# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:44:06 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: [1-[2-(phenylsulfonylamino)ethyl]piperidin-4-yl]methyl 1~{H}-indole-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(OCC1CCN(CCN[S](=O)(=O)c2ccccc2)CC1)c3c[nH]c4ccccc34
#
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
 E8K  E8K  '[1-[2-(phenylsulfonylamino)ethyl]piperidin-4-yl]methyl 1~{H}-indole-3-carboxylate'  ligand  58  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E8K
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
 E8K  O3   O  OS    0  -0.656  -6.2547   1.5320  -1.9106
 E8K  S    S  S     0   1.376  -6.4430   1.3697  -0.4785
 E8K  O2   O  OS    0  -0.657  -7.4374   2.1679   0.2192
 E8K  C7   C  CR6   0  -0.199  -6.7797  -0.3425  -0.1631
 E8K  C12  C  CR16  0  -0.231  -6.4219  -1.2976  -1.1053
 E8K  C11  C  CR16  0  -0.243  -6.6513  -2.6373  -0.8250
 E8K  C10  C  CR16  0  -0.236  -7.2303  -3.0080   0.3808
 E8K  C9   C  CR16  0  -0.243  -7.5847  -2.0417   1.3146
 E8K  C8   C  CR16  0  -0.236  -7.3605  -0.7004   1.0481
 E8K  N1   N  NC1   0  -0.729  -5.0012   1.7051   0.2421
 E8K  C6   C  CH2   0  -0.293  -3.8126   0.9680  -0.1811
 E8K  C5   C  CH2   0  -0.280  -2.5850   1.6200   0.4429
 E8K  N    N  NT    0  -0.424  -1.3852   0.8592   0.1621
 E8K  C4   C  CH2   0  -0.289  -1.2328  -0.2683   1.0674
 E8K  C3   C  CH2   0  -0.429  -0.0381  -1.1273   0.6894
 E8K  C13  C  CH2   0  -0.284  -0.1968   1.6968   0.1684
 E8K  C14  C  CH2   0  -0.422   1.0394   0.9108  -0.2404
 E8K  C2   C  CH1   0  -0.297   1.2438  -0.2992   0.6660
 E8K  C1   C  CH2   0  -0.146   2.4072  -1.1715   0.2402
 E8K  O1   O  O2    0  -0.473   3.6058  -0.3980   0.3309
 E8K  C    C  C     0   0.536   4.7488  -0.9581  -0.0566
 E8K  O    O  O     0  -0.469   4.8250  -2.0921  -0.4783
 E8K  C15  C  CR5   0  -0.204   5.8794  -0.0598   0.0890
 E8K  C22  C  CR56  0   0.087   7.2549  -0.3532  -0.2059
 E8K  C17  C  CR56  0   0.350   7.9816   0.8153   0.0976
 E8K  N2   N  NR15  0  -0.674   7.0862   1.7536   0.5456
 E8K  C16  C  CR15  0   0.003   5.8414   1.2397   0.5435
 E8K  C21  C  CR16  0  -0.370   7.9462  -1.4708  -0.6865
 E8K  C20  C  CR16  0  -0.259   9.3166  -1.3876  -0.8432
 E8K  C19  C  CR16  0  -0.281  10.0187  -0.2132  -0.5317
 E8K  C18  C  CR16  0  -0.296   9.3616   0.9056  -0.0577
 E8K  H1   H  HCR6  0   0.286  -5.9773  -1.0088  -2.0476
 E8K  H2   H  HCR6  0   0.273  -6.3800  -3.3899  -1.5530
 E8K  H3   H  HCR6  0   0.273  -7.4086  -4.0533   0.5949
 E8K  H4   H  HCR6  0   0.274  -8.0402  -2.3324   2.2514
 E8K  H5   H  HCR6  0   0.284  -7.6416   0.0500   1.7750
 E8K  H6   H  HNC1  0   0.409  -5.1010   1.7598   1.2512
 E8K  H7   H  HCH2  0   0.241  -3.8811  -0.0896   0.0949
 E8K  H8   H  HCH2  0   0.262  -3.7305   1.0214  -1.2658
 E8K  H9   H  HCH2  0   0.249  -2.4791   2.6208   0.0197
 E8K  H10  H  HCH2  0   0.206  -2.7409   1.7549   1.5267
 E8K  H12  H  HCH2  0   0.193  -1.1197   0.0764   2.1111
 E8K  H13  H  HCH2  0   0.240  -2.1358  -0.8804   1.0392
 E8K  H14  H  HCH2  0   0.238   0.0486  -1.9496   1.4040
 E8K  H15  H  HCH2  0   0.221  -0.2117  -1.5732  -0.2955
 E8K  H16  H  HCH2  0   0.239  -0.3494   2.5214  -0.5313
 E8K  H17  H  HCH2  0   0.189  -0.0246   2.1492   1.1613
 E8K  H18  H  HCH2  0   0.216   0.9282   0.5735  -1.2766
 E8K  H19  H  HCH2  0   0.239   1.9050   1.5751  -0.2084
 E8K  H20  H  HCH1  0   0.230   1.4333   0.0561   1.6872
 E8K  H21  H  HCH2  0   0.238   2.4817  -2.0468   0.8920
 E8K  H22  H  HCH2  0   0.225   2.2630  -1.5252  -0.7852
 E8K  H23  H  HNR5  0   0.422   7.3189   2.6897   0.8366
 E8K  H24  H  HCR5  0   0.300   5.0011   1.8336   0.8656
 E8K  H25  H  HCR6  0   0.248   7.4215  -2.3826  -0.9341
 E8K  H26  H  HCR6  0   0.252   9.8618  -2.2462  -1.2132
 E8K  H27  H  HCR6  0   0.255  11.0921  -0.1831  -0.6652
 E8K  H28  H  HCR6  0   0.266   9.8976   1.8140   0.1857

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
 E8K  O2   S    double    1.454  0.020  1.454
 E8K  C12  C11  aromatic  1.388  0.020  1.388
 E8K  C12  C7   aromatic  1.389  0.020  1.389
 E8K  C11  C10  aromatic  1.388  0.020  1.388
 E8K  S    C7   single    1.773  0.020  1.773
 E8K  S    N1   single    1.646  0.020  1.646
 E8K  S    O3   double    1.453  0.020  1.453
 E8K  C7   C8   aromatic  1.390  0.020  1.390
 E8K  N1   C6   single    1.461  0.020  1.461
 E8K  C10  C9   aromatic  1.390  0.020  1.390
 E8K  C8   C9   aromatic  1.386  0.020  1.386
 E8K  C5   C6   single    1.524  0.020  1.524
 E8K  C5   N    single    1.448  0.020  1.448
 E8K  C4   N    single    1.454  0.020  1.454
 E8K  C4   C3   single    1.519  0.020  1.519
 E8K  N    C13  single    1.454  0.020  1.454
 E8K  C13  C14  single    1.521  0.020  1.521
 E8K  C3   C2   single    1.526  0.020  1.526
 E8K  C2   C14  single    1.526  0.020  1.526
 E8K  C2   C1   single    1.515  0.020  1.515
 E8K  C1   O1   single    1.429  0.020  1.429
 E8K  O1   C    single    1.331  0.020  1.331
 E8K  C    O    double    1.212  0.020  1.212
 E8K  C    C15  single    1.451  0.020  1.451
 E8K  C21  C20  aromatic  1.382  0.020  1.382
 E8K  C21  C22  aromatic  1.399  0.020  1.399
 E8K  C20  C19  aromatic  1.403  0.020  1.403
 E8K  C15  C22  aromatic  1.437  0.020  1.437
 E8K  C15  C16  aromatic  1.377  0.020  1.377
 E8K  C22  C17  aromatic  1.409  0.020  1.409
 E8K  C19  C18  aromatic  1.381  0.020  1.381
 E8K  C16  N2   aromatic  1.347  0.020  1.347
 E8K  C17  C18  aromatic  1.392  0.020  1.392
 E8K  C17  N2   aromatic  1.372  0.020  1.372
 E8K  C12  H1   single    0.930  0.020  1.080
 E8K  C11  H2   single    0.930  0.020  1.080
 E8K  C10  H3   single    0.930  0.020  1.080
 E8K  C9   H4   single    0.930  0.020  1.080
 E8K  C8   H5   single    0.930  0.020  1.080
 E8K  N1   H6   single    0.890  0.020  1.040
 E8K  C6   H7   single    0.970  0.020  1.090
 E8K  C6   H8   single    0.970  0.020  1.090
 E8K  C5   H9   single    0.970  0.020  1.090
 E8K  C5   H10  single    0.970  0.020  1.090
 E8K  C4   H12  single    0.970  0.020  1.090
 E8K  C4   H13  single    0.970  0.020  1.090
 E8K  C3   H14  single    0.970  0.020  1.090
 E8K  C3   H15  single    0.970  0.020  1.090
 E8K  C13  H16  single    0.970  0.020  1.090
 E8K  C13  H17  single    0.970  0.020  1.090
 E8K  C14  H18  single    0.970  0.020  1.090
 E8K  C14  H19  single    0.970  0.020  1.090
 E8K  C2   H20  single    0.970  0.020  1.090
 E8K  C1   H21  single    0.970  0.020  1.090
 E8K  C1   H22  single    0.970  0.020  1.090
 E8K  N2   H23  single    0.860  0.020  1.020
 E8K  C16  H24  single    0.930  0.020  1.080
 E8K  C21  H25  single    0.930  0.020  1.080
 E8K  C20  H26  single    0.930  0.020  1.080
 E8K  C19  H27  single    0.930  0.020  1.080
 E8K  C18  H28  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
 E8K  N1   S    C7   106.56  3.000
 E8K  N1   S    O2   106.09  3.000
 E8K  C7   S    O2   108.36  3.000
 E8K  N1   S    O3   107.16  3.000
 E8K  C7   S    O3   107.92  3.000
 E8K  O2   S    O3   120.02  3.000
 E8K  C8   C7   C12  121.45  3.000
 E8K  C8   C7   S    118.88  3.000
 E8K  C12  C7   S    119.64  3.000
 E8K  H1   C12  C11  120.12  3.000
 E8K  H1   C12  C7   120.90  3.000
 E8K  C11  C12  C7   118.97  3.000
 E8K  H2   C11  C10  120.24  3.000
 E8K  H2   C11  C12  119.62  3.000
 E8K  C10  C11  C12  120.14  3.000
 E8K  H3   C10  C9   119.79  3.000
 E8K  H3   C10  C11  119.92  3.000
 E8K  C9   C10  C11  120.29  3.000
 E8K  H4   C9   C8   119.66  3.000
 E8K  H4   C9   C10  120.17  3.000
 E8K  C8   C9   C10  120.17  3.000
 E8K  H5   C8   C9   120.01  3.000
 E8K  H5   C8   C7   121.02  3.000
 E8K  C9   C8   C7   118.97  3.000
 E8K  H6   N1   C6   113.27  3.000
 E8K  H6   N1   S    111.09  3.000
 E8K  C6   N1   S    118.87  3.000
 E8K  H8   C6   H7   107.64  3.000
 E8K  H8   C6   C5   109.04  3.000
 E8K  H7   C6   C5   111.12  3.000
 E8K  H8   C6   N1   108.97  3.000
 E8K  H7   C6   N1   111.30  3.000
 E8K  C5   C6   N1   108.72  3.000
 E8K  H10  C5   H9   106.40  3.000
 E8K  H10  C5   N    111.83  3.000
 E8K  H9   C5   N    109.03  3.000
 E8K  H10  C5   C6   109.93  3.000
 E8K  H9   C5   C6   108.16  3.000
 E8K  N    C5   C6   111.30  3.000
 E8K  C13  N    C4   111.00  3.000
 E8K  C13  N    C5   111.94  3.000
 E8K  C4   N    C5   111.93  3.000
 E8K  H13  C4   H12  106.50  3.000
 E8K  H13  C4   C3   109.09  3.000
 E8K  H12  C4   C3   109.32  3.000
 E8K  H13  C4   N    109.40  3.000
 E8K  H12  C4   N    110.91  3.000
 E8K  C3   C4   N    111.47  3.000
 E8K  H15  C3   H14  107.12  3.000
 E8K  H15  C3   C2   109.90  3.000
 E8K  H14  C3   C2   110.59  3.000
 E8K  H15  C3   C4   109.22  3.000
 E8K  H14  C3   C4   108.97  3.000
 E8K  C2   C3   C4   110.95  3.000
 E8K  H17  C13  H16  106.77  3.000
 E8K  H17  C13  C14  109.06  3.000
 E8K  H16  C13  C14  109.36  3.000
 E8K  H17  C13  N    111.55  3.000
 E8K  H16  C13  N    108.54  3.000
 E8K  C14  C13  N    111.43  3.000
 E8K  H19  C14  H18  107.19  3.000
 E8K  H19  C14  C2   111.04  3.000
 E8K  H18  C14  C2   109.35  3.000
 E8K  H19  C14  C13  108.79  3.000
 E8K  H18  C14  C13  109.32  3.000
 E8K  C2   C14  C13  111.05  3.000
 E8K  H20  C2   C1   108.37  3.000
 E8K  H20  C2   C14  108.61  3.000
 E8K  C1   C2   C14  113.11  3.000
 E8K  H20  C2   C3   107.84  3.000
 E8K  C1   C2   C3   109.69  3.000
 E8K  C14  C2   C3   109.09  3.000
 E8K  H22  C1   H21  107.98  3.000
 E8K  H22  C1   O1   110.18  3.000
 E8K  H21  C1   O1   109.76  3.000
 E8K  H22  C1   C2   110.38  3.000
 E8K  H21  C1   C2   110.21  3.000
 E8K  O1   C1   C2   108.33  3.000
 E8K  C    O1   C1   118.30  3.000
 E8K  C15  C    O    124.40  3.000
 E8K  C15  C    O1   112.30  3.000
 E8K  O    C    O1   123.30  3.000
 E8K  C16  C15  C22  106.67  3.000
 E8K  C16  C15  C    126.56  3.000
 E8K  C22  C15  C    126.77  3.000
 E8K  C21  C22  C17  118.78  3.000
 E8K  C17  C22  C15  106.26  3.000
 E8K  C21  C22  C15  134.95  3.000
 E8K  C18  C17  N2   129.73  3.000
 E8K  N2   C17  C22  107.51  3.000
 E8K  C18  C17  C22  122.76  3.000
 E8K  H23  N2   C16  124.64  3.000
 E8K  H23  N2   C17  125.38  3.000
 E8K  C16  N2   C17  109.98  3.000
 E8K  H24  C16  N2   120.64  3.000
 E8K  H24  C16  C15  129.78  3.000
 E8K  N2   C16  C15  109.58  3.000
 E8K  H25  C21  C20  120.41  3.000
 E8K  H25  C21  C22  120.84  3.000
 E8K  C20  C21  C22  118.74  3.000
 E8K  H26  C20  C19  119.19  3.000
 E8K  H26  C20  C21  119.38  3.000
 E8K  C19  C20  C21  121.43  3.000
 E8K  H27  C19  C18  119.45  3.000
 E8K  H27  C19  C20  119.49  3.000
 E8K  C18  C19  C20  121.06  3.000
 E8K  H28  C18  C19  121.42  3.000
 E8K  H28  C18  C17  121.36  3.000
 E8K  C19  C18  C17  117.22  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
 E8K  CONST_01  C10  C11  C12  C7     0.00   0.0  0
 E8K  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 E8K  CONST_03  C9   C10  C11  C12    0.00   0.0  0
 E8K  CONST_04  C9   C8   C7   C12    0.00   0.0  0
 E8K  CONST_05  C8   C7   C12  C11    0.00   0.0  0
 E8K  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 E8K  CONST_07  C20  C21  C22  C15  180.00   0.0  0
 E8K  CONST_08  C18  C17  C22  C15  180.00   0.0  0
 E8K  CONST_09  N2   C17  C22  C15    0.00   0.0  0
 E8K  CONST_10  C17  N2   C16  C15    0.00   0.0  0
 E8K  CONST_11  C19  C20  C21  C22    0.00   0.0  0
 E8K  CONST_12  N2   C16  C15  C22    0.00   0.0  0
 E8K  CONST_13  C19  C18  C17  C22    0.00   0.0  0
 E8K  CONST_14  C16  N2   C17  C22    0.00   0.0  0
 E8K  CONST_15  C20  C21  C22  C17    0.00   0.0  0
 E8K  CONST_16  C16  C15  C22  C17    0.00   0.0  0
 E8K  CONST_17  C20  C19  C18  C17    0.00   0.0  0
 E8K  CONST_18  C21  C22  C17  N2   180.00   0.0  0
 E8K  CONST_19  C19  C18  C17  N2   180.00   0.0  0
 E8K  CONST_20  C21  C22  C15  C16  180.00   0.0  0
 E8K  CONST_21  C18  C17  N2   C16  180.00   0.0  0
 E8K  CONST_22  C18  C19  C20  C21    0.00   0.0  0
 E8K  CONST_23  C18  C17  C22  C21    0.00   0.0  0
 E8K  CONST_24  C11  C12  C7   S    180.00   0.0  0
 E8K  CONST_25  C9   C8   C7   S    180.00   0.0  0
 E8K  CONST_26  C21  C22  C15  C      0.00   0.0  0
 E8K  CONST_27  C17  C22  C15  C    180.00   0.0  0
 E8K  CONST_28  N2   C16  C15  C    180.00   0.0  0
 E8K  CONST_29  H2   C11  C12  C7   180.00   0.0  0
 E8K  CONST_30  H4   C9   C8   C7   180.00   0.0  0
 E8K  CONST_31  H3   C10  C11  C12  180.00   0.0  0
 E8K  CONST_32  H5   C8   C7   C12  180.00   0.0  0
 E8K  CONST_33  H1   C12  C11  C10  180.00   0.0  0
 E8K  CONST_34  H25  C21  C22  C15    0.00   0.0  0
 E8K  CONST_35  H23  N2   C16  C15  180.00   0.0  0
 E8K  CONST_36  H26  C20  C21  C22  180.00   0.0  0
 E8K  CONST_37  H24  C16  C15  C22  180.00   0.0  0
 E8K  CONST_38  H28  C18  C17  C22  180.00   0.0  0
 E8K  CONST_39  H27  C19  C18  C17  180.00   0.0  0
 E8K  Var_01    C2   C3   C4   N     57.02  30.0  1
 E8K  Var_02    C2   C14  C13  N    -56.77  30.0  1
 E8K  Var_03    C14  C13  N    C4    58.85  30.0  1
 E8K  Var_04    C13  N    C4   C3   -59.03  30.0  1
 E8K  Var_05    C12  C7   S    O3    19.97  30.0  2
 E8K  Var_06    C4   N    C5   C6   -81.48  30.0  3
 E8K  Var_07    C22  C15  C    O1   178.48  30.0  2
 E8K  Var_08    C6   N1   S    C7    60.08  30.0  3
 E8K  Var_09    N    C5   C6   N1   174.61  30.0  1
 E8K  Var_10    C15  C    O1   C1   179.94  30.0  3
 E8K  Var_11    C5   C6   N1   S    170.11  30.0  3
 E8K  Var_12    H21  C1   O1   C     62.54  30.0  1

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
 E8K  chir_01  C2  C3  C14  C1  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
 E8K  plan-1  S    0.020
 E8K  plan-1  C7   0.020
 E8K  plan-1  C12  0.020
 E8K  plan-1  C11  0.020
 E8K  plan-1  C10  0.020
 E8K  plan-1  C9   0.020
 E8K  plan-1  C8   0.020
 E8K  plan-1  H1   0.020
 E8K  plan-1  H2   0.020
 E8K  plan-1  H3   0.020
 E8K  plan-1  H4   0.020
 E8K  plan-1  H5   0.020
 E8K  plan-2  O1   0.020
 E8K  plan-2  C    0.020
 E8K  plan-2  O    0.020
 E8K  plan-2  C15  0.020
 E8K  plan-3  C    0.020
 E8K  plan-3  C15  0.020
 E8K  plan-3  C22  0.020
 E8K  plan-3  C17  0.020
 E8K  plan-3  N2   0.020
 E8K  plan-3  C16  0.020
 E8K  plan-3  C21  0.020
 E8K  plan-3  C20  0.020
 E8K  plan-3  C19  0.020
 E8K  plan-3  C18  0.020
 E8K  plan-3  H23  0.020
 E8K  plan-3  H24  0.020
 E8K  plan-3  H25  0.020
 E8K  plan-3  H26  0.020
 E8K  plan-3  H27  0.020
 E8K  plan-3  H28  0.020

