# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 16:57:07 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-[(3~{R})-12-(4-morpholin-4-ylcyclohexyl)oxy-7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9,11-tetraen-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C[C@H]1CCc2sc3ncnc(O[C@@H]4CC[C@H](CC4)N5CCOCC5)c3c12
#
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
 CJQ  CJQ  2-[(3~{R})-12-(4-morpholin-4-ylcyclohexyl)oxy-7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9,11-tetraen-3-yl]ethanamide  ligand  57  29  .  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_CJQ
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
 CJQ  C1   C  CR6   0   0.516   1.3018   1.4482  -0.0439
 CJQ  C2   C  CR56  0  -0.040   2.6704   1.1539   0.0824
 CJQ  C3   C  CR55  0   0.258   3.3900  -0.0500   0.3339
 CJQ  C7   C  CH2   0  -0.460   4.3968  -2.0798   1.0050
 CJQ  C8   C  CR15  0  -0.336   3.0475  -1.4992   0.5052
 CJQ  C9   C  CH2   0  -0.567   2.5795  -2.1159  -0.8154
 CJQ  C10  C  C     0   0.521   2.1329  -3.5524  -0.6413
 CJQ  C11  C  CH1   0   0.053  -0.9524   0.6338  -0.1201
 CJQ  C12  C  CH2   0  -0.468  -1.6128   1.1253   1.1585
 CJQ  C13  C  CH2   0  -0.450  -3.1237   1.2286   0.9627
 CJQ  C14  C  CH1   0  -0.047  -3.7127  -0.1137   0.5322
 CJQ  C15  C  CH2   0  -0.468  -3.0262  -0.6015  -0.7508
 CJQ  C16  C  CH2   0  -0.451  -1.5164  -0.7074  -0.5550
 CJQ  C19  C  CH2   0  -0.184  -7.2881  -1.2363   0.6813
 CJQ  C20  C  CH2   0  -0.304  -5.7870  -1.3824   0.5167
 CJQ  O    O  O     0  -0.496   1.4129  -3.8939   0.2873
 CJQ  N2   N  NH2   0  -0.802   2.5680  -4.4075  -1.5775
 CJQ  C6   C  CH2   0  -0.484   5.5117  -1.0990   0.5691
 CJQ  C4   C  CR55  0  -0.243   4.7250   0.1510   0.3622
 CJQ  C5   C  CR56  0  -0.018   3.5197   2.2531  -0.0661
 CJQ  S    S  S2    0   0.224   5.1904   1.7953   0.0924
 CJQ  N1   N  N     0  -0.421   3.1151   3.4988  -0.2989
 CJQ  C    C  CR16  0   0.044   1.8097   3.6351  -0.3926
 CJQ  N    N  N     0  -0.460   0.8889   2.6751  -0.2785
 CJQ  O1   O  O2    0  -0.469   0.4600   0.4413   0.0711
 CJQ  N3   N  NT    0  -0.439  -5.1678  -0.0713   0.4849
 CJQ  O2   O  O2    0  -0.487  -7.8465  -0.4537  -0.3514
 CJQ  C18  C  CH2   0  -0.181  -7.2432   0.8207  -0.3972
 CJQ  C17  C  CH2   0  -0.314  -5.7398   0.7236  -0.5855
 CJQ  H1   H  HCH2  0   0.257   4.3794  -2.1345   2.0939
 CJQ  H2   H  HCH2  0   0.244   4.5786  -3.0902   0.6367
 CJQ  H3   H  HCR5  0   0.261   2.2627  -1.6439   1.2495
 CJQ  H4   H  HCH2  0   0.284   1.7184  -1.5570  -1.1927
 CJQ  H5   H  HCH2  0   0.255   3.3660  -2.0305  -1.5695
 CJQ  H6   H  HCH1  0   0.237  -1.1086   1.3678  -0.9165
 CJQ  H7   H  HCH2  0   0.228  -1.3929   0.4216   1.9681
 CJQ  H8   H  HCH2  0   0.250  -1.2050   2.0954   1.4475
 CJQ  H9   H  HCH2  0   0.241  -3.5986   1.5541   1.8904
 CJQ  H10  H  HCH2  0   0.223  -3.3325   1.9979   0.2118
 CJQ  H11  H  HCH1  0   0.223  -3.4674  -0.8325   1.3251
 CJQ  H12  H  HCH2  0   0.245  -3.4212  -1.5748  -1.0512
 CJQ  H13  H  HCH2  0   0.224  -3.2369   0.0914  -1.5722
 CJQ  H14  H  HCH2  0   0.245  -1.0335  -1.0317  -1.4799
 CJQ  H15  H  HCH2  0   0.229  -1.2945  -1.4618   0.2075
 CJQ  H17  H  HCH2  0   0.197  -7.5040  -0.7885   1.6619
 CJQ  H18  H  HCH2  0   0.238  -5.3922  -1.9478   1.3646
 CJQ  H19  H  HCH2  0   0.196  -5.5835  -1.9756  -0.3904
 CJQ  H20  H  HNH2  0   0.406   3.1570  -4.1118  -2.3363
 CJQ  H21  H  HNH2  0   0.398   2.2826  -5.3733  -1.5613
 CJQ  H22  H  HCH2  0   0.263   6.2914  -1.0014   1.3253
 CJQ  H23  H  HCH2  0   0.259   6.0019  -1.4095  -0.3578
 CJQ  H24  H  HCR6  0   0.265   1.4347   4.6341  -0.5820
 CJQ  H26  H  HCH2  0   0.233  -7.6919   1.3630  -1.2311
 CJQ  H27  H  HCH2  0   0.197  -7.4574   1.3791   0.5256
 CJQ  H28  H  HCH2  0   0.242  -5.3279   1.7346  -0.5657
 CJQ  H29  H  HCH2  0   0.202  -5.5277   0.3075  -1.5837
 CJQ  H16  H  HCH2  0   0.233  -7.7687  -2.2154   0.6454

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
 CJQ  N1   C    aromatic  1.316  0.020  1.316
 CJQ  N1   C5   aromatic  1.330  0.020  1.330
 CJQ  C    N    aromatic  1.335  0.020  1.335
 CJQ  S    C5   aromatic  1.740  0.020  1.740
 CJQ  S    C4   aromatic  1.730  0.020  1.730
 CJQ  C5   C2   aromatic  1.397  0.020  1.397
 CJQ  N    C1   aromatic  1.316  0.020  1.316
 CJQ  C2   C1   aromatic  1.406  0.020  1.406
 CJQ  C2   C3   aromatic  1.425  0.020  1.425
 CJQ  C1   O1   single    1.317  0.020  1.317
 CJQ  C4   C3   aromatic  1.350  0.020  1.350
 CJQ  C4   C6   single    1.491  0.020  1.491
 CJQ  C3   C8   single    1.499  0.020  1.499
 CJQ  C6   C7   single    1.548  0.020  1.548
 CJQ  O1   C11  single    1.438  0.020  1.438
 CJQ  C11  C16  single    1.519  0.020  1.519
 CJQ  C11  C12  single    1.521  0.020  1.521
 CJQ  C16  C15  single    1.526  0.020  1.526
 CJQ  C15  C14  single    1.535  0.020  1.535
 CJQ  C8   C7   single    1.552  0.020  1.552
 CJQ  C8   C9   single    1.531  0.020  1.531
 CJQ  C17  C18  single    1.518  0.020  1.518
 CJQ  C17  N3   single    1.451  0.020  1.451
 CJQ  C12  C13  single    1.527  0.020  1.527
 CJQ  C9   C10  single    1.514  0.020  1.514
 CJQ  C18  O2   single    1.411  0.020  1.411
 CJQ  C13  C14  single    1.528  0.020  1.528
 CJQ  C14  N3   single    1.456  0.020  1.456
 CJQ  N3   C20  single    1.450  0.020  1.450
 CJQ  O2   C19  single    1.411  0.020  1.411
 CJQ  C10  N2   single    1.340  0.020  1.340
 CJQ  C10  O    double    1.224  0.020  1.224
 CJQ  C20  C19  single    1.517  0.020  1.517
 CJQ  C7   H1   single    0.970  0.020  1.090
 CJQ  C7   H2   single    0.970  0.020  1.090
 CJQ  C8   H3   single    0.970  0.020  1.090
 CJQ  C9   H4   single    0.970  0.020  1.090
 CJQ  C9   H5   single    0.970  0.020  1.090
 CJQ  C11  H6   single    0.970  0.020  1.090
 CJQ  C12  H7   single    0.970  0.020  1.090
 CJQ  C12  H8   single    0.970  0.020  1.090
 CJQ  C13  H9   single    0.970  0.020  1.090
 CJQ  C13  H10  single    0.970  0.020  1.090
 CJQ  C14  H11  single    0.970  0.020  1.090
 CJQ  C15  H12  single    0.970  0.020  1.090
 CJQ  C15  H13  single    0.970  0.020  1.090
 CJQ  C16  H14  single    0.970  0.020  1.090
 CJQ  C16  H15  single    0.970  0.020  1.090
 CJQ  C19  H16  single    0.970  0.020  1.090
 CJQ  C19  H17  single    0.970  0.020  1.090
 CJQ  C20  H18  single    0.970  0.020  1.090
 CJQ  C20  H19  single    0.970  0.020  1.090
 CJQ  N2   H20  single    0.860  0.020  1.020
 CJQ  N2   H21  single    0.860  0.020  1.020
 CJQ  C6   H22  single    0.970  0.020  1.090
 CJQ  C6   H23  single    0.970  0.020  1.090
 CJQ  C    H24  single    0.930  0.020  1.080
 CJQ  C18  H26  single    0.970  0.020  1.090
 CJQ  C18  H27  single    0.970  0.020  1.090
 CJQ  C17  H28  single    0.970  0.020  1.090
 CJQ  C17  H29  single    0.970  0.020  1.090

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
 CJQ  O1   C1   N    121.86  3.000
 CJQ  O1   C1   C2   117.02  3.000
 CJQ  N    C1   C2   121.12  3.000
 CJQ  C5   C2   C3   112.12  3.000
 CJQ  C3   C2   C1   133.20  3.000
 CJQ  C5   C2   C1   114.68  3.000
 CJQ  C4   C3   C8   111.56  3.000
 CJQ  C8   C3   C2   136.19  3.000
 CJQ  C4   C3   C2   112.16  3.000
 CJQ  H2   C7   H1   107.06  3.000
 CJQ  H2   C7   C6   111.84  3.000
 CJQ  H1   C7   C6   108.94  3.000
 CJQ  H2   C7   C8   112.51  3.000
 CJQ  H1   C7   C8   109.06  3.000
 CJQ  C6   C7   C8   107.38  3.000
 CJQ  H3   C8   C9   108.37  3.000
 CJQ  H3   C8   C7   110.85  3.000
 CJQ  C9   C8   C7   113.15  3.000
 CJQ  H3   C8   C3   111.74  3.000
 CJQ  C9   C8   C3   111.15  3.000
 CJQ  C7   C8   C3   101.53  3.000
 CJQ  H5   C9   H4   106.78  3.000
 CJQ  H5   C9   C10  111.45  3.000
 CJQ  H4   C9   C10  106.99  3.000
 CJQ  H5   C9   C8   110.10  3.000
 CJQ  H4   C9   C8   109.42  3.000
 CJQ  C10  C9   C8   111.91  3.000
 CJQ  N2   C10  O    122.88  3.000
 CJQ  O    C10  C9   121.70  3.000
 CJQ  N2   C10  C9   115.41  3.000
 CJQ  H6   C11  O1   109.06  3.000
 CJQ  H6   C11  C16  109.33  3.000
 CJQ  O1   C11  C16  106.54  3.000
 CJQ  H6   C11  C12  109.46  3.000
 CJQ  C16  C11  C12  111.41  3.000
 CJQ  O1   C11  C12  110.98  3.000
 CJQ  H8   C12  H7   107.48  3.000
 CJQ  H8   C12  C13  110.10  3.000
 CJQ  H7   C12  C13  109.69  3.000
 CJQ  H8   C12  C11  110.35  3.000
 CJQ  H7   C12  C11  109.07  3.000
 CJQ  C13  C12  C11  110.11  3.000
 CJQ  H10  C13  H9   106.87  3.000
 CJQ  H10  C13  C14  110.52  3.000
 CJQ  H9   C13  C14  109.50  3.000
 CJQ  H10  C13  C12  108.91  3.000
 CJQ  H9   C13  C12  109.97  3.000
 CJQ  C14  C13  C12  110.99  3.000
 CJQ  H11  C14  N3   105.41  3.000
 CJQ  H11  C14  C15  107.19  3.000
 CJQ  N3   C14  C15  115.41  3.000
 CJQ  H11  C14  C13  106.59  3.000
 CJQ  N3   C14  C13  111.64  3.000
 CJQ  C15  C14  C13  110.02  3.000
 CJQ  H13  C15  H12  106.73  3.000
 CJQ  H13  C15  C16  109.30  3.000
 CJQ  H12  C15  C16  109.34  3.000
 CJQ  H13  C15  C14  109.87  3.000
 CJQ  H12  C15  C14  110.57  3.000
 CJQ  C16  C15  C14  110.94  3.000
 CJQ  H15  C16  H14  107.17  3.000
 CJQ  H15  C16  C15  109.73  3.000
 CJQ  H14  C16  C15  110.44  3.000
 CJQ  H15  C16  C11  109.49  3.000
 CJQ  H14  C16  C11  109.91  3.000
 CJQ  C15  C16  C11  110.06  3.000
 CJQ  H17  C19  H16  107.96  3.000
 CJQ  H17  C19  O2   110.43  3.000
 CJQ  H16  C19  O2   107.41  3.000
 CJQ  H17  C19  C20  109.29  3.000
 CJQ  H16  C19  C20  110.23  3.000
 CJQ  O2   C19  C20  111.44  3.000
 CJQ  H19  C20  H18  107.05  3.000
 CJQ  H19  C20  N3   112.92  3.000
 CJQ  H18  C20  N3   109.30  3.000
 CJQ  H19  C20  C19  108.88  3.000
 CJQ  H18  C20  C19  108.85  3.000
 CJQ  N3   C20  C19  109.74  3.000
 CJQ  H21  N2   H20  117.41  3.000
 CJQ  H21  N2   C10  120.56  3.000
 CJQ  H20  N2   C10  122.00  3.000
 CJQ  H23  C6   H22  107.02  3.000
 CJQ  H23  C6   C4   110.90  3.000
 CJQ  H22  C6   C4   113.47  3.000
 CJQ  H23  C6   C7   112.44  3.000
 CJQ  H22  C6   C7   112.12  3.000
 CJQ  C4   C6   C7   100.97  3.000
 CJQ  S    C4   C6   132.56  3.000
 CJQ  C6   C4   C3   113.55  3.000
 CJQ  S    C4   C3   113.84  3.000
 CJQ  N1   C5   S    123.67  3.000
 CJQ  S    C5   C2   111.54  3.000
 CJQ  N1   C5   C2   124.79  3.000
 CJQ  C5   S    C4    90.34  3.000
 CJQ  C    N1   C5   114.28  3.000
 CJQ  H24  C    N    116.05  3.000
 CJQ  H24  C    N1   116.82  3.000
 CJQ  N    C    N1   127.13  3.000
 CJQ  C    N    C1   117.99  3.000
 CJQ  C11  O1   C1   120.90  3.000
 CJQ  C17  N3   C20  110.07  3.000
 CJQ  C20  N3   C14  113.55  3.000
 CJQ  C17  N3   C14  115.71  3.000
 CJQ  C18  O2   C19  110.83  3.000
 CJQ  H27  C18  H26  107.99  3.000
 CJQ  H27  C18  C17  109.24  3.000
 CJQ  H26  C18  C17  110.13  3.000
 CJQ  H27  C18  O2   110.37  3.000
 CJQ  H26  C18  O2   107.33  3.000
 CJQ  C17  C18  O2   111.70  3.000
 CJQ  H29  C17  H28  107.06  3.000
 CJQ  H29  C17  C18  109.09  3.000
 CJQ  H28  C17  C18  108.18  3.000
 CJQ  H29  C17  N3   112.68  3.000
 CJQ  H28  C17  N3   110.20  3.000
 CJQ  C18  C17  N3   109.51  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
 CJQ  CONST_01  N1   C    N    C1      0.00   0.0  0
 CJQ  CONST_02  N1   C5   C2   C1      0.00   0.0  0
 CJQ  CONST_03  S    C5   C2   C1    180.00   0.0  0
 CJQ  CONST_04  C4   C3   C2   C1    180.00   0.0  0
 CJQ  CONST_05  C    N1   C5   C2      0.00   0.0  0
 CJQ  CONST_06  C4   S    C5   C2      0.00   0.0  0
 CJQ  CONST_07  C    N    C1   C2      0.00   0.0  0
 CJQ  CONST_08  S    C4   C3   C2      0.00   0.0  0
 CJQ  CONST_09  N1   C5   C2   C3    180.00   0.0  0
 CJQ  CONST_10  S    C5   C2   C3      0.00   0.0  0
 CJQ  CONST_11  N    C1   C2   C3    180.00   0.0  0
 CJQ  CONST_12  C5   S    C4   C3      0.00   0.0  0
 CJQ  CONST_13  N1   C5   S    C4    180.00   0.0  0
 CJQ  CONST_14  C5   C2   C3   C4      0.00   0.0  0
 CJQ  CONST_15  N    C    N1   C5      0.00   0.0  0
 CJQ  CONST_16  N    C1   C2   C5      0.00   0.0  0
 CJQ  CONST_17  C    N1   C5   S     180.00   0.0  0
 CJQ  CONST_18  O1   C1   C2   C3      0.00   0.0  0
 CJQ  CONST_19  O1   C1   C2   C5    180.00   0.0  0
 CJQ  CONST_20  O1   C1   N    C     180.00   0.0  0
 CJQ  CONST_21  H24  C    N    C1    180.00   0.0  0
 CJQ  CONST_22  H20  N2   C10  C9      0.00   0.0  0
 CJQ  CONST_23  H21  N2   C10  C9    180.00   0.0  0
 CJQ  Var_01    C7   C6   C4   C3    -13.04  30.0  1
 CJQ  Var_02    C4   C6   C7   C8     21.15  30.0  1
 CJQ  Var_03    C14  C15  C16  C11   -57.10  30.0  1
 CJQ  Var_04    C14  C13  C12  C11    57.07  30.0  1
 CJQ  Var_05    C18  C17  N3   C14  -172.62  30.0  1
 CJQ  Var_06    C19  C20  N3   C14   171.25  30.0  1
 CJQ  Var_07    C17  C18  O2   C19    57.39  30.0  1
 CJQ  Var_08    O2   C18  C17  N3    -57.25  30.0  1
 CJQ  Var_09    O2   C19  C20  N3     57.40  30.0  1
 CJQ  Var_10    N    C1   O1   C11     3.01  30.0  2
 CJQ  Var_11    N2   C10  C9   C8   -135.73  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
 CJQ  chir_01  C8   C3  C7   C9   positiv
 CJQ  chir_02  C11  O1  C16  C12  negativ
 CJQ  chir_03  C14  N3  C15  C13  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
 CJQ  plan-1  C9   0.020
 CJQ  plan-1  C10  0.020
 CJQ  plan-1  O    0.020
 CJQ  plan-1  N2   0.020
 CJQ  plan-1  H20  0.020
 CJQ  plan-1  H21  0.020
 CJQ  plan-2  C1   0.020
 CJQ  plan-2  C2   0.020
 CJQ  plan-2  C3   0.020
 CJQ  plan-2  C8   0.020
 CJQ  plan-2  C6   0.020
 CJQ  plan-2  C4   0.020
 CJQ  plan-2  C5   0.020
 CJQ  plan-2  S    0.020
 CJQ  plan-2  N1   0.020
 CJQ  plan-2  C    0.020
 CJQ  plan-2  N    0.020
 CJQ  plan-2  O1   0.020
 CJQ  plan-2  H24  0.020

