# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:05:13 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-thiophen-2-yl-4~{H}-pyrazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NN=C(C1)c2sccc2
#
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
 J9N  J9N  5-thiophen-2-yl-4~{H}-pyrazol-3-amine  ligand  18  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J9N
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
 J9N  N01  N  NH2   0  -0.830   3.9181  -0.7953   0.0502
 J9N  C02  C  CR5   0   0.463   2.7432  -0.1676   0.0212
 J9N  C03  C  CH2   0  -0.654   1.4284  -0.8759   0.0136
 J9N  C04  C  CR5   0   0.235   0.5451   0.3282   0.0085
 J9N  C05  C  CR5   0  -0.220  -0.8994   0.3168   0.0000
 J9N  S06  S  S2    0   0.224  -1.7693  -1.1734  -0.0009
 J9N  C07  C  CR15  0  -0.465  -3.2781  -0.3675  -0.0121
 J9N  C08  C  CR15  0  -0.171  -3.1217   0.9872  -0.0144
 J9N  C09  C  CR15  0  -0.220  -1.7625   1.3820  -0.0078
 J9N  N10  N  N     0  -0.289   1.2389   1.4096   0.0107
 J9N  N11  N  N     0  -0.364   2.5974   1.1243   0.0168
 J9N  H1   H  HNH2  0   0.413   3.9755  -1.7939  -0.0378
 J9N  H2   H  HNH2  0   0.402   4.7751  -0.2729  -0.0163
 J9N  H3   H  HCH2  0   0.321   1.3038  -1.5106  -0.8682
 J9N  H4   H  HCR5  0   0.300  -4.1968  -0.9333  -0.0174
 J9N  H5   H  HCR5  0   0.271  -3.9498   1.6810  -0.0217
 J9N  H6   H  HCR5  0   0.264  -1.4305   2.4102  -0.0088
 J9N  H8   H  HCH2  0   0.321   1.2946  -1.5118   0.8929

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
 J9N  N11  N10  single    1.388  0.020  1.388
 J9N  N11  C02  double    1.300  0.020  1.300
 J9N  N10  C04  double    1.285  0.020  1.285
 J9N  C02  N01  single    1.332  0.020  1.332
 J9N  C02  C03  single    1.493  0.020  1.493
 J9N  C04  C03  single    1.493  0.020  1.493
 J9N  C04  C05  single    1.445  0.020  1.445
 J9N  C05  C09  aromatic  1.371  0.020  1.371
 J9N  C05  S06  aromatic  1.726  0.020  1.726
 J9N  C09  C08  aromatic  1.415  0.020  1.415
 J9N  S06  C07  aromatic  1.711  0.020  1.711
 J9N  C08  C07  aromatic  1.364  0.020  1.364
 J9N  N01  H1   single    0.860  0.020  1.020
 J9N  N01  H2   single    0.860  0.020  1.020
 J9N  C03  H3   single    0.970  0.020  1.090
 J9N  C07  H4   single    0.930  0.020  1.080
 J9N  C08  H5   single    0.930  0.020  1.080
 J9N  C09  H6   single    0.930  0.020  1.080
 J9N  C03  H8   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
 J9N  H2   N01  H1   117.52  3.000
 J9N  H2   N01  C02  120.34  3.000
 J9N  H1   N01  C02  121.14  3.000
 J9N  N11  C02  C03  111.87  3.000
 J9N  C03  C02  N01  123.57  3.000
 J9N  N11  C02  N01  124.55  3.000
 J9N  H8   C03  H3   107.28  3.000
 J9N  H8   C03  C04  113.53  3.000
 J9N  H3   C03  C04  113.44  3.000
 J9N  H8   C03  C02  112.30  3.000
 J9N  H3   C03  C02  112.31  3.000
 J9N  C04  C03  C02   97.95  3.000
 J9N  N10  C04  C05  123.14  3.000
 J9N  C05  C04  C03  125.81  3.000
 J9N  N10  C04  C03  111.05  3.000
 J9N  C09  C05  S06  110.71  3.000
 J9N  S06  C05  C04  120.73  3.000
 J9N  C09  C05  C04  128.57  3.000
 J9N  C07  S06  C05   92.17  3.000
 J9N  H4   C07  C08  128.21  3.000
 J9N  H4   C07  S06  120.27  3.000
 J9N  C08  C07  S06  111.53  3.000
 J9N  H5   C08  C09  123.85  3.000
 J9N  H5   C08  C07  123.38  3.000
 J9N  C09  C08  C07  112.78  3.000
 J9N  H6   C09  C08  124.09  3.000
 J9N  H6   C09  C05  123.08  3.000
 J9N  C08  C09  C05  112.83  3.000
 J9N  N11  N10  C04  110.83  3.000
 J9N  N10  N11  C02  108.30  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
 J9N  CONST_01  C07  C08  C09  C05     0.00   0.0  0
 J9N  CONST_02  C08  C07  S06  C05     0.00   0.0  0
 J9N  CONST_03  C08  C09  C05  S06     0.00   0.0  0
 J9N  CONST_04  C09  C08  C07  S06     0.00   0.0  0
 J9N  CONST_05  C09  C05  S06  C07     0.00   0.0  0
 J9N  CONST_06  C08  C09  C05  C04   180.00   0.0  0
 J9N  CONST_07  C07  S06  C05  C04   180.00   0.0  0
 J9N  CONST_08  N10  N11  C02  C03     0.00   0.0  0
 J9N  CONST_09  N10  N11  C02  N01   180.00   0.0  0
 J9N  CONST_10  H6   C09  C05  C04     0.00   0.0  0
 J9N  CONST_11  H5   C08  C09  C05   180.00   0.0  0
 J9N  CONST_12  H4   C07  S06  C05   180.00   0.0  0
 J9N  CONST_13  H1   N01  C02  C03     0.00   0.0  0
 J9N  CONST_14  H2   N01  C02  C03   180.00   0.0  0
 J9N  Var_01    N10  C04  C03  C02     0.09  30.0  1
 J9N  Var_02    C09  C05  C04  C03  -179.85  30.0  2
 J9N  Var_03    N11  C02  C03  C04    -0.17  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
 J9N  plan-1  C04  0.020
 J9N  plan-1  C05  0.020
 J9N  plan-1  S06  0.020
 J9N  plan-1  C07  0.020
 J9N  plan-1  C08  0.020
 J9N  plan-1  C09  0.020
 J9N  plan-1  H4   0.020
 J9N  plan-1  H5   0.020
 J9N  plan-1  H6   0.020
 J9N  plan-2  N01  0.020
 J9N  plan-2  C02  0.020
 J9N  plan-2  C03  0.020
 J9N  plan-2  N10  0.020
 J9N  plan-2  N11  0.020
 J9N  plan-2  H1   0.020
 J9N  plan-2  H2   0.020

