# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:45:29 2020
#   Inital geometry file: a 29 line input string
#   Ligand name: 4-iodo-1H-pyrazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1c[nH]nc1
#
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
 PYZ  PYZ  '4-iodo-1H-pyrazole       '  ligand  9  6  .  2022-07-22  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_PYZ
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
 PYZ  N1   N  NR15  0  -0.412   0.6532   0.0113   2.9736
 PYZ  N2   N  N     0  -0.259  -0.6707   0.0227   3.0589
 PYZ  C3   C  CR15  0  -0.050  -1.0996   0.0223   1.8115
 PYZ  C4   C  CR5   0  -0.411  -0.0157   0.0104   0.9184
 PYZ  I4   I  I     0   0.070  -0.0811   0.0045  -1.1480
 PYZ  C5   C  CR15  0   0.049   1.1078   0.0035   1.7131
 PYZ  HN1  H  HNR5  0   0.430   1.2095   0.0092   3.8146
 PYZ  H3   H  HCR5  0   0.276  -2.1545   0.0304   1.5855
 PYZ  H5   H  HCR5  0   0.308   2.1578  -0.0057   1.4738

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
 PYZ  N1  N2   aromatic  1.327  0.020  1.327
 PYZ  N1  C5   aromatic  1.340  0.020  1.340
 PYZ  N1  HN1  single    0.860  0.020  1.020
 PYZ  N2  C3   aromatic  1.319  0.020  1.319
 PYZ  C3  C4   aromatic  1.404  0.020  1.404
 PYZ  C3  H3   single    0.930  0.020  1.080
 PYZ  C4  I4   single    2.067  0.020  2.067
 PYZ  C4  C5   aromatic  1.376  0.020  1.376
 PYZ  C5  H5   single    0.930  0.020  1.080

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
 PYZ  HN1  N1  C5  126.69  3.000
 PYZ  HN1  N1  N2  119.79  3.000
 PYZ  C5   N1  N2  113.52  3.000
 PYZ  C3   N2  N1  105.29  3.000
 PYZ  H3   C3  C4  128.42  3.000
 PYZ  H3   C3  N2  121.06  3.000
 PYZ  C4   C3  N2  110.51  3.000
 PYZ  C5   C4  I4  127.09  3.000
 PYZ  C5   C4  C3  105.24  3.000
 PYZ  I4   C4  C3  127.67  3.000
 PYZ  H5   C5  C4  131.89  3.000
 PYZ  H5   C5  N1  122.67  3.000
 PYZ  C4   C5  N1  105.44  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
 PYZ  CONST_01  C4   C3  N2  N1    0.00  0.0  0
 PYZ  CONST_02  C3   C4  C5  N1    0.00  0.0  0
 PYZ  CONST_03  C4   C5  N1  N2    0.00  0.0  0
 PYZ  CONST_04  C5   C4  C3  N2    0.00  0.0  0
 PYZ  CONST_05  C5   N1  N2  C3    0.00  0.0  0
 PYZ  CONST_06  I4   C4  C5  N1  180.00  0.0  0
 PYZ  CONST_07  I4   C4  C3  N2  180.00  0.0  0
 PYZ  CONST_08  H3   C3  N2  N1  180.00  0.0  0
 PYZ  CONST_09  H5   C5  N1  N2  180.00  0.0  0
 PYZ  CONST_10  HN1  N1  N2  C3  180.00  0.0  0

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
 PYZ  plan-1  N1   0.020
 PYZ  plan-1  N2   0.020
 PYZ  plan-1  C3   0.020
 PYZ  plan-1  C4   0.020
 PYZ  plan-1  I4   0.020
 PYZ  plan-1  C5   0.020
 PYZ  plan-1  HN1  0.020
 PYZ  plan-1  H3   0.020
 PYZ  plan-1  H5   0.020

