# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:25:29 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 4-phenylpyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc(cc1)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
 5SH  5SH  '4-phenylpyridine         '  ligand  21  12  .  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_5SH
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
 5SH  CAF  C  CR16  0  -0.305  -1.4733   1.1452  -0.3774
 5SH  CAB  C  CR16  0  -0.239  -2.8602   1.1453  -0.3857
 5SH  CAA  C  CR16  0  -0.261  -3.5609   0.0013  -0.0270
 5SH  CAC  C  CR16  0  -0.239  -2.8649  -1.1441   0.3373
 5SH  CAG  C  CR16  0  -0.305  -1.4782  -1.1465   0.3399
 5SH  CAK  C  CR6   0   0.092  -0.7644  -0.0012  -0.0160
 5SH  CAL  C  CR6   0   0.172   0.7103  -0.0024  -0.0102
 5SH  CAH  C  CR16  0  -0.378   1.4396   1.1225   0.3715
 5SH  CAD  C  CR16  0  -0.060   2.8238   1.0695   0.3598
 5SH  NAJ  N  N     0  -0.408   3.5177  -0.0049   0.0013
 5SH  CAE  C  CR16  0  -0.060   2.8249  -1.0780  -0.3631
 5SH  CAI  C  CR16  0  -0.378   1.4406  -1.1286  -0.3862
 5SH  H1   H  HCR6  0   0.259  -0.9404   2.0392  -0.6764
 5SH  H2   H  HCR6  0   0.261  -3.3934   2.0399  -0.6798
 5SH  H3   H  HCR6  0   0.261  -4.6430   0.0018  -0.0307
 5SH  H4   H  HCR6  0   0.261  -3.4023  -2.0376   0.6269
 5SH  H5   H  HCR6  0   0.259  -0.9491  -2.0411   0.6438
 5SH  H6   H  HCR6  0   0.269   0.9438   2.0278   0.6957
 5SH  H7   H  HCR6  0   0.265   3.3972   1.9391   0.6619
 5SH  H8   H  HCR6  0   0.265   3.3991  -1.9485  -0.6606
 5SH  H9   H  HCR6  0   0.269   0.9465  -2.0330  -0.7153

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
 5SH  NAJ  CAE  aromatic  1.328  0.020  1.328
 5SH  NAJ  CAD  aromatic  1.328  0.020  1.328
 5SH  CAE  CAI  aromatic  1.385  0.020  1.385
 5SH  CAD  CAH  aromatic  1.385  0.020  1.385
 5SH  CAI  CAL  aromatic  1.394  0.020  1.394
 5SH  CAH  CAL  aromatic  1.394  0.020  1.394
 5SH  CAL  CAK  single    1.475  0.020  1.475
 5SH  CAK  CAG  aromatic  1.396  0.020  1.396
 5SH  CAK  CAF  aromatic  1.395  0.020  1.395
 5SH  CAG  CAC  aromatic  1.387  0.020  1.387
 5SH  CAF  CAB  aromatic  1.387  0.020  1.387
 5SH  CAC  CAA  aromatic  1.389  0.020  1.389
 5SH  CAB  CAA  aromatic  1.389  0.020  1.389
 5SH  CAF  H1   single    0.930  0.020  1.080
 5SH  CAB  H2   single    0.930  0.020  1.080
 5SH  CAA  H3   single    0.930  0.020  1.080
 5SH  CAC  H4   single    0.930  0.020  1.080
 5SH  CAG  H5   single    0.930  0.020  1.080
 5SH  CAH  H6   single    0.930  0.020  1.080
 5SH  CAD  H7   single    0.930  0.020  1.080
 5SH  CAE  H8   single    0.930  0.020  1.080
 5SH  CAI  H9   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
 5SH  H1   CAF  CAK  119.99  3.000
 5SH  H1   CAF  CAB  119.36  3.000
 5SH  CAK  CAF  CAB  120.64  3.000
 5SH  H2   CAB  CAA  120.17  3.000
 5SH  H2   CAB  CAF  119.63  3.000
 5SH  CAA  CAB  CAF  120.19  3.000
 5SH  H3   CAA  CAC  120.16  3.000
 5SH  H3   CAA  CAB  120.22  3.000
 5SH  CAC  CAA  CAB  119.62  3.000
 5SH  H4   CAC  CAG  119.65  3.000
 5SH  H4   CAC  CAA  120.15  3.000
 5SH  CAG  CAC  CAA  120.20  3.000
 5SH  H5   CAG  CAK  119.98  3.000
 5SH  H5   CAG  CAC  119.37  3.000
 5SH  CAK  CAG  CAC  120.63  3.000
 5SH  CAL  CAK  CAG  120.65  3.000
 5SH  CAG  CAK  CAF  118.71  3.000
 5SH  CAL  CAK  CAF  120.64  3.000
 5SH  CAI  CAL  CAH  116.86  3.000
 5SH  CAH  CAL  CAK  121.57  3.000
 5SH  CAI  CAL  CAK  121.57  3.000
 5SH  H6   CAH  CAD  119.50  3.000
 5SH  H6   CAH  CAL  121.18  3.000
 5SH  CAD  CAH  CAL  119.31  3.000
 5SH  H7   CAD  NAJ  116.59  3.000
 5SH  H7   CAD  CAH  119.69  3.000
 5SH  NAJ  CAD  CAH  123.72  3.000
 5SH  CAE  NAJ  CAD  117.07  3.000
 5SH  H8   CAE  CAI  119.68  3.000
 5SH  H8   CAE  NAJ  116.59  3.000
 5SH  CAI  CAE  NAJ  123.73  3.000
 5SH  H9   CAI  CAE  119.47  3.000
 5SH  H9   CAI  CAL  121.21  3.000
 5SH  CAE  CAI  CAL  119.31  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
 5SH  CONST_03  CAC  CAG  CAK  CAF    0.00  0.0  0
 5SH  CONST_04  CAC  CAA  CAB  CAF    0.00  0.0  0
 5SH  CONST_05  CAL  CAK  CAF  CAB  180.00  0.0  0
 5SH  CONST_06  CAG  CAK  CAF  CAB    0.00  0.0  0
 5SH  CONST_07  CAG  CAC  CAA  CAB    0.00  0.0  0
 5SH  CONST_08  CAK  CAG  CAC  CAA    0.00  0.0  0
 5SH  CONST_09  CAK  CAF  CAB  CAA    0.00  0.0  0
 5SH  CONST_10  CAL  CAK  CAG  CAC  180.00  0.0  0
 5SH  CONST_13  CAE  CAI  CAL  CAK  180.00  0.0  0
 5SH  CONST_14  CAD  CAH  CAL  CAK  180.00  0.0  0
 5SH  CONST_15  NAJ  CAE  CAI  CAL    0.00  0.0  0
 5SH  CONST_16  NAJ  CAD  CAH  CAL    0.00  0.0  0
 5SH  CONST_17  CAE  NAJ  CAD  CAH    0.00  0.0  0
 5SH  CONST_18  CAE  CAI  CAL  CAH    0.00  0.0  0
 5SH  CONST_19  CAI  CAE  NAJ  CAD    0.00  0.0  0
 5SH  CONST_20  CAI  CAL  CAH  CAD    0.00  0.0  0
 5SH  CONST_21  H5   CAG  CAK  CAF  180.00  0.0  0
 5SH  CONST_22  H3   CAA  CAB  CAF  180.00  0.0  0
 5SH  CONST_23  H4   CAC  CAA  CAB  180.00  0.0  0
 5SH  CONST_24  H1   CAF  CAB  CAA  180.00  0.0  0
 5SH  CONST_25  H2   CAB  CAA  CAC  180.00  0.0  0
 5SH  CONST_26  H9   CAI  CAL  CAK    0.00  0.0  0
 5SH  CONST_27  H6   CAH  CAL  CAK    0.00  0.0  0
 5SH  CONST_28  H8   CAE  CAI  CAL  180.00  0.0  0
 5SH  CONST_29  H7   CAD  CAH  CAL  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
 5SH  plan-1  CAF  0.020
 5SH  plan-1  CAB  0.020
 5SH  plan-1  CAA  0.020
 5SH  plan-1  CAC  0.020
 5SH  plan-1  CAG  0.020
 5SH  plan-1  CAK  0.020
 5SH  plan-1  CAL  0.020
 5SH  plan-1  H1   0.020
 5SH  plan-1  H2   0.020
 5SH  plan-1  H3   0.020
 5SH  plan-1  H4   0.020
 5SH  plan-1  H5   0.020
 5SH  plan-2  CAK  0.020
 5SH  plan-2  CAL  0.020
 5SH  plan-2  CAH  0.020
 5SH  plan-2  CAD  0.020
 5SH  plan-2  NAJ  0.020
 5SH  plan-2  CAE  0.020
 5SH  plan-2  CAI  0.020
 5SH  plan-2  H6   0.020
 5SH  plan-2  H7   0.020
 5SH  plan-2  H8   0.020
 5SH  plan-2  H9   0.020

