# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:00:02 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-methyl-3-[(3R)-piperidin-3-yl]-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(C(N)=O)c(n1)[C@@H]2CCCNC2
#
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
 K3Y  K3Y  1-methyl-3-[(3R)-piperidin-3-yl]-1H-pyrazole-4-carboxamide  ligand  31  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K3Y
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
 K3Y  N1   N  NH2   0  -0.817   2.7888  -2.5341  -0.3269
 K3Y  N3   N  NH1   0  -0.582  -3.2324   0.4095   1.2711
 K3Y  C4   C  CR5   0   0.368   0.4036   0.2970   0.1124
 K3Y  C5   C  CH1   0  -0.338  -1.0368  -0.0963   0.1874
 K3Y  C6   C  CH2   0  -0.419  -1.7055   0.0079  -1.1901
 K3Y  C7   C  CH2   0  -0.449  -3.1854  -0.3481  -1.1052
 K3Y  C8   C  CH2   0  -0.313  -3.8779   0.4854  -0.0307
 K3Y  N    N  NR5   0  -0.263   2.0951   1.5811   0.1428
 K3Y  C    C  CH3   0  -0.507   2.8080   2.8289   0.2744
 K3Y  O    O  O     0  -0.483   0.5846  -2.5733  -0.7941
 K3Y  C1   C  CR15  0   0.059   2.6016   0.3778  -0.1265
 K3Y  C2   C  CR5   0  -0.338   1.5385  -0.5074  -0.1601
 K3Y  C3   C  C     0   0.433   1.5807  -1.9484  -0.4472
 K3Y  C9   C  CH2   0  -0.283  -1.8212   0.7481   1.2017
 K3Y  N2   N  N     0  -0.315   0.7706   1.5510   0.2974
 K3Y  H1   H  HNH2  0   0.401   2.8720  -3.5274  -0.4687
 K3Y  H2   H  HNH2  0   0.405   3.5605  -2.0797   0.1291
 K3Y  H5   H  HCH1  0   0.235  -1.0870  -1.1421   0.5044
 K3Y  H6   H  HCH2  0   0.213  -1.5950   1.0344  -1.5570
 K3Y  H7   H  HCH2  0   0.238  -1.1921  -0.6402  -1.9024
 K3Y  H8   H  HCH2  0   0.227  -3.6697  -0.1930  -2.0727
 K3Y  H9   H  HCH2  0   0.213  -3.2945  -1.4107  -0.8623
 K3Y  H10  H  HCH2  0   0.232  -4.9211   0.1811   0.0797
 K3Y  H11  H  HCH2  0   0.212  -3.8903   1.5365  -0.3405
 K3Y  H12  H  HCH3  0   0.263   2.6857   3.2288   1.2790
 K3Y  H13  H  HCH3  0   0.260   3.8634   2.6542   0.0880
 K3Y  H14  H  HCH3  0   0.263   2.4344   3.5527  -0.4470
 K3Y  H15  H  HCR5  0   0.303   3.6583   0.2367  -0.2908
 K3Y  H16  H  HCH2  0   0.215  -1.7386   1.8060   0.9341
 K3Y  H17  H  HCH2  0   0.234  -1.3871   0.6408   2.1986
 K3Y  H3   H  HNH1  0   0.336  -3.3270  -0.5346   1.6288

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
 K3Y  O   C3   double    1.226  0.020  1.226
 K3Y  C3  N1   single    1.348  0.020  1.348
 K3Y  C3  C2   single    1.470  0.020  1.470
 K3Y  C2  C1   aromatic  1.384  0.020  1.384
 K3Y  C2  C4   aromatic  1.418  0.020  1.418
 K3Y  C1  N    aromatic  1.333  0.020  1.333
 K3Y  C6  C7   single    1.525  0.020  1.525
 K3Y  C6  C5   single    1.535  0.020  1.535
 K3Y  C4  C5   single    1.495  0.020  1.495
 K3Y  C4  N2   aromatic  1.320  0.020  1.320
 K3Y  C9  C5   single    1.535  0.020  1.535
 K3Y  C9  N3   single    1.453  0.020  1.453
 K3Y  C8  C7   single    1.526  0.020  1.526
 K3Y  C8  N3   single    1.455  0.020  1.455
 K3Y  N   C    single    1.443  0.020  1.443
 K3Y  N   N2   aromatic  1.334  0.020  1.334
 K3Y  N1  H1   single    0.860  0.020  1.020
 K3Y  N1  H2   single    0.860  0.020  1.020
 K3Y  N3  H3   single    0.890  0.020  1.040
 K3Y  C5  H5   single    0.970  0.020  1.090
 K3Y  C6  H6   single    0.970  0.020  1.090
 K3Y  C6  H7   single    0.970  0.020  1.090
 K3Y  C7  H8   single    0.970  0.020  1.090
 K3Y  C7  H9   single    0.970  0.020  1.090
 K3Y  C8  H10  single    0.970  0.020  1.090
 K3Y  C8  H11  single    0.970  0.020  1.090
 K3Y  C   H12  single    0.970  0.020  1.090
 K3Y  C   H13  single    0.970  0.020  1.090
 K3Y  C   H14  single    0.970  0.020  1.090
 K3Y  C1  H15  single    0.930  0.020  1.080
 K3Y  C9  H16  single    0.970  0.020  1.090
 K3Y  C9  H17  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
 K3Y  H2   N1  H1   116.52  3.000
 K3Y  H2   N1  C3   122.16  3.000
 K3Y  H1   N1  C3   119.35  3.000
 K3Y  H3   N3  C9   108.93  3.000
 K3Y  H3   N3  C8   108.83  3.000
 K3Y  C9   N3  C8   112.09  3.000
 K3Y  N2   C4  C2   110.09  3.000
 K3Y  N2   C4  C5   120.73  3.000
 K3Y  C2   C4  C5   129.17  3.000
 K3Y  H5   C5  C9   108.11  3.000
 K3Y  H5   C5  C6   107.76  3.000
 K3Y  C9   C5  C6   109.46  3.000
 K3Y  H5   C5  C4   108.07  3.000
 K3Y  C9   C5  C4   112.37  3.000
 K3Y  C6   C5  C4   110.91  3.000
 K3Y  H7   C6  H6   106.88  3.000
 K3Y  H7   C6  C7   110.76  3.000
 K3Y  H6   C6  C7   109.59  3.000
 K3Y  H7   C6  C5   109.91  3.000
 K3Y  H6   C6  C5   108.68  3.000
 K3Y  C7   C6  C5   110.92  3.000
 K3Y  H9   C7  H8   106.84  3.000
 K3Y  H9   C7  C8   109.18  3.000
 K3Y  H8   C7  C8   110.17  3.000
 K3Y  H9   C7  C6   109.60  3.000
 K3Y  H8   C7  C6   110.34  3.000
 K3Y  C8   C7  C6   110.62  3.000
 K3Y  H11  C8  H10  106.56  3.000
 K3Y  H11  C8  C7   109.27  3.000
 K3Y  H10  C8  C7   110.64  3.000
 K3Y  H11  C8  N3   107.93  3.000
 K3Y  H10  C8  N3   108.58  3.000
 K3Y  C7   C8  N3   113.59  3.000
 K3Y  N2   N   C1   112.36  3.000
 K3Y  N2   N   C    119.97  3.000
 K3Y  C1   N   C    127.68  3.000
 K3Y  H14  C   H13  109.08  3.000
 K3Y  H14  C   H12  109.22  3.000
 K3Y  H13  C   H12  109.08  3.000
 K3Y  H14  C   N    110.19  3.000
 K3Y  H13  C   N    108.98  3.000
 K3Y  H12  C   N    110.27  3.000
 K3Y  H15  C1  C2   131.70  3.000
 K3Y  H15  C1  N    121.40  3.000
 K3Y  C2   C1  N    106.89  3.000
 K3Y  C3   C2  C1   127.58  3.000
 K3Y  C1   C2  C4   104.32  3.000
 K3Y  C3   C2  C4   128.09  3.000
 K3Y  C2   C3  O    122.11  3.000
 K3Y  C2   C3  N1   115.74  3.000
 K3Y  O    C3  N1   122.14  3.000
 K3Y  H17  C9  H16  106.74  3.000
 K3Y  H17  C9  C5   110.24  3.000
 K3Y  H16  C9  C5   109.36  3.000
 K3Y  H17  C9  N3   108.63  3.000
 K3Y  H16  C9  N3   108.08  3.000
 K3Y  C5   C9  N3   113.55  3.000
 K3Y  N    N2  C4   106.34  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
 K3Y  CONST_01  N    C1  C2  C4     0.00   0.0  0
 K3Y  CONST_02  C1   N   N2  C4     0.00   0.0  0
 K3Y  CONST_03  C2   C4  N2  N      0.00   0.0  0
 K3Y  CONST_04  N2   C4  C2  C1     0.00   0.0  0
 K3Y  CONST_05  N2   N   C1  C2     0.00   0.0  0
 K3Y  CONST_06  C1   C2  C4  C5   180.00   0.0  0
 K3Y  CONST_07  N    N2  C4  C5   180.00   0.0  0
 K3Y  CONST_08  C    N   N2  C4   180.00   0.0  0
 K3Y  CONST_09  C3   C2  C4  C5     0.00   0.0  0
 K3Y  CONST_10  C3   C2  C1  N    180.00   0.0  0
 K3Y  CONST_11  C2   C1  N   C    180.00   0.0  0
 K3Y  CONST_12  N2   C4  C2  C3   180.00   0.0  0
 K3Y  CONST_13  H15  C1  C2  C4   180.00   0.0  0
 K3Y  CONST_14  H1   N1  C3  C2   180.00   0.0  0
 K3Y  CONST_15  H2   N1  C3  C2     0.00   0.0  0
 K3Y  Var_01    C6   C7  C8  N3   -53.55  30.0  1
 K3Y  Var_02    C8   C7  C6  C5    53.26  30.0  1
 K3Y  Var_03    C8   N3  C9  C5   -55.10  30.0  1
 K3Y  Var_04    C9   N3  C8  C7    54.13  30.0  1
 K3Y  Var_05    C1   C2  C3  N1    18.38  30.0  2
 K3Y  Var_06    H12  C   N   C1  -118.06  30.0  2

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
 K3Y  chir_01  C5  C6  C4  C9  negativ

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
 K3Y  plan-1  C4   0.020
 K3Y  plan-1  C5   0.020
 K3Y  plan-1  N    0.020
 K3Y  plan-1  C    0.020
 K3Y  plan-1  C1   0.020
 K3Y  plan-1  C2   0.020
 K3Y  plan-1  C3   0.020
 K3Y  plan-1  N2   0.020
 K3Y  plan-1  H15  0.020
 K3Y  plan-2  N1   0.020
 K3Y  plan-2  O    0.020
 K3Y  plan-2  C2   0.020
 K3Y  plan-2  C3   0.020
 K3Y  plan-2  H1   0.020
 K3Y  plan-2  H2   0.020

