# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:06:22 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 2-nitrobenzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(O)c1[N+]([O-])=O
#
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
 38L  38L  '2-nitrobenzene-1,3-diol  '  ligand  16  11  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_38L
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
 38L  OAK  O  O      0  -0.389  -2.2412   0.5640   0.8088
 38L  NAG  N  N      1   0.313  -1.6629  -0.0330  -0.0701
 38L  OAJ  O  O     -1  -0.373  -2.2085  -0.7853  -0.8422
 38L  CAA  C  CR6    0   0.082  -0.2189  -0.0160  -0.0488
 38L  CAF  C  CR6    0   0.317   0.4813  -1.2293  -0.0711
 38L  OAH  O  OH1    0  -0.602  -0.2116  -2.3838   0.0244
 38L  CAE  C  CR16   0  -0.321   1.8638  -1.2064  -0.0961
 38L  CAD  C  CR16   0  -0.202   2.5345   0.0097  -0.1084
 38L  CAC  C  CR16   0  -0.417   1.8469   1.2059  -0.0716
 38L  CAB  C  CR6    0   0.413   0.4527   1.2101  -0.0343
 38L  OAI  O  OH1    0  -0.649  -0.2550   2.3392  -0.0272
 38L  H1   H  HOH1   0   0.504   0.1072  -3.0080  -0.6389
 38L  H2   H  HCR6   0   0.271   2.4308  -2.1280  -0.0986
 38L  H3   H  HCR6   0   0.287   3.6157   0.0083  -0.1281
 38L  H4   H  HCR6   0   0.272   2.3673   2.1561  -0.0726
 38L  H5   H  HOH1   0   0.494   0.3233   3.1085  -0.0904

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
 38L  OAI  CAB  single    1.333  0.020  1.333
 38L  CAB  CAC  aromatic  1.395  0.020  1.395
 38L  CAB  CAA  aromatic  1.398  0.020  1.398
 38L  OAK  NAG  double    1.210  0.020  1.210
 38L  CAC  CAD  aromatic  1.380  0.020  1.380
 38L  NAG  CAA  single    1.444  0.020  1.444
 38L  NAG  OAJ  single    1.208  0.020  1.208
 38L  CAA  CAF  aromatic  1.401  0.020  1.401
 38L  CAD  CAE  aromatic  1.389  0.020  1.389
 38L  CAF  CAE  aromatic  1.383  0.020  1.383
 38L  CAF  OAH  single    1.350  0.020  1.350
 38L  OAH  H1   single    0.850  0.020  0.980
 38L  CAE  H2   single    0.930  0.020  1.080
 38L  CAD  H3   single    0.930  0.020  1.080
 38L  CAC  H4   single    0.930  0.020  1.080
 38L  OAI  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
 38L  CAA  NAG  OAJ  117.92  3.000
 38L  OAJ  NAG  OAK  123.76  3.000
 38L  CAA  NAG  OAK  117.48  3.000
 38L  CAB  CAA  CAF  121.31  3.000
 38L  CAF  CAA  NAG  119.29  3.000
 38L  CAB  CAA  NAG  119.39  3.000
 38L  CAE  CAF  OAH  121.91  3.000
 38L  OAH  CAF  CAA  118.88  3.000
 38L  CAE  CAF  CAA  119.05  3.000
 38L  H1   OAH  CAF  109.57  3.000
 38L  H2   CAE  CAD  119.52  3.000
 38L  H2   CAE  CAF  120.65  3.000
 38L  CAD  CAE  CAF  119.83  3.000
 38L  H3   CAD  CAC  119.97  3.000
 38L  H3   CAD  CAE  118.81  3.000
 38L  CAC  CAD  CAE  121.21  3.000
 38L  H4   CAC  CAB  118.53  3.000
 38L  H4   CAC  CAD  121.39  3.000
 38L  CAB  CAC  CAD  120.08  3.000
 38L  OAI  CAB  CAC  122.25  3.000
 38L  CAC  CAB  CAA  118.51  3.000
 38L  OAI  CAB  CAA  119.21  3.000
 38L  H5   OAI  CAB  110.92  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
 38L  CONST_01  CAD  CAC  CAB  CAA    0.00  0.0  0
 38L  CONST_02  CAD  CAE  CAF  CAA    0.00  0.0  0
 38L  CONST_03  CAC  CAB  CAA  CAF    0.00  0.0  0
 38L  CONST_04  CAC  CAD  CAE  CAF    0.00  0.0  0
 38L  CONST_05  CAB  CAC  CAD  CAE    0.00  0.0  0
 38L  CONST_06  CAB  CAA  CAF  CAE    0.00  0.0  0
 38L  CONST_07  CAC  CAB  CAA  NAG  180.00  0.0  0
 38L  CONST_08  CAE  CAF  CAA  NAG  180.00  0.0  0
 38L  CONST_09  OAI  CAB  CAA  CAF  180.00  0.0  0
 38L  CONST_10  CAB  CAA  CAF  OAH  180.00  0.0  0
 38L  CONST_11  CAD  CAE  CAF  OAH  180.00  0.0  0
 38L  CONST_12  OAI  CAB  CAC  CAD  180.00  0.0  0
 38L  CONST_13  H4   CAC  CAB  CAA  180.00  0.0  0
 38L  CONST_14  H2   CAE  CAF  CAA  180.00  0.0  0
 38L  CONST_15  H3   CAD  CAE  CAF  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
 38L  plan-1  NAG  0.020
 38L  plan-1  CAA  0.020
 38L  plan-1  CAF  0.020
 38L  plan-1  OAH  0.020
 38L  plan-1  CAE  0.020
 38L  plan-1  CAD  0.020
 38L  plan-1  CAC  0.020
 38L  plan-1  CAB  0.020
 38L  plan-1  OAI  0.020
 38L  plan-1  H2   0.020
 38L  plan-1  H3   0.020
 38L  plan-1  H4   0.020
 38L  plan-2  OAK  0.020
 38L  plan-2  NAG  0.020
 38L  plan-2  OAJ  0.020
 38L  plan-2  CAA  0.020

