02  3.000
 RRP  H22   C22  C23   119.64  3.000
 RRP  H22   C22  C24   120.13  3.000
 RRP  C23   C22  C24   120.23  3.000
 RRP  H23   C23  C25   119.68  3.000
 RRP  H23   C23  C22   119.93  3.000
 RRP  C25   C23  C22   120.38  3.000
 RRP  H25   C25  C23   119.61  3.000
 RRP  H25   C25  C27   120.33  3.000
 RRP  C23   C25  C27   120.05  3.000
 RRP  H212  C21  H211  107.29  3.000
 RRP  H212  C21  N2    108.71  3.000
 RRP  H211  C21  N2    107.94  3.000
 RRP  H212  C21  C24   110.70  3.000
 RRP  H211  C21  C24   109.85  3.000
 RRP  N2    C21  C24   112.18  3.000
 RRP  C2    N2   C8    123.15  3.000
 RRP  C2    N2   C21   116.06  3.000
 RRP  C8    N2   C21   120.29  3.000
 RRP  C4    C8   O1    117.54  3.000
 RRP  C4    C8   N2    118.63  3.000
 RRP  O1    C8   N2    123.78  3.000
 RRP  H42   C4   H41   107.66  3.000
 RRP  H42   C4   N1    111.90  3.000
 RRP  H41   C4   N1    110.01  3.000
 RRP  H42   C4   C8    106.12  3.000
 RRP  H41   C4   C8    106.75  3.000
 RRP  N1    C4   C8    114.07  3.000
 RRP  S4    N1   C7    118.40  3.000
 RRP  S4    N1   C4    116.13  3.000
 RRP  C7    N1   C4    112.56  3.000
 RRP  H72   C7   H71   108.45  3.000
 RRP  H72   C7   C2    108.51  3.000
 RRP  H71   C7   C2    110.88  3.000
 RRP  H72   C7   N1    110.50  3.000
 RRP  H71   C7   N1    111.36  3.000
 RRP  C2    C7   N1    107.11  3.000
 RRP  H22A  C2   H21   107.57  3.000
 RRP  H22A  C2   C7    108.77  3.000
 RRP  H21   C2   C7    109.78  3.000
 RRP  H22A  C2   N2    108.37  3.000
 RRP  H21   C2   N2    110.70  3.000
 RRP  C7    C2   N2    111.55  3.000
 RRP  C1    S4   O9    107.13  3.000
 RRP  C1    S4   O8    107.48  3.000
 RRP  O9    S4   O8    121.32  3.000
 RRP  C1    S4   N1    105.98  3.000
 RRP  O9    S4   N1    107.07  3.000
 RRP  O8    S4   N1    106.93  3.000
 RRP  S2    C1   C3    114.34  3.000
 RRP  S2    C1   S4    119.59  3.000
 RRP  C3    C1   S4    125.92  3.000
 RRP  H3    C3   C6    124.07  3.000
 RRP  H3    C3   C1    124.38  3.000
 RRP  C6    C3   C1    111.54  3.000
 RRP  C11   C6   C5    119.10  3.000
 RRP  C11   C6   C3    128.83  3.000
 RRP  C5    C6   C3    112.07  3.000
 RRP  C10   C5   S2    126.11  3.000
 RRP  C10   C5   C6    122.00  3.000
 RRP  S2    C5   C6    111.89  3.000
 RRP  C5    S2   C1     90.16  3.000
 RRP  H10   C10  C14   121.40  3.000
 RRP  H10   C10  C5    121.54  3.000
 RRP  C14   C10  C5    117.06  3.000
 RRP  C15   C14  CL    118.55  3.000
 RRP  C15   C14  C10   122.41  3.000
 RRP  CL    C14  C10   119.04  3.000
 RRP  H15   C15  C11   120.25  3.000
 RRP  H15   C15  C14   119.93  3.000
 RRP  C11   C15  C14   119.82  3.000
 RRP  H11   C11  C15   120.17  3.000
 RRP  H11   C11  C6    120.21  3.000
 RRP  C15   C11  C6    119.62  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
 RRP  CONST_01  C22   C24  C26  C27     0.00   0.0  0
 RRP  CONST_02  C22   C23  C25  C27     0.00   0.0  0
 RRP  CONST_03  C23   C25  C27  C26     0.00   0.0  0
 RRP  CONST_04  C23   C22  C24  C26     0.00   0.0  0
 RRP  CONST_05  C25   C27  C26  C24     0.00   0.0  0
 RRP  CONST_06  C25   C23  C22  C24     0.00   0.0  0
 RRP  CONST_07  C5    C6   C3   C1      0.00   0.0  0
 RRP  CONST_08  C11   C6   C3   C1    180.00   0.0  0
 RRP  CONST_09  C6    C5   S2   C1      0.00   0.0  0
 RRP  CONST_10  C10   C5   S2   C1    180.00   0.0  0
 RRP  CONST_11  C5    S2   C1   C3      0.00   0.0  0
 RRP  CONST_12  S2    C5   C6   C3      0.00   0.0  0
 RRP  CONST_13  C10   C5   C6   C3    180.00   0.0  0
 RRP  CONST_14  C15   C11  C6   C3    180.00   0.0  0
 RRP  CONST_15  S2    C1   C3   C6      0.00   0.0  0
 RRP  CONST_16  C14   C10  C5   C6      0.00   0.0  0
 RRP  CONST_17  C14   C15  C11  C6      0.00   0.0  0
 RRP  CONST_18  C15   C11  C6   C5      0.00   0.0  0
 RRP  CONST_19  C15   C14  C10  C5      0.00   0.0  0
 RRP  CONST_20  C11   C6   C5   S2    180.00   0.0  0
 RRP  CONST_21  C14   C10  C5   S2    180.00   0.0  0
 RRP  CONST_22  C11   C6   C5   C10     0.00   0.0  0
 RRP  CONST_23  C11   C15  C14  C10     0.00   0.0  0
 RRP  CONST_24  C2    N2   C8   C4      0.00   0.0  0
 RRP  CONST_25  C24   C26  C27  C28   180.00   0.0  0
 RRP  CONST_26  C23   C25  C27  C28   180.00   0.0  0
 RRP  CONST_27  C21   C24  C26  C27   180.00   0.0  0
 RRP  CONST_28  C21   C24  C22  C23   180.00   0.0  0
 RRP  CONST_29  C6    C3   C1   S4    180.00   0.0  0
 RRP  CONST_30  C5    S2   C1   S4    180.00   0.0  0
 RRP  CONST_31  CL    C14  C10  C5    180.00   0.0  0
 RRP  CONST_32  C11   C15  C14  CL    180.00   0.0  0
 RRP  CONST_33  C4    C8   N2   C21   180.00   0.0  0
 RRP  CONST_34  C2    N2   C8   O1    180.00   0.0  0
 RRP  CONST_35  H23   C23  C25  C27   180.00   0.0  0
 RRP  CONST_36  H25   C25  C27  C26   180.00   0.0  0
 RRP  CONST_37  H22   C22  C24  C26   180.00   0.0  0
 RRP  CONST_38  H26   C26  C24  C22   180.00   0.0  0
 RRP  CONST_39  H11   C11  C6   C3      0.00   0.0  0
 RRP  CONST_40  H10   C10  C5   C6    180.00   0.0  0
 RRP  CONST_41  H15   C15  C11  C6    180.00   0.0  0
 RRP  CONST_42  H3    C3   C6   C5    180.00   0.0  0
 RRP  CONST_43  O1    C8   N2   C21     0.00   0.0  0
 RRP  CONST_44  H29   N29  C28  C27     0.00   0.0  0
 RRP  CONST_45  H301  N30  C28  C27   180.00   0.0  0
 RRP  Var_01    N1    C4   C8   N2    -13.48  30.0  1
 RRP  Var_02    N1    C7   C2   N2     54.90  30.0  1
 RRP  Var_03    C7    C2   N2   C8    -28.13  30.0  1
 RRP  Var_04    N2    C21  C24  C26  -109.65  30.0  2
 RRP  Var_05    C8    N2   C21  C24  -100.49  30.0  3
 RRP  Var_06    C3    C1   S4   N1     90.90  30.0  2
 RRP  Var_07    C26   C27  C28  N29   -35.92  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
 RRP  chir_01  N1  S4  C7  C4  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
 RRP  plan-1  C28   0.020
 RRP  plan-1  C27   0.020
 RRP  plan-1  C26   0.020
 RRP  plan-1  C24   0.020
 RRP  plan-1  C22   0.020
 RRP  plan-1  C23   0.020
 RRP  plan-1  C25   0.020
 RRP  plan-1  C21   0.020
 RRP  plan-1  H26   0.020
 RRP  plan-1  H22   0.020
 RRP  plan-1  H23   0.020
 RRP  plan-1  H25   0.020
 RRP  plan-2  S4    0.020
 RRP  plan-2  C1    0.020
 RRP  plan-2  C3    0.020
 RRP  plan-2  C6    0.020
 RRP  plan-2  C5    0.020
 RRP  plan-2  S2    0.020
 RRP  plan-2  C10   0.020
 RRP  plan-2  C14   0.020
 RRP  plan-2  CL    0.020
 RRP  plan-2  C15   0.020
 RRP  plan-2  C11   0.020
 RRP  plan-2  H3    0.020
 RRP  plan-2  H10   0.020
 RRP  plan-2  H15   0.020
 RRP  plan-2  H11   0.020
 RRP  plan-3  C21   0.020
 RRP  plan-3  N2    0.020
 RRP  plan-3  C8    0.020
 RRP  plan-3  O1    0.020
 RRP  plan-3  C4    0.020
 RRP  plan-3  C2    0.020
 RRP  plan-4  N29   0.020
 RRP  plan-4  C28   0.020
 RRP  plan-4  N30   0.020
 RRP  plan-4  C27   0.020
 RRP  plan-4  H29   0.020
 RRP  plan-4  H301  0.020
 RRP  plan-4  H302  0.020

