# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:18:42 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 1-(2-azanylpyridin-4-yl)-3-[5-[4-(5-methyl-1,2,4-oxadiazol-3-yl)phenoxy]pentyl]imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(n1)c2ccc(OCCCCCN3CCN(C3=O)c4ccnc(N)c4)cc2
#
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
 EQ9  EQ9  1-(2-azanylpyridin-4-yl)-3-[5-[4-(5-methyl-1,2,4-oxadiazol-3-yl)phenoxy]pentyl]imidazolidin-2-one  ligand  57  31  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EQ9
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
 EQ9  C15  C  CR16  0  -0.335   -4.9610  -0.4991  -1.4440
 EQ9  C16  C  CR16  0  -0.367   -4.7079   0.4114   0.7732
 EQ9  C17  C  CR16  0  -0.266   -6.0823   0.3592   0.9360
 EQ9  C18  C  CR6   0  -0.019   -6.9118  -0.1170  -0.0757
 EQ9  C13  C  CH2   0  -0.174   -1.9193   0.4841   0.3029
 EQ9  C7   C  CH2   0  -0.316    6.1889   2.1214  -0.5234
 EQ9  C6   C  CR5   0   0.750    5.0929   0.4482   0.6834
 EQ9  N2   N  NR5   0  -0.630    6.2179   0.7352  -0.0787
 EQ9  C10  C  CH2   0  -0.436    1.9176   0.9831   0.1441
 EQ9  C9   C  CH2   0  -0.288    2.9342   1.5052   1.1546
 EQ9  C8   C  CH2   0  -0.290    4.7302   2.5140  -0.3114
 EQ9  C2   C  CR16  0  -0.069    9.6275  -0.2840  -0.8877
 EQ9  C1   C  CR6   0   0.456    8.5849  -2.1075  -0.0369
 EQ9  N1   N  N     0  -0.470    9.6902  -1.5667  -0.5507
 EQ9  C5   C  CR16  0  -0.467    7.3922  -1.3951   0.1457
 EQ9  C4   C  CR6   0   0.470    7.3493  -0.0502  -0.2058
 EQ9  C3   C  CR16  0  -0.448    8.5179   0.5199  -0.7429
 EQ9  C22  C  CH3   0  -0.761  -11.6975  -0.8490  -0.8709
 EQ9  C11  C  CH2   0  -0.432    0.5084   0.9641   0.7215
 EQ9  C12  C  CH2   0  -0.455   -0.5229   0.4602  -0.2811
 EQ9  C14  C  CR6   0   0.395   -4.1346  -0.0159  -0.4256
 EQ9  C19  C  CR16  0  -0.269   -6.3285  -0.5474  -1.2689
 EQ9  C20  C  CR5   0   0.320   -8.3591  -0.1699   0.0939
 EQ9  C21  C  CR5   0   0.510  -10.3695  -0.5075  -0.3216
 EQ9  N3   N  NR5   0  -0.509    4.2875   1.5357   0.6541
 EQ9  N5   N  N     0  -0.167   -8.9696   0.2162   1.1756
 EQ9  N6   N  N     0  -0.467   -9.2091  -0.6316  -0.8725
 EQ9  O1   O  O2    0  -0.469   -2.8205   0.0016  -0.6857
 EQ9  O2   O  O     0  -0.325  -10.2928  -0.0054   0.9043
 EQ9  H20  H  HCR6  0   0.268   -4.5196  -0.8359  -2.3732
 EQ9  H21  H  HCR6  0   0.285   -4.1050   0.7883   1.5876
 EQ9  H22  H  HCR6  0   0.264   -6.5054   0.6998   1.8720
 EQ9  H19  H  HCH2  0   0.226   -1.9734  -0.1435   1.1998
 EQ9  H18  H  HCH2  0   0.225   -2.1881   1.5055   0.5948
 EQ9  H4   H  HCH2  0   0.263    6.8616   2.7352   0.0809
 EQ9  H5   H  HCH2  0   0.272    6.4849   2.2112  -1.5672
 EQ9  H12  H  HCH2  0   0.227    1.9327   1.6088  -0.7534
 EQ9  H13  H  HCH2  0   0.229    2.2044  -0.0252  -0.1684
 EQ9  H10  H  HCH2  0   0.248    2.6693   2.5195   1.4625
 EQ9  H11  H  HCH2  0   0.251    2.9185   0.8886   2.0542
 EQ9  H7   H  HCH2  0   0.264    4.6328   3.5278   0.0757
 EQ9  H6   H  HCH2  0   0.250    4.1563   2.4498  -1.2409
 EQ9  H1   H  HCR6  0   0.255   10.5336   0.1424  -1.3056
 EQ9  H3   H  HCR6  0   0.283    6.5328  -1.9013   0.5526
 EQ9  H2   H  HCR6  0   0.275    8.5743   1.5557  -1.0414
 EQ9  H25  H  HCH3  0   0.284  -12.1629  -1.6406  -0.2834
 EQ9  H24  H  HCH3  0   0.282  -12.3601   0.0155  -0.8485
 EQ9  H26  H  HCH3  0   0.279  -11.5928  -1.1887  -1.8969
 EQ9  H14  H  HCH2  0   0.225    0.4912   0.3316   1.6150
 EQ9  H15  H  HCH2  0   0.224    0.2360   1.9720   1.0519
 EQ9  H16  H  HCH2  0   0.234   -0.2693  -0.5580  -0.5892
 EQ9  H17  H  HCH2  0   0.232   -0.4984   1.0849  -1.1788
 EQ9  H23  H  HCR6  0   0.261   -6.9496  -0.9240  -2.0707
 EQ9  H9   H  HNH2  0   0.380    9.4113  -3.9541  -0.0514
 EQ9  H8   H  HNH2  0   0.388    7.8067  -3.9200   0.4759
 EQ9  O3   O  O     0  -0.504    4.8713  -0.5857   1.2866
 EQ9  N4   N  NH2   0  -0.838    8.6675  -3.4125   0.3571

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
 EQ9  C22  C21  single    1.477  0.020  1.477
 EQ9  C21  N6   aromatic  1.290  0.020  1.290
 EQ9  C21  O2   aromatic  1.327  0.020  1.327
 EQ9  N6   C20  aromatic  1.367  0.020  1.367
 EQ9  O2   N5   aromatic  1.369  0.020  1.369
 EQ9  N5   C20  aromatic  1.301  0.020  1.301
 EQ9  C20  C18  single    1.458  0.020  1.458
 EQ9  C19  C18  aromatic  1.396  0.020  1.396
 EQ9  C19  C15  aromatic  1.379  0.020  1.379
 EQ9  C18  C17  aromatic  1.392  0.020  1.392
 EQ9  C15  C14  aromatic  1.398  0.020  1.398
 EQ9  C17  C16  aromatic  1.385  0.020  1.385
 EQ9  C14  C16  aromatic  1.396  0.020  1.396
 EQ9  C14  O1   single    1.340  0.020  1.340
 EQ9  C13  O1   single    1.422  0.020  1.422
 EQ9  C13  C12  single    1.514  0.020  1.514
 EQ9  C12  C11  single    1.524  0.020  1.524
 EQ9  C11  C10  single    1.523  0.020  1.523
 EQ9  C10  C9   single    1.526  0.020  1.526
 EQ9  C9   N3   single    1.443  0.020  1.443
 EQ9  N3   C8   single    1.444  0.020  1.444
 EQ9  N3   C6   single    1.354  0.020  1.354
 EQ9  C8   C7   single    1.525  0.020  1.525
 EQ9  C6   O3   double    1.217  0.020  1.217
 EQ9  C6   N2   single    1.389  0.020  1.389
 EQ9  C7   N2   single    1.456  0.020  1.456
 EQ9  N2   C4   single    1.383  0.020  1.383
 EQ9  C4   C3   aromatic  1.407  0.020  1.407
 EQ9  C4   C5   aromatic  1.391  0.020  1.391
 EQ9  C3   C2   aromatic  1.378  0.020  1.378
 EQ9  C5   C1   aromatic  1.401  0.020  1.401
 EQ9  C2   N1   aromatic  1.328  0.020  1.328
 EQ9  C1   N1   aromatic  1.333  0.020  1.333
 EQ9  C1   N4   single    1.366  0.020  1.366
 EQ9  C15  H20  single    0.930  0.020  1.080
 EQ9  C16  H21  single    0.930  0.020  1.080
 EQ9  C17  H22  single    0.930  0.020  1.080
 EQ9  C13  H19  single    0.970  0.020  1.090
 EQ9  C13  H18  single    0.970  0.020  1.090
 EQ9  C7   H4   single    0.970  0.020  1.090
 EQ9  C7   H5   single    0.970  0.020  1.090
 EQ9  C10  H12  single    0.970  0.020  1.090
 EQ9  C10  H13  single    0.970  0.020  1.090
 EQ9  C9   H10  single    0.970  0.020  1.090
 EQ9  C9   H11  single    0.970  0.020  1.090
 EQ9  C8   H7   single    0.970  0.020  1.090
 EQ9  C8   H6   single    0.970  0.020  1.090
 EQ9  C2   H1   single    0.930  0.020  1.080
 EQ9  C5   H3   single    0.930  0.020  1.080
 EQ9  C3   H2   single    0.930  0.020  1.080
 EQ9  C22  H25  single    0.970  0.020  1.090
 EQ9  C22  H24  single    0.970  0.020  1.090
 EQ9  C22  H26  single    0.970  0.020  1.090
 EQ9  C11  H14  single    0.970  0.020  1.090
 EQ9  C11  H15  single    0.970  0.020  1.090
 EQ9  C12  H16  single    0.970  0.020  1.090
 EQ9  C12  H17  single    0.970  0.020  1.090
 EQ9  C19  H23  single    0.930  0.020  1.080
 EQ9  N4   H9   single    0.890  0.020  1.040
 EQ9  N4   H8   single    0.890  0.020  1.040

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
 EQ9  H20  C15  C19  120.15  3.000
 EQ9  H20  C15  C14  119.46  3.000
 EQ9  C19  C15  C14  120.38  3.000
 EQ9  H21  C16  C14  121.65  3.000
 EQ9  H21  C16  C17  118.55  3.000
 EQ9  C14  C16  C17  119.80  3.000
 EQ9  H22  C17  C18  120.21  3.000
 EQ9  H22  C17  C16  118.54  3.000
 EQ9  C18  C17  C16  121.25  3.000
 EQ9  C20  C18  C19  120.19  3.000
 EQ9  C19  C18  C17  118.53  3.000
 EQ9  C20  C18  C17  121.28  3.000
 EQ9  H18  C13  H19  107.68  3.000
 EQ9  H18  C13  O1   110.24  3.000
 EQ9  H19  C13  O1   110.08  3.000
 EQ9  H18  C13  C12  110.11  3.000
 EQ9  H19  C13  C12  110.62  3.000
 EQ9  O1   C13  C12  108.12  3.000
 EQ9  H5   C7   H4   108.45  3.000
 EQ9  H5   C7   C8   111.84  3.000
 EQ9  H4   C7   C8   111.54  3.000
 EQ9  H5   C7   N2   111.46  3.000
 EQ9  H4   C7   N2   110.71  3.000
 EQ9  C8   C7   N2   102.80  3.000
 EQ9  O3   C6   N3   125.79  3.000
 EQ9  O3   C6   N2   126.50  3.000
 EQ9  N3   C6   N2   107.70  3.000
 EQ9  C4   N2   C6   126.56  3.000
 EQ9  C4   N2   C7   121.93  3.000
 EQ9  C6   N2   C7   110.37  3.000
 EQ9  H13  C10  H12  106.81  3.000
 EQ9  H13  C10  C11  109.84  3.000
 EQ9  H12  C10  C11  109.32  3.000
 EQ9  H13  C10  C9   109.27  3.000
 EQ9  H12  C10  C9   109.79  3.000
 EQ9  C11  C10  C9   111.70  3.000
 EQ9  H11  C9   H10  106.79  3.000
 EQ9  H11  C9   N3   108.15  3.000
 EQ9  H10  C9   N3   107.79  3.000
 EQ9  H11  C9   C10  110.08  3.000
 EQ9  H10  C9   C10  110.05  3.000
 EQ9  N3   C9   C10  113.72  3.000
 EQ9  H6   C8   H7   108.03  3.000
 EQ9  H6   C8   N3   111.56  3.000
 EQ9  H7   C8   N3   111.43  3.000
 EQ9  H6   C8   C7   111.62  3.000
 EQ9  H7   C8   C7   111.98  3.000
 EQ9  N3   C8   C7   102.22  3.000
 EQ9  H1   C2   C3   118.93  3.000
 EQ9  H1   C2   N1   115.97  3.000
 EQ9  C3   C2   N1   125.10  3.000
 EQ9  N4   C1   C5   119.98  3.000
 EQ9  N4   C1   N1   116.65  3.000
 EQ9  C5   C1   N1   123.34  3.000
 EQ9  C1   N1   C2   116.77  3.000
 EQ9  H3   C5   C4   121.69  3.000
 EQ9  H3   C5   C1   119.30  3.000
 EQ9  C4   C5   C1   119.01  3.000
 EQ9  C3   C4   C5   117.57  3.000
 EQ9  C5   C4   N2   123.45  3.000
 EQ9  C3   C4   N2   118.98  3.000
 EQ9  H2   C3   C4   122.54  3.000
 EQ9  H2   C3   C2   119.25  3.000
 EQ9  C4   C3   C2   118.21  3.000
 EQ9  H26  C22  H24  109.04  3.000
 EQ9  H26  C22  H25  108.86  3.000
 EQ9  H24  C22  H25  107.79  3.000
 EQ9  H26  C22  C21  109.69  3.000
 EQ9  H24  C22  C21  110.84  3.000
 EQ9  H25  C22  C21  110.56  3.000
 EQ9  H15  C11  H14  106.36  3.000
 EQ9  H15  C11  C12  109.54  3.000
 EQ9  H14  C11  C12  109.58  3.000
 EQ9  H15  C11  C10  109.46  3.000
 EQ9  H14  C11  C10  109.34  3.000
 EQ9  C12  C11  C10  112.39  3.000
 EQ9  H17  C12  H16  107.18  3.000
 EQ9  H17  C12  C11  109.63  3.000
 EQ9  H16  C12  C11  109.65  3.000
 EQ9  H17  C12  C13  109.16  3.000
 EQ9  H16  C12  C13  109.71  3.000
 EQ9  C11  C12  C13  111.42  3.000
 EQ9  O1   C14  C16  124.44  3.000
 EQ9  O1   C14  C15  116.30  3.000
 EQ9  C16  C14  C15  119.26  3.000
 EQ9  H23  C19  C18  120.05  3.000
 EQ9  H23  C19  C15  119.16  3.000
 EQ9  C18  C19  C15  120.79  3.000
 EQ9  N6   C20  N5   113.34  3.000
 EQ9  N5   C20  C18  123.49  3.000
 EQ9  N6   C20  C18  123.16  3.000
 EQ9  O2   C21  N6   112.26  3.000
 EQ9  O2   C21  C22  118.88  3.000
 EQ9  N6   C21  C22  128.86  3.000
 EQ9  C8   N3   C9   122.25  3.000
 EQ9  C8   N3   C6   112.11  3.000
 EQ9  C9   N3   C6   122.24  3.000
 EQ9  O2   N5   C20  103.94  3.000
 EQ9  C21  N6   C20  102.99  3.000
 EQ9  C14  O1   C13  119.42  3.000
 EQ9  N5   O2   C21  107.47  3.000
 EQ9  H8   N4   H9   114.11  3.000
 EQ9  H8   N4   C1   117.66  3.000
 EQ9  H9   N4   C1   116.21  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
 EQ9  CONST_01  C20  C18  C19  C15   180.00   0.0  0
 EQ9  CONST_02  C17  C18  C19  C15     0.00   0.0  0
 EQ9  CONST_03  C17  C16  C14  C15     0.00   0.0  0
 EQ9  CONST_04  C20  C18  C17  C16   180.00   0.0  0
 EQ9  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 EQ9  CONST_06  C19  C15  C14  C16     0.00   0.0  0
 EQ9  CONST_07  N6   C20  C18  C17   180.00   0.0  0
 EQ9  CONST_08  N5   C20  C18  C17     0.00   0.0  0
 EQ9  CONST_09  C21  N6   C20  C18   180.00   0.0  0
 EQ9  CONST_10  O2   N5   C20  C18   180.00   0.0  0
 EQ9  CONST_11  C14  C15  C19  C18     0.00   0.0  0
 EQ9  CONST_12  C14  C16  C17  C18     0.00   0.0  0
 EQ9  CONST_13  C5   C4   C3   C2      0.00   0.0  0
 EQ9  CONST_14  C5   C1   N1   C2      0.00   0.0  0
 EQ9  CONST_15  C3   C4   C5   C1      0.00   0.0  0
 EQ9  CONST_16  C3   C2   N1   C1      0.00   0.0  0
 EQ9  CONST_17  C4   C3   C2   N1      0.00   0.0  0
 EQ9  CONST_18  C4   C5   C1   N1      0.00   0.0  0
 EQ9  CONST_19  N6   C20  C18  C19     0.00   0.0  0
 EQ9  CONST_20  N5   C20  C18  C19   180.00   0.0  0
 EQ9  CONST_21  O2   C21  N6   C20     0.00   0.0  0
 EQ9  CONST_22  C21  O2   N5   C20     0.00   0.0  0
 EQ9  CONST_23  N5   C20  N6   C21     0.00   0.0  0
 EQ9  CONST_24  N6   C21  O2   N5      0.00   0.0  0
 EQ9  CONST_25  O2   N5   C20  N6      0.00   0.0  0
 EQ9  CONST_26  C2   C3   C4   N2    180.00   0.0  0
 EQ9  CONST_27  C1   C5   C4   N2    180.00   0.0  0
 EQ9  CONST_29  N3   C6   N2   C7      0.00   0.0  0
 EQ9  CONST_31  C8   N3   C6   N2      0.00   0.0  0
 EQ9  CONST_33  C4   N2   C7   C8    180.00   0.0  0
 EQ9  CONST_34  N3   C6   N2   C4    180.00   0.0  0
 EQ9  CONST_35  O1   C14  C16  C17   180.00   0.0  0
 EQ9  CONST_36  N4   C1   N1   C2    180.00   0.0  0
 EQ9  CONST_37  N4   C1   C5   C4    180.00   0.0  0
 EQ9  CONST_38  C20  N6   C21  C22   180.00   0.0  0
 EQ9  CONST_39  N5   O2   C21  C22   180.00   0.0  0
 EQ9  CONST_40  O1   C14  C15  C19   180.00   0.0  0
 EQ9  CONST_41  C9   N3   C8   C7    180.00   0.0  0
 EQ9  CONST_42  O3   C6   N2   C7    180.00   0.0  0
 EQ9  CONST_43  C9   N3   C6   N2    180.00   0.0  0
 EQ9  CONST_44  O3   C6   N3   C8    180.00   0.0  0
 EQ9  CONST_45  O3   C6   N2   C4      0.00   0.0  0
 EQ9  CONST_46  H21  C16  C14  C15   180.00   0.0  0
 EQ9  CONST_47  H20  C15  C14  C16   180.00   0.0  0
 EQ9  CONST_48  H23  C19  C18  C17   180.00   0.0  0
 EQ9  CONST_49  H2   C3   C4   N2      0.00   0.0  0
 EQ9  CONST_50  H3   C5   C4   N2      0.00   0.0  0
 EQ9  CONST_51  H1   C2   N1   C1    180.00   0.0  0
 EQ9  CONST_52  H22  C17  C16  C14   180.00   0.0  0
 EQ9  CONST_53  O3   C6   N3   C9      0.00   0.0  0
 EQ9  Var_01    C3   C4   N2   C7      1.98  30.0  2
 EQ9  Var_02    H7   C8   N3   C6   -139.48  30.0  1
 EQ9  Var_03    H4   C7   N2   C6    102.39  30.0  1
 EQ9  Var_04    C10  C9   N3   C6    -84.16  30.0  2
 EQ9  Var_05    H25  C22  C21  N6    116.36  30.0  2
 EQ9  Var_06    N3   C9   C10  C11   179.72  30.0  3
 EQ9  Var_07    H19  C13  O1   C14    62.06  30.0  1
 EQ9  Var_08    C10  C11  C12  C13  -178.53  30.0  3
 EQ9  Var_09    C12  C11  C10  C9    179.33  30.0  1
 EQ9  Var_10    O1   C13  C12  C11  -179.95  30.0  1

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
 EQ9  plan-1  C18  0.020
 EQ9  plan-1  C22  0.020
 EQ9  plan-1  C20  0.020
 EQ9  plan-1  C21  0.020
 EQ9  plan-1  N5   0.020
 EQ9  plan-1  N6   0.020
 EQ9  plan-1  O2   0.020
 EQ9  plan-2  N2   0.020
 EQ9  plan-2  C2   0.020
 EQ9  plan-2  C1   0.020
 EQ9  plan-2  N1   0.020
 EQ9  plan-2  C5   0.020
 EQ9  plan-2  C4   0.020
 EQ9  plan-2  C3   0.020
 EQ9  plan-2  H1   0.020
 EQ9  plan-2  H3   0.020
 EQ9  plan-2  H2   0.020
 EQ9  plan-2  N4   0.020
 EQ9  plan-3  C15  0.020
 EQ9  plan-3  C16  0.020
 EQ9  plan-3  C17  0.020
 EQ9  plan-3  C18  0.020
 EQ9  plan-3  C14  0.020
 EQ9  plan-3  C19  0.020
 EQ9  plan-3  C20  0.020
 EQ9  plan-3  O1   0.020
 EQ9  plan-3  H20  0.020
 EQ9  plan-3  H21  0.020
 EQ9  plan-3  H22  0.020
 EQ9  plan-3  H23  0.020
 EQ9  plan-4  C1   0.020
 EQ9  plan-4  H9   0.020
 EQ9  plan-4  H8   0.020
 EQ9  plan-4  N4   0.020
 EQ9  plan-5  C7   0.020
 EQ9  plan-5  C6   0.020
 EQ9  plan-5  N2   0.020
 EQ9  plan-5  C9   0.020
 EQ9  plan-5  C8   0.020
 EQ9  plan-5  C4   0.020
 EQ9  plan-5  N3   0.020
 EQ9  plan-5  O3   0.020

