# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:50:24 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1C(=O)n2ncc(C#N)c2N=C1c3cnn(c3)C4CCN(CC4)C(=O)C=C
#
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
 B7K  B7K  7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  53  30  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B7K
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
 B7K  N    N  NR5   0  -0.438   4.4431   0.7307  -0.2149
 B7K  C    C  C     0   0.610   4.5419  -0.6466  -0.3814
 B7K  O    O  O     0  -0.370   5.5970  -1.1856  -0.5687
 B7K  C1   C  CR5   0   0.710   3.2521   1.3982  -0.1974
 B7K  C10  C  CR5   0  -0.215   0.7490  -1.1180  -0.6641
 B7K  C11  C  CR15  0   0.105  -0.4945  -0.4991  -0.6947
 B7K  C12  C  CH1   0  -0.081  -2.8387  -1.3325  -1.0113
 B7K  C13  C  CH2   0  -0.459  -3.2919   0.0016  -1.5870
 B7K  C14  C  CH2   0  -0.325  -4.8160   0.0591  -1.5945
 B7K  C16  C  C1    0  -0.333  -6.4650   0.6372   1.7708
 B7K  C17  C  C2    0  -0.468  -7.2857   1.5010   2.3593
 B7K  C18  C  CH2   0  -0.329  -4.9653  -1.4280   0.2986
 B7K  C19  C  CH2   0  -0.424  -3.4492  -1.5639   0.3685
 B7K  C2   C  CR5   0  -0.319   3.5854   2.7291  -0.0562
 B7K  C20  C  CR15  0  -0.062   0.4579  -2.4758  -0.9294
 B7K  C3   C  CSP   0   0.002   2.6899   3.8125   0.0011
 B7K  C4   C  CR15  0   0.037   5.0066   2.7468  -0.0066
 B7K  C5   C  CH1   0  -0.530   3.2210  -1.3574  -0.2352
 B7K  C6   C  CH1   0  -0.245   3.1375  -2.0419   1.1765
 B7K  C7   C  CH3   0  -0.652   4.1170  -3.2018   1.3045
 B7K  C8   C  CH3   0  -0.680   3.2886  -1.0503   2.3236
 B7K  C9   C  C     0   0.272   2.0138  -0.4773  -0.4313
 B7K  N1   N  N     0  -0.451   2.0456   0.8122  -0.3583
 B7K  N2   N  NS    0  -0.245   1.9603   4.7043   0.0483
 B7K  N3   N  N     0  -0.253   5.5094   1.5507  -0.1123
 B7K  N4   N  NR5   0  -0.289  -1.3880  -1.4476  -0.9622
 B7K  N5   N  NT    0  -0.465  -5.3425  -0.1400  -0.2549
 B7K  N6   N  N     0  -0.266  -0.8285  -2.6568  -1.1052
 B7K  O1   O  O     0  -0.503  -6.2747   1.9111  -0.2027
 B7K  H1   H  HCR5  0   0.312  -0.7600   0.5322  -0.5334
 B7K  H2   H  HCH1  0   0.279  -3.1675  -2.1296  -1.6828
 B7K  H3   H  HCH2  0   0.247  -2.9129   0.8385  -0.9942
 B7K  H4   H  HCH2  0   0.270  -2.9216   0.1226  -2.6068
 B7K  H5   H  HCH2  0   0.280  -5.1544   1.0134  -1.9849
 B7K  H6   H  HCH2  0   0.251  -5.2143  -0.7247  -2.2471
 B7K  H7   H  H     0   0.272  -6.1201  -0.2183   2.3335
 B7K  H8   H  H     0   0.257  -7.6633   2.3764   1.8483
 B7K  H9   H  H     0   0.261  -7.6077   1.3510   3.3804
 B7K  H10  H  HCH2  0   0.257  -5.3757  -2.2122  -0.3460
 B7K  H11  H  HCH2  0   0.279  -5.3959  -1.5873   1.2806
 B7K  H12  H  HCH2  0   0.264  -3.1947  -2.5613   0.7315
 B7K  H13  H  HCH2  0   0.246  -3.0449  -0.8387   1.0803
 B7K  H14  H  HCR5  0   0.277   1.1384  -3.3101  -1.0153
 B7K  H15  H  HCR5  0   0.305   5.6443   3.6102   0.1030
 B7K  H16  H  HCH1  0   0.337   3.2054  -2.1555  -0.9826
 B7K  H17  H  HCH1  0   0.274   2.1296  -2.4610   1.2254
 B7K  H18  H  HCH3  0   0.237   4.0303  -3.8943   0.4665
 B7K  H19  H  HCH3  0   0.235   5.1520  -2.8674   1.3652
 B7K  H20  H  HCH3  0   0.244   3.8987  -3.7552   2.2183
 B7K  H21  H  HCH3  0   0.243   2.5652  -0.2355   2.2739
 B7K  H22  H  HCH3  0   0.259   3.1265  -1.5641   3.2709
 B7K  H23  H  HCH3  0   0.234   4.2899  -0.6170   2.3645
 B7K  C15  C  C     0   0.544  -6.0194   0.8548   0.3659

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
 B7K  C13  C12  single    1.522  0.020  1.522
 B7K  C13  C14  single    1.525  0.020  1.525
 B7K  C12  C19  single    1.527  0.020  1.527
 B7K  C12  N4   single    1.456  0.020  1.456
 B7K  C16  C17  double    1.329  0.020  1.329
 B7K  C16  C15  single    1.490  0.020  1.490
 B7K  N6   N4   aromatic  1.340  0.020  1.340
 B7K  N6   C20  aromatic  1.311  0.020  1.311
 B7K  C19  C18  single    1.524  0.020  1.524
 B7K  O1   C15  double    1.226  0.020  1.226
 B7K  C15  N5   single    1.354  0.020  1.354
 B7K  C14  N5   single    1.453  0.020  1.453
 B7K  N4   C11  aromatic  1.330  0.020  1.330
 B7K  N5   C18  single    1.452  0.020  1.452
 B7K  C20  C10  aromatic  1.414  0.020  1.414
 B7K  C11  C10  aromatic  1.389  0.020  1.389
 B7K  C10  C9   single    1.437  0.020  1.437
 B7K  N2   C3   triple    1.153  0.020  1.153
 B7K  C7   C6   single    1.524  0.020  1.524
 B7K  C3   C2   single    1.407  0.020  1.407
 B7K  N1   C9   double    1.292  0.020  1.292
 B7K  N1   C1   single    1.351  0.020  1.351
 B7K  C9   C5   single    1.507  0.020  1.507
 B7K  C1   C2   aromatic  1.379  0.020  1.379
 B7K  C1   N    aromatic  1.365  0.020  1.365
 B7K  C2   C4   aromatic  1.422  0.020  1.422
 B7K  C5   C6   single    1.571  0.020  1.571
 B7K  C5   C    single    1.507  0.020  1.507
 B7K  C6   C8   single    1.524  0.020  1.524
 B7K  N    C    single    1.391  0.020  1.391
 B7K  N    N3   aromatic  1.349  0.020  1.349
 B7K  C    O    double    1.199  0.020  1.199
 B7K  C4   N3   aromatic  1.302  0.020  1.302
 B7K  C11  H1   single    0.930  0.020  1.080
 B7K  C12  H2   single    0.970  0.020  1.090
 B7K  C13  H3   single    0.970  0.020  1.090
 B7K  C13  H4   single    0.970  0.020  1.090
 B7K  C14  H5   single    0.970  0.020  1.090
 B7K  C14  H6   single    0.970  0.020  1.090
 B7K  C16  H7   single    0.930  0.020  1.080
 B7K  C17  H8   single    0.930  0.020  1.080
 B7K  C17  H9   single    0.930  0.020  1.080
 B7K  C18  H10  single    0.970  0.020  1.090
 B7K  C18  H11  single    0.970  0.020  1.090
 B7K  C19  H12  single    0.970  0.020  1.090
 B7K  C19  H13  single    0.970  0.020  1.090
 B7K  C20  H14  single    0.930  0.020  1.080
 B7K  C4   H15  single    0.930  0.020  1.080
 B7K  C5   H16  single    0.970  0.020  1.090
 B7K  C6   H17  single    0.970  0.020  1.090
 B7K  C7   H18  single    0.970  0.020  1.090
 B7K  C7   H19  single    0.970  0.020  1.090
 B7K  C7   H20  single    0.970  0.020  1.090
 B7K  C8   H21  single    0.970  0.020  1.090
 B7K  C8   H22  single    0.970  0.020  1.090
 B7K  C8   H23  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
 B7K  N3   N    C1   113.04  3.000
 B7K  N3   N    C    123.70  3.000
 B7K  C1   N    C    123.20  3.000
 B7K  C5   C    O    125.04  3.000
 B7K  O    C    N    121.75  3.000
 B7K  C5   C    N    113.15  3.000
 B7K  N1   C1   C2   130.28  3.000
 B7K  C2   C1   N    105.20  3.000
 B7K  N1   C1   N    124.43  3.000
 B7K  C9   C10  C20  129.79  3.000
 B7K  C9   C10  C11  126.36  3.000
 B7K  C20  C10  C11  103.85  3.000
 B7K  H1   C11  N4   123.18  3.000
 B7K  H1   C11  C10  130.08  3.000
 B7K  N4   C11  C10  106.74  3.000
 B7K  H2   C12  N4   105.24  3.000
 B7K  H2   C12  C19  108.93  3.000
 B7K  N4   C12  C19  110.86  3.000
 B7K  H2   C12  C13  108.50  3.000
 B7K  N4   C12  C13  112.25  3.000
 B7K  C19  C12  C13  110.83  3.000
 B7K  H4   C13  H3   107.71  3.000
 B7K  H4   C13  C14  109.28  3.000
 B7K  H3   C13  C14  108.67  3.000
 B7K  H4   C13  C12  110.45  3.000
 B7K  H3   C13  C12  111.26  3.000
 B7K  C14  C13  C12  109.42  3.000
 B7K  H6   C14  H5   107.56  3.000
 B7K  H6   C14  N5   108.64  3.000
 B7K  H5   C14  N5   109.83  3.000
 B7K  H6   C14  C13  109.84  3.000
 B7K  H5   C14  C13  110.27  3.000
 B7K  N5   C14  C13  110.63  3.000
 B7K  H7   C16  C17  118.77  3.000
 B7K  H7   C16  C15  120.74  3.000
 B7K  C17  C16  C15  120.49  3.000
 B7K  H9   C17  H8   117.03  3.000
 B7K  H9   C17  C16  120.80  3.000
 B7K  H8   C17  C16  122.17  3.000
 B7K  H11  C18  H10  106.21  3.000
 B7K  H11  C18  N5   111.87  3.000
 B7K  H10  C18  N5   108.28  3.000
 B7K  H11  C18  C19  109.91  3.000
 B7K  H10  C18  C19  109.64  3.000
 B7K  N5   C18  C19  110.80  3.000
 B7K  H13  C19  H12  107.66  3.000
 B7K  H13  C19  C18  109.79  3.000
 B7K  H12  C19  C18  109.19  3.000
 B7K  H13  C19  C12  109.87  3.000
 B7K  H12  C19  C12  110.23  3.000
 B7K  C18  C19  C12  110.06  3.000
 B7K  C4   C2   C3   128.69  3.000
 B7K  C4   C2   C1   104.89  3.000
 B7K  C3   C2   C1   126.40  3.000
 B7K  H14  C20  N6   120.07  3.000
 B7K  H14  C20  C10  128.83  3.000
 B7K  N6   C20  C10  111.09  3.000
 B7K  N2   C3   C2   180.00  3.000
 B7K  H15  C4   N3   121.01  3.000
 B7K  H15  C4   C2   127.17  3.000
 B7K  N3   C4   C2   111.82  3.000
 B7K  H16  C5   C9   109.02  3.000
 B7K  H16  C5   C6   107.18  3.000
 B7K  C9   C5   C6   109.20  3.000
 B7K  H16  C5   C    106.88  3.000
 B7K  C6   C5   C    109.83  3.000
 B7K  C9   C5   C    114.46  3.000
 B7K  H17  C6   C8   107.90  3.000
 B7K  H17  C6   C7   107.29  3.000
 B7K  C8   C6   C7   111.62  3.000
 B7K  H17  C6   C5   104.86  3.000
 B7K  C8   C6   C5   112.81  3.000
 B7K  C7   C6   C5   111.90  3.000
 B7K  H20  C7   H19  107.42  3.000
 B7K  H20  C7   H18  107.81  3.000
 B7K  H19  C7   H18  108.26  3.000
 B7K  H20  C7   C6   109.15  3.000
 B7K  H19  C7   C6   112.44  3.000
 B7K  H18  C7   C6   111.58  3.000
 B7K  H23  C8   H22  106.91  3.000
 B7K  H23  C8   H21  108.26  3.000
 B7K  H22  C8   H21  107.05  3.000
 B7K  H23  C8   C6   112.17  3.000
 B7K  H22  C8   C6   109.45  3.000
 B7K  H21  C8   C6   112.71  3.000
 B7K  N1   C9   C5   123.77  3.000
 B7K  C5   C9   C10  117.77  3.000
 B7K  N1   C9   C10  118.42  3.000
 B7K  C9   N1   C1   117.50  3.000
 B7K  C4   N3   N    105.03  3.000
 B7K  N6   N4   C12  118.93  3.000
 B7K  N6   N4   C11  112.61  3.000
 B7K  C12  N4   C11  128.29  3.000
 B7K  C18  N5   C15  127.37  3.000
 B7K  C18  N5   C14  112.27  3.000
 B7K  C15  N5   C14  120.21  3.000
 B7K  N4   N6   C20  105.72  3.000
 B7K  O1   C15  N5   121.63  3.000
 B7K  N5   C15  C16  118.33  3.000
 B7K  O1   C15  C16  120.04  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
 B7K  CONST_01  C4   C2   C1   N       0.00   0.0  0
 B7K  CONST_02  C2   C4   N3   N       0.00   0.0  0
 B7K  CONST_03  N3   C4   C2   C1      0.00   0.0  0
 B7K  CONST_04  C4   N3   N    C1      0.00   0.0  0
 B7K  CONST_05  N4   N6   C20  C10     0.00   0.0  0
 B7K  CONST_06  N6   N4   C11  C10     0.00   0.0  0
 B7K  CONST_07  C20  N6   N4   C11     0.00   0.0  0
 B7K  CONST_08  N6   C20  C10  C11     0.00   0.0  0
 B7K  CONST_09  N3   N    C1   C2      0.00   0.0  0
 B7K  CONST_10  N4   C11  C10  C20     0.00   0.0  0
 B7K  CONST_11  C12  N4   C11  C10   180.00   0.0  0
 B7K  CONST_12  C20  N6   N4   C12   180.00   0.0  0
 B7K  CONST_13  N6   C20  C10  C9    180.00   0.0  0
 B7K  CONST_14  N4   C11  C10  C9    180.00   0.0  0
 B7K  CONST_15  C3   C2   C1   N     180.00   0.0  0
 B7K  CONST_16  N1   C1   C2   C3      0.00   0.0  0
 B7K  CONST_17  N3   C4   C2   C3    180.00   0.0  0
 B7K  CONST_18  H15  C4   N3   N     180.00   0.0  0
 B7K  CONST_19  H14  C20  C10  C11   180.00   0.0  0
 B7K  CONST_20  H1   C11  N4   C12     0.00   0.0  0
 B7K  CONST_21  C16  C15  N5   C14   180.00   0.0  0
 B7K  CONST_22  O1   C15  N5   C14     0.00   0.0  0
 B7K  CONST_23  C18  N5   C15  C16     0.00   0.0  0
 B7K  CONST_24  O1   C15  N5   C18   180.00   0.0  0
 B7K  Var_01    C10  C9   N1   C1   -177.18  30.0  1
 B7K  Var_02    C5   C    N    C1    -12.72  30.0  1
 B7K  Var_03    N1   C9   C10  C11    -6.70  30.0  2
 B7K  Var_04    N5   C14  C13  C12    57.20  30.0  1
 B7K  Var_05    N5   C18  C19  C12   -55.54  30.0  1
 B7K  Var_06    C18  N5   C14  C13   -60.35  30.0  1
 B7K  Var_07    C19  C18  N5   C14    59.39  30.0  1
 B7K  Var_08    N5   C15  C16  C17  -170.72  30.0  2
 B7K  Var_09    H18  C7   C6   C5    -50.68  30.0  3
 B7K  Var_10    H21  C8   C6   C5     55.57  30.0  3
 B7K  Var_11    H8   C17  C16  C15     0.54   0.0  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
 B7K  chir_01  C12  C13  C19  N4  positiv
 B7K  chir_02  C5   C9   C6   C   positiv

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
 B7K  plan-1  C10  0.020
 B7K  plan-1  C11  0.020
 B7K  plan-1  C12  0.020
 B7K  plan-1  C20  0.020
 B7K  plan-1  C9   0.020
 B7K  plan-1  N4   0.020
 B7K  plan-1  N6   0.020
 B7K  plan-1  H1   0.020
 B7K  plan-1  H14  0.020
 B7K  plan-2  N    0.020
 B7K  plan-2  C    0.020
 B7K  plan-2  C1   0.020
 B7K  plan-2  C2   0.020
 B7K  plan-2  C3   0.020
 B7K  plan-2  C4   0.020
 B7K  plan-2  N1   0.020
 B7K  plan-2  N2   0.020
 B7K  plan-2  N3   0.020
 B7K  plan-2  H15  0.020
 B7K  plan-3  C14  0.020
 B7K  plan-3  C16  0.020
 B7K  plan-3  C18  0.020
 B7K  plan-3  N5   0.020
 B7K  plan-3  O1   0.020
 B7K  plan-3  C15  0.020
 B7K  plan-4  N    0.020
 B7K  plan-4  C    0.020
 B7K  plan-4  O    0.020
 B7K  plan-4  C5   0.020
 B7K  plan-5  C16  0.020
 B7K  plan-5  C17  0.020
 B7K  plan-5  H7   0.020
 B7K  plan-5  H8   0.020
 B7K  plan-5  H9   0.020
 B7K  plan-5  C15  0.020

