# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:40:58 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-[trans-4-(4-cyanophenoxy)cyclohexyl]-3-[(4-oxo-3,4-dihydroquinazolin-2-yl)sulfanyl]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)Oc4ccc(cc4)C#N
#
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
 2D6  2D6  N-[trans-4-(4-cyanophenoxy)cyclohexyl]-3-[(4-oxo-3,4-dihydroquinazolin-2-yl)sulfanyl]propanamide  ligand  56  32  .  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_2D6
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
 2D6  N4   N  NH1   0  -0.642   -0.6879   1.2748  -0.1848
 2D6  C8   C  C     0   0.589    0.4277   0.5287  -0.1030
 2D6  O2   O  O     0  -0.481    0.5043  -0.6121  -0.5270
 2D6  C9   C  CH2   0  -0.577    1.5949   1.2178   0.5815
 2D6  C10  C  CH2   0  -0.534    2.9219   0.6342   0.1274
 2D6  S1   S  S2    0   0.072    4.2383   1.4999   1.0261
 2D6  C11  C  CR6   0   0.344    5.6366   0.5587   0.5626
 2D6  N2   N  NR16  0  -0.697    6.8045   0.9867   1.1255
 2D6  C12  C  CR6   0   0.556    8.0299   0.3895   0.9030
 2D6  O3   O  O     0  -0.440    9.0373   0.8174   1.4303
 2D6  N3   N  N     0  -0.452    5.5511  -0.4397  -0.2329
 2D6  C13  C  CR66  0   0.271    6.7089  -1.1209  -0.5291
 2D6  C14  C  CR66  0  -0.113    7.9550  -0.7556   0.0039
 2D6  C15  C  CR16  0  -0.257    9.1043  -1.4787  -0.3223
 2D6  C16  C  CR16  0  -0.241    9.0200  -2.5588  -1.1730
 2D6  C17  C  CR16  0  -0.215    7.7813  -2.9253  -1.7086
 2D6  C18  C  CR16  0  -0.297    6.6403  -2.2200  -1.3945
 2D6  C19  C  CH2   0  -0.443   -4.0917   1.4773  -1.8341
 2D6  C20  C  CH2   0  -0.448   -2.7424   1.9444  -1.3014
 2D6  C21  C  CH1   0  -0.046   -1.9512   0.7882  -0.6984
 2D6  C22  C  CH2   0  -0.423   -2.7689   0.0725   0.3770
 2D6  C23  C  CH2   0  -0.471   -4.1160  -0.3921  -0.1664
 2D6  C24  C  CH1   0   0.050   -4.8917   0.7849  -0.7431
 2D6  O1   O  O2    0  -0.481   -6.1203   0.3660  -1.3339
 2D6  C1   C  CR6   0   0.417   -7.1868   0.0751  -0.5811
 2D6  C2   C  CR16  0  -0.348   -7.2470   0.2035   0.8077
 2D6  C3   C  CR16  0  -0.218   -8.4129  -0.1169   1.4807
 2D6  C4   C  CR6   0  -0.014   -9.5343  -0.5685   0.7904
 2D6  C5   C  CR16  0  -0.209   -9.4734  -0.6947  -0.6002
 2D6  C6   C  CR16  0  -0.332   -8.3152  -0.3782  -1.2746
 2D6  C7   C  CSP   0   0.019  -10.7265  -0.9007   1.4977
 2D6  N1   N  NS    0  -0.196  -11.6847  -1.1712   2.0778
 2D6  H1   H  HNH1  0   0.368   -0.6768   2.1916   0.2312
 2D6  H2   H  HCH2  0   0.253    1.5609   2.2935   0.3943
 2D6  H3   H  HCH2  0   0.283    1.4717   1.0856   1.6607
 2D6  H4   H  HCH2  0   0.292    2.9860  -0.4272   0.3513
 2D6  H5   H  HCH2  0   0.284    3.0706   0.7741  -0.9418
 2D6  H6   H  HNR6  0   0.403    6.8031   1.7855   1.7457
 2D6  H7   H  HCR6  0   0.253   10.0568  -1.1856   0.0980
 2D6  H8   H  HCR6  0   0.246    9.9070  -3.1223  -1.4264
 2D6  H9   H  HCR6  0   0.248    7.7173  -3.7730  -2.3772
 2D6  H10  H  HCR6  0   0.247    5.6802  -2.4999  -1.8065
 2D6  H12  H  HCH2  0   0.228   -3.9402   0.7839  -2.6669
 2D6  H13  H  HCH2  0   0.258   -2.1698   2.4098  -2.1047
 2D6  H14  H  HCH2  0   0.206   -2.9012   2.7182  -0.5407
 2D6  H15  H  HCH1  0   0.241   -1.7256   0.0746  -1.4953
 2D6  H16  H  HCH2  0   0.255   -2.2119  -0.7838   0.7593
 2D6  H17  H  HCH2  0   0.207   -2.9205   0.7504   1.2239
 2D6  H18  H  HCH2  0   0.230   -3.9627  -1.1341  -0.9564
 2D6  H19  H  HCH2  0   0.252   -4.6772  -0.8933   0.6245
 2D6  H20  H  HCH1  0   0.209   -5.0939   1.5197   0.0484
 2D6  H21  H  HCR6  0   0.264   -6.4048   0.5512   1.3876
 2D6  H22  H  HCR6  0   0.262   -8.4439  -0.0150   2.5568
 2D6  H23  H  HCR6  0   0.260  -10.3370  -1.0418  -1.1505
 2D6  H24  H  HCR6  0   0.255   -8.2721  -0.4758  -2.3512
 2D6  H11  H  HCH2  0   0.254   -4.6507   2.3299  -2.2227

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
 2D6  C20  C19  single    1.524  0.020  1.524
 2D6  C20  C21  single    1.525  0.020  1.525
 2D6  C19  C24  single    1.520  0.020  1.520
 2D6  O2   C8   double    1.219  0.020  1.219
 2D6  C8   C9   single    1.518  0.020  1.518
 2D6  C8   N4   single    1.345  0.020  1.345
 2D6  C9   C10  single    1.519  0.020  1.519
 2D6  N4   C21  single    1.448  0.020  1.448
 2D6  C21  C22  single    1.529  0.020  1.529
 2D6  C17  C18  aromatic  1.378  0.020  1.378
 2D6  C17  C16  aromatic  1.398  0.020  1.398
 2D6  C24  O1   single    1.426  0.020  1.426
 2D6  C24  C23  single    1.523  0.020  1.523
 2D6  O1   C1   single    1.337  0.020  1.337
 2D6  C18  C13  aromatic  1.401  0.020  1.401
 2D6  C16  C15  aromatic  1.377  0.020  1.377
 2D6  C10  S1   single    1.814  0.020  1.814
 2D6  C1   C6   aromatic  1.400  0.020  1.400
 2D6  C1   C2   aromatic  1.396  0.020  1.396
 2D6  C6   C5   aromatic  1.377  0.020  1.377
 2D6  C13  N3   single    1.376  0.020  1.376
 2D6  C13  C14  aromatic  1.404  0.020  1.404
 2D6  C22  C23  single    1.525  0.020  1.525
 2D6  N3   C11  double    1.279  0.020  1.279
 2D6  C2   C3   aromatic  1.384  0.020  1.384
 2D6  C15  C14  aromatic  1.397  0.020  1.397
 2D6  C5   C4   aromatic  1.398  0.020  1.398
 2D6  C14  C12  single    1.458  0.020  1.458
 2D6  C3   C4   aromatic  1.392  0.020  1.392
 2D6  C11  S1   single    1.748  0.020  1.748
 2D6  C11  N2   single    1.365  0.020  1.365
 2D6  C4   C7   single    1.425  0.020  1.425
 2D6  C12  N2   single    1.381  0.020  1.381
 2D6  C12  O3   double    1.215  0.020  1.215
 2D6  C7   N1   triple    1.152  0.020  1.152
 2D6  N4   H1   single    0.860  0.020  1.020
 2D6  C9   H2   single    0.970  0.020  1.090
 2D6  C9   H3   single    0.970  0.020  1.090
 2D6  C10  H4   single    0.970  0.020  1.090
 2D6  C10  H5   single    0.970  0.020  1.090
 2D6  N2   H6   single    0.860  0.020  1.020
 2D6  C15  H7   single    0.930  0.020  1.080
 2D6  C16  H8   single    0.930  0.020  1.080
 2D6  C17  H9   single    0.930  0.020  1.080
 2D6  C18  H10  single    0.930  0.020  1.080
 2D6  C19  H11  single    0.970  0.020  1.090
 2D6  C19  H12  single    0.970  0.020  1.090
 2D6  C20  H13  single    0.970  0.020  1.090
 2D6  C20  H14  single    0.970  0.020  1.090
 2D6  C21  H15  single    0.970  0.020  1.090
 2D6  C22  H16  single    0.970  0.020  1.090
 2D6  C22  H17  single    0.970  0.020  1.090
 2D6  C23  H18  single    0.970  0.020  1.090
 2D6  C23  H19  single    0.970  0.020  1.090
 2D6  C24  H20  single    0.970  0.020  1.090
 2D6  C2   H21  single    0.930  0.020  1.080
 2D6  C3   H22  single    0.930  0.020  1.080
 2D6  C5   H23  single    0.930  0.020  1.080
 2D6  C6   H24  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
 2D6  H1   N4   C21  117.53  3.000
 2D6  H1   N4   C8   118.10  3.000
 2D6  C21  N4   C8   123.99  3.000
 2D6  C9   C8   O2   122.21  3.000
 2D6  C9   C8   N4   114.42  3.000
 2D6  O2   C8   N4   123.37  3.000
 2D6  H3   C9   H2   106.53  3.000
 2D6  H3   C9   C10  110.29  3.000
 2D6  H2   C9   C10  110.74  3.000
 2D6  H3   C9   C8   107.66  3.000
 2D6  H2   C9   C8   110.22  3.000
 2D6  C10  C9   C8   111.24  3.000
 2D6  H5   C10  H4   108.65  3.000
 2D6  H5   C10  S1   109.04  3.000
 2D6  H4   C10  S1   108.74  3.000
 2D6  H5   C10  C9   111.32  3.000
 2D6  H4   C10  C9   111.42  3.000
 2D6  S1   C10  C9   107.61  3.000
 2D6  C11  S1   C10  101.08  3.000
 2D6  N3   C11  N2   123.93  3.000
 2D6  N2   C11  S1   113.97  3.000
 2D6  N3   C11  S1   122.11  3.000
 2D6  H6   N2   C12  116.20  3.000
 2D6  H6   N2   C11  119.95  3.000
 2D6  C12  N2   C11  123.85  3.000
 2D6  C14  C12  O3   125.94  3.000
 2D6  O3   C12  N2   120.89  3.000
 2D6  C14  C12  N2   113.17  3.000
 2D6  C13  N3   C11  117.65  3.000
 2D6  C18  C13  C14  118.84  3.000
 2D6  C14  C13  N3   122.45  3.000
 2D6  C18  C13  N3   118.71  3.000
 2D6  C15  C14  C13  120.47  3.000
 2D6  C15  C14  C12  120.56  3.000
 2D6  C13  C14  C12  118.96  3.000
 2D6  H7   C15  C16  120.43  3.000
 2D6  H7   C15  C14  119.58  3.000
 2D6  C16  C15  C14  119.99  3.000
 2D6  H8   C16  C17  120.03  3.000
 2D6  H8   C16  C15  120.22  3.000
 2D6  C17  C16  C15  119.76  3.000
 2D6  H9   C17  C18  119.55  3.000
 2D6  H9   C17  C16  119.64  3.000
 2D6  C18  C17  C16  120.80  3.000
 2D6  H10  C18  C17  121.06  3.000
 2D6  H10  C18  C13  118.81  3.000
 2D6  C17  C18  C13  120.14  3.000
 2D6  H12  C19  H11  107.17  3.000
 2D6  H12  C19  C24  109.30  3.000
 2D6  H11  C19  C24  110.00  3.000
 2D6  H12  C19  C20  109.74  3.000
 2D6  H11  C19  C20  109.79  3.000
 2D6  C24  C19  C20  110.78  3.000
 2D6  H14  C20  H13  106.61  3.000
 2D6  H14  C20  C21  109.63  3.000
 2D6  H13  C20  C21  110.01  3.000
 2D6  H14  C20  C19  109.30  3.000
 2D6  H13  C20  C19  109.76  3.000
 2D6  C21  C20  C19  111.41  3.000
 2D6  H15  C21  C22  108.51  3.000
 2D6  H15  C21  C20  108.29  3.000
 2D6  C22  C21  C20  110.83  3.000
 2D6  H15  C21  N4   107.33  3.000
 2D6  C22  C21  N4   111.99  3.000
 2D6  C20  C21  N4   109.76  3.000
 2D6  H17  C22  H16  106.60  3.000
 2D6  H17  C22  C23  109.98  3.000
 2D6  H16  C22  C23  109.68  3.000
 2D6  H17  C22  C21  109.16  3.000
 2D6  H16  C22  C21  109.93  3.000
 2D6  C23  C22  C21  111.37  3.000
 2D6  H19  C23  H18  106.48  3.000
 2D6  H19  C23  C24  111.55  3.000
 2D6  H18  C23  C24  108.78  3.000
 2D6  H19  C23  C22  109.62  3.000
 2D6  H18  C23  C22  109.88  3.000
 2D6  C24  C23  C22  110.45  3.000
 2D6  H20  C24  O1   109.65  3.000
 2D6  H20  C24  C23  109.74  3.000
 2D6  O1   C24  C23  111.63  3.000
 2D6  H20  C24  C19  108.02  3.000
 2D6  C23  C24  C19  110.84  3.000
 2D6  O1   C24  C19  106.85  3.000
 2D6  C1   O1   C24  121.17  3.000
 2D6  C6   C1   C2   119.20  3.000
 2D6  C2   C1   O1   125.06  3.000
 2D6  C6   C1   O1   115.74  3.000
 2D6  H21  C2   C3   118.06  3.000
 2D6  H21  C2   C1   122.01  3.000
 2D6  C3   C2   C1   119.93  3.000
 2D6  H22  C3   C4   120.06  3.000
 2D6  H22  C3   C2   119.10  3.000
 2D6  C4   C3   C2   120.84  3.000
 2D6  C7   C4   C5   120.60  3.000
 2D6  C7   C4   C3   120.21  3.000
 2D6  C5   C4   C3   119.18  3.000
 2D6  H23  C5   C6   119.75  3.000
 2D6  H23  C5   C4   120.04  3.000
 2D6  C6   C5   C4   120.21  3.000
 2D6  H24  C6   C5   120.01  3.000
 2D6  H24  C6   C1   119.34  3.000
 2D6  C5   C6   C1   120.64  3.000
 2D6  N1   C7   C4   180.00  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
 2D6  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 2D6  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 2D6  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 2D6  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 2D6  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 2D6  CONST_06  C18  C13  C14  C15     0.00   0.0  0
 2D6  CONST_07  C4   C5   C6   C1      0.00   0.0  0
 2D6  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 2D6  CONST_09  C5   C6   C1   C2      0.00   0.0  0
 2D6  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 2D6  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 2D6  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 2D6  CONST_13  C14  C12  N2   C11     0.00   0.0  0
 2D6  CONST_14  C13  N3   C11  N2      0.00   0.0  0
 2D6  CONST_15  N3   C11  N2   C12     0.00   0.0  0
 2D6  CONST_16  C5   C6   C1   O1    180.00   0.0  0
 2D6  CONST_17  C3   C2   C1   O1    180.00   0.0  0
 2D6  CONST_18  C7   C4   C3   C2    180.00   0.0  0
 2D6  CONST_19  C7   C4   C5   C6    180.00   0.0  0
 2D6  CONST_20  C13  N3   C11  S1    180.00   0.0  0
 2D6  CONST_21  C12  N2   C11  S1    180.00   0.0  0
 2D6  CONST_22  O3   C12  N2   C11   180.00   0.0  0
 2D6  CONST_23  H7   C15  C14  C12     0.00   0.0  0
 2D6  CONST_24  H10  C18  C13  N3      0.00   0.0  0
 2D6  CONST_25  H9   C17  C18  C13   180.00   0.0  0
 2D6  CONST_26  H8   C16  C15  C14   180.00   0.0  0
 2D6  CONST_27  H23  C5   C6   C1    180.00   0.0  0
 2D6  CONST_28  H22  C3   C2   C1    180.00   0.0  0
 2D6  CONST_29  H24  C6   C1   C2    180.00   0.0  0
 2D6  CONST_30  H21  C2   C3   C4    180.00   0.0  0
 2D6  CONST_31  H6   N2   C11  N3    180.00   0.0  0
 2D6  CONST_32  C21  N4   C8   O2      0.00   0.0  0
 2D6  CONST_33  C21  N4   C8   C9    180.00   0.0  0
 2D6  CONST_34  H1   N4   C8   O2    180.00   0.0  0
 2D6  Var_01    C24  C19  C20  C21    56.09  30.0  1
 2D6  Var_02    C24  C23  C22  C21   -56.39  30.0  1
 2D6  Var_03    C6   C1   O1   C24  -177.40  30.0  2
 2D6  Var_04    N3   C11  S1   C10     0.79  30.0  3
 2D6  Var_05    H4   C10  S1   C11    51.37  30.0  2
 2D6  Var_06    C10  C9   C8   N4   -155.12  30.0  3
 2D6  Var_07    S1   C10  C9   C8   -178.85  30.0  3

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
 2D6  chir_01  C21  C20  N4   C22  negativ
 2D6  chir_02  C24  O1   C23  C19  negativ

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
 2D6  plan-1  O1   0.020
 2D6  plan-1  C1   0.020
 2D6  plan-1  C2   0.020
 2D6  plan-1  C3   0.020
 2D6  plan-1  C4   0.020
 2D6  plan-1  C5   0.020
 2D6  plan-1  C6   0.020
 2D6  plan-1  C7   0.020
 2D6  plan-1  N1   0.020
 2D6  plan-1  H21  0.020
 2D6  plan-1  H22  0.020
 2D6  plan-1  H23  0.020
 2D6  plan-1  H24  0.020
 2D6  plan-2  S1   0.020
 2D6  plan-2  C11  0.020
 2D6  plan-2  N2   0.020
 2D6  plan-2  C12  0.020
 2D6  plan-2  O3   0.020
 2D6  plan-2  N3   0.020
 2D6  plan-2  C13  0.020
 2D6  plan-2  C14  0.020
 2D6  plan-2  C15  0.020
 2D6  plan-2  C16  0.020
 2D6  plan-2  C17  0.020
 2D6  plan-2  C18  0.020
 2D6  plan-2  H6   0.020
 2D6  plan-2  H7   0.020
 2D6  plan-2  H8   0.020
 2D6  plan-2  H9   0.020
 2D6  plan-2  H10  0.020
 2D6  plan-3  N4   0.020
 2D6  plan-3  C8   0.020
 2D6  plan-3  O2   0.020
 2D6  plan-3  C9   0.020
 2D6  plan-3  C21  0.020
 2D6  plan-3  H1   0.020

