# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 19:17:17 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 3-[(4-oxo-3,4-dihydroquinazolin-2-yl)sulfanyl]-N-[trans-4-(5-phenyl-1,3,4-oxadiazol-2-yl)cyclohexyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCSC1=Nc2ccccc2C(=O)N1)N[C@H]3CC[C@@H](CC3)c4oc(nn4)c5ccccc5
#
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
 2C6  2C6  3-[(4-oxo-3,4-dihydroquinazolin-2-yl)sulfanyl]-N-[trans-4-(5-phenyl-1,3,4-oxadiazol-2-yl)cyclohexyl]propanamide  ligand  59  34  .  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_2C6
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
 2C6  N1   N  NR16  0  -0.703    7.5256  -1.4064   0.5817
 2C6  C9   C  CR6   0   0.550    8.7486  -0.7700   0.5233
 2C6  O1   O  O     0  -0.446    9.7801  -1.3743   0.7473
 2C6  C10  C  CR66  0  -0.115    8.6471   0.6423   0.1747
 2C6  C11  C  CR16  0  -0.275    9.7937   1.4340   0.0715
 2C6  C15  C  CR16  0  -0.262    9.6832   2.7665  -0.2613
 2C6  C16  C  CR16  0  -0.236    8.4201   3.3214  -0.4941
 2C6  C17  C  CR16  0  -0.315    7.2818   2.5509  -0.3960
 2C6  C7   C  CR66  0   0.267    7.3775   1.1943  -0.0588
 2C6  N2   N  N     0  -0.455    6.2223   0.4529   0.0320
 2C6  C8   C  CR6   0   0.340    6.3347  -0.7847   0.3403
 2C6  S1   S  S2    0   0.062    4.9434  -1.8329   0.4914
 2C6  C18  C  CR5   0   0.522   -5.5906   0.1572  -0.4320
 2C6  N4   N  N     0  -0.310   -5.8687   1.1714  -1.1722
 2C6  N5   N  N     0  -0.316   -7.2189   1.3739  -1.0834
 2C6  C19  C  CR5   0   0.480   -7.6789   0.4678  -0.2919
 2C6  C20  C  CR6   0  -0.028   -9.0503   0.2473   0.1359
 2C6  O2   O  O     0  -0.419   -6.6973  -0.3339   0.1519
 2C6  C21  C  CR16  0  -0.288   -9.3866  -0.8245   0.9625
 2C6  C22  C  CR16  0  -0.240  -10.7043  -1.0081   1.3537
 2C6  C23  C  CR16  0  -0.248  -11.6905  -0.1291   0.9274
 2C6  C24  C  CR16  0  -0.239  -11.3565   0.9395   0.1035
 2C6  C25  C  CR16  0  -0.270  -10.0438   1.1292  -0.2926
 2C6  C1   C  CH2   0  -0.466   -2.2752  -1.6115  -1.2050
 2C6  C2   C  CH1   0  -0.039   -1.3407  -0.6322  -0.5025
 2C6  C3   C  CH2   0  -0.442   -1.9692  -0.1123   0.7896
 2C6  C4   C  CH2   0  -0.427   -3.3284   0.5237   0.5281
 2C6  C5   C  CH1   0  -0.393   -4.2685  -0.4679  -0.1696
 2C6  C6   C  CH2   0  -0.423   -3.6386  -0.9849  -1.4684
 2C6  C12  C  CH2   0  -0.545    3.5948  -0.6932   0.0703
 2C6  C13  C  CH2   0  -0.598    2.2937  -1.4672   0.1931
 2C6  C14  C  C     0   0.575    1.0967  -0.5954  -0.1464
 2C6  O3   O  O     0  -0.494    1.1907   0.6136  -0.2952
 2C6  N3   N  NH1   0  -0.653   -0.0590  -1.2673  -0.2658
 2C6  H1   H  HNR6  0   0.430    7.5396  -2.3921   0.8140
 2C6  H2   H  HCR6  0   0.270   10.7650   0.9942   0.2548
 2C6  H3   H  HCR6  0   0.267   10.5683   3.3824  -0.3437
 2C6  H4   H  HCR6  0   0.270    8.3349   4.3685  -0.7539
 2C6  H5   H  HCR6  0   0.267    6.3033   2.9762  -0.5768
 2C6  H6   H  HCR6  0   0.265   -8.6309  -1.5196   1.3032
 2C6  H7   H  HCR6  0   0.267  -10.9589  -1.8426   1.9932
 2C6  H8   H  HCR6  0   0.267  -12.7172  -0.2752   1.2362
 2C6  H9   H  HCR6  0   0.267  -12.1211   1.6284  -0.2301
 2C6  H10  H  HCR6  0   0.265   -9.7871   1.9634  -0.9321
 2C6  H11  H  HCH2  0   0.255   -1.8313  -1.9348  -2.1489
 2C6  H12  H  HCH2  0   0.229   -2.3994  -2.5087  -0.5876
 2C6  H13  H  HCH1  0   0.242   -1.1692   0.2165  -1.1714
 2C6  H14  H  HCH2  0   0.223   -2.0799  -0.9415   1.4965
 2C6  H15  H  HCH2  0   0.251   -1.3049   0.6175   1.2565
 2C6  H16  H  HCH2  0   0.256   -3.7701   0.8586   1.4686
 2C6  H17  H  HCH2  0   0.234   -3.2110   1.4121  -0.0996
 2C6  H18  H  HCH1  0   0.275   -4.4306  -1.3183   0.5007
 2C6  H19  H  HCH2  0   0.236   -3.5328  -0.1566  -2.1749
 2C6  H20  H  HCH2  0   0.257   -4.2969  -1.7185  -1.9376
 2C6  H21  H  HCH2  0   0.293    3.6232   0.1510   0.7551
 2C6  H22  H  HCH2  0   0.293    3.7501  -0.3284  -0.9430
 2C6  H23  H  HCH2  0   0.282    2.2980  -2.3431  -0.4609
 2C6  H24  H  HCH2  0   0.292    2.1658  -1.8426   1.2130
 2C6  H25  H  HNH1  0   0.397   -0.0576  -2.2581  -0.0780

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
 2C6  C3   C4   single    1.523  0.020  1.523
 2C6  C3   C2   single    1.528  0.020  1.528
 2C6  C4   C5   single    1.534  0.020  1.534
 2C6  O3   C14  double    1.222  0.020  1.222
 2C6  C14  N3   single    1.342  0.020  1.342
 2C6  C14  C13  single    1.519  0.020  1.519
 2C6  C2   N3   single    1.450  0.020  1.450
 2C6  C2   C1   single    1.525  0.020  1.525
 2C6  N4   N5   aromatic  1.368  0.020  1.368
 2C6  N4   C18  aromatic  1.286  0.020  1.286
 2C6  C13  C12  single    1.519  0.020  1.519
 2C6  N5   C19  aromatic  1.288  0.020  1.288
 2C6  C18  C5   single    1.486  0.020  1.486
 2C6  C18  O2   aromatic  1.344  0.020  1.344
 2C6  C5   C6   single    1.533  0.020  1.533
 2C6  C16  C17  aromatic  1.378  0.020  1.378
 2C6  C16  C15  aromatic  1.399  0.020  1.399
 2C6  C19  O2   aromatic  1.343  0.020  1.343
 2C6  C19  C20  single    1.453  0.020  1.453
 2C6  C17  C7   aromatic  1.401  0.020  1.401
 2C6  C21  C20  aromatic  1.395  0.020  1.395
 2C6  C21  C22  aromatic  1.387  0.020  1.387
 2C6  C20  C25  aromatic  1.396  0.020  1.396
 2C6  C15  C11  aromatic  1.378  0.020  1.378
 2C6  C1   C6   single    1.523  0.020  1.523
 2C6  C12  S1   single    1.815  0.020  1.815
 2C6  C22  C23  aromatic  1.388  0.020  1.388
 2C6  C7   N2   single    1.376  0.020  1.376
 2C6  C7   C10  aromatic  1.404  0.020  1.404
 2C6  C25  C24  aromatic  1.384  0.020  1.384
 2C6  N2   C8   double    1.280  0.020  1.280
 2C6  C23  C24  aromatic  1.390  0.020  1.390
 2C6  C11  C10  aromatic  1.397  0.020  1.397
 2C6  C10  C9   single    1.458  0.020  1.458
 2C6  C8   S1   single    1.749  0.020  1.749
 2C6  C8   N1   single    1.365  0.020  1.365
 2C6  C9   N1   single    1.380  0.020  1.380
 2C6  C9   O1   double    1.216  0.020  1.216
 2C6  N1   H1   single    0.860  0.020  1.020
 2C6  C11  H2   single    0.930  0.020  1.080
 2C6  C15  H3   single    0.930  0.020  1.080
 2C6  C16  H4   single    0.930  0.020  1.080
 2C6  C17  H5   single    0.930  0.020  1.080
 2C6  C21  H6   single    0.930  0.020  1.080
 2C6  C22  H7   single    0.930  0.020  1.080
 2C6  C23  H8   single    0.930  0.020  1.080
 2C6  C24  H9   single    0.930  0.020  1.080
 2C6  C25  H10  single    0.930  0.020  1.080
 2C6  C1   H11  single    0.970  0.020  1.090
 2C6  C1   H12  single    0.970  0.020  1.090
 2C6  C2   H13  single    0.970  0.020  1.090
 2C6  C3   H14  single    0.970  0.020  1.090
 2C6  C3   H15  single    0.970  0.020  1.090
 2C6  C4   H16  single    0.970  0.020  1.090
 2C6  C4   H17  single    0.970  0.020  1.090
 2C6  C5   H18  single    0.970  0.020  1.090
 2C6  C6   H19  single    0.970  0.020  1.090
 2C6  C6   H20  single    0.970  0.020  1.090
 2C6  C12  H21  single    0.970  0.020  1.090
 2C6  C12  H22  single    0.970  0.020  1.090
 2C6  C13  H23  single    0.970  0.020  1.090
 2C6  C13  H24  single    0.970  0.020  1.090
 2C6  N3   H25  single    0.860  0.020  1.020

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
 2C6  H1   N1   C8   119.73  3.000
 2C6  H1   N1   C9   116.50  3.000
 2C6  C8   N1   C9   123.77  3.000
 2C6  C10  C9   O1   125.75  3.000
 2C6  O1   C9   N1   120.98  3.000
 2C6  C10  C9   N1   113.27  3.000
 2C6  C7   C10  C11  120.46  3.000
 2C6  C11  C10  C9   120.62  3.000
 2C6  C7   C10  C9   118.92  3.000
 2C6  H2   C11  C15  120.40  3.000
 2C6  H2   C11  C10  119.59  3.000
 2C6  C15  C11  C10  120.00  3.000
 2C6  H3   C15  C16  120.02  3.000
 2C6  H3   C15  C11  120.23  3.000
 2C6  C16  C15  C11  119.74  3.000
 2C6  H4   C16  C17  119.54  3.000
 2C6  H4   C16  C15  119.65  3.000
 2C6  C17  C16  C15  120.80  3.000
 2C6  H5   C17  C7   118.86  3.000
 2C6  H5   C17  C16  121.01  3.000
 2C6  C7   C17  C16  120.14  3.000
 2C6  N2   C7   C17  118.71  3.000
 2C6  N2   C7   C10  122.44  3.000
 2C6  C17  C7   C10  118.85  3.000
 2C6  C8   N2   C7   117.59  3.000
 2C6  S1   C8   N2   122.04  3.000
 2C6  S1   C8   N1   113.95  3.000
 2C6  N2   C8   N1   124.01  3.000
 2C6  C12  S1   C8   101.23  3.000
 2C6  C5   C18  O2   120.14  3.000
 2C6  O2   C18  N4   111.11  3.000
 2C6  C5   C18  N4   128.75  3.000
 2C6  N5   N4   C18  107.03  3.000
 2C6  C19  N5   N4   106.75  3.000
 2C6  O2   C19  C20  120.12  3.000
 2C6  C20  C19  N5   128.65  3.000
 2C6  O2   C19  N5   111.22  3.000
 2C6  C25  C20  C21  119.73  3.000
 2C6  C25  C20  C19  119.03  3.000
 2C6  C21  C20  C19  121.24  3.000
 2C6  C19  O2   C18  103.90  3.000
 2C6  H6   C21  C22  119.33  3.000
 2C6  H6   C21  C20  120.80  3.000
 2C6  C22  C21  C20  119.87  3.000
 2C6  H7   C22  C23  120.18  3.000
 2C6  H7   C22  C21  119.51  3.000
 2C6  C23  C22  C21  120.31  3.000
 2C6  H8   C23  C24  120.06  3.000
 2C6  H8   C23  C22  120.07  3.000
 2C6  C24  C23  C22  119.87  3.000
 2C6  H9   C24  C25  119.65  3.000
 2C6  H9   C24  C23  120.16  3.000
 2C6  C25  C24  C23  120.19  3.000
 2C6  H10  C25  C24  119.99  3.000
 2C6  H10  C25  C20  119.98  3.000
 2C6  C24  C25  C20  120.04  3.000
 2C6  H12  C1   H11  106.89  3.000
 2C6  H12  C1   C6   109.43  3.000
 2C6  H11  C1   C6   109.64  3.000
 2C6  H12  C1   C2   109.60  3.000
 2C6  H11  C1   C2   109.83  3.000
 2C6  C6   C1   C2   111.34  3.000
 2C6  H13  C2   N3   107.52  3.000
 2C6  H13  C2   C3   108.51  3.000
 2C6  N3   C2   C3   112.00  3.000
 2C6  H13  C2   C1   108.21  3.000
 2C6  N3   C2   C1   109.61  3.000
 2C6  C3   C2   C1   110.86  3.000
 2C6  H15  C3   H14  106.96  3.000
 2C6  H15  C3   C4   109.71  3.000
 2C6  H14  C3   C4   109.67  3.000
 2C6  H15  C3   C2   109.81  3.000
 2C6  H14  C3   C2   109.25  3.000
 2C6  C4   C3   C2   111.34  3.000
 2C6  H17  C4   H16  106.77  3.000
 2C6  H17  C4   C5   109.25  3.000
 2C6  H16  C4   C5   110.01  3.000
 2C6  H17  C4   C3   109.98  3.000
 2C6  H16  C4   C3   109.95  3.000
 2C6  C5   C4   C3   110.80  3.000
 2C6  H18  C5   C6   108.51  3.000
 2C6  H18  C5   C4   108.32  3.000
 2C6  C6   C5   C4   110.58  3.000
 2C6  H18  C5   C18  107.65  3.000
 2C6  C6   C5   C18  110.97  3.000
 2C6  C4   C5   C18  110.71  3.000
 2C6  H20  C6   H19  106.83  3.000
 2C6  H20  C6   C5   110.06  3.000
 2C6  H19  C6   C5   109.36  3.000
 2C6  H20  C6   C1   109.73  3.000
 2C6  H19  C6   C1   109.67  3.000
 2C6  C5   C6   C1   111.09  3.000
 2C6  H22  C12  H21  108.81  3.000
 2C6  H22  C12  C13  111.62  3.000
 2C6  H21  C12  C13  111.53  3.000
 2C6  H22  C12  S1   108.70  3.000
 2C6  H21  C12  S1   108.79  3.000
 2C6  C13  C12  S1   107.32  3.000
 2C6  H24  C13  H23  106.45  3.000
 2C6  H24  C13  C14  108.25  3.000
 2C6  H23  C13  C14  109.22  3.000
 2C6  H24  C13  C12  110.50  3.000
 2C6  H23  C13  C12  110.89  3.000
 2C6  C14  C13  C12  111.37  3.000
 2C6  N3   C14  O3   123.42  3.000
 2C6  N3   C14  C13  114.27  3.000
 2C6  O3   C14  C13  122.31  3.000
 2C6  H25  N3   C14  118.29  3.000
 2C6  H25  N3   C2   117.52  3.000
 2C6  C14  N3   C2   123.82  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
 2C6  CONST_01  C16  C17  C7   C10     0.00   0.0  0
 2C6  CONST_02  C16  C15  C11  C10     0.00   0.0  0
 2C6  CONST_03  C17  C16  C15  C11     0.00   0.0  0
 2C6  CONST_04  C17  C7   C10  C11     0.00   0.0  0
 2C6  CONST_05  C7   C17  C16  C15     0.00   0.0  0
 2C6  CONST_06  C7   C10  C11  C15     0.00   0.0  0
 2C6  CONST_07  C19  N5   N4   C18     0.00   0.0  0
 2C6  CONST_08  N5   C19  O2   C18     0.00   0.0  0
 2C6  CONST_09  C20  C19  O2   C18   180.00   0.0  0
 2C6  CONST_10  O2   C19  N5   N4      0.00   0.0  0
 2C6  CONST_11  C20  C19  N5   N4    180.00   0.0  0
 2C6  CONST_12  C19  O2   C18  N4      0.00   0.0  0
 2C6  CONST_13  O2   C18  N4   N5      0.00   0.0  0
 2C6  CONST_14  C21  C20  C19  N5    180.00   0.0  0
 2C6  CONST_15  C25  C20  C19  N5      0.00   0.0  0
 2C6  CONST_16  C22  C21  C20  C19   180.00   0.0  0
 2C6  CONST_17  C24  C25  C20  C19   180.00   0.0  0
 2C6  CONST_18  C23  C22  C21  C20     0.00   0.0  0
 2C6  CONST_19  C23  C24  C25  C20     0.00   0.0  0
 2C6  CONST_20  C21  C20  C19  O2      0.00   0.0  0
 2C6  CONST_21  C25  C20  C19  O2    180.00   0.0  0
 2C6  CONST_22  C24  C25  C20  C21     0.00   0.0  0
 2C6  CONST_23  C24  C23  C22  C21     0.00   0.0  0
 2C6  CONST_24  C25  C20  C21  C22     0.00   0.0  0
 2C6  CONST_25  C25  C24  C23  C22     0.00   0.0  0
 2C6  CONST_26  C5   C18  N4   N5    180.00   0.0  0
 2C6  CONST_27  C5   C18  O2   C19   180.00   0.0  0
 2C6  CONST_28  C7   N2   C8   N1      0.00   0.0  0
 2C6  CONST_29  N2   C8   N1   C9      0.00   0.0  0
 2C6  CONST_30  C8   N1   C9   C10     0.00   0.0  0
 2C6  CONST_31  S1   C8   N1   C9    180.00   0.0  0
 2C6  CONST_32  C8   N1   C9   O1    180.00   0.0  0
 2C6  CONST_33  S1   C8   N2   C7    180.00   0.0  0
 2C6  CONST_34  H2   C11  C10  C9      0.00   0.0  0
 2C6  CONST_35  H5   C17  C7   C10   180.00   0.0  0
 2C6  CONST_36  H3   C15  C11  C10   180.00   0.0  0
 2C6  CONST_37  H4   C16  C15  C11   180.00   0.0  0
 2C6  CONST_38  H6   C21  C20  C19     0.00   0.0  0
 2C6  CONST_39  H10  C25  C20  C19     0.00   0.0  0
 2C6  CONST_40  H7   C22  C21  C20   180.00   0.0  0
 2C6  CONST_41  H9   C24  C25  C20   180.00   0.0  0
 2C6  CONST_42  H8   C23  C22  C21   180.00   0.0  0
 2C6  CONST_43  H1   N1   C9   C10   180.00   0.0  0
 2C6  CONST_44  O3   C14  N3   C2      0.00   0.0  0
 2C6  CONST_45  C13  C14  N3   C2    180.00   0.0  0
 2C6  CONST_46  H25  N3   C14  C13     0.00   0.0  0
 2C6  Var_01    C5   C4   C3   C2     56.42  30.0  1
 2C6  Var_02    C5   C6   C1   C2    -55.99  30.0  1
 2C6  Var_03    C13  C12  S1   C8   -178.64  30.0  1
 2C6  Var_04    C14  C13  C12  S1   -179.80  30.0  1
 2C6  Var_05    O3   C14  C13  C12   -10.14  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2C6  chir_01  C2  C3  N3   C1  negativ
 2C6  chir_02  C5  C6  C18  C4  positiv

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
 2C6  plan-1  C18  0.020
 2C6  plan-1  N4   0.020
 2C6  plan-1  N5   0.020
 2C6  plan-1  C19  0.020
 2C6  plan-1  C20  0.020
 2C6  plan-1  O2   0.020
 2C6  plan-1  C5   0.020
 2C6  plan-2  C19  0.020
 2C6  plan-2  C20  0.020
 2C6  plan-2  C21  0.020
 2C6  plan-2  C22  0.020
 2C6  plan-2  C23  0.020
 2C6  plan-2  C24  0.020
 2C6  plan-2  C25  0.020
 2C6  plan-2  H6   0.020
 2C6  plan-2  H7   0.020
 2C6  plan-2  H8   0.020
 2C6  plan-2  H9   0.020
 2C6  plan-2  H10  0.020
 2C6  plan-3  N1   0.020
 2C6  plan-3  C9   0.020
 2C6  plan-3  O1   0.020
 2C6  plan-3  C10  0.020
 2C6  plan-3  C11  0.020
 2C6  plan-3  C15  0.020
 2C6  plan-3  C16  0.020
 2C6  plan-3  C17  0.020
 2C6  plan-3  C7   0.020
 2C6  plan-3  N2   0.020
 2C6  plan-3  C8   0.020
 2C6  plan-3  S1   0.020
 2C6  plan-3  H1   0.020
 2C6  plan-3  H2   0.020
 2C6  plan-3  H3   0.020
 2C6  plan-3  H4   0.020
 2C6  plan-3  H5   0.020
 2C6  plan-4  C2   0.020
 2C6  plan-4  C13  0.020
 2C6  plan-4  C14  0.020
 2C6  plan-4  O3   0.020
 2C6  plan-4  N3   0.020
 2C6  plan-4  H25  0.020

