# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:08:43 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 7-phenyl-1-[5-(pyridin-2-yl)-1,3,4-oxadiazol-2-yl]heptan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCCCCCc1ccccc1)c2oc(nn2)c3ccccn3
#
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
 JG1  JG1  7-phenyl-1-[5-(pyridin-2-yl)-1,3,4-oxadiazol-2-yl]heptan-1-one  ligand  46  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JG1
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
 JG1  N1    N  N     0  -0.414    6.6761   0.8930  -0.0333
 JG1  C2    C  CR6   0   0.130    6.2845  -0.3759   0.0058
 JG1  C3    C  CR16  0  -0.286    7.1597  -1.4552   0.0270
 JG1  C4    C  CR16  0  -0.149    8.5186  -1.1859   0.0064
 JG1  C5    C  CR16  0  -0.303    8.9390   0.1338  -0.0340
 JG1  C6    C  CR16  0  -0.074    7.9769   1.1364  -0.0526
 JG1  C7    C  CR5   0   0.494    4.8447  -0.6073   0.0263
 JG1  N8    N  N     0  -0.300    4.2154  -1.7376   0.0594
 JG1  N9    N  N     0  -0.269    2.8918  -1.4414   0.0641
 JG1  C10   C  CR5   0   0.401    2.7995  -0.1577   0.0342
 JG1  O11   O  O     0  -0.384    4.0035   0.4259   0.0100
 JG1  C12   C  C     0   0.331    1.5805   0.6894   0.0226
 JG1  C13   C  CH2   0  -0.573    0.2736  -0.0402   0.0302
 JG1  O14   O  O     0  -0.361    1.7086   1.8886   0.0088
 JG1  C15   C  CH2   0  -0.422   -0.9435   0.8706   0.0326
 JG1  C16   C  CH2   0  -0.418   -2.2429   0.0744   0.0280
 JG1  C17   C  CH2   0  -0.419   -3.4748   0.9704   0.0275
 JG1  C18   C  CH2   0  -0.411   -4.7830   0.1909   0.0086
 JG1  C19   C  CH2   0  -0.506   -6.0083   1.1069   0.0060
 JG1  C20   C  CR6   0   0.139   -7.2981   0.3364  -0.0238
 JG1  C21   C  CR16  0  -0.314   -7.8760  -0.0437  -1.2339
 JG1  C22   C  CR16  0  -0.240   -9.0479  -0.7879  -1.2639
 JG1  C23   C  CR16  0  -0.276   -9.6637  -1.1682  -0.0782
 JG1  C24   C  CR16  0  -0.239   -9.0975  -0.7971   1.1346
 JG1  C25   C  CR16  0  -0.315   -7.9254  -0.0526   1.1582
 JG1  H3    H  HCR6  0   0.286    6.7891  -2.4703   0.0596
 JG1  H4    H  HCR6  0   0.287    9.2356  -1.9951   0.0209
 JG1  H5    H  HCR6  0   0.284    9.9894   0.3877  -0.0521
 JG1  H6    H  HCR6  0   0.276    8.2722   2.1783  -0.0843
 JG1  H13   H  HCH2  0   0.285    0.2575  -0.7075  -0.8388
 JG1  H13A  H  HCH2  0   0.285    0.2624  -0.7083   0.8983
 JG1  H15   H  HCH2  0   0.231   -0.9191   1.5211   0.9111
 JG1  H15A  H  HCH2  0   0.230   -0.9180   1.5271  -0.8420
 JG1  H16   H  HCH2  0   0.216   -2.2684  -0.5799  -0.8502
 JG1  H16A  H  HCH2  0   0.216   -2.2725  -0.5867   0.9009
 JG1  H17   H  HCH2  0   0.214   -3.4516   1.6200   0.9094
 JG1  H17A  H  HCH2  0   0.214   -3.4376   1.6368  -0.8415
 JG1  H18   H  HCH2  0   0.220   -4.8132  -0.4551  -0.8753
 JG1  H18A  H  HCH2  0   0.221   -4.8299  -0.4748   0.8768
 JG1  H19   H  HCH2  0   0.237   -5.9796   1.7460   0.8931
 JG1  H19A  H  HCH2  0   0.236   -5.9543   1.7731  -0.8598
 JG1  H21   H  HCR6  0   0.244   -7.4057   0.2498  -2.1655
 JG1  H22   H  HCR6  0   0.252   -9.4839  -1.0656  -2.2153
 JG1  H23   H  HCR6  0   0.252  -10.5791  -1.7458  -0.0998
 JG1  H24   H  HCR6  0   0.252   -9.5714  -1.0833   2.0650
 JG1  H25   H  HCR6  0   0.244   -7.4937   0.2337   2.1105

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
 JG1  N1   C2    aromatic  1.328  0.020  1.328
 JG1  N1   C6    aromatic  1.324  0.020  1.324
 JG1  C7   C2    single    1.458  0.020  1.458
 JG1  C2   C3    aromatic  1.390  0.020  1.390
 JG1  C3   C4    aromatic  1.386  0.020  1.386
 JG1  C3   H3    single    0.930  0.020  1.080
 JG1  C5   C4    aromatic  1.386  0.020  1.386
 JG1  C4   H4    single    0.930  0.020  1.080
 JG1  C6   C5    aromatic  1.390  0.020  1.390
 JG1  C5   H5    single    0.930  0.020  1.080
 JG1  C6   H6    single    0.930  0.020  1.080
 JG1  N8   C7    aromatic  1.294  0.020  1.294
 JG1  C7   O11   aromatic  1.332  0.020  1.332
 JG1  N9   N8    aromatic  1.356  0.020  1.356
 JG1  N9   C10   aromatic  1.287  0.020  1.287
 JG1  C10  C12   single    1.484  0.020  1.484
 JG1  C10  O11   aromatic  1.338  0.020  1.338
 JG1  C13  C12   single    1.497  0.020  1.497
 JG1  C12  O14   double    1.206  0.020  1.206
 JG1  C15  C13   single    1.520  0.020  1.520
 JG1  C13  H13   single    0.970  0.020  1.090
 JG1  C13  H13A  single    0.970  0.020  1.090
 JG1  C16  C15   single    1.524  0.020  1.524
 JG1  C15  H15   single    0.970  0.020  1.090
 JG1  C15  H15A  single    0.970  0.020  1.090
 JG1  C17  C16   single    1.523  0.020  1.523
 JG1  C16  H16   single    0.970  0.020  1.090
 JG1  C16  H16A  single    0.970  0.020  1.090
 JG1  C17  C18   single    1.523  0.020  1.523
 JG1  C17  H17   single    0.970  0.020  1.090
 JG1  C17  H17A  single    0.970  0.020  1.090
 JG1  C19  C18   single    1.530  0.020  1.530
 JG1  C18  H18   single    0.970  0.020  1.090
 JG1  C18  H18A  single    0.970  0.020  1.090
 JG1  C19  C20   single    1.503  0.020  1.503
 JG1  C19  H19   single    0.970  0.020  1.090
 JG1  C19  H19A  single    0.970  0.020  1.090
 JG1  C21  C20   aromatic  1.394  0.020  1.394
 JG1  C20  C25   aromatic  1.394  0.020  1.394
 JG1  C21  C22   aromatic  1.389  0.020  1.389
 JG1  C21  H21   single    0.930  0.020  1.080
 JG1  C22  C23   aromatic  1.389  0.020  1.389
 JG1  C22  H22   single    0.930  0.020  1.080
 JG1  C23  C24   aromatic  1.389  0.020  1.389
 JG1  C23  H23   single    0.930  0.020  1.080
 JG1  C25  C24   aromatic  1.389  0.020  1.389
 JG1  C24  H24   single    0.930  0.020  1.080
 JG1  C25  H25   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
 JG1  C6    N1   C2   117.76  3.000
 JG1  C7    C2   C3   119.88  3.000
 JG1  C3    C2   N1   123.82  3.000
 JG1  C7    C2   N1   116.29  3.000
 JG1  H3    C3   C4   121.27  3.000
 JG1  H3    C3   C2   120.92  3.000
 JG1  C4    C3   C2   117.81  3.000
 JG1  H4    C4   C5   120.80  3.000
 JG1  H4    C4   C3   120.32  3.000
 JG1  C5    C4   C3   118.88  3.000
 JG1  H5    C5   C6   120.20  3.000
 JG1  H5    C5   C4   121.27  3.000
 JG1  C6    C5   C4   118.53  3.000
 JG1  H6    C6   C5   120.37  3.000
 JG1  H6    C6   N1   116.44  3.000
 JG1  C5    C6   N1   123.20  3.000
 JG1  O11   C7   N8   111.75  3.000
 JG1  O11   C7   C2   120.00  3.000
 JG1  N8    C7   C2   128.25  3.000
 JG1  N9    N8   C7   106.49  3.000
 JG1  C10   N9   N8   106.72  3.000
 JG1  C12   C10  O11  119.33  3.000
 JG1  O11   C10  N9   111.76  3.000
 JG1  C12   C10  N9   128.91  3.000
 JG1  C10   O11  C7   103.27  3.000
 JG1  O14   C12  C13  125.27  3.000
 JG1  O14   C12  C10  118.70  3.000
 JG1  C13   C12  C10  116.03  3.000
 JG1  H13A  C13  H13  104.88  3.000
 JG1  H13A  C13  C15  110.85  3.000
 JG1  H13   C13  C15  110.76  3.000
 JG1  H13A  C13  C12  108.07  3.000
 JG1  H13   C13  C12  107.80  3.000
 JG1  C15   C13  C12  114.02  3.000
 JG1  H15A  C15  H15  106.54  3.000
 JG1  H15A  C15  C16  109.33  3.000
 JG1  H15   C15  C16  109.41  3.000
 JG1  H15A  C15  C13  109.86  3.000
 JG1  H15   C15  C13  109.88  3.000
 JG1  C16   C15  C13  111.70  3.000
 JG1  H16A  C16  H16  106.13  3.000
 JG1  H16A  C16  C17  109.48  3.000
 JG1  H16   C16  C17  109.40  3.000
 JG1  H16A  C16  C15  109.62  3.000
 JG1  H16   C16  C15  109.53  3.000
 JG1  C17   C16  C15  112.48  3.000
 JG1  H17A  C17  H17  106.08  3.000
 JG1  H17A  C17  C18  109.31  3.000
 JG1  H17   C17  C18  109.37  3.000
 JG1  H17A  C17  C16  109.30  3.000
 JG1  H17   C17  C16  109.35  3.000
 JG1  C18   C17  C16  113.18  3.000
 JG1  H18A  C18  H18  106.27  3.000
 JG1  H18A  C18  C19  109.33  3.000
 JG1  H18   C18  C19  109.25  3.000
 JG1  H18A  C18  C17  109.76  3.000
 JG1  H18   C18  C17  109.61  3.000
 JG1  C19   C18  C17  112.43  3.000
 JG1  H19A  C19  H19  106.55  3.000
 JG1  H19A  C19  C20  109.81  3.000
 JG1  H19   C19  C20  109.77  3.000
 JG1  H19A  C19  C18  109.06  3.000
 JG1  H19   C19  C18  109.12  3.000
 JG1  C20   C19  C18  112.36  3.000
 JG1  C25   C20  C21  118.27  3.000
 JG1  C25   C20  C19  120.84  3.000
 JG1  C21   C20  C19  120.86  3.000
 JG1  H21   C21  C22  119.51  3.000
 JG1  H21   C21  C20  119.50  3.000
 JG1  C22   C21  C20  120.99  3.000
 JG1  H22   C22  C23  120.09  3.000
 JG1  H22   C22  C21  119.76  3.000
 JG1  C23   C22  C21  120.15  3.000
 JG1  H23   C23  C24  120.30  3.000
 JG1  H23   C23  C22  120.25  3.000
 JG1  C24   C23  C22  119.44  3.000
 JG1  H24   C24  C25  119.77  3.000
 JG1  H24   C24  C23  120.09  3.000
 JG1  C25   C24  C23  120.14  3.000
 JG1  H25   C25  C24  119.51  3.000
 JG1  H25   C25  C20  119.48  3.000
 JG1  C24   C25  C20  121.01  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
 JG1  CONST_01  N8   C7   C2   N1    180.00   0.0  0
 JG1  CONST_02  O11  C7   C2   N1      0.00   0.0  0
 JG1  CONST_03  C4   C3   C2   N1      0.00   0.0  0
 JG1  CONST_04  C4   C5   C6   N1      0.00   0.0  0
 JG1  CONST_05  C5   C6   N1   C2      0.00   0.0  0
 JG1  CONST_06  N9   N8   C7   C2    180.00   0.0  0
 JG1  CONST_07  C10  O11  C7   C2    180.00   0.0  0
 JG1  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 JG1  CONST_09  C6   N1   C2   C3      0.00   0.0  0
 JG1  CONST_10  N8   C7   C2   C3      0.00   0.0  0
 JG1  CONST_11  O11  C7   C2   C3    180.00   0.0  0
 JG1  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 JG1  CONST_13  C7   C2   C3   C4    180.00   0.0  0
 JG1  CONST_14  C7   C2   N1   C6    180.00   0.0  0
 JG1  CONST_15  C10  N9   N8   C7      0.00   0.0  0
 JG1  CONST_16  N9   C10  O11  C7      0.00   0.0  0
 JG1  CONST_17  C10  O11  C7   N8      0.00   0.0  0
 JG1  CONST_18  O11  C10  N9   N8      0.00   0.0  0
 JG1  CONST_19  O11  C7   N8   N9      0.00   0.0  0
 JG1  CONST_20  C23  C22  C21  C20     0.00   0.0  0
 JG1  CONST_21  C23  C24  C25  C20     0.00   0.0  0
 JG1  CONST_22  C24  C25  C20  C21     0.00   0.0  0
 JG1  CONST_23  C24  C23  C22  C21     0.00   0.0  0
 JG1  CONST_24  C25  C20  C21  C22     0.00   0.0  0
 JG1  CONST_25  C25  C24  C23  C22     0.00   0.0  0
 JG1  CONST_26  C12  C10  O11  C7    180.00   0.0  0
 JG1  CONST_27  C12  C10  N9   N8    180.00   0.0  0
 JG1  CONST_28  C22  C21  C20  C19   180.00   0.0  0
 JG1  CONST_29  C24  C25  C20  C19   180.00   0.0  0
 JG1  CONST_30  H3   C3   C2   N1    180.00   0.0  0
 JG1  CONST_31  H5   C5   C6   N1    180.00   0.0  0
 JG1  CONST_32  H6   C6   N1   C2    180.00   0.0  0
 JG1  CONST_33  H4   C4   C3   C2    180.00   0.0  0
 JG1  CONST_34  H22  C22  C21  C20   180.00   0.0  0
 JG1  CONST_35  H24  C24  C25  C20   180.00   0.0  0
 JG1  CONST_36  H25  C25  C20  C21   180.00   0.0  0
 JG1  CONST_37  H23  C23  C22  C21   180.00   0.0  0
 JG1  CONST_38  H21  C21  C22  C23   180.00   0.0  0
 JG1  Var_01    C13  C12  C10  N9     -0.81  30.0  2
 JG1  Var_02    C21  C20  C19  C18   -88.20  30.0  2
 JG1  Var_03    C15  C13  C12  C10   179.39  30.0  1
 JG1  Var_04    C20  C19  C18  C17   179.54  30.0  1
 JG1  Var_05    C16  C15  C13  C12   179.50  30.0  1
 JG1  Var_06    C17  C16  C15  C13  -179.88  30.0  1
 JG1  Var_07    C18  C17  C16  C15   179.41  30.0  1
 JG1  Var_08    C19  C18  C17  C16  -179.91  30.0  3

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
 JG1  plan-1  C2   0.020
 JG1  plan-1  C7   0.020
 JG1  plan-1  N8   0.020
 JG1  plan-1  N9   0.020
 JG1  plan-1  C10  0.020
 JG1  plan-1  O11  0.020
 JG1  plan-1  C12  0.020
 JG1  plan-2  N1   0.020
 JG1  plan-2  C2   0.020
 JG1  plan-2  C3   0.020
 JG1  plan-2  C4   0.020
 JG1  plan-2  C5   0.020
 JG1  plan-2  C6   0.020
 JG1  plan-2  C7   0.020
 JG1  plan-2  H3   0.020
 JG1  plan-2  H4   0.020
 JG1  plan-2  H5   0.020
 JG1  plan-2  H6   0.020
 JG1  plan-3  C19  0.020
 JG1  plan-3  C20  0.020
 JG1  plan-3  C21  0.020
 JG1  plan-3  C22  0.020
 JG1  plan-3  C23  0.020
 JG1  plan-3  C24  0.020
 JG1  plan-3  C25  0.020
 JG1  plan-3  H21  0.020
 JG1  plan-3  H22  0.020
 JG1  plan-3  H23  0.020
 JG1  plan-3  H24  0.020
 JG1  plan-3  H25  0.020
 JG1  plan-4  C10  0.020
 JG1  plan-4  C12  0.020
 JG1  plan-4  C13  0.020
 JG1  plan-4  O14  0.020

