# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:47:07 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-[5-(5-amino-1,3,4-thiadiazol-2-yl)-1H-indol-3-yl]-N-cyclopentylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1sc(nn1)c2ccc3[nH]cc(c4cccc(NC5CCCC5)n4)c3c2
#
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
 3U6  3U6  6-[5-(5-amino-1,3,4-thiadiazol-2-yl)-1H-indol-3-yl]-N-cyclopentylpyridin-2-amine  ligand  47  27  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3U6
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
 3U6  C17  C  CH2   0  -0.449  -4.8987  -1.5695   1.0661
 3U6  C18  C  CH2   0  -0.446  -5.6384  -2.9229   1.1344
 3U6  C19  C  CH2   0  -0.453  -5.2893  -3.6590  -0.1725
 3U6  C20  C  CH2   0  -0.448  -3.9845  -3.0205  -0.6308
 3U6  C16  C  CH1   0  -0.079  -4.2033  -1.5449  -0.3108
 3U6  N6   N  NH1   0  -0.670  -2.9804  -0.7856  -0.3821
 3U6  C15  C  CR6   0   0.486  -2.9244   0.5735  -0.3464
 3U6  N5   N  N     0  -0.507  -1.7094   1.0950  -0.1636
 3U6  C14  C  CR16  0  -0.415  -4.0588   1.3842  -0.5189
 3U6  C13  C  CR16  0  -0.154  -3.8757   2.7533  -0.5128
 3U6  C12  C  CR16  0  -0.390  -2.6133   3.2962  -0.3343
 3U6  C9   C  CR6   0   0.194  -1.5444   2.4163  -0.1545
 3U6  C8   C  CR5   0  -0.035  -0.1839   2.9036   0.0503
 3U6  C2   C  CR56  0   0.090   1.0369   2.1404   0.0963
 3U6  C3   C  CR16  0  -0.426   1.3516   0.7874  -0.0287
 3U6  C7   C  CR15  0  -0.065   0.1851   4.2139   0.2367
 3U6  N1   N  NR15  0  -0.685   1.5297   4.3065   0.3882
 3U6  C1   C  CR56  0   0.355   2.0852   3.0648   0.3067
 3U6  C6   C  CR16  0  -0.282   3.4177   2.6745   0.3966
 3U6  C5   C  CR16  0  -0.344   3.7001   1.3322   0.2687
 3U6  C4   C  CR6   0   0.110   2.6789   0.3842   0.0558
 3U6  C10  C  CR5   0   0.019   2.9973  -1.0352  -0.0784
 3U6  S1   S  S2    0   0.145   4.6312  -1.6517   0.0067
 3U6  N3   N  N     0  -0.272   2.1314  -1.9701  -0.2718
 3U6  N2   N  N     0  -0.300   2.6503  -3.2098  -0.3753
 3U6  C11  C  CR5   0   0.295   3.9443  -3.2256  -0.2498
 3U6  N4   N  NH2   0  -0.823   4.6987  -4.3427  -0.2517
 3U6  H1   H  HCH2  0   0.236  -5.5676  -0.7184   1.2012
 3U6  H2   H  HCH2  0   0.229  -4.1375  -1.5042   1.8467
 3U6  H3   H  HCH2  0   0.229  -5.2931  -3.4966   1.9954
 3U6  H4   H  HCH2  0   0.231  -6.7154  -2.8010   1.2517
 3U6  H5   H  HCH2  0   0.235  -5.2110  -4.7382  -0.0388
 3U6  H6   H  HCH2  0   0.225  -6.0626  -3.4854  -0.9248
 3U6  H7   H  HCH2  0   0.224  -3.1447  -3.4030  -0.0402
 3U6  H8   H  HCH2  0   0.243  -3.7583  -3.1942  -1.6837
 3U6  H9   H  HCH1  0   0.240  -4.8967  -1.1424  -1.0562
 3U6  H10  H  HNH1  0   0.370  -2.1486  -1.2440  -0.0405
 3U6  H11  H  HCR6  0   0.266  -5.0449   0.9629  -0.6537
 3U6  H12  H  HCR6  0   0.261  -4.7285   3.4064  -0.6494
 3U6  H13  H  HCR6  0   0.250  -2.4694   4.3673  -0.3396
 3U6  H14  H  HCR6  0   0.257   0.5684   0.0608  -0.1824
 3U6  H15  H  HCR5  0   0.295  -0.4248   5.1026   0.2771
 3U6  H16  H  HNR5  0   0.418   2.0302   5.1644   0.5534
 3U6  H17  H  HCR6  0   0.271   4.2079   3.3957   0.5589
 3U6  H18  H  HCR6  0   0.251   4.7346   1.0175   0.3366
 3U6  H19  H  HNH2  0   0.405   4.2535  -5.1761  -0.6027
 3U6  H20  H  HNH2  0   0.411   5.6776  -4.2695  -0.4713

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
 3U6  C6   C5   aromatic  1.378  0.020  1.378
 3U6  C6   C1   aromatic  1.391  0.020  1.391
 3U6  C5   C4   aromatic  1.410  0.020  1.410
 3U6  N1   C1   aromatic  1.363  0.020  1.363
 3U6  N1   C7   aromatic  1.356  0.020  1.356
 3U6  C1   C2   aromatic  1.413  0.020  1.413
 3U6  N3   N2   aromatic  1.348  0.020  1.348
 3U6  N3   C10  aromatic  1.289  0.020  1.289
 3U6  C4   C10  single    1.461  0.020  1.461
 3U6  C4   C3   aromatic  1.390  0.020  1.390
 3U6  N2   C11  aromatic  1.300  0.020  1.300
 3U6  C7   C8   aromatic  1.374  0.020  1.374
 3U6  C10  S1   aromatic  1.748  0.020  1.748
 3U6  C2   C3   aromatic  1.395  0.020  1.395
 3U6  C2   C8   aromatic  1.441  0.020  1.441
 3U6  C8   C9   single    1.459  0.020  1.459
 3U6  C11  S1   aromatic  1.736  0.020  1.736
 3U6  C11  N4   single    1.348  0.020  1.348
 3U6  C9   C12  aromatic  1.396  0.020  1.396
 3U6  C9   N5   aromatic  1.332  0.020  1.332
 3U6  C12  C13  aromatic  1.386  0.020  1.386
 3U6  N5   C15  aromatic  1.335  0.020  1.335
 3U6  C20  C16  single    1.526  0.020  1.526
 3U6  C20  C19  single    1.523  0.020  1.523
 3U6  C13  C14  aromatic  1.381  0.020  1.381
 3U6  C15  C14  aromatic  1.405  0.020  1.405
 3U6  C15  N6   single    1.361  0.020  1.361
 3U6  C16  N6   single    1.441  0.020  1.441
 3U6  C16  C17  single    1.543  0.020  1.543
 3U6  C19  C18  single    1.540  0.020  1.540
 3U6  C18  C17  single    1.544  0.020  1.544
 3U6  C17  H1   single    0.970  0.020  1.090
 3U6  C17  H2   single    0.970  0.020  1.090
 3U6  C18  H3   single    0.970  0.020  1.090
 3U6  C18  H4   single    0.970  0.020  1.090
 3U6  C19  H5   single    0.970  0.020  1.090
 3U6  C19  H6   single    0.970  0.020  1.090
 3U6  C20  H7   single    0.970  0.020  1.090
 3U6  C20  H8   single    0.970  0.020  1.090
 3U6  C16  H9   single    0.970  0.020  1.090
 3U6  N6   H10  single    0.890  0.020  1.040
 3U6  C14  H11  single    0.930  0.020  1.080
 3U6  C13  H12  single    0.930  0.020  1.080
 3U6  C12  H13  single    0.930  0.020  1.080
 3U6  C3   H14  single    0.930  0.020  1.080
 3U6  C7   H15  single    0.930  0.020  1.080
 3U6  N1   H16  single    0.860  0.020  1.020
 3U6  C6   H17  single    0.930  0.020  1.080
 3U6  C5   H18  single    0.930  0.020  1.080
 3U6  N4   H19  single    0.890  0.020  1.040
 3U6  N4   H20  single    0.890  0.020  1.040

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
 3U6  H2   C17  H1   106.99  3.000
 3U6  H2   C17  C16  108.83  3.000
 3U6  H1   C17  C16  112.00  3.000
 3U6  H2   C17  C18  110.77  3.000
 3U6  H1   C17  C18  112.62  3.000
 3U6  C16  C17  C18  105.63  3.000
 3U6  H4   C18  H3   106.66  3.000
 3U6  H4   C18  C19  111.63  3.000
 3U6  H3   C18  C19  110.29  3.000
 3U6  H4   C18  C17  112.34  3.000
 3U6  H3   C18  C17  110.14  3.000
 3U6  C19  C18  C17  105.84  3.000
 3U6  H6   C19  H5   107.00  3.000
 3U6  H6   C19  C20  109.42  3.000
 3U6  H5   C19  C20  112.97  3.000
 3U6  H6   C19  C18  110.36  3.000
 3U6  H5   C19  C18  112.67  3.000
 3U6  C20  C19  C18  104.43  3.000
 3U6  H8   C20  H7   107.80  3.000
 3U6  H8   C20  C16  112.71  3.000
 3U6  H7   C20  C16  109.54  3.000
 3U6  H8   C20  C19  113.66  3.000
 3U6  H7   C20  C19  110.37  3.000
 3U6  C16  C20  C19  102.68  3.000
 3U6  H9   C16  N6   108.07  3.000
 3U6  H9   C16  C20  107.68  3.000
 3U6  N6   C16  C20  112.18  3.000
 3U6  H9   C16  C17  109.15  3.000
 3U6  N6   C16  C17  115.78  3.000
 3U6  C20  C16  C17  103.67  3.000
 3U6  H10  N6   C15  114.26  3.000
 3U6  H10  N6   C16  116.32  3.000
 3U6  C15  N6   C16  124.05  3.000
 3U6  C14  C15  N5   121.76  3.000
 3U6  C14  C15  N6   122.68  3.000
 3U6  N5   C15  N6   115.55  3.000
 3U6  C9   N5   C15  120.10  3.000
 3U6  H11  C14  C13  120.52  3.000
 3U6  H11  C14  C15  121.81  3.000
 3U6  C13  C14  C15  117.67  3.000
 3U6  H12  C13  C12  119.83  3.000
 3U6  H12  C13  C14  119.53  3.000
 3U6  C12  C13  C14  120.64  3.000
 3U6  H13  C12  C9   121.56  3.000
 3U6  H13  C12  C13  120.59  3.000
 3U6  C9   C12  C13  117.85  3.000
 3U6  C8   C9   C12  121.42  3.000
 3U6  C12  C9   N5   121.98  3.000
 3U6  C8   C9   N5   116.60  3.000
 3U6  C7   C8   C2   105.86  3.000
 3U6  C2   C8   C9   128.14  3.000
 3U6  C7   C8   C9   126.00  3.000
 3U6  C1   C2   C3   118.71  3.000
 3U6  C3   C2   C8   134.62  3.000
 3U6  C1   C2   C8   106.67  3.000
 3U6  H14  C3   C4   120.43  3.000
 3U6  H14  C3   C2   120.13  3.000
 3U6  C4   C3   C2   119.44  3.000
 3U6  H15  C7   N1   120.01  3.000
 3U6  H15  C7   C8   129.71  3.000
 3U6  N1   C7   C8   110.28  3.000
 3U6  H16  N1   C1   125.70  3.000
 3U6  H16  N1   C7   124.70  3.000
 3U6  C1   N1   C7   109.59  3.000
 3U6  C6   C1   N1   129.95  3.000
 3U6  N1   C1   C2   107.61  3.000
 3U6  C6   C1   C2   122.44  3.000
 3U6  H17  C6   C5   120.91  3.000
 3U6  H17  C6   C1   121.47  3.000
 3U6  C5   C6   C1   117.62  3.000
 3U6  H18  C5   C4   120.39  3.000
 3U6  H18  C5   C6   118.22  3.000
 3U6  C4   C5   C6   121.39  3.000
 3U6  C10  C4   C5   120.62  3.000
 3U6  C10  C4   C3   118.98  3.000
 3U6  C5   C4   C3   120.40  3.000
 3U6  N3   C10  S1   112.29  3.000
 3U6  S1   C10  C4   122.81  3.000
 3U6  N3   C10  C4   124.90  3.000
 3U6  C11  S1   C10   86.72  3.000
 3U6  N2   N3   C10  114.84  3.000
 3U6  C11  N2   N3   112.76  3.000
 3U6  N4   C11  N2   124.53  3.000
 3U6  N4   C11  S1   122.01  3.000
 3U6  N2   C11  S1   113.39  3.000
 3U6  H20  N4   H19  114.45  3.000
 3U6  H20  N4   C11  118.98  3.000
 3U6  H19  N4   C11  116.01  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
 3U6  CONST_01  C8   C9   N5   C15  180.00   0.0  0
 3U6  CONST_02  C12  C9   N5   C15    0.00   0.0  0
 3U6  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 3U6  CONST_04  C7   C8   C9   N5   180.00   0.0  0
 3U6  CONST_05  C2   C8   C9   N5     0.00   0.0  0
 3U6  CONST_06  C13  C12  C9   N5     0.00   0.0  0
 3U6  CONST_07  C13  C14  C15  N5     0.00   0.0  0
 3U6  CONST_08  C9   C12  C13  C14    0.00   0.0  0
 3U6  CONST_09  C9   N5   C15  C14    0.00   0.0  0
 3U6  CONST_10  C8   C9   C12  C13  180.00   0.0  0
 3U6  CONST_11  C7   C8   C9   C12    0.00   0.0  0
 3U6  CONST_12  C2   C8   C9   C12  180.00   0.0  0
 3U6  CONST_13  N1   C7   C8   C9   180.00   0.0  0
 3U6  CONST_14  C1   C2   C8   C9   180.00   0.0  0
 3U6  CONST_15  C3   C2   C8   C9     0.00   0.0  0
 3U6  CONST_16  C1   N1   C7   C8     0.00   0.0  0
 3U6  CONST_17  C6   C1   C2   C8   180.00   0.0  0
 3U6  CONST_18  N1   C1   C2   C8     0.00   0.0  0
 3U6  CONST_19  C4   C3   C2   C8   180.00   0.0  0
 3U6  CONST_20  C5   C6   C1   C2     0.00   0.0  0
 3U6  CONST_21  C7   N1   C1   C2     0.00   0.0  0
 3U6  CONST_22  C5   C4   C3   C2     0.00   0.0  0
 3U6  CONST_23  C10  C4   C3   C2   180.00   0.0  0
 3U6  CONST_24  N1   C7   C8   C2     0.00   0.0  0
 3U6  CONST_25  C6   C5   C4   C3     0.00   0.0  0
 3U6  CONST_26  N3   C10  C4   C3     0.00   0.0  0
 3U6  CONST_27  S1   C10  C4   C3   180.00   0.0  0
 3U6  CONST_28  C6   C1   C2   C3     0.00   0.0  0
 3U6  CONST_29  N1   C1   C2   C3   180.00   0.0  0
 3U6  CONST_30  C7   C8   C2   C3   180.00   0.0  0
 3U6  CONST_31  C6   C1   N1   C7   180.00   0.0  0
 3U6  CONST_32  C1   C2   C8   C7     0.00   0.0  0
 3U6  CONST_33  C5   C6   C1   N1   180.00   0.0  0
 3U6  CONST_34  C4   C5   C6   C1     0.00   0.0  0
 3U6  CONST_35  C4   C3   C2   C1     0.00   0.0  0
 3U6  CONST_36  C10  C4   C5   C6   180.00   0.0  0
 3U6  CONST_37  N3   C10  C4   C5   180.00   0.0  0
 3U6  CONST_38  S1   C10  C4   C5     0.00   0.0  0
 3U6  CONST_39  N2   N3   C10  C4   180.00   0.0  0
 3U6  CONST_40  C11  S1   C10  C4   180.00   0.0  0
 3U6  CONST_41  C11  N2   N3   C10    0.00   0.0  0
 3U6  CONST_42  N2   C11  S1   C10    0.00   0.0  0
 3U6  CONST_43  N2   N3   C10  S1     0.00   0.0  0
 3U6  CONST_44  N3   N2   C11  S1     0.00   0.0  0
 3U6  CONST_45  C11  S1   C10  N3     0.00   0.0  0
 3U6  CONST_46  C9   N5   C15  N6   180.00   0.0  0
 3U6  CONST_47  C13  C14  C15  N6   180.00   0.0  0
 3U6  CONST_48  N4   C11  S1   C10  180.00   0.0  0
 3U6  CONST_49  N4   C11  N2   N3   180.00   0.0  0
 3U6  CONST_50  N5   C15  N6   C16  180.00   0.0  0
 3U6  CONST_51  C14  C15  N6   C16    0.00   0.0  0
 3U6  CONST_52  H12  C13  C14  C15  180.00   0.0  0
 3U6  CONST_53  H13  C12  C9   N5   180.00   0.0  0
 3U6  CONST_54  H11  C14  C15  N5   180.00   0.0  0
 3U6  CONST_55  H15  C7   C8   C9     0.00   0.0  0
 3U6  CONST_56  H16  N1   C7   C8   180.00   0.0  0
 3U6  CONST_57  H14  C3   C2   C8     0.00   0.0  0
 3U6  CONST_58  H17  C6   C1   C2   180.00   0.0  0
 3U6  CONST_59  H18  C5   C4   C3   180.00   0.0  0
 3U6  CONST_60  H10  N6   C15  N5     0.00   0.0  0
 3U6  CONST_61  H19  N4   C11  S1   180.00   0.0  0
 3U6  Var_01    C20  C19  C18  C17   22.76  30.0  1
 3U6  Var_02    C16  C20  C19  C18  -39.65  30.0  1
 3U6  Var_03    C16  C17  C18  C19    2.67  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
 3U6  chir_01  C16  C20  N6  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
 3U6  plan-1  C4   0.020
 3U6  plan-1  C10  0.020
 3U6  plan-1  S1   0.020
 3U6  plan-1  N3   0.020
 3U6  plan-1  N2   0.020
 3U6  plan-1  C11  0.020
 3U6  plan-1  N4   0.020
 3U6  plan-2  N6   0.020
 3U6  plan-2  C15  0.020
 3U6  plan-2  N5   0.020
 3U6  plan-2  C14  0.020
 3U6  plan-2  C13  0.020
 3U6  plan-2  C12  0.020
 3U6  plan-2  C9   0.020
 3U6  plan-2  C8   0.020
 3U6  plan-2  H11  0.020
 3U6  plan-2  H12  0.020
 3U6  plan-2  H13  0.020
 3U6  plan-3  C9   0.020
 3U6  plan-3  C8   0.020
 3U6  plan-3  C2   0.020
 3U6  plan-3  C3   0.020
 3U6  plan-3  C7   0.020
 3U6  plan-3  N1   0.020
 3U6  plan-3  C1   0.020
 3U6  plan-3  C6   0.020
 3U6  plan-3  C5   0.020
 3U6  plan-3  C4   0.020
 3U6  plan-3  C10  0.020
 3U6  plan-3  H14  0.020
 3U6  plan-3  H15  0.020
 3U6  plan-3  H16  0.020
 3U6  plan-3  H17  0.020
 3U6  plan-3  H18  0.020
 3U6  plan-4  C16  0.020
 3U6  plan-4  N6   0.020
 3U6  plan-4  C15  0.020
 3U6  plan-4  H10  0.020
 3U6  plan-5  C11  0.020
 3U6  plan-5  N4   0.020
 3U6  plan-5  H19  0.020
 3U6  plan-5  H20  0.020

