# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:07:39 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: (1H-pyrazol-4-yl)(pyrrolidin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCCC1)c2c[nH]nc2
#
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
 UXD  UXD  (1H-pyrazol-4-yl)(pyrrolidin-1-yl)methanone  ligand  23  12  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UXD
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
 UXD  N1   N  NR15  0  -0.430  -23.7073  12.7117  27.0883
 UXD  C4   C  CH2   0  -0.286  -19.8135  14.5570  26.8176
 UXD  C5   C  CR5   0  -0.260  -21.9147  12.6922  25.8536
 UXD  C6   C  CR15  0   0.041  -22.6175  13.4255  26.7941
 UXD  C7   C  CR15  0  -0.053  -22.7092  11.5394  25.6666
 UXD  N    N  NT    0  -0.483  -19.8112  13.8749  25.5275
 UXD  C    C  C     0   0.504  -20.6854  12.9565  25.0855
 UXD  O    O  O     0  -0.514  -20.4810  12.3287  24.0467
 UXD  C1   C  CH2   0  -0.258  -18.6064  14.1704  24.7546
 UXD  C2   C  CH2   0  -0.488  -17.9595  15.3125  25.5281
 UXD  C3   C  CH2   0  -0.470  -18.3715  15.0268  26.9673
 UXD  N2   N  N     0  -0.263  -23.7831  11.5609  26.4243
 UXD  H1   H  HNR5  0   0.428  -24.4382  12.9691  27.7332
 UXD  H3   H  HCH2  0   0.258  -20.1185  13.8873  27.6220
 UXD  H4   H  HCR5  0   0.300  -22.4465  14.3873  27.2466
 UXD  H5   H  HCR5  0   0.264  -22.5155  10.7049  25.0108
 UXD  H6   H  HCH2  0   0.246  -18.8549  14.4401  23.7280
 UXD  H7   H  HCH2  0   0.235  -17.9509  13.2954  24.7190
 UXD  H8   H  HCH2  0   0.253  -16.8803  15.3447  25.3846
 UXD  H9   H  HCH2  0   0.239  -18.3689  16.2711  25.2017
 UXD  H10  H  HCH2  0   0.241  -17.7584  14.2256  27.3856
 UXD  H11  H  HCH2  0   0.253  -18.2905  15.8909  27.6252
 UXD  H2   H  HCH2  0   0.242  -20.4933  15.4143  26.8086

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
 UXD  O   C    double    1.231  0.020  1.231
 UXD  C1  C2   single    1.524  0.020  1.524
 UXD  C1  N    single    1.462  0.020  1.462
 UXD  C   N    single    1.343  0.020  1.343
 UXD  C   C5   single    1.473  0.020  1.473
 UXD  C7  C5   aromatic  1.412  0.020  1.412
 UXD  C7  N2   aromatic  1.314  0.020  1.314
 UXD  C2  C3   single    1.524  0.020  1.524
 UXD  N   C4   single    1.459  0.020  1.459
 UXD  C5  C6   aromatic  1.384  0.020  1.384
 UXD  N2  N1   aromatic  1.331  0.020  1.331
 UXD  C3  C4   single    1.524  0.020  1.524
 UXD  C6  N1   aromatic  1.336  0.020  1.336
 UXD  N1  H1   single    0.860  0.020  1.020
 UXD  C4  H2   single    0.970  0.020  1.090
 UXD  C4  H3   single    0.970  0.020  1.090
 UXD  C6  H4   single    0.930  0.020  1.080
 UXD  C7  H5   single    0.930  0.020  1.080
 UXD  C1  H6   single    0.970  0.020  1.090
 UXD  C1  H7   single    0.970  0.020  1.090
 UXD  C2  H8   single    0.970  0.020  1.090
 UXD  C2  H9   single    0.970  0.020  1.090
 UXD  C3  H10  single    0.970  0.020  1.090
 UXD  C3  H11  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
 UXD  H1   N1  N2   119.91  3.000
 UXD  H1   N1  C6   126.58  3.000
 UXD  N2   N1  C6   113.50  3.000
 UXD  H3   C4  H2   108.27  3.000
 UXD  H3   C4  C3   112.43  3.000
 UXD  H2   C4  C3   110.31  3.000
 UXD  H3   C4  N    111.45  3.000
 UXD  H2   C4  N    111.09  3.000
 UXD  C3   C4  N    103.26  3.000
 UXD  C    C5  C7   123.14  3.000
 UXD  C7   C5  C6   103.70  3.000
 UXD  C    C5  C6   133.06  3.000
 UXD  H4   C6  C5   132.71  3.000
 UXD  H4   C6  N1   120.96  3.000
 UXD  C5   C6  N1   106.31  3.000
 UXD  H5   C7  N2   120.64  3.000
 UXD  H5   C7  C5   127.65  3.000
 UXD  N2   C7  C5   111.71  3.000
 UXD  C1   N   C    120.06  3.000
 UXD  C    N   C4   127.56  3.000
 UXD  C1   N   C4   111.98  3.000
 UXD  O    C   N    121.23  3.000
 UXD  N    C   C5   119.62  3.000
 UXD  O    C   C5   119.15  3.000
 UXD  H7   C1  H6   107.70  3.000
 UXD  H7   C1  C2   111.20  3.000
 UXD  H6   C1  C2   112.92  3.000
 UXD  H7   C1  N    110.45  3.000
 UXD  H6   C1  N    111.10  3.000
 UXD  C2   C1  N    103.47  3.000
 UXD  H9   C2  H8   107.82  3.000
 UXD  H9   C2  C3   110.20  3.000
 UXD  H8   C2  C3   113.45  3.000
 UXD  H9   C2  C1   110.31  3.000
 UXD  H8   C2  C1   112.08  3.000
 UXD  C3   C2  C1   102.95  3.000
 UXD  H11  C3  H10  107.99  3.000
 UXD  H11  C3  C2   113.68  3.000
 UXD  H10  C3  C2   110.33  3.000
 UXD  H11  C3  C4   111.98  3.000
 UXD  H10  C3  C4   110.04  3.000
 UXD  C2   C3  C4   102.76  3.000
 UXD  C7   N2  N1   104.78  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
 UXD  CONST_01  C5  C7  N2  N1    0.00   0.0  0
 UXD  CONST_02  C7  C5  C6  N1    0.00   0.0  0
 UXD  CONST_03  N2  N1  C6  C5    0.00   0.0  0
 UXD  CONST_04  N2  C7  C5  C6    0.00   0.0  0
 UXD  CONST_05  C7  N2  N1  C6    0.00   0.0  0
 UXD  CONST_06  C   C5  C6  N1  180.00   0.0  0
 UXD  CONST_07  N2  C7  C5  C   180.00   0.0  0
 UXD  CONST_08  C5  C   N   C4    0.00   0.0  0
 UXD  CONST_09  C1  N   C   C5  180.00   0.0  0
 UXD  CONST_10  H5  C7  N2  N1  180.00   0.0  0
 UXD  CONST_11  H1  N1  C6  C5  180.00   0.0  0
 UXD  CONST_12  H4  C6  C5  C7  180.00   0.0  0
 UXD  CONST_13  O   C   N   C4  180.00   0.0  0
 UXD  CONST_14  C1  N   C   O     0.00   0.0  0
 UXD  Var_01    C2  C1  N   C4  -10.81  30.0  1
 UXD  Var_02    C1  C2  C3  C4  -39.61  30.0  1
 UXD  Var_03    C3  C2  C1  N    31.00  30.0  1
 UXD  Var_04    C2  C3  C4  N    32.76  30.0  1
 UXD  Var_05    C3  C4  N   C1  -13.87  30.0  1
 UXD  Var_06    N   C   C5  C6   21.03  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
 UXD  plan-1  N1  0.020
 UXD  plan-1  C5  0.020
 UXD  plan-1  C6  0.020
 UXD  plan-1  C7  0.020
 UXD  plan-1  C   0.020
 UXD  plan-1  N2  0.020
 UXD  plan-1  H1  0.020
 UXD  plan-1  H4  0.020
 UXD  plan-1  H5  0.020
 UXD  plan-2  C4  0.020
 UXD  plan-2  C5  0.020
 UXD  plan-2  N   0.020
 UXD  plan-2  C   0.020
 UXD  plan-2  O   0.020
 UXD  plan-2  C1  0.020

