# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:25:51 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-azanyl-5-[(2~{S})-3-methylbutan-2-yl]-7-[1-methyl-5-(2-oxidanylpropan-2-yl)pyrazol-3-yl]-1~{H}-pyrazolo[4,3-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C)N1C=C(c2cc(n(C)n2)C(C)(C)O)c3[nH]nc(N)c3C1=O
#
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
 5U3  5U3  3-azanyl-5-[(2~{S})-3-methylbutan-2-yl]-7-[1-methyl-5-(2-oxidanylpropan-2-yl)pyrazol-3-yl]-1~{H}-pyrazolo[4,3-c]pyridin-4-one  ligand  52  26  .  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_5U3
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
 5U3  C4   C  CH1   0  -0.069  -2.8748   2.0762  -0.5287
 5U3  C6   C  CH3   0  -0.668  -3.5665   2.1044  -1.8874
 5U3  C8   C  CR16  0  -0.074  -0.8200   0.7996  -0.2431
 5U3  C10  C  CR5   0   0.348   1.4225  -0.2275  -0.0131
 5U3  C17  C  CH3   0  -0.658   5.7461   0.6810  -1.1696
 5U3  C20  C  CR56  0   0.528  -0.7439  -1.5151   0.0817
 5U3  C24  C  CR5   0   0.391  -2.4645  -2.9221   0.2144
 5U3  C26  C  CR56  0  -0.366  -2.1322  -1.5503   0.0302
 5U3  C2   C  CH1   0  -0.241  -3.7674   2.4835   0.6558
 5U3  C3   C  CH3   0  -0.664  -4.2825   3.9068   0.4516
 5U3  N7   N  NR6   0  -0.555  -2.1859   0.7848  -0.3054
 5U3  C9   C  CR6   0  -0.083  -0.0302  -0.2912  -0.0590
 5U3  C11  C  CR15  0  -0.608   2.2835   0.8812  -0.0962
 5U3  C12  C  CR5   0   0.435   3.5535   0.3577   0.0115
 5U3  N13  N  NR5   0  -0.323   3.4009  -0.9806   0.1505
 5U3  C14  C  CH3   0  -0.541   4.3899  -2.0346   0.1759
 5U3  N15  N  N     0  -0.350   2.1185  -1.3428   0.1285
 5U3  C16  C  CT    0   0.133   4.8634   1.1225  -0.0051
 5U3  C18  C  CH3   0  -0.678   5.6012   0.9939   1.3297
 5U3  O19  O  OH1   0  -0.657   4.5683   2.4836  -0.2482
 5U3  N21  N  NR15  0  -0.559  -0.3404  -2.7687   0.2770
 5U3  N23  N  N     0  -0.301  -1.3736  -3.6422   0.3577
 5U3  N25  N  NH2   0  -0.849  -3.7217  -3.4544   0.3052
 5U3  C27  C  CR6   0   0.551  -2.9304  -0.3891  -0.1852
 5U3  O28  O  O     0  -0.498  -4.1558  -0.3907  -0.2629
 5U3  H1   H  HCH1  0   0.246  -2.0656   2.8104  -0.5670
 5U3  H2   H  HCH3  0   0.239  -4.4708   1.5005  -1.9025
 5U3  H3   H  HCH3  0   0.242  -3.8319   3.1275  -2.1486
 5U3  H4   H  HCH3  0   0.239  -2.8935   1.7375  -2.6629
 5U3  H5   H  HCR6  0   0.298  -0.3763   1.7783  -0.3608
 5U3  H6   H  HCH3  0   0.243   5.2144   0.7646  -2.1183
 5U3  H7   H  HCH3  0   0.247   6.6357   1.3103  -1.2160
 5U3  H8   H  HCH3  0   0.237   6.0795  -0.3491  -1.0601
 5U3  H9   H  HCH3  0   0.234  -3.6482   2.7106   2.8026
 5U3  H10  H  HCH3  0   0.230  -2.6794   1.3756   2.2023
 5U3  H11  H  HCH3  0   0.216  -2.1297   3.0368   1.9735
 5U3  H12  H  HCH1  0   0.239  -4.6292   1.8150   0.6937
 5U3  H13  H  HCH3  0   0.235  -4.9345   3.9930  -0.4173
 5U3  H14  H  HCH3  0   0.234  -4.8595   4.2265   1.3202
 5U3  H15  H  HCH3  0   0.217  -3.4582   4.6137   0.3267
 5U3  H16  H  HCR5  0   0.266   2.0189   1.9182  -0.2158
 5U3  H17  H  HCH3  0   0.261   4.6576  -2.3486  -0.8325
 5U3  H18  H  HCH3  0   0.257   5.2864  -1.7156   0.6956
 5U3  H19  H  HCH3  0   0.277   3.9706  -2.8819   0.7105
 5U3  H20  H  HCH3  0   0.248   6.5045   1.6053   1.3078
 5U3  H21  H  HCH3  0   0.242   4.9751   1.3389   2.1552
 5U3  H22  H  HCH3  0   0.237   5.9037  -0.0276   1.5539
 5U3  H23  H  HOH1  0   0.452   4.1651   2.8612   0.5416
 5U3  H24  H  HNR5  0   0.416   0.6144  -3.0817   0.3584
 5U3  H25  H  HNH2  0   0.383  -4.4369  -2.9232  -0.1641
 5U3  H26  H  HNH2  0   0.379  -3.7840  -4.4424   0.1162
 5U3  C1   C  CH3   0  -0.659  -3.0110   2.3895   1.9775

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
 5U3  C17  C16  single    1.526  0.020  1.526
 5U3  N23  N21  aromatic  1.355  0.020  1.355
 5U3  N23  C24  aromatic  1.315  0.020  1.315
 5U3  C14  N13  single    1.446  0.020  1.446
 5U3  N21  C20  aromatic  1.331  0.020  1.331
 5U3  N25  C24  single    1.368  0.020  1.368
 5U3  C24  C26  aromatic  1.423  0.020  1.423
 5U3  N13  N15  aromatic  1.333  0.020  1.333
 5U3  N13  C12  aromatic  1.354  0.020  1.354
 5U3  N15  C10  aromatic  1.322  0.020  1.322
 5U3  C16  C12  single    1.517  0.020  1.517
 5U3  C16  O19  single    1.414  0.020  1.414
 5U3  C16  C18  single    1.531  0.020  1.531
 5U3  C12  C11  aromatic  1.378  0.020  1.378
 5U3  C20  C26  aromatic  1.390  0.020  1.390
 5U3  C20  C9   single    1.424  0.020  1.424
 5U3  C10  C11  aromatic  1.406  0.020  1.406
 5U3  C10  C9   single    1.455  0.020  1.455
 5U3  C26  C27  single    1.425  0.020  1.425
 5U3  C9   C8   double    1.359  0.020  1.359
 5U3  C27  O28  double    1.228  0.020  1.228
 5U3  C27  N7   single    1.395  0.020  1.395
 5U3  C8   N7   single    1.367  0.020  1.367
 5U3  C6   C4   single    1.525  0.020  1.525
 5U3  N7   C4   single    1.481  0.020  1.481
 5U3  C4   C2   single    1.538  0.020  1.538
 5U3  C2   C3   single    1.527  0.020  1.527
 5U3  C2   C1   single    1.526  0.020  1.526
 5U3  C4   H1   single    0.970  0.020  1.090
 5U3  C6   H2   single    0.970  0.020  1.090
 5U3  C6   H3   single    0.970  0.020  1.090
 5U3  C6   H4   single    0.970  0.020  1.090
 5U3  C8   H5   single    0.930  0.020  1.080
 5U3  C17  H6   single    0.970  0.020  1.090
 5U3  C17  H7   single    0.970  0.020  1.090
 5U3  C17  H8   single    0.970  0.020  1.090
 5U3  C1   H9   single    0.970  0.020  1.090
 5U3  C1   H10  single    0.970  0.020  1.090
 5U3  C1   H11  single    0.970  0.020  1.090
 5U3  C2   H12  single    0.970  0.020  1.090
 5U3  C3   H13  single    0.970  0.020  1.090
 5U3  C3   H14  single    0.970  0.020  1.090
 5U3  C3   H15  single    0.970  0.020  1.090
 5U3  C11  H16  single    0.930  0.020  1.080
 5U3  C14  H17  single    0.970  0.020  1.090
 5U3  C14  H18  single    0.970  0.020  1.090
 5U3  C14  H19  single    0.970  0.020  1.090
 5U3  C18  H20  single    0.970  0.020  1.090
 5U3  C18  H21  single    0.970  0.020  1.090
 5U3  C18  H22  single    0.970  0.020  1.090
 5U3  O19  H23  single    0.850  0.020  0.980
 5U3  N21  H24  single    0.860  0.020  1.020
 5U3  N25  H25  single    0.890  0.020  1.040
 5U3  N25  H26  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
 5U3  H1   C4   N7   104.28  3.000
 5U3  H1   C4   C2   106.18  3.000
 5U3  N7   C4   C2   112.63  3.000
 5U3  H1   C4   C6   106.98  3.000
 5U3  C2   C4   C6   114.71  3.000
 5U3  N7   C4   C6   111.20  3.000
 5U3  H4   C6   H3   107.21  3.000
 5U3  H4   C6   H2   108.45  3.000
 5U3  H3   C6   H2   108.41  3.000
 5U3  H4   C6   C4   110.34  3.000
 5U3  H3   C6   C4   109.99  3.000
 5U3  H2   C6   C4   112.29  3.000
 5U3  H5   C8   C9   120.19  3.000
 5U3  H5   C8   N7   114.51  3.000
 5U3  C9   C8   N7   125.30  3.000
 5U3  N15  C10  C11  110.43  3.000
 5U3  C11  C10  C9   130.09  3.000
 5U3  N15  C10  C9   119.48  3.000
 5U3  H8   C17  H7   107.49  3.000
 5U3  H8   C17  H6   108.03  3.000
 5U3  H7   C17  H6   108.45  3.000
 5U3  H8   C17  C16  111.97  3.000
 5U3  H7   C17  C16  109.71  3.000
 5U3  H6   C17  C16  111.07  3.000
 5U3  N21  C20  C9   132.22  3.000
 5U3  C9   C20  C26  121.26  3.000
 5U3  N21  C20  C26  106.52  3.000
 5U3  N25  C24  N23  122.82  3.000
 5U3  N25  C24  C26  126.73  3.000
 5U3  N23  C24  C26  110.38  3.000
 5U3  C27  C26  C24  132.37  3.000
 5U3  C27  C26  C20  122.98  3.000
 5U3  C24  C26  C20  104.65  3.000
 5U3  H12  C2   C3   108.00  3.000
 5U3  H12  C2   C1   108.89  3.000
 5U3  C3   C2   C1   109.90  3.000
 5U3  H12  C2   C4   108.83  3.000
 5U3  C1   C2   C4   111.29  3.000
 5U3  C3   C2   C4   109.85  3.000
 5U3  H15  C3   H14  107.48  3.000
 5U3  H15  C3   H13  107.99  3.000
 5U3  H14  C3   H13  107.18  3.000
 5U3  H15  C3   C2   111.32  3.000
 5U3  H14  C3   C2   110.19  3.000
 5U3  H13  C3   C2   112.46  3.000
 5U3  C27  N7   C8   122.56  3.000
 5U3  C8   N7   C4   117.53  3.000
 5U3  C27  N7   C4   119.91  3.000
 5U3  C20  C9   C10  122.35  3.000
 5U3  C10  C9   C8   123.32  3.000
 5U3  C20  C9   C8   114.33  3.000
 5U3  H16  C11  C12  126.95  3.000
 5U3  H16  C11  C10  127.98  3.000
 5U3  C12  C11  C10  105.08  3.000
 5U3  C16  C12  N13  126.63  3.000
 5U3  C16  C12  C11  127.12  3.000
 5U3  N13  C12  C11  106.24  3.000
 5U3  N15  N13  C14  117.42  3.000
 5U3  N15  N13  C12  112.04  3.000
 5U3  C14  N13  C12  130.19  3.000
 5U3  H19  C14  H18  108.23  3.000
 5U3  H19  C14  H17  109.00  3.000
 5U3  H18  C14  H17  108.99  3.000
 5U3  H19  C14  N13  108.26  3.000
 5U3  H18  C14  N13  111.07  3.000
 5U3  H17  C14  N13  111.22  3.000
 5U3  N13  N15  C10  106.21  3.000
 5U3  O19  C16  C18  109.36  3.000
 5U3  C18  C16  C12  111.37  3.000
 5U3  O19  C16  C12  107.87  3.000
 5U3  C18  C16  C17  111.24  3.000
 5U3  O19  C16  C17  105.54  3.000
 5U3  C12  C16  C17  111.21  3.000
 5U3  H22  C18  H21  107.46  3.000
 5U3  H22  C18  H20  107.46  3.000
 5U3  H21  C18  H20  108.23  3.000
 5U3  H22  C18  C16  113.10  3.000
 5U3  H21  C18  C16  110.87  3.000
 5U3  H20  C18  C16  109.54  3.000
 5U3  H23  O19  C16  108.88  3.000
 5U3  H24  N21  N23  121.14  3.000
 5U3  H24  N21  C20  126.25  3.000
 5U3  N23  N21  C20  112.61  3.000
 5U3  N21  N23  C24  105.84  3.000
 5U3  H26  N25  H25  112.69  3.000
 5U3  H26  N25  C24  115.20  3.000
 5U3  H25  N25  C24  114.61  3.000
 5U3  O28  C27  N7   121.88  3.000
 5U3  N7   C27  C26  113.55  3.000
 5U3  O28  C27  C26  124.56  3.000
 5U3  H11  C1   H10  107.83  3.000
 5U3  H11  C1   H9   107.42  3.000
 5U3  H10  C1   H9   107.19  3.000
 5U3  H11  C1   C2   111.09  3.000
 5U3  H10  C1   C2   112.75  3.000
 5U3  H9   C1   C2   110.33  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
 5U3  CONST_01  C12  N13  N15  C10     0.00   0.0  0
 5U3  CONST_02  N13  C12  C11  C10     0.00   0.0  0
 5U3  CONST_03  C24  N23  N21  C20     0.00   0.0  0
 5U3  CONST_04  N23  C24  C26  C20     0.00   0.0  0
 5U3  CONST_05  N21  C20  C26  C24     0.00   0.0  0
 5U3  CONST_06  N21  N23  C24  C26     0.00   0.0  0
 5U3  CONST_07  N23  N21  C20  C26     0.00   0.0  0
 5U3  CONST_08  N15  N13  C12  C11     0.00   0.0  0
 5U3  CONST_09  N13  N15  C10  C11     0.00   0.0  0
 5U3  CONST_10  N15  C10  C11  C12     0.00   0.0  0
 5U3  CONST_11  N13  N15  C10  C9    180.00   0.0  0
 5U3  CONST_12  C12  C11  C10  C9    180.00   0.0  0
 5U3  CONST_13  C26  C27  N7   C8      0.00   0.0  0
 5U3  CONST_14  C14  N13  N15  C10   180.00   0.0  0
 5U3  CONST_15  C16  C12  C11  C10   180.00   0.0  0
 5U3  CONST_16  N25  C24  C26  C20   180.00   0.0  0
 5U3  CONST_17  C14  N13  C12  C11   180.00   0.0  0
 5U3  CONST_18  C16  C12  N13  N15   180.00   0.0  0
 5U3  CONST_19  N25  C24  N23  N21   180.00   0.0  0
 5U3  CONST_20  C27  C26  C24  N25     0.00   0.0  0
 5U3  CONST_21  C26  C27  N7   C4    180.00   0.0  0
 5U3  CONST_22  O28  C27  N7   C8    180.00   0.0  0
 5U3  CONST_23  H24  N21  N23  C24   180.00   0.0  0
 5U3  CONST_24  H16  C11  C10  C9      0.00   0.0  0
 5U3  CONST_25  O28  C27  N7   C4      0.00   0.0  0
 5U3  Var_01    N15  C10  C9   C8   -177.91  30.0  2
 5U3  Var_02    N13  C12  C16  C17    61.39  30.0  2
 5U3  Var_03    H17  C14  N13  C12   -84.24  30.0  2
 5U3  Var_04    H6   C17  C16  C12    54.68  30.0  3
 5U3  Var_05    H20  C18  C16  C12  -176.38  30.0  3
 5U3  Var_06    H13  C3   C2   C4     64.39  30.0  3
 5U3  Var_07    H9   C1   C2   C4    178.27  30.0  3

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
 5U3  chir_01  C4  C6  N7  C2  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
 5U3  plan-1  C10  0.020
 5U3  plan-1  C9   0.020
 5U3  plan-1  C11  0.020
 5U3  plan-1  C12  0.020
 5U3  plan-1  N13  0.020
 5U3  plan-1  C14  0.020
 5U3  plan-1  N15  0.020
 5U3  plan-1  C16  0.020
 5U3  plan-1  H16  0.020
 5U3  plan-2  C4   0.020
 5U3  plan-2  C8   0.020
 5U3  plan-2  C10  0.020
 5U3  plan-2  C20  0.020
 5U3  plan-2  C24  0.020
 5U3  plan-2  C26  0.020
 5U3  plan-2  N7   0.020
 5U3  plan-2  C9   0.020
 5U3  plan-2  N21  0.020
 5U3  plan-2  N23  0.020
 5U3  plan-2  N25  0.020
 5U3  plan-2  C27  0.020
 5U3  plan-2  O28  0.020
 5U3  plan-2  H5   0.020
 5U3  plan-2  H24  0.020
 5U3  plan-3  C24  0.020
 5U3  plan-3  N25  0.020
 5U3  plan-3  H25  0.020
 5U3  plan-3  H26  0.020

