# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:22:43 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1[nH]nc(C(=O)NCc2ccc(Cl)cc2)c1Cl
#
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
 WDU  WDU  4-chloro-N-(4-chlorobenzyl)-5-nitro-1H-pyrazole-3-carboxamide  ligand  28  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WDU
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
 WDU  C15  C   CR16   0  -0.289  -3.4700  -0.5242  -1.1848
 WDU  C16  C   CR16   0  -0.290  -3.5235  -0.5553   1.2088
 WDU  C17  C   CR16   0  -0.197  -4.6413   0.2174  -1.2113
 WDU  C18  C   CR16   0  -0.197  -4.6954   0.1869   1.2025
 WDU  C14  C   CR6    0   0.055  -2.8999  -0.9220   0.0207
 WDU  C19  C   CR6    0  -0.049  -5.2437   0.5664  -0.0123
 WDU  C2   C   CR5    0  -0.231   3.2133  -0.3635  -0.0501
 WDU  C1   C   CR5    0   0.225   1.8186  -0.1993  -0.0174
 WDU  C5   C   CR5    0   0.617   3.6952   0.9283  -0.0004
 WDU  C4   C   C      0   0.564   0.7727  -1.2524  -0.0401
 WDU  C11  C   CH2    0  -0.314  -1.6196  -1.7074   0.0389
 WDU  N3   N   N      0  -0.248   1.5076   1.0882   0.0452
 WDU  N7   N   NR15   0  -0.438   2.6297   1.7480   0.0540
 WDU  N8   N   NH1    0  -0.650  -0.4847  -0.8018   0.0305
 WDU  N10  N   N      1   0.329   5.0200   1.4374  -0.0013
 WDU  O13  O   O     -1  -0.376   5.1425   2.6404   0.0390
 WDU  O9   O   O      0  -0.473   1.0725  -2.4327  -0.1193
 WDU  O12  O   O      0  -0.359   5.9222   0.6394  -0.0411
 WDU  CL1  CL  CL     0  -0.127  -6.7113   1.4875  -0.0340
 WDU  H1   H   HCR6   0   0.267  -3.0006  -0.7980  -2.1216
 WDU  H2   H   HCR6   0   0.268  -3.0965  -0.8551   2.1578
 WDU  H3   H   HCR6   0   0.282  -5.0798   0.5119  -2.1550
 WDU  H4   H   HCR6   0   0.282  -5.1745   0.4585   2.1332
 WDU  H5   H   HCH2   0   0.263  -1.5832  -2.3462   0.9247
 WDU  H6   H   HCH2   0   0.264  -1.5692  -2.3639  -0.8321
 WDU  H8   H   HNH1   0   0.416  -0.6510   0.1884   0.1261
 WDU  H7   H   HNR5   0   0.457   2.6319   2.7594   0.0976
 WDU  CL6  CL  CL     0  -0.051   4.1014  -1.7973  -0.1303

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
 WDU  C15  C17  aromatic  1.387  0.020  1.387
 WDU  C15  C14  aromatic  1.392  0.020  1.392
 WDU  C17  C19  aromatic  1.386  0.020  1.386
 WDU  C11  C14  single    1.502  0.020  1.502
 WDU  C11  N8   single    1.452  0.020  1.452
 WDU  C14  C16  aromatic  1.391  0.020  1.391
 WDU  O9   C4   double    1.220  0.020  1.220
 WDU  N8   C4   single    1.338  0.020  1.338
 WDU  C19  CL1  single    1.733  0.020  1.733
 WDU  C19  C18  aromatic  1.386  0.020  1.386
 WDU  C4   C1   single    1.484  0.020  1.484
 WDU  C16  C18  aromatic  1.387  0.020  1.387
 WDU  C1   N3   aromatic  1.326  0.020  1.326
 WDU  C1   C2   aromatic  1.405  0.020  1.405
 WDU  N3   N7   aromatic  1.302  0.020  1.302
 WDU  C2   CL6  single    1.689  0.020  1.689
 WDU  C2   C5   aromatic  1.380  0.020  1.380
 WDU  N7   C5   aromatic  1.345  0.020  1.345
 WDU  C5   N10  single    1.419  0.020  1.419
 WDU  N10  O13  single    1.210  0.020  1.210
 WDU  N10  O12  double    1.205  0.020  1.205
 WDU  C15  H1   single    0.930  0.020  1.080
 WDU  C16  H2   single    0.930  0.020  1.080
 WDU  C17  H3   single    0.930  0.020  1.080
 WDU  C18  H4   single    0.930  0.020  1.080
 WDU  C11  H5   single    0.970  0.020  1.090
 WDU  C11  H6   single    0.970  0.020  1.090
 WDU  N8   H8   single    0.860  0.020  1.020
 WDU  N7   H7   single    0.860  0.020  1.020

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
 WDU  H1   C15  C14  119.97  3.000
 WDU  H1   C15  C17  119.00  3.000
 WDU  C14  C15  C17  121.03  3.000
 WDU  H2   C16  C14  119.92  3.000
 WDU  H2   C16  C18  119.02  3.000
 WDU  C14  C16  C18  121.06  3.000
 WDU  H3   C17  C19  120.66  3.000
 WDU  H3   C17  C15  120.32  3.000
 WDU  C19  C17  C15  119.02  3.000
 WDU  H4   C18  C19  120.68  3.000
 WDU  H4   C18  C16  120.32  3.000
 WDU  C19  C18  C16  118.99  3.000
 WDU  C11  C14  C16  120.63  3.000
 WDU  C16  C14  C15  118.75  3.000
 WDU  C11  C14  C15  120.61  3.000
 WDU  CL1  C19  C18  119.45  3.000
 WDU  C18  C19  C17  121.15  3.000
 WDU  CL1  C19  C17  119.40  3.000
 WDU  CL6  C2   C5   127.81  3.000
 WDU  C5   C2   C1   103.68  3.000
 WDU  CL6  C2   C1   128.51  3.000
 WDU  N3   C1   C4   121.62  3.000
 WDU  N3   C1   C2   110.33  3.000
 WDU  C4   C1   C2   128.05  3.000
 WDU  N10  C5   N7   121.38  3.000
 WDU  N10  C5   C2   131.45  3.000
 WDU  N7   C5   C2   107.18  3.000
 WDU  O9   C4   N8   124.07  3.000
 WDU  N8   C4   C1   115.00  3.000
 WDU  O9   C4   C1   120.93  3.000
 WDU  H6   C11  H5   107.07  3.000
 WDU  H6   C11  N8   109.53  3.000
 WDU  H5   C11  N8   110.08  3.000
 WDU  H6   C11  C14  110.12  3.000
 WDU  H5   C11  C14  110.11  3.000
 WDU  N8   C11  C14  109.88  3.000
 WDU  N7   N3   C1   106.87  3.000
 WDU  H7   N7   N3   120.56  3.000
 WDU  H7   N7   C5   127.50  3.000
 WDU  N3   N7   C5   111.94  3.000
 WDU  H8   N8   C11  118.87  3.000
 WDU  H8   N8   C4   119.39  3.000
 WDU  C11  N8   C4   121.67  3.000
 WDU  O12  N10  O13  125.71  3.000
 WDU  O12  N10  C5   117.47  3.000
 WDU  O13  N10  C5   116.82  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
 WDU  CONST_01  C18  C19  C17  C15     0.00   0.0  0
 WDU  CONST_02  C18  C16  C14  C15     0.00   0.0  0
 WDU  CONST_03  C17  C15  C14  C16     0.00   0.0  0
 WDU  CONST_04  C17  C19  C18  C16     0.00   0.0  0
 WDU  CONST_05  C19  C17  C15  C14     0.00   0.0  0
 WDU  CONST_06  C19  C18  C16  C14     0.00   0.0  0
 WDU  CONST_07  N7   N3   C1   C2      0.00   0.0  0
 WDU  CONST_08  N3   N7   C5   C2      0.00   0.0  0
 WDU  CONST_09  C5   N7   N3   C1      0.00   0.0  0
 WDU  CONST_10  N7   C5   C2   C1      0.00   0.0  0
 WDU  CONST_11  N3   C1   C2   C5      0.00   0.0  0
 WDU  CONST_12  CL1  C19  C17  C15   180.00   0.0  0
 WDU  CONST_13  CL1  C19  C18  C16   180.00   0.0  0
 WDU  CONST_14  C11  C14  C15  C17   180.00   0.0  0
 WDU  CONST_15  C11  C14  C16  C18   180.00   0.0  0
 WDU  CONST_16  N10  C5   C2   C1    180.00   0.0  0
 WDU  CONST_17  C4   C1   C2   C5    180.00   0.0  0
 WDU  CONST_18  N7   N3   C1   C4    180.00   0.0  0
 WDU  CONST_19  CL6  C2   C1   N3    180.00   0.0  0
 WDU  CONST_20  N10  C5   N7   N3    180.00   0.0  0
 WDU  CONST_21  CL6  C2   C5   N7    180.00   0.0  0
 WDU  CONST_22  H2   C16  C14  C15   180.00   0.0  0
 WDU  CONST_23  H1   C15  C14  C16   180.00   0.0  0
 WDU  CONST_24  H4   C18  C19  C17   180.00   0.0  0
 WDU  CONST_25  H3   C17  C19  C18   180.00   0.0  0
 WDU  CONST_26  H7   N7   C5   C2    180.00   0.0  0
 WDU  CONST_27  O13  N10  C5   C2    180.00   0.0  0
 WDU  CONST_28  O12  N10  C5   C2      0.00   0.0  0
 WDU  CONST_29  O13  N10  C5   N7      0.00   0.0  0
 WDU  CONST_30  O12  N10  C5   N7    180.00   0.0  0
 WDU  CONST_31  C11  N8   C4   C1    180.00   0.0  0
 WDU  CONST_32  H8   N8   C4   C1      0.00   0.0  0
 WDU  CONST_33  O9   C4   N8   C11     0.00   0.0  0
 WDU  Var_01    N8   C11  C14  C15    87.43  30.0  3
 WDU  Var_02    O9   C4   C1   C2     -1.43  30.0  2
 WDU  Var_03    C4   N8   C11  C14  -175.79  30.0  3

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
 WDU  plan-1  C2   0.020
 WDU  plan-1  C1   0.020
 WDU  plan-1  C5   0.020
 WDU  plan-1  C4   0.020
 WDU  plan-1  N3   0.020
 WDU  plan-1  N7   0.020
 WDU  plan-1  N10  0.020
 WDU  plan-1  H7   0.020
 WDU  plan-1  CL6  0.020
 WDU  plan-2  C15  0.020
 WDU  plan-2  C16  0.020
 WDU  plan-2  C17  0.020
 WDU  plan-2  C18  0.020
 WDU  plan-2  C14  0.020
 WDU  plan-2  C19  0.020
 WDU  plan-2  C11  0.020
 WDU  plan-2  CL1  0.020
 WDU  plan-2  H1   0.020
 WDU  plan-2  H2   0.020
 WDU  plan-2  H3   0.020
 WDU  plan-2  H4   0.020
 WDU  plan-3  C1   0.020
 WDU  plan-3  C4   0.020
 WDU  plan-3  C11  0.020
 WDU  plan-3  N8   0.020
 WDU  plan-3  O9   0.020
 WDU  plan-3  H8   0.020
 WDU  plan-4  C5   0.020
 WDU  plan-4  N10  0.020
 WDU  plan-4  O13  0.020
 WDU  plan-4  O12  0.020

