# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:27:57 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 3,3'-oxydipyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O(c1cccnc1)c2cccnc2
#
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
 3OP  3OP  '3,3'-oxydipyridine       '  ligand  21  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 PERFECT
;

data_comp_3OP
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
 3OP  C4   C  CR6   0   0.282  -1.1620  -0.3989  -0.0238
 3OP  C5   C  CR16  0  -0.195   1.7844  -0.2556   1.1981
 3OP  C6   C  CR16  0  -0.246  -1.1704   0.9871  -0.0008
 3OP  C7   C  CR16  0  -0.320   3.0446   0.3198   1.1660
 3OP  C8   C  CR16  0  -0.309  -2.4019   1.6271   0.0187
 3OP  C9   C  CR16  0  -0.065   3.6348   0.5671  -0.0652
 3OP  C10  C  CR16  0  -0.086  -3.5607   0.8699   0.0144
 3OP  N12  N  N     0  -0.389  -3.5465  -0.4594  -0.0070
 3OP  C2   C  CR16  0  -0.125  -2.3791  -1.0788  -0.0242
 3OP  O13  O  O2    0  -0.503  -0.0424  -1.1693  -0.0522
 3OP  C3   C  CR6   0   0.209   1.1830  -0.5594  -0.0114
 3OP  N11  N  N     0  -0.393   3.0531   0.2740  -1.2221
 3OP  C1   C  CR16  0  -0.109   1.8476  -0.2769  -1.1961
 3OP  H2   H  HCR6  0   0.296  -0.2591   1.5702   0.0011
 3OP  H3   H  HCR6  0   0.283   3.5617   0.5721   2.0811
 3OP  H4   H  HCR6  0   0.279  -2.4544   2.7068   0.0364
 3OP  H5   H  HCR6  0   0.272   4.6184   1.0192  -0.1174
 3OP  H6   H  HCR6  0   0.265  -4.5328   1.3485   0.0286
 3OP  H7   H  HCR6  0   0.275  -2.3883  -2.1640  -0.0415
 3OP  H8   H  HCR6  0   0.282   1.3862  -0.5152  -2.1492
 3OP  H1   H  HCR6  0   0.296   1.2879  -0.4691   2.1361

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
 3OP  C7   C9   aromatic  1.388  0.020  1.388
 3OP  C7   C5   aromatic  1.386  0.020  1.386
 3OP  C9   N11  aromatic  1.328  0.020  1.328
 3OP  C5   C3   aromatic  1.385  0.020  1.385
 3OP  N11  C1   aromatic  1.326  0.020  1.326
 3OP  C3   C1   aromatic  1.387  0.020  1.387
 3OP  C3   O13  single    1.369  0.020  1.369
 3OP  C2   N12  aromatic  1.322  0.020  1.322
 3OP  C2   C4   aromatic  1.394  0.020  1.394
 3OP  N12  C10  aromatic  1.330  0.020  1.330
 3OP  O13  C4   single    1.359  0.020  1.359
 3OP  C4   C6   aromatic  1.386  0.020  1.386
 3OP  C10  C8   aromatic  1.384  0.020  1.384
 3OP  C6   C8   aromatic  1.388  0.020  1.388
 3OP  C5   H1   single    0.930  0.020  1.080
 3OP  C6   H2   single    0.930  0.020  1.080
 3OP  C7   H3   single    0.930  0.020  1.080
 3OP  C8   H4   single    0.930  0.020  1.080
 3OP  C9   H5   single    0.930  0.020  1.080
 3OP  C10  H6   single    0.930  0.020  1.080
 3OP  C2   H7   single    0.930  0.020  1.080
 3OP  C1   H8   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
 3OP  O13  C4   C2   116.27  3.000
 3OP  O13  C4   C6   124.89  3.000
 3OP  C2   C4   C6   118.83  3.000
 3OP  H1   C5   C3   120.96  3.000
 3OP  H1   C5   C7   121.27  3.000
 3OP  C3   C5   C7   117.77  3.000
 3OP  H2   C6   C8   119.92  3.000
 3OP  H2   C6   C4   122.26  3.000
 3OP  C8   C6   C4   117.82  3.000
 3OP  H3   C7   C9   120.40  3.000
 3OP  H3   C7   C5   120.82  3.000
 3OP  C9   C7   C5   118.78  3.000
 3OP  H4   C8   C10  120.37  3.000
 3OP  H4   C8   C6   120.25  3.000
 3OP  C10  C8   C6   119.37  3.000
 3OP  H5   C9   N11  116.60  3.000
 3OP  H5   C9   C7   120.21  3.000
 3OP  N11  C9   C7   123.19  3.000
 3OP  H6   C10  N12  116.83  3.000
 3OP  H6   C10  C8   120.62  3.000
 3OP  N12  C10  C8   122.55  3.000
 3OP  C2   N12  C10  118.57  3.000
 3OP  H7   C2   N12  117.47  3.000
 3OP  H7   C2   C4   119.67  3.000
 3OP  N12  C2   C4   122.86  3.000
 3OP  C3   O13  C4   118.94  3.000
 3OP  C1   C3   O13  119.60  3.000
 3OP  O13  C3   C5   120.83  3.000
 3OP  C1   C3   C5   119.55  3.000
 3OP  C1   N11  C9   118.24  3.000
 3OP  H8   C1   N11  117.42  3.000
 3OP  H8   C1   C3   120.10  3.000
 3OP  N11  C1   C3   122.48  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
 3OP  CONST_01  C10  N12  C2   C4     0.00   0.0  0
 3OP  CONST_02  C10  C8   C6   C4     0.00   0.0  0
 3OP  CONST_03  N11  C9   C7   C5     0.00   0.0  0
 3OP  CONST_04  N11  C1   C3   C5     0.00   0.0  0
 3OP  CONST_05  N12  C2   C4   C6     0.00   0.0  0
 3OP  CONST_06  N12  C10  C8   C6     0.00   0.0  0
 3OP  CONST_07  C1   N11  C9   C7     0.00   0.0  0
 3OP  CONST_08  C1   C3   C5   C7     0.00   0.0  0
 3OP  CONST_09  C2   N12  C10  C8     0.00   0.0  0
 3OP  CONST_10  C2   C4   C6   C8     0.00   0.0  0
 3OP  CONST_11  C3   C5   C7   C9     0.00   0.0  0
 3OP  CONST_12  C3   C1   N11  C9     0.00   0.0  0
 3OP  CONST_13  O13  C3   C5   C7   180.00   0.0  0
 3OP  CONST_14  O13  C4   C6   C8   180.00   0.0  0
 3OP  CONST_15  O13  C4   C2   N12  180.00   0.0  0
 3OP  CONST_16  N11  C1   C3   O13  180.00   0.0  0
 3OP  CONST_17  H4   C8   C6   C4   180.00   0.0  0
 3OP  CONST_18  H5   C9   C7   C5   180.00   0.0  0
 3OP  CONST_19  H8   C1   C3   C5   180.00   0.0  0
 3OP  CONST_20  H7   C2   C4   C6   180.00   0.0  0
 3OP  CONST_21  H6   C10  C8   C6   180.00   0.0  0
 3OP  CONST_22  H1   C5   C7   C9   180.00   0.0  0
 3OP  CONST_23  H2   C6   C8   C10  180.00   0.0  0
 3OP  CONST_24  H3   C7   C5   C3   180.00   0.0  0
 3OP  Var_01    C5   C3   O13  C4    87.50  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
 3OP  plan-1  C5   0.020
 3OP  plan-1  C7   0.020
 3OP  plan-1  C9   0.020
 3OP  plan-1  O13  0.020
 3OP  plan-1  C3   0.020
 3OP  plan-1  N11  0.020
 3OP  plan-1  C1   0.020
 3OP  plan-1  H3   0.020
 3OP  plan-1  H5   0.020
 3OP  plan-1  H8   0.020
 3OP  plan-1  H1   0.020
 3OP  plan-2  C4   0.020
 3OP  plan-2  C6   0.020
 3OP  plan-2  C8   0.020
 3OP  plan-2  C10  0.020
 3OP  plan-2  N12  0.020
 3OP  plan-2  C2   0.020
 3OP  plan-2  O13  0.020
 3OP  plan-2  H2   0.020
 3OP  plan-2  H4   0.020
 3OP  plan-2  H6   0.020
 3OP  plan-2  H7   0.020

