# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 21:02:09 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 4,4'-disulfanediyldipyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S(Sc1ccncc1)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
 D4G  D4G  4,4'-disulfanediyldipyridine  ligand  22  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D4G
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
 D4G  C3   C  CR16  0  -0.329  -3.0513  -0.2366   0.9002
 D4G  C2   C  CR16  0  -0.051  -3.9578   0.7428   0.5305
 D4G  N_1  N  N     0  -0.408  -3.7630   1.5893  -0.4744
 D4G  C1   C  CR16  0  -0.053  -2.6289   1.4758  -1.1525
 D4G  C5   C  CR16  0  -0.310  -1.6475   0.5359  -0.8730
 D4G  C4   C  CR6   0  -0.025  -1.8668  -0.3407   0.1775
 D4G  S_1  S  S2    0   0.055  -0.7330  -1.5925   0.7109
 D4G  S_2  S  S2    0   0.055   0.7636  -1.5843  -0.6714
 D4G  C6   C  CR6   0  -0.025   1.8829  -0.3193  -0.1382
 D4G  C7   C  CR16  0  -0.310   1.6512   0.5572   0.9099
 D4G  C8   C  CR16  0  -0.053   2.6218   1.5078   1.1903
 D4G  N_2  N  N     0  -0.408   3.7569   1.6316   0.5154
 D4G  C9   C  CR16  0  -0.051   3.9635   0.7854  -0.4871
 D4G  C10  C  CR16  0  -0.329   3.0682  -0.2044  -0.8576
 D4G  H3   H  HCR6  0   0.290  -3.2745  -0.8948   1.7301
 D4G  H2   H  HCR6  0   0.274  -4.8883   0.8405   1.0781
 D4G  H1   H  HCR6  0   0.274  -2.4797   2.1710  -1.9709
 D4G  H5   H  HCR6  0   0.283  -0.7494   0.5005  -1.4740
 D4G  H7   H  HCR6  0   0.283   0.7514   0.5141   1.5077
 D4G  H8   H  HCR6  0   0.274   2.4629   2.2036   2.0063
 D4G  H9   H  HCR6  0   0.274   4.8943   0.8919  -1.0325
 D4G  H10  H  HCR6  0   0.290   3.3008  -0.8619  -1.6854

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
 D4G  C3   C2   aromatic  1.385  0.020  1.385
 D4G  C3   C4   aromatic  1.391  0.020  1.391
 D4G  C3   H3   single    0.930  0.020  1.080
 D4G  C2   N_1  aromatic  1.328  0.020  1.328
 D4G  C2   H2   single    0.930  0.020  1.080
 D4G  N_1  C1   aromatic  1.326  0.020  1.326
 D4G  C1   C5   aromatic  1.387  0.020  1.387
 D4G  C1   H1   single    0.930  0.020  1.080
 D4G  C5   C4   aromatic  1.386  0.020  1.386
 D4G  C5   H5   single    0.930  0.020  1.080
 D4G  C4   S_1  single    1.771  0.020  1.771
 D4G  S_1  S_2  single    2.037  0.020  2.037
 D4G  S_2  C6   single    1.771  0.020  1.771
 D4G  C6   C7   aromatic  1.386  0.020  1.386
 D4G  C6   C10  aromatic  1.391  0.020  1.391
 D4G  C7   C8   aromatic  1.387  0.020  1.387
 D4G  C7   H7   single    0.930  0.020  1.080
 D4G  C8   N_2  aromatic  1.326  0.020  1.326
 D4G  C8   H8   single    0.930  0.020  1.080
 D4G  N_2  C9   aromatic  1.328  0.020  1.328
 D4G  C9   C10  aromatic  1.385  0.020  1.385
 D4G  C9   H9   single    0.930  0.020  1.080
 D4G  C10  H10  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
 D4G  H3   C3   C4   121.88  3.000
 D4G  H3   C3   C2   119.98  3.000
 D4G  C4   C3   C2   118.13  3.000
 D4G  H2   C2   N_1  116.78  3.000
 D4G  H2   C2   C3   119.39  3.000
 D4G  N_1  C2   C3   123.83  3.000
 D4G  C1   N_1  C2   117.23  3.000
 D4G  H1   C1   C5   119.29  3.000
 D4G  H1   C1   N_1  116.66  3.000
 D4G  C5   C1   N_1  124.05  3.000
 D4G  H5   C5   C4   122.15  3.000
 D4G  H5   C5   C1   119.85  3.000
 D4G  C4   C5   C1   117.99  3.000
 D4G  S_1  C4   C5   125.04  3.000
 D4G  S_1  C4   C3   116.20  3.000
 D4G  C5   C4   C3   118.76  3.000
 D4G  S_2  S_1  C4   105.25  3.000
 D4G  C6   S_2  S_1  105.24  3.000
 D4G  C10  C6   C7   118.77  3.000
 D4G  C10  C6   S_2  116.21  3.000
 D4G  C7   C6   S_2  125.01  3.000
 D4G  H7   C7   C8   119.86  3.000
 D4G  H7   C7   C6   122.15  3.000
 D4G  C8   C7   C6   117.99  3.000
 D4G  H8   C8   N_2  116.65  3.000
 D4G  H8   C8   C7   119.30  3.000
 D4G  N_2  C8   C7   124.05  3.000
 D4G  C9   N_2  C8   117.24  3.000
 D4G  H9   C9   C10  119.38  3.000
 D4G  H9   C9   N_2  116.79  3.000
 D4G  C10  C9   N_2  123.83  3.000
 D4G  H10  C10  C9   119.98  3.000
 D4G  H10  C10  C6   121.89  3.000
 D4G  C9   C10  C6   118.12  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
 D4G  CONST_01  C1   N_1  C2   C3     0.00   0.0  0
 D4G  CONST_02  C1   C5   C4   C3     0.00   0.0  0
 D4G  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 D4G  CONST_04  C5   C1   N_1  C2     0.00   0.0  0
 D4G  CONST_05  C4   C3   C2   N_1    0.00   0.0  0
 D4G  CONST_06  C4   C5   C1   N_1    0.00   0.0  0
 D4G  CONST_07  N_2  C8   C7   C6     0.00   0.0  0
 D4G  CONST_08  N_2  C9   C10  C6     0.00   0.0  0
 D4G  CONST_09  C9   C10  C6   C7     0.00   0.0  0
 D4G  CONST_10  C9   N_2  C8   C7     0.00   0.0  0
 D4G  CONST_11  C10  C6   C7   C8     0.00   0.0  0
 D4G  CONST_12  C10  C9   N_2  C8     0.00   0.0  0
 D4G  CONST_13  S_1  C4   C3   C2   180.00   0.0  0
 D4G  CONST_14  S_1  C4   C5   C1   180.00   0.0  0
 D4G  CONST_15  C8   C7   C6   S_2  180.00   0.0  0
 D4G  CONST_16  C9   C10  C6   S_2  180.00   0.0  0
 D4G  CONST_17  H5   C5   C4   C3   180.00   0.0  0
 D4G  CONST_18  H1   C1   N_1  C2   180.00   0.0  0
 D4G  CONST_19  H3   C3   C2   N_1  180.00   0.0  0
 D4G  CONST_20  H2   C2   N_1  C1   180.00   0.0  0
 D4G  CONST_21  H8   C8   C7   C6   180.00   0.0  0
 D4G  CONST_22  H9   C9   C10  C6   180.00   0.0  0
 D4G  CONST_23  H10  C10  C6   C7   180.00   0.0  0
 D4G  CONST_24  H7   C7   C8   N_2  180.00   0.0  0
 D4G  Var_01    C7   C6   S_2  S_1   -7.08  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
 D4G  plan-1  C3   0.020
 D4G  plan-1  C2   0.020
 D4G  plan-1  N_1  0.020
 D4G  plan-1  C1   0.020
 D4G  plan-1  C5   0.020
 D4G  plan-1  C4   0.020
 D4G  plan-1  S_1  0.020
 D4G  plan-1  H3   0.020
 D4G  plan-1  H2   0.020
 D4G  plan-1  H1   0.020
 D4G  plan-1  H5   0.020
 D4G  plan-2  S_2  0.020
 D4G  plan-2  C6   0.020
 D4G  plan-2  C7   0.020
 D4G  plan-2  C8   0.020
 D4G  plan-2  N_2  0.020
 D4G  plan-2  C9   0.020
 D4G  plan-2  C10  0.020
 D4G  plan-2  H7   0.020
 D4G  plan-2  H8   0.020
 D4G  plan-2  H9   0.020
 D4G  plan-2  H10  0.020

