# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 09:21:54 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc(C(=O)NCC2CCC2)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
 HR5  HR5  ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide  ligand  32  15  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HR5
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
 HR5  N1   N  NR5   0  -0.314   3.3850  -0.5974  -0.1222
 HR5  C4   C  CH3   0  -0.526   4.8258  -0.6325  -0.2120
 HR5  C5   C  C     0   0.489   0.0749   0.8478   0.0057
 HR5  C6   C  CH2   0  -0.253  -2.3161   0.8611   0.5994
 HR5  C7   C  C     0  -0.267  -3.3961  -0.1953   0.5380
 HR5  C8   C  C     0  -0.436  -4.8497   0.2875   0.3606
 HR5  C10  C  C     0  -0.433  -3.5453  -1.0068  -0.7647
 HR5  O    O  O     0  -0.501   0.0322   1.9750  -0.4788
 HR5  N2   N  NH1   0  -0.652  -1.0032   0.2551   0.5528
 HR5  C9   C  C     0  -0.453  -5.0746  -0.8768  -0.6237
 HR5  C2   C  CR5   0  -0.341   1.3050   0.0409   0.0123
 HR5  C3   C  CR15  0  -0.069   1.4422  -1.3538   0.1674
 HR5  N    N  N     0  -0.277   2.6985  -1.7252   0.0830
 HR5  C1   C  CR5   0   0.467   2.6048   0.4949  -0.1744
 HR5  C    C  CH3   0  -0.753   3.1729   1.8530  -0.3743
 HR5  H1   H  HCH3  0   0.262   5.1702   0.0309  -1.0020
 HR5  H2   H  HCH3  0   0.262   5.2856  -0.3297   0.7286
 HR5  H3   H  HCH3  0   0.274   5.1312  -1.6470  -0.4479
 HR5  H4   H  HCH2  0   0.233  -2.4172   1.5338  -0.2528
 HR5  H5   H  HCH2  0   0.236  -2.4329   1.4702   1.5033
 HR5  H6   H  H     0   0.240  -3.3211  -0.8655   1.4004
 HR5  H7   H  H     0   0.232  -5.4804   0.3338   1.2485
 HR5  H8   H  H     0   0.223  -4.8889   1.2564  -0.1422
 HR5  H9   H  H     0   0.222  -3.1646  -0.4515  -1.6250
 HR5  H10  H  H     0   0.230  -3.1224  -2.0112  -0.7885
 HR5  H11  H  HNH1  0   0.397  -0.8784  -0.6062   1.0596
 HR5  H12  H  H     0   0.226  -5.5114  -1.7458  -0.1305
 HR5  H13  H  H     0   0.228  -5.6482  -0.6667  -1.5264
 HR5  H14  H  HCR5  0   0.260   0.6703  -2.0961   0.3102
 HR5  H15  H  HCH3  0   0.262   3.6190   1.9498  -1.3660
 HR5  H16  H  HCH3  0   0.275   2.3990   2.6067  -0.2805
 HR5  H17  H  HCH3  0   0.259   3.9539   2.0665   0.3567

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
 HR5  C9   C10  single    1.541  0.020  1.541
 HR5  C9   C8   single    1.541  0.020  1.541
 HR5  C10  C7   single    1.542  0.020  1.542
 HR5  C8   C7   single    1.542  0.020  1.542
 HR5  C7   C6   single    1.512  0.020  1.512
 HR5  C    C1   single    1.486  0.020  1.486
 HR5  C6   N2   single    1.447  0.020  1.447
 HR5  N2   C5   single    1.346  0.020  1.346
 HR5  C1   N1   aromatic  1.343  0.020  1.343
 HR5  C1   C2   aromatic  1.389  0.020  1.389
 HR5  C4   N1   single    1.444  0.020  1.444
 HR5  C5   C2   single    1.471  0.020  1.471
 HR5  C5   O    double    1.228  0.020  1.228
 HR5  N1   N    aromatic  1.336  0.020  1.336
 HR5  C2   C3   aromatic  1.410  0.020  1.410
 HR5  N    C3   aromatic  1.313  0.020  1.313
 HR5  C4   H1   single    0.970  0.020  1.090
 HR5  C4   H2   single    0.970  0.020  1.090
 HR5  C4   H3   single    0.970  0.020  1.090
 HR5  C6   H4   single    0.970  0.020  1.090
 HR5  C6   H5   single    0.970  0.020  1.090
 HR5  C7   H6   single    0.970  0.020  1.090
 HR5  C8   H7   single    0.970  0.020  1.090
 HR5  C8   H8   single    0.970  0.020  1.090
 HR5  C10  H9   single    0.970  0.020  1.090
 HR5  C10  H10  single    0.970  0.020  1.090
 HR5  N2   H11  single    0.860  0.020  1.020
 HR5  C9   H12  single    0.970  0.020  1.090
 HR5  C9   H13  single    0.970  0.020  1.090
 HR5  C3   H14  single    0.930  0.020  1.080
 HR5  C    H15  single    0.970  0.020  1.090
 HR5  C    H16  single    0.970  0.020  1.090
 HR5  C    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
 HR5  C1   N1   N    113.20  3.000
 HR5  N    N1   C4   120.11  3.000
 HR5  C1   N1   C4   126.65  3.000
 HR5  H3   C4   H2   109.18  3.000
 HR5  H3   C4   H1   108.86  3.000
 HR5  H2   C4   H1   108.89  3.000
 HR5  H3   C4   N1   108.48  3.000
 HR5  H2   C4   N1   111.13  3.000
 HR5  H1   C4   N1   110.26  3.000
 HR5  C2   C5   N2   115.23  3.000
 HR5  C2   C5   O    122.30  3.000
 HR5  N2   C5   O    122.46  3.000
 HR5  H5   C6   H4   106.96  3.000
 HR5  H5   C6   N2   110.85  3.000
 HR5  H4   C6   N2   108.51  3.000
 HR5  H5   C6   C7   110.22  3.000
 HR5  H4   C6   C7   109.46  3.000
 HR5  N2   C6   C7   110.75  3.000
 HR5  H6   C7   C10  110.48  3.000
 HR5  H6   C7   C8   110.30  3.000
 HR5  C10  C7   C8    88.64  3.000
 HR5  H6   C7   C6   110.29  3.000
 HR5  C8   C7   C6   117.34  3.000
 HR5  C10  C7   C6   118.10  3.000
 HR5  H8   C8   H7   108.45  3.000
 HR5  H8   C8   C9   111.77  3.000
 HR5  H7   C8   C9   117.90  3.000
 HR5  H8   C8   C7   111.38  3.000
 HR5  H7   C8   C7   117.71  3.000
 HR5  C9   C8   C7    88.54  3.000
 HR5  H10  C10  H9   108.43  3.000
 HR5  H10  C10  C9   117.68  3.000
 HR5  H9   C10  C9   112.02  3.000
 HR5  H10  C10  C7   117.76  3.000
 HR5  H9   C10  C7   111.35  3.000
 HR5  C9   C10  C7    88.53  3.000
 HR5  H11  N2   C6   117.03  3.000
 HR5  H11  N2   C5   118.80  3.000
 HR5  C6   N2   C5   123.74  3.000
 HR5  H13  C9   H12  108.50  3.000
 HR5  H13  C9   C10  117.55  3.000
 HR5  H12  C9   C10  111.81  3.000
 HR5  H13  C9   C8   117.40  3.000
 HR5  H12  C9   C8   111.82  3.000
 HR5  C10  C9   C8    88.70  3.000
 HR5  C1   C2   C3   104.29  3.000
 HR5  C3   C2   C5   128.64  3.000
 HR5  C1   C2   C5   127.04  3.000
 HR5  H14  C3   N    119.86  3.000
 HR5  H14  C3   C2   128.65  3.000
 HR5  N    C3   C2   111.47  3.000
 HR5  C3   N    N1   105.23  3.000
 HR5  C    C1   C2   132.41  3.000
 HR5  C2   C1   N1   105.81  3.000
 HR5  C    C1   N1   121.77  3.000
 HR5  H17  C    H16  108.48  3.000
 HR5  H17  C    H15  107.38  3.000
 HR5  H16  C    H15  107.97  3.000
 HR5  H17  C    C1   111.26  3.000
 HR5  H16  C    C1   110.55  3.000
 HR5  H15  C    C1   111.07  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
 HR5  CONST_01  C3   C2  C1   N1    0.00   0.0  0
 HR5  CONST_02  C2   C3  N    N1    0.00   0.0  0
 HR5  CONST_03  N    N1  C1   C2    0.00   0.0  0
 HR5  CONST_04  C1   N1  N    C3    0.00   0.0  0
 HR5  CONST_05  C1   C2  C3   N     0.00   0.0  0
 HR5  CONST_06  C5   C2  C1   N1  180.00   0.0  0
 HR5  CONST_07  C2   C1  N1   C4  180.00   0.0  0
 HR5  CONST_08  C3   N   N1   C4  180.00   0.0  0
 HR5  CONST_09  N    C3  C2   C5  180.00   0.0  0
 HR5  CONST_10  C    C1  C2   C3  180.00   0.0  0
 HR5  CONST_11  C    C1  N1   N   180.00   0.0  0
 HR5  CONST_12  H14  C3  N    N1  180.00   0.0  0
 HR5  CONST_13  C2   C5  N2   C6  180.00   0.0  0
 HR5  CONST_14  H11  N2  C5   C2    0.00   0.0  0
 HR5  CONST_15  O    C5  N2   C6    0.00   0.0  0
 HR5  Var_01    C8   C9  C10  C7   17.75  30.0  1
 HR5  Var_02    C1   C2  C5   O    17.77  30.0  2
 HR5  Var_03    H15  C   C1   N1   66.27  30.0  2
 HR5  Var_04    H1   C4  N1   N   139.32  30.0  2
 HR5  Var_05    C7   C6  N2   C5  148.95  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
 HR5  chir_01  C7  C10  C8  C6  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
 HR5  plan-1  N1   0.020
 HR5  plan-1  C4   0.020
 HR5  plan-1  C5   0.020
 HR5  plan-1  C2   0.020
 HR5  plan-1  C3   0.020
 HR5  plan-1  N    0.020
 HR5  plan-1  C1   0.020
 HR5  plan-1  C    0.020
 HR5  plan-1  H14  0.020
 HR5  plan-2  C5   0.020
 HR5  plan-2  C6   0.020
 HR5  plan-2  O    0.020
 HR5  plan-2  N2   0.020
 HR5  plan-2  C2   0.020
 HR5  plan-2  H11  0.020

