# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 11:13:17 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: ~{N}-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C1=CC=CN(Cc2ccccc2)C1=O
#
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
 QCW  QCW  ~{N}-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3-carboxamide  ligand  32  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QCW
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
 QCW  C10  C  CR16  0  -0.120  43.6097  16.3124   7.8283
 QCW  C17  C  CH2   0  -0.460  41.2331  18.9444  10.0740
 QCW  C20  C  CR6   0   0.155  40.7701  18.2859  11.3461
 QCW  C21  C  CR16  0  -0.290  39.6839  17.4124  11.3488
 QCW  C01  C  CH3   0  -0.535  39.9508  14.9072   4.9314
 QCW  N05  N  NH1   0  -0.655  40.5117  15.6690   6.0215
 QCW  C07  C  C     0   0.553  41.8021  15.5825   6.3499
 QCW  O08  O  O     0  -0.509  42.5829  14.8447   5.7541
 QCW  C09  C  CR6   0  -0.299  42.2878  16.4242   7.4912
 QCW  C12  C  CR16  0  -0.366  44.1665  17.0547   8.8798
 QCW  C14  C  CR16  0   0.098  43.3509  17.8981   9.5615
 QCW  N16  N  NR6   0  -0.497  42.0440  18.0330   9.2538
 QCW  C23  C  CR16  0  -0.223  39.2885  16.7901  12.5235
 QCW  C25  C  CR16  0  -0.243  39.9694  17.0331  13.7098
 QCW  C27  C  CR16  0  -0.221  41.0458  17.9076  13.7170
 QCW  C29  C  CR16  0  -0.295  41.4406  18.5303  12.5403
 QCW  C31  C  CR6   0   0.615  41.4252  17.3184   8.2319
 QCW  O32  O  O     0  -0.512  40.2222  17.4834   8.0247
 QCW  H1   H  HCR6  0   0.283  44.2363  15.6322   7.2673
 QCW  H2   H  HCH2  0   0.297  41.8477  19.8156  10.2972
 QCW  H3   H  HCH2  0   0.304  40.3934  19.2849   9.4745
 QCW  H4   H  HCR6  0   0.262  39.1463  17.2191  10.4296
 QCW  H5   H  HCH3  0   0.245  38.8810  15.0947   4.9018
 QCW  H6   H  HCH3  0   0.248  40.3779  15.1974   3.9701
 QCW  H7   H  HCH3  0   0.250  40.1113  13.8372   5.0646
 QCW  H8   H  HNH1  0   0.426  39.9265  16.3113   6.5326
 QCW  H9   H  HCR6  0   0.259  45.2080  16.9722   9.1467
 QCW  H10  H  HCR6  0   0.283  43.7133  18.5055  10.3788
 QCW  H11  H  HCR6  0   0.239  38.4429  16.1153  12.5134
 QCW  H12  H  HCR6  0   0.240  39.6608  16.5439  14.6241
 QCW  H13  H  HCR6  0   0.239  41.5777  18.1093  14.6371
 QCW  H14  H  HCR6  0   0.229  42.2763  19.2199  12.5605

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
 QCW  C01  N05  single    1.443  0.020  1.443
 QCW  O08  C07  double    1.228  0.020  1.228
 QCW  N05  C07  single    1.334  0.020  1.334
 QCW  C07  C09  single    1.499  0.020  1.499
 QCW  C09  C10  double    1.369  0.020  1.369
 QCW  C09  C31  single    1.446  0.020  1.446
 QCW  C10  C12  single    1.402  0.020  1.402
 QCW  O32  C31  double    1.232  0.020  1.232
 QCW  C31  N16  single    1.392  0.020  1.392
 QCW  C12  C14  double    1.357  0.020  1.357
 QCW  N16  C14  single    1.349  0.020  1.349
 QCW  N16  C17  single    1.470  0.020  1.470
 QCW  C17  C20  single    1.505  0.020  1.505
 QCW  C21  C20  aromatic  1.394  0.020  1.394
 QCW  C21  C23  aromatic  1.387  0.020  1.387
 QCW  C20  C29  aromatic  1.391  0.020  1.391
 QCW  C23  C25  aromatic  1.389  0.020  1.389
 QCW  C29  C27  aromatic  1.389  0.020  1.389
 QCW  C25  C27  aromatic  1.387  0.020  1.387
 QCW  C10  H1   single    0.930  0.020  1.080
 QCW  C17  H2   single    0.970  0.020  1.090
 QCW  C17  H3   single    0.970  0.020  1.090
 QCW  C21  H4   single    0.930  0.020  1.080
 QCW  C01  H5   single    0.970  0.020  1.090
 QCW  C01  H6   single    0.970  0.020  1.090
 QCW  C01  H7   single    0.970  0.020  1.090
 QCW  N05  H8   single    0.860  0.020  1.020
 QCW  C12  H9   single    0.930  0.020  1.080
 QCW  C14  H10  single    0.930  0.020  1.080
 QCW  C23  H11  single    0.930  0.020  1.080
 QCW  C25  H12  single    0.930  0.020  1.080
 QCW  C27  H13  single    0.930  0.020  1.080
 QCW  C29  H14  single    0.930  0.020  1.080

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
 QCW  H1   C10  C12  119.45  3.000
 QCW  H1   C10  C09  118.89  3.000
 QCW  C12  C10  C09  121.66  3.000
 QCW  H3   C17  H2   107.36  3.000
 QCW  H3   C17  N16  108.23  3.000
 QCW  H2   C17  N16  107.39  3.000
 QCW  H3   C17  C20  111.45  3.000
 QCW  H2   C17  C20  110.50  3.000
 QCW  N16  C17  C20  111.71  3.000
 QCW  C29  C20  C21  118.95  3.000
 QCW  C29  C20  C17  120.02  3.000
 QCW  C21  C20  C17  121.02  3.000
 QCW  H4   C21  C23  119.84  3.000
 QCW  H4   C21  C20  119.82  3.000
 QCW  C23  C21  C20  120.33  3.000
 QCW  H7   C01  H6   108.13  3.000
 QCW  H7   C01  H5   108.52  3.000
 QCW  H6   C01  H5   108.39  3.000
 QCW  H7   C01  N05  111.62  3.000
 QCW  H6   C01  N05  111.90  3.000
 QCW  H5   C01  N05  108.18  3.000
 QCW  H8   N05  C07  118.55  3.000
 QCW  H8   N05  C01  119.58  3.000
 QCW  C07  N05  C01  121.84  3.000
 QCW  C09  C07  O08  120.04  3.000
 QCW  C09  C07  N05  117.67  3.000
 QCW  O08  C07  N05  122.30  3.000
 QCW  C31  C09  C07  122.94  3.000
 QCW  C31  C09  C10  120.02  3.000
 QCW  C07  C09  C10  117.04  3.000
 QCW  H9   C12  C14  120.25  3.000
 QCW  H9   C12  C10  121.92  3.000
 QCW  C14  C12  C10  117.84  3.000
 QCW  H10  C14  N16  116.17  3.000
 QCW  H10  C14  C12  121.84  3.000
 QCW  N16  C14  C12  121.99  3.000
 QCW  C31  N16  C14  123.13  3.000
 QCW  C14  N16  C17  117.97  3.000
 QCW  C31  N16  C17  118.86  3.000
 QCW  H11  C23  C25  120.01  3.000
 QCW  H11  C23  C21  119.66  3.000
 QCW  C25  C23  C21  120.33  3.000
 QCW  H12  C25  C27  120.14  3.000
 QCW  H12  C25  C23  120.18  3.000
 QCW  C27  C25  C23  119.68  3.000
 QCW  H13  C27  C29  119.83  3.000
 QCW  H13  C27  C25  120.24  3.000
 QCW  C29  C27  C25  119.93  3.000
 QCW  H14  C29  C27  119.25  3.000
 QCW  H14  C29  C20  119.97  3.000
 QCW  C27  C29  C20  120.77  3.000
 QCW  O32  C31  N16  119.26  3.000
 QCW  N16  C31  C09  115.35  3.000
 QCW  O32  C31  C09  125.39  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
 QCW  CONST_01  C25  C23  C21  C20    0.00   0.0  0
 QCW  CONST_02  C25  C27  C29  C20    0.00   0.0  0
 QCW  CONST_03  C27  C29  C20  C21    0.00   0.0  0
 QCW  CONST_04  C27  C25  C23  C21    0.00   0.0  0
 QCW  CONST_05  C29  C20  C21  C23    0.00   0.0  0
 QCW  CONST_06  C29  C27  C25  C23    0.00   0.0  0
 QCW  CONST_07  C14  N16  C31  C09    0.00   0.0  0
 QCW  CONST_08  C23  C21  C20  C17  180.00   0.0  0
 QCW  CONST_09  C27  C29  C20  C17  180.00   0.0  0
 QCW  CONST_10  C09  C31  N16  C17  180.00   0.0  0
 QCW  CONST_11  O32  C31  N16  C14  180.00   0.0  0
 QCW  CONST_12  H11  C23  C21  C20  180.00   0.0  0
 QCW  CONST_13  H13  C27  C29  C20  180.00   0.0  0
 QCW  CONST_14  H14  C29  C20  C21  180.00   0.0  0
 QCW  CONST_15  H12  C25  C23  C21  180.00   0.0  0
 QCW  CONST_16  H4   C21  C23  C25  180.00   0.0  0
 QCW  CONST_17  O32  C31  N16  C17    0.00   0.0  0
 QCW  CONST_18  C09  C07  N05  C01  180.00   0.0  0
 QCW  CONST_19  H8   N05  C07  C09    0.00   0.0  0
 QCW  CONST_20  O08  C07  N05  C01    0.00   0.0  0
 QCW  Var_01    C31  N16  C17  C20   95.68  30.0  2
 QCW  Var_02    N16  C17  C20  C21  -79.27  30.0  2
 QCW  Var_03    O08  C07  C09  C10   -0.70  30.0  2
 QCW  Var_04    H5   C01  N05  C07  176.31  30.0  3

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
 QCW  plan-1  C17  0.020
 QCW  plan-1  C20  0.020
 QCW  plan-1  C21  0.020
 QCW  plan-1  C23  0.020
 QCW  plan-1  C25  0.020
 QCW  plan-1  C27  0.020
 QCW  plan-1  C29  0.020
 QCW  plan-1  H4   0.020
 QCW  plan-1  H11  0.020
 QCW  plan-1  H12  0.020
 QCW  plan-1  H13  0.020
 QCW  plan-1  H14  0.020
 QCW  plan-2  C10  0.020
 QCW  plan-2  C17  0.020
 QCW  plan-2  C07  0.020
 QCW  plan-2  C09  0.020
 QCW  plan-2  C12  0.020
 QCW  plan-2  C14  0.020
 QCW  plan-2  N16  0.020
 QCW  plan-2  C31  0.020
 QCW  plan-2  O32  0.020
 QCW  plan-2  H1   0.020
 QCW  plan-2  H9   0.020
 QCW  plan-2  H10  0.020
 QCW  plan-3  C01  0.020
 QCW  plan-3  N05  0.020
 QCW  plan-3  C07  0.020
 QCW  plan-3  O08  0.020
 QCW  plan-3  C09  0.020
 QCW  plan-3  H8   0.020

