# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 02:14:24 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: N,N-dimethyl-1-[4-(4-methyl-1H-pyrazol-1-yl)pyridin-3-yl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)C1CCN(CC1)c2cnccc2n3cc(C)cn3
#
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
 05D  05D  "N,N-dimethyl-1-[4-(4-methyl-1H-pyrazol-1-yl)pyridin-3-yl]piperidine-4-carboxamide"  ligand  46  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_05D
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
 05D  C4   C  CR16  0  -0.143  13.8600  -1.5418  -21.9785
 05D  C5   C  CR15  0   0.024  17.8806  -2.6065  -23.4844
 05D  C6   C  CR5   0  -0.155  19.0374  -3.3363  -23.5541
 05D  C7   C  CR6   0   0.398  15.6561  -3.0241  -22.4601
 05D  C8   C  CR6   0   0.237  15.2338  -1.7174  -22.1617
 05D  C10  C  CH2   0  -0.424  16.8022   1.6299  -22.5589
 05D  C13  C  CH2   0  -0.321  17.0663  -0.7312  -20.9358
 05D  C15  C  CH3   0  -0.739  20.3050  -2.9798  -24.2530
 05D  C17  C  CH3   0  -0.536  17.7757   4.3697  -20.6075
 05D  C1   C  CR16  0  -0.366  14.7197  -4.0459  -22.4931
 05D  C2   C  CR16  0  -0.086  13.3878  -3.7431  -22.2712
 05D  C3   C  CR15  0  -0.057  18.7464  -4.4983  -22.8041
 05D  C9   C  C     0   0.590  18.9837   2.5210  -21.7139
 05D  C11  C  CH2   0  -0.413  18.2670   0.1692  -21.1664
 05D  C12  C  CH2   0  -0.310  15.6451   0.6789  -22.2907
 05D  C14  C  CH1   0  -0.415  17.8109   1.6052  -21.4044
 05D  C16  C  CH3   0  -0.514  20.0340   4.6713  -21.6238
 05D  N18  N  N     0  -0.396  12.9577  -2.5113  -22.0371
 05D  N19  N  N     0  -0.279  17.5222  -4.4837  -22.3266
 05D  N20  N  NR5   0  -0.398  16.9997  -3.3225  -22.7374
 05D  N21  N  NT    0  -0.508  16.1461  -0.6656  -22.0701
 05D  O23  O  O     0  -0.500  19.9771   2.0948  -22.2924
 05D  H1   H  HCR6  0   0.273  13.4752  -0.5512  -21.7642
 05D  H2   H  HCR5  0   0.296  17.6235  -1.6491  -23.9048
 05D  H3   H  HCH2  0   0.239  17.3018   1.3402  -23.4875
 05D  H4   H  HCH2  0   0.249  16.3989   2.6337  -22.7099
 05D  H5   H  HCH2  0   0.228  16.5473  -0.4336  -20.0116
 05D  H6   H  HCH2  0   0.264  17.4014  -1.7571  -20.7876
 05D  H7   H  HCH3  0   0.243  21.1299  -2.8582  -23.5494
 05D  H8   H  HCH3  0   0.243  20.5998  -3.7511  -24.9653
 05D  H9   H  HCH3  0   0.245  20.2000  -2.0449  -24.8014
 05D  H10  H  HCH3  0   0.258  17.7669   5.4503  -20.7260
 05D  H11  H  HCH3  0   0.254  16.8171   4.0063  -20.9705
 05D  H12  H  HCH3  0   0.242  17.8482   4.1491  -19.5399
 05D  H13  H  HCR6  0   0.280  15.0211  -5.0596  -22.7160
 05D  H14  H  HCR6  0   0.264  12.6420  -4.5291  -22.2988
 05D  H15  H  HCR5  0   0.262  19.3980  -5.3353  -22.5989
 05D  H16  H  HCH2  0   0.233  18.8326  -0.1998  -22.0236
 05D  H17  H  HCH2  0   0.243  18.9214   0.1142  -20.2938
 05D  H18  H  HCH2  0   0.215  15.0700   1.0520  -21.4292
 05D  H19  H  HCH2  0   0.258  14.9763   0.6746  -23.1528
 05D  H20  H  HCH1  0   0.261  17.2970   1.9398  -20.4977
 05D  H21  H  HCH3  0   0.241  19.7985   5.6882  -21.3235
 05D  H22  H  HCH3  0   0.236  20.9141   4.3483  -21.0649
 05D  H23  H  HCH3  0   0.240  20.2913   4.6818  -22.6828
 05D  N22  N  NT    0  -0.454  18.8854   3.8209  -21.3652

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
 05D  C15  C6   single    1.491  0.020  1.491
 05D  C6   C5   aromatic  1.370  0.020  1.370
 05D  C6   C3   aromatic  1.413  0.020  1.413
 05D  C5   N20  aromatic  1.359  0.020  1.359
 05D  C3   N19  aromatic  1.314  0.020  1.314
 05D  N20  N19  aromatic  1.338  0.020  1.338
 05D  N20  C7   single    1.404  0.020  1.404
 05D  C10  C12  single    1.522  0.020  1.522
 05D  C10  C14  single    1.533  0.020  1.533
 05D  C7   C1   aromatic  1.386  0.020  1.386
 05D  C7   C8   aromatic  1.405  0.020  1.405
 05D  C1   C2   aromatic  1.384  0.020  1.384
 05D  C12  N21  single    1.452  0.020  1.452
 05D  C2   N18  aromatic  1.326  0.020  1.326
 05D  C8   N21  single    1.395  0.020  1.395
 05D  C8   C4   aromatic  1.397  0.020  1.397
 05D  N21  C13  single    1.462  0.020  1.462
 05D  O23  C9   double    1.226  0.020  1.226
 05D  C4   N18  aromatic  1.326  0.020  1.326
 05D  C9   C14  single    1.520  0.020  1.520
 05D  C9   N22  single    1.350  0.020  1.350
 05D  C16  N22  single    1.452  0.020  1.452
 05D  C14  C11  single    1.525  0.020  1.525
 05D  C11  C13  single    1.518  0.020  1.518
 05D  N22  C17  single    1.452  0.020  1.452
 05D  C4   H1   single    0.930  0.020  1.080
 05D  C5   H2   single    0.930  0.020  1.080
 05D  C10  H3   single    0.970  0.020  1.090
 05D  C10  H4   single    0.970  0.020  1.090
 05D  C13  H5   single    0.970  0.020  1.090
 05D  C13  H6   single    0.970  0.020  1.090
 05D  C15  H7   single    0.970  0.020  1.090
 05D  C15  H8   single    0.970  0.020  1.090
 05D  C15  H9   single    0.970  0.020  1.090
 05D  C17  H10  single    0.970  0.020  1.090
 05D  C17  H11  single    0.970  0.020  1.090
 05D  C17  H12  single    0.970  0.020  1.090
 05D  C1   H13  single    0.930  0.020  1.080
 05D  C2   H14  single    0.930  0.020  1.080
 05D  C3   H15  single    0.930  0.020  1.080
 05D  C11  H16  single    0.970  0.020  1.090
 05D  C11  H17  single    0.970  0.020  1.090
 05D  C12  H18  single    0.970  0.020  1.090
 05D  C12  H19  single    0.970  0.020  1.090
 05D  C14  H20  single    0.970  0.020  1.090
 05D  C16  H21  single    0.970  0.020  1.090
 05D  C16  H22  single    0.970  0.020  1.090
 05D  C16  H23  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
 05D  H1   C4   N18  115.81  3.000
 05D  H1   C4   C8   119.33  3.000
 05D  N18  C4   C8   124.86  3.000
 05D  H2   C5   N20  121.90  3.000
 05D  H2   C5   C6   130.96  3.000
 05D  N20  C5   C6   107.14  3.000
 05D  C3   C6   C15  128.35  3.000
 05D  C3   C6   C5   103.72  3.000
 05D  C15  C6   C5   127.93  3.000
 05D  N20  C7   C1   119.02  3.000
 05D  C1   C7   C8   119.17  3.000
 05D  N20  C7   C8   121.81  3.000
 05D  N21  C8   C7   121.22  3.000
 05D  N21  C8   C4   122.66  3.000
 05D  C7   C8   C4   116.12  3.000
 05D  H4   C10  H3   107.14  3.000
 05D  H4   C10  C14  111.21  3.000
 05D  H3   C10  C14  109.55  3.000
 05D  H4   C10  C12  108.54  3.000
 05D  H3   C10  C12  109.37  3.000
 05D  C14  C10  C12  110.94  3.000
 05D  H6   C13  H5   106.58  3.000
 05D  H6   C13  N21  109.96  3.000
 05D  H5   C13  N21  110.02  3.000
 05D  H6   C13  C11  109.62  3.000
 05D  H5   C13  C11  109.88  3.000
 05D  N21  C13  C11  110.69  3.000
 05D  H9   C15  H8   107.72  3.000
 05D  H9   C15  H7   107.57  3.000
 05D  H8   C15  H7   107.20  3.000
 05D  H9   C15  C6   111.06  3.000
 05D  H8   C15  C6   111.53  3.000
 05D  H7   C15  C6   111.55  3.000
 05D  H12  C17  H11  108.49  3.000
 05D  H12  C17  H10  107.93  3.000
 05D  H11  C17  H10  106.78  3.000
 05D  H12  C17  N22  112.52  3.000
 05D  H11  C17  N22  111.92  3.000
 05D  H10  C17  N22  108.97  3.000
 05D  H13  C1   C2   120.44  3.000
 05D  H13  C1   C7   120.52  3.000
 05D  C2   C1   C7   119.01  3.000
 05D  H14  C2   N18  117.08  3.000
 05D  H14  C2   C1   119.97  3.000
 05D  N18  C2   C1   122.95  3.000
 05D  H15  C3   N19  120.09  3.000
 05D  H15  C3   C6   127.85  3.000
 05D  N19  C3   C6   112.06  3.000
 05D  O23  C9   N22  121.05  3.000
 05D  N22  C9   C14  118.14  3.000
 05D  O23  C9   C14  120.79  3.000
 05D  H17  C11  H16  107.46  3.000
 05D  H17  C11  C14  110.57  3.000
 05D  H16  C11  C14  110.54  3.000
 05D  H17  C11  C13  108.82  3.000
 05D  H16  C11  C13  109.19  3.000
 05D  C14  C11  C13  110.21  3.000
 05D  H19  C12  H18  107.42  3.000
 05D  H19  C12  N21  109.14  3.000
 05D  H18  C12  N21  112.04  3.000
 05D  H19  C12  C10  109.22  3.000
 05D  H18  C12  C10  108.87  3.000
 05D  N21  C12  C10  110.08  3.000
 05D  H20  C14  C11  107.39  3.000
 05D  H20  C14  C9   110.29  3.000
 05D  C11  C14  C9   111.61  3.000
 05D  H20  C14  C10  108.06  3.000
 05D  C11  C14  C10  109.23  3.000
 05D  C9   C14  C10  110.16  3.000
 05D  H23  C16  H22  108.06  3.000
 05D  H23  C16  H21  108.11  3.000
 05D  H22  C16  H21  108.07  3.000
 05D  H23  C16  N22  111.43  3.000
 05D  H22  C16  N22  111.92  3.000
 05D  H21  C16  N22  109.12  3.000
 05D  C2   N18  C4   117.81  3.000
 05D  N20  N19  C3   105.18  3.000
 05D  N19  N20  C7   119.84  3.000
 05D  C7   N20  C5   128.09  3.000
 05D  N19  N20  C5   111.90  3.000
 05D  C12  N21  C13  112.12  3.000
 05D  C13  N21  C8   115.38  3.000
 05D  C12  N21  C8   117.55  3.000
 05D  C16  N22  C9   117.41  3.000
 05D  C16  N22  C17  118.44  3.000
 05D  C9   N22  C17  123.69  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
 05D  CONST_01  N20  C7   C8   C4    180.00   0.0  0
 05D  CONST_02  C1   C7   C8   C4      0.00   0.0  0
 05D  CONST_03  C1   C2   N18  C4      0.00   0.0  0
 05D  CONST_04  N19  C3   C6   C5      0.00   0.0  0
 05D  CONST_05  C3   N19  N20  C5      0.00   0.0  0
 05D  CONST_08  N19  N20  C5   C6      0.00   0.0  0
 05D  CONST_09  C7   N20  C5   C6    180.00   0.0  0
 05D  CONST_10  N20  N19  C3   C6      0.00   0.0  0
 05D  CONST_11  C3   N19  N20  C7    180.00   0.0  0
 05D  CONST_12  N18  C2   C1   C7      0.00   0.0  0
 05D  CONST_13  N18  C4   C8   C7      0.00   0.0  0
 05D  CONST_15  C2   C1   C7   C8      0.00   0.0  0
 05D  CONST_16  C2   N18  C4   C8      0.00   0.0  0
 05D  CONST_18  N20  C7   C1   C2    180.00   0.0  0
 05D  CONST_19  N20  C5   C6   C3      0.00   0.0  0
 05D  CONST_20  N21  C8   C7   C1    180.00   0.0  0
 05D  CONST_21  N21  C8   C4   N18   180.00   0.0  0
 05D  CONST_22  N21  C8   C7   N20     0.00   0.0  0
 05D  CONST_23  N20  C5   C6   C15   180.00   0.0  0
 05D  CONST_24  N19  C3   C6   C15   180.00   0.0  0
 05D  CONST_25  H14  C2   N18  C4    180.00   0.0  0
 05D  CONST_26  H15  C3   C6   C5    180.00   0.0  0
 05D  CONST_27  H2   C5   N20  C7      0.00   0.0  0
 05D  CONST_28  H14  C2   C1   C7    180.00   0.0  0
 05D  CONST_29  H1   C4   C8   C7    180.00   0.0  0
 05D  CONST_30  H13  C1   C7   C8    180.00   0.0  0
 05D  CONST_31  H1   C4   N18  C2    180.00   0.0  0
 05D  CONST_32  H2   C5   C6   C3    180.00   0.0  0
 05D  CONST_33  H13  C1   C2   N18   180.00   0.0  0
 05D  CONST_34  H2   C5   N20  N19   180.00   0.0  0
 05D  CONST_35  H15  C3   N19  N20   180.00   0.0  0
 05D  CONST_36  H13  C1   C7   N20     0.00   0.0  0
 05D  CONST_37  H1   C4   C8   N21     0.00   0.0  0
 05D  CONST_38  C14  C9   N22  C17     0.00   0.0  0
 05D  CONST_39  C16  N22  C9   C14   180.00   0.0  0
 05D  CONST_40  O23  C9   N22  C17   180.00   0.0  0
 05D  CONST_41  O23  C9   N22  C16     0.00   0.0  0
 05D  Var_01    C12  N21  C8   C4    -23.32  30.0  2
 05D  Var_02    C13  N21  C8   C4    112.54  30.0  2
 05D  Var_03    C12  N21  C8   C7    156.05  30.0  2
 05D  Var_04    C13  N21  C8   C7    -68.09  30.0  2
 05D  Var_05    C10  C12  N21  C8   -163.39  30.0  1
 05D  Var_06    C11  C13  N21  C8    161.73  30.0  1
 05D  Var_07    C13  N21  C12  C10    59.39  30.0  1
 05D  Var_08    C12  N21  C13  C11   -60.07  30.0  1
 05D  Var_09    N21  C12  C10  C14   -56.90  30.0  1
 05D  Var_10    N21  C13  C11  C14    57.36  30.0  1
 05D  Var_11    H18  C12  N21  C8     75.31  30.0  1
 05D  Var_12    H19  C12  N21  C8    -43.53  30.0  1
 05D  Var_13    H5   C13  N21  C8    -76.64  30.0  1
 05D  Var_14    H6   C13  N21  C8     40.46  30.0  1
 05D  Var_15    H18  C12  N21  C13   -61.91  30.0  1
 05D  Var_16    H19  C12  N21  C13   179.25  30.0  1
 05D  Var_17    H5   C13  N21  C12    61.57  30.0  1
 05D  Var_18    H6   C13  N21  C12   178.66  30.0  1
 05D  Var_19    H18  C12  C10  C14    66.27  30.0  1
 05D  Var_20    H19  C12  C10  C14  -176.71  30.0  1
 05D  Var_21    H5   C13  C11  C14   -64.36  30.0  1
 05D  Var_22    H6   C13  C11  C14   178.83  30.0  1
 05D  Var_23    H3   C10  C12  N21    64.04  30.0  1
 05D  Var_24    H4   C10  C12  N21  -179.38  30.0  1
 05D  Var_25    H16  C11  C13  N21   -64.23  30.0  1
 05D  Var_26    H17  C11  C13  N21   178.76  30.0  1
 05D  Var_27    H7   C15  C6   C5    115.92  30.0  2
 05D  Var_28    H8   C15  C6   C5   -124.24  30.0  2
 05D  Var_29    H9   C15  C6   C5     -4.08  30.0  2
 05D  Var_30    H7   C15  C6   C3    -63.74  30.0  2
 05D  Var_31    H8   C15  C6   C3     56.10  30.0  2
 05D  Var_32    H9   C15  C6   C3    176.26  30.0  2
 05D  Var_33    H21  C16  N22  C17    -9.25  30.0  3
 05D  Var_34    H22  C16  N22  C17   110.32  30.0  3
 05D  Var_35    H23  C16  N22  C17  -128.55  30.0  3
 05D  Var_36    H21  C16  N22  C9    178.17  30.0  3
 05D  Var_37    H22  C16  N22  C9    -62.26  30.0  3
 05D  Var_38    H23  C16  N22  C9     58.87  30.0  3
 05D  Var_39    H10  C17  N22  C9   -162.30  30.0  3
 05D  Var_40    H11  C17  N22  C9    -44.45  30.0  3
 05D  Var_41    H12  C17  N22  C9     78.03  30.0  3
 05D  Var_42    H10  C17  N22  C16    25.62  30.0  3
 05D  Var_43    H11  C17  N22  C16   143.48  30.0  3
 05D  Var_44    H12  C17  N22  C16   -94.05  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
 05D  chir_01  C14  C10  C9  C11  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
 05D  plan-1  C5   0.020
 05D  plan-1  C6   0.020
 05D  plan-1  C7   0.020
 05D  plan-1  C15  0.020
 05D  plan-1  C3   0.020
 05D  plan-1  N19  0.020
 05D  plan-1  N20  0.020
 05D  plan-1  H2   0.020
 05D  plan-1  H15  0.020
 05D  plan-2  C4   0.020
 05D  plan-2  C7   0.020
 05D  plan-2  C8   0.020
 05D  plan-2  C1   0.020
 05D  plan-2  C2   0.020
 05D  plan-2  N18  0.020
 05D  plan-2  N20  0.020
 05D  plan-2  N21  0.020
 05D  plan-2  H1   0.020
 05D  plan-2  H13  0.020
 05D  plan-2  H14  0.020
 05D  plan-3  C17  0.020
 05D  plan-3  C9   0.020
 05D  plan-3  C14  0.020
 05D  plan-3  C16  0.020
 05D  plan-3  O23  0.020
 05D  plan-3  N22  0.020

