# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:21:50 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 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=C1NC=CC(=C1)N2CCc3n[nH]c(c4ccncc4)c3C2
#
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
 4VB  4VB  4-[3-(pyridin-4-yl)-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]pyridin-2(1H)-one  ligand  37  22  .  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_4VB
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
 4VB  C2   C  CR5   0   0.442  -2.2381   0.8569  -0.1644
 4VB  C3   C  CR5   0  -0.195  -0.8779   1.0612  -0.0078
 4VB  C11  C  CR16  0  -0.400  -2.5511  -1.6100  -0.2473
 4VB  C12  C  CR16  0  -0.053  -3.3852  -2.7072  -0.1084
 4VB  C14  C  CR16  0  -0.058  -5.1685  -1.4050   0.3987
 4VB  C15  C  CR16  0  -0.371  -4.4221  -0.2439   0.2927
 4VB  C16  C  CR6   0   0.532   2.6605   0.1401   0.2234
 4VB  C17  C  CR16  0  -0.463   3.9079   0.8328   0.0693
 4VB  C18  C  CR16  0   0.051   5.0383   0.1135  -0.1061
 4VB  C20  C  CR6   0   0.524   3.8854  -1.9977   0.0131
 4VB  C21  C  CR16  0  -0.601   2.6881  -1.2457   0.1970
 4VB  N1   N  NR15  0  -0.520  -2.7548   2.0788  -0.4248
 4VB  C4   C  CR5   0   0.233  -0.7039   2.4408  -0.1846
 4VB  N5   N  N     0  -0.277  -1.8492   3.0444  -0.4456
 4VB  C6   C  CH2   0  -0.360   0.2345   0.1194   0.3161
 4VB  N7   N  NT    0  -0.532   1.4977   0.8361   0.3543
 4VB  C8   C  CH2   0  -0.339   1.4466   2.1899   0.8889
 4VB  C9   C  CH2   0  -0.503   0.6178   3.1005  -0.0082
 4VB  C10  C  CR6   0   0.145  -3.0705  -0.3328  -0.0435
 4VB  N13  N  N     0  -0.406  -4.6721  -2.6219   0.2067
 4VB  N19  N  NR16  0  -0.669   5.0325  -1.2353  -0.1323
 4VB  O22  O  O     0  -0.536   3.9623  -3.2286  -0.0106
 4VB  H2   H  HCR6  0   0.271  -2.9879  -3.7036  -0.2654
 4VB  H3   H  HCR6  0   0.270  -6.2192  -1.3440   0.6595
 4VB  H4   H  HCR6  0   0.271  -4.8973   0.7071   0.4934
 4VB  H5   H  HCR6  0   0.281   3.9807   1.9078   0.0402
 4VB  H6   H  HCR6  0   0.308   5.9994   0.5865  -0.2457
 4VB  H7   H  HCR6  0   0.272   1.7946  -1.8332   0.3473
 4VB  H8   H  HNR5  0   0.424  -3.7145   2.2983  -0.6421
 4VB  H9   H  HCH2  0   0.257   0.0379  -0.4058   1.2615
 4VB  H10  H  HCH2  0   0.268   0.3103  -0.6452  -0.4595
 4VB  H11  H  HCH2  0   0.257   1.0023   2.1619   1.8904
 4VB  H12  H  HCH2  0   0.276   2.4483   2.5867   1.0122
 4VB  H13  H  HCH2  0   0.260   1.1250   3.2428  -0.9663
 4VB  H14  H  HCH2  0   0.260   0.5114   4.0833   0.4537
 4VB  H15  H  HNR6  0   0.415   5.9042  -1.7270  -0.2667
 4VB  H1   H  HCR6  0   0.267  -1.5206  -1.7685  -0.5310

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
 4VB  C9   C8   single    1.523  0.020  1.523
 4VB  C9   C4   single    1.488  0.020  1.488
 4VB  C8   N7   single    1.456  0.020  1.456
 4VB  N5   C4   aromatic  1.321  0.020  1.321
 4VB  N5   N1   aromatic  1.324  0.020  1.324
 4VB  C4   C3   aromatic  1.402  0.020  1.402
 4VB  O22  C20  double    1.234  0.020  1.234
 4VB  C21  C20  single    1.426  0.020  1.426
 4VB  C21  C16  double    1.386  0.020  1.386
 4VB  N7   C16  single    1.362  0.020  1.362
 4VB  N7   C6   single    1.453  0.020  1.453
 4VB  N1   C2   aromatic  1.352  0.020  1.352
 4VB  C3   C2   aromatic  1.384  0.020  1.384
 4VB  C3   C6   single    1.493  0.020  1.493
 4VB  C20  N19  single    1.385  0.020  1.385
 4VB  C16  C17  single    1.435  0.020  1.435
 4VB  C2   C10  single    1.457  0.020  1.457
 4VB  N19  C18  single    1.349  0.020  1.349
 4VB  C17  C18  double    1.351  0.020  1.351
 4VB  C10  C15  aromatic  1.396  0.020  1.396
 4VB  C10  C11  aromatic  1.394  0.020  1.394
 4VB  C15  C14  aromatic  1.384  0.020  1.384
 4VB  C14  N13  aromatic  1.328  0.020  1.328
 4VB  C11  C12  aromatic  1.385  0.020  1.385
 4VB  C12  N13  aromatic  1.328  0.020  1.328
 4VB  C11  H1   single    0.930  0.020  1.080
 4VB  C12  H2   single    0.930  0.020  1.080
 4VB  C14  H3   single    0.930  0.020  1.080
 4VB  C15  H4   single    0.930  0.020  1.080
 4VB  C17  H5   single    0.930  0.020  1.080
 4VB  C18  H6   single    0.930  0.020  1.080
 4VB  C21  H7   single    0.930  0.020  1.080
 4VB  N1   H8   single    0.860  0.020  1.020
 4VB  C6   H9   single    0.970  0.020  1.090
 4VB  C6   H10  single    0.970  0.020  1.090
 4VB  C8   H11  single    0.970  0.020  1.090
 4VB  C8   H12  single    0.970  0.020  1.090
 4VB  C9   H13  single    0.970  0.020  1.090
 4VB  C9   H14  single    0.970  0.020  1.090
 4VB  N19  H15  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
 4VB  C10  C2   N1   122.38  3.000
 4VB  C10  C2   C3   132.26  3.000
 4VB  N1   C2   C3   105.31  3.000
 4VB  C6   C3   C4   123.76  3.000
 4VB  C6   C3   C2   131.57  3.000
 4VB  C4   C3   C2   104.65  3.000
 4VB  H1   C11  C10  121.89  3.000
 4VB  H1   C11  C12  118.97  3.000
 4VB  C10  C11  C12  119.12  3.000
 4VB  H2   C12  N13  116.66  3.000
 4VB  H2   C12  C11  119.52  3.000
 4VB  N13  C12  C11  123.82  3.000
 4VB  H3   C14  N13  116.65  3.000
 4VB  H3   C14  C15  119.59  3.000
 4VB  N13  C14  C15  123.76  3.000
 4VB  H4   C15  C10  121.74  3.000
 4VB  H4   C15  C14  119.08  3.000
 4VB  C10  C15  C14  119.16  3.000
 4VB  N7   C16  C21  122.00  3.000
 4VB  N7   C16  C17  120.39  3.000
 4VB  C21  C16  C17  117.59  3.000
 4VB  H5   C17  C18  118.09  3.000
 4VB  H5   C17  C16  122.89  3.000
 4VB  C18  C17  C16  118.96  3.000
 4VB  H6   C18  N19  116.05  3.000
 4VB  H6   C18  C17  121.87  3.000
 4VB  N19  C18  C17  122.08  3.000
 4VB  O22  C20  N19  119.72  3.000
 4VB  N19  C20  C21  114.75  3.000
 4VB  O22  C20  C21  125.53  3.000
 4VB  H7   C21  C20  115.21  3.000
 4VB  H7   C21  C16  121.65  3.000
 4VB  C20  C21  C16  123.12  3.000
 4VB  H8   N1   N5   119.26  3.000
 4VB  H8   N1   C2   127.03  3.000
 4VB  N5   N1   C2   113.62  3.000
 4VB  C9   C4   N5   126.24  3.000
 4VB  N5   C4   C3   111.54  3.000
 4VB  C9   C4   C3   122.12  3.000
 4VB  C4   N5   N1   104.87  3.000
 4VB  H10  C6   H9   106.79  3.000
 4VB  H10  C6   N7   107.69  3.000
 4VB  H9   C6   N7   111.63  3.000
 4VB  H10  C6   C3   109.83  3.000
 4VB  H9   C6   C3   110.77  3.000
 4VB  N7   C6   C3   110.02  3.000
 4VB  C8   N7   C6   115.96  3.000
 4VB  C6   N7   C16  119.20  3.000
 4VB  C8   N7   C16  122.71  3.000
 4VB  H12  C8   H11  106.26  3.000
 4VB  H12  C8   C9   110.54  3.000
 4VB  H11  C8   C9   109.44  3.000
 4VB  H12  C8   N7   110.45  3.000
 4VB  H11  C8   N7   109.02  3.000
 4VB  C9   C8   N7   111.01  3.000
 4VB  H14  C9   H13  107.39  3.000
 4VB  H14  C9   C8   110.01  3.000
 4VB  H13  C9   C8   109.97  3.000
 4VB  H14  C9   C4   111.28  3.000
 4VB  H13  C9   C4   111.47  3.000
 4VB  C8   C9   C4   106.75  3.000
 4VB  C15  C10  C11  117.04  3.000
 4VB  C11  C10  C2   121.54  3.000
 4VB  C15  C10  C2   121.42  3.000
 4VB  C14  N13  C12  117.10  3.000
 4VB  H15  N19  C20  117.44  3.000
 4VB  H15  N19  C18  119.06  3.000
 4VB  C20  N19  C18  123.50  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
 4VB  CONST_01  C4   N5   N1   C2     0.00   0.0  0
 4VB  CONST_02  N5   C4   C3   C2     0.00   0.0  0
 4VB  CONST_03  C14  C15  C10  C2   180.00   0.0  0
 4VB  CONST_04  C12  C11  C10  C2   180.00   0.0  0
 4VB  CONST_05  N1   N5   C4   C3     0.00   0.0  0
 4VB  CONST_06  N5   N1   C2   C3     0.00   0.0  0
 4VB  CONST_10  C14  C15  C10  C11    0.00   0.0  0
 4VB  CONST_11  C14  N13  C12  C11    0.00   0.0  0
 4VB  CONST_12  C15  C10  C11  C12    0.00   0.0  0
 4VB  CONST_13  C15  C14  N13  C12    0.00   0.0  0
 4VB  CONST_15  C4   C3   C2   N1     0.00   0.0  0
 4VB  CONST_16  C10  C2   C3   C4   180.00   0.0  0
 4VB  CONST_17  C10  C2   N1   N5   180.00   0.0  0
 4VB  CONST_18  N13  C14  C15  C10    0.00   0.0  0
 4VB  CONST_19  N13  C12  C11  C10    0.00   0.0  0
 4VB  CONST_20  C10  C2   C3   C6     0.00   0.0  0
 4VB  CONST_21  C21  C20  N19  C18    0.00   0.0  0
 4VB  CONST_22  O22  C20  N19  C18  180.00   0.0  0
 4VB  CONST_23  H4   C15  C10  C2     0.00   0.0  0
 4VB  CONST_24  H1   C11  C10  C2     0.00   0.0  0
 4VB  CONST_25  H8   N1   C2   C3   180.00   0.0  0
 4VB  CONST_26  H3   C14  N13  C12  180.00   0.0  0
 4VB  CONST_27  H2   C12  N13  C14  180.00   0.0  0
 4VB  CONST_28  H15  N19  C20  C21  180.00   0.0  0
 4VB  Var_01    N7   C6   C3   C2   179.42  30.0  1
 4VB  Var_02    C8   C9   C4   C3   -22.69  30.0  1
 4VB  Var_03    C8   N7   C6   C3    36.09  30.0  1
 4VB  Var_04    C9   C8   N7   C16  131.44  30.0  1
 4VB  Var_05    N7   C8   C9   C4    53.81  30.0  1

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
 4VB  plan-1  C16  0.020
 4VB  plan-1  C17  0.020
 4VB  plan-1  C18  0.020
 4VB  plan-1  C20  0.020
 4VB  plan-1  C21  0.020
 4VB  plan-1  N7   0.020
 4VB  plan-1  N19  0.020
 4VB  plan-1  O22  0.020
 4VB  plan-1  H5   0.020
 4VB  plan-1  H6   0.020
 4VB  plan-1  H7   0.020
 4VB  plan-1  H15  0.020
 4VB  plan-2  C2   0.020
 4VB  plan-2  C11  0.020
 4VB  plan-2  C12  0.020
 4VB  plan-2  C14  0.020
 4VB  plan-2  C15  0.020
 4VB  plan-2  C10  0.020
 4VB  plan-2  N13  0.020
 4VB  plan-2  H2   0.020
 4VB  plan-2  H3   0.020
 4VB  plan-2  H4   0.020
 4VB  plan-2  H1   0.020
 4VB  plan-3  C2   0.020
 4VB  plan-3  C3   0.020
 4VB  plan-3  N1   0.020
 4VB  plan-3  C4   0.020
 4VB  plan-3  N5   0.020
 4VB  plan-3  C6   0.020
 4VB  plan-3  C9   0.020
 4VB  plan-3  C10  0.020
 4VB  plan-3  H8   0.020
 4VB  plan-4  C16  0.020
 4VB  plan-4  C6   0.020
 4VB  plan-4  N7   0.020
 4VB  plan-4  C8   0.020

