# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:20:09 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-{[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}-1-(1H-pyrrolo[3,2-c]pyridin-2-ylmethyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(cc1)/C=C/[S](=O)(=O)N2CCN(Cc3[nH]c4ccncc4c3)C(=O)C2
#
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
 RRR  RRR  4-{[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}-1-(1H-pyrrolo[3,2-c]pyridin-2-ylmethyl)piperazin-2-one  ligand  45  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RRR
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
 RRR  N10   N   NR15   0  -0.723   1.7963  -4.9224   3.0985
 RRR  C4    C   CR56   0   0.430   3.0108  -5.4787   3.3331
 RRR  C5    C   CR56   0  -0.021   3.6619  -5.6136   2.0886
 RRR  C6    C   CR16   0  -0.132   4.9425  -6.1685   2.0868
 RRR  N1    N   N      0  -0.424   5.5436  -6.5630   3.1939
 RRR  C2    C   CR16   0  -0.102   4.8995  -6.4247   4.3650
 RRR  C3    C   CR16   0  -0.373   3.6347  -5.8926   4.5074
 RRR  C12   C   CR15   0  -0.435   2.7695  -5.1095   1.0945
 RRR  C11   C   CR5    0   0.375   1.6434  -4.7016   1.7480
 RRR  C13   C   CH2    0  -0.442   0.4100  -4.0652   1.1998
 RRR  N14   N   NT     0  -0.456   0.4336  -2.6127   1.3024
 RRR  C17   C   C      0   0.553   1.0848  -1.9114   0.3577
 RRR  O44   O   O      0  -0.491   1.5824  -2.4265  -0.6314
 RRR  C18   C   CH2    0  -0.393   1.1640  -0.4005   0.4917
 RRR  N19   N   N     -1  -0.585   0.7774   0.0883   1.8067
 RRR  C20   C   CH2    0  -0.342  -0.4240  -0.5613   2.3111
 RRR  C21   C   CH2    0  -0.263  -0.0889  -2.0175   2.5205
 RRR  S28   S   S      0   1.373   0.9388   1.7167   2.0788
 RRR  O37   O   OS     0  -0.655   2.2242   2.0963   1.5181
 RRR  O45   O   OS     0  -0.646   0.6726   1.9300   3.4912
 RRR  C29   C   C1     0  -0.511  -0.3118   2.4992   1.1362
 RRR  C30   C   C1     0  -0.152  -1.3941   3.0194   1.7232
 RRR  C31   C   CR5    0  -0.164  -2.4770   3.6651   1.0219
 RRR  C35   C   CR15   0  -0.235  -2.6533   3.8803  -0.3214
 RRR  C34   C   CR15   0  -0.108  -3.8537   4.5534  -0.6293
 RRR  C33   C   CR5    0  -0.257  -4.5723   4.8401   0.4943
 RRR  CL36  CL  CL     0  -0.060  -6.0746   5.6385   0.5668
 RRR  S32   S   S2     0   0.324  -3.8071   4.3008   1.9257
 RRR  H10   H   HNR5   0   0.414   1.0914  -4.7553   3.7987
 RRR  H6    H   HCR6   0   0.255   5.4895  -6.2931   1.1571
 RRR  H2    H   HCR6   0   0.256   5.4370  -6.7613   5.2443
 RRR  H3    H   HCR6   0   0.273   3.1693  -5.8046   5.4798
 RRR  H12   H   HCR5   0   0.254   2.9373  -5.0464   0.0315
 RRR  H131  H   HCH2   0   0.293   0.2898  -4.3519   0.1574
 RRR  H132  H   HCH2   0   0.289  -0.4751  -4.4188   1.7318
 RRR  H181  H   HCH2   0   0.308   2.1938  -0.1210   0.2784
 RRR  H182  H   HCH2   0   0.280   0.5340   0.0096  -0.3092
 RRR  H201  H   HCH2   0   0.261  -1.2600  -0.4555   1.6099
 RRR  H202  H   HCH2   0   0.293  -0.7172  -0.1300   3.2651
 RRR  H211  H   HCH2   0   0.257   0.6285  -2.1159   3.3402
 RRR  H212  H   HCH2   0   0.269  -0.9958  -2.5531   2.8027
 RRR  H29   H   H      0   0.324  -0.1337   2.5099   0.0673
 RRR  H30   H   H      0   0.308  -1.4798   2.9688   2.8036
 RRR  H35   H   HCR5   0   0.282  -1.9446   3.5671  -1.0751
 RRR  H34   H   HCR5   0   0.298  -4.1717   4.8111  -1.6282

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
 RRR  N10  C4    aromatic  1.356  0.020  1.356
 RRR  N10  C11   aromatic  1.377  0.020  1.377
 RRR  N10  H10   single    0.860  0.020  1.020
 RRR  C4   C5    aromatic  1.411  0.020  1.411
 RRR  C4   C3    aromatic  1.393  0.020  1.393
 RRR  C5   C6    aromatic  1.396  0.020  1.396
 RRR  C5   C12   aromatic  1.428  0.020  1.428
 RRR  C6   N1    aromatic  1.320  0.020  1.320
 RRR  C6   H6    single    0.930  0.020  1.080
 RRR  N1   C2    aromatic  1.344  0.020  1.344
 RRR  C2   C3    aromatic  1.380  0.020  1.380
 RRR  C2   H2    single    0.930  0.020  1.080
 RRR  C3   H3    single    0.930  0.020  1.080
 RRR  C12  C11   aromatic  1.364  0.020  1.364
 RRR  C12  H12   single    0.930  0.020  1.080
 RRR  C11  C13   single    1.492  0.020  1.492
 RRR  C13  N14   single    1.456  0.020  1.456
 RRR  C13  H131  single    0.970  0.020  1.090
 RRR  C13  H132  single    0.970  0.020  1.090
 RRR  N14  C17   single    1.345  0.020  1.345
 RRR  N14  C21   single    1.453  0.020  1.453
 RRR  C17  O44   double    1.221  0.020  1.221
 RRR  C17  C18   single    1.519  0.020  1.519
 RRR  C18  N19   single    1.455  0.020  1.455
 RRR  C18  H181  single    0.970  0.020  1.090
 RRR  C18  H182  single    0.970  0.020  1.090
 RRR  N19  C20   single    1.456  0.020  1.456
 RRR  N19  S28   single    1.659  0.020  1.659
 RRR  C20  C21   single    1.509  0.020  1.509
 RRR  C20  H201  single    0.970  0.020  1.090
 RRR  C20  H202  single    0.970  0.020  1.090
 RRR  C21  H211  single    0.970  0.020  1.090
 RRR  C21  H212  single    0.970  0.020  1.090
 RRR  S28  O37   double    1.453  0.020  1.453
 RRR  S28  O45   double    1.453  0.020  1.453
 RRR  S28  C29   single    1.751  0.020  1.751
 RRR  C29  C30   double    1.337  0.020  1.337
 RRR  C29  H29   single    0.930  0.020  1.080
 RRR  C30  C31   single    1.443  0.020  1.443
 RRR  C30  H30   single    0.930  0.020  1.080
 RRR  C31  C35   aromatic  1.372  0.020  1.372
 RRR  C31  S32   aromatic  1.729  0.020  1.729
 RRR  C35  C34   aromatic  1.410  0.020  1.410
 RRR  C35  H35   single    0.930  0.020  1.080
 RRR  C34  C33   aromatic  1.364  0.020  1.364
 RRR  C34  H34   single    0.930  0.020  1.080
 RRR  C33  CL36  single    1.703  0.020  1.703
 RRR  C33  S32   aromatic  1.710  0.020  1.710

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
 RRR  H10   N10  C11   125.26  3.000
 RRR  H10   N10  C4    125.05  3.000
 RRR  C11   N10  C4    109.57  3.000
 RRR  C3    C4   C5    120.57  3.000
 RRR  C3    C4   N10   131.98  3.000
 RRR  C5    C4   N10   107.45  3.000
 RRR  C12   C5   C6    135.48  3.000
 RRR  C12   C5   C4    106.97  3.000
 RRR  C6    C5   C4    117.55  3.000
 RRR  H6    C6   N1    117.03  3.000
 RRR  H6    C6   C5    120.59  3.000
 RRR  N1    C6   C5    122.38  3.000
 RRR  C2    N1   C6    118.81  3.000
 RRR  H2    C2   C3    119.38  3.000
 RRR  H2    C2   N1    115.93  3.000
 RRR  C3    C2   N1    124.69  3.000
 RRR  H3    C3   C2    121.25  3.000
 RRR  H3    C3   C4    122.76  3.000
 RRR  C2    C3   C4    116.00  3.000
 RRR  H12   C12  C11   125.68  3.000
 RRR  H12   C12  C5    127.58  3.000
 RRR  C11   C12  C5    106.74  3.000
 RRR  C13   C11  C12   129.32  3.000
 RRR  C13   C11  N10   121.37  3.000
 RRR  C12   C11  N10   109.28  3.000
 RRR  H132  C13  H131  106.98  3.000
 RRR  H132  C13  N14   107.58  3.000
 RRR  H131  C13  N14   109.41  3.000
 RRR  H132  C13  C11   110.67  3.000
 RRR  H131  C13  C11   109.33  3.000
 RRR  N14   C13  C11   112.71  3.000
 RRR  C21   N14  C17   123.33  3.000
 RRR  C21   N14  C13   117.51  3.000
 RRR  C17   N14  C13   118.59  3.000
 RRR  C18   C17  O44   118.03  3.000
 RRR  C18   C17  N14   118.82  3.000
 RRR  O44   C17  N14   123.11  3.000
 RRR  H182  C18  H181  107.70  3.000
 RRR  H182  C18  N19   112.40  3.000
 RRR  H181  C18  N19   110.02  3.000
 RRR  H182  C18  C17   106.09  3.000
 RRR  H181  C18  C17   106.71  3.000
 RRR  N19   C18  C17   113.58  3.000
 RRR  S28   N19  C20   117.48  3.000
 RRR  S28   N19  C18   116.88  3.000
 RRR  C20   N19  C18   112.48  3.000
 RRR  H202  C20  H201  108.50  3.000
 RRR  H202  C20  C21   108.72  3.000
 RRR  H201  C20  C21   110.56  3.000
 RRR  H202  C20  N19   110.46  3.000
 RRR  H201  C20  N19   111.38  3.000
 RRR  C21   C20  N19   107.19  3.000
 RRR  H212  C21  H211  107.90  3.000
 RRR  H212  C21  C20   108.98  3.000
 RRR  H211  C21  C20   109.67  3.000
 RRR  H212  C21  N14   108.35  3.000
 RRR  H211  C21  N14   110.83  3.000
 RRR  C20   C21  N14   111.03  3.000
 RRR  C29   S28  O45   109.08  3.000
 RRR  C29   S28  O37   107.91  3.000
 RRR  O45   S28  O37   119.92  3.000
 RRR  C29   S28  N19   106.32  3.000
 RRR  O45   S28  N19   106.60  3.000
 RRR  O37   S28  N19   106.22  3.000
 RRR  H29   C29  C30   124.23  3.000
 RRR  H29   C29  S28   114.71  3.000
 RRR  C30   C29  S28   121.06  3.000
 RRR  H30   C30  C31   116.47  3.000
 RRR  H30   C30  C29   118.89  3.000
 RRR  C31   C30  C29   124.64  3.000
 RRR  S32   C31  C35   110.81  3.000
 RRR  S32   C31  C30   119.20  3.000
 RRR  C35   C31  C30   129.99  3.000
 RRR  H35   C35  C34   122.97  3.000
 RRR  H35   C35  C31   123.58  3.000
 RRR  C34   C35  C31   113.45  3.000
 RRR  H34   C34  C33   123.83  3.000
 RRR  H34   C34  C35   124.52  3.000
 RRR  C33   C34  C35   111.65  3.000
 RRR  S32   C33  CL36  120.46  3.000
 RRR  S32   C33  C34   112.79  3.000
 RRR  CL36  C33  C34   126.75  3.000
 RRR  C33   S32  C31    91.30  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
 RRR  CONST_01  C6    C5   C4   N10  180.00   0.0  0
 RRR  CONST_02  C12   C5   C4   N10    0.00   0.0  0
 RRR  CONST_03  C2    C3   C4   N10  180.00   0.0  0
 RRR  CONST_04  C5    C12  C11  N10    0.00   0.0  0
 RRR  CONST_05  C12   C11  N10  C4     0.00   0.0  0
 RRR  CONST_06  N1    C6   C5   C4     0.00   0.0  0
 RRR  CONST_07  C11   C12  C5   C4     0.00   0.0  0
 RRR  CONST_08  N1    C2   C3   C4     0.00   0.0  0
 RRR  CONST_09  C11   N10  C4   C5     0.00   0.0  0
 RRR  CONST_10  C2    C3   C4   C5     0.00   0.0  0
 RRR  CONST_11  C2    N1   C6   C5     0.00   0.0  0
 RRR  CONST_12  C3    C4   C5   C6     0.00   0.0  0
 RRR  CONST_13  C11   C12  C5   C6   180.00   0.0  0
 RRR  CONST_14  C3    C2   N1   C6     0.00   0.0  0
 RRR  CONST_15  C12   C5   C6   N1   180.00   0.0  0
 RRR  CONST_16  C11   N10  C4   C3   180.00   0.0  0
 RRR  CONST_17  C12   C5   C4   C3   180.00   0.0  0
 RRR  CONST_18  C33   C34  C35  C31    0.00   0.0  0
 RRR  CONST_19  C34   C33  S32  C31    0.00   0.0  0
 RRR  CONST_20  C33   S32  C31  C35    0.00   0.0  0
 RRR  CONST_21  S32   C33  C34  C35    0.00   0.0  0
 RRR  CONST_22  S32   C31  C35  C34    0.00   0.0  0
 RRR  CONST_23  C21   N14  C17  C18    0.00   0.0  0
 RRR  CONST_24  C13   C11  N10  C4   180.00   0.0  0
 RRR  CONST_25  C13   C11  C12  C5   180.00   0.0  0
 RRR  CONST_26  C34   C35  C31  C30  180.00   0.0  0
 RRR  CONST_27  C33   S32  C31  C30  180.00   0.0  0
 RRR  CONST_28  CL36  C33  S32  C31  180.00   0.0  0
 RRR  CONST_29  CL36  C33  C34  C35  180.00   0.0  0
 RRR  CONST_30  C18   C17  N14  C13  180.00   0.0  0
 RRR  CONST_31  C21   N14  C17  O44  180.00   0.0  0
 RRR  CONST_32  H3    C3   C4   N10    0.00   0.0  0
 RRR  CONST_33  H12   C12  C11  N10  180.00   0.0  0
 RRR  CONST_34  H6    C6   C5   C4   180.00   0.0  0
 RRR  CONST_35  H2    C2   C3   C4   180.00   0.0  0
 RRR  CONST_36  H10   N10  C4   C5   180.00   0.0  0
 RRR  CONST_37  H34   C34  C35  C31  180.00   0.0  0
 RRR  CONST_38  H35   C35  C34  C33  180.00   0.0  0
 RRR  CONST_39  O44   C17  N14  C13    0.00   0.0  0
 RRR  CONST_40  C31   C30  C29  S28  180.00   0.0  0
 RRR  CONST_41  H29   C29  C30  C31    0.00   0.0  0
 RRR  CONST_42  H30   C30  C29  S28    0.00   0.0  0
 RRR  Var_01    N19   C18  C17  N14   13.40  30.0  1
 RRR  Var_02    N19   C20  C21  N14  -55.08  30.0  1
 RRR  Var_03    C20   C21  N14  C17   27.70  30.0  1
 RRR  Var_04    N14   C13  C11  N10   81.83  30.0  2
 RRR  Var_05    C17   N14  C13  C11   82.59  30.0  3
 RRR  Var_06    C35   C31  C30  C29    0.45  30.0  2
 RRR  Var_07    C30   C29  S28  N19  106.27  30.0  3

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
 RRR  chir_01  N19  S28  C20  C18  negativ

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
 RRR  plan-1  C30   0.020
 RRR  plan-1  C31   0.020
 RRR  plan-1  C35   0.020
 RRR  plan-1  C34   0.020
 RRR  plan-1  C33   0.020
 RRR  plan-1  CL36  0.020
 RRR  plan-1  S32   0.020
 RRR  plan-1  H35   0.020
 RRR  plan-1  H34   0.020
 RRR  plan-2  N10   0.020
 RRR  plan-2  C4    0.020
 RRR  plan-2  C5    0.020
 RRR  plan-2  C6    0.020
 RRR  plan-2  N1    0.020
 RRR  plan-2  C2    0.020
 RRR  plan-2  C3    0.020
 RRR  plan-2  C12   0.020
 RRR  plan-2  C11   0.020
 RRR  plan-2  C13   0.020
 RRR  plan-2  H10   0.020
 RRR  plan-2  H6    0.020
 RRR  plan-2  H2    0.020
 RRR  plan-2  H3    0.020
 RRR  plan-2  H12   0.020
 RRR  plan-3  C13   0.020
 RRR  plan-3  N14   0.020
 RRR  plan-3  C17   0.020
 RRR  plan-3  O44   0.020
 RRR  plan-3  C18   0.020
 RRR  plan-3  C21   0.020
 RRR  plan-4  S28   0.020
 RRR  plan-4  C29   0.020
 RRR  plan-4  C30   0.020
 RRR  plan-4  C31   0.020
 RRR  plan-4  H29   0.020
 RRR  plan-4  H30   0.020

