# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:46:36 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C1=CC(=CN(Cc2ccccc2)C1=O)C(=O)NC3CC3
#
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
 QCZ  QCZ  ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide  ligand  43  24  .  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_QCZ
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
 QCZ  C10  C  CR16  0  -0.161  16.6098   -7.4227   8.3996
 QCZ  C13  C  CR16  0   0.097  18.2822   -6.9669  10.0050
 QCZ  C20  C  CR16  0  -0.309  18.7004   -4.8055  12.7514
 QCZ  C22  C  CR16  0  -0.241  18.0806   -4.2758  13.8749
 QCZ  C24  C  CR16  0  -0.260  17.3532   -3.0973  13.7749
 QCZ  C26  C  CR16  0  -0.241  17.2543   -2.4507  12.5496
 QCZ  C28  C  CR16  0  -0.291  17.8727   -2.9831  11.4267
 QCZ  C01  C  CH3   0  -0.515  14.8911   -4.0551   5.3294
 QCZ  N05  N  NH1   0  -0.661  15.7414   -4.5077   6.4028
 QCZ  C07  C  C     0   0.572  15.7039   -5.7636   6.8513
 QCZ  O08  O  O     0  -0.504  14.9428   -6.6077   6.3865
 QCZ  C09  C  CR6   0  -0.290  16.6423   -6.1293   7.9625
 QCZ  C12  C  CR6   0  -0.176  17.4412   -7.8814   9.4378
 QCZ  N15  N  NR6   0  -0.500  18.3409   -5.6917   9.5977
 QCZ  C16  C  CH2   0  -0.461  19.2519   -4.7758  10.3051
 QCZ  C19  C  CR6   0   0.153  18.5968   -4.1691  11.5173
 QCZ  C30  C  CR6   0   0.613  17.5410   -5.1783   8.5756
 QCZ  O31  O  O     0  -0.495  17.6442   -3.9925   8.2729
 QCZ  C32  C  C     0   0.555  17.4582   -9.2659   9.9836
 QCZ  O33  O  O     0  -0.483  18.0248   -9.5158  11.0380
 QCZ  N34  N  NH1   0  -0.673  16.8205  -10.2029   9.2599
 QCZ  C36  C  CH1   0  -0.080  16.7556  -11.5647   9.6782
 QCZ  C38  C  CH2   0  -0.512  15.4806  -12.3022   9.4258
 QCZ  C41  C  CH2   0  -0.483  15.8655  -11.9258  10.8234
 QCZ  H1   H  HCR6  0   0.274  15.8995   -8.0866   7.9233
 QCZ  H2   H  HCR6  0   0.316  18.9478   -7.2441  10.8107
 QCZ  H3   H  HCR6  0   0.256  19.2807   -5.7163  12.8438
 QCZ  H4   H  HCR6  0   0.260  18.1731   -4.7795  14.8282
 QCZ  H5   H  HCR6  0   0.260  16.8705   -2.6812  14.6495
 QCZ  H6   H  HCR6  0   0.259  16.6959   -1.5272  12.4674
 QCZ  H7   H  HCR6  0   0.258  17.7913   -2.4735  10.4756
 QCZ  H8   H  HCH3  0   0.249  15.0786   -2.9971   5.1698
 QCZ  H9   H  HCH3  0   0.237  15.0967   -4.5849   4.3981
 QCZ  H10  H  HCH3  0   0.238  13.8349   -4.1854   5.5677
 QCZ  H11  H  HNH1  0   0.417  16.3953   -3.8671   6.8301
 QCZ  H12  H  HCH2  0   0.303  20.1281   -5.3549  10.5925
 QCZ  H13  H  HCH2  0   0.304  19.5830   -4.0131   9.6058
 QCZ  H14  H  HNH1  0   0.411  16.5155   -9.9915   8.3241
 QCZ  H15  H  HCH1  0   0.270  17.6791  -12.1263   9.5754
 QCZ  H16  H  HCH2  0   0.259  14.6681  -11.7568   8.9623
 QCZ  H17  H  HCH2  0   0.260  15.5537  -13.3393   9.1265
 QCZ  H18  H  HCH2  0   0.257  15.3137  -11.1259  11.2993
 QCZ  H19  H  HCH2  0   0.257  16.2062  -12.7020  11.4959

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
 QCZ  C01  N05  single    1.442  0.020  1.442
 QCZ  O08  C07  double    1.228  0.020  1.228
 QCZ  N05  C07  single    1.334  0.020  1.334
 QCZ  C07  C09  single    1.500  0.020  1.500
 QCZ  C09  C10  double    1.366  0.020  1.366
 QCZ  C09  C30  single    1.445  0.020  1.445
 QCZ  O31  C30  double    1.228  0.020  1.228
 QCZ  C10  C12  single    1.407  0.020  1.407
 QCZ  C30  N15  single    1.396  0.020  1.396
 QCZ  C12  C32  single    1.488  0.020  1.488
 QCZ  C12  C13  double    1.366  0.020  1.366
 QCZ  N15  C13  single    1.340  0.020  1.340
 QCZ  N15  C16  single    1.473  0.020  1.473
 QCZ  N34  C32  single    1.345  0.020  1.345
 QCZ  N34  C36  single    1.426  0.020  1.426
 QCZ  C38  C36  single    1.494  0.020  1.494
 QCZ  C38  C41  single    1.498  0.020  1.498
 QCZ  C32  O33  double    1.223  0.020  1.223
 QCZ  C36  C41  single    1.495  0.020  1.495
 QCZ  C16  C19  single    1.506  0.020  1.506
 QCZ  C28  C19  aromatic  1.393  0.020  1.393
 QCZ  C28  C26  aromatic  1.388  0.020  1.388
 QCZ  C19  C20  aromatic  1.392  0.020  1.392
 QCZ  C26  C24  aromatic  1.389  0.020  1.389
 QCZ  C20  C22  aromatic  1.388  0.020  1.388
 QCZ  C24  C22  aromatic  1.388  0.020  1.388
 QCZ  C10  H1   single    0.930  0.020  1.080
 QCZ  C13  H2   single    0.930  0.020  1.080
 QCZ  C20  H3   single    0.930  0.020  1.080
 QCZ  C22  H4   single    0.930  0.020  1.080
 QCZ  C24  H5   single    0.930  0.020  1.080
 QCZ  C26  H6   single    0.930  0.020  1.080
 QCZ  C28  H7   single    0.930  0.020  1.080
 QCZ  C01  H8   single    0.970  0.020  1.090
 QCZ  C01  H9   single    0.970  0.020  1.090
 QCZ  C01  H10  single    0.970  0.020  1.090
 QCZ  N05  H11  single    0.860  0.020  1.020
 QCZ  C16  H12  single    0.970  0.020  1.090
 QCZ  C16  H13  single    0.970  0.020  1.090
 QCZ  N34  H14  single    0.860  0.020  1.020
 QCZ  C36  H15  single    0.970  0.020  1.090
 QCZ  C38  H16  single    0.970  0.020  1.090
 QCZ  C38  H17  single    0.970  0.020  1.090
 QCZ  C41  H18  single    0.970  0.020  1.090
 QCZ  C41  H19  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
 QCZ  H1   C10  C12  120.83  3.000
 QCZ  H1   C10  C09  117.10  3.000
 QCZ  C12  C10  C09  122.06  3.000
 QCZ  H2   C13  N15  116.33  3.000
 QCZ  H2   C13  C12  121.13  3.000
 QCZ  N15  C13  C12  122.54  3.000
 QCZ  H3   C20  C19  119.96  3.000
 QCZ  H3   C20  C22  119.39  3.000
 QCZ  C19  C20  C22  120.65  3.000
 QCZ  H4   C22  C24  120.22  3.000
 QCZ  H4   C22  C20  119.81  3.000
 QCZ  C24  C22  C20  119.97  3.000
 QCZ  H5   C24  C26  120.14  3.000
 QCZ  H5   C24  C22  120.12  3.000
 QCZ  C26  C24  C22  119.74  3.000
 QCZ  H6   C26  C28  119.71  3.000
 QCZ  H6   C26  C24  120.07  3.000
 QCZ  C28  C26  C24  120.22  3.000
 QCZ  H7   C28  C19  119.83  3.000
 QCZ  H7   C28  C26  119.80  3.000
 QCZ  C19  C28  C26  120.37  3.000
 QCZ  H10  C01  H9   108.12  3.000
 QCZ  H10  C01  H8   108.40  3.000
 QCZ  H9   C01  H8   108.36  3.000
 QCZ  H10  C01  N05  111.77  3.000
 QCZ  H9   C01  N05  111.82  3.000
 QCZ  H8   C01  N05  108.26  3.000
 QCZ  H11  N05  C07  118.23  3.000
 QCZ  H11  N05  C01  119.83  3.000
 QCZ  C07  N05  C01  121.94  3.000
 QCZ  C09  C07  O08  120.05  3.000
 QCZ  C09  C07  N05  117.45  3.000
 QCZ  O08  C07  N05  122.50  3.000
 QCZ  C30  C09  C07  122.89  3.000
 QCZ  C30  C09  C10  120.16  3.000
 QCZ  C07  C09  C10  116.95  3.000
 QCZ  C32  C12  C13  117.62  3.000
 QCZ  C13  C12  C10  116.88  3.000
 QCZ  C32  C12  C10  125.49  3.000
 QCZ  C30  N15  C16  118.52  3.000
 QCZ  C16  N15  C13  118.22  3.000
 QCZ  C30  N15  C13  123.20  3.000
 QCZ  H13  C16  H12  107.34  3.000
 QCZ  H13  C16  C19  111.59  3.000
 QCZ  H12  C16  C19  110.61  3.000
 QCZ  H13  C16  N15  108.41  3.000
 QCZ  H12  C16  N15  107.08  3.000
 QCZ  C19  C16  N15  111.60  3.000
 QCZ  C16  C19  C28  121.14  3.000
 QCZ  C28  C19  C20  119.05  3.000
 QCZ  C16  C19  C20  119.81  3.000
 QCZ  O31  C30  N15  119.17  3.000
 QCZ  N15  C30  C09  115.16  3.000
 QCZ  O31  C30  C09  125.67  3.000
 QCZ  N34  C32  O33  122.78  3.000
 QCZ  O33  C32  C12  120.77  3.000
 QCZ  N34  C32  C12  116.45  3.000
 QCZ  H14  N34  C36  117.35  3.000
 QCZ  H14  N34  C32  119.84  3.000
 QCZ  C36  N34  C32  121.94  3.000
 QCZ  H15  C36  C41  117.01  3.000
 QCZ  H15  C36  C38  117.03  3.000
 QCZ  C41  C36  C38   60.14  3.000
 QCZ  H15  C36  N34  115.30  3.000
 QCZ  C41  C36  N34  118.85  3.000
 QCZ  C38  C36  N34  117.42  3.000
 QCZ  H17  C38  H16  114.53  3.000
 QCZ  H17  C38  C41  118.80  3.000
 QCZ  H16  C38  C41  117.75  3.000
 QCZ  H17  C38  C36  117.52  3.000
 QCZ  H16  C38  C36  117.64  3.000
 QCZ  C41  C38  C36   59.94  3.000
 QCZ  H19  C41  H18  114.68  3.000
 QCZ  H19  C41  C38  118.72  3.000
 QCZ  H18  C41  C38  117.72  3.000
 QCZ  H19  C41  C36  117.52  3.000
 QCZ  H18  C41  C36  117.52  3.000
 QCZ  C38  C41  C36   59.92  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
 QCZ  CONST_01  C26  C28  C19  C20     0.00   0.0  0
 QCZ  CONST_02  C26  C24  C22  C20     0.00   0.0  0
 QCZ  CONST_03  C28  C19  C20  C22     0.00   0.0  0
 QCZ  CONST_04  C28  C26  C24  C22     0.00   0.0  0
 QCZ  CONST_05  C19  C28  C26  C24     0.00   0.0  0
 QCZ  CONST_06  C19  C20  C22  C24     0.00   0.0  0
 QCZ  CONST_07  C09  C30  N15  C13     0.00   0.0  0
 QCZ  CONST_08  C16  C19  C20  C22   180.00   0.0  0
 QCZ  CONST_09  C16  C19  C28  C26   180.00   0.0  0
 QCZ  CONST_10  O31  C30  N15  C13   180.00   0.0  0
 QCZ  CONST_11  C16  N15  C30  C09   180.00   0.0  0
 QCZ  CONST_12  H7   C28  C19  C20   180.00   0.0  0
 QCZ  CONST_13  H5   C24  C22  C20   180.00   0.0  0
 QCZ  CONST_14  H6   C26  C24  C22   180.00   0.0  0
 QCZ  CONST_15  H3   C20  C22  C24   180.00   0.0  0
 QCZ  CONST_16  H4   C22  C24  C26   180.00   0.0  0
 QCZ  CONST_17  C36  N34  C32  C12   180.00   0.0  0
 QCZ  CONST_18  O31  C30  N15  C16     0.00   0.0  0
 QCZ  CONST_19  C09  C07  N05  C01   180.00   0.0  0
 QCZ  CONST_20  C36  N34  C32  O33     0.00   0.0  0
 QCZ  CONST_21  H11  N05  C07  C09     0.00   0.0  0
 QCZ  CONST_22  H14  N34  C32  C12     0.00   0.0  0
 QCZ  CONST_23  O08  C07  N05  C01     0.00   0.0  0
 QCZ  Var_01    C19  C16  N15  C13   -86.19  30.0  3
 QCZ  Var_02    N15  C16  C19  C20    90.32  30.0  1
 QCZ  Var_03    C41  C38  C36  N34  -109.21  30.0  1
 QCZ  Var_04    H18  C41  C38  C36   107.39  30.0  1
 QCZ  Var_05    O08  C07  C09  C10     0.76  30.0  2
 QCZ  Var_06    N34  C32  C12  C10    13.49  30.0  2
 QCZ  Var_07    C38  C36  N34  C32   142.26  30.0  3
 QCZ  Var_08    H8   C01  N05  C07   178.02  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
 QCZ  chir_01  C36  N34  C38  C41  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
 QCZ  plan-1  C20  0.020
 QCZ  plan-1  C22  0.020
 QCZ  plan-1  C24  0.020
 QCZ  plan-1  C26  0.020
 QCZ  plan-1  C28  0.020
 QCZ  plan-1  C16  0.020
 QCZ  plan-1  C19  0.020
 QCZ  plan-1  H3   0.020
 QCZ  plan-1  H4   0.020
 QCZ  plan-1  H5   0.020
 QCZ  plan-1  H6   0.020
 QCZ  plan-1  H7   0.020
 QCZ  plan-2  C10  0.020
 QCZ  plan-2  C13  0.020
 QCZ  plan-2  C07  0.020
 QCZ  plan-2  C09  0.020
 QCZ  plan-2  C12  0.020
 QCZ  plan-2  N15  0.020
 QCZ  plan-2  C16  0.020
 QCZ  plan-2  C30  0.020
 QCZ  plan-2  O31  0.020
 QCZ  plan-2  C32  0.020
 QCZ  plan-2  H1   0.020
 QCZ  plan-2  H2   0.020
 QCZ  plan-3  C12  0.020
 QCZ  plan-3  C32  0.020
 QCZ  plan-3  O33  0.020
 QCZ  plan-3  N34  0.020
 QCZ  plan-3  C36  0.020
 QCZ  plan-3  H14  0.020
 QCZ  plan-4  C01  0.020
 QCZ  plan-4  N05  0.020
 QCZ  plan-4  C07  0.020
 QCZ  plan-4  O08  0.020
 QCZ  plan-4  C09  0.020
 QCZ  plan-4  H11  0.020

