# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:47:50 2021
#   Inital geometry file: a 48 line input string
#   Ligand name: 2,3-bis(oxidanyl)benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(C#N)c1O
#
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
 P3K  P3K  2,3-bis(oxidanyl)benzenecarbonitrile  ligand  15  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P3K
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
 P3K  C4  C  CR16  0  -0.261  -38.3186  6.4983  7.5001
 P3K  C5  C  CR16  0  -0.359  -38.2446  5.4499  6.5835
 P3K  C6  C  CR6   0   0.301  -37.4485  5.5380  5.4558
 P3K  C7  C  CR6   0   0.290  -36.6984  6.7033  5.2263
 P3K  N1  N  NS    0  -0.240  -35.4123  9.8795  5.7008
 P3K  C3  C  CR16  0  -0.273  -37.5931  7.6481  7.2914
 P3K  C2  C  CR6   0  -0.090  -36.7832  7.7457  6.1513
 P3K  O1  O  OH1   0  -0.620  -37.3369  4.5647  4.5357
 P3K  O2  O  OH1   0  -0.591  -35.9478  6.7306  4.1205
 P3K  H1  H  HCR6  0   0.273  -38.9491  6.4024  8.3727
 P3K  H2  H  HCR6  0   0.288  -38.8213  4.5477  6.7546
 P3K  H3  H  HCR6  0   0.281  -37.6375  8.4744  7.9867
 P3K  H4  H  HOH1  0   0.481  -37.8824  3.8091  4.7823
 P3K  H5  H  HOH1  0   0.485  -35.4451  7.5504  4.0392
 P3K  C1  C  CSP   0   0.036  -36.0289  8.9286  5.9148

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
 P3K  O2  C7  single    1.337  0.020  1.337
 P3K  O1  C6  single    1.344  0.020  1.344
 P3K  C7  C6  aromatic  1.405  0.020  1.405
 P3K  C7  C2  aromatic  1.396  0.020  1.396
 P3K  C6  C5  aromatic  1.383  0.020  1.383
 P3K  N1  C1  triple    1.153  0.020  1.153
 P3K  C1  C2  single    1.423  0.020  1.423
 P3K  C2  C3  aromatic  1.402  0.020  1.402
 P3K  C5  C4  aromatic  1.395  0.020  1.395
 P3K  C3  C4  aromatic  1.375  0.020  1.375
 P3K  C4  H1  single    0.930  0.020  1.080
 P3K  C5  H2  single    0.930  0.020  1.080
 P3K  C3  H3  single    0.930  0.020  1.080
 P3K  O1  H4  single    0.850  0.020  0.980
 P3K  O2  H5  single    0.850  0.020  0.980

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
 P3K  H1  C4  C3  120.29  3.000
 P3K  H1  C4  C5  119.66  3.000
 P3K  C3  C4  C5  120.05  3.000
 P3K  H2  C5  C6  119.19  3.000
 P3K  H2  C5  C4  119.58  3.000
 P3K  C6  C5  C4  121.23  3.000
 P3K  O1  C6  C7  116.39  3.000
 P3K  C7  C6  C5  119.56  3.000
 P3K  O1  C6  C5  124.04  3.000
 P3K  O2  C7  C2  124.53  3.000
 P3K  C2  C7  C6  118.60  3.000
 P3K  O2  C7  C6  116.87  3.000
 P3K  H3  C3  C2  119.58  3.000
 P3K  H3  C3  C4  121.32  3.000
 P3K  C2  C3  C4  119.10  3.000
 P3K  C1  C2  C3  119.96  3.000
 P3K  C3  C2  C7  121.46  3.000
 P3K  C1  C2  C7  118.59  3.000
 P3K  H4  O1  C6  110.22  3.000
 P3K  H5  O2  C7  112.31  3.000
 P3K  C2  C1  N1  180.00  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
 P3K  CONST_01  C7  C6  C5  C4    0.00  0.0  0
 P3K  CONST_02  C7  C2  C3  C4    0.00  0.0  0
 P3K  CONST_03  C2  C7  C6  C5    0.00  0.0  0
 P3K  CONST_04  C2  C3  C4  C5    0.00  0.0  0
 P3K  CONST_05  C3  C2  C7  C6    0.00  0.0  0
 P3K  CONST_06  C3  C4  C5  C6    0.00  0.0  0
 P3K  CONST_07  O1  C6  C5  C4  180.00  0.0  0
 P3K  CONST_08  C1  C2  C3  C4  180.00  0.0  0
 P3K  CONST_09  O2  C7  C6  C5  180.00  0.0  0
 P3K  CONST_10  C1  C2  C7  C6  180.00  0.0  0
 P3K  CONST_11  O2  C7  C2  C3  180.00  0.0  0
 P3K  CONST_12  O1  C6  C7  C2  180.00  0.0  0
 P3K  CONST_13  H3  C3  C4  C5  180.00  0.0  0
 P3K  CONST_14  H1  C4  C5  C6  180.00  0.0  0
 P3K  CONST_15  H2  C5  C6  C7  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
 P3K  plan-1  C4  0.020
 P3K  plan-1  C5  0.020
 P3K  plan-1  C6  0.020
 P3K  plan-1  C7  0.020
 P3K  plan-1  N1  0.020
 P3K  plan-1  C3  0.020
 P3K  plan-1  C2  0.020
 P3K  plan-1  O1  0.020
 P3K  plan-1  O2  0.020
 P3K  plan-1  H1  0.020
 P3K  plan-1  H2  0.020
 P3K  plan-1  H3  0.020
 P3K  plan-1  C1  0.020

