# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:54:12 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-benzylpyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(c1ccccc1)c2ccncc2
#
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
 3QO  3QO  '4-benzylpyridine         '  ligand  24  13  .  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_3QO
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
 3QO  CAA   C  CR16  0  -0.270   3.5341  -0.0128  -0.9190
 3QO  CAB   C  CR16  0  -0.239   2.9632   1.1891  -0.5206
 3QO  CAC   C  CR16  0  -0.238   2.9622  -1.2108  -0.5109
 3QO  CAD   C  CR16  0  -0.058  -2.9248  -1.1282  -0.5942
 3QO  CAE   C  CR16  0  -0.057  -2.9455   1.1386  -0.5603
 3QO  CAF   C  CR16  0  -0.307   1.8288   1.1909   0.2799
 3QO  CAG   C  CR16  0  -0.308   1.8275  -1.2048   0.2896
 3QO  CAH   C  CR16  0  -0.376  -1.8079  -1.1831   0.2249
 3QO  CAI   C  CR16  0  -0.378  -1.8294   1.1894   0.2606
 3QO  NAK   N  N     0  -0.413  -3.4937   0.0064  -0.9868
 3QO  CAL   C  CR6   0   0.154   1.2487  -0.0051   0.6944
 3QO  CAM   C  CR6   0   0.245  -1.2347   0.0021   0.6728
 3QO  HAA   H  HCR6  0   0.255   4.4204  -0.0155  -1.5399
 3QO  HAB   H  HCR6  0   0.256   3.4052   2.1286  -0.8269
 3QO  HAC   H  HCR6  0   0.256   3.4025  -2.1533  -0.8102
 3QO  HAE   H  HCR6  0   0.263  -3.4206   2.0591  -0.8822
 3QO  HAF   H  HCR6  0   0.248   1.3931   2.1343   0.5881
 3QO  HAG   H  HCR6  0   0.249   1.3909  -2.1452   0.6054
 3QO  HAH   H  HCR6  0   0.263  -1.3975  -2.1437   0.5103
 3QO  HAI   H  HCR6  0   0.263  -1.4356   2.1481   0.5740
 3QO  CAJ   C  CH2   0  -0.627  -0.0029  -0.0003   1.5381
 3QO  HAD   H  HCR6  0   0.263  -3.3832  -2.0468  -0.9441
 3QO  HAJ   H  HCH2  0   0.279  -0.0151  -0.8777   2.1873
 3QO  HAJA  H  HCH2  0   0.279  -0.0098   0.8784   2.1854

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
 3QO  CAB  CAA   aromatic  1.389  0.020  1.389
 3QO  CAA  CAC   aromatic  1.389  0.020  1.389
 3QO  CAA  HAA   single    0.930  0.020  1.080
 3QO  CAB  CAF   aromatic  1.388  0.020  1.388
 3QO  CAB  HAB   single    0.930  0.020  1.080
 3QO  CAC  CAG   aromatic  1.389  0.020  1.389
 3QO  CAC  HAC   single    0.930  0.020  1.080
 3QO  CAH  CAD   aromatic  1.386  0.020  1.386
 3QO  CAD  NAK   aromatic  1.329  0.020  1.329
 3QO  CAD  HAD   single    0.930  0.020  1.080
 3QO  CAI  CAE   aromatic  1.386  0.020  1.386
 3QO  NAK  CAE   aromatic  1.328  0.020  1.328
 3QO  CAE  HAE   single    0.930  0.020  1.080
 3QO  CAF  CAL   aromatic  1.392  0.020  1.392
 3QO  CAF  HAF   single    0.930  0.020  1.080
 3QO  CAL  CAG   aromatic  1.392  0.020  1.392
 3QO  CAG  HAG   single    0.930  0.020  1.080
 3QO  CAH  CAM   aromatic  1.391  0.020  1.391
 3QO  CAH  HAH   single    0.930  0.020  1.080
 3QO  CAM  CAI   aromatic  1.390  0.020  1.390
 3QO  CAI  HAI   single    0.930  0.020  1.080
 3QO  CAL  CAJ   single    1.509  0.020  1.509
 3QO  CAJ  CAM   single    1.505  0.020  1.505
 3QO  CAJ  HAJ   single    0.970  0.020  1.090
 3QO  CAJ  HAJA  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
 3QO  HAA   CAA  CAC  120.25  3.000
 3QO  HAA   CAA  CAB  120.22  3.000
 3QO  CAC   CAA  CAB  119.53  3.000
 3QO  HAB   CAB  CAF  119.71  3.000
 3QO  HAB   CAB  CAA  120.13  3.000
 3QO  CAF   CAB  CAA  120.15  3.000
 3QO  HAC   CAC  CAG  119.70  3.000
 3QO  HAC   CAC  CAA  120.15  3.000
 3QO  CAG   CAC  CAA  120.15  3.000
 3QO  HAD   CAD  NAK  116.55  3.000
 3QO  HAD   CAD  CAH  119.84  3.000
 3QO  NAK   CAD  CAH  123.61  3.000
 3QO  HAE   CAE  NAK  116.57  3.000
 3QO  HAE   CAE  CAI  119.81  3.000
 3QO  NAK   CAE  CAI  123.62  3.000
 3QO  HAF   CAF  CAL  119.70  3.000
 3QO  HAF   CAF  CAB  119.57  3.000
 3QO  CAL   CAF  CAB  120.72  3.000
 3QO  HAG   CAG  CAL  119.70  3.000
 3QO  HAG   CAG  CAC  119.57  3.000
 3QO  CAL   CAG  CAC  120.73  3.000
 3QO  HAH   CAH  CAM  120.99  3.000
 3QO  HAH   CAH  CAD  119.75  3.000
 3QO  CAM   CAH  CAD  119.25  3.000
 3QO  HAI   CAI  CAM  120.98  3.000
 3QO  HAI   CAI  CAE  119.78  3.000
 3QO  CAM   CAI  CAE  119.25  3.000
 3QO  CAE   NAK  CAD  117.15  3.000
 3QO  CAJ   CAL  CAG  120.66  3.000
 3QO  CAJ   CAL  CAF  120.60  3.000
 3QO  CAG   CAL  CAF  118.72  3.000
 3QO  CAJ   CAM  CAI  121.45  3.000
 3QO  CAJ   CAM  CAH  121.40  3.000
 3QO  CAI   CAM  CAH  117.13  3.000
 3QO  HAJA  CAJ  HAJ  107.12  3.000
 3QO  HAJA  CAJ  CAM  109.54  3.000
 3QO  HAJ   CAJ  CAM  109.51  3.000
 3QO  HAJA  CAJ  CAL  109.83  3.000
 3QO  HAJ   CAJ  CAL  109.83  3.000
 3QO  CAM   CAJ  CAL  110.93  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
 3QO  CONST_01  CAL  CAF  CAB  CAA    0.00   0.0  0
 3QO  CONST_02  CAL  CAG  CAC  CAA    0.00   0.0  0
 3QO  CONST_03  CAG  CAC  CAA  CAB    0.00   0.0  0
 3QO  CONST_04  CAG  CAL  CAF  CAB    0.00   0.0  0
 3QO  CONST_05  CAF  CAB  CAA  CAC    0.00   0.0  0
 3QO  CONST_06  CAF  CAL  CAG  CAC    0.00   0.0  0
 3QO  CONST_07  CAI  CAM  CAH  CAD    0.00   0.0  0
 3QO  CONST_08  CAI  CAE  NAK  CAD    0.00   0.0  0
 3QO  CONST_09  CAH  CAM  CAI  CAE    0.00   0.0  0
 3QO  CONST_10  CAH  CAD  NAK  CAE    0.00   0.0  0
 3QO  CONST_11  CAM  CAH  CAD  NAK    0.00   0.0  0
 3QO  CONST_12  CAM  CAI  CAE  NAK    0.00   0.0  0
 3QO  CONST_13  CAJ  CAL  CAF  CAB  180.00   0.0  0
 3QO  CONST_14  CAJ  CAL  CAG  CAC  180.00   0.0  0
 3QO  CONST_15  CAJ  CAM  CAH  CAD  180.00   0.0  0
 3QO  CONST_16  CAJ  CAM  CAI  CAE  180.00   0.0  0
 3QO  CONST_17  HAF  CAF  CAB  CAA  180.00   0.0  0
 3QO  CONST_18  HAG  CAG  CAC  CAA  180.00   0.0  0
 3QO  CONST_19  HAC  CAC  CAA  CAB  180.00   0.0  0
 3QO  CONST_20  HAB  CAB  CAA  CAC  180.00   0.0  0
 3QO  CONST_21  HAE  CAE  NAK  CAD  180.00   0.0  0
 3QO  CONST_22  HAD  CAD  NAK  CAE  180.00   0.0  0
 3QO  CONST_23  HAA  CAA  CAB  CAF  180.00   0.0  0
 3QO  CONST_24  HAI  CAI  CAM  CAH  180.00   0.0  0
 3QO  CONST_25  HAH  CAH  CAM  CAI  180.00   0.0  0
 3QO  Var_01    CAM  CAJ  CAL  CAF   89.04  30.0  2
 3QO  Var_02    CAL  CAJ  CAM  CAH   88.06  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
 3QO  plan-1  CAA  0.020
 3QO  plan-1  CAB  0.020
 3QO  plan-1  CAC  0.020
 3QO  plan-1  CAF  0.020
 3QO  plan-1  CAG  0.020
 3QO  plan-1  CAL  0.020
 3QO  plan-1  HAA  0.020
 3QO  plan-1  HAB  0.020
 3QO  plan-1  HAC  0.020
 3QO  plan-1  HAF  0.020
 3QO  plan-1  HAG  0.020
 3QO  plan-1  CAJ  0.020
 3QO  plan-2  CAD  0.020
 3QO  plan-2  CAE  0.020
 3QO  plan-2  CAH  0.020
 3QO  plan-2  CAI  0.020
 3QO  plan-2  NAK  0.020
 3QO  plan-2  CAM  0.020
 3QO  plan-2  HAE  0.020
 3QO  plan-2  HAH  0.020
 3QO  plan-2  HAI  0.020
 3QO  plan-2  CAJ  0.020
 3QO  plan-2  HAD  0.020

