# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:54:30 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n[nH]c(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
 46X  46X  3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile  ligand  24  13  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_46X
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
 46X  C4   C  CH2   0  -0.292  -2.2596   0.9119  -0.9421
 46X  C5   C  CR5   0  -0.321   1.1599   0.0379   0.4972
 46X  C6   C  CSP   0  -0.005   1.1975  -0.7698   1.6362
 46X  N1   N  NR15  0  -0.550   0.5632   1.3150  -1.1694
 46X  C7   C  CR5   0   0.451   2.2878   0.6445  -0.1375
 46X  N2   N  NT    0  -0.530  -1.2560   0.2708  -0.1024
 46X  N3   N  NS    0  -0.287   1.2800  -1.4300   2.5841
 46X  N4   N  NH2   0  -0.844   3.5898   0.5245   0.2743
 46X  N    N  N     0  -0.328   1.9262   1.4006  -1.1378
 46X  C    C  CR5   0   0.742   0.0502   0.5074  -0.2334
 46X  C3   C  CH2   0  -0.483  -3.5723   0.4602  -0.3133
 46X  C2   C  CH2   0  -0.474  -3.2306  -0.9121   0.2600
 46X  C1   C  CH2   0  -0.280  -1.8181  -0.7240   0.8013
 46X  H1   H  HCH2  0   0.255  -2.1444   1.9983  -0.9341
 46X  H2   H  HCH2  0   0.246  -2.1762   0.5719  -1.9801
 46X  H3   H  HNR5  0   0.427   0.0625   1.7803  -1.9080
 46X  H4   H  HNH2  0   0.382   4.2660   0.8023  -0.4209
 46X  H5   H  HNH2  0   0.385   3.8279  -0.3712   0.6712
 46X  H6   H  HCH2  0   0.246  -3.8601   1.1443   0.4874
 46X  H7   H  HCH2  0   0.258  -4.3826   0.4331  -1.0399
 46X  H8   H  HCH2  0   0.257  -3.9239  -1.2403   1.0328
 46X  H9   H  HCH2  0   0.244  -3.2283  -1.6627  -0.5328
 46X  H10  H  HCH2  0   0.256  -1.2401  -1.6493   0.7801
 46X  H11  H  HCH2  0   0.244  -1.8312  -0.3555   1.8314

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
 46X  N4  C7   single    1.371  0.020  1.371
 46X  C7  N    aromatic  1.305  0.020  1.305
 46X  C7  C5   aromatic  1.429  0.020  1.429
 46X  N   N1   aromatic  1.366  0.020  1.366
 46X  N1  C    aromatic  1.338  0.020  1.338
 46X  C5  C6   single    1.397  0.020  1.397
 46X  C5  C    aromatic  1.409  0.020  1.409
 46X  C6  N3   triple    1.158  0.020  1.158
 46X  C   N2   single    1.334  0.020  1.334
 46X  N2  C4   single    1.457  0.020  1.457
 46X  N2  C1   single    1.457  0.020  1.457
 46X  C4  C3   single    1.524  0.020  1.524
 46X  C1  C2   single    1.524  0.020  1.524
 46X  C2  C3   single    1.526  0.020  1.526
 46X  C4  H1   single    0.970  0.020  1.090
 46X  C4  H2   single    0.970  0.020  1.090
 46X  N1  H3   single    0.860  0.020  1.020
 46X  N4  H4   single    0.890  0.020  1.040
 46X  N4  H5   single    0.890  0.020  1.040
 46X  C3  H6   single    0.970  0.020  1.090
 46X  C3  H7   single    0.970  0.020  1.090
 46X  C2  H8   single    0.970  0.020  1.090
 46X  C2  H9   single    0.970  0.020  1.090
 46X  C1  H10  single    0.970  0.020  1.090
 46X  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
 46X  H2   C4  H1   107.91  3.000
 46X  H2   C4  C3   111.38  3.000
 46X  H1   C4  C3   112.49  3.000
 46X  H2   C4  N2   110.92  3.000
 46X  H1   C4  N2   111.14  3.000
 46X  C3   C4  N2   103.01  3.000
 46X  C    C5  C7   104.47  3.000
 46X  C    C5  C6   129.54  3.000
 46X  C7   C5  C6   125.89  3.000
 46X  N3   C6  C5   180.00  3.000
 46X  H3   N1  C    126.98  3.000
 46X  H3   N1  N    118.98  3.000
 46X  C    N1  N    113.83  3.000
 46X  N    C7  N4   122.97  3.000
 46X  N    C7  C5   111.57  3.000
 46X  N4   C7  C5   125.38  3.000
 46X  C1   N2  C    124.04  3.000
 46X  C1   N2  C4   113.09  3.000
 46X  C    N2  C4   122.67  3.000
 46X  H5   N4  H4   110.95  3.000
 46X  H5   N4  C7   114.85  3.000
 46X  H4   N4  C7   113.93  3.000
 46X  C7   N   N1   104.95  3.000
 46X  N2   C   N1   123.44  3.000
 46X  N2   C   C5   131.39  3.000
 46X  N1   C   C5   105.17  3.000
 46X  H7   C3  H6   107.99  3.000
 46X  H7   C3  C2   113.26  3.000
 46X  H6   C3  C2   110.30  3.000
 46X  H7   C3  C4   111.91  3.000
 46X  H6   C3  C4   110.12  3.000
 46X  C2   C3  C4   103.22  3.000
 46X  H9   C2  H8   108.03  3.000
 46X  H9   C2  C1   109.92  3.000
 46X  H8   C2  C1   112.03  3.000
 46X  H9   C2  C3   110.24  3.000
 46X  H8   C2  C3   113.28  3.000
 46X  C1   C2  C3   103.29  3.000
 46X  H11  C1  H10  108.08  3.000
 46X  H11  C1  C2   111.39  3.000
 46X  H10  C1  C2   112.29  3.000
 46X  H11  C1  N2   111.02  3.000
 46X  H10  C1  N2   111.26  3.000
 46X  C2   C1  N2   102.80  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
 46X  CONST_01  N1  N   C7  C5     0.00   0.0  0
 46X  CONST_02  N   N1  C   C5     0.00   0.0  0
 46X  CONST_03  C7  C5  C   N1     0.00   0.0  0
 46X  CONST_04  C   N1  N   C7     0.00   0.0  0
 46X  CONST_05  C   C5  C7  N      0.00   0.0  0
 46X  CONST_06  N2  C   C5  C7   180.00   0.0  0
 46X  CONST_07  N   N1  C   N2   180.00   0.0  0
 46X  CONST_08  N   C7  C5  C6   180.00   0.0  0
 46X  CONST_09  N1  C   C5  C6   180.00   0.0  0
 46X  CONST_10  N2  C   C5  C6     0.00   0.0  0
 46X  CONST_11  N4  C7  N   N1   180.00   0.0  0
 46X  CONST_12  C   C5  C7  N4   180.00   0.0  0
 46X  CONST_13  H3  N1  C   C5   180.00   0.0  0
 46X  Var_01    N1  C   N2  C4    -2.29  30.0  3
 46X  Var_02    C2  C1  N2  C4    12.60  30.0  1
 46X  Var_03    C1  C2  C3  C4    38.56  30.0  1
 46X  Var_04    C2  C3  C4  N2   -30.43  30.0  1
 46X  Var_05    C3  C2  C1  N2   -31.21  30.0  1
 46X  Var_06    C3  C4  N2  C   -173.58  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
 46X  plan-1  C5  0.020
 46X  plan-1  C6  0.020
 46X  plan-1  N1  0.020
 46X  plan-1  C7  0.020
 46X  plan-1  N2  0.020
 46X  plan-1  N3  0.020
 46X  plan-1  N4  0.020
 46X  plan-1  N   0.020
 46X  plan-1  C   0.020
 46X  plan-1  H3  0.020
 46X  plan-2  C7  0.020
 46X  plan-2  N4  0.020
 46X  plan-2  H4  0.020
 46X  plan-2  H5  0.020

