# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 13:21:31 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: ethyl (4~{S})-4-[4-[(1-methylcyclobutyl)carbamoyl]piperidin-1-yl]azepane-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1CCC[C@@H](CC1)N2CCC(CC2)C(=O)NC3(C)CCC3
#
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
 QK8  QK8  "ethyl (4~{S})-4-[4-[(1-methylcyclobutyl)carbamoyl]piperidin-1-yl]azepane-1-carboxylate"  ligand  61  26  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QK8
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
 QK8  C1   C  CH2   0  -0.280  -20.9787  21.8096  5.8239
 QK8  N1   N  NH1   0  -0.660  -24.4652  23.7408  7.6307
 QK8  O1   O  O     0  -0.494  -23.6588  23.0349  9.6190
 QK8  C2   C  CH2   0  -0.430  -21.8969  22.7993  6.5260
 QK8  N2   N  NT    0  -0.483  -20.7592  17.0685  2.9231
 QK8  O2   O  O     0  -0.526  -21.0183  14.9480  3.7096
 QK8  C3   C  CH1   0  -0.387  -22.6819  22.0994  7.6360
 QK8  N3   N  NT    0  -0.428  -21.7438  20.7050  5.2789
 QK8  O3   O  O2    0  -0.485  -22.7708  16.1062  2.9082
 QK8  C4   C  CH2   0  -0.414  -23.4033  20.8759  7.0621
 QK8  C5   C  CH2   0  -0.292  -22.4155  19.9736  6.3362
 QK8  C6   C  C     0   0.557  -23.6374  23.0064  8.3948
 QK8  C7   C  C     0   0.147  -25.4457  24.6945  8.1273
 QK8  C8   C  C     0  -0.427  -26.5940  23.9946  8.8992
 QK8  C9   C  C     0  -0.445  -27.3871  23.8945  7.5840
 QK8  C10  C  CH1   0  -0.060  -21.0068  19.8905  4.3185
 QK8  C11  C  CH2   0  -0.423  -21.9933  19.1782  3.3927
 QK8  C12  C  CH2   0  -0.330  -21.3590  18.2633  2.3509
 QK8  C13  C  CH2   0  -0.285  -19.3502  17.1127  3.2778
 QK8  C15  C  CH2   0  -0.453  -19.9429  18.9718  4.9437
 QK8  C17  C  CH2   0  -0.184  -23.6314  14.9792  3.0921
 QK8  C18  C  CH3   0  -0.687  -23.5307  13.9824  1.9577
 QK8  C19  C  C     0  -0.462  -26.4649  24.9784  6.9998
 QK8  C20  C  CH3   0  -0.659  -24.7869  25.9017  8.7680
 QK8  C14  C  CH2   0  -0.478  -18.9417  18.4354  3.9186
 QK8  H1   H  HCH2  0   0.190  -20.2020  21.4786  6.5352
 QK8  H2   H  HCH2  0   0.236  -20.4590  22.3152  5.0066
 QK8  H3   H  HNH1  0   0.396  -24.3600  23.6824  6.6304
 QK8  H4   H  HCH2  0   0.241  -21.3059  23.6210  6.9367
 QK8  H5   H  HCH2  0   0.219  -22.5678  23.2285  5.7762
 QK8  H6   H  HCH1  0   0.246  -21.9626  21.7408  8.3795
 QK8  H8   H  HCH2  0   0.222  -24.1845  21.1887  6.3630
 QK8  H9   H  HCH2  0   0.238  -23.8896  20.3133  7.8625
 QK8  H10  H  HCH2  0   0.241  -22.9564  19.1248  5.9157
 QK8  H11  H  HCH2  0   0.195  -21.7048  19.5590  7.0718
 QK8  H12  H  H     0   0.238  -26.3551  23.0733  9.4272
 QK8  H13  H  H     0   0.228  -27.0618  24.6865  9.6015
 QK8  H14  H  H     0   0.231  -28.4528  24.1162  7.6234
 QK8  H15  H  H     0   0.229  -27.2529  22.9296  7.0950
 QK8  H16  H  HCH1  0   0.220  -20.4598  20.6071  3.6934
 QK8  H17  H  HCH2  0   0.230  -22.5752  19.9422  2.8704
 QK8  H18  H  HCH2  0   0.226  -22.7113  18.5889  3.9681
 QK8  H19  H  HCH2  0   0.250  -20.5815  18.7923  1.7954
 QK8  H20  H  HCH2  0   0.263  -22.1068  17.9826  1.6113
 QK8  H21  H  HCH2  0   0.249  -19.1557  16.3047  3.9789
 QK8  H22  H  HCH2  0   0.236  -18.7318  16.9256  2.3938
 QK8  H23  H  HCH2  0   0.225  -20.4082  18.1438  5.4889
 QK8  H24  H  HCH2  0   0.241  -19.3929  19.5504  5.6906
 QK8  H25  H  HCH2  0   0.240  -24.6330  15.4055  3.1323
 QK8  H26  H  HCH2  0   0.229  -23.4354  14.5019  4.0529
 QK8  H27  H  HCH3  0   0.236  -24.2755  13.1991  2.1024
 QK8  H28  H  HCH3  0   0.232  -23.7289  14.4560  0.9960
 QK8  H29  H  HCH3  0   0.235  -22.5519  13.5069  1.9169
 QK8  H30  H  H     0   0.240  -26.8898  25.9768  7.1091
 QK8  H31  H  H     0   0.239  -26.1178  24.8661  5.9701
 QK8  H32  H  HCH3  0   0.234  -24.2123  25.6229  9.6500
 QK8  H33  H  HCH3  0   0.224  -24.1155  26.3937  8.0615
 QK8  H34  H  HCH3  0   0.223  -25.5435  26.6252  9.0731
 QK8  H35  H  HCH2  0   0.250  -17.9719  18.2681  4.3920
 QK8  H36  H  HCH2  0   0.229  -18.7650  19.1962  3.1530
 QK8  C16  C  C     0   0.762  -21.4764  15.9630  3.2178

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
 QK8  C18  C17  single  1.513  0.020  1.513
 QK8  C17  O3   single  1.430  0.020  1.430
 QK8  O3   C16  single  1.339  0.020  1.339
 QK8  C12  N2   single  1.454  0.020  1.454
 QK8  C12  C11  single  1.525  0.020  1.525
 QK8  C16  N2   single  1.350  0.020  1.350
 QK8  C16  O2   double  1.217  0.020  1.217
 QK8  N2   C13  single  1.454  0.020  1.454
 QK8  C13  C14  single  1.525  0.020  1.525
 QK8  C11  C10  single  1.529  0.020  1.529
 QK8  C14  C15  single  1.530  0.020  1.530
 QK8  C10  C15  single  1.538  0.020  1.538
 QK8  C10  N3   single  1.459  0.020  1.459
 QK8  N3   C1   single  1.450  0.020  1.450
 QK8  N3   C5   single  1.450  0.020  1.450
 QK8  C1   C2   single  1.522  0.020  1.522
 QK8  C2   C3   single  1.529  0.020  1.529
 QK8  C5   C4   single  1.522  0.020  1.522
 QK8  C19  C7   single  1.546  0.020  1.546
 QK8  C19  C9   single  1.538  0.020  1.538
 QK8  C4   C3   single  1.532  0.020  1.532
 QK8  N1   C7   single  1.455  0.020  1.455
 QK8  N1   C6   single  1.345  0.020  1.345
 QK8  C3   C6   single  1.520  0.020  1.520
 QK8  C7   C20  single  1.517  0.020  1.517
 QK8  C7   C8   single  1.551  0.020  1.551
 QK8  C6   O1   double  1.225  0.020  1.225
 QK8  C9   C8   single  1.539  0.020  1.539
 QK8  C1   H1   single  0.970  0.020  1.090
 QK8  C1   H2   single  0.970  0.020  1.090
 QK8  N1   H3   single  0.860  0.020  1.020
 QK8  C2   H4   single  0.970  0.020  1.090
 QK8  C2   H5   single  0.970  0.020  1.090
 QK8  C3   H6   single  0.970  0.020  1.090
 QK8  C4   H8   single  0.970  0.020  1.090
 QK8  C4   H9   single  0.970  0.020  1.090
 QK8  C5   H10  single  0.970  0.020  1.090
 QK8  C5   H11  single  0.970  0.020  1.090
 QK8  C8   H12  single  0.970  0.020  1.090
 QK8  C8   H13  single  0.970  0.020  1.090
 QK8  C9   H14  single  0.970  0.020  1.090
 QK8  C9   H15  single  0.970  0.020  1.090
 QK8  C10  H16  single  0.970  0.020  1.090
 QK8  C11  H17  single  0.970  0.020  1.090
 QK8  C11  H18  single  0.970  0.020  1.090
 QK8  C12  H19  single  0.970  0.020  1.090
 QK8  C12  H20  single  0.970  0.020  1.090
 QK8  C13  H21  single  0.970  0.020  1.090
 QK8  C13  H22  single  0.970  0.020  1.090
 QK8  C15  H23  single  0.970  0.020  1.090
 QK8  C15  H24  single  0.970  0.020  1.090
 QK8  C17  H25  single  0.970  0.020  1.090
 QK8  C17  H26  single  0.970  0.020  1.090
 QK8  C18  H27  single  0.970  0.020  1.090
 QK8  C18  H28  single  0.970  0.020  1.090
 QK8  C18  H29  single  0.970  0.020  1.090
 QK8  C19  H30  single  0.970  0.020  1.090
 QK8  C19  H31  single  0.970  0.020  1.090
 QK8  C20  H32  single  0.970  0.020  1.090
 QK8  C20  H33  single  0.970  0.020  1.090
 QK8  C20  H34  single  0.970  0.020  1.090
 QK8  C14  H35  single  0.970  0.020  1.090
 QK8  C14  H36  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
 QK8  H2   C1   H1   106.62  3.000
 QK8  H2   C1   N3   108.80  3.000
 QK8  H1   C1   N3   112.64  3.000
 QK8  H2   C1   C2   109.34  3.000
 QK8  H1   C1   C2   108.80  3.000
 QK8  N3   C1   C2   110.52  3.000
 QK8  H3   N1   C7   116.56  3.000
 QK8  H3   N1   C6   117.92  3.000
 QK8  C7   N1   C6   125.36  3.000
 QK8  H5   C2   H4   107.12  3.000
 QK8  H5   C2   C3   111.24  3.000
 QK8  H4   C2   C3   110.43  3.000
 QK8  H5   C2   C1   108.00  3.000
 QK8  H4   C2   C1   109.65  3.000
 QK8  C3   C2   C1   110.31  3.000
 QK8  C16  N2   C13  119.11  3.000
 QK8  C13  N2   C12  118.08  3.000
 QK8  C16  N2   C12  122.65  3.000
 QK8  H6   C3   C6   105.62  3.000
 QK8  H6   C3   C4   107.59  3.000
 QK8  C6   C3   C4   111.56  3.000
 QK8  H6   C3   C2   107.79  3.000
 QK8  C6   C3   C2   114.32  3.000
 QK8  C4   C3   C2   109.60  3.000
 QK8  C10  N3   C5   115.61  3.000
 QK8  C5   N3   C1   110.76  3.000
 QK8  C10  N3   C1   113.96  3.000
 QK8  C17  O3   C16  117.90  3.000
 QK8  H9   C4   H8   107.31  3.000
 QK8  H9   C4   C5   109.45  3.000
 QK8  H8   C4   C5   109.16  3.000
 QK8  H9   C4   C3   110.27  3.000
 QK8  H8   C4   C3   110.32  3.000
 QK8  C5   C4   C3   110.27  3.000
 QK8  H11  C5   H10  106.50  3.000
 QK8  H11  C5   C4   108.83  3.000
 QK8  H10  C5   C4   108.86  3.000
 QK8  H11  C5   N3   112.16  3.000
 QK8  H10  C5   N3   109.94  3.000
 QK8  C4   C5   N3   110.44  3.000
 QK8  C3   C6   O1   121.58  3.000
 QK8  O1   C6   N1   122.99  3.000
 QK8  C3   C6   N1   115.41  3.000
 QK8  C20  C7   C19  116.62  3.000
 QK8  C20  C7   C8   118.06  3.000
 QK8  C19  C7   C8    87.57  3.000
 QK8  C8   C7   N1   111.90  3.000
 QK8  C20  C7   N1   111.91  3.000
 QK8  C19  C7   N1   108.40  3.000
 QK8  H13  C8   H12  108.58  3.000
 QK8  H13  C8   C9   111.73  3.000
 QK8  H12  C8   C9   118.20  3.000
 QK8  H13  C8   C7   110.59  3.000
 QK8  H12  C8   C7   117.45  3.000
 QK8  C9   C8   C7    89.17  3.000
 QK8  H15  C9   H14  108.47  3.000
 QK8  H15  C9   C19  112.31  3.000
 QK8  H14  C9   C19  117.18  3.000
 QK8  H15  C9   C8   112.18  3.000
 QK8  H14  C9   C8   117.39  3.000
 QK8  C19  C9   C8    88.27  3.000
 QK8  H16  C10  C15  106.07  3.000
 QK8  H16  C10  C11  106.32  3.000
 QK8  C15  C10  C11  114.46  3.000
 QK8  H16  C10  N3   105.21  3.000
 QK8  C15  C10  N3   114.53  3.000
 QK8  C11  C10  N3   109.43  3.000
 QK8  H18  C11  H17  106.19  3.000
 QK8  H18  C11  C12  108.03  3.000
 QK8  H17  C11  C12  108.32  3.000
 QK8  H18  C11  C10  110.88  3.000
 QK8  H17  C11  C10  107.89  3.000
 QK8  C12  C11  C10  115.14  3.000
 QK8  H20  C12  H19  105.57  3.000
 QK8  H20  C12  C11  109.47  3.000
 QK8  H19  C12  C11  110.67  3.000
 QK8  H20  C12  N2   109.80  3.000
 QK8  H19  C12  N2   107.73  3.000
 QK8  C11  C12  N2   113.31  3.000
 QK8  H22  C13  H21  107.01  3.000
 QK8  H22  C13  C14  109.63  3.000
 QK8  H21  C13  C14  109.00  3.000
 QK8  H22  C13  N2   110.20  3.000
 QK8  H21  C13  N2   107.95  3.000
 QK8  C14  C13  N2   112.86  3.000
 QK8  H24  C15  H23  105.89  3.000
 QK8  H24  C15  C14  108.30  3.000
 QK8  H23  C15  C14  110.27  3.000
 QK8  H24  C15  C10  108.03  3.000
 QK8  H23  C15  C10  111.10  3.000
 QK8  C14  C15  C10  112.93  3.000
 QK8  H26  C17  H25  107.70  3.000
 QK8  H26  C17  C18  111.11  3.000
 QK8  H25  C17  C18  110.28  3.000
 QK8  H26  C17  O3   110.49  3.000
 QK8  H25  C17  O3   104.46  3.000
 QK8  C18  C17  O3   112.50  3.000
 QK8  H29  C18  H28  108.66  3.000
 QK8  H29  C18  H27  107.77  3.000
 QK8  H28  C18  H27  107.75  3.000
 QK8  H29  C18  C17  112.05  3.000
 QK8  H28  C18  C17  111.28  3.000
 QK8  H27  C18  C17  109.16  3.000
 QK8  H31  C19  H30  108.20  3.000
 QK8  H31  C19  C9   118.42  3.000
 QK8  H30  C19  C9   111.93  3.000
 QK8  H31  C19  C7   117.32  3.000
 QK8  H30  C19  C7   110.60  3.000
 QK8  C9   C19  C7    89.37  3.000
 QK8  H34  C20  H33  107.99  3.000
 QK8  H34  C20  H32  108.02  3.000
 QK8  H33  C20  H32  108.36  3.000
 QK8  H34  C20  C7   110.18  3.000
 QK8  H33  C20  C7   110.63  3.000
 QK8  H32  C20  C7   111.55  3.000
 QK8  H36  C14  H35  105.46  3.000
 QK8  H36  C14  C15  109.32  3.000
 QK8  H35  C14  C15  110.15  3.000
 QK8  H36  C14  C13  110.63  3.000
 QK8  H35  C14  C13  106.68  3.000
 QK8  C15  C14  C13  114.21  3.000
 QK8  O3   C16  O2   123.13  3.000
 QK8  O2   C16  N2   124.81  3.000
 QK8  O3   C16  N2   112.05  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
 QK8  CONST_01  C7   N1   C6   C3    180.00   0.0  0
 QK8  CONST_02  C7   N1   C6   O1      0.00   0.0  0
 QK8  CONST_03  H3   N1   C6   C3      0.00   0.0  0
 QK8  CONST_04  H3   N1   C6   O1    180.00   0.0  0
 QK8  Var_01    C4   C5   N3   C1     61.94  30.0  1
 QK8  Var_02    C10  N3   C1   C2    165.67  30.0  1
 QK8  Var_03    C5   N3   C1   C2    -61.93  30.0  1
 QK8  Var_04    N3   C1   C2   C3     57.77  30.0  1
 QK8  Var_05    N3   C5   C4   C3    -57.78  30.0  1
 QK8  Var_06    C10  N3   C5   C4   -166.51  30.0  1
 QK8  Var_07    C8   C9   C19  C7     17.88  30.0  1
 QK8  Var_08    H10  C5   N3   C1   -177.92  30.0  1
 QK8  Var_09    H11  C5   N3   C1    -59.64  30.0  1
 QK8  Var_10    H1   C1   C2   C3    -66.39  30.0  1
 QK8  Var_11    H2   C1   C2   C3    177.52  30.0  1
 QK8  Var_12    H10  C5   C4   C3   -178.57  30.0  1
 QK8  Var_13    H11  C5   C4   C3     65.75  30.0  1
 QK8  Var_14    H4   C2   C1   N3    179.61  30.0  1
 QK8  Var_15    H5   C2   C1   N3    -63.99  30.0  1
 QK8  Var_16    H8   C4   C5   N3     63.57  30.0  1
 QK8  Var_17    H9   C4   C5   N3   -179.25  30.0  1
 QK8  Var_18    H1   C1   N3   C5     60.00  30.0  1
 QK8  Var_19    H2   C1   N3   C5    178.00  30.0  1
 QK8  Var_20    H14  C9   C19  C7    138.00  30.0  1
 QK8  Var_21    H15  C9   C19  C7    -95.44  30.0  1
 QK8  Var_22    H14  C9   C8   C7   -137.77  30.0  1
 QK8  Var_23    H15  C9   C8   C7     95.61  30.0  1
 QK8  Var_24    H30  C19  C9   C8    -94.14  30.0  1
 QK8  Var_25    H31  C19  C9   C8    138.94  30.0  1
 QK8  Var_26    H1   C1   N3   C10   -72.40  30.0  1
 QK8  Var_27    H2   C1   N3   C10    45.60  30.0  1
 QK8  Var_28    H10  C5   N3   C10   -46.36  30.0  1
 QK8  Var_29    H11  C5   N3   C10    71.92  30.0  1
 QK8  Var_30    H12  C8   C9   C19  -138.85  30.0  1
 QK8  Var_31    H13  C8   C9   C19    94.07  30.0  1
 QK8  Var_32    C17  O3   C16  N2    176.21  30.0  1
 QK8  Var_33    C17  O3   C16  O2     -3.93  30.0  1
 QK8  Var_34    C18  C17  O3   C16   -80.09  30.0  1
 QK8  Var_35    H27  C18  C17  O3   -174.48  30.0  3
 QK8  Var_36    H28  C18  C17  O3    -55.68  30.0  3
 QK8  Var_37    H29  C18  C17  O3     66.21  30.0  3
 QK8  Var_38    H25  C17  O3   C16   160.29  30.0  1
 QK8  Var_39    H26  C17  O3   C16    44.73  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
 QK8  chir_01  C3   C2   C4   C6   positiv
 QK8  chir_02  C7   C8   C20  C19  positiv
 QK8  chir_03  C10  C11  C15  N3   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
 QK8  plan-1  N1   0.020
 QK8  plan-1  O1   0.020
 QK8  plan-1  C3   0.020
 QK8  plan-1  C6   0.020
 QK8  plan-1  C7   0.020
 QK8  plan-1  H3   0.020
 QK8  plan-2  N2   0.020
 QK8  plan-2  O2   0.020
 QK8  plan-2  O3   0.020
 QK8  plan-2  C16  0.020

