# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:29:55 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: N-{5-[(3S)-3-{[5-(acetylamino)-1,3,4-thiadiazol-2-yl]amino}pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1sc(N[C@H]2CCN(C2)c3sc(NC(C)=O)nn3)nn1
#
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
 Q9A  Q9A  N-{5-[(3S)-3-{[5-(acetylamino)-1,3,4-thiadiazol-2-yl]amino}pyrrolidin-1-yl]-1,3,4-thiadiazol-2-yl}acetamide  ligand  40  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Q9A
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
 Q9A  C10  C  CH2   0  -0.516  -20.5195  -23.5271  44.2750
 Q9A  N12  N  NT    0  -0.497  -21.3932  -25.2435  45.5775
 Q9A  C13  C  CH2   0  -0.252  -19.9957  -25.1261  45.9546
 Q9A  C17  C  CR5   0   0.320  -24.0386  -27.3922  46.9770
 Q9A  C20  C  CH3   0  -0.783  -27.5231  -28.7042  47.0994
 Q9A  C01  C  CH3   0  -0.793  -13.7345  -30.4300  43.0106
 Q9A  C02  C  C     0   0.501  -14.7867  -29.6215  43.7179
 Q9A  C04  C  CR5   0   0.286  -16.0647  -27.5662  43.5001
 Q9A  C07  C  CR5   0   0.339  -17.9375  -26.1275  43.7802
 Q9A  C09  C  CH1   0  -0.143  -19.3775  -24.4213  44.7482
 Q9A  C11  C  CH2   0  -0.280  -21.7648  -24.3891  44.4645
 Q9A  C14  C  CR5   0   0.346  -22.2336  -26.0750  46.1994
 Q9A  C19  C  C     0   0.519  -26.3814  -27.8722  46.5946
 Q9A  N05  N  N     0  -0.223  -16.1202  -27.0279  44.6610
 Q9A  N06  N  N     0  -0.334  -17.1854  -26.2177  44.8403
 Q9A  N08  N  NH1   0  -0.659  -19.0378  -25.3638  43.6969
 Q9A  N15  N  N     0  -0.350  -21.9131  -26.8309  47.2093
 Q9A  N16  N  N     0  -0.289  -22.9575  -27.5827  47.6425
 Q9A  O21  O  O     0  -0.457  -26.4588  -27.0879  45.6664
 Q9A  O24  O  O     0  -0.444  -15.3250  -29.9575  44.7493
 Q9A  S22  S  S2    0   0.153  -23.9014  -26.2285  45.6909
 Q9A  S23  S  S2    0   0.165  -17.3875  -27.1078  42.4531
 Q9A  H1   H  HCH2  0   0.278  -20.3984  -23.1752  43.2507
 Q9A  H2   H  HCH2  0   0.278  -20.5657  -22.6515  44.9228
 Q9A  H3   H  HCH2  0   0.264  -19.5539  -26.1019  46.1527
 Q9A  H4   H  HCH2  0   0.250  -19.8775  -24.5138  46.8542
 Q9A  H5   H  HCH3  0   0.273  -28.4244  -28.4876  46.5333
 Q9A  H6   H  HCH3  0   0.279  -27.2930  -29.7664  47.0062
 Q9A  H7   H  HCH3  0   0.277  -27.7075  -28.5005  48.1549
 Q9A  H8   H  HCH3  0   0.271  -13.4882  -31.3168  43.5874
 Q9A  H9   H  HCH3  0   0.276  -14.0906  -30.7381  42.0263
 Q9A  H10  H  HCH3  0   0.274  -12.8288  -29.8418  42.8598
 Q9A  H11  H  HCH1  0   0.283  -18.4938  -23.8483  45.0376
 Q9A  H12  H  HCH2  0   0.262  -22.6444  -23.7821  44.6941
 Q9A  H13  H  HCH2  0   0.250  -21.9935  -24.9805  43.5709
 Q9A  H14  H  HNH1  0   0.428  -14.6566  -28.2672  42.1808
 Q9A  H15  H  HNH1  0   0.413  -19.4517  -25.2289  42.7888
 Q9A  H16  H  HNH1  0   0.429  -25.1638  -28.7091  48.0317
 Q9A  N18  N  NH1   0  -0.684  -25.2083  -28.0537  47.2639
 Q9A  N03  N  NH1   0  -0.709  -15.0936  -28.4492  43.0722

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
 Q9A  C01  C02  single    1.504  0.020  1.504
 Q9A  N03  C02  single    1.373  0.020  1.373
 Q9A  N03  C04  single    1.381  0.020  1.381
 Q9A  S23  C04  aromatic  1.748  0.020  1.748
 Q9A  S23  C07  aromatic  1.739  0.020  1.739
 Q9A  C02  O24  double    1.211  0.020  1.211
 Q9A  C04  N05  aromatic  1.281  0.020  1.281
 Q9A  C07  N08  single    1.342  0.020  1.342
 Q9A  C07  N06  aromatic  1.303  0.020  1.303
 Q9A  N08  C09  single    1.452  0.020  1.452
 Q9A  C11  C10  single    1.526  0.020  1.526
 Q9A  C11  N12  single    1.452  0.020  1.452
 Q9A  N05  N06  aromatic  1.350  0.020  1.350
 Q9A  C10  C09  single    1.526  0.020  1.526
 Q9A  C09  C13  single    1.528  0.020  1.528
 Q9A  S22  C14  aromatic  1.750  0.020  1.750
 Q9A  S22  C17  aromatic  1.740  0.020  1.740
 Q9A  N12  C14  single    1.336  0.020  1.336
 Q9A  N12  C13  single    1.452  0.020  1.452
 Q9A  C14  N15  aromatic  1.302  0.020  1.302
 Q9A  C17  N18  single    1.374  0.020  1.374
 Q9A  C17  N16  aromatic  1.284  0.020  1.284
 Q9A  N18  C19  single    1.363  0.020  1.363
 Q9A  C19  C20  single    1.500  0.020  1.500
 Q9A  C19  O21  double    1.218  0.020  1.218
 Q9A  N15  N16  aromatic  1.358  0.020  1.358
 Q9A  C10  H1   single    0.970  0.020  1.090
 Q9A  C10  H2   single    0.970  0.020  1.090
 Q9A  C13  H3   single    0.970  0.020  1.090
 Q9A  C13  H4   single    0.970  0.020  1.090
 Q9A  C20  H5   single    0.970  0.020  1.090
 Q9A  C20  H6   single    0.970  0.020  1.090
 Q9A  C20  H7   single    0.970  0.020  1.090
 Q9A  C01  H8   single    0.970  0.020  1.090
 Q9A  C01  H9   single    0.970  0.020  1.090
 Q9A  C01  H10  single    0.970  0.020  1.090
 Q9A  C09  H11  single    0.970  0.020  1.090
 Q9A  C11  H12  single    0.970  0.020  1.090
 Q9A  C11  H13  single    0.970  0.020  1.090
 Q9A  N03  H14  single    0.860  0.020  1.020
 Q9A  N08  H15  single    0.890  0.020  1.040
 Q9A  N18  H16  single    0.860  0.020  1.020

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
 Q9A  H2   C10  H1   107.69  3.000
 Q9A  H2   C10  C11  110.20  3.000
 Q9A  H1   C10  C11  112.94  3.000
 Q9A  H2   C10  C09  108.55  3.000
 Q9A  H1   C10  C09  113.43  3.000
 Q9A  C11  C10  C09  103.96  3.000
 Q9A  C14  N12  C11  124.22  3.000
 Q9A  C14  N12  C13  122.33  3.000
 Q9A  C11  N12  C13  113.45  3.000
 Q9A  H4   C13  H3   107.93  3.000
 Q9A  H4   C13  C09  110.31  3.000
 Q9A  H3   C13  C09  113.13  3.000
 Q9A  H4   C13  N12  111.26  3.000
 Q9A  H3   C13  N12  111.42  3.000
 Q9A  C09  C13  N12  102.81  3.000
 Q9A  S22  C17  N18  122.91  3.000
 Q9A  N18  C17  N16  122.50  3.000
 Q9A  S22  C17  N16  114.59  3.000
 Q9A  H7   C20  H6   107.47  3.000
 Q9A  H7   C20  H5   109.07  3.000
 Q9A  H6   C20  H5   108.95  3.000
 Q9A  H7   C20  C19  110.53  3.000
 Q9A  H6   C20  C19  110.54  3.000
 Q9A  H5   C20  C19  110.22  3.000
 Q9A  H10  C01  H9   107.37  3.000
 Q9A  H10  C01  H8   108.99  3.000
 Q9A  H9   C01  H8   108.82  3.000
 Q9A  H10  C01  C02  110.87  3.000
 Q9A  H9   C01  C02  110.35  3.000
 Q9A  H8   C01  C02  110.36  3.000
 Q9A  O24  C02  N03  122.56  3.000
 Q9A  O24  C02  C01  124.22  3.000
 Q9A  N03  C02  C01  113.22  3.000
 Q9A  S23  C04  N05  113.57  3.000
 Q9A  N05  C04  N03  125.47  3.000
 Q9A  S23  C04  N03  120.95  3.000
 Q9A  S23  C07  N08  122.19  3.000
 Q9A  N08  C07  N06  124.28  3.000
 Q9A  S23  C07  N06  113.53  3.000
 Q9A  H11  C09  N08  110.06  3.000
 Q9A  H11  C09  C13  111.11  3.000
 Q9A  N08  C09  C13  111.52  3.000
 Q9A  H11  C09  C10  112.36  3.000
 Q9A  C13  C09  C10  102.26  3.000
 Q9A  N08  C09  C10  109.32  3.000
 Q9A  H13  C11  H12  107.64  3.000
 Q9A  H13  C11  N12  111.16  3.000
 Q9A  H12  C11  N12  111.83  3.000
 Q9A  H13  C11  C10  111.96  3.000
 Q9A  H12  C11  C10  111.65  3.000
 Q9A  N12  C11  C10  102.64  3.000
 Q9A  S22  C14  N15  114.15  3.000
 Q9A  N15  C14  N12  124.60  3.000
 Q9A  S22  C14  N12  121.25  3.000
 Q9A  O21  C19  N18  120.99  3.000
 Q9A  O21  C19  C20  124.43  3.000
 Q9A  N18  C19  C20  114.58  3.000
 Q9A  N06  N05  C04  114.00  3.000
 Q9A  N05  N06  C07  112.89  3.000
 Q9A  H15  N08  C09  118.02  3.000
 Q9A  H15  N08  C07  117.98  3.000
 Q9A  C09  N08  C07  121.08  3.000
 Q9A  N16  N15  C14  112.32  3.000
 Q9A  N15  N16  C17  113.59  3.000
 Q9A  C14  S22  C17   85.35  3.000
 Q9A  C07  S23  C04   85.99  3.000
 Q9A  H16  N18  C19  119.83  3.000
 Q9A  H16  N18  C17  115.68  3.000
 Q9A  C19  N18  C17  124.48  3.000
 Q9A  H14  N03  C04  117.58  3.000
 Q9A  H14  N03  C02  118.20  3.000
 Q9A  C04  N03  C02  123.88  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
 Q9A  CONST_01  N15  C14  S22  C17     0.00   0.0  0
 Q9A  CONST_02  C14  N15  N16  C17     0.00   0.0  0
 Q9A  CONST_03  N06  C07  S23  C04     0.00   0.0  0
 Q9A  CONST_04  C07  N06  N05  C04     0.00   0.0  0
 Q9A  CONST_05  N05  C04  S23  C07     0.00   0.0  0
 Q9A  CONST_06  N16  C17  S22  C14     0.00   0.0  0
 Q9A  CONST_07  S23  C07  N06  N05     0.00   0.0  0
 Q9A  CONST_08  S23  C04  N05  N06     0.00   0.0  0
 Q9A  CONST_09  S22  C17  N16  N15     0.00   0.0  0
 Q9A  CONST_10  S22  C14  N15  N16     0.00   0.0  0
 Q9A  CONST_11  C17  S22  C14  N12   180.00   0.0  0
 Q9A  CONST_12  N16  N15  C14  N12   180.00   0.0  0
 Q9A  CONST_13  N08  C07  S23  C04   180.00   0.0  0
 Q9A  CONST_14  N03  C04  S23  C07   180.00   0.0  0
 Q9A  CONST_15  N18  C17  S22  C14   180.00   0.0  0
 Q9A  CONST_16  N06  N05  C04  N03   180.00   0.0  0
 Q9A  CONST_17  N08  C07  N06  N05   180.00   0.0  0
 Q9A  CONST_18  N18  C17  N16  N15   180.00   0.0  0
 Q9A  CONST_19  S23  C07  N08  C09   180.00   0.0  0
 Q9A  CONST_20  N06  C07  N08  C09     0.00   0.0  0
 Q9A  CONST_23  S22  C17  N18  C19     0.00   0.0  0
 Q9A  CONST_24  N16  C17  N18  C19   180.00   0.0  0
 Q9A  CONST_26  H15  N08  C07  N06   180.00   0.0  0
 Q9A  CONST_27  H16  N18  C17  N16     0.00   0.0  0
 Q9A  CONST_28  C20  C19  N18  C17   180.00   0.0  0
 Q9A  CONST_29  O21  C19  N18  C17     0.00   0.0  0
 Q9A  CONST_30  C04  N03  C02  C01   180.00   0.0  0
 Q9A  CONST_31  O24  C02  N03  C04     0.00   0.0  0
 Q9A  Var_01    C14  N12  C11  C10   172.30  30.0  1
 Q9A  Var_02    C09  C10  C11  N12    29.13  30.0  1
 Q9A  Var_03    S22  C14  N12  C13  -178.18  30.0  2
 Q9A  Var_04    C11  N12  C13  C09   -15.61  30.0  1
 Q9A  Var_05    H8   C01  C02  N03   176.84  30.0  3
 Q9A  Var_06    H5   C20  C19  N18   178.69  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
 Q9A  chir_01  C09  N08  C10  C13  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
 Q9A  plan-1  C01  0.020
 Q9A  plan-1  C02  0.020
 Q9A  plan-1  C04  0.020
 Q9A  plan-1  O24  0.020
 Q9A  plan-1  H14  0.020
 Q9A  plan-1  N03  0.020
 Q9A  plan-2  N12  0.020
 Q9A  plan-2  C17  0.020
 Q9A  plan-2  C14  0.020
 Q9A  plan-2  N15  0.020
 Q9A  plan-2  N16  0.020
 Q9A  plan-2  S22  0.020
 Q9A  plan-2  N18  0.020
 Q9A  plan-3  C04  0.020
 Q9A  plan-3  C07  0.020
 Q9A  plan-3  N05  0.020
 Q9A  plan-3  N06  0.020
 Q9A  plan-3  N08  0.020
 Q9A  plan-3  S23  0.020
 Q9A  plan-3  N03  0.020
 Q9A  plan-4  C17  0.020
 Q9A  plan-4  C20  0.020
 Q9A  plan-4  C19  0.020
 Q9A  plan-4  O21  0.020
 Q9A  plan-4  H16  0.020
 Q9A  plan-4  N18  0.020
 Q9A  plan-5  C07  0.020
 Q9A  plan-5  C09  0.020
 Q9A  plan-5  N08  0.020
 Q9A  plan-5  H15  0.020

