# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:22:04 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: (1~{S})-2,2-bis(fluoranyl)-~{N}-[4-(3-methyl-6-oxidanylidene-2,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc2NC(=O)C=C([C@@H]3CC[C@H](CC3)NC(=O)[C@@H]4CC4(F)F)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
 NTQ  NTQ  (1~{S})-2,2-bis(fluoranyl)-~{N}-[4-(3-methyl-6-oxidanylidene-2,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]cyclopropane-1-carboxamide  ligand  45  25  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NTQ
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
 NTQ  C1   C  CH3   0  -0.770  17.1027   2.3409   1.7630
 NTQ  C2   C  CR5   0   0.371  15.9762   1.6227   1.1133
 NTQ  C5   C  CR56  0   0.517  14.1927   0.8596   0.0622
 NTQ  C6   C  CR56  0  -0.251  14.8534   2.0565   0.4063
 NTQ  C7   C  CR6   0   0.317  14.3047   3.3108  -0.0083
 NTQ  C8   C  CR16  0  -0.596  13.1532   3.2696  -0.7265
 NTQ  C12  C  CH1   0  -0.358  14.9701   4.5957   0.3997
 NTQ  C15  C  CH1   0  -0.038  15.0714   7.3983   1.3359
 NTQ  C16  C  CH2   0  -0.461  15.2379   6.2336   2.3057
 NTQ  C17  C  CH2   0  -0.431  14.5126   4.9888   1.8121
 NTQ  O20  O  O     0  -0.494  14.5801  10.1458   0.8238
 NTQ  C21  C  CH1   0  -0.553  16.4469  10.8132   2.1526
 NTQ  C23  C  CH2   0  -0.571  15.9844  12.2730   2.2568
 NTQ  N3   N  NR15  0  -0.480  15.8844   0.2908   1.1272
 NTQ  N4   N  N     0  -0.309  14.8126  -0.2143   0.4947
 NTQ  C9   C  CR6   0   0.538  12.4523   2.0425  -1.0800
 NTQ  O10  O  O     0  -0.501  11.4046   2.0226  -1.7181
 NTQ  N11  N  NR16  0  -0.735  13.0313   0.8729  -0.6518
 NTQ  C13  C  CH2   0  -0.428  14.7497   5.7666  -0.5556
 NTQ  C14  C  CH2   0  -0.438  15.5065   6.9997  -0.0737
 NTQ  N18  N  NH1   0  -0.659  15.8125   8.5419   1.8341
 NTQ  C22  C  CT    0   0.742  17.0368  11.8901   1.3239
 NTQ  F24  F  F     0  -0.315  18.3120  12.2513   1.5568
 NTQ  F25  F  F     0  -0.307  16.8207  11.9149  -0.0010
 NTQ  H1   H  HCH3  0   0.266  16.7417   3.0422   2.5145
 NTQ  H2   H  HCH3  0   0.276  17.7755   1.6436   2.2601
 NTQ  H3   H  HCH3  0   0.270  17.6846   2.9058   1.0351
 NTQ  H4   H  HCR6  0   0.260  12.6818   4.1789  -1.0734
 NTQ  H5   H  HCH1  0   0.247  16.0496   4.4139   0.4378
 NTQ  H6   H  HCH1  0   0.243  14.0135   7.6761   1.3074
 NTQ  H7   H  HCH2  0   0.227  16.3050   6.0095   2.4216
 NTQ  H8   H  HCH2  0   0.253  14.8635   6.5149   3.2925
 NTQ  H9   H  HCH2  0   0.237  13.4332   5.1712   1.7940
 NTQ  H10  H  HCH2  0   0.248  14.6738   4.1678   2.5146
 NTQ  H11  H  HCH1  0   0.317  17.0689  10.4546   2.9658
 NTQ  H12  H  HCH2  0   0.299  16.2555  12.8071   3.1576
 NTQ  H13  H  HCH2  0   0.290  15.0061  12.5005   1.8526
 NTQ  H14  H  HNR5  0   0.425  16.5483  -0.3438   1.5442
 NTQ  H15  H  HNR6  0   0.409  12.5688   0.0011  -0.8713
 NTQ  H16  H  HCH2  0   0.227  13.6840   6.0061  -0.6199
 NTQ  H17  H  HCH2  0   0.248  15.0721   5.4994  -1.5640
 NTQ  H18  H  HCH2  0   0.221  16.5828   6.7965  -0.0720
 NTQ  H19  H  HCH2  0   0.246  15.3410   7.8310  -0.7618
 NTQ  H20  H  HNH1  0   0.402  16.6313   8.3579   2.3928
 NTQ  C19  C  C     0   0.600  15.5198   9.8145   1.5318

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
 NTQ  O10  C9   double    1.227  0.020  1.227
 NTQ  C9   N11  single    1.373  0.020  1.373
 NTQ  C9   C8   single    1.457  0.020  1.457
 NTQ  N11  C5   single    1.363  0.020  1.363
 NTQ  C8   C7   double    1.358  0.020  1.358
 NTQ  C13  C14  single    1.525  0.020  1.525
 NTQ  C13  C12  single    1.527  0.020  1.527
 NTQ  C5   N4   aromatic  1.313  0.020  1.313
 NTQ  C5   C6   aromatic  1.410  0.020  1.410
 NTQ  F25  C22  single    1.343  0.020  1.343
 NTQ  N4   N3   aromatic  1.343  0.020  1.343
 NTQ  C7   C6   single    1.430  0.020  1.430
 NTQ  C7   C12  single    1.503  0.020  1.503
 NTQ  C14  C15  single    1.528  0.020  1.528
 NTQ  C6   C2   aromatic  1.396  0.020  1.396
 NTQ  C12  C17  single    1.536  0.020  1.536
 NTQ  O20  C19  double    1.222  0.020  1.222
 NTQ  N3   C2   aromatic  1.335  0.020  1.335
 NTQ  C2   C1   single    1.486  0.020  1.486
 NTQ  C22  F24  single    1.346  0.020  1.346
 NTQ  C22  C23  single    1.458  0.020  1.458
 NTQ  C22  C21  single    1.481  0.020  1.481
 NTQ  C15  N18  single    1.451  0.020  1.451
 NTQ  C15  C16  single    1.525  0.020  1.525
 NTQ  C19  N18  single    1.340  0.020  1.340
 NTQ  C19  C21  single    1.497  0.020  1.497
 NTQ  C23  C21  single    1.535  0.020  1.535
 NTQ  C17  C16  single    1.523  0.020  1.523
 NTQ  C1   H1   single    0.970  0.020  1.090
 NTQ  C1   H2   single    0.970  0.020  1.090
 NTQ  C1   H3   single    0.970  0.020  1.090
 NTQ  C8   H4   single    0.930  0.020  1.080
 NTQ  C12  H5   single    0.970  0.020  1.090
 NTQ  C15  H6   single    0.970  0.020  1.090
 NTQ  C16  H7   single    0.970  0.020  1.090
 NTQ  C16  H8   single    0.970  0.020  1.090
 NTQ  C17  H9   single    0.970  0.020  1.090
 NTQ  C17  H10  single    0.970  0.020  1.090
 NTQ  C21  H11  single    0.970  0.020  1.090
 NTQ  C23  H12  single    0.970  0.020  1.090
 NTQ  C23  H13  single    0.970  0.020  1.090
 NTQ  N3   H14  single    0.860  0.020  1.020
 NTQ  N11  H15  single    0.860  0.020  1.020
 NTQ  C13  H16  single    0.970  0.020  1.090
 NTQ  C13  H17  single    0.970  0.020  1.090
 NTQ  C14  H18  single    0.970  0.020  1.090
 NTQ  C14  H19  single    0.970  0.020  1.090
 NTQ  N18  H20  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
 NTQ  H3   C1   H2   107.88  3.000
 NTQ  H3   C1   H1   107.70  3.000
 NTQ  H2   C1   H1   107.58  3.000
 NTQ  H3   C1   C2   111.31  3.000
 NTQ  H2   C1   C2   111.01  3.000
 NTQ  H1   C1   C2   111.20  3.000
 NTQ  N3   C2   C6   105.07  3.000
 NTQ  N3   C2   C1   122.00  3.000
 NTQ  C6   C2   C1   132.94  3.000
 NTQ  N11  C5   N4   125.63  3.000
 NTQ  N4   C5   C6   113.12  3.000
 NTQ  N11  C5   C6   121.25  3.000
 NTQ  C7   C6   C5   119.60  3.000
 NTQ  C7   C6   C2   136.70  3.000
 NTQ  C5   C6   C2   103.69  3.000
 NTQ  C12  C7   C8   123.01  3.000
 NTQ  C12  C7   C6   120.06  3.000
 NTQ  C8   C7   C6   116.88  3.000
 NTQ  H4   C8   C9   114.88  3.000
 NTQ  H4   C8   C7   120.93  3.000
 NTQ  C9   C8   C7   124.19  3.000
 NTQ  H5   C12  C13  106.93  3.000
 NTQ  H5   C12  C17  107.70  3.000
 NTQ  C13  C12  C17  109.63  3.000
 NTQ  H5   C12  C7   107.69  3.000
 NTQ  C17  C12  C7   109.66  3.000
 NTQ  C13  C12  C7   114.94  3.000
 NTQ  H6   C15  N18  107.62  3.000
 NTQ  H6   C15  C14  108.51  3.000
 NTQ  N18  C15  C14  112.14  3.000
 NTQ  H6   C15  C16  108.43  3.000
 NTQ  N18  C15  C16  109.14  3.000
 NTQ  C14  C15  C16  110.87  3.000
 NTQ  H8   C16  H7   106.90  3.000
 NTQ  H8   C16  C17  109.88  3.000
 NTQ  H7   C16  C17  109.31  3.000
 NTQ  H8   C16  C15  109.91  3.000
 NTQ  H7   C16  C15  109.25  3.000
 NTQ  C17  C16  C15  111.48  3.000
 NTQ  H10  C17  H9   106.35  3.000
 NTQ  H10  C17  C16  109.60  3.000
 NTQ  H9   C17  C16  109.80  3.000
 NTQ  H10  C17  C12  110.80  3.000
 NTQ  H9   C17  C12  108.73  3.000
 NTQ  C16  C17  C12  111.43  3.000
 NTQ  H11  C21  C22  115.55  3.000
 NTQ  H11  C21  C23  115.87  3.000
 NTQ  C22  C21  C23   57.76  3.000
 NTQ  H11  C21  C19  116.44  3.000
 NTQ  C23  C21  C19  118.42  3.000
 NTQ  C22  C21  C19  119.97  3.000
 NTQ  H13  C23  H12  115.69  3.000
 NTQ  H13  C23  C22  117.95  3.000
 NTQ  H12  C23  C22  118.80  3.000
 NTQ  H13  C23  C21  116.54  3.000
 NTQ  H12  C23  C21  116.79  3.000
 NTQ  C22  C23  C21   59.28  3.000
 NTQ  H14  N3   N4   118.90  3.000
 NTQ  H14  N3   C2   125.92  3.000
 NTQ  N4   N3   C2   115.16  3.000
 NTQ  N3   N4   C5   102.96  3.000
 NTQ  N11  C9   O10  120.56  3.000
 NTQ  N11  C9   C8   116.03  3.000
 NTQ  O10  C9   C8   123.42  3.000
 NTQ  H15  N11  C9   118.27  3.000
 NTQ  H15  N11  C5   119.67  3.000
 NTQ  C9   N11  C5   122.05  3.000
 NTQ  H17  C13  H16  106.67  3.000
 NTQ  H17  C13  C14  110.07  3.000
 NTQ  H16  C13  C14  108.97  3.000
 NTQ  H17  C13  C12  110.33  3.000
 NTQ  H16  C13  C12  110.19  3.000
 NTQ  C14  C13  C12  110.53  3.000
 NTQ  H19  C14  H18  106.93  3.000
 NTQ  H19  C14  C13  109.95  3.000
 NTQ  H18  C14  C13  109.76  3.000
 NTQ  H19  C14  C15  109.85  3.000
 NTQ  H18  C14  C15  109.08  3.000
 NTQ  C13  C14  C15  111.17  3.000
 NTQ  H20  N18  C19  118.41  3.000
 NTQ  H20  N18  C15  117.47  3.000
 NTQ  C19  N18  C15  124.01  3.000
 NTQ  F25  C22  F24  108.56  3.000
 NTQ  F24  C22  C23  120.19  3.000
 NTQ  F25  C22  C23  120.70  3.000
 NTQ  C23  C22  C21   62.96  3.000
 NTQ  F24  C22  C21  118.40  3.000
 NTQ  F25  C22  C21  120.09  3.000
 NTQ  N18  C19  C21  113.86  3.000
 NTQ  C21  C19  O20  122.37  3.000
 NTQ  N18  C19  O20  123.77  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
 NTQ  CONST_01  N4   C5   C6   C2     0.00   0.0  0
 NTQ  CONST_02  C5   N4   N3   C2     0.00   0.0  0
 NTQ  CONST_03  N3   C2   C6   C5     0.00   0.0  0
 NTQ  CONST_04  N3   N4   C5   C6     0.00   0.0  0
 NTQ  CONST_05  N4   N3   C2   C6     0.00   0.0  0
 NTQ  CONST_06  C8   C9   N11  C5     0.00   0.0  0
 NTQ  CONST_07  C5   C6   C2   C1   180.00   0.0  0
 NTQ  CONST_08  C7   C6   C2   C1     0.00   0.0  0
 NTQ  CONST_09  N4   N3   C2   C1   180.00   0.0  0
 NTQ  CONST_10  O10  C9   N11  C5   180.00   0.0  0
 NTQ  CONST_11  H14  N3   N4   C5   180.00   0.0  0
 NTQ  CONST_12  H15  N11  C9   C8   180.00   0.0  0
 NTQ  CONST_13  C21  C19  N18  C15  180.00   0.0  0
 NTQ  CONST_14  O20  C19  N18  C15    0.00   0.0  0
 NTQ  CONST_15  H20  N18  C19  C21    0.00   0.0  0
 NTQ  Var_01    C15  C14  C13  C12  -58.02  30.0  1
 NTQ  Var_02    C15  C16  C17  C12   55.50  30.0  1
 NTQ  Var_03    C23  C22  C21  C19  106.61  30.0  1
 NTQ  Var_04    F25  C22  C23  C21  110.58  30.0  1
 NTQ  Var_05    C22  C21  C19  O20  -48.77  30.0  3
 NTQ  Var_06    H1   C1   C2   C6    57.82  30.0  2

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
 NTQ  chir_01  C12  C13  C7   C17  positiv
 NTQ  chir_02  C15  N18  C16  C14  positiv
 NTQ  chir_03  C21  C22  C19  C23  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
 NTQ  plan-1  C15  0.020
 NTQ  plan-1  O20  0.020
 NTQ  plan-1  C21  0.020
 NTQ  plan-1  N18  0.020
 NTQ  plan-1  H20  0.020
 NTQ  plan-1  C19  0.020
 NTQ  plan-2  C1   0.020
 NTQ  plan-2  C2   0.020
 NTQ  plan-2  C5   0.020
 NTQ  plan-2  C6   0.020
 NTQ  plan-2  C7   0.020
 NTQ  plan-2  C8   0.020
 NTQ  plan-2  C12  0.020
 NTQ  plan-2  N3   0.020
 NTQ  plan-2  N4   0.020
 NTQ  plan-2  C9   0.020
 NTQ  plan-2  O10  0.020
 NTQ  plan-2  N11  0.020
 NTQ  plan-2  H4   0.020
 NTQ  plan-2  H14  0.020
 NTQ  plan-2  H15  0.020

