# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:53:05 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: N-{5-[(3R)-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
 Q94  Q94  N-{5-[(3R)-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 PERFECT
;

data_comp_Q94
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
 Q94  C14  C  CR5   0   0.345  15.6447  18.2672  41.5664
 Q94  C19  C  C     0   0.534  12.4000  21.3626  42.2240
 Q94  N16  N  N     0  -0.287  14.3076  19.2073  40.0803
 Q94  N18  N  NH1   0  -0.692  12.8712  20.7189  41.1224
 Q94  C01  C  CH3   0  -0.783  23.9859  21.6672  46.7252
 Q94  C02  C  C     0   0.539  23.1701  20.7945  45.8200
 Q94  C04  C  CR5   0   0.322  21.1227  19.5201  45.6742
 Q94  C07  C  CR5   0   0.314  19.8941  18.0995  44.2402
 Q94  C09  C  CR15  0  -0.140  18.2034  16.5349  43.4715
 Q94  C10  C  CH2   0  -0.519  17.9787  15.6167  42.2741
 Q94  C11  C  CH2   0  -0.260  17.3067  16.5094  41.2359
 Q94  C13  C  CH2   0  -0.268  16.9345  17.3869  43.4696
 Q94  C17  C  CR5   0   0.316  13.8884  19.7936  41.1426
 Q94  C20  C  CH3   0  -0.781  11.3037  22.3542  41.9717
 Q94  N05  N  N     0  -0.289  20.0197  19.1195  46.1958
 Q94  N06  N  N     0  -0.326  19.3087  18.2981  45.3793
 Q94  N08  N  NH1   0  -0.659  19.3839  17.3485  43.2398
 Q94  N12  N  NR5   0  -0.496  16.6011  17.4769  42.0607
 Q94  N15  N  N     0  -0.349  15.3166  18.3284  40.3079
 Q94  O21  O  O     0  -0.464  12.8681  21.1445  43.3279
 Q94  O24  O  O     0  -0.461  23.5143  20.4874  44.6923
 Q94  S22  S  S2    0   0.155  14.7062  19.3218  42.6025
 Q94  S23  S  S2    0   0.179  21.4202  18.9335  44.0654
 Q94  H1   H  HNH1  0   0.429  12.4672  20.9074  40.2160
 Q94  H2   H  HCH3  0   0.281  24.2271  22.5964  46.2110
 Q94  H3   H  HCH3  0   0.263  23.4868  21.9036  47.6620
 Q94  H4   H  HCH3  0   0.283  24.9267  21.1650  46.9512
 Q94  H5   H  HCR5  0   0.280  18.2940  15.9769  44.4069
 Q94  H6   H  HCH2  0   0.274  17.3055  14.8125  42.5732
 Q94  H7   H  HCH2  0   0.274  18.8962  15.1561  41.9076
 Q94  H8   H  HCH2  0   0.255  16.6157  15.9560  40.5986
 Q94  H9   H  HCH2  0   0.245  18.0303  17.0075  40.5840
 Q94  H10  H  HCH2  0   0.266  17.0977  18.3718  43.9124
 Q94  H11  H  HCH2  0   0.255  16.1448  16.8856  44.0403
 Q94  H12  H  HCH3  0   0.277  10.5262  22.2359  42.7239
 Q94  H13  H  HCH3  0   0.283  11.7078  23.3627  42.0708
 Q94  H14  H  HCH3  0   0.262  10.8584  22.2613  40.9835
 Q94  H15  H  HNH1  0   0.430  21.7290  20.6012  47.2805
 Q94  H16  H  HNH1  0   0.407  20.0371  17.0049  42.5531
 Q94  N03  N  NH1   0  -0.693  21.9971  20.3418  46.3418

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
 Q94  O21  C19  double    1.219  0.020  1.219
 Q94  N16  N15  aromatic  1.357  0.020  1.357
 Q94  N16  C17  aromatic  1.284  0.020  1.284
 Q94  N15  C14  aromatic  1.302  0.020  1.302
 Q94  C19  C20  single    1.500  0.020  1.500
 Q94  C19  N18  single    1.360  0.020  1.360
 Q94  C11  N12  single    1.454  0.020  1.454
 Q94  C11  C10  single    1.525  0.020  1.525
 Q94  C17  N18  single    1.375  0.020  1.375
 Q94  C17  S22  aromatic  1.739  0.020  1.739
 Q94  C14  N12  single    1.335  0.020  1.335
 Q94  C14  S22  aromatic  1.751  0.020  1.751
 Q94  N12  C13  single    1.451  0.020  1.451
 Q94  C10  C09  single    1.526  0.020  1.526
 Q94  N08  C09  single    1.452  0.020  1.452
 Q94  N08  C07  single    1.351  0.020  1.351
 Q94  C09  C13  single    1.528  0.020  1.528
 Q94  S23  C07  aromatic  1.748  0.020  1.748
 Q94  S23  C04  aromatic  1.738  0.020  1.738
 Q94  C07  N06  aromatic  1.296  0.020  1.296
 Q94  O24  C02  double    1.218  0.020  1.218
 Q94  N06  N05  aromatic  1.359  0.020  1.359
 Q94  C04  N05  aromatic  1.284  0.020  1.284
 Q94  C04  N03  single    1.373  0.020  1.373
 Q94  C02  N03  single    1.361  0.020  1.361
 Q94  C02  C01  single    1.499  0.020  1.499
 Q94  N18  H1   single    0.860  0.020  1.020
 Q94  C01  H2   single    0.970  0.020  1.090
 Q94  C01  H3   single    0.970  0.020  1.090
 Q94  C01  H4   single    0.970  0.020  1.090
 Q94  C09  H5   single    0.970  0.020  1.090
 Q94  C10  H6   single    0.970  0.020  1.090
 Q94  C10  H7   single    0.970  0.020  1.090
 Q94  C11  H8   single    0.970  0.020  1.090
 Q94  C11  H9   single    0.970  0.020  1.090
 Q94  C13  H10  single    0.970  0.020  1.090
 Q94  C13  H11  single    0.970  0.020  1.090
 Q94  C20  H12  single    0.970  0.020  1.090
 Q94  C20  H13  single    0.970  0.020  1.090
 Q94  C20  H14  single    0.970  0.020  1.090
 Q94  N03  H15  single    0.860  0.020  1.020
 Q94  N08  H16  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
 Q94  S22  C14  N15  114.11  3.000
 Q94  S22  C14  N12  121.41  3.000
 Q94  N15  C14  N12  124.48  3.000
 Q94  O21  C19  C20  123.47  3.000
 Q94  C20  C19  N18  115.47  3.000
 Q94  O21  C19  N18  121.05  3.000
 Q94  N15  N16  C17  113.56  3.000
 Q94  H1   N18  C17  115.76  3.000
 Q94  H1   N18  C19  119.99  3.000
 Q94  C17  N18  C19  124.25  3.000
 Q94  H4   C01  H3   108.52  3.000
 Q94  H4   C01  H2   107.45  3.000
 Q94  H3   C01  H2   108.84  3.000
 Q94  H4   C01  C02  109.07  3.000
 Q94  H3   C01  C02  113.39  3.000
 Q94  H2   C01  C02  109.41  3.000
 Q94  O24  C02  N03  120.95  3.000
 Q94  N03  C02  C01  115.54  3.000
 Q94  O24  C02  C01  123.50  3.000
 Q94  S23  C04  N05  114.69  3.000
 Q94  N05  C04  N03  122.42  3.000
 Q94  S23  C04  N03  122.89  3.000
 Q94  S23  C07  N08  121.40  3.000
 Q94  S23  C07  N06  114.15  3.000
 Q94  N08  C07  N06  124.43  3.000
 Q94  H5   C09  N08  110.81  3.000
 Q94  H5   C09  C13  110.76  3.000
 Q94  N08  C09  C13  111.24  3.000
 Q94  H5   C09  C10  112.13  3.000
 Q94  C13  C09  C10  102.25  3.000
 Q94  N08  C09  C10  109.37  3.000
 Q94  H7   C10  H6   107.46  3.000
 Q94  H7   C10  C11  112.91  3.000
 Q94  H6   C10  C11  110.26  3.000
 Q94  H7   C10  C09  113.22  3.000
 Q94  H6   C10  C09  108.64  3.000
 Q94  C11  C10  C09  104.29  3.000
 Q94  H9   C11  H8   107.57  3.000
 Q94  H9   C11  N12  110.86  3.000
 Q94  H8   C11  N12  111.20  3.000
 Q94  H9   C11  C10  112.37  3.000
 Q94  H8   C11  C10  112.32  3.000
 Q94  N12  C11  C10  102.54  3.000
 Q94  H11  C13  H10  108.01  3.000
 Q94  H11  C13  N12  111.63  3.000
 Q94  H10  C13  N12  111.85  3.000
 Q94  H11  C13  C09  110.04  3.000
 Q94  H10  C13  C09  112.22  3.000
 Q94  N12  C13  C09  103.10  3.000
 Q94  S22  C17  N18  122.88  3.000
 Q94  S22  C17  N16  114.67  3.000
 Q94  N18  C17  N16  122.46  3.000
 Q94  H14  C20  H13  108.25  3.000
 Q94  H14  C20  H12  109.04  3.000
 Q94  H13  C20  H12  107.60  3.000
 Q94  H14  C20  C19  113.30  3.000
 Q94  H13  C20  C19  108.98  3.000
 Q94  H12  C20  C19  109.52  3.000
 Q94  N06  N05  C04  113.20  3.000
 Q94  N05  N06  C07  112.60  3.000
 Q94  H16  N08  C09  116.38  3.000
 Q94  H16  N08  C07  116.69  3.000
 Q94  C09  N08  C07  120.02  3.000
 Q94  C13  N12  C11  113.46  3.000
 Q94  C13  N12  C14  124.11  3.000
 Q94  C11  N12  C14  122.09  3.000
 Q94  N16  N15  C14  112.32  3.000
 Q94  C17  S22  C14   85.34  3.000
 Q94  C07  S23  C04   85.36  3.000
 Q94  H15  N03  C04  115.88  3.000
 Q94  H15  N03  C02  119.96  3.000
 Q94  C04  N03  C02  124.15  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
 Q94  CONST_01  C17  N16  N15  C14     0.00   0.0  0
 Q94  CONST_02  N16  C17  S22  C14     0.00   0.0  0
 Q94  CONST_03  S22  C14  N15  N16     0.00   0.0  0
 Q94  CONST_04  N06  C07  S23  C04     0.00   0.0  0
 Q94  CONST_05  C07  N06  N05  C04     0.00   0.0  0
 Q94  CONST_06  N05  C04  S23  C07     0.00   0.0  0
 Q94  CONST_07  N15  C14  S22  C17     0.00   0.0  0
 Q94  CONST_08  S23  C07  N06  N05     0.00   0.0  0
 Q94  CONST_09  S23  C04  N05  N06     0.00   0.0  0
 Q94  CONST_10  S22  C17  N16  N15     0.00   0.0  0
 Q94  CONST_11  N12  C14  N15  N16   180.00   0.0  0
 Q94  CONST_12  N12  C14  S22  C17   180.00   0.0  0
 Q94  CONST_13  N18  C17  S22  C14   180.00   0.0  0
 Q94  CONST_14  N15  N16  C17  N18   180.00   0.0  0
 Q94  CONST_15  N08  C07  S23  C04   180.00   0.0  0
 Q94  CONST_16  N03  C04  S23  C07   180.00   0.0  0
 Q94  CONST_17  N06  N05  C04  N03   180.00   0.0  0
 Q94  CONST_18  N08  C07  N06  N05   180.00   0.0  0
 Q94  CONST_19  S23  C07  N08  C09   180.00   0.0  0
 Q94  CONST_20  N06  C07  N08  C09     0.00   0.0  0
 Q94  CONST_21  N16  C17  N18  C19   180.00   0.0  0
 Q94  CONST_22  S22  C17  N18  C19     0.00   0.0  0
 Q94  CONST_23  S23  C04  N03  C02     0.00   0.0  0
 Q94  CONST_24  N05  C04  N03  C02   180.00   0.0  0
 Q94  CONST_25  H1   N18  C17  N16     0.00   0.0  0
 Q94  CONST_26  H15  N03  C04  N05     0.00   0.0  0
 Q94  CONST_28  C04  N03  C02  C01   180.00   0.0  0
 Q94  CONST_29  O24  C02  N03  C04     0.00   0.0  0
 Q94  CONST_30  O21  C19  N18  C17     0.00   0.0  0
 Q94  CONST_31  C20  C19  N18  C17   180.00   0.0  0
 Q94  Var_01    C10  C11  N12  C14  -164.91  30.0  1
 Q94  Var_02    C09  C13  N12  C14  -171.61  30.0  1
 Q94  Var_03    N12  C11  C10  C09   -28.93  30.0  1
 Q94  Var_04    N15  C14  N12  C11    -5.25  30.0  1
 Q94  Var_05    H12  C20  C19  N18   136.02  30.0  3
 Q94  Var_06    H2   C01  C02  N03  -127.01  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
 Q94  chir_01  C09  C10  N08  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
 Q94  plan-1  C14  0.020
 Q94  plan-1  N16  0.020
 Q94  plan-1  N18  0.020
 Q94  plan-1  C17  0.020
 Q94  plan-1  N12  0.020
 Q94  plan-1  N15  0.020
 Q94  plan-1  S22  0.020
 Q94  plan-2  C19  0.020
 Q94  plan-2  N18  0.020
 Q94  plan-2  C17  0.020
 Q94  plan-2  C20  0.020
 Q94  plan-2  O21  0.020
 Q94  plan-2  H1   0.020
 Q94  plan-3  C04  0.020
 Q94  plan-3  C07  0.020
 Q94  plan-3  N05  0.020
 Q94  plan-3  N06  0.020
 Q94  plan-3  N08  0.020
 Q94  plan-3  S23  0.020
 Q94  plan-3  N03  0.020
 Q94  plan-4  C01  0.020
 Q94  plan-4  C02  0.020
 Q94  plan-4  C04  0.020
 Q94  plan-4  O24  0.020
 Q94  plan-4  H15  0.020
 Q94  plan-4  N03  0.020
 Q94  plan-5  C07  0.020
 Q94  plan-5  C09  0.020
 Q94  plan-5  N08  0.020
 Q94  plan-5  H16  0.020

