# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 09:41:41 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: ~{N}-[(1-azanylcyclohexyl)methyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=CC1=O)C(=O)NCC2(N)CCCCC2
#
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
 D9T  D9T  ~{N}-[(1-azanylcyclohexyl)methyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide  ligand  40  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D9T
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
 D9T  C13  C  CR6   0   0.049  -2.8587   0.2813  -0.0570
 D9T  C15  C  C     0  -0.424  -3.0614  -0.9637   0.8279
 D9T  C17  C  C     0  -0.427  -5.5297  -0.9986   0.3351
 D9T  C01  C  CH3   0  -0.521   5.4308   1.0010  -0.3848
 D9T  C03  C  CR16  0   0.076   3.0118   0.9158  -0.2047
 D9T  C04  C  CR6   0  -0.204   1.8224   0.2955   0.0467
 D9T  C05  C  CR16  0  -0.137   1.8677  -1.0855   0.3648
 D9T  C06  C  CR16  0  -0.451   3.0505  -1.7462   0.4188
 D9T  C07  C  CR6   0   0.568   4.3014  -1.0834   0.1705
 D9T  C09  C  C     0   0.527   0.5762   1.0946  -0.0759
 D9T  C12  C  CH2   0  -0.247  -1.8048   1.2065   0.5652
 D9T  C16  C  C     0  -0.440  -4.2448  -1.8183   0.3817
 D9T  C18  C  C     0  -0.449  -5.3655   0.2244  -0.5602
 D9T  C19  C  C     0  -0.402  -4.1711   1.0710  -0.1289
 D9T  N02  N  NR6   0  -0.505   4.1923   0.2757  -0.1338
 D9T  N11  N  NH1   0  -0.669  -0.4850   0.6185   0.6041
 D9T  N14  N  NH2   0  -0.798  -2.4211  -0.0390  -1.4119
 D9T  O08  O  O     0  -0.501   5.4045  -1.6148   0.2045
 D9T  O10  O  O     0  -0.488   0.5439   2.1142  -0.7528
 D9T  H1   H  H     0   0.222  -2.1494  -1.5701   0.8274
 D9T  H2   H  H     0   0.212  -3.2267  -0.6476   1.8643
 D9T  H3   H  H     0   0.228  -6.3626  -1.6140  -0.0128
 D9T  H4   H  H     0   0.209  -5.7833  -0.6705   1.3491
 D9T  H5   H  HCH3  0   0.265   6.0928   0.9264   0.4743
 D9T  H6   H  HCH3  0   0.265   5.9392   0.5970  -1.2576
 D9T  H7   H  HCH3  0   0.261   5.1990   2.0462  -0.5623
 D9T  H8   H  HCR6  0   0.312   3.0555   1.9644  -0.4637
 D9T  H9   H  HCR6  0   0.269   0.9546  -1.6412   0.5405
 D9T  H10  H  HCR6  0   0.280   3.0888  -2.8034   0.6414
 D9T  H11  H  HCH2  0   0.253  -1.7493   2.1295  -0.0100
 D9T  H12  H  HCH2  0   0.243  -2.1108   1.4678   1.5817
 D9T  H13  H  H     0   0.207  -4.0466  -2.2475  -0.6063
 D9T  H14  H  H     0   0.233  -4.3579  -2.6666   1.0604
 D9T  H15  H  H     0   0.212  -5.2551  -0.0951  -1.6019
 D9T  H16  H  H     0   0.234  -6.2695   0.8376  -0.5344
 D9T  H17  H  H     0   0.216  -4.3818   1.4900   0.8614
 D9T  H18  H  H     0   0.230  -4.0411   1.9180  -0.8083
 D9T  H19  H  HNH1  0   0.407  -0.3311  -0.1082   1.2837
 D9T  H20  H  HNH2  0   0.338  -1.5686  -0.5868  -1.3724
 D9T  H21  H  HNH2  0   0.345  -3.0973  -0.6361  -1.8710

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
 D9T  O10  C09  double  1.224  0.020  1.224
 D9T  C09  N11  single  1.347  0.020  1.347
 D9T  C09  C04  single  1.485  0.020  1.485
 D9T  N14  C13  single  1.459  0.020  1.459
 D9T  C12  N11  single  1.445  0.020  1.445
 D9T  C12  C13  single  1.534  0.020  1.534
 D9T  C04  C03  double  1.365  0.020  1.365
 D9T  C04  C05  single  1.418  0.020  1.418
 D9T  C03  N02  single  1.345  0.020  1.345
 D9T  C15  C13  single  1.541  0.020  1.541
 D9T  C15  C16  single  1.526  0.020  1.526
 D9T  C05  C06  double  1.356  0.020  1.356
 D9T  C13  C19  single  1.533  0.020  1.533
 D9T  N02  C01  single  1.457  0.020  1.457
 D9T  N02  C07  single  1.397  0.020  1.397
 D9T  C06  C07  single  1.437  0.020  1.437
 D9T  C07  O08  double  1.225  0.020  1.225
 D9T  C16  C17  single  1.525  0.020  1.525
 D9T  C19  C18  single  1.526  0.020  1.526
 D9T  C17  C18  single  1.525  0.020  1.525
 D9T  C15  H1   single  0.970  0.020  1.090
 D9T  C15  H2   single  0.970  0.020  1.090
 D9T  C17  H3   single  0.970  0.020  1.090
 D9T  C17  H4   single  0.970  0.020  1.090
 D9T  C01  H5   single  0.970  0.020  1.090
 D9T  C01  H6   single  0.970  0.020  1.090
 D9T  C01  H7   single  0.970  0.020  1.090
 D9T  C03  H8   single  0.930  0.020  1.080
 D9T  C05  H9   single  0.930  0.020  1.080
 D9T  C06  H10  single  0.930  0.020  1.080
 D9T  C12  H11  single  0.970  0.020  1.090
 D9T  C12  H12  single  0.970  0.020  1.090
 D9T  C16  H13  single  0.970  0.020  1.090
 D9T  C16  H14  single  0.970  0.020  1.090
 D9T  C18  H15  single  0.970  0.020  1.090
 D9T  C18  H16  single  0.970  0.020  1.090
 D9T  C19  H17  single  0.970  0.020  1.090
 D9T  C19  H18  single  0.970  0.020  1.090
 D9T  N11  H19  single  0.860  0.020  1.020
 D9T  N14  H20  single  0.890  0.020  1.040
 D9T  N14  H21  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
 D9T  N14  C13  C19  109.03  3.000
 D9T  C19  C13  C12  107.24  3.000
 D9T  N14  C13  C12  107.64  3.000
 D9T  C19  C13  C15  109.29  3.000
 D9T  C12  C13  C15  110.17  3.000
 D9T  N14  C13  C15  113.28  3.000
 D9T  H2   C15  H1   106.60  3.000
 D9T  H2   C15  C16  108.72  3.000
 D9T  H1   C15  C16  109.60  3.000
 D9T  H2   C15  C13  109.26  3.000
 D9T  H1   C15  C13  109.73  3.000
 D9T  C16  C15  C13  112.74  3.000
 D9T  H4   C17  H3   106.68  3.000
 D9T  H4   C17  C18  109.16  3.000
 D9T  H3   C17  C18  110.30  3.000
 D9T  H4   C17  C16  109.13  3.000
 D9T  H3   C17  C16  110.45  3.000
 D9T  C18  C17  C16  111.00  3.000
 D9T  H7   C01  H6   109.05  3.000
 D9T  H7   C01  H5   109.00  3.000
 D9T  H6   C01  H5   108.90  3.000
 D9T  H7   C01  N02  109.03  3.000
 D9T  H6   C01  N02  110.52  3.000
 D9T  H5   C01  N02  110.31  3.000
 D9T  H8   C03  N02  116.03  3.000
 D9T  H8   C03  C04  121.35  3.000
 D9T  N02  C03  C04  122.61  3.000
 D9T  C09  C04  C05  124.70  3.000
 D9T  C05  C04  C03  117.14  3.000
 D9T  C09  C04  C03  118.13  3.000
 D9T  H9   C05  C06  118.61  3.000
 D9T  H9   C05  C04  120.60  3.000
 D9T  C06  C05  C04  120.76  3.000
 D9T  H10  C06  C07  117.11  3.000
 D9T  H10  C06  C05  121.04  3.000
 D9T  C07  C06  C05  121.85  3.000
 D9T  O08  C07  N02  119.90  3.000
 D9T  O08  C07  C06  125.38  3.000
 D9T  N02  C07  C06  114.72  3.000
 D9T  O10  C09  N11  123.54  3.000
 D9T  N11  C09  C04  115.41  3.000
 D9T  O10  C09  C04  121.05  3.000
 D9T  H12  C12  H11  107.62  3.000
 D9T  H12  C12  N11  109.13  3.000
 D9T  H11  C12  N11  108.21  3.000
 D9T  H12  C12  C13  109.21  3.000
 D9T  H11  C12  C13  109.39  3.000
 D9T  N11  C12  C13  113.13  3.000
 D9T  H14  C16  H13  105.96  3.000
 D9T  H14  C16  C17  110.44  3.000
 D9T  H13  C16  C17  109.61  3.000
 D9T  H14  C16  C15  109.48  3.000
 D9T  H13  C16  C15  110.04  3.000
 D9T  C17  C16  C15  111.18  3.000
 D9T  H16  C18  H15  105.64  3.000
 D9T  H16  C18  C19  109.24  3.000
 D9T  H15  C18  C19  110.59  3.000
 D9T  H16  C18  C17  110.32  3.000
 D9T  H15  C18  C17  109.60  3.000
 D9T  C19  C18  C17  111.31  3.000
 D9T  H18  C19  H17  106.75  3.000
 D9T  H18  C19  C18  110.31  3.000
 D9T  H17  C19  C18  108.48  3.000
 D9T  H18  C19  C13  109.04  3.000
 D9T  H17  C19  C13  108.61  3.000
 D9T  C18  C19  C13  113.42  3.000
 D9T  C07  N02  C03  122.90  3.000
 D9T  C07  N02  C01  117.09  3.000
 D9T  C03  N02  C01  120.01  3.000
 D9T  H19  N11  C12  116.83  3.000
 D9T  H19  N11  C09  118.38  3.000
 D9T  C12  N11  C09  124.19  3.000
 D9T  H21  N14  H20  105.11  3.000
 D9T  H21  N14  C13  110.50  3.000
 D9T  H20  N14  C13  109.53  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
 D9T  CONST_01  C06  C07  N02  C03    0.00   0.0  0
 D9T  CONST_02  C06  C07  N02  C01  180.00   0.0  0
 D9T  CONST_03  O08  C07  N02  C03  180.00   0.0  0
 D9T  CONST_04  O08  C07  N02  C01    0.00   0.0  0
 D9T  CONST_05  C12  N11  C09  C04  180.00   0.0  0
 D9T  CONST_06  H19  N11  C09  C04    0.00   0.0  0
 D9T  CONST_07  O10  C09  N11  C12    0.00   0.0  0
 D9T  Var_01    C17  C16  C15  C13  -56.02  30.0  1
 D9T  Var_02    C17  C18  C19  C13   54.79  30.0  1
 D9T  Var_03    C18  C17  C16  C15   55.71  30.0  1
 D9T  Var_04    C19  C18  C17  C16  -54.90  30.0  1
 D9T  Var_05    O10  C09  C04  C03   22.00  30.0  2
 D9T  Var_06    H5   C01  N02  C03  122.41  30.0  3
 D9T  Var_07    C09  N11  C12  C13  115.60  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
 D9T  chir_01  C13  C12  C15  C19  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
 D9T  plan-1  C01  0.020
 D9T  plan-1  C03  0.020
 D9T  plan-1  C04  0.020
 D9T  plan-1  C05  0.020
 D9T  plan-1  C06  0.020
 D9T  plan-1  C07  0.020
 D9T  plan-1  C09  0.020
 D9T  plan-1  N02  0.020
 D9T  plan-1  O08  0.020
 D9T  plan-1  H8   0.020
 D9T  plan-1  H9   0.020
 D9T  plan-1  H10  0.020
 D9T  plan-2  C04  0.020
 D9T  plan-2  C09  0.020
 D9T  plan-2  C12  0.020
 D9T  plan-2  N11  0.020
 D9T  plan-2  O10  0.020
 D9T  plan-2  H19  0.020

