# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:58:34 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cccc(c1)c2onc(n2)c3cccnc3
#
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
 NSE  NSE  3-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]benzonitrile  ligand  27  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NSE
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
 NSE  C4   C  CSP   0   0.059  -5.2916   0.8466   0.0043
 NSE  C14  C  CR16  0  -0.055   5.6873  -0.4798  -0.0329
 NSE  C5   C  CR16  0  -0.265  -2.8823   0.5006   0.0092
 NSE  C6   C  CR16  0  -0.249  -1.9931  -1.7426  -0.0091
 NSE  C11  C  CR5   0   0.355   1.6210   0.4507   0.0045
 NSE  C7   C  CR5   0   0.598  -0.4297   0.1484   0.0086
 NSE  C8   C  CR6   0  -0.053  -1.7921  -0.3621   0.0034
 NSE  C9   C  CR6   0  -0.106   3.0537   0.1755  -0.0079
 NSE  C10  C  CR16  0  -0.074   3.5110  -1.1394  -0.0448
 NSE  C12  C  CR16  0  -0.161   3.9978   1.1990   0.0168
 NSE  C13  C  CR16  0  -0.312   5.3386   0.8637   0.0043
 NSE  N1   N  NS    0  -0.240  -6.2027   1.5509   0.0047
 NSE  N2   N  N     0  -0.471   0.6712  -0.5264  -0.0104
 NSE  C3   C  CR6   0   0.029  -4.1667  -0.0334   0.0013
 NSE  N3   N  N     0  -0.144   1.1286   1.6543   0.0313
 NSE  N4   N  N     0  -0.397   4.7959  -1.4632  -0.0573
 NSE  O1   O  O     0  -0.332  -0.2210   1.4570   0.0340
 NSE  C2   C  CR16  0  -0.228  -3.2766  -2.2612  -0.0159
 NSE  C1   C  CR16  0  -0.225  -4.3713  -1.4129  -0.0111
 NSE  H1   H  HCR6  0   0.275   6.7314  -0.7710  -0.0431
 NSE  H2   H  HCR6  0   0.293  -2.7523   1.5739   0.0183
 NSE  H3   H  HCR6  0   0.285  -1.1423  -2.4099  -0.0132
 NSE  H4   H  HCR6  0   0.273   2.8029  -1.9596  -0.0650
 NSE  H5   H  HCR6  0   0.278   3.6927   2.2367   0.0464
 NSE  H6   H  HCR6  0   0.282   6.1041   1.6260   0.0233
 NSE  H7   H  HCR6  0   0.288  -3.4251  -3.3316  -0.0252
 NSE  H8   H  HCR6  0   0.296  -5.3760  -1.8122  -0.0172

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
 NSE  C13  C14  aromatic  1.388  0.020  1.388
 NSE  C13  C12  aromatic  1.382  0.020  1.382
 NSE  C14  N4   aromatic  1.328  0.020  1.328
 NSE  C12  C9   aromatic  1.393  0.020  1.393
 NSE  N4   C10  aromatic  1.325  0.020  1.325
 NSE  C9   C10  aromatic  1.393  0.020  1.393
 NSE  C9   C11  single    1.459  0.020  1.459
 NSE  N3   C11  aromatic  1.301  0.020  1.301
 NSE  N3   O1   aromatic  1.364  0.020  1.364
 NSE  C11  N2   aromatic  1.363  0.020  1.363
 NSE  O1   C7   aromatic  1.325  0.020  1.325
 NSE  N2   C7   aromatic  1.291  0.020  1.291
 NSE  C7   C8   single    1.455  0.020  1.455
 NSE  C8   C6   aromatic  1.395  0.020  1.395
 NSE  C8   C5   aromatic  1.390  0.020  1.390
 NSE  C6   C2   aromatic  1.384  0.020  1.384
 NSE  C5   C3   aromatic  1.391  0.020  1.391
 NSE  C2   C1   aromatic  1.385  0.020  1.385
 NSE  C3   C1   aromatic  1.395  0.020  1.395
 NSE  C3   C4   single    1.428  0.020  1.428
 NSE  C4   N1   triple    1.152  0.020  1.152
 NSE  C14  H1   single    0.930  0.020  1.080
 NSE  C5   H2   single    0.930  0.020  1.080
 NSE  C6   H3   single    0.930  0.020  1.080
 NSE  C10  H4   single    0.930  0.020  1.080
 NSE  C12  H5   single    0.930  0.020  1.080
 NSE  C13  H6   single    0.930  0.020  1.080
 NSE  C2   H7   single    0.930  0.020  1.080
 NSE  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
 NSE  C3   C4   N1   180.00  3.000
 NSE  H1   C14  N4   116.59  3.000
 NSE  H1   C14  C13  120.14  3.000
 NSE  N4   C14  C13  123.27  3.000
 NSE  H2   C5   C3   119.48  3.000
 NSE  H2   C5   C8   121.45  3.000
 NSE  C3   C5   C8   119.07  3.000
 NSE  H3   C6   C2   119.89  3.000
 NSE  H3   C6   C8   119.82  3.000
 NSE  C2   C6   C8   120.29  3.000
 NSE  N3   C11  N2   113.57  3.000
 NSE  N2   C11  C9   123.31  3.000
 NSE  N3   C11  C9   123.12  3.000
 NSE  O1   C7   N2   112.46  3.000
 NSE  N2   C7   C8   127.94  3.000
 NSE  O1   C7   C8   119.60  3.000
 NSE  C7   C8   C6   118.83  3.000
 NSE  C6   C8   C5   120.07  3.000
 NSE  C7   C8   C5   121.10  3.000
 NSE  C12  C9   C10  118.15  3.000
 NSE  C10  C9   C11  120.05  3.000
 NSE  C12  C9   C11  121.80  3.000
 NSE  H4   C10  N4   116.65  3.000
 NSE  H4   C10  C9   120.03  3.000
 NSE  N4   C10  C9   123.32  3.000
 NSE  H5   C12  C13  120.43  3.000
 NSE  H5   C12  C9   120.94  3.000
 NSE  C13  C12  C9   118.63  3.000
 NSE  H6   C13  C12  121.06  3.000
 NSE  H6   C13  C14  120.34  3.000
 NSE  C12  C13  C14  118.60  3.000
 NSE  C7   N2   C11  102.67  3.000
 NSE  C1   C3   C5   121.01  3.000
 NSE  C1   C3   C4   119.60  3.000
 NSE  C5   C3   C4   119.39  3.000
 NSE  O1   N3   C11  103.93  3.000
 NSE  C10  N4   C14  118.03  3.000
 NSE  N3   O1   C7   107.37  3.000
 NSE  H7   C2   C1   119.88  3.000
 NSE  H7   C2   C6   119.90  3.000
 NSE  C1   C2   C6   120.22  3.000
 NSE  H8   C1   C2   120.55  3.000
 NSE  H8   C1   C3   120.11  3.000
 NSE  C2   C1   C3   119.34  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
 NSE  CONST_01  C9   C12  C13  C14    0.00  0.0  0
 NSE  CONST_02  C9   C10  N4   C14    0.00  0.0  0
 NSE  CONST_03  O1   C7   C8   C5     0.00  0.0  0
 NSE  CONST_04  N2   C7   C8   C5   180.00  0.0  0
 NSE  CONST_05  C2   C6   C8   C5     0.00  0.0  0
 NSE  CONST_06  C2   C1   C3   C5     0.00  0.0  0
 NSE  CONST_07  O1   C7   C8   C6   180.00  0.0  0
 NSE  CONST_08  N2   C7   C8   C6     0.00  0.0  0
 NSE  CONST_09  C3   C5   C8   C6     0.00  0.0  0
 NSE  CONST_10  C3   C1   C2   C6     0.00  0.0  0
 NSE  CONST_11  C13  C12  C9   C11  180.00  0.0  0
 NSE  CONST_12  N4   C10  C9   C11  180.00  0.0  0
 NSE  CONST_13  C7   O1   N3   C11    0.00  0.0  0
 NSE  CONST_14  O1   C7   N2   C11    0.00  0.0  0
 NSE  CONST_15  C8   C7   N2   C11  180.00  0.0  0
 NSE  CONST_16  C9   C11  N2   C7   180.00  0.0  0
 NSE  CONST_17  N3   C11  N2   C7     0.00  0.0  0
 NSE  CONST_18  C2   C6   C8   C7   180.00  0.0  0
 NSE  CONST_19  C3   C5   C8   C7   180.00  0.0  0
 NSE  CONST_20  N3   O1   C7   C8   180.00  0.0  0
 NSE  CONST_21  C1   C2   C6   C8     0.00  0.0  0
 NSE  CONST_22  C1   C3   C5   C8     0.00  0.0  0
 NSE  CONST_23  O1   N3   C11  C9   180.00  0.0  0
 NSE  CONST_24  C13  C14  N4   C10    0.00  0.0  0
 NSE  CONST_25  C13  C12  C9   C10    0.00  0.0  0
 NSE  CONST_26  N3   C11  C9   C10  180.00  0.0  0
 NSE  CONST_27  N2   C11  C9   C10    0.00  0.0  0
 NSE  CONST_28  N4   C14  C13  C12    0.00  0.0  0
 NSE  CONST_29  N4   C10  C9   C12    0.00  0.0  0
 NSE  CONST_30  N3   C11  C9   C12    0.00  0.0  0
 NSE  CONST_31  N2   C11  C9   C12  180.00  0.0  0
 NSE  CONST_32  O1   N3   C11  N2     0.00  0.0  0
 NSE  CONST_33  N3   O1   C7   N2     0.00  0.0  0
 NSE  CONST_34  C8   C5   C3   C4   180.00  0.0  0
 NSE  CONST_35  C2   C1   C3   C4   180.00  0.0  0
 NSE  CONST_36  H5   C12  C13  C14  180.00  0.0  0
 NSE  CONST_37  H4   C10  N4   C14  180.00  0.0  0
 NSE  CONST_38  H3   C6   C8   C5   180.00  0.0  0
 NSE  CONST_39  H8   C1   C3   C5   180.00  0.0  0
 NSE  CONST_40  H2   C5   C8   C6   180.00  0.0  0
 NSE  CONST_41  H7   C2   C6   C8   180.00  0.0  0
 NSE  CONST_42  H6   C13  C12  C9   180.00  0.0  0
 NSE  CONST_43  H1   C14  N4   C10  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
 NSE  plan-1  C11  0.020
 NSE  plan-1  C7   0.020
 NSE  plan-1  C8   0.020
 NSE  plan-1  C9   0.020
 NSE  plan-1  N2   0.020
 NSE  plan-1  N3   0.020
 NSE  plan-1  O1   0.020
 NSE  plan-2  C4   0.020
 NSE  plan-2  C5   0.020
 NSE  plan-2  C6   0.020
 NSE  plan-2  C7   0.020
 NSE  plan-2  C8   0.020
 NSE  plan-2  N1   0.020
 NSE  plan-2  C3   0.020
 NSE  plan-2  C2   0.020
 NSE  plan-2  C1   0.020
 NSE  plan-2  H2   0.020
 NSE  plan-2  H3   0.020
 NSE  plan-2  H7   0.020
 NSE  plan-2  H8   0.020
 NSE  plan-3  C14  0.020
 NSE  plan-3  C11  0.020
 NSE  plan-3  C9   0.020
 NSE  plan-3  C10  0.020
 NSE  plan-3  C12  0.020
 NSE  plan-3  C13  0.020
 NSE  plan-3  N4   0.020
 NSE  plan-3  H1   0.020
 NSE  plan-3  H4   0.020
 NSE  plan-3  H5   0.020
 NSE  plan-3  H6   0.020

