# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:02:44 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[4-(3-methyl-6-oxidanylidene-1,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n[nH]c2NC(=O)C=C([C@H]3CC[C@@H](CC3)CC#N)c12
#
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
 NTW  NTW  2-[4-(3-methyl-6-oxidanylidene-1,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]ethanenitrile  ligand  38  20  .  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_NTW
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
 NTW  C2   C  CSP   0   0.116  14.2978   9.5269   2.9959
 NTW  C3   C  CH2   0  -0.532  15.2372   8.6611   2.3004
 NTW  C4   C  CH1   0  -0.248  14.5546   7.4561   1.6403
 NTW  C6   C  CH2   0  -0.422  15.5880   6.6596   0.8502
 NTW  C7   C  CH2   0  -0.430  14.9831   5.4141   0.2176
 NTW  C8   C  CH1   0  -0.350  14.3057   4.5256   1.2729
 NTW  C11  C  CH2   0  -0.427  13.8571   6.5668   2.6665
 NTW  C12  C  CR6   0   0.304  13.8101   3.2628   0.6250
 NTW  C18  C  CR56  0   0.693  14.2396   1.0846  -0.3282
 NTW  C24  C  CR56  0  -0.213  14.7229   2.2042   0.3339
 NTW  N1   N  NS    0  -0.277  13.5434  10.2068   3.5377
 NTW  C10  C  CH2   0  -0.423  13.2449   5.3291   2.0208
 NTW  C13  C  CR16  0  -0.594  12.5126   3.0923   0.2442
 NTW  C14  C  CR6   0   0.537  12.0127   1.9187  -0.4418
 NTW  O15  O  O     0  -0.497  10.8476   1.7596  -0.7882
 NTW  N16  N  NR16  0  -0.737  12.9525   0.9371  -0.7068
 NTW  N19  N  NR15  0  -0.519  15.2554   0.2363  -0.4870
 NTW  N20  N  N     0  -0.280  16.3961   0.7283   0.0382
 NTW  C22  C  CR5   0   0.200  16.1032   1.9053   0.5387
 NTW  H1   H  HCH2  0   0.300  15.9898   8.3297   3.0207
 NTW  H2   H  HCH2  0   0.312  15.7557   9.2667   1.5535
 NTW  H3   H  HCH1  0   0.246  13.8032   7.8388   0.9406
 NTW  H4   H  HCH2  0   0.222  16.4059   6.3650   1.5182
 NTW  H5   H  HCH2  0   0.245  16.0316   7.2873   0.0734
 NTW  H6   H  HCH2  0   0.235  14.2407   5.6952  -0.5362
 NTW  H7   H  HCH2  0   0.245  15.7605   4.8580  -0.3112
 NTW  H8   H  HCH1  0   0.246  15.0694   4.2423   2.0060
 NTW  H9   H  HCH2  0   0.222  14.5813   6.2639   3.4315
 NTW  H10  H  HCH2  0   0.246  13.0745   7.1261   3.1858
 NTW  H11  H  HCH3  0   0.263  18.1045   2.1775   1.2020
 NTW  H12  H  HCH3  0   0.251  17.3042   3.6758   0.7339
 NTW  H13  H  HCH3  0   0.254  16.8975   2.9048   2.2598
 NTW  H14  H  HCH2  0   0.225  12.4504   5.6433   1.3367
 NTW  H15  H  HCH2  0   0.247  12.7728   4.7074   2.7850
 NTW  H16  H  HCR6  0   0.262  11.7721   3.8560   0.4361
 NTW  H17  H  HNR6  0   0.421  12.6449   0.1007  -1.1849
 NTW  H18  H  HNR5  0   0.425  15.2534  -0.6660  -0.9351
 NTW  C23  C  CH3   0  -0.767  17.1551   2.7101   1.2184

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
 NTW  O15  C14  double    1.226  0.020  1.226
 NTW  N16  C14  single    1.385  0.020  1.385
 NTW  N16  C18  single    1.350  0.020  1.350
 NTW  C14  C13  single    1.448  0.020  1.448
 NTW  C18  N19  aromatic  1.333  0.020  1.333
 NTW  C18  C24  aromatic  1.388  0.020  1.388
 NTW  C13  C12  double    1.363  0.020  1.363
 NTW  N19  N20  aromatic  1.349  0.020  1.349
 NTW  C7   C6   single    1.522  0.020  1.522
 NTW  C7   C8   single    1.537  0.020  1.537
 NTW  C24  C12  single    1.428  0.020  1.428
 NTW  C24  C22  aromatic  1.427  0.020  1.427
 NTW  C12  C8   single    1.503  0.020  1.503
 NTW  N20  C22  aromatic  1.312  0.020  1.312
 NTW  C6   C4   single    1.525  0.020  1.525
 NTW  C22  C23  single    1.489  0.020  1.489
 NTW  C8   C10  single    1.527  0.020  1.527
 NTW  C4   C3   single    1.534  0.020  1.534
 NTW  C4   C11  single    1.527  0.020  1.527
 NTW  C10  C11  single    1.524  0.020  1.524
 NTW  C3   C2   single    1.455  0.020  1.455
 NTW  C2   N1   triple    1.151  0.020  1.151
 NTW  C3   H1   single    0.970  0.020  1.090
 NTW  C3   H2   single    0.970  0.020  1.090
 NTW  C4   H3   single    0.970  0.020  1.090
 NTW  C6   H4   single    0.970  0.020  1.090
 NTW  C6   H5   single    0.970  0.020  1.090
 NTW  C7   H6   single    0.970  0.020  1.090
 NTW  C7   H7   single    0.970  0.020  1.090
 NTW  C8   H8   single    0.970  0.020  1.090
 NTW  C11  H9   single    0.970  0.020  1.090
 NTW  C11  H10  single    0.970  0.020  1.090
 NTW  C23  H11  single    0.970  0.020  1.090
 NTW  C23  H12  single    0.970  0.020  1.090
 NTW  C23  H13  single    0.970  0.020  1.090
 NTW  C10  H14  single    0.970  0.020  1.090
 NTW  C10  H15  single    0.970  0.020  1.090
 NTW  C13  H16  single    0.930  0.020  1.080
 NTW  N16  H17  single    0.860  0.020  1.020
 NTW  N19  H18  single    0.860  0.020  1.020

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
 NTW  N1   C2   C3   180.00  3.000
 NTW  H2   C3   H1   106.96  3.000
 NTW  H2   C3   C4   110.64  3.000
 NTW  H1   C3   C4   110.60  3.000
 NTW  H2   C3   C2   107.66  3.000
 NTW  H1   C3   C2   108.06  3.000
 NTW  C4   C3   C2   112.70  3.000
 NTW  H3   C4   C11  108.63  3.000
 NTW  H3   C4   C6   108.43  3.000
 NTW  C11  C4   C6   110.70  3.000
 NTW  H3   C4   C3   107.79  3.000
 NTW  C11  C4   C3   111.82  3.000
 NTW  C6   C4   C3   109.36  3.000
 NTW  H5   C6   H4   106.54  3.000
 NTW  H5   C6   C7   109.63  3.000
 NTW  H4   C6   C7   109.26  3.000
 NTW  H5   C6   C4   110.08  3.000
 NTW  H4   C6   C4   109.28  3.000
 NTW  C7   C6   C4   111.92  3.000
 NTW  H7   C7   H6   106.26  3.000
 NTW  H7   C7   C8   110.60  3.000
 NTW  H6   C7   C8   108.81  3.000
 NTW  H7   C7   C6   109.56  3.000
 NTW  H6   C7   C6   110.21  3.000
 NTW  C8   C7   C6   111.27  3.000
 NTW  H8   C8   C10  107.01  3.000
 NTW  H8   C8   C12  107.51  3.000
 NTW  C10  C8   C12  115.10  3.000
 NTW  H8   C8   C7   107.55  3.000
 NTW  C10  C8   C7   109.78  3.000
 NTW  C12  C8   C7   109.57  3.000
 NTW  H10  C11  H9   106.43  3.000
 NTW  H10  C11  C10  109.22  3.000
 NTW  H9   C11  C10  109.67  3.000
 NTW  H10  C11  C4   110.39  3.000
 NTW  H9   C11  C4   109.16  3.000
 NTW  C10  C11  C4   111.83  3.000
 NTW  C13  C12  C24  117.31  3.000
 NTW  C24  C12  C8   119.99  3.000
 NTW  C13  C12  C8   122.64  3.000
 NTW  N19  C18  N16  128.59  3.000
 NTW  N19  C18  C24  107.76  3.000
 NTW  N16  C18  C24  123.65  3.000
 NTW  C22  C24  C18  103.67  3.000
 NTW  C22  C24  C12  138.10  3.000
 NTW  C18  C24  C12  118.22  3.000
 NTW  H15  C10  H14  106.67  3.000
 NTW  H15  C10  C11  109.84  3.000
 NTW  H14  C10  C11  108.86  3.000
 NTW  H15  C10  C8   110.09  3.000
 NTW  H14  C10  C8   110.44  3.000
 NTW  C11  C10  C8   110.84  3.000
 NTW  H16  C13  C14  114.84  3.000
 NTW  H16  C13  C12  120.94  3.000
 NTW  C14  C13  C12  124.21  3.000
 NTW  N16  C14  O15  119.93  3.000
 NTW  N16  C14  C13  115.52  3.000
 NTW  O15  C14  C13  124.54  3.000
 NTW  H17  N16  C14  118.06  3.000
 NTW  H17  N16  C18  120.87  3.000
 NTW  C14  N16  C18  121.07  3.000
 NTW  H18  N19  N20  120.11  3.000
 NTW  H18  N19  C18  128.43  3.000
 NTW  N20  N19  C18  111.47  3.000
 NTW  C22  N20  N19  106.68  3.000
 NTW  N20  C22  C24  110.43  3.000
 NTW  N20  C22  C23  120.09  3.000
 NTW  C24  C22  C23  129.48  3.000
 NTW  H13  C23  H12  107.37  3.000
 NTW  H13  C23  H11  107.93  3.000
 NTW  H12  C23  H11  107.90  3.000
 NTW  H13  C23  C22  111.44  3.000
 NTW  H12  C23  C22  111.86  3.000
 NTW  H11  C23  C22  110.17  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
 NTW  CONST_01  C22  N20  N19  C18     0.00   0.0  0
 NTW  CONST_02  N20  C22  C24  C18     0.00   0.0  0
 NTW  CONST_03  N20  N19  C18  C24     0.00   0.0  0
 NTW  CONST_04  N19  N20  C22  C24     0.00   0.0  0
 NTW  CONST_05  C22  C24  C18  N19     0.00   0.0  0
 NTW  CONST_06  C13  C14  N16  C18     0.00   0.0  0
 NTW  CONST_07  C23  C22  C24  C12     0.00   0.0  0
 NTW  CONST_08  C23  C22  C24  C18   180.00   0.0  0
 NTW  CONST_09  N19  N20  C22  C23   180.00   0.0  0
 NTW  CONST_10  O15  C14  N16  C18   180.00   0.0  0
 NTW  CONST_11  H18  N19  C18  C24   180.00   0.0  0
 NTW  CONST_12  H17  N16  C14  C13   180.00   0.0  0
 NTW  Var_01    C8   C7   C6   C4    -55.65  30.0  1
 NTW  Var_02    C8   C10  C11  C4     57.00  30.0  1
 NTW  Var_03    H11  C23  C22  C24   179.58  30.0  2
 NTW  Var_04    H1   C3   C2   N1   -145.19  30.0  1

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
 NTW  chir_01  C4  C6   C3   C11  positiv
 NTW  chir_02  C8  C10  C12  C7   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
 NTW  plan-1  C8   0.020
 NTW  plan-1  C12  0.020
 NTW  plan-1  C18  0.020
 NTW  plan-1  C24  0.020
 NTW  plan-1  C13  0.020
 NTW  plan-1  C14  0.020
 NTW  plan-1  O15  0.020
 NTW  plan-1  N16  0.020
 NTW  plan-1  N19  0.020
 NTW  plan-1  N20  0.020
 NTW  plan-1  C22  0.020
 NTW  plan-1  H16  0.020
 NTW  plan-1  H17  0.020
 NTW  plan-1  H18  0.020
 NTW  plan-1  C23  0.020

