# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:07:09 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-azanyl-5-(2-methylphenyl)-7-(1-methylpyrazol-3-yl)-1~{H}-pyrazolo[4,3-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc(n1)C2=CN(C(=O)c3c(N)n[nH]c23)c4ccccc4C
#
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
 5U4  5U4  3-azanyl-5-(2-methylphenyl)-7-(1-methylpyrazol-3-yl)-1~{H}-pyrazolo[4,3-c]pyridin-4-one  ligand  40  24  .  2022-07-23  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_5U4
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
 5U4  C4   C  CR16  0  -0.230   4.9508   2.1288  -0.3296
 5U4  C5   C  CR16  0  -0.283   4.2626   1.8289  -1.4961
 5U4  C6   C  CR16  0  -0.246   3.0548   1.1508  -1.4197
 5U4  C7   C  CR6   0   0.234   2.5477   0.7813  -0.1844
 5U4  C10  C  CR6   0  -0.074  -1.1064   0.3442  -0.0912
 5U4  C13  C  CR15  0   0.043  -3.7927   2.7809  -0.2166
 5U4  C17  C  CR56  0   0.531  -1.1545  -1.0791  -0.0043
 5U4  C21  C  CR5   0   0.396  -0.4690  -3.1971   0.1037
 5U4  C24  C  CR6   0   0.531   1.3063  -1.2940  -0.0554
 5U4  C2   C  CR6   0   0.104   3.2219   1.0704   1.0018
 5U4  C3   C  CR16  0  -0.320   4.4320   1.7522   0.9017
 5U4  N8   N  NR6   0  -0.635   1.2898   0.1024  -0.1293
 5U4  C9   C  CR16  0  -0.068   0.1480   0.8594  -0.1469
 5U4  C11  C  CR5   0   0.352  -2.3056   1.1680  -0.1180
 5U4  C12  C  CR15  0  -0.571  -2.4364   2.5642  -0.2489
 5U4  N14  N  NR5   0  -0.248  -4.3824   1.5813  -0.0797
 5U4  N16  N  N     0  -0.355  -3.4979   0.5948  -0.0163
 5U4  N18  N  NR15  0  -0.555  -2.1779  -1.9261   0.0663
 5U4  N20  N  N     0  -0.299  -1.7835  -3.2201   0.1296
 5U4  C23  C  CR56  0  -0.377   0.0005  -1.8568   0.0158
 5U4  O25  O  O     0  -0.483   2.3654  -1.9084  -0.0593
 5U4  H1   H  HCR6  0   0.261   5.8926   2.6600  -0.3757
 5U4  H2   H  HCR6  0   0.263   4.6611   2.1165  -2.4597
 5U4  H3   H  HCR6  0   0.265   2.5033   0.9072  -2.3191
 5U4  H4   H  HCR5  0   0.298  -4.3665   3.6908  -0.2875
 5U4  H5   H  HCH3  0   0.261  -6.0324   0.9322   1.0281
 5U4  H6   H  HCH3  0   0.261  -6.3498   2.2126  -0.1527
 5U4  H7   H  HCH3  0   0.263  -6.0836   0.5529  -0.7044
 5U4  H8   H  HCH3  0   0.254   2.6747  -0.4251   2.4471
 5U4  H9   H  HCH3  0   0.256   3.2708   1.0759   3.1433
 5U4  H10  H  HCH3  0   0.249   1.6442   0.9974   2.4757
 5U4  H11  H  HCR6  0   0.256   4.9759   1.9916   1.8076
 5U4  H12  H  HCR6  0   0.308   0.3177   1.9254  -0.2083
 5U4  H13  H  HCR5  0   0.267  -1.6647   3.3079  -0.3558
 5U4  H14  H  HNR5  0   0.418  -3.1556  -1.6795   0.0747
 5U4  H15  H  HNH2  0   0.384   1.2223  -4.2494  -0.1668
 5U4  H16  H  HNH2  0   0.381  -0.1655  -5.1831  -0.0499
 5U4  C1   C  CH3   0  -0.735   2.6720   0.6605   2.3347
 5U4  N22  N  NH2   0  -0.848   0.2940  -4.3263   0.2157
 5U4  C15  C  CH3   0  -0.507  -5.7926   1.2990   0.0316

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
 5U4  N20  N18  aromatic  1.354  0.020  1.354
 5U4  N20  C21  aromatic  1.315  0.020  1.315
 5U4  C15  N14  single    1.443  0.020  1.443
 5U4  N18  C17  aromatic  1.330  0.020  1.330
 5U4  N22  C21  single    1.367  0.020  1.367
 5U4  C21  C23  aromatic  1.423  0.020  1.423
 5U4  N14  N16  aromatic  1.326  0.020  1.326
 5U4  N14  C13  aromatic  1.344  0.020  1.344
 5U4  N16  C11  aromatic  1.327  0.020  1.327
 5U4  C13  C12  aromatic  1.374  0.020  1.374
 5U4  C17  C23  aromatic  1.393  0.020  1.393
 5U4  C17  C10  single    1.427  0.020  1.427
 5U4  C23  C24  single    1.424  0.020  1.424
 5U4  C11  C12  aromatic  1.408  0.020  1.408
 5U4  C11  C10  single    1.455  0.020  1.455
 5U4  C10  C9   double    1.357  0.020  1.357
 5U4  C24  O25  double    1.224  0.020  1.224
 5U4  C24  N8   single    1.398  0.020  1.398
 5U4  C6   C5   aromatic  1.387  0.020  1.387
 5U4  C6   C7   aromatic  1.386  0.020  1.386
 5U4  C9   N8   single    1.370  0.020  1.370
 5U4  N8   C7   single    1.431  0.020  1.431
 5U4  C5   C4   aromatic  1.387  0.020  1.387
 5U4  C7   C2   aromatic  1.395  0.020  1.395
 5U4  C4   C3   aromatic  1.388  0.020  1.388
 5U4  C2   C3   aromatic  1.393  0.020  1.393
 5U4  C2   C1   single    1.499  0.020  1.499
 5U4  C4   H1   single    0.930  0.020  1.080
 5U4  C5   H2   single    0.930  0.020  1.080
 5U4  C6   H3   single    0.930  0.020  1.080
 5U4  C13  H4   single    0.930  0.020  1.080
 5U4  C15  H5   single    0.970  0.020  1.090
 5U4  C15  H6   single    0.970  0.020  1.090
 5U4  C15  H7   single    0.970  0.020  1.090
 5U4  C1   H8   single    0.970  0.020  1.090
 5U4  C1   H9   single    0.970  0.020  1.090
 5U4  C1   H10  single    0.970  0.020  1.090
 5U4  C3   H11  single    0.930  0.020  1.080
 5U4  C9   H12  single    0.930  0.020  1.080
 5U4  C12  H13  single    0.930  0.020  1.080
 5U4  N18  H14  single    0.860  0.020  1.020
 5U4  N22  H15  single    0.890  0.020  1.040
 5U4  N22  H16  single    0.890  0.020  1.040

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
 5U4  H1   C4   C3   119.74  3.000
 5U4  H1   C4   C5   120.13  3.000
 5U4  C3   C4   C5   120.12  3.000
 5U4  H2   C5   C6   119.99  3.000
 5U4  H2   C5   C4   120.59  3.000
 5U4  C6   C5   C4   119.42  3.000
 5U4  H3   C6   C7   119.62  3.000
 5U4  H3   C6   C5   120.51  3.000
 5U4  C7   C6   C5   119.87  3.000
 5U4  N8   C7   C2   119.39  3.000
 5U4  C2   C7   C6   121.75  3.000
 5U4  N8   C7   C6   118.86  3.000
 5U4  C11  C10  C9   123.10  3.000
 5U4  C9   C10  C17  114.35  3.000
 5U4  C11  C10  C17  122.55  3.000
 5U4  H4   C13  N14  121.78  3.000
 5U4  H4   C13  C12  131.07  3.000
 5U4  N14  C13  C12  107.15  3.000
 5U4  C23  C17  N18  106.36  3.000
 5U4  C23  C17  C10  122.01  3.000
 5U4  N18  C17  C10  131.63  3.000
 5U4  C23  C21  N22  126.78  3.000
 5U4  C23  C21  N20  110.34  3.000
 5U4  N22  C21  N20  122.80  3.000
 5U4  O25  C24  C23  126.52  3.000
 5U4  O25  C24  N8   120.74  3.000
 5U4  C23  C24  N8   112.74  3.000
 5U4  C3   C2   C1   121.10  3.000
 5U4  C1   C2   C7   121.48  3.000
 5U4  C3   C2   C7   117.42  3.000
 5U4  H11  C3   C2   118.97  3.000
 5U4  H11  C3   C4   119.61  3.000
 5U4  C2   C3   C4   121.42  3.000
 5U4  C9   N8   C24  124.21  3.000
 5U4  C9   N8   C7   118.04  3.000
 5U4  C24  N8   C7   117.75  3.000
 5U4  H12  C9   N8   114.50  3.000
 5U4  H12  C9   C10  121.44  3.000
 5U4  N8   C9   C10  124.06  3.000
 5U4  N16  C11  C12  110.61  3.000
 5U4  C12  C11  C10  129.75  3.000
 5U4  N16  C11  C10  119.65  3.000
 5U4  H13  C12  C11  128.85  3.000
 5U4  H13  C12  C13  126.92  3.000
 5U4  C11  C12  C13  104.23  3.000
 5U4  N16  N14  C15  120.17  3.000
 5U4  N16  N14  C13  112.10  3.000
 5U4  C15  N14  C13  127.71  3.000
 5U4  N14  N16  C11  105.91  3.000
 5U4  H14  N18  N20  121.04  3.000
 5U4  H14  N18  C17  126.21  3.000
 5U4  N20  N18  C17  112.75  3.000
 5U4  N18  N20  C21  105.87  3.000
 5U4  C24  C23  C21  132.70  3.000
 5U4  C24  C23  C17  122.63  3.000
 5U4  C21  C23  C17  104.67  3.000
 5U4  H10  C1   H9   107.72  3.000
 5U4  H10  C1   H8   107.23  3.000
 5U4  H9   C1   H8   107.56  3.000
 5U4  H10  C1   C2   112.10  3.000
 5U4  H9   C1   C2   110.76  3.000
 5U4  H8   C1   C2   111.27  3.000
 5U4  H16  N22  H15  112.65  3.000
 5U4  H16  N22  C21  115.22  3.000
 5U4  H15  N22  C21  114.85  3.000
 5U4  H7   C15  H6   108.96  3.000
 5U4  H7   C15  H5   109.24  3.000
 5U4  H6   C15  H5   109.02  3.000
 5U4  H7   C15  N14  110.09  3.000
 5U4  H6   C15  N14  108.89  3.000
 5U4  H5   C15  N14  110.61  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
 5U4  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 5U4  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 5U4  CONST_03  C2   C7   C6   C5      0.00   0.0  0
 5U4  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 5U4  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 5U4  CONST_06  C3   C2   C7   C6      0.00   0.0  0
 5U4  CONST_07  C11  N16  N14  C13     0.00   0.0  0
 5U4  CONST_08  N16  C11  C12  C13     0.00   0.0  0
 5U4  CONST_09  C21  N20  N18  C17     0.00   0.0  0
 5U4  CONST_10  N20  C21  C23  C17     0.00   0.0  0
 5U4  CONST_11  N18  C17  C23  C21     0.00   0.0  0
 5U4  CONST_12  N14  C13  C12  C11     0.00   0.0  0
 5U4  CONST_13  N16  N14  C13  C12     0.00   0.0  0
 5U4  CONST_14  N14  N16  C11  C12     0.00   0.0  0
 5U4  CONST_15  C23  C21  N20  N18     0.00   0.0  0
 5U4  CONST_16  C23  C17  N18  N20     0.00   0.0  0
 5U4  CONST_17  N8   C7   C6   C5    180.00   0.0  0
 5U4  CONST_18  N14  N16  C11  C10   180.00   0.0  0
 5U4  CONST_19  C13  C12  C11  C10   180.00   0.0  0
 5U4  CONST_20  N8   C7   C2   C3    180.00   0.0  0
 5U4  CONST_21  C23  C24  N8   C7    180.00   0.0  0
 5U4  CONST_22  C23  C24  N8   C9      0.00   0.0  0
 5U4  CONST_23  C1   C2   C3   C4    180.00   0.0  0
 5U4  CONST_24  C1   C2   C7   C6    180.00   0.0  0
 5U4  CONST_25  C11  N16  N14  C15   180.00   0.0  0
 5U4  CONST_26  C12  C13  N14  C15   180.00   0.0  0
 5U4  CONST_27  N22  C21  C23  C17   180.00   0.0  0
 5U4  CONST_28  N22  C21  C23  C24     0.00   0.0  0
 5U4  CONST_29  N8   C7   C2   C1      0.00   0.0  0
 5U4  CONST_30  N22  C21  N20  N18   180.00   0.0  0
 5U4  CONST_31  O25  C24  N8   C7      0.00   0.0  0
 5U4  CONST_32  O25  C24  N8   C9    180.00   0.0  0
 5U4  CONST_33  H3   C6   C5   C4    180.00   0.0  0
 5U4  CONST_34  H11  C3   C4   C5    180.00   0.0  0
 5U4  CONST_35  H1   C4   C5   C6    180.00   0.0  0
 5U4  CONST_36  H2   C5   C6   C7    180.00   0.0  0
 5U4  CONST_37  H14  N18  C17  C10     0.00   0.0  0
 5U4  CONST_38  H13  C12  C11  C10     0.00   0.0  0
 5U4  CONST_39  H4   C13  C12  C11   180.00   0.0  0
 5U4  Var_01    C24  N8   C7   C6     96.24  30.0  2
 5U4  Var_02    N16  C11  C10  C17     2.20  30.0  2
 5U4  Var_03    H8   C1   C2   C7     67.29  30.0  2
 5U4  Var_04    H5   C15  N14  C13  -111.83  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
 5U4  plan-1  C10  0.020
 5U4  plan-1  C13  0.020
 5U4  plan-1  C11  0.020
 5U4  plan-1  C12  0.020
 5U4  plan-1  N14  0.020
 5U4  plan-1  N16  0.020
 5U4  plan-1  H4   0.020
 5U4  plan-1  H13  0.020
 5U4  plan-1  C15  0.020
 5U4  plan-2  C4   0.020
 5U4  plan-2  C5   0.020
 5U4  plan-2  C6   0.020
 5U4  plan-2  C7   0.020
 5U4  plan-2  C2   0.020
 5U4  plan-2  C3   0.020
 5U4  plan-2  N8   0.020
 5U4  plan-2  H1   0.020
 5U4  plan-2  H2   0.020
 5U4  plan-2  H3   0.020
 5U4  plan-2  H11  0.020
 5U4  plan-2  C1   0.020
 5U4  plan-3  C7   0.020
 5U4  plan-3  C10  0.020
 5U4  plan-3  C17  0.020
 5U4  plan-3  C21  0.020
 5U4  plan-3  C24  0.020
 5U4  plan-3  N8   0.020
 5U4  plan-3  C9   0.020
 5U4  plan-3  C11  0.020
 5U4  plan-3  N18  0.020
 5U4  plan-3  N20  0.020
 5U4  plan-3  C23  0.020
 5U4  plan-3  O25  0.020
 5U4  plan-3  H12  0.020
 5U4  plan-3  H14  0.020
 5U4  plan-3  N22  0.020
 5U4  plan-4  C21  0.020
 5U4  plan-4  H15  0.020
 5U4  plan-4  H16  0.020
 5U4  plan-4  N22  0.020

