# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:56:29 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}5-cyclopropyl-1-(1~{H}-indol-4-ylmethyl)-~{N}3-methyl-2-oxidanylidene-pyridine-3,5-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C1=CC(=CN(Cc2cccc3[nH]ccc23)C1=O)C(=O)NC4CC4
#
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
 QD5  QD5  ~{N}5-cyclopropyl-1-(1~{H}-indol-4-ylmethyl)-~{N}3-methyl-2-oxidanylidene-pyridine-3,5-dicarboxamide  ligand  47  27  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QD5
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
 QD5  C10  C  CR16  0  -0.161  43.5698  16.6695   8.4892
 QD5  C13  C  CR16  0   0.080  43.1910  18.5815   9.8275
 QD5  C20  C  CR16  0  -0.324  38.6825  18.9903  10.9857
 QD5  C22  C  CR16  0  -0.277  37.7835  18.4736  11.9305
 QD5  C24  C  CR16  0  -0.313  38.2337  17.8607  13.0817
 QD5  C26  C  CR56  0   0.348  39.6125  17.7869  13.2682
 QD5  C01  C  CH3   0  -0.514  40.0090  14.4022   6.0570
 QD5  N05  N  NH1   0  -0.661  40.5254  15.4265   6.9311
 QD5  C07  C  C     0   0.570  41.8159  15.4845   7.2655
 QD5  O08  O  O     0  -0.505  42.6391  14.6671   6.8624
 QD5  C09  C  CR6   0  -0.301  42.2439  16.6023   8.1674
 QD5  C12  C  CR6   0  -0.185  44.0830  17.6773   9.3252
 QD5  N15  N  NR6   0  -0.499  41.8832  18.5350   9.5435
 QD5  C16  C  CH2   0  -0.434  40.9793  19.5226  10.1491
 QD5  C19  C  CR6   0   0.075  40.0505  18.9219  11.1661
 QD5  N27  N  NR15  0  -0.676  40.3263  17.2586  14.3038
 QD5  C29  C  CR15  0  -0.019  41.6572  17.4299  14.0717
 QD5  C31  C  CR15  0  -0.440  41.8402  18.0700  12.8790
 QD5  C33  C  CR56  0   0.057  40.5381  18.3117  12.3357
 QD5  C34  C  CR6   0   0.614  41.3216  17.5866   8.6864
 QD5  O35  O  O     0  -0.483  40.1224  17.6535   8.4371
 QD5  C36  C  C     0   0.547  45.5058  17.8132   9.7353
 QD5  O37  O  O     0  -0.482  45.8159  18.4786  10.7135
 QD5  N38  N  NH1   0  -0.669  46.4087  17.1684   8.9746
 QD5  C40  C  CH1   0  -0.080  47.8063  17.2307   9.2516
 QD5  C42  C  CH2   0  -0.513  48.6189  16.0079   8.9753
 QD5  C45  C  CH2   0  -0.483  48.3543  16.4294  10.3881
 QD5  H1   H  HCR6  0   0.273  44.2204  15.9037   8.0849
 QD5  H2   H  HCR6  0   0.329  43.5109  19.3887  10.4714
 QD5  H3   H  HCR6  0   0.244  38.2915  19.4508  10.0872
 QD5  H4   H  HCR6  0   0.251  36.7201  18.5519  11.7461
 QD5  H5   H  HCR6  0   0.261  37.5443  17.4568  13.8123
 QD5  H6   H  HCH3  0   0.248  38.9411  14.5622   5.9386
 QD5  H7   H  HCH3  0   0.237  40.4731  14.4389   5.0703
 QD5  H8   H  HCH3  0   0.237  40.1634  13.4035   6.4675
 QD5  H9   H  HNH1  0   0.417  39.9063  16.1388   7.2921
 QD5  H10  H  HCH2  0   0.289  41.6124  20.2814  10.6096
 QD5  H11  H  HCH2  0   0.299  40.4146  20.0104   9.3564
 QD5  H12  H  HNR5  0   0.412  39.9348  16.8192  15.1198
 QD5  H13  H  HCR5  0   0.284  42.3882  17.0785  14.7819
 QD5  H14  H  HCR5  0   0.232  42.8007  18.3293  12.4659
 QD5  H15  H  HNH1  0   0.410  46.1300  16.7989   8.0800
 QD5  H16  H  HCH1  0   0.270  48.2743  18.1900   9.0524
 QD5  H17  H  HCH2  0   0.259  48.1012  15.1320   8.6049
 QD5  H18  H  HCH2  0   0.260  49.6107  16.1495   8.5669
 QD5  H19  H  HCH2  0   0.257  47.6552  15.8388  10.9655
 QD5  H20  H  HCH2  0   0.257  49.1634  16.8610  10.9626

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
 QD5  C01  N05  single    1.442  0.020  1.442
 QD5  O08  C07  double    1.228  0.020  1.228
 QD5  N05  C07  single    1.334  0.020  1.334
 QD5  C07  C09  single    1.499  0.020  1.499
 QD5  C09  C10  double    1.366  0.020  1.366
 QD5  C09  C34  single    1.445  0.020  1.445
 QD5  O35  C34  double    1.227  0.020  1.227
 QD5  C10  C12  single    1.406  0.020  1.406
 QD5  C34  N15  single    1.396  0.020  1.396
 QD5  C12  C36  single    1.487  0.020  1.487
 QD5  C12  C13  double    1.366  0.020  1.366
 QD5  N15  C13  single    1.339  0.020  1.339
 QD5  N15  C16  single    1.469  0.020  1.469
 QD5  N38  C36  single    1.345  0.020  1.345
 QD5  N38  C40  single    1.426  0.020  1.426
 QD5  C36  O37  double    1.223  0.020  1.223
 QD5  C42  C40  single    1.494  0.020  1.494
 QD5  C42  C45  single    1.498  0.020  1.498
 QD5  C40  C45  single    1.495  0.020  1.495
 QD5  C16  C19  single    1.503  0.020  1.503
 QD5  C20  C19  aromatic  1.382  0.020  1.382
 QD5  C20  C22  aromatic  1.403  0.020  1.403
 QD5  C19  C33  aromatic  1.406  0.020  1.406
 QD5  C22  C24  aromatic  1.380  0.020  1.380
 QD5  C33  C31  aromatic  1.431  0.020  1.431
 QD5  C33  C26  aromatic  1.415  0.020  1.415
 QD5  C31  C29  aromatic  1.366  0.020  1.366
 QD5  C24  C26  aromatic  1.393  0.020  1.393
 QD5  C26  N27  aromatic  1.364  0.020  1.364
 QD5  C29  N27  aromatic  1.362  0.020  1.362
 QD5  C10  H1   single    0.930  0.020  1.080
 QD5  C13  H2   single    0.930  0.020  1.080
 QD5  C20  H3   single    0.930  0.020  1.080
 QD5  C22  H4   single    0.930  0.020  1.080
 QD5  C24  H5   single    0.930  0.020  1.080
 QD5  C01  H6   single    0.970  0.020  1.090
 QD5  C01  H7   single    0.970  0.020  1.090
 QD5  C01  H8   single    0.970  0.020  1.090
 QD5  N05  H9   single    0.860  0.020  1.020
 QD5  C16  H10  single    0.970  0.020  1.090
 QD5  C16  H11  single    0.970  0.020  1.090
 QD5  N27  H12  single    0.860  0.020  1.020
 QD5  C29  H13  single    0.930  0.020  1.080
 QD5  C31  H14  single    0.930  0.020  1.080
 QD5  N38  H15  single    0.860  0.020  1.020
 QD5  C40  H16  single    0.970  0.020  1.090
 QD5  C42  H17  single    0.970  0.020  1.090
 QD5  C42  H18  single    0.970  0.020  1.090
 QD5  C45  H19  single    0.970  0.020  1.090
 QD5  C45  H20  single    0.970  0.020  1.090

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
 QD5  H1   C10  C12  120.62  3.000
 QD5  H1   C10  C09  117.41  3.000
 QD5  C12  C10  C09  121.97  3.000
 QD5  H2   C13  N15  116.18  3.000
 QD5  H2   C13  C12  121.34  3.000
 QD5  N15  C13  C12  122.47  3.000
 QD5  H3   C20  C19  119.15  3.000
 QD5  H3   C20  C22  118.96  3.000
 QD5  C19  C20  C22  121.90  3.000
 QD5  H4   C22  C24  119.67  3.000
 QD5  H4   C22  C20  119.23  3.000
 QD5  C24  C22  C20  121.09  3.000
 QD5  H5   C24  C26  121.34  3.000
 QD5  H5   C24  C22  121.39  3.000
 QD5  C26  C24  C22  117.27  3.000
 QD5  C33  C26  N27  107.56  3.000
 QD5  N27  C26  C24  129.79  3.000
 QD5  C33  C26  C24  122.65  3.000
 QD5  H8   C01  H7   108.12  3.000
 QD5  H8   C01  H6   108.37  3.000
 QD5  H7   C01  H6   108.34  3.000
 QD5  H8   C01  N05  111.81  3.000
 QD5  H7   C01  N05  111.83  3.000
 QD5  H6   C01  N05  108.27  3.000
 QD5  H9   N05  C07  118.18  3.000
 QD5  H9   N05  C01  119.86  3.000
 QD5  C07  N05  C01  121.94  3.000
 QD5  C09  C07  O08  120.17  3.000
 QD5  C09  C07  N05  117.35  3.000
 QD5  O08  C07  N05  122.48  3.000
 QD5  C34  C09  C07  122.81  3.000
 QD5  C34  C09  C10  120.09  3.000
 QD5  C07  C09  C10  117.10  3.000
 QD5  C36  C12  C13  117.58  3.000
 QD5  C13  C12  C10  117.04  3.000
 QD5  C36  C12  C10  125.35  3.000
 QD5  C34  N15  C16  117.53  3.000
 QD5  C16  N15  C13  119.34  3.000
 QD5  C34  N15  C13  123.13  3.000
 QD5  H11  C16  H10  107.27  3.000
 QD5  H11  C16  C19  110.57  3.000
 QD5  H10  C16  C19  110.57  3.000
 QD5  H11  C16  N15  108.67  3.000
 QD5  H10  C16  N15  106.54  3.000
 QD5  C19  C16  N15  112.98  3.000
 QD5  C33  C19  C16  121.47  3.000
 QD5  C33  C19  C20  118.25  3.000
 QD5  C16  C19  C20  120.26  3.000
 QD5  H12  N27  C29  125.00  3.000
 QD5  H12  N27  C26  125.53  3.000
 QD5  C29  N27  C26  109.47  3.000
 QD5  H13  C29  C31  129.58  3.000
 QD5  H13  C29  N27  120.62  3.000
 QD5  C31  C29  N27  109.80  3.000
 QD5  H14  C31  C33  128.68  3.000
 QD5  H14  C31  C29  124.55  3.000
 QD5  C33  C31  C29  106.78  3.000
 QD5  C31  C33  C19  134.77  3.000
 QD5  C31  C33  C26  106.40  3.000
 QD5  C19  C33  C26  118.83  3.000
 QD5  O35  C34  N15  118.74  3.000
 QD5  N15  C34  C09  115.24  3.000
 QD5  O35  C34  C09  126.01  3.000
 QD5  N38  C36  O37  122.88  3.000
 QD5  O37  C36  C12  120.86  3.000
 QD5  N38  C36  C12  116.26  3.000
 QD5  H15  N38  C40  117.37  3.000
 QD5  H15  N38  C36  119.50  3.000
 QD5  C40  N38  C36  121.80  3.000
 QD5  H16  C40  C45  117.08  3.000
 QD5  H16  C40  C42  117.05  3.000
 QD5  C45  C40  C42   60.16  3.000
 QD5  H16  C40  N38  115.17  3.000
 QD5  C45  C40  N38  118.92  3.000
 QD5  C42  C40  N38  117.48  3.000
 QD5  H18  C42  H17  114.52  3.000
 QD5  H18  C42  C45  118.76  3.000
 QD5  H17  C42  C45  117.76  3.000
 QD5  H18  C42  C40  117.47  3.000
 QD5  H17  C42  C40  117.73  3.000
 QD5  C45  C42  C40   59.94  3.000
 QD5  H20  C45  H19  114.67  3.000
 QD5  H20  C45  C42  118.75  3.000
 QD5  H19  C45  C42  117.63  3.000
 QD5  H20  C45  C40  117.65  3.000
 QD5  H19  C45  C40  117.48  3.000
 QD5  C42  C45  C40   59.90  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
 QD5  CONST_01  C31  C33  C19  C20   180.00   0.0  0
 QD5  CONST_02  C26  C33  C19  C20     0.00   0.0  0
 QD5  CONST_03  C26  C24  C22  C20     0.00   0.0  0
 QD5  CONST_04  C33  C19  C20  C22     0.00   0.0  0
 QD5  CONST_05  C33  C26  C24  C22     0.00   0.0  0
 QD5  CONST_06  N27  C26  C24  C22   180.00   0.0  0
 QD5  CONST_07  C19  C20  C22  C24     0.00   0.0  0
 QD5  CONST_08  C19  C33  C26  C24     0.00   0.0  0
 QD5  CONST_09  C31  C33  C26  C24   180.00   0.0  0
 QD5  CONST_10  C29  N27  C26  C24   180.00   0.0  0
 QD5  CONST_11  C29  C31  C33  C26     0.00   0.0  0
 QD5  CONST_12  C31  C29  N27  C26     0.00   0.0  0
 QD5  CONST_13  C29  C31  C33  C19   180.00   0.0  0
 QD5  CONST_14  N27  C26  C33  C19   180.00   0.0  0
 QD5  CONST_15  C31  C33  C26  N27     0.00   0.0  0
 QD5  CONST_16  C33  C31  C29  N27     0.00   0.0  0
 QD5  CONST_17  C33  C26  N27  C29     0.00   0.0  0
 QD5  CONST_18  C09  C34  N15  C13     0.00   0.0  0
 QD5  CONST_19  C16  C19  C20  C22   180.00   0.0  0
 QD5  CONST_20  C16  C19  C33  C26   180.00   0.0  0
 QD5  CONST_21  C31  C33  C19  C16     0.00   0.0  0
 QD5  CONST_22  O35  C34  N15  C13   180.00   0.0  0
 QD5  CONST_23  C16  N15  C34  C09   180.00   0.0  0
 QD5  CONST_24  H5   C24  C22  C20   180.00   0.0  0
 QD5  CONST_25  H3   C20  C22  C24   180.00   0.0  0
 QD5  CONST_26  H12  N27  C26  C24     0.00   0.0  0
 QD5  CONST_27  H14  C31  C33  C26   180.00   0.0  0
 QD5  CONST_28  H4   C22  C24  C26   180.00   0.0  0
 QD5  CONST_29  H13  C29  N27  C26   180.00   0.0  0
 QD5  CONST_30  C40  N38  C36  C12   180.00   0.0  0
 QD5  CONST_31  O35  C34  N15  C16     0.00   0.0  0
 QD5  CONST_32  C09  C07  N05  C01   180.00   0.0  0
 QD5  CONST_33  C40  N38  C36  O37     0.00   0.0  0
 QD5  CONST_34  H9   N05  C07  C09     0.00   0.0  0
 QD5  CONST_35  H15  N38  C36  C12     0.00   0.0  0
 QD5  CONST_36  O08  C07  N05  C01     0.00   0.0  0
 QD5  Var_01    C19  C16  N15  C13  -110.63  30.0  3
 QD5  Var_02    N15  C16  C19  C20  -119.52  30.0  1
 QD5  Var_03    C45  C42  C40  N38  -109.28  30.0  1
 QD5  Var_04    H19  C45  C42  C40   107.37  30.0  1
 QD5  Var_05    O08  C07  C09  C10     0.98  30.0  2
 QD5  Var_06    N38  C36  C12  C10    19.21  30.0  2
 QD5  Var_07    C42  C40  N38  C36   145.16  30.0  3
 QD5  Var_08    H6   C01  N05  C07   179.81  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
 QD5  chir_01  C40  N38  C42  C45  both

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
 QD5  plan-1  C10  0.020
 QD5  plan-1  C13  0.020
 QD5  plan-1  C07  0.020
 QD5  plan-1  C09  0.020
 QD5  plan-1  C12  0.020
 QD5  plan-1  N15  0.020
 QD5  plan-1  C16  0.020
 QD5  plan-1  C34  0.020
 QD5  plan-1  O35  0.020
 QD5  plan-1  C36  0.020
 QD5  plan-1  H1   0.020
 QD5  plan-1  H2   0.020
 QD5  plan-2  C20  0.020
 QD5  plan-2  C22  0.020
 QD5  plan-2  C24  0.020
 QD5  plan-2  C26  0.020
 QD5  plan-2  C16  0.020
 QD5  plan-2  C19  0.020
 QD5  plan-2  N27  0.020
 QD5  plan-2  C29  0.020
 QD5  plan-2  C31  0.020
 QD5  plan-2  C33  0.020
 QD5  plan-2  H3   0.020
 QD5  plan-2  H4   0.020
 QD5  plan-2  H5   0.020
 QD5  plan-2  H12  0.020
 QD5  plan-2  H13  0.020
 QD5  plan-2  H14  0.020
 QD5  plan-3  C12  0.020
 QD5  plan-3  C36  0.020
 QD5  plan-3  O37  0.020
 QD5  plan-3  N38  0.020
 QD5  plan-3  C40  0.020
 QD5  plan-3  H15  0.020
 QD5  plan-4  C01  0.020
 QD5  plan-4  N05  0.020
 QD5  plan-4  C07  0.020
 QD5  plan-4  O08  0.020
 QD5  plan-4  C09  0.020
 QD5  plan-4  H9   0.020

