# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:02:07 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-azanyl-3-pyrrolidin-1-yl-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(N2CCCC2)c1C#N
#
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
 E9Q  E9Q  5-azanyl-3-pyrrolidin-1-yl-1~{H}-pyrazole-4-carbonitrile  ligand  24  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9Q
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
 E9Q  C4   C  CH2   0  -0.283  -2.2447   1.2364   0.1115
 E9Q  C5   C  CR5   0  -0.284   1.1978  -0.3338  -0.1428
 E9Q  C6   C  CSP   0  -0.006   1.2850  -1.7202  -0.2992
 E9Q  N1   N  N     0  -0.347   0.4514   1.7737   0.1813
 E9Q  C7   C  CR5   0   0.615   2.3066   0.5237  -0.0812
 E9Q  N2   N  NR5   0  -0.516  -1.2489   0.1772   0.1095
 E9Q  N3   N  NS    0  -0.282   1.4003  -2.8651  -0.4262
 E9Q  N4   N  NH2   0  -0.840   3.6185   0.2474  -0.2478
 E9Q  N    N  NR15  0  -0.499   1.8113   1.7406   0.1186
 E9Q  C    C  CR5   0   0.531   0.0665   0.5282   0.0373
 E9Q  C3   C  CH2   0  -0.477  -3.5789   0.4875   0.1431
 E9Q  C2   C  CH2   0  -0.467  -3.2606  -0.9476  -0.3205
 E9Q  C1   C  CH2   0  -0.301  -1.7675  -0.9493  -0.6503
 E9Q  H2   H  HCH2  0   0.246  -2.1078   1.8928   0.9713
 E9Q  H1   H  HCH2  0   0.220  -2.1620   1.8589  -0.7887
 E9Q  H4   H  HNH2  0   0.406   3.9001  -0.7069  -0.0908
 E9Q  H5   H  HNH2  0   0.407   4.2814   0.9173   0.1088
 E9Q  H    H  HNR5  0   0.423   2.3300   2.6001   0.2020
 E9Q  H7   H  HCH2  0   0.244  -3.9927   0.4804   1.1511
 E9Q  H6   H  HCH2  0   0.243  -4.3104   0.9749  -0.4993
 E9Q  H8   H  HCH2  0   0.245  -3.4728  -1.6614   0.4753
 E9Q  H9   H  HCH2  0   0.244  -3.8494  -1.2467  -1.1865
 E9Q  H10  H  HCH2  0   0.225  -1.6004  -0.8156  -1.7271
 E9Q  H11  H  HCH2  0   0.254  -1.2907  -1.8828  -0.3541

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
 E9Q  N4  C7   single    1.351  0.020  1.351
 E9Q  N3  C6   triple    1.158  0.020  1.158
 E9Q  C6  C5   single    1.398  0.020  1.398
 E9Q  C7  C5   aromatic  1.403  0.020  1.403
 E9Q  C7  N    aromatic  1.329  0.020  1.329
 E9Q  C5  C    aromatic  1.434  0.020  1.434
 E9Q  N   N1   aromatic  1.362  0.020  1.362
 E9Q  C   N1   aromatic  1.312  0.020  1.312
 E9Q  C   N2   single    1.363  0.020  1.363
 E9Q  C1  N2   single    1.454  0.020  1.454
 E9Q  C1  C2   single    1.529  0.020  1.529
 E9Q  N2  C4   single    1.454  0.020  1.454
 E9Q  C2  C3   single    1.541  0.020  1.541
 E9Q  C4  C3   single    1.530  0.020  1.530
 E9Q  C4  H2   single    0.970  0.020  1.090
 E9Q  C4  H1   single    0.970  0.020  1.090
 E9Q  N4  H4   single    0.890  0.020  1.040
 E9Q  N4  H5   single    0.890  0.020  1.040
 E9Q  N   H    single    0.860  0.020  1.020
 E9Q  C3  H7   single    0.970  0.020  1.090
 E9Q  C3  H6   single    0.970  0.020  1.090
 E9Q  C2  H8   single    0.970  0.020  1.090
 E9Q  C2  H9   single    0.970  0.020  1.090
 E9Q  C1  H10  single    0.970  0.020  1.090
 E9Q  C1  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
 E9Q  H1   C4  H2   107.21  3.000
 E9Q  H1   C4  C3   111.11  3.000
 E9Q  H2   C4  C3   112.82  3.000
 E9Q  H1   C4  N2   111.13  3.000
 E9Q  H2   C4  N2   110.71  3.000
 E9Q  C3   C4  N2   103.93  3.000
 E9Q  C    C5  C7   104.51  3.000
 E9Q  C    C5  C6   131.27  3.000
 E9Q  C7   C5  C6   124.18  3.000
 E9Q  N3   C6  C5   180.00  3.000
 E9Q  C    N1  N    105.36  3.000
 E9Q  N    C7  N4   124.59  3.000
 E9Q  N    C7  C5   105.77  3.000
 E9Q  N4   C7  C5   129.57  3.000
 E9Q  C1   N2  C    121.05  3.000
 E9Q  C1   N2  C4   108.71  3.000
 E9Q  C    N2  C4   118.26  3.000
 E9Q  H5   N4  H4   113.00  3.000
 E9Q  H5   N4  C7   117.34  3.000
 E9Q  H4   N4  C7   116.48  3.000
 E9Q  H    N   C7   127.00  3.000
 E9Q  H    N   N1   119.32  3.000
 E9Q  C7   N   N1   113.66  3.000
 E9Q  N2   C   N1   121.45  3.000
 E9Q  N2   C   C5   127.82  3.000
 E9Q  N1   C   C5   110.69  3.000
 E9Q  H6   C3  H7   107.08  3.000
 E9Q  H6   C3  C2   112.22  3.000
 E9Q  H7   C3  C2   110.52  3.000
 E9Q  H6   C3  C4   110.76  3.000
 E9Q  H7   C3  C4   110.69  3.000
 E9Q  C2   C3  C4   105.63  3.000
 E9Q  H9   C2  H8   107.19  3.000
 E9Q  H9   C2  C1   110.85  3.000
 E9Q  H8   C2  C1   110.30  3.000
 E9Q  H9   C2  C3   112.53  3.000
 E9Q  H8   C2  C3   110.49  3.000
 E9Q  C1   C2  C3   105.52  3.000
 E9Q  H11  C1  H10  107.73  3.000
 E9Q  H11  C1  C2   111.69  3.000
 E9Q  H10  C1  C2   111.10  3.000
 E9Q  H11  C1  N2   111.45  3.000
 E9Q  H10  C1  N2   111.34  3.000
 E9Q  C2   C1  N2   103.57  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
 E9Q  CONST_01  N1  N   C7  C5     0.00   0.0  0
 E9Q  CONST_02  N   N1  C   C5     0.00   0.0  0
 E9Q  CONST_03  C7  C5  C   N1     0.00   0.0  0
 E9Q  CONST_04  C   N1  N   C7     0.00   0.0  0
 E9Q  CONST_05  C   C5  C7  N      0.00   0.0  0
 E9Q  CONST_06  N2  C   C5  C7   180.00   0.0  0
 E9Q  CONST_07  N   N1  C   N2   180.00   0.0  0
 E9Q  CONST_08  N   C7  C5  C6   180.00   0.0  0
 E9Q  CONST_09  N1  C   C5  C6   180.00   0.0  0
 E9Q  CONST_10  N2  C   C5  C6     0.00   0.0  0
 E9Q  CONST_11  N4  C7  N   N1   180.00   0.0  0
 E9Q  CONST_12  C   C5  C7  N4   180.00   0.0  0
 E9Q  CONST_13  H   N   C7  C5   180.00   0.0  0
 E9Q  Var_01    C5  C   N2  C4  -171.67  30.0  1
 E9Q  Var_02    C2  C1  N2  C4   -35.96  30.0  1
 E9Q  Var_03    C1  C2  C3  C4    -2.11  30.0  1
 E9Q  Var_04    C3  C2  C1  N2    22.17  30.0  1
 E9Q  Var_05    C2  C3  C4  N2   -18.76  30.0  1
 E9Q  Var_06    C3  C4  N2  C    177.80  30.0  1

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
 E9Q  plan-1  C5  0.020
 E9Q  plan-1  C6  0.020
 E9Q  plan-1  N1  0.020
 E9Q  plan-1  C7  0.020
 E9Q  plan-1  N2  0.020
 E9Q  plan-1  N3  0.020
 E9Q  plan-1  N4  0.020
 E9Q  plan-1  N   0.020
 E9Q  plan-1  C   0.020
 E9Q  plan-1  H   0.020
 E9Q  plan-2  C7  0.020
 E9Q  plan-2  N4  0.020
 E9Q  plan-2  H4  0.020
 E9Q  plan-2  H5  0.020

