# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:12:51 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-(4-nitrophenyl)-1H-pyrazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(cc1)c2cc[nH]n2
#
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
 VC3  VC3  3-(4-nitrophenyl)-1H-pyrazole  ligand  21  14  .  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_VC3
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
 VC3  N1   N  N      1   0.328  73.8964  66.8106   0.9609
 VC3  N2   N  N      0  -0.289  78.9342  65.6557   4.8489
 VC3  C3   C  CR5    0   0.281  78.6938  65.2764   3.6001
 VC3  N4   N  NR15   0  -0.408  80.1100  65.1395   5.1483
 VC3  C5   C  CR6    0   0.237  75.1199  66.4204   1.6343
 VC3  C6   C  CR15   0  -0.522  79.7591  64.4948   3.1031
 VC3  O7   O  O     -1  -0.383  73.7577  66.4949  -0.1985
 VC3  O8   O  O      0  -0.383  73.0723  67.4330   1.5907
 VC3  C9   C  CR6    0   0.088  77.4606  65.6712   2.9245
 VC3  C10  C  CR15   0   0.032  80.6535  64.4334   4.1424
 VC3  C11  C  CR16   0  -0.246  76.0613  65.6640   0.9511
 VC3  C12  C  CR16   0  -0.250  75.3273  66.8093   2.9516
 VC3  C13  C  CR16   0  -0.326  77.2232  65.2947   1.6010
 VC3  C14  C  CR16   0  -0.287  76.4938  66.4339   3.5865
 VC3  H4   H  HNR5   0   0.428  80.5074  65.2981   6.0610
 VC3  H6   H  HCR5   0   0.270  79.8650  64.0374   2.1338
 VC3  H10  H  HCR5   0   0.299  81.6118  63.9506   4.2359
 VC3  H11  H  HCR6   0   0.298  75.9008  65.3587  -0.0724
 VC3  H12  H  HCR6   0   0.297  74.5956  67.3998   3.4831
 VC3  H13  H  HCR6   0   0.266  77.9505  64.7044   1.0609
 VC3  H14  H  HCR6   0   0.271  76.6565  66.7381   4.6110

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
 VC3  N1   C5   single    1.450  0.020  1.450
 VC3  N1   O7   single    1.210  0.020  1.210
 VC3  N1   O8   double    1.210  0.020  1.210
 VC3  N2   C3   aromatic  1.327  0.020  1.327
 VC3  N2   N4   aromatic  1.319  0.020  1.319
 VC3  C3   C6   aromatic  1.412  0.020  1.412
 VC3  C3   C9   single    1.461  0.020  1.461
 VC3  N4   C10  aromatic  1.344  0.020  1.344
 VC3  C5   C11  aromatic  1.388  0.020  1.388
 VC3  C5   C12  aromatic  1.389  0.020  1.389
 VC3  C6   C10  aromatic  1.373  0.020  1.373
 VC3  C9   C13  aromatic  1.396  0.020  1.396
 VC3  C9   C14  aromatic  1.398  0.020  1.398
 VC3  C11  C13  aromatic  1.382  0.020  1.382
 VC3  C12  C14  aromatic  1.380  0.020  1.380
 VC3  N4   H4   single    0.860  0.020  1.020
 VC3  C6   H6   single    0.930  0.020  1.080
 VC3  C10  H10  single    0.930  0.020  1.080
 VC3  C11  H11  single    0.930  0.020  1.080
 VC3  C12  H12  single    0.930  0.020  1.080
 VC3  C13  H13  single    0.930  0.020  1.080
 VC3  C14  H14  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
 VC3  O8   N1   O7   123.72  3.000
 VC3  O8   N1   C5   118.13  3.000
 VC3  O7   N1   C5   118.15  3.000
 VC3  N4   N2   C3   105.26  3.000
 VC3  C9   C3   C6   128.61  3.000
 VC3  C9   C3   N2   120.73  3.000
 VC3  C6   C3   N2   110.67  3.000
 VC3  H4   N4   C10  126.94  3.000
 VC3  H4   N4   N2   119.70  3.000
 VC3  C10  N4   N2   113.36  3.000
 VC3  C12  C5   C11  121.22  3.000
 VC3  C12  C5   N1   119.41  3.000
 VC3  C11  C5   N1   119.37  3.000
 VC3  H6   C6   C10  126.76  3.000
 VC3  H6   C6   C3   128.77  3.000
 VC3  C10  C6   C3   104.47  3.000
 VC3  C14  C9   C13  118.57  3.000
 VC3  C14  C9   C3   120.82  3.000
 VC3  C13  C9   C3   120.61  3.000
 VC3  H10  C10  C6   131.72  3.000
 VC3  H10  C10  N4   122.04  3.000
 VC3  C6   C10  N4   106.24  3.000
 VC3  H11  C11  C13  119.69  3.000
 VC3  H11  C11  C5   121.33  3.000
 VC3  C13  C11  C5   118.99  3.000
 VC3  H12  C12  C14  119.66  3.000
 VC3  H12  C12  C5   121.24  3.000
 VC3  C14  C12  C5   119.10  3.000
 VC3  H13  C13  C11  118.46  3.000
 VC3  H13  C13  C9   120.41  3.000
 VC3  C11  C13  C9   121.12  3.000
 VC3  H14  C14  C12  119.12  3.000
 VC3  H14  C14  C9   119.88  3.000
 VC3  C12  C14  C9   121.00  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
 VC3  CONST_01  C10  C6   C3   N2     0.00  0.0  0
 VC3  CONST_02  C13  C9   C3   N2   180.00  0.0  0
 VC3  CONST_03  C14  C9   C3   N2     0.00  0.0  0
 VC3  CONST_04  C6   C10  N4   N2     0.00  0.0  0
 VC3  CONST_05  C10  N4   N2   C3     0.00  0.0  0
 VC3  CONST_06  N4   C10  C6   C3     0.00  0.0  0
 VC3  CONST_07  C11  C13  C9   C3   180.00  0.0  0
 VC3  CONST_08  C12  C14  C9   C3   180.00  0.0  0
 VC3  CONST_09  C6   C3   N2   N4     0.00  0.0  0
 VC3  CONST_10  C9   C3   N2   N4   180.00  0.0  0
 VC3  CONST_11  C9   C13  C11  C5     0.00  0.0  0
 VC3  CONST_12  C9   C14  C12  C5     0.00  0.0  0
 VC3  CONST_13  C13  C9   C3   C6     0.00  0.0  0
 VC3  CONST_14  C14  C9   C3   C6   180.00  0.0  0
 VC3  CONST_15  C10  C6   C3   C9   180.00  0.0  0
 VC3  CONST_16  C14  C12  C5   C11    0.00  0.0  0
 VC3  CONST_17  C14  C9   C13  C11    0.00  0.0  0
 VC3  CONST_18  C13  C11  C5   C12    0.00  0.0  0
 VC3  CONST_19  C13  C9   C14  C12    0.00  0.0  0
 VC3  CONST_20  C13  C11  C5   N1   180.00  0.0  0
 VC3  CONST_21  C14  C12  C5   N1   180.00  0.0  0
 VC3  CONST_22  H6   C6   C3   N2   180.00  0.0  0
 VC3  CONST_23  H10  C10  N4   N2   180.00  0.0  0
 VC3  CONST_24  H4   N4   N2   C3   180.00  0.0  0
 VC3  CONST_25  H13  C13  C9   C3     0.00  0.0  0
 VC3  CONST_26  H14  C14  C9   C3     0.00  0.0  0
 VC3  CONST_27  H11  C11  C13  C9   180.00  0.0  0
 VC3  CONST_28  H12  C12  C14  C9   180.00  0.0  0
 VC3  CONST_29  C11  C5   N1   O7     0.00  0.0  0
 VC3  CONST_30  C12  C5   N1   O7   180.00  0.0  0
 VC3  CONST_31  C11  C5   N1   O8   180.00  0.0  0
 VC3  CONST_32  C12  C5   N1   O8     0.00  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
 VC3  plan-1  N2   0.020
 VC3  plan-1  C3   0.020
 VC3  plan-1  N4   0.020
 VC3  plan-1  C6   0.020
 VC3  plan-1  C9   0.020
 VC3  plan-1  C10  0.020
 VC3  plan-1  H4   0.020
 VC3  plan-1  H6   0.020
 VC3  plan-1  H10  0.020
 VC3  plan-2  N1   0.020
 VC3  plan-2  C3   0.020
 VC3  plan-2  C5   0.020
 VC3  plan-2  C9   0.020
 VC3  plan-2  C11  0.020
 VC3  plan-2  C12  0.020
 VC3  plan-2  C13  0.020
 VC3  plan-2  C14  0.020
 VC3  plan-2  H11  0.020
 VC3  plan-2  H12  0.020
 VC3  plan-2  H13  0.020
 VC3  plan-2  H14  0.020
 VC3  plan-3  N1   0.020
 VC3  plan-3  C5   0.020
 VC3  plan-3  O7   0.020
 VC3  plan-3  O8   0.020

