# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 13:58:21 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2[nH]c3cc(NC(=O)[C@H](N)C4CCCCC4)cc5C(=O)NN=Cc2c35
#
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
 9DB  9DB  (2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide  ligand  56  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9DB
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
 9DB  C1   C  CR15  0   0.045  -4.8226   2.4460   0.1267
 9DB  C2   C  CR5   0  -0.202  -4.6181   1.1100  -0.1748
 9DB  C3   C  CR15  0  -0.108  -5.9159   0.6239  -0.4370
 9DB  C4   C  CR5   0   0.373  -3.3569   0.4090  -0.2198
 9DB  C5   C  CR56  0   0.347  -1.1463   0.1958  -0.5186
 9DB  C6   C  CR16  0  -0.370   0.2023   0.4145  -0.7636
 9DB  C7   C  CR6   0   0.349   1.0552  -0.6711  -0.6435
 9DB  C8   C  C     0   0.508   3.4409  -0.8675  -0.1117
 9DB  C18  C  C     0   0.499  -1.2255  -3.5194   0.2935
 9DB  N5   N  NH1   0  -0.537  -2.5333  -3.8153   0.5821
 9DB  N6   N  N     0  -0.243  -3.7137  -3.1669   0.7699
 9DB  C19  C  C1    0  -0.187  -3.9360  -1.9347   0.5285
 9DB  C20  C  CR5   0  -0.129  -3.0509  -0.9157   0.0476
 9DB  N1   N  N     0  -0.269  -6.8174   1.5737  -0.3041
 9DB  N    N  NR5   0  -0.265  -6.1394   2.6654   0.0380
 9DB  C    C  CH3   0  -0.505  -6.8383   3.9068   0.2749
 9DB  C21  C  CR56  0   0.171  -1.6475  -1.0622  -0.1477
 9DB  N2   N  NR15  0  -0.765  -2.2055   1.0580  -0.5539
 9DB  C17  C  CR6   0  -0.115  -0.7758  -2.1443  -0.0372
 9DB  C16  C  CR16  0  -0.346   0.5695  -1.9387  -0.2910
 9DB  N3   N  NH1   0  -0.740   2.4233  -0.4877  -0.9219
 9DB  O    O  O     0  -0.470   3.2745  -1.4929   0.9220
 9DB  C9   C  CH1   0  -0.203   4.8336  -0.4627  -0.5930
 9DB  N4   N  NH2   0  -0.776   5.7526  -1.5842  -0.5812
 9DB  C10  C  CH1   0  -0.225   5.3732   0.6918   0.2667
 9DB  C15  C  CH2   0  -0.410   6.7270   1.1659  -0.2642
 9DB  C14  C  CH2   0  -0.433   7.2871   2.3324   0.5434
 9DB  C13  C  CH2   0  -0.430   6.3018   3.4934   0.5959
 9DB  C12  C  CH2   0  -0.427   4.9558   3.0331   1.1405
 9DB  C11  C  CH2   0  -0.439   4.3903   1.8631   0.3405
 9DB  H1   H  HCR5  0   0.303  -4.1311   3.2256   0.4048
 9DB  H2   H  HCR5  0   0.267  -6.2091  -0.3694  -0.7408
 9DB  H3   H  HCR6  0   0.282   0.5778   1.3930  -1.0358
 9DB  H4   H  HNH1  0   0.408  -2.6469  -4.7965   0.7904
 9DB  H5   H  H     0   0.254  -4.9565  -1.6427   0.7512
 9DB  H6   H  HCH3  0   0.265  -7.3695   4.2154  -0.6230
 9DB  H7   H  HCH3  0   0.265  -7.5484   3.7881   1.0901
 9DB  H8   H  HCH3  0   0.262  -6.1163   4.6726   0.5411
 9DB  H9   H  HNR5  0   0.422  -2.1564   2.0213  -0.8469
 9DB  H10  H  HCR6  0   0.269   1.2528  -2.7728  -0.2426
 9DB  H11  H  HNH1  0   0.410   2.6517   0.1021  -1.7077
 9DB  H12  H  HCH1  0   0.244   4.7641  -0.1039  -1.6264
 9DB  H13  H  HNH2  0   0.342   5.7782  -1.9920   0.3462
 9DB  H14  H  HNH2  0   0.353   5.4223  -2.3135  -1.2013
 9DB  H16  H  HCH1  0   0.218   5.5182   0.3074   1.2867
 9DB  H17  H  HCH2  0   0.234   7.4329   0.3351  -0.2689
 9DB  H18  H  HCH2  0   0.203   6.6059   1.4791  -1.3087
 9DB  H19  H  HCH2  0   0.208   7.5096   1.9970   1.5624
 9DB  H20  H  HCH2  0   0.226   8.2374   2.6563   0.1118
 9DB  H21  H  HCH2  0   0.226   6.6996   4.3075   1.2069
 9DB  H22  H  HCH2  0   0.207   6.1664   3.8985  -0.4135
 9DB  H23  H  HCH2  0   0.210   5.0742   2.7250   2.1851
 9DB  H24  H  HCH2  0   0.228   4.2403   3.8587   1.1413
 9DB  H25  H  HCH2  0   0.211   4.1490   2.1978  -0.6759
 9DB  H26  H  HCH2  0   0.235   3.4459   1.5520   0.7951
 9DB  O1   O  O     0  -0.453  -0.4288  -4.4438   0.3070

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
 9DB  C    N    single    1.444  0.020  1.444
 9DB  N    C1   aromatic  1.338  0.020  1.338
 9DB  N    N1   aromatic  1.330  0.020  1.330
 9DB  C1   C2   aromatic  1.385  0.020  1.385
 9DB  N4   C9   single    1.450  0.020  1.450
 9DB  N1   C3   aromatic  1.316  0.020  1.316
 9DB  C2   C3   aromatic  1.410  0.020  1.410
 9DB  C2   C4   single    1.444  0.020  1.444
 9DB  N2   C4   aromatic  1.363  0.020  1.363
 9DB  N2   C5   aromatic  1.366  0.020  1.366
 9DB  O    C8   double    1.220  0.020  1.220
 9DB  C9   C8   single    1.528  0.020  1.528
 9DB  C9   C10  single    1.537  0.020  1.537
 9DB  C8   N3   single    1.355  0.020  1.355
 9DB  C4   C20  aromatic  1.386  0.020  1.386
 9DB  C11  C10  single    1.531  0.020  1.531
 9DB  C11  C12  single    1.526  0.020  1.526
 9DB  C6   C5   aromatic  1.388  0.020  1.388
 9DB  C6   C7   aromatic  1.386  0.020  1.386
 9DB  C5   C21  aromatic  1.404  0.020  1.404
 9DB  C10  C15  single    1.529  0.020  1.529
 9DB  C12  C13  single    1.523  0.020  1.523
 9DB  N3   C7   single    1.408  0.020  1.408
 9DB  C7   C16  aromatic  1.402  0.020  1.402
 9DB  C20  C21  aromatic  1.424  0.020  1.424
 9DB  C20  C19  single    1.433  0.020  1.433
 9DB  C21  C17  aromatic  1.394  0.020  1.394
 9DB  C15  C14  single    1.525  0.020  1.525
 9DB  C13  C14  single    1.524  0.020  1.524
 9DB  C16  C17  aromatic  1.384  0.020  1.384
 9DB  C19  N6   double    1.275  0.020  1.275
 9DB  C17  C18  single    1.484  0.020  1.484
 9DB  N6   N5   single    1.360  0.020  1.360
 9DB  C18  N5   single    1.372  0.020  1.372
 9DB  C18  O1   double    1.220  0.020  1.220
 9DB  C1   H1   single    0.930  0.020  1.080
 9DB  C3   H2   single    0.930  0.020  1.080
 9DB  C6   H3   single    0.930  0.020  1.080
 9DB  N5   H4   single    0.860  0.020  1.020
 9DB  C19  H5   single    0.930  0.020  1.080
 9DB  C    H6   single    0.970  0.020  1.090
 9DB  C    H7   single    0.970  0.020  1.090
 9DB  C    H8   single    0.970  0.020  1.090
 9DB  N2   H9   single    0.860  0.020  1.020
 9DB  C16  H10  single    0.930  0.020  1.080
 9DB  N3   H11  single    0.860  0.020  1.020
 9DB  C9   H12  single    0.970  0.020  1.090
 9DB  N4   H13  single    0.890  0.020  1.040
 9DB  N4   H14  single    0.890  0.020  1.040
 9DB  C10  H16  single    0.970  0.020  1.090
 9DB  C15  H17  single    0.970  0.020  1.090
 9DB  C15  H18  single    0.970  0.020  1.090
 9DB  C14  H19  single    0.970  0.020  1.090
 9DB  C14  H20  single    0.970  0.020  1.090
 9DB  C13  H21  single    0.970  0.020  1.090
 9DB  C13  H22  single    0.970  0.020  1.090
 9DB  C12  H23  single    0.970  0.020  1.090
 9DB  C12  H24  single    0.970  0.020  1.090
 9DB  C11  H25  single    0.970  0.020  1.090
 9DB  C11  H26  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
 9DB  H1   C1   N    121.98  3.000
 9DB  H1   C1   C2   131.21  3.000
 9DB  N    C1   C2   106.80  3.000
 9DB  C4   C2   C3   129.10  3.000
 9DB  C4   C2   C1   127.18  3.000
 9DB  C3   C2   C1   103.72  3.000
 9DB  H2   C3   N1   120.43  3.000
 9DB  H2   C3   C2   128.28  3.000
 9DB  N1   C3   C2   111.27  3.000
 9DB  N2   C4   C20  108.42  3.000
 9DB  C20  C4   C2   130.63  3.000
 9DB  N2   C4   C2   120.95  3.000
 9DB  N2   C5   C21  107.19  3.000
 9DB  C21  C5   C6   122.32  3.000
 9DB  N2   C5   C6   130.49  3.000
 9DB  H3   C6   C7   121.08  3.000
 9DB  H3   C6   C5   121.58  3.000
 9DB  C7   C6   C5   117.34  3.000
 9DB  N3   C7   C16  120.25  3.000
 9DB  C16  C7   C6   121.11  3.000
 9DB  N3   C7   C6   118.61  3.000
 9DB  C9   C8   O    121.81  3.000
 9DB  C9   C8   N3   114.95  3.000
 9DB  O    C8   N3   123.24  3.000
 9DB  C17  C18  N5   122.39  3.000
 9DB  N5   C18  O1   117.18  3.000
 9DB  C17  C18  O1   120.43  3.000
 9DB  H4   N5   N6   109.72  3.000
 9DB  H4   N5   C18  111.12  3.000
 9DB  N6   N5   C18  138.93  3.000
 9DB  C19  N6   N5   125.87  3.000
 9DB  H5   C19  C20  117.30  3.000
 9DB  H5   C19  N6   112.66  3.000
 9DB  C20  C19  N6   130.03  3.000
 9DB  C21  C20  C19  125.55  3.000
 9DB  C19  C20  C4   127.47  3.000
 9DB  C21  C20  C4   106.82  3.000
 9DB  N    N1   C3   105.61  3.000
 9DB  C    N    N1   120.07  3.000
 9DB  N1   N    C1   112.60  3.000
 9DB  C    N    C1   127.33  3.000
 9DB  H8   C    H7   109.10  3.000
 9DB  H8   C    H6   109.08  3.000
 9DB  H7   C    H6   109.32  3.000
 9DB  H8   C    N    108.94  3.000
 9DB  H7   C    N    110.19  3.000
 9DB  H6   C    N    110.17  3.000
 9DB  C17  C21  C20  133.24  3.000
 9DB  C17  C21  C5   119.56  3.000
 9DB  C20  C21  C5   107.20  3.000
 9DB  H9   N2   C5   124.94  3.000
 9DB  H9   N2   C4   124.56  3.000
 9DB  C5   N2   C4   110.37  3.000
 9DB  C16  C17  C21  118.54  3.000
 9DB  C16  C17  C18  118.23  3.000
 9DB  C21  C17  C18  123.19  3.000
 9DB  H10  C16  C17  119.48  3.000
 9DB  H10  C16  C7   119.38  3.000
 9DB  C17  C16  C7   121.12  3.000
 9DB  H11  N3   C8   117.36  3.000
 9DB  H11  N3   C7   116.75  3.000
 9DB  C8   N3   C7   125.09  3.000
 9DB  H12  C9   C10  107.68  3.000
 9DB  H12  C9   N4   107.52  3.000
 9DB  C10  C9   N4   110.73  3.000
 9DB  H12  C9   C8   109.01  3.000
 9DB  C10  C9   C8   110.04  3.000
 9DB  N4   C9   C8   111.73  3.000
 9DB  H14  N4   H13  106.19  3.000
 9DB  H14  N4   C9   110.20  3.000
 9DB  H13  N4   C9   109.56  3.000
 9DB  H16  C10  C11  107.91  3.000
 9DB  H16  C10  C15  108.28  3.000
 9DB  C11  C10  C15  110.36  3.000
 9DB  H16  C10  C9   107.61  3.000
 9DB  C15  C10  C9   110.45  3.000
 9DB  C11  C10  C9   112.10  3.000
 9DB  H18  C15  H17  106.55  3.000
 9DB  H18  C15  C14  109.04  3.000
 9DB  H17  C15  C14  110.32  3.000
 9DB  H18  C15  C10  108.74  3.000
 9DB  H17  C15  C10  109.78  3.000
 9DB  C14  C15  C10  112.23  3.000
 9DB  H20  C14  H19  106.35  3.000
 9DB  H20  C14  C13  110.49  3.000
 9DB  H19  C14  C13  109.42  3.000
 9DB  H20  C14  C15  109.69  3.000
 9DB  H19  C14  C15  109.45  3.000
 9DB  C13  C14  C15  111.31  3.000
 9DB  H22  C13  H21  106.54  3.000
 9DB  H22  C13  C12  109.38  3.000
 9DB  H21  C13  C12  110.29  3.000
 9DB  H22  C13  C14  109.25  3.000
 9DB  H21  C13  C14  110.58  3.000
 9DB  C12  C13  C14  110.70  3.000
 9DB  H24  C12  H23  106.42  3.000
 9DB  H24  C12  C11  109.69  3.000
 9DB  H23  C12  C11  108.93  3.000
 9DB  H24  C12  C13  110.52  3.000
 9DB  H23  C12  C13  109.30  3.000
 9DB  C11  C12  C13  111.82  3.000
 9DB  H26  C11  H25  106.38  3.000
 9DB  H26  C11  C12  108.68  3.000
 9DB  H25  C11  C12  109.48  3.000
 9DB  H26  C11  C10  110.91  3.000
 9DB  H25  C11  C10  109.27  3.000
 9DB  C12  C11  C10  111.96  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
 9DB  CONST_01  C3   N1   N    C1     0.00   0.0  0
 9DB  CONST_02  N1   C3   C2   C1     0.00   0.0  0
 9DB  CONST_05  N1   N    C1   C2     0.00   0.0  0
 9DB  CONST_06  N    N1   C3   C2     0.00   0.0  0
 9DB  CONST_07  C5   N2   C4   C2   180.00   0.0  0
 9DB  CONST_08  C21  C20  C4   C2   180.00   0.0  0
 9DB  CONST_09  N    C1   C2   C3     0.00   0.0  0
 9DB  CONST_12  N    C1   C2   C4   180.00   0.0  0
 9DB  CONST_13  N1   C3   C2   C4   180.00   0.0  0
 9DB  CONST_14  C6   C5   N2   C4   180.00   0.0  0
 9DB  CONST_15  C21  C5   N2   C4     0.00   0.0  0
 9DB  CONST_16  C5   C21  C20  C4     0.00   0.0  0
 9DB  CONST_17  C17  C21  C20  C4   180.00   0.0  0
 9DB  CONST_18  C20  C4   N2   C5     0.00   0.0  0
 9DB  CONST_19  C16  C7   C6   C5     0.00   0.0  0
 9DB  CONST_20  C16  C17  C21  C5     0.00   0.0  0
 9DB  CONST_21  C20  C21  C5   C6   180.00   0.0  0
 9DB  CONST_22  C17  C21  C5   C6     0.00   0.0  0
 9DB  CONST_23  C17  C16  C7   C6     0.00   0.0  0
 9DB  CONST_24  N2   C5   C6   C7   180.00   0.0  0
 9DB  CONST_25  C21  C5   C6   C7     0.00   0.0  0
 9DB  CONST_26  C21  C17  C16  C7     0.00   0.0  0
 9DB  CONST_27  N2   C5   C21  C20    0.00   0.0  0
 9DB  CONST_28  C16  C17  C21  C20  180.00   0.0  0
 9DB  CONST_29  N2   C4   C20  C21    0.00   0.0  0
 9DB  CONST_30  C17  C21  C5   N2   180.00   0.0  0
 9DB  CONST_31  C19  C20  C4   C2     0.00   0.0  0
 9DB  CONST_32  C17  C18  N5   N6     0.00   0.0  0
 9DB  CONST_33  C    N    C1   C2   180.00   0.0  0
 9DB  CONST_34  C    N    N1   C3   180.00   0.0  0
 9DB  CONST_35  N3   C7   C6   C5   180.00   0.0  0
 9DB  CONST_36  N3   C7   C16  C17  180.00   0.0  0
 9DB  CONST_37  N6   N5   C18  O1   180.00   0.0  0
 9DB  CONST_38  H2   C3   C2   C1   180.00   0.0  0
 9DB  CONST_39  H9   N2   C4   C2     0.00   0.0  0
 9DB  CONST_40  H1   C1   C2   C3   180.00   0.0  0
 9DB  CONST_41  H10  C16  C7   C6   180.00   0.0  0
 9DB  CONST_42  H3   C6   C5   C21  180.00   0.0  0
 9DB  CONST_43  H4   N5   C18  C17  180.00   0.0  0
 9DB  CONST_47  O    C8   N3   C7     0.00   0.0  0
 9DB  CONST_48  C9   C8   N3   C7   180.00   0.0  0
 9DB  Var_01    N6   C19  C20  C4   178.75  30.0  1
 9DB  Var_02    C20  C19  N6   N5    -1.72  30.0  1
 9DB  Var_03    C21  C17  C18  N5    -3.34  30.0  1
 9DB  Var_04    C13  C12  C11  C10   55.12  30.0  1
 9DB  Var_05    C13  C14  C15  C10  -55.73  30.0  1
 9DB  Var_06    C12  C13  C14  C15   55.41  30.0  1
 9DB  Var_07    C11  C12  C13  C14  -55.33  30.0  1
 9DB  Var_08    H6   C    N    C1   119.96  30.0  2

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
 9DB  chir_01  C9   N4   C8   C10  negativ
 9DB  chir_02  C10  C15  C11  C9   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
 9DB  plan-1  C1   0.020
 9DB  plan-1  C2   0.020
 9DB  plan-1  C3   0.020
 9DB  plan-1  C4   0.020
 9DB  plan-1  N1   0.020
 9DB  plan-1  N    0.020
 9DB  plan-1  C    0.020
 9DB  plan-1  H1   0.020
 9DB  plan-1  H2   0.020
 9DB  plan-2  C2   0.020
 9DB  plan-2  C4   0.020
 9DB  plan-2  C5   0.020
 9DB  plan-2  C6   0.020
 9DB  plan-2  C7   0.020
 9DB  plan-2  C18  0.020
 9DB  plan-2  C19  0.020
 9DB  plan-2  C20  0.020
 9DB  plan-2  C21  0.020
 9DB  plan-2  N2   0.020
 9DB  plan-2  C17  0.020
 9DB  plan-2  C16  0.020
 9DB  plan-2  N3   0.020
 9DB  plan-2  H3   0.020
 9DB  plan-2  H9   0.020
 9DB  plan-2  H10  0.020
 9DB  plan-3  C7   0.020
 9DB  plan-3  C8   0.020
 9DB  plan-3  N3   0.020
 9DB  plan-3  O    0.020
 9DB  plan-3  C9   0.020
 9DB  plan-3  H11  0.020
 9DB  plan-4  C18  0.020
 9DB  plan-4  N5   0.020
 9DB  plan-4  N6   0.020
 9DB  plan-4  C17  0.020
 9DB  plan-4  H4   0.020
 9DB  plan-4  O1   0.020

