# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:34:00 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-benzyl-4-[3-(pyridin-4-yl)-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C=C(C=CN1Cc2ccccc2)N3CCc4n[nH]c(c5ccncc5)c4C3
#
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
 4V8  4V8  1-benzyl-4-[3-(pyridin-4-yl)-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]pyridin-2(1H)-one  ligand  50  29  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4V8
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
 4V8  C2   C  CR5   0   0.443  -4.0761   0.4790  -0.5477
 4V8  C3   C  CR5   0  -0.191  -2.8631   1.0598  -0.2187
 4V8  C11  C  CR16  0  -0.370  -5.9735  -1.1148  -0.2991
 4V8  C12  C  CR16  0  -0.058  -6.4172  -2.4117  -0.1050
 4V8  C14  C  CR16  0  -0.053  -4.3031  -3.2175   0.0025
 4V8  C15  C  CR16  0  -0.404  -3.7537  -1.9610  -0.1928
 4V8  C16  C  CR6   0   0.535   0.6587   1.1556   0.8137
 4V8  C17  C  CR16  0  -0.474   1.7171   2.1207   0.8164
 4V8  C18  C  CR16  0   0.056   2.9877   1.7049   1.0117
 4V8  C20  C  CR6   0   0.571   2.3588  -0.5934   1.2330
 4V8  C21  C  CR16  0  -0.596   1.0150  -0.1645   1.0290
 4V8  C24  C  CR6   0   0.147   5.3198  -0.5244   0.1060
 4V8  C25  C  CR16  0  -0.301   5.6260   0.3224  -0.9570
 4V8  C26  C  CR16  0  -0.242   6.1675  -0.1817  -2.1308
 4V8  C27  C  CR16  0  -0.266   6.4149  -1.5435  -2.2531
 4V8  C28  C  CR16  0  -0.244   6.1189  -2.3936  -1.1962
 4V8  C29  C  CR16  0  -0.288   5.5712  -1.8860  -0.0249
 4V8  N1   N  NR15  0  -0.522  -4.8082   1.4727  -1.1004
 4V8  C4   C  CR5   0   0.234  -2.9929   2.3990  -0.6093
 4V8  N5   N  N     0  -0.276  -4.1745   2.6343  -1.1499
 4V8  C6   C  CH2   0  -0.363  -1.6395   0.4978   0.4242
 4V8  N7   N  NT    0  -0.536  -0.6288   1.5309   0.5751
 4V8  C8   C  CH2   0  -0.336  -1.1135   2.8805   0.8323
 4V8  C9   C  CH2   0  -0.504  -1.9270   3.4020  -0.3460
 4V8  C10  C  CR6   0   0.149  -4.6012  -0.8653  -0.3501
 4V8  N13  N  N     0  -0.406  -5.6085  -3.4544   0.0469
 4V8  N19  N  NR6   0  -0.508   3.3260   0.4108   1.2154
 4V8  O22  O  O     0  -0.531   2.6981  -1.7609   1.4348
 4V8  H1   H  HCR6  0   0.266  -6.7030  -0.3208  -0.3860
 4V8  H2   H  HCR6  0   0.270  -7.4819  -2.6117  -0.0638
 4V8  H3   H  HCR6  0   0.271  -3.6482  -4.0729   0.1250
 4V8  H4   H  HCR6  0   0.270  -2.6790  -1.8622  -0.2387
 4V8  H5   H  HCR6  0   0.282   1.5548   3.1705   0.6345
 4V8  H6   H  HCR6  0   0.302   3.8045   2.4126   1.0085
 4V8  H7   H  HCR6  0   0.272   0.2783  -0.9521   1.0831
 4V8  H8   H  HCH2  0   0.283   4.8162  -0.6746   2.1903
 4V8  H9   H  HCH2  0   0.281   5.2680   0.9376   1.6718
 4V8  H10  H  HCR6  0   0.247   5.4489   1.3886  -0.8687
 4V8  H11  H  HCR6  0   0.256   6.4033   0.4891  -2.9469
 4V8  H12  H  HCR6  0   0.257   6.8407  -1.9386  -3.1662
 4V8  H13  H  HCR6  0   0.255   6.3123  -3.4550  -1.2836
 4V8  H14  H  HCR6  0   0.250   5.3367  -2.5533   0.7941
 4V8  H15  H  HNR5  0   0.422  -5.7277   1.3977  -1.5069
 4V8  H16  H  HCH2  0   0.257  -1.8855   0.0241   1.3856
 4V8  H17  H  HCH2  0   0.269  -1.2204  -0.2842  -0.2134
 4V8  H18  H  HCH2  0   0.256  -1.7368   2.8770   1.7337
 4V8  H19  H  HCH2  0   0.276  -0.2823   3.5459   1.0361
 4V8  H20  H  HCH2  0   0.260  -1.2767   3.5318  -1.2153
 4V8  H21  H  HCH2  0   0.260  -2.3510   4.3777  -0.1046
 4V8  C23  C  CH2   0  -0.428   4.7286   0.0386   1.3731

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
 4V8  C9   C8   single    1.524  0.020  1.524
 4V8  C9   C4   single    1.487  0.020  1.487
 4V8  C8   N7   single    1.457  0.020  1.457
 4V8  N5   C4   aromatic  1.321  0.020  1.321
 4V8  N5   N1   aromatic  1.324  0.020  1.324
 4V8  C4   C3   aromatic  1.401  0.020  1.401
 4V8  O22  C20  double    1.232  0.020  1.232
 4V8  C21  C16  double    1.384  0.020  1.384
 4V8  C21  C20  single    1.425  0.020  1.425
 4V8  N7   C16  single    1.362  0.020  1.362
 4V8  N7   C6   single    1.453  0.020  1.453
 4V8  C27  C26  aromatic  1.389  0.020  1.389
 4V8  C27  C28  aromatic  1.388  0.020  1.388
 4V8  N1   C2   aromatic  1.352  0.020  1.352
 4V8  C3   C6   single    1.492  0.020  1.492
 4V8  C3   C2   aromatic  1.385  0.020  1.385
 4V8  C26  C25  aromatic  1.388  0.020  1.388
 4V8  C28  C29  aromatic  1.389  0.020  1.389
 4V8  C16  C17  single    1.432  0.020  1.432
 4V8  C20  N19  single    1.394  0.020  1.394
 4V8  C2   C10  single    1.457  0.020  1.457
 4V8  C25  C24  aromatic  1.393  0.020  1.393
 4V8  C29  C24  aromatic  1.391  0.020  1.391
 4V8  C24  C23  single    1.507  0.020  1.507
 4V8  N19  C23  single    1.460  0.020  1.460
 4V8  N19  C18  single    1.353  0.020  1.353
 4V8  C17  C18  double    1.351  0.020  1.351
 4V8  C11  C10  aromatic  1.396  0.020  1.396
 4V8  C11  C12  aromatic  1.384  0.020  1.384
 4V8  C10  C15  aromatic  1.394  0.020  1.394
 4V8  C12  N13  aromatic  1.328  0.020  1.328
 4V8  C15  C14  aromatic  1.385  0.020  1.385
 4V8  N13  C14  aromatic  1.327  0.020  1.327
 4V8  C11  H1   single    0.930  0.020  1.080
 4V8  C12  H2   single    0.930  0.020  1.080
 4V8  C14  H3   single    0.930  0.020  1.080
 4V8  C15  H4   single    0.930  0.020  1.080
 4V8  C17  H5   single    0.930  0.020  1.080
 4V8  C18  H6   single    0.930  0.020  1.080
 4V8  C21  H7   single    0.930  0.020  1.080
 4V8  C23  H8   single    0.970  0.020  1.090
 4V8  C23  H9   single    0.970  0.020  1.090
 4V8  C25  H10  single    0.930  0.020  1.080
 4V8  C26  H11  single    0.930  0.020  1.080
 4V8  C27  H12  single    0.930  0.020  1.080
 4V8  C28  H13  single    0.930  0.020  1.080
 4V8  C29  H14  single    0.930  0.020  1.080
 4V8  N1   H15  single    0.860  0.020  1.020
 4V8  C6   H16  single    0.970  0.020  1.090
 4V8  C6   H17  single    0.970  0.020  1.090
 4V8  C8   H18  single    0.970  0.020  1.090
 4V8  C8   H19  single    0.970  0.020  1.090
 4V8  C9   H20  single    0.970  0.020  1.090
 4V8  C9   H21  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
 4V8  C10  C2   N1   122.57  3.000
 4V8  C10  C2   C3   132.12  3.000
 4V8  N1   C2   C3   105.26  3.000
 4V8  C6   C3   C4   123.79  3.000
 4V8  C6   C3   C2   131.51  3.000
 4V8  C4   C3   C2   104.69  3.000
 4V8  H1   C11  C10  121.93  3.000
 4V8  H1   C11  C12  118.86  3.000
 4V8  C10  C11  C12  119.19  3.000
 4V8  H2   C12  N13  116.67  3.000
 4V8  H2   C12  C11  119.53  3.000
 4V8  N13  C12  C11  123.80  3.000
 4V8  H3   C14  N13  116.70  3.000
 4V8  H3   C14  C15  119.48  3.000
 4V8  N13  C14  C15  123.82  3.000
 4V8  H4   C15  C10  121.88  3.000
 4V8  H4   C15  C14  118.92  3.000
 4V8  C10  C15  C14  119.19  3.000
 4V8  N7   C16  C21  122.23  3.000
 4V8  N7   C16  C17  120.87  3.000
 4V8  C21  C16  C17  116.88  3.000
 4V8  H5   C17  C18  117.76  3.000
 4V8  H5   C17  C16  123.01  3.000
 4V8  C18  C17  C16  119.19  3.000
 4V8  H6   C18  N19  115.96  3.000
 4V8  H6   C18  C17  120.58  3.000
 4V8  N19  C18  C17  123.46  3.000
 4V8  O22  C20  N19  119.56  3.000
 4V8  N19  C20  C21  115.81  3.000
 4V8  O22  C20  C21  124.62  3.000
 4V8  H7   C21  C20  114.62  3.000
 4V8  H7   C21  C16  121.86  3.000
 4V8  C20  C21  C16  123.50  3.000
 4V8  C29  C24  C25  118.92  3.000
 4V8  C29  C24  C23  121.05  3.000
 4V8  C25  C24  C23  120.03  3.000
 4V8  H10  C25  C26  119.33  3.000
 4V8  H10  C25  C24  119.98  3.000
 4V8  C26  C25  C24  120.69  3.000
 4V8  H11  C26  C27  120.15  3.000
 4V8  H11  C26  C25  119.85  3.000
 4V8  C27  C26  C25  120.00  3.000
 4V8  H12  C27  C28  120.17  3.000
 4V8  H12  C27  C26  120.15  3.000
 4V8  C28  C27  C26  119.68  3.000
 4V8  H13  C28  C29  119.79  3.000
 4V8  H13  C28  C27  120.06  3.000
 4V8  C29  C28  C27  120.15  3.000
 4V8  H14  C29  C28  119.89  3.000
 4V8  H14  C29  C24  119.56  3.000
 4V8  C28  C29  C24  120.56  3.000
 4V8  H15  N1   N5   119.12  3.000
 4V8  H15  N1   C2   127.15  3.000
 4V8  N5   N1   C2   113.63  3.000
 4V8  C9   C4   N5   126.42  3.000
 4V8  N5   C4   C3   111.55  3.000
 4V8  C9   C4   C3   121.94  3.000
 4V8  C4   N5   N1   104.87  3.000
 4V8  H17  C6   H16  106.72  3.000
 4V8  H17  C6   N7   107.62  3.000
 4V8  H16  C6   N7   111.78  3.000
 4V8  H17  C6   C3   109.44  3.000
 4V8  H16  C6   C3   110.82  3.000
 4V8  N7   C6   C3   110.32  3.000
 4V8  C8   N7   C6   116.46  3.000
 4V8  C6   N7   C16  118.66  3.000
 4V8  C8   N7   C16  122.60  3.000
 4V8  H19  C8   H18  106.46  3.000
 4V8  H19  C8   C9   110.16  3.000
 4V8  H18  C8   C9   109.48  3.000
 4V8  H19  C8   N7   110.28  3.000
 4V8  H18  C8   N7   109.36  3.000
 4V8  C9   C8   N7   110.98  3.000
 4V8  H21  C9   H20  107.52  3.000
 4V8  H21  C9   C8   110.03  3.000
 4V8  H20  C9   C8   109.75  3.000
 4V8  H21  C9   C4   111.34  3.000
 4V8  H20  C9   C4   111.45  3.000
 4V8  C8   C9   C4   106.78  3.000
 4V8  C15  C10  C11  116.94  3.000
 4V8  C15  C10  C2   121.43  3.000
 4V8  C11  C10  C2   121.62  3.000
 4V8  C14  N13  C12  117.05  3.000
 4V8  C23  N19  C20  118.79  3.000
 4V8  C23  N19  C18  120.02  3.000
 4V8  C20  N19  C18  121.15  3.000
 4V8  H9   C23  H8   107.15  3.000
 4V8  H9   C23  N19  107.15  3.000
 4V8  H8   C23  N19  109.00  3.000
 4V8  H9   C23  C24  110.14  3.000
 4V8  H8   C23  C24  110.78  3.000
 4V8  N19  C23  C24  112.42  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
 4V8  CONST_01  C4   N5   N1   C2      0.00   0.0  0
 4V8  CONST_02  N5   C4   C3   C2      0.00   0.0  0
 4V8  CONST_03  C12  C11  C10  C2    180.00   0.0  0
 4V8  CONST_04  C14  C15  C10  C2    180.00   0.0  0
 4V8  CONST_05  N1   N5   C4   C3      0.00   0.0  0
 4V8  CONST_06  N5   N1   C2   C3      0.00   0.0  0
 4V8  CONST_10  C14  C15  C10  C11     0.00   0.0  0
 4V8  CONST_11  C14  N13  C12  C11     0.00   0.0  0
 4V8  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 4V8  CONST_13  C15  C14  N13  C12     0.00   0.0  0
 4V8  CONST_15  C27  C26  C25  C24     0.00   0.0  0
 4V8  CONST_16  C27  C28  C29  C24     0.00   0.0  0
 4V8  CONST_17  C28  C27  C26  C25     0.00   0.0  0
 4V8  CONST_18  C28  C29  C24  C25     0.00   0.0  0
 4V8  CONST_19  C29  C28  C27  C26     0.00   0.0  0
 4V8  CONST_20  C29  C24  C25  C26     0.00   0.0  0
 4V8  CONST_21  C4   C3   C2   N1      0.00   0.0  0
 4V8  CONST_22  C10  C2   C3   C4    180.00   0.0  0
 4V8  CONST_23  C10  C2   N1   N5    180.00   0.0  0
 4V8  CONST_24  N13  C12  C11  C10     0.00   0.0  0
 4V8  CONST_25  N13  C14  C15  C10     0.00   0.0  0
 4V8  CONST_26  C10  C2   C3   C6      0.00   0.0  0
 4V8  CONST_27  C21  C20  N19  C18     0.00   0.0  0
 4V8  CONST_28  C26  C25  C24  C23   180.00   0.0  0
 4V8  CONST_29  C28  C29  C24  C23   180.00   0.0  0
 4V8  CONST_30  O22  C20  N19  C18   180.00   0.0  0
 4V8  CONST_31  C23  N19  C20  C21   180.00   0.0  0
 4V8  CONST_32  H1   C11  C10  C2      0.00   0.0  0
 4V8  CONST_33  H4   C15  C10  C2      0.00   0.0  0
 4V8  CONST_34  H15  N1   C2   C3    180.00   0.0  0
 4V8  CONST_35  H3   C14  N13  C12   180.00   0.0  0
 4V8  CONST_36  H2   C12  N13  C14   180.00   0.0  0
 4V8  CONST_37  H11  C26  C25  C24   180.00   0.0  0
 4V8  CONST_38  H13  C28  C29  C24   180.00   0.0  0
 4V8  CONST_39  H12  C27  C26  C25   180.00   0.0  0
 4V8  CONST_40  H14  C29  C24  C25   180.00   0.0  0
 4V8  CONST_41  H10  C25  C26  C27   180.00   0.0  0
 4V8  CONST_42  O22  C20  N19  C23     0.00   0.0  0
 4V8  Var_01    N7   C6   C3   C2   -179.03  30.0  1
 4V8  Var_02    C8   C9   C4   C3    -23.55  30.0  1
 4V8  Var_03    C8   N7   C6   C3     33.46  30.0  1
 4V8  Var_04    C9   C8   N7   C16   133.50  30.0  1
 4V8  Var_05    N7   C8   C9   C4     54.35  30.0  1
 4V8  Var_06    C24  C23  N19  C18   -99.93  30.0  3
 4V8  Var_07    N19  C23  C24  C25    74.27  30.0  2

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
 4V8  plan-1  C2   0.020
 4V8  plan-1  C11  0.020
 4V8  plan-1  C12  0.020
 4V8  plan-1  C14  0.020
 4V8  plan-1  C15  0.020
 4V8  plan-1  C10  0.020
 4V8  plan-1  N13  0.020
 4V8  plan-1  H1   0.020
 4V8  plan-1  H2   0.020
 4V8  plan-1  H3   0.020
 4V8  plan-1  H4   0.020
 4V8  plan-2  C16  0.020
 4V8  plan-2  C17  0.020
 4V8  plan-2  C18  0.020
 4V8  plan-2  C20  0.020
 4V8  plan-2  C21  0.020
 4V8  plan-2  N7   0.020
 4V8  plan-2  N19  0.020
 4V8  plan-2  O22  0.020
 4V8  plan-2  H5   0.020
 4V8  plan-2  H6   0.020
 4V8  plan-2  H7   0.020
 4V8  plan-2  C23  0.020
 4V8  plan-3  C2   0.020
 4V8  plan-3  C3   0.020
 4V8  plan-3  N1   0.020
 4V8  plan-3  C4   0.020
 4V8  plan-3  N5   0.020
 4V8  plan-3  C6   0.020
 4V8  plan-3  C9   0.020
 4V8  plan-3  C10  0.020
 4V8  plan-3  H15  0.020
 4V8  plan-4  C24  0.020
 4V8  plan-4  C25  0.020
 4V8  plan-4  C26  0.020
 4V8  plan-4  C27  0.020
 4V8  plan-4  C28  0.020
 4V8  plan-4  C29  0.020
 4V8  plan-4  H10  0.020
 4V8  plan-4  H11  0.020
 4V8  plan-4  H12  0.020
 4V8  plan-4  H13  0.020
 4V8  plan-4  H14  0.020
 4V8  plan-4  C23  0.020
 4V8  plan-5  C16  0.020
 4V8  plan-5  C6   0.020
 4V8  plan-5  N7   0.020
 4V8  plan-5  C8   0.020

