# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:57:20 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-(pyridin-2-yl)-2-(1,3,5-trimethyl-1H-pyrazol-4-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(C)c(CC(=O)Nc2ccccn2)c1C
#
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
 47U  47U  N-(pyridin-2-yl)-2-(1,3,5-trimethyl-1H-pyrazol-4-yl)acetamide  ligand  34  18  .  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_47U
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
 47U  C4   C  CH3   0  -0.746   2.7912   2.2296  -1.0488
 47U  C5   C  CR5   0  -0.157   1.9836  -0.1884  -0.5083
 47U  C6   C  CH2   0  -0.754   0.6423  -0.2274  -1.1427
 47U  N1   N  NR5   0  -0.324   3.9395   0.4288   0.2351
 47U  C7   C  C     0   0.553  -0.4951   0.0527  -0.1689
 47U  C8   C  CR6   0   0.525  -2.9925  -0.0725  -0.1805
 47U  N2   N  NH1   0  -0.734  -1.7175  -0.2428  -0.7079
 47U  C9   C  CR16  0  -0.405  -4.0775  -0.4094  -1.0006
 47U  C10  C  CR16  0  -0.144  -5.3516  -0.2480  -0.4997
 47U  C11  C  CR16  0  -0.345  -5.5173   0.2408   0.7923
 47U  C12  C  CR16  0  -0.064  -4.3776   0.5402   1.5140
 47U  N3   N  N     0  -0.426  -3.1401   0.3889   1.0483
 47U  O    O  O     0  -0.429  -0.3185   0.5041   0.9390
 47U  C3   C  CR5   0   0.403   2.8758   0.8634  -0.4710
 47U  C2   C  CH3   0  -0.521   5.1719   1.1376   0.4724
 47U  N    N  N     0  -0.320   3.7992  -0.8335   0.6480
 47U  C1   C  CR5   0   0.254   2.6151  -1.2210   0.2132
 47U  C    C  CH3   0  -0.745   2.0797  -2.5806   0.5044
 47U  H1   H  HCH3  0   0.257   3.5901   2.4178  -1.7682
 47U  H2   H  HCH3  0   0.260   1.8429   2.3608  -1.5666
 47U  H3   H  HCH3  0   0.258   2.8541   2.9995  -0.2780
 47U  H4   H  HCH2  0   0.303   0.5716   0.5147  -1.9453
 47U  H5   H  HCH2  0   0.286   0.4699  -1.1936  -1.6274
 47U  H6   H  HNH1  0   0.423  -1.6989  -0.6158  -1.6450
 47U  H7   H  HCR6  0   0.280  -3.9172  -0.7851  -2.0031
 47U  H8   H  HCR6  0   0.276  -6.2088  -0.4989  -1.1105
 47U  H9   H  HCR6  0   0.269  -6.4975   0.3842   1.2239
 47U  H10  H  HCR6  0   0.262  -4.4578   0.9243   2.5250
 47U  H11  H  HCH3  0   0.251   5.8347   1.0874  -0.3919
 47U  H12  H  HCH3  0   0.255   4.9696   2.1827   0.6972
 47U  H13  H  HCH3  0   0.265   5.6724   0.6908   1.3268
 47U  H14  H  HCH3  0   0.241   1.7398  -3.0788  -0.4054
 47U  H15  H  HCH3  0   0.248   2.8402  -3.2085   0.9660
 47U  H16  H  HCH3  0   0.243   1.2257  -2.5366   1.1832

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
 47U  C4   C3   single    1.486  0.020  1.486
 47U  C2   N1   single    1.441  0.020  1.441
 47U  C3   N1   aromatic  1.349  0.020  1.349
 47U  C3   C5   aromatic  1.380  0.020  1.380
 47U  N1   N    aromatic  1.336  0.020  1.336
 47U  C5   C6   single    1.484  0.020  1.484
 47U  C5   C1   aromatic  1.409  0.020  1.409
 47U  C6   C7   single    1.523  0.020  1.523
 47U  N    C1   aromatic  1.320  0.020  1.320
 47U  C1   C    single    1.490  0.020  1.490
 47U  C7   N2   single    1.368  0.020  1.368
 47U  C7   O    double    1.209  0.020  1.209
 47U  N2   C8   single    1.390  0.020  1.390
 47U  C8   N3   aromatic  1.321  0.020  1.321
 47U  C8   C9   aromatic  1.401  0.020  1.401
 47U  N3   C12  aromatic  1.331  0.020  1.331
 47U  C9   C10  aromatic  1.379  0.020  1.379
 47U  C12  C11  aromatic  1.382  0.020  1.382
 47U  C10  C11  aromatic  1.391  0.020  1.391
 47U  C4   H1   single    0.970  0.020  1.090
 47U  C4   H2   single    0.970  0.020  1.090
 47U  C4   H3   single    0.970  0.020  1.090
 47U  C6   H4   single    0.970  0.020  1.090
 47U  C6   H5   single    0.970  0.020  1.090
 47U  N2   H6   single    0.860  0.020  1.020
 47U  C9   H7   single    0.930  0.020  1.080
 47U  C10  H8   single    0.930  0.020  1.080
 47U  C11  H9   single    0.930  0.020  1.080
 47U  C12  H10  single    0.930  0.020  1.080
 47U  C2   H11  single    0.970  0.020  1.090
 47U  C2   H12  single    0.970  0.020  1.090
 47U  C2   H13  single    0.970  0.020  1.090
 47U  C    H14  single    0.970  0.020  1.090
 47U  C    H15  single    0.970  0.020  1.090
 47U  C    H16  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
 47U  H3   C4   H2   107.53  3.000
 47U  H3   C4   H1   107.56  3.000
 47U  H2   C4   H1   107.66  3.000
 47U  H3   C4   C3   111.76  3.000
 47U  H2   C4   C3   110.21  3.000
 47U  H1   C4   C3   111.91  3.000
 47U  C1   C5   C3   104.77  3.000
 47U  C1   C5   C6   127.19  3.000
 47U  C3   C5   C6   128.02  3.000
 47U  H5   C6   H4   105.27  3.000
 47U  H5   C6   C7   109.13  3.000
 47U  H4   C6   C7   107.19  3.000
 47U  H5   C6   C5   110.78  3.000
 47U  H4   C6   C5   110.71  3.000
 47U  C7   C6   C5   113.37  3.000
 47U  N    N1   C2   120.25  3.000
 47U  N    N1   C3   112.56  3.000
 47U  C2   N1   C3   127.02  3.000
 47U  O    C7   N2   124.89  3.000
 47U  O    C7   C6   123.04  3.000
 47U  N2   C7   C6   112.06  3.000
 47U  N3   C8   C9   122.82  3.000
 47U  C9   C8   N2   117.30  3.000
 47U  N3   C8   N2   119.88  3.000
 47U  H6   N2   C8   114.50  3.000
 47U  H6   N2   C7   115.42  3.000
 47U  C8   N2   C7   130.05  3.000
 47U  H7   C9   C10  120.93  3.000
 47U  H7   C9   C8   120.72  3.000
 47U  C10  C9   C8   118.35  3.000
 47U  H8   C10  C11  120.75  3.000
 47U  H8   C10  C9   120.00  3.000
 47U  C11  C10  C9   119.25  3.000
 47U  H9   C11  C12  120.72  3.000
 47U  H9   C11  C10  121.70  3.000
 47U  C12  C11  C10  117.58  3.000
 47U  H10  C12  N3   115.80  3.000
 47U  H10  C12  C11  120.17  3.000
 47U  N3   C12  C11  124.03  3.000
 47U  C12  N3   C8   117.98  3.000
 47U  N1   C3   C5   106.17  3.000
 47U  C5   C3   C4   130.81  3.000
 47U  N1   C3   C4   123.01  3.000
 47U  H13  C2   H12  108.55  3.000
 47U  H13  C2   H11  108.93  3.000
 47U  H12  C2   H11  108.73  3.000
 47U  H13  C2   N1   108.73  3.000
 47U  H12  C2   N1   110.33  3.000
 47U  H11  C2   N1   111.50  3.000
 47U  C1   N    N1   105.66  3.000
 47U  C    C1   N    121.74  3.000
 47U  C    C1   C5   127.43  3.000
 47U  N    C1   C5   110.83  3.000
 47U  H16  C    H15  107.81  3.000
 47U  H16  C    H14  107.05  3.000
 47U  H15  C    H14  107.91  3.000
 47U  H16  C    C1   111.46  3.000
 47U  H15  C    C1   110.98  3.000
 47U  H14  C    C1   111.44  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
 47U  CONST_01  N    N1   C3   C5      0.00   0.0  0
 47U  CONST_02  N1   N    C1   C5      0.00   0.0  0
 47U  CONST_03  C1   C5   C3   N1      0.00   0.0  0
 47U  CONST_04  C11  C12  N3   C8      0.00   0.0  0
 47U  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 47U  CONST_06  C12  N3   C8   C9      0.00   0.0  0
 47U  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 47U  CONST_08  N3   C8   C9   C10     0.00   0.0  0
 47U  CONST_09  N3   C12  C11  C10     0.00   0.0  0
 47U  CONST_10  C1   N    N1   C3      0.00   0.0  0
 47U  CONST_11  N    C1   C5   C3      0.00   0.0  0
 47U  CONST_12  N    N1   C3   C4    180.00   0.0  0
 47U  CONST_13  C1   C5   C3   C4    180.00   0.0  0
 47U  CONST_14  C2   N1   C3   C5    180.00   0.0  0
 47U  CONST_15  N1   C3   C5   C6    180.00   0.0  0
 47U  CONST_16  N    C1   C5   C6    180.00   0.0  0
 47U  CONST_17  C    C1   N    N1    180.00   0.0  0
 47U  CONST_18  C12  N3   C8   N2    180.00   0.0  0
 47U  CONST_19  C10  C9   C8   N2    180.00   0.0  0
 47U  CONST_20  C    C1   C5   C3    180.00   0.0  0
 47U  CONST_21  C1   N    N1   C2    180.00   0.0  0
 47U  CONST_22  H10  C12  N3   C8    180.00   0.0  0
 47U  CONST_23  H8   C10  C9   C8    180.00   0.0  0
 47U  CONST_24  H9   C11  C10  C9    180.00   0.0  0
 47U  CONST_25  H7   C9   C10  C11   180.00   0.0  0
 47U  CONST_26  N3   C8   N2   C7      0.00   0.0  0
 47U  CONST_27  C9   C8   N2   C7    180.00   0.0  0
 47U  CONST_28  H6   N2   C8   C9      0.00   0.0  0
 47U  CONST_29  C8   N2   C7   C6    180.00   0.0  0
 47U  CONST_30  O    C7   N2   C8      0.00   0.0  0
 47U  Var_01    C3   C5   C6   C7    -96.43  30.0  2
 47U  Var_02    H1   C4   C3   C5   -119.24  30.0  2
 47U  Var_03    H14  C    C1   C5     52.12  30.0  2
 47U  Var_04    H11  C2   N1   C3    -79.03  30.0  2
 47U  Var_05    N2   C7   C6   C5   -168.09  30.0  3

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
 47U  plan-1  C4   0.020
 47U  plan-1  C5   0.020
 47U  plan-1  C6   0.020
 47U  plan-1  N1   0.020
 47U  plan-1  C3   0.020
 47U  plan-1  C2   0.020
 47U  plan-1  N    0.020
 47U  plan-1  C1   0.020
 47U  plan-1  C    0.020
 47U  plan-2  C8   0.020
 47U  plan-2  N2   0.020
 47U  plan-2  C9   0.020
 47U  plan-2  C10  0.020
 47U  plan-2  C11  0.020
 47U  plan-2  C12  0.020
 47U  plan-2  N3   0.020
 47U  plan-2  H7   0.020
 47U  plan-2  H8   0.020
 47U  plan-2  H9   0.020
 47U  plan-2  H10  0.020
 47U  plan-3  C6   0.020
 47U  plan-3  C7   0.020
 47U  plan-3  C8   0.020
 47U  plan-3  N2   0.020
 47U  plan-3  O    0.020
 47U  plan-3  H6   0.020

