# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:41:23 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[(6-chloro-1-benzothiophen-2-yl)sulfonyl]-1-{[1-(2-hydroxyethyl)-1H-pyrrolo[3,2-c]pyridin-2-yl]methyl}piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCn1c(CN2CCN(CC2=O)[S](=O)(=O)c3sc4cc(Cl)ccc4c3)cc5cnccc15
#
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
 RDR  RDR  4-[(6-chloro-1-benzothiophen-2-yl)sulfonyl]-1-{[1-(2-hydroxyethyl)-1H-pyrrolo[3,2-c]pyridin-2-yl]methyl}piperazin-2-one  ligand  54  33  .  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_RDR
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
 RDR  O15   O   OH1    0  -0.665   4.2289   0.2431  -6.4539
 RDR  C10   C   CH2    0  -0.140   2.9737  -0.2578  -6.0688
 RDR  C6    C   CH2    0  -0.372   2.0837   0.9369  -5.7562
 RDR  N2    N   NR5    0  -0.580   0.7624   0.5164  -5.3469
 RDR  C5    C   CR56   0   0.447  -0.2624   0.2323  -6.1985
 RDR  C7    C   CR56   0  -0.015  -1.3508  -0.2267  -5.4310
 RDR  C11   C   CR16   0  -0.139  -2.5213  -0.5687  -6.1070
 RDR  N16   N   N      0  -0.423  -2.6317  -0.4755  -7.4202
 RDR  C14   C   CR16   0  -0.100  -1.5797  -0.0351  -8.1276
 RDR  C9    C   CR16   0  -0.380  -0.3658   0.3343  -7.5827
 RDR  C3    C   CR15   0  -0.457  -0.9303  -0.2166  -4.0672
 RDR  C1    C   CR5    0   0.369   0.3568   0.2336  -4.0585
 RDR  C4    C   CH2    0  -0.392   1.2778   0.4414  -2.8974
 RDR  N8    N   NT     0  -0.473   0.6307   0.1415  -1.6403
 RDR  C12   C   C      0   0.550  -0.1327   1.0911  -1.0671
 RDR  O18   O   O      0  -0.483  -0.2243   2.2255  -1.5059
 RDR  C17   C   CH2    0  -0.405  -0.8852   0.7479   0.2050
 RDR  N20   N   N     -1  -0.574  -0.9320  -0.6791   0.4797
 RDR  C19   C   CH2    0  -0.355   0.3686  -1.3151   0.3084
 RDR  C13   C   CH2    0  -0.258   0.7182  -1.2274  -1.1562
 RDR  S21   S   S      0   1.389  -1.8782  -1.1499   1.7503
 RDR  O23   O   OS     0  -0.631  -3.1496  -0.4718   1.5999
 RDR  O24   O   OS     0  -0.635  -1.7980  -2.5951   1.8274
 RDR  C22   C   CR5    0  -0.445  -1.1078  -0.5193   3.1907
 RDR  C25   C   CR15   0  -0.166  -1.3430   0.6873   3.7576
 RDR  C27   C   CR56   0   0.216  -0.4783   0.9208   4.8701
 RDR  C28   C   CR56   0  -0.222   0.3991  -0.1551   5.0918
 RDR  S26   S   S2     0   0.310   0.1505  -1.4359   3.9553
 RDR  C30   C   CR16   0  -0.226   1.3304  -0.1474   6.1263
 RDR  C32   C   CR6    0  -0.048   1.3631   0.9709   6.9316
 RDR  CL33  CL  CL     0  -0.107   2.5043   1.0366   8.2292
 RDR  C31   C   CR16   0  -0.207   0.5039   2.0609   6.7387
 RDR  C29   C   CR16   0  -0.308  -0.4138   2.0359   5.7142
 RDR  H15   H   HOH1   0   0.461   4.7964  -0.5001  -6.6767
 RDR  H101  H   HCH2   0   0.207   2.5070  -0.8558  -6.8616
 RDR  H102  H   HCH2   0   0.204   3.0408  -0.9010  -5.1817
 RDR  H61   H   HCH2   0   0.279   2.5269   1.5459  -4.9676
 RDR  H62   H   HCH2   0   0.278   1.9880   1.5794  -6.6327
 RDR  H11   H   HCR6   0   0.256  -3.3888  -0.9287  -5.5627
 RDR  H14   H   HCR6   0   0.256  -1.7200   0.0232  -9.2009
 RDR  H9    H   HCR6   0   0.275   0.4436   0.6792  -8.2128
 RDR  H3    H   HCR5   0   0.252  -1.5132  -0.5036  -3.2060
 RDR  H41   H   HCH2   0   0.286   2.1555  -0.2053  -2.9815
 RDR  H42   H   HCH2   0   0.295   1.6494   1.4677  -2.8807
 RDR  H171  H   HCH2   0   0.314  -1.8932   1.1403   0.0858
 RDR  H172  H   HCH2   0   0.285  -0.3998   1.3058   1.0184
 RDR  H191  H   HCH2   0   0.265   1.1333  -0.8244   0.9218
 RDR  H192  H   HCH2   0   0.300   0.3224  -2.3644   0.5884
 RDR  H131  H   HCH2   0   0.262   0.0619  -1.8822  -1.7352
 RDR  H132  H   HCH2   0   0.275   1.7419  -1.5764  -1.2945
 RDR  H25   H   HCR5   0   0.307  -2.0927   1.3870   3.4163
 RDR  H30   H   HCR6   0   0.300   2.0008  -0.9798   6.2914
 RDR  H31   H   HCR6   0   0.289   0.5649   2.9182   7.3943
 RDR  H29   H   HCR6   0   0.279  -1.0805   2.8737   5.5600

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
 RDR  O15  C10   single    1.405  0.020  1.405
 RDR  O15  H15   single    0.850  0.020  0.980
 RDR  C10  C6    single    1.522  0.020  1.522
 RDR  C10  H101  single    0.970  0.020  1.090
 RDR  C10  H102  single    0.970  0.020  1.090
 RDR  C6   N2    single    1.446  0.020  1.446
 RDR  C6   H61   single    0.970  0.020  1.090
 RDR  C6   H62   single    0.970  0.020  1.090
 RDR  N2   C5    aromatic  1.362  0.020  1.362
 RDR  N2   C1    aromatic  1.380  0.020  1.380
 RDR  C5   C7    aromatic  1.409  0.020  1.409
 RDR  C5   C9    aromatic  1.392  0.020  1.392
 RDR  C7   C11   aromatic  1.394  0.020  1.394
 RDR  C7   C3    aromatic  1.427  0.020  1.427
 RDR  C11  N16   aromatic  1.321  0.020  1.321
 RDR  C11  H11   single    0.930  0.020  1.080
 RDR  N16  C14   aromatic  1.342  0.020  1.342
 RDR  C14  C9    aromatic  1.381  0.020  1.381
 RDR  C14  H14   single    0.930  0.020  1.080
 RDR  C9   H9    single    0.930  0.020  1.080
 RDR  C3   C1    aromatic  1.364  0.020  1.364
 RDR  C3   H3    single    0.930  0.020  1.080
 RDR  C1   C4    single    1.496  0.020  1.496
 RDR  C4   N8    single    1.445  0.020  1.445
 RDR  C4   H41   single    0.970  0.020  1.090
 RDR  C4   H42   single    0.970  0.020  1.090
 RDR  N8   C12   single    1.346  0.020  1.346
 RDR  N8   C13   single    1.455  0.020  1.455
 RDR  C12  O18   double    1.220  0.020  1.220
 RDR  C12  C17   single    1.517  0.020  1.517
 RDR  C17  N20   single    1.454  0.020  1.454
 RDR  C17  H171  single    0.970  0.020  1.090
 RDR  C17  H172  single    0.970  0.020  1.090
 RDR  N20  C19   single    1.458  0.020  1.458
 RDR  N20  S21   single    1.653  0.020  1.653
 RDR  C19  C13   single    1.508  0.020  1.508
 RDR  C19  H191  single    0.970  0.020  1.090
 RDR  C19  H192  single    0.970  0.020  1.090
 RDR  C13  H131  single    0.970  0.020  1.090
 RDR  C13  H132  single    0.970  0.020  1.090
 RDR  S21  O23   double    1.449  0.020  1.449
 RDR  S21  O24   double    1.449  0.020  1.449
 RDR  S21  C22   single    1.751  0.020  1.751
 RDR  C22  C25   aromatic  1.354  0.020  1.354
 RDR  C22  S26   aromatic  1.734  0.020  1.734
 RDR  C25  C27   aromatic  1.428  0.020  1.428
 RDR  C25  H25   single    0.930  0.020  1.080
 RDR  C27  C28   aromatic  1.406  0.020  1.406
 RDR  C27  C29   aromatic  1.400  0.020  1.400
 RDR  C28  S26   aromatic  1.730  0.020  1.730
 RDR  C28  C30   aromatic  1.392  0.020  1.392
 RDR  C30  C32   aromatic  1.378  0.020  1.378
 RDR  C30  H30   single    0.930  0.020  1.080
 RDR  C32  CL33  single    1.729  0.020  1.729
 RDR  C32  C31   aromatic  1.401  0.020  1.401
 RDR  C31  C29   aromatic  1.376  0.020  1.376
 RDR  C31  H31   single    0.930  0.020  1.080
 RDR  C29  H29   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
 RDR  H15   O15  C10   108.38  3.000
 RDR  H102  C10  H101  106.89  3.000
 RDR  H102  C10  C6    109.24  3.000
 RDR  H101  C10  C6    109.11  3.000
 RDR  H102  C10  O15   112.07  3.000
 RDR  H101  C10  O15   112.10  3.000
 RDR  C6    C10  O15   107.38  3.000
 RDR  H62   C6   H61   106.72  3.000
 RDR  H62   C6   N2    108.58  3.000
 RDR  H61   C6   N2    109.22  3.000
 RDR  H62   C6   C10   110.39  3.000
 RDR  H61   C6   C10   110.44  3.000
 RDR  N2    C6   C10   111.36  3.000
 RDR  C1    N2   C5    108.65  3.000
 RDR  C1    N2   C6    126.34  3.000
 RDR  C5    N2   C6    124.83  3.000
 RDR  C9    C5   C7    120.56  3.000
 RDR  C9    C5   N2    131.47  3.000
 RDR  C7    C5   N2    107.97  3.000
 RDR  C3    C7   C11   135.43  3.000
 RDR  C3    C7   C5    106.90  3.000
 RDR  C11   C7   C5    117.67  3.000
 RDR  H11   C11  N16   117.06  3.000
 RDR  H11   C11  C7    120.61  3.000
 RDR  N16   C11  C7    122.33  3.000
 RDR  C14   N16  C11   118.79  3.000
 RDR  H14   C14  C9    119.34  3.000
 RDR  H14   C14  N16   115.98  3.000
 RDR  C9    C14  N16   124.67  3.000
 RDR  H9    C9   C14   120.86  3.000
 RDR  H9    C9   C5    123.16  3.000
 RDR  C14   C9   C5    115.98  3.000
 RDR  H3    C3   C1    126.35  3.000
 RDR  H3    C3   C7    127.00  3.000
 RDR  C1    C3   C7    106.65  3.000
 RDR  C4    C1   C3    129.17  3.000
 RDR  C4    C1   N2    121.00  3.000
 RDR  C3    C1   N2    109.83  3.000
 RDR  H42   C4   H41   106.50  3.000
 RDR  H42   C4   N8    109.52  3.000
 RDR  H41   C4   N8    107.67  3.000
 RDR  H42   C4   C1    110.61  3.000
 RDR  H41   C4   C1    110.62  3.000
 RDR  N8    C4   C1    111.75  3.000
 RDR  C13   N8   C12   123.79  3.000
 RDR  C13   N8   C4    117.25  3.000
 RDR  C12   N8   C4    118.53  3.000
 RDR  C17   C12  O18   118.34  3.000
 RDR  C17   C12  N8    118.59  3.000
 RDR  O18   C12  N8    123.05  3.000
 RDR  H172  C17  H171  107.88  3.000
 RDR  H172  C17  N20   111.87  3.000
 RDR  H171  C17  N20   110.17  3.000
 RDR  H172  C17  C12   106.65  3.000
 RDR  H171  C17  C12   106.62  3.000
 RDR  N20   C17  C12   113.35  3.000
 RDR  S21   N20  C19   118.48  3.000
 RDR  S21   N20  C17   116.31  3.000
 RDR  C19   N20  C17   112.16  3.000
 RDR  H192  C19  H191  108.52  3.000
 RDR  H192  C19  C13   108.43  3.000
 RDR  H191  C19  C13   110.83  3.000
 RDR  H192  C19  N20   110.67  3.000
 RDR  H191  C19  N20   111.18  3.000
 RDR  C13   C19  N20   107.18  3.000
 RDR  H132  C13  H131  107.74  3.000
 RDR  H132  C13  C19   108.79  3.000
 RDR  H131  C13  C19   109.90  3.000
 RDR  H132  C13  N8    108.39  3.000
 RDR  H131  C13  N8    110.57  3.000
 RDR  C19   C13  N8    111.34  3.000
 RDR  C22   S21  O24   106.92  3.000
 RDR  C22   S21  O23   107.63  3.000
 RDR  O24   S21  O23   121.38  3.000
 RDR  C22   S21  N20   106.14  3.000
 RDR  O24   S21  N20   107.05  3.000
 RDR  O23   S21  N20   106.82  3.000
 RDR  S26   C22  C25   114.36  3.000
 RDR  S26   C22  S21   119.44  3.000
 RDR  C25   C22  S21   126.09  3.000
 RDR  H25   C25  C27   124.06  3.000
 RDR  H25   C25  C22   124.42  3.000
 RDR  C27   C25  C22   111.52  3.000
 RDR  C29   C27  C28   119.06  3.000
 RDR  C29   C27  C25   128.88  3.000
 RDR  C28   C27  C25   112.06  3.000
 RDR  C30   C28  S26   126.04  3.000
 RDR  C30   C28  C27   122.04  3.000
 RDR  S26   C28  C27   111.92  3.000
 RDR  C28   S26  C22    90.15  3.000
 RDR  H30   C30  C32   121.37  3.000
 RDR  H30   C30  C28   121.60  3.000
 RDR  C32   C30  C28   117.03  3.000
 RDR  C31   C32  CL33  118.58  3.000
 RDR  C31   C32  C30   122.42  3.000
 RDR  CL33  C32  C30   119.00  3.000
 RDR  H31   C31  C29   120.26  3.000
 RDR  H31   C31  C32   119.92  3.000
 RDR  C29   C31  C32   119.83  3.000
 RDR  H29   C29  C31   120.21  3.000
 RDR  H29   C29  C27   120.17  3.000
 RDR  C31   C29  C27   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
 RDR  CONST_01  C11   C7   C5   N2     180.00   0.0  0
 RDR  CONST_02  C3    C7   C5   N2       0.00   0.0  0
 RDR  CONST_03  C14   C9   C5   N2     180.00   0.0  0
 RDR  CONST_04  C7    C3   C1   N2       0.00   0.0  0
 RDR  CONST_05  C3    C1   N2   C5       0.00   0.0  0
 RDR  CONST_06  N16   C11  C7   C5       0.00   0.0  0
 RDR  CONST_07  C1    C3   C7   C5       0.00   0.0  0
 RDR  CONST_08  N16   C14  C9   C5       0.00   0.0  0
 RDR  CONST_09  C1    N2   C5   C7       0.00   0.0  0
 RDR  CONST_10  C14   C9   C5   C7       0.00   0.0  0
 RDR  CONST_11  C14   N16  C11  C7       0.00   0.0  0
 RDR  CONST_12  C9    C5   C7   C11      0.00   0.0  0
 RDR  CONST_13  C1    C3   C7   C11    180.00   0.0  0
 RDR  CONST_14  C9    C14  N16  C11      0.00   0.0  0
 RDR  CONST_15  C3    C7   C11  N16    180.00   0.0  0
 RDR  CONST_16  C1    N2   C5   C9     180.00   0.0  0
 RDR  CONST_17  C3    C7   C5   C9     180.00   0.0  0
 RDR  CONST_18  C28   C27  C25  C22      0.00   0.0  0
 RDR  CONST_19  C29   C27  C25  C22    180.00   0.0  0
 RDR  CONST_20  C27   C28  S26  C22      0.00   0.0  0
 RDR  CONST_21  C30   C28  S26  C22    180.00   0.0  0
 RDR  CONST_22  C28   S26  C22  C25      0.00   0.0  0
 RDR  CONST_23  S26   C28  C27  C25      0.00   0.0  0
 RDR  CONST_24  C30   C28  C27  C25    180.00   0.0  0
 RDR  CONST_25  C31   C29  C27  C25    180.00   0.0  0
 RDR  CONST_26  S26   C22  C25  C27      0.00   0.0  0
 RDR  CONST_27  C32   C30  C28  C27      0.00   0.0  0
 RDR  CONST_28  C32   C31  C29  C27      0.00   0.0  0
 RDR  CONST_29  C31   C29  C27  C28      0.00   0.0  0
 RDR  CONST_30  C31   C32  C30  C28      0.00   0.0  0
 RDR  CONST_31  C29   C27  C28  S26    180.00   0.0  0
 RDR  CONST_32  C32   C30  C28  S26    180.00   0.0  0
 RDR  CONST_33  C29   C27  C28  C30      0.00   0.0  0
 RDR  CONST_34  C29   C31  C32  C30      0.00   0.0  0
 RDR  CONST_35  C13   N8   C12  C17      0.00   0.0  0
 RDR  CONST_36  C7    C5   N2   C6     180.00   0.0  0
 RDR  CONST_37  C9    C5   N2   C6       0.00   0.0  0
 RDR  CONST_38  C3    C1   N2   C6     180.00   0.0  0
 RDR  CONST_39  C4    C1   N2   C5     180.00   0.0  0
 RDR  CONST_40  C4    C1   C3   C7     180.00   0.0  0
 RDR  CONST_41  C27   C25  C22  S21    180.00   0.0  0
 RDR  CONST_42  C28   S26  C22  S21    180.00   0.0  0
 RDR  CONST_43  CL33  C32  C30  C28    180.00   0.0  0
 RDR  CONST_44  C29   C31  C32  CL33   180.00   0.0  0
 RDR  CONST_45  C17   C12  N8   C4     180.00   0.0  0
 RDR  CONST_46  C13   N8   C12  O18    180.00   0.0  0
 RDR  CONST_47  H9    C9   C5   N2       0.00   0.0  0
 RDR  CONST_48  H3    C3   C1   N2     180.00   0.0  0
 RDR  CONST_49  H11   C11  C7   C5     180.00   0.0  0
 RDR  CONST_50  H14   C14  C9   C5     180.00   0.0  0
 RDR  CONST_51  H29   C29  C27  C25      0.00   0.0  0
 RDR  CONST_52  H30   C30  C28  C27    180.00   0.0  0
 RDR  CONST_53  H31   C31  C29  C27    180.00   0.0  0
 RDR  CONST_54  H25   C25  C27  C28    180.00   0.0  0
 RDR  CONST_55  O18   C12  N8   C4       0.00   0.0  0
 RDR  Var_01    N20   C17  C12  N8     -13.71  30.0  1
 RDR  Var_02    N20   C19  C13  N8      53.23  30.0  1
 RDR  Var_03    C19   C13  N8   C12    -24.19  30.0  1
 RDR  Var_04    N8    C4   C1   N2     177.35  30.0  2
 RDR  Var_05    C12   N8   C4   C1     -83.13  30.0  3
 RDR  Var_06    C25   C22  S21  N20     90.28  30.0  2
 RDR  Var_07    C5    N2   C6   C10    -85.48  30.0  2
 RDR  Var_08    N2    C6   C10  O15   -179.95  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
 RDR  chir_01  N20  S21  C19  C17  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
 RDR  plan-1  C6    0.020
 RDR  plan-1  N2    0.020
 RDR  plan-1  C5    0.020
 RDR  plan-1  C7    0.020
 RDR  plan-1  C11   0.020
 RDR  plan-1  N16   0.020
 RDR  plan-1  C14   0.020
 RDR  plan-1  C9    0.020
 RDR  plan-1  C3    0.020
 RDR  plan-1  C1    0.020
 RDR  plan-1  C4    0.020
 RDR  plan-1  H11   0.020
 RDR  plan-1  H14   0.020
 RDR  plan-1  H9    0.020
 RDR  plan-1  H3    0.020
 RDR  plan-2  S21   0.020
 RDR  plan-2  C22   0.020
 RDR  plan-2  C25   0.020
 RDR  plan-2  C27   0.020
 RDR  plan-2  C28   0.020
 RDR  plan-2  S26   0.020
 RDR  plan-2  C30   0.020
 RDR  plan-2  C32   0.020
 RDR  plan-2  CL33  0.020
 RDR  plan-2  C31   0.020
 RDR  plan-2  C29   0.020
 RDR  plan-2  H25   0.020
 RDR  plan-2  H30   0.020
 RDR  plan-2  H31   0.020
 RDR  plan-2  H29   0.020
 RDR  plan-3  C4    0.020
 RDR  plan-3  N8    0.020
 RDR  plan-3  C12   0.020
 RDR  plan-3  O18   0.020
 RDR  plan-3  C17   0.020
 RDR  plan-3  C13   0.020

