# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:55:57 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: ~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-6-(1-methylpyrazol-4-yl)pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cccc(n2)C(=O)Nc3cn(C)nc3C(N)=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
 6YD  6YD  ~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-6-(1-methylpyrazol-4-yl)pyridine-2-carboxamide  ligand  39  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6YD
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
 6YD  N01  N  NH1   0  -0.743  -1.2183   0.7681  -0.0055
 6YD  C02  C  C     0   0.515  -0.8349   2.0568   0.0044
 6YD  O03  O  O     0  -0.462  -1.6029   3.0051   0.0181
 6YD  C04  C  CR6   0   0.109   0.6546   2.2348  -0.0046
 6YD  N05  N  N     0  -0.488   1.3820   1.1265  -0.0172
 6YD  C06  C  CR6   0   0.238   2.7082   1.2074  -0.0277
 6YD  C07  C  CR16  0  -0.343   3.3537   2.4485  -0.0254
 6YD  C08  C  CR16  0  -0.144   2.5915   3.6008  -0.0123
 6YD  C09  C  CR16  0  -0.306   1.2058   3.5058  -0.0015
 6YD  C10  C  CR5   0  -0.173   3.4405  -0.0494  -0.0409
 6YD  C11  C  CR15  0  -0.103   4.8297  -0.2819  -0.0754
 6YD  N12  N  N     0  -0.274   5.1005  -1.5712  -0.0731
 6YD  N13  N  NR5   0  -0.266   3.9176  -2.1824  -0.0362
 6YD  C14  C  CR15  0   0.057   2.8945  -1.3209  -0.0179
 6YD  C15  C  CR5   0   0.115  -2.5223   0.3131  -0.0055
 6YD  C16  C  CR15  0   0.015  -3.7126   1.0121   0.0104
 6YD  N17  N  NR5   0  -0.254  -4.6920   0.0807   0.0086
 6YD  N18  N  N     0  -0.280  -4.2347  -1.1477  -0.0113
 6YD  C19  C  CR5   0   0.071  -2.9124  -1.0421  -0.0182
 6YD  C20  C  CH3   0  -0.507  -6.1157   0.3295  -0.0183
 6YD  C21  C  C     0   0.510  -2.0265  -2.2202  -0.0308
 6YD  N22  N  NH2   0  -0.806  -2.6375  -3.4083  -0.0385
 6YD  O23  O  O     0  -0.494  -0.8046  -2.0814  -0.0341
 6YD  C24  C  CH3   0  -0.505   3.8500  -3.6245  -0.0362
 6YD  H1   H  HNH1  0   0.426  -0.4889   0.0639  -0.0170
 6YD  H2   H  HCR6  0   0.270   4.4334   2.5100  -0.0327
 6YD  H3   H  HCR6  0   0.280   3.0724   4.5699  -0.0101
 6YD  H4   H  HCR6  0   0.275   0.5798   4.3863   0.0089
 6YD  H5   H  HCR5  0   0.262   5.6339   0.4382  -0.1010
 6YD  H6   H  HCR5  0   0.295   1.8674  -1.6478   0.0114
 6YD  H7   H  HCR5  0   0.306  -3.9300   2.0645   0.0255
 6YD  H8   H  HCH3  0   0.267  -6.5254   0.0944  -0.9989
 6YD  H9   H  HCH3  0   0.269  -6.6075  -0.2802   0.7351
 6YD  H10  H  HCH3  0   0.264  -6.2946   1.3774   0.2012
 6YD  H11  H  HNH2  0   0.413  -3.6409  -3.4818  -0.0336
 6YD  H12  H  HNH2  0   0.408  -2.0990  -4.2589  -0.0463
 6YD  H13  H  HCH3  0   0.264   4.4390  -4.0245   0.7859
 6YD  H14  H  HCH3  0   0.259   2.8153  -3.9297   0.0895
 6YD  H15  H  HCH3  0   0.263   4.2267  -4.0236  -0.9760

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
 6YD  C24  N13  single    1.444  0.020  1.444
 6YD  N13  N12  aromatic  1.332  0.020  1.332
 6YD  N13  C14  aromatic  1.338  0.020  1.338
 6YD  N12  C11  aromatic  1.317  0.020  1.317
 6YD  C14  C10  aromatic  1.384  0.020  1.384
 6YD  C11  C10  aromatic  1.409  0.020  1.409
 6YD  N22  C21  single    1.336  0.020  1.336
 6YD  O23  C21  double    1.230  0.020  1.230
 6YD  C10  C06  single    1.455  0.020  1.455
 6YD  C21  C19  single    1.474  0.020  1.474
 6YD  C06  N05  aromatic  1.329  0.020  1.329
 6YD  C06  C07  aromatic  1.399  0.020  1.399
 6YD  N05  C04  aromatic  1.326  0.020  1.326
 6YD  C19  N18  aromatic  1.327  0.020  1.327
 6YD  C19  C15  aromatic  1.410  0.020  1.410
 6YD  C07  C08  aromatic  1.382  0.020  1.382
 6YD  N18  N17  aromatic  1.311  0.020  1.311
 6YD  N01  C15  single    1.381  0.020  1.381
 6YD  N01  C02  single    1.345  0.020  1.345
 6YD  C15  C16  aromatic  1.380  0.020  1.380
 6YD  C04  C02  single    1.500  0.020  1.500
 6YD  C04  C09  aromatic  1.385  0.020  1.385
 6YD  C08  C09  aromatic  1.389  0.020  1.389
 6YD  C02  O03  double    1.220  0.020  1.220
 6YD  N17  C16  aromatic  1.352  0.020  1.352
 6YD  N17  C20  single    1.446  0.020  1.446
 6YD  N01  H1   single    0.860  0.020  1.020
 6YD  C07  H2   single    0.930  0.020  1.080
 6YD  C08  H3   single    0.930  0.020  1.080
 6YD  C09  H4   single    0.930  0.020  1.080
 6YD  C11  H5   single    0.930  0.020  1.080
 6YD  C14  H6   single    0.930  0.020  1.080
 6YD  C16  H7   single    0.930  0.020  1.080
 6YD  C20  H8   single    0.970  0.020  1.090
 6YD  C20  H9   single    0.970  0.020  1.090
 6YD  C20  H10  single    0.970  0.020  1.090
 6YD  N22  H11  single    0.860  0.020  1.020
 6YD  N22  H12  single    0.860  0.020  1.020
 6YD  C24  H13  single    0.970  0.020  1.090
 6YD  C24  H14  single    0.970  0.020  1.090
 6YD  C24  H15  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
 6YD  H1   N01  C15  116.77  3.000
 6YD  H1   N01  C02  117.43  3.000
 6YD  C15  N01  C02  125.80  3.000
 6YD  C04  C02  O03  122.19  3.000
 6YD  O03  C02  N01  124.43  3.000
 6YD  C04  C02  N01  113.38  3.000
 6YD  C09  C04  N05  123.27  3.000
 6YD  C09  C04  C02  120.26  3.000
 6YD  N05  C04  C02  116.47  3.000
 6YD  C06  N05  C04  119.80  3.000
 6YD  C10  C06  C07  122.30  3.000
 6YD  C07  C06  N05  120.96  3.000
 6YD  C10  C06  N05  116.74  3.000
 6YD  H2   C07  C08  120.22  3.000
 6YD  H2   C07  C06  120.73  3.000
 6YD  C08  C07  C06  119.04  3.000
 6YD  H3   C08  C09  120.32  3.000
 6YD  H3   C08  C07  120.13  3.000
 6YD  C09  C08  C07  119.56  3.000
 6YD  H4   C09  C08  121.48  3.000
 6YD  H4   C09  C04  121.15  3.000
 6YD  C08  C09  C04  117.37  3.000
 6YD  C14  C10  C11  103.75  3.000
 6YD  C11  C10  C06  129.73  3.000
 6YD  C14  C10  C06  126.51  3.000
 6YD  H5   C11  N12  119.97  3.000
 6YD  H5   C11  C10  128.67  3.000
 6YD  N12  C11  C10  111.36  3.000
 6YD  N13  N12  C11  105.46  3.000
 6YD  C24  N13  C14  127.41  3.000
 6YD  C14  N13  N12  112.59  3.000
 6YD  C24  N13  N12  120.00  3.000
 6YD  H6   C14  N13  122.25  3.000
 6YD  H6   C14  C10  130.90  3.000
 6YD  N13  C14  C10  106.84  3.000
 6YD  C19  C15  C16  104.37  3.000
 6YD  C16  C15  N01  130.34  3.000
 6YD  C19  C15  N01  125.29  3.000
 6YD  H7   C16  N17  121.89  3.000
 6YD  H7   C16  C15  132.10  3.000
 6YD  N17  C16  C15  106.01  3.000
 6YD  C20  N17  N18  120.30  3.000
 6YD  C20  N17  C16  126.52  3.000
 6YD  N18  N17  C16  113.14  3.000
 6YD  C19  N18  N17  105.86  3.000
 6YD  C21  C19  N18  122.38  3.000
 6YD  N18  C19  C15  110.62  3.000
 6YD  C21  C19  C15  127.01  3.000
 6YD  H10  C20  H9   109.08  3.000
 6YD  H10  C20  H8   109.18  3.000
 6YD  H9   C20  H8   109.45  3.000
 6YD  H10  C20  N17  108.95  3.000
 6YD  H9   C20  N17  109.65  3.000
 6YD  H8   C20  N17  110.50  3.000
 6YD  O23  C21  N22  123.69  3.000
 6YD  O23  C21  C19  120.46  3.000
 6YD  N22  C21  C19  115.85  3.000
 6YD  H12  N22  H11  118.15  3.000
 6YD  H12  N22  C21  120.45  3.000
 6YD  H11  N22  C21  121.40  3.000
 6YD  H15  C24  H14  109.06  3.000
 6YD  H15  C24  H13  109.30  3.000
 6YD  H14  C24  H13  108.97  3.000
 6YD  H15  C24  N13  110.50  3.000
 6YD  H14  C24  N13  108.99  3.000
 6YD  H13  C24  N13  110.00  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
 6YD  CONST_01  C10  C06  N05  C04  180.00   0.0  0
 6YD  CONST_02  C07  C06  N05  C04    0.00   0.0  0
 6YD  CONST_03  C07  C08  C09  C04    0.00   0.0  0
 6YD  CONST_04  C14  C10  C06  N05    0.00   0.0  0
 6YD  CONST_05  C11  C10  C06  N05  180.00   0.0  0
 6YD  CONST_06  C08  C07  C06  N05    0.00   0.0  0
 6YD  CONST_07  C08  C09  C04  N05    0.00   0.0  0
 6YD  CONST_08  N13  C14  C10  C06  180.00   0.0  0
 6YD  CONST_09  N12  C11  C10  C06  180.00   0.0  0
 6YD  CONST_10  C09  C04  N05  C06    0.00   0.0  0
 6YD  CONST_11  C09  C08  C07  C06    0.00   0.0  0
 6YD  CONST_12  C14  C10  C06  C07  180.00   0.0  0
 6YD  CONST_13  C11  C10  C06  C07    0.00   0.0  0
 6YD  CONST_14  C10  C06  C07  C08  180.00   0.0  0
 6YD  CONST_15  N12  N13  C14  C10    0.00   0.0  0
 6YD  CONST_16  N13  N12  C11  C10    0.00   0.0  0
 6YD  CONST_17  C14  N13  N12  C11    0.00   0.0  0
 6YD  CONST_18  N13  C14  C10  C11    0.00   0.0  0
 6YD  CONST_19  C14  C10  C11  N12    0.00   0.0  0
 6YD  CONST_20  N17  N18  C19  C15    0.00   0.0  0
 6YD  CONST_21  N18  N17  C16  C15    0.00   0.0  0
 6YD  CONST_22  N18  C19  C15  C16    0.00   0.0  0
 6YD  CONST_23  C19  N18  N17  C16    0.00   0.0  0
 6YD  CONST_24  C19  C15  C16  N17    0.00   0.0  0
 6YD  CONST_25  N18  C19  C15  N01  180.00   0.0  0
 6YD  CONST_26  N17  C16  C15  N01  180.00   0.0  0
 6YD  CONST_27  C06  N05  C04  C02  180.00   0.0  0
 6YD  CONST_28  C08  C09  C04  C02  180.00   0.0  0
 6YD  CONST_29  C24  N13  C14  C10  180.00   0.0  0
 6YD  CONST_30  C24  N13  N12  C11  180.00   0.0  0
 6YD  CONST_31  C20  N17  C16  C15  180.00   0.0  0
 6YD  CONST_32  C21  C19  C15  C16  180.00   0.0  0
 6YD  CONST_33  C21  C19  N18  N17  180.00   0.0  0
 6YD  CONST_34  C20  N17  N18  C19  180.00   0.0  0
 6YD  CONST_35  H3   C08  C09  C04  180.00   0.0  0
 6YD  CONST_36  H2   C07  C06  N05  180.00   0.0  0
 6YD  CONST_37  H4   C09  C04  N05  180.00   0.0  0
 6YD  CONST_38  H6   C14  C10  C06    0.00   0.0  0
 6YD  CONST_39  H5   C11  C10  C06    0.00   0.0  0
 6YD  CONST_40  H7   C16  N17  N18  180.00   0.0  0
 6YD  CONST_41  C15  N01  C02  C04  180.00   0.0  0
 6YD  CONST_42  N22  C21  C19  C15  180.00   0.0  0
 6YD  CONST_43  C19  C15  N01  C02  180.00   0.0  0
 6YD  CONST_44  C16  C15  N01  C02    0.00   0.0  0
 6YD  CONST_45  H1   N01  C15  C16  180.00   0.0  0
 6YD  CONST_46  C15  N01  C02  O03    0.00   0.0  0
 6YD  CONST_47  H11  N22  C21  C19    0.00   0.0  0
 6YD  CONST_48  H12  N22  C21  C19  180.00   0.0  0
 6YD  Var_01    N05  C04  C02  N01   -0.17  30.0  3
 6YD  Var_02    H13  C24  N13  N12   55.39  30.0  2
 6YD  Var_03    H8   C20  N17  C16  106.54  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
 6YD  plan-1  C06  0.020
 6YD  plan-1  C10  0.020
 6YD  plan-1  C11  0.020
 6YD  plan-1  N12  0.020
 6YD  plan-1  N13  0.020
 6YD  plan-1  C14  0.020
 6YD  plan-1  C24  0.020
 6YD  plan-1  H5   0.020
 6YD  plan-1  H6   0.020
 6YD  plan-2  C02  0.020
 6YD  plan-2  C04  0.020
 6YD  plan-2  N05  0.020
 6YD  plan-2  C06  0.020
 6YD  plan-2  C07  0.020
 6YD  plan-2  C08  0.020
 6YD  plan-2  C09  0.020
 6YD  plan-2  C10  0.020
 6YD  plan-2  H2   0.020
 6YD  plan-2  H3   0.020
 6YD  plan-2  H4   0.020
 6YD  plan-3  N01  0.020
 6YD  plan-3  C02  0.020
 6YD  plan-3  O03  0.020
 6YD  plan-3  C04  0.020
 6YD  plan-3  C15  0.020
 6YD  plan-3  H1   0.020
 6YD  plan-4  N01  0.020
 6YD  plan-4  C15  0.020
 6YD  plan-4  C16  0.020
 6YD  plan-4  N17  0.020
 6YD  plan-4  N18  0.020
 6YD  plan-4  C19  0.020
 6YD  plan-4  C20  0.020
 6YD  plan-4  C21  0.020
 6YD  plan-4  N22  0.020
 6YD  plan-4  O23  0.020
 6YD  plan-4  H7   0.020
 6YD  plan-4  H11  0.020
 6YD  plan-4  H12  0.020

