# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 21:06:19 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 8-[4-[2-(4-propanoylpiperazin-1-yl)ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCN(CC1)CCc2cnn(c2)c3nccc4C(=O)NC=Nc34
#
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
 B7Z  B7Z  8-[4-[2-(4-propanoylpiperazin-1-yl)ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  51  28  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B7Z
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
 B7Z  C1   C  CR16  0   0.151  -5.0226   2.3326   0.8546
 B7Z  C2   C  CR66  0   0.155  -4.6173   0.2561   0.0721
 B7Z  C3   C  CR66  0  -0.018  -5.9272  -0.1616   0.3316
 B7Z  C4   C  CR16  0  -0.356  -6.3011  -1.4845   0.1056
 B7Z  C5   C  CR16  0  -0.063  -5.3451  -2.3515  -0.3692
 B7Z  C6   C  CR6   0   0.444  -3.7512  -0.7185  -0.4765
 B7Z  N1   N  N     0  -0.429  -4.1662   1.5156   0.3648
 B7Z  O3   O  O     0  -0.507   7.7176   0.3442   1.7995
 B7Z  C7   C  CR15  0   0.031  -1.3419  -1.1901  -0.6290
 B7Z  N    N  NR16  0  -0.659  -6.3274   2.0418   1.0900
 B7Z  C    C  CR6   0   0.580  -6.8878   0.8069   0.8706
 B7Z  C10  C  CH2   0  -0.254   1.9100  -0.3499   0.0055
 B7Z  C11  C  CH2   0  -0.282   4.0827   0.0655  -0.9541
 B7Z  C12  C  CH2   0  -0.313   5.5343  -0.3829  -0.9768
 B7Z  C13  C  C     0   0.563   7.2771   0.3306   0.6567
 B7Z  C14  C  CH2   0  -0.597   8.0243   1.0178  -0.4732
 B7Z  C15  C  CH3   0  -0.650   9.3332   1.6428  -0.0227
 B7Z  C19  C  CH2   0  -0.308   5.3461  -0.9984   1.3516
 B7Z  C20  C  CH2   0  -0.284   3.9017  -0.5324   1.3359
 B7Z  C21  C  CR15  0  -0.064  -0.8396   0.6461  -1.7113
 B7Z  C8   C  CR5   0  -0.148  -0.2736  -0.5393  -1.1866
 B7Z  C9   C  CH2   0  -0.543   1.1629  -0.9438  -1.1896
 B7Z  N2   N  N     0  -0.402  -4.1027  -1.9640  -0.6676
 B7Z  N3   N  NR5   0  -0.371  -2.4298  -0.3995  -0.8217
 B7Z  N4   N  NT    0  -0.430   3.3189  -0.6950   0.0167
 B7Z  N5   N  NT    0  -0.462   6.1176  -0.2916   0.3469
 B7Z  N7   N  N     0  -0.266  -2.1324   0.7177  -1.4920
 B7Z  O    O  O     0  -0.434  -8.0546   0.5706   1.1074
 B7Z  H1   H  HCR6  0   0.307  -4.7236   3.3396   1.1159
 B7Z  H2   H  HCR6  0   0.286  -7.3068  -1.8238   0.3097
 B7Z  H3   H  HCR6  0   0.281  -5.5750  -3.3958  -0.5360
 B7Z  H4   H  HCR5  0   0.292  -1.4090  -2.1315  -0.1083
 B7Z  H5   H  HNR6  0   0.440  -6.9211   2.7700   1.4672
 B7Z  H6   H  HCH2  0   0.201   1.7572   0.7421   0.0331
 B7Z  H7   H  HCH2  0   0.238   1.4562  -0.7459   0.9178
 B7Z  H8   H  HCH2  0   0.200   4.0402   1.1485  -0.7433
 B7Z  H9   H  HCH2  0   0.247   3.6720  -0.0839  -1.9537
 B7Z  H10  H  HCH2  0   0.240   5.5887  -1.4198  -1.3254
 B7Z  H11  H  HCH2  0   0.273   6.0811   0.2291  -1.6877
 B7Z  H12  H  HCH2  0   0.265   8.2154   0.2950  -1.2709
 B7Z  H13  H  HCH2  0   0.265   7.3809   1.7826  -0.9178
 B7Z  H14  H  HCH3  0   0.230   9.8303   2.1086  -0.8730
 B7Z  H15  H  HCH3  0   0.227   9.1759   2.4118   0.7321
 B7Z  H16  H  HCH3  0   0.226  10.0129   0.8994   0.3919
 B7Z  H17  H  HCH2  0   0.262   5.7785  -0.8285   2.3336
 B7Z  H18  H  HCH2  0   0.236   5.3863  -2.0741   1.1470
 B7Z  H19  H  HCH2  0   0.245   3.3351  -1.1294   2.0537
 B7Z  H20  H  HCH2  0   0.198   3.8582   0.5160   1.6778
 B7Z  H21  H  HCR5  0   0.262  -0.3348   1.4355  -2.2495
 B7Z  H22  H  HCH2  0   0.249   1.6191  -0.6193  -2.1278
 B7Z  H23  H  HCH2  0   0.245   1.2521  -2.0315  -1.1572

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
 B7Z  C21  C8   aromatic  1.414  0.020  1.414
 B7Z  C21  N7   aromatic  1.313  0.020  1.313
 B7Z  C9   C8   single    1.492  0.020  1.492
 B7Z  C9   C10  single    1.530  0.020  1.530
 B7Z  C19  C20  single    1.518  0.020  1.518
 B7Z  C19  N5   single    1.451  0.020  1.451
 B7Z  C8   C7   aromatic  1.370  0.020  1.370
 B7Z  N7   N3   aromatic  1.336  0.020  1.336
 B7Z  C20  N4   single    1.451  0.020  1.451
 B7Z  C7   N3   aromatic  1.359  0.020  1.359
 B7Z  N3   C6   single    1.402  0.020  1.402
 B7Z  N4   C10  single    1.451  0.020  1.451
 B7Z  N4   C11  single    1.451  0.020  1.451
 B7Z  N2   C6   aromatic  1.308  0.020  1.308
 B7Z  N2   C5   aromatic  1.335  0.020  1.335
 B7Z  C6   C2   aromatic  1.415  0.020  1.415
 B7Z  C14  C13  single    1.519  0.020  1.519
 B7Z  C14  C15  single    1.519  0.020  1.519
 B7Z  N5   C12  single    1.449  0.020  1.449
 B7Z  N5   C13  single    1.352  0.020  1.352
 B7Z  N1   C2   single    1.369  0.020  1.369
 B7Z  N1   C1   double    1.281  0.020  1.281
 B7Z  C2   C3   aromatic  1.399  0.020  1.399
 B7Z  C5   C4   aromatic  1.375  0.020  1.375
 B7Z  C12  C11  single    1.519  0.020  1.519
 B7Z  C13  O3   double    1.225  0.020  1.225
 B7Z  C1   N    single    1.357  0.020  1.357
 B7Z  C3   C4   aromatic  1.393  0.020  1.393
 B7Z  C3   C    single    1.467  0.020  1.467
 B7Z  N    C    single    1.374  0.020  1.374
 B7Z  C    O    double    1.214  0.020  1.214
 B7Z  C1   H1   single    0.930  0.020  1.080
 B7Z  C4   H2   single    0.930  0.020  1.080
 B7Z  C5   H3   single    0.930  0.020  1.080
 B7Z  C7   H4   single    0.930  0.020  1.080
 B7Z  N    H5   single    0.860  0.020  1.020
 B7Z  C10  H6   single    0.970  0.020  1.090
 B7Z  C10  H7   single    0.970  0.020  1.090
 B7Z  C11  H8   single    0.970  0.020  1.090
 B7Z  C11  H9   single    0.970  0.020  1.090
 B7Z  C12  H10  single    0.970  0.020  1.090
 B7Z  C12  H11  single    0.970  0.020  1.090
 B7Z  C14  H12  single    0.970  0.020  1.090
 B7Z  C14  H13  single    0.970  0.020  1.090
 B7Z  C15  H14  single    0.970  0.020  1.090
 B7Z  C15  H15  single    0.970  0.020  1.090
 B7Z  C15  H16  single    0.970  0.020  1.090
 B7Z  C19  H17  single    0.970  0.020  1.090
 B7Z  C19  H18  single    0.970  0.020  1.090
 B7Z  C20  H19  single    0.970  0.020  1.090
 B7Z  C20  H20  single    0.970  0.020  1.090
 B7Z  C21  H21  single    0.930  0.020  1.080
 B7Z  C9   H22  single    0.970  0.020  1.090
 B7Z  C9   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
 B7Z  H1   C1   N    115.02  3.000
 B7Z  H1   C1   N1   120.06  3.000
 B7Z  N    C1   N1   124.91  3.000
 B7Z  N1   C2   C6   120.99  3.000
 B7Z  N1   C2   C3   122.91  3.000
 B7Z  C6   C2   C3   116.07  3.000
 B7Z  C    C3   C4   120.72  3.000
 B7Z  C    C3   C2   118.96  3.000
 B7Z  C4   C3   C2   120.31  3.000
 B7Z  H2   C4   C5   120.95  3.000
 B7Z  H2   C4   C3   121.14  3.000
 B7Z  C5   C4   C3   117.91  3.000
 B7Z  H3   C5   N2   116.31  3.000
 B7Z  H3   C5   C4   120.92  3.000
 B7Z  N2   C5   C4   122.76  3.000
 B7Z  N3   C6   N2   115.71  3.000
 B7Z  N2   C6   C2   123.23  3.000
 B7Z  N3   C6   C2   121.04  3.000
 B7Z  C2   N1   C1   116.62  3.000
 B7Z  H4   C7   N3   121.80  3.000
 B7Z  H4   C7   C8   131.32  3.000
 B7Z  N3   C7   C8   106.88  3.000
 B7Z  H5   N    C    117.83  3.000
 B7Z  H5   N    C1   118.31  3.000
 B7Z  C    N    C1   123.85  3.000
 B7Z  O    C    N    122.41  3.000
 B7Z  O    C    C3   124.94  3.000
 B7Z  N    C    C3   112.65  3.000
 B7Z  H7   C10  H6   106.27  3.000
 B7Z  H7   C10  N4   108.10  3.000
 B7Z  H6   C10  N4   111.71  3.000
 B7Z  H7   C10  C9   107.98  3.000
 B7Z  H6   C10  C9   109.65  3.000
 B7Z  N4   C10  C9   112.84  3.000
 B7Z  H9   C11  H8   107.14  3.000
 B7Z  H9   C11  N4   110.07  3.000
 B7Z  H8   C11  N4   111.48  3.000
 B7Z  H9   C11  C12  107.80  3.000
 B7Z  H8   C11  C12  109.21  3.000
 B7Z  N4   C11  C12  111.00  3.000
 B7Z  H11  C12  H10  107.47  3.000
 B7Z  H11  C12  N5   111.09  3.000
 B7Z  H10  C12  N5   109.29  3.000
 B7Z  H11  C12  C11  108.94  3.000
 B7Z  H10  C12  C11  109.36  3.000
 B7Z  N5   C12  C11  110.63  3.000
 B7Z  N5   C13  C14  117.37  3.000
 B7Z  N5   C13  O3   121.83  3.000
 B7Z  C14  C13  O3   120.80  3.000
 B7Z  H13  C14  H12  105.57  3.000
 B7Z  H13  C14  C15  109.86  3.000
 B7Z  H12  C14  C15  109.74  3.000
 B7Z  H13  C14  C13  109.23  3.000
 B7Z  H12  C14  C13  109.25  3.000
 B7Z  C15  C14  C13  112.92  3.000
 B7Z  H16  C15  H15  107.96  3.000
 B7Z  H16  C15  H14  107.70  3.000
 B7Z  H15  C15  H14  107.75  3.000
 B7Z  H16  C15  C14  111.70  3.000
 B7Z  H15  C15  C14  111.82  3.000
 B7Z  H14  C15  C14  109.73  3.000
 B7Z  H18  C19  H17  107.92  3.000
 B7Z  H18  C19  N5   109.24  3.000
 B7Z  H17  C19  N5   109.76  3.000
 B7Z  H18  C19  C20  109.54  3.000
 B7Z  H17  C19  C20  109.89  3.000
 B7Z  N5   C19  C20  110.45  3.000
 B7Z  H20  C20  H19  107.17  3.000
 B7Z  H20  C20  N4   111.85  3.000
 B7Z  H19  C20  N4   109.14  3.000
 B7Z  H20  C20  C19  109.02  3.000
 B7Z  H19  C20  C19  108.61  3.000
 B7Z  N4   C20  C19  110.93  3.000
 B7Z  H21  C21  N7   120.21  3.000
 B7Z  H21  C21  C8   127.59  3.000
 B7Z  N7   C21  C8   112.19  3.000
 B7Z  C9   C8   C21  127.71  3.000
 B7Z  C9   C8   C7   128.52  3.000
 B7Z  C21  C8   C7   103.72  3.000
 B7Z  H23  C9   H22  106.70  3.000
 B7Z  H23  C9   C8   110.40  3.000
 B7Z  H22  C9   C8   108.85  3.000
 B7Z  H23  C9   C10  108.89  3.000
 B7Z  H22  C9   C10  110.59  3.000
 B7Z  C8   C9   C10  111.31  3.000
 B7Z  C6   N2   C5   119.58  3.000
 B7Z  N7   N3   C7   112.30  3.000
 B7Z  C7   N3   C6   125.96  3.000
 B7Z  N7   N3   C6   121.55  3.000
 B7Z  C20  N4   C11  109.77  3.000
 B7Z  C11  N4   C10  112.43  3.000
 B7Z  C20  N4   C10  111.74  3.000
 B7Z  C19  N5   C13  121.45  3.000
 B7Z  C13  N5   C12  125.69  3.000
 B7Z  C19  N5   C12  112.82  3.000
 B7Z  N3   N7   C21  104.91  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
 B7Z  CONST_03  C5   N2   C6   C2      0.00   0.0  0
 B7Z  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 B7Z  CONST_05  N3   C6   C2   C3    180.00   0.0  0
 B7Z  CONST_06  N2   C6   C2   C3      0.00   0.0  0
 B7Z  CONST_07  N2   C5   C4   C3      0.00   0.0  0
 B7Z  CONST_08  C6   N2   C5   C4      0.00   0.0  0
 B7Z  CONST_09  C6   C2   C3   C4      0.00   0.0  0
 B7Z  CONST_10  N3   C6   N2   C5    180.00   0.0  0
 B7Z  CONST_11  C21  N7   N3   C6    180.00   0.0  0
 B7Z  CONST_12  C8   C7   N3   C6    180.00   0.0  0
 B7Z  CONST_13  N7   C21  C8   C7      0.00   0.0  0
 B7Z  CONST_14  C21  N7   N3   C7      0.00   0.0  0
 B7Z  CONST_16  N3   C7   C8   C21     0.00   0.0  0
 B7Z  CONST_17  N3   N7   C21  C8      0.00   0.0  0
 B7Z  CONST_18  N7   N3   C7   C8      0.00   0.0  0
 B7Z  CONST_20  N3   C6   C2   N1      0.00   0.0  0
 B7Z  CONST_21  C3   C    N    C1      0.00   0.0  0
 B7Z  CONST_22  N    C1   N1   C2      0.00   0.0  0
 B7Z  CONST_23  C    N    C1   N1      0.00   0.0  0
 B7Z  CONST_24  N7   C21  C8   C9    180.00   0.0  0
 B7Z  CONST_25  N3   C7   C8   C9    180.00   0.0  0
 B7Z  CONST_26  O    C    N    C1    180.00   0.0  0
 B7Z  CONST_27  H2   C4   C3   C2    180.00   0.0  0
 B7Z  CONST_28  H3   C5   C4   C3    180.00   0.0  0
 B7Z  CONST_29  H4   C7   N3   C6      0.00   0.0  0
 B7Z  CONST_30  H21  C21  C8   C7    180.00   0.0  0
 B7Z  CONST_31  H1   C1   N1   C2    180.00   0.0  0
 B7Z  CONST_32  H5   N    C    C3    180.00   0.0  0
 B7Z  CONST_33  C19  N5   C13  O3      0.00   0.0  0
 B7Z  CONST_34  C12  N5   C13  O3    180.00   0.0  0
 B7Z  CONST_35  C14  C13  N5   C12     0.00   0.0  0
 B7Z  CONST_36  C19  N5   C13  C14   180.00   0.0  0
 B7Z  Var_01    C19  C20  N4   C11   -58.91  30.0  1
 B7Z  Var_02    C19  N5   C12  C11    53.65  30.0  1
 B7Z  Var_03    C20  C19  N5   C12   -53.92  30.0  1
 B7Z  Var_04    C20  N4   C11  C12    58.57  30.0  1
 B7Z  Var_05    N5   C19  C20  N4     56.25  30.0  1
 B7Z  Var_06    N5   C12  C11  N4    -55.69  30.0  1
 B7Z  Var_07    C10  C9   C8   C7    -91.66  30.0  2
 B7Z  Var_08    C9   C10  N4   C11    75.71  30.0  3
 B7Z  Var_09    N4   C10  C9   C8   -178.54  30.0  3
 B7Z  Var_10    N5   C13  C14  C15  -178.07  30.0  3
 B7Z  Var_11    H14  C15  C14  C13   179.29  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
 B7Z  plan-1  C6   0.020
 B7Z  plan-1  C7   0.020
 B7Z  plan-1  C21  0.020
 B7Z  plan-1  C8   0.020
 B7Z  plan-1  C9   0.020
 B7Z  plan-1  N3   0.020
 B7Z  plan-1  N7   0.020
 B7Z  plan-1  H4   0.020
 B7Z  plan-1  H21  0.020
 B7Z  plan-2  C1   0.020
 B7Z  plan-2  C2   0.020
 B7Z  plan-2  C3   0.020
 B7Z  plan-2  C4   0.020
 B7Z  plan-2  C5   0.020
 B7Z  plan-2  C6   0.020
 B7Z  plan-2  N1   0.020
 B7Z  plan-2  N    0.020
 B7Z  plan-2  C    0.020
 B7Z  plan-2  N2   0.020
 B7Z  plan-2  N3   0.020
 B7Z  plan-2  O    0.020
 B7Z  plan-2  H1   0.020
 B7Z  plan-2  H2   0.020
 B7Z  plan-2  H3   0.020
 B7Z  plan-2  H5   0.020
 B7Z  plan-3  O3   0.020
 B7Z  plan-3  C12  0.020
 B7Z  plan-3  C13  0.020
 B7Z  plan-3  C14  0.020
 B7Z  plan-3  C19  0.020
 B7Z  plan-3  N5   0.020

