# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:42:33 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-(4-nitrobenzyl)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(Cc2ccncc2)cc1
#
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
 3QU  3QU  4-(4-nitrobenzyl)pyridine  ligand  26  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3QU
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
 3QU  OAA   O  O      0  -0.380  -4.2954  -1.0335  -0.8855
 3QU  OAB   O  O     -1  -0.380  -4.3304   1.0960  -0.7742
 3QU  CAC   C  CR16   0  -0.055   3.8251   1.1388  -0.9562
 3QU  CAD   C  CR16   0  -0.055   3.8795  -1.1280  -0.9222
 3QU  CAE   C  CR16   0  -0.373   2.9128   1.1861   0.0863
 3QU  CAF   C  CR16   0  -0.378   2.9683  -1.1874   0.1215
 3QU  CAG   C  CR16   0  -0.302  -0.6074   1.2015   0.9068
 3QU  CAH   C  CR16   0  -0.297  -0.5868  -1.1950   0.8219
 3QU  CAI   C  CR16   0  -0.248  -1.8653   1.2225   0.3316
 3QU  CAJ   C  CR16   0  -0.248  -1.8439  -1.1968   0.2448
 3QU  NAL   N  N      0  -0.411   4.3068   0.0082  -1.4607
 3QU  CAM   C  CR6    0   0.240   2.4630  -0.0040   0.6465
 3QU  CAN   C  CR6    0   0.172   0.0470  -0.0015   1.1597
 3QU  CAO   C  CR6    0   0.236  -2.4708   0.0177   0.0047
 3QU  NAP   N  N      1   0.330  -3.7943   0.0274  -0.5950
 3QU  HAD   H  HCR6   0   0.265   4.2825  -2.0445  -1.3393
 3QU  HAE   H  HCR6   0   0.265   2.5648   2.1439   0.4525
 3QU  HAF   H  HCR6   0   0.266   2.6643  -2.1486   0.5167
 3QU  HAG   H  HCR6   0   0.271  -0.1344   2.1394   1.1675
 3QU  HAH   H  HCR6   0   0.270  -0.0974  -2.1406   1.0165
 3QU  HAI   H  HCR6   0   0.298  -2.3573   2.1663   0.1477
 3QU  HAJ   H  HCR6   0   0.298  -2.3186  -2.1342  -0.0049
 3QU  CAK   C  CH2    0  -0.628   1.4341  -0.0114   1.7467
 3QU  HAC   H  HCR6   0   0.265   4.1826   2.0604  -1.4023
 3QU  HAK   H  HCH2   0   0.290   1.5648  -0.8964   2.3713
 3QU  HAKA  H  HCH2   0   0.290   1.5703   0.8605   2.3883

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
 3QU  OAA  NAP   double    1.209  0.020  1.209
 3QU  CAC  NAL   aromatic  1.328  0.020  1.328
 3QU  CAD  NAL   aromatic  1.328  0.020  1.328
 3QU  CAE  CAC   aromatic  1.386  0.020  1.386
 3QU  CAF  CAD   aromatic  1.387  0.020  1.387
 3QU  CAH  CAN   aromatic  1.393  0.020  1.393
 3QU  CAI  CAG   aromatic  1.383  0.020  1.383
 3QU  CAJ  CAH   aromatic  1.383  0.020  1.383
 3QU  CAJ  CAO   aromatic  1.388  0.020  1.388
 3QU  CAK  CAM   single    1.506  0.020  1.506
 3QU  CAM  CAE   aromatic  1.390  0.020  1.390
 3QU  CAM  CAF   aromatic  1.390  0.020  1.390
 3QU  CAN  CAG   aromatic  1.392  0.020  1.392
 3QU  CAN  CAK   single    1.506  0.020  1.506
 3QU  CAO  CAI   aromatic  1.387  0.020  1.387
 3QU  NAP  OAB   single    1.209  0.020  1.209
 3QU  NAP  CAO   single    1.453  0.020  1.453
 3QU  CAC  HAC   single    0.930  0.020  1.080
 3QU  CAD  HAD   single    0.930  0.020  1.080
 3QU  CAE  HAE   single    0.930  0.020  1.080
 3QU  CAF  HAF   single    0.930  0.020  1.080
 3QU  CAG  HAG   single    0.930  0.020  1.080
 3QU  CAH  HAH   single    0.930  0.020  1.080
 3QU  CAI  HAI   single    0.930  0.020  1.080
 3QU  CAJ  HAJ   single    0.930  0.020  1.080
 3QU  CAK  HAK   single    0.970  0.020  1.090
 3QU  CAK  HAKA  single    0.970  0.020  1.090

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
 3QU  HAC   CAC  NAL  116.59  3.000
 3QU  HAC   CAC  CAE  119.82  3.000
 3QU  NAL   CAC  CAE  123.59  3.000
 3QU  HAD   CAD  NAL  116.58  3.000
 3QU  HAD   CAD  CAF  119.83  3.000
 3QU  NAL   CAD  CAF  123.59  3.000
 3QU  HAE   CAE  CAM  121.13  3.000
 3QU  HAE   CAE  CAC  119.74  3.000
 3QU  CAM   CAE  CAC  119.13  3.000
 3QU  HAF   CAF  CAM  121.06  3.000
 3QU  HAF   CAF  CAD  119.81  3.000
 3QU  CAM   CAF  CAD  119.13  3.000
 3QU  HAG   CAG  CAN  119.97  3.000
 3QU  HAG   CAG  CAI  118.97  3.000
 3QU  CAN   CAG  CAI  121.06  3.000
 3QU  HAH   CAH  CAN  119.95  3.000
 3QU  HAH   CAH  CAJ  119.00  3.000
 3QU  CAN   CAH  CAJ  121.05  3.000
 3QU  HAI   CAI  CAO  121.32  3.000
 3QU  HAI   CAI  CAG  119.89  3.000
 3QU  CAO   CAI  CAG  118.79  3.000
 3QU  HAJ   CAJ  CAO  121.40  3.000
 3QU  HAJ   CAJ  CAH  119.81  3.000
 3QU  CAO   CAJ  CAH  118.79  3.000
 3QU  CAD   NAL  CAC  117.23  3.000
 3QU  CAK   CAM  CAF  121.34  3.000
 3QU  CAF   CAM  CAE  117.33  3.000
 3QU  CAK   CAM  CAE  121.30  3.000
 3QU  CAK   CAN  CAH  120.52  3.000
 3QU  CAK   CAN  CAG  120.61  3.000
 3QU  CAH   CAN  CAG  118.84  3.000
 3QU  NAP   CAO  CAJ  119.26  3.000
 3QU  NAP   CAO  CAI  119.27  3.000
 3QU  CAJ   CAO  CAI  121.47  3.000
 3QU  CAO   NAP  OAB  118.10  3.000
 3QU  CAO   NAP  OAA  118.09  3.000
 3QU  OAB   NAP  OAA  123.81  3.000
 3QU  HAKA  CAK  HAK  107.25  3.000
 3QU  HAKA  CAK  CAN  109.81  3.000
 3QU  HAK   CAK  CAN  109.80  3.000
 3QU  HAKA  CAK  CAM  109.90  3.000
 3QU  HAK   CAK  CAM  109.89  3.000
 3QU  CAN   CAK  CAM  110.14  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
 3QU  CONST_01  CAF  CAD  NAL  CAC    0.00   0.0  0
 3QU  CONST_02  CAF  CAM  CAE  CAC    0.00   0.0  0
 3QU  CONST_03  CAE  CAC  NAL  CAD    0.00   0.0  0
 3QU  CONST_04  CAE  CAM  CAF  CAD    0.00   0.0  0
 3QU  CONST_05  CAJ  CAO  CAI  CAG    0.00   0.0  0
 3QU  CONST_06  CAJ  CAH  CAN  CAG    0.00   0.0  0
 3QU  CONST_07  CAI  CAG  CAN  CAH    0.00   0.0  0
 3QU  CONST_08  CAI  CAO  CAJ  CAH    0.00   0.0  0
 3QU  CONST_09  CAM  CAE  CAC  NAL    0.00   0.0  0
 3QU  CONST_10  CAM  CAF  CAD  NAL    0.00   0.0  0
 3QU  CONST_11  CAO  CAJ  CAH  CAN    0.00   0.0  0
 3QU  CONST_12  CAO  CAI  CAG  CAN    0.00   0.0  0
 3QU  CONST_13  CAK  CAM  CAE  CAC  180.00   0.0  0
 3QU  CONST_14  CAK  CAM  CAF  CAD  180.00   0.0  0
 3QU  CONST_15  NAP  CAO  CAI  CAG  180.00   0.0  0
 3QU  CONST_16  NAP  CAO  CAJ  CAH  180.00   0.0  0
 3QU  CONST_17  CAK  CAN  CAG  CAI  180.00   0.0  0
 3QU  CONST_18  CAK  CAN  CAH  CAJ  180.00   0.0  0
 3QU  CONST_19  HAD  CAD  NAL  CAC  180.00   0.0  0
 3QU  CONST_20  HAC  CAC  NAL  CAD  180.00   0.0  0
 3QU  CONST_21  HAF  CAF  CAM  CAE  180.00   0.0  0
 3QU  CONST_22  HAE  CAE  CAM  CAF  180.00   0.0  0
 3QU  CONST_23  HAH  CAH  CAN  CAG  180.00   0.0  0
 3QU  CONST_24  HAG  CAG  CAN  CAH  180.00   0.0  0
 3QU  CONST_25  HAJ  CAJ  CAO  CAI  180.00   0.0  0
 3QU  CONST_26  HAI  CAI  CAO  CAJ  180.00   0.0  0
 3QU  CONST_27  CAJ  CAO  NAP  OAA    0.00   0.0  0
 3QU  CONST_28  CAI  CAO  NAP  OAA  180.00   0.0  0
 3QU  CONST_29  CAJ  CAO  NAP  OAB  180.00   0.0  0
 3QU  CONST_30  CAI  CAO  NAP  OAB    0.00   0.0  0
 3QU  Var_01    CAN  CAK  CAM  CAE   86.88  30.0  3
 3QU  Var_02    CAM  CAK  CAN  CAG  -90.62  30.0  2

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
 3QU  plan-1  CAC  0.020
 3QU  plan-1  CAD  0.020
 3QU  plan-1  CAE  0.020
 3QU  plan-1  CAF  0.020
 3QU  plan-1  NAL  0.020
 3QU  plan-1  CAM  0.020
 3QU  plan-1  HAD  0.020
 3QU  plan-1  HAE  0.020
 3QU  plan-1  HAF  0.020
 3QU  plan-1  CAK  0.020
 3QU  plan-1  HAC  0.020
 3QU  plan-2  CAG  0.020
 3QU  plan-2  CAH  0.020
 3QU  plan-2  CAI  0.020
 3QU  plan-2  CAJ  0.020
 3QU  plan-2  CAN  0.020
 3QU  plan-2  CAO  0.020
 3QU  plan-2  NAP  0.020
 3QU  plan-2  HAG  0.020
 3QU  plan-2  HAH  0.020
 3QU  plan-2  HAI  0.020
 3QU  plan-2  HAJ  0.020
 3QU  plan-2  CAK  0.020
 3QU  plan-3  OAA  0.020
 3QU  plan-3  OAB  0.020
 3QU  plan-3  CAO  0.020
 3QU  plan-3  NAP  0.020

