# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:08:11 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (2~{S})-6-azanyl-2-[[(2~{R})-1-[[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]carbamoylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](NC(=O)N[C@H](CC1CCCCC1)C(=O)N[C@H]2C[C@H]3CC[C@@H]2C3)C(O)=O
#
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
 7B6  7B6  '(2~{S})-6-azanyl-2-[[(2~{R})-1-[[(1~{R},2~{S},4~{S})-2-bicyclo[2.2.1]heptanyl]amino]-3-cyclohexyl-1-oxidanylidene-propan-2-yl]carbamoylamino]hexanoic acid'  ligand  70  31  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7B6
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
 7B6  C2   C  CH2    0  -0.272  -6.9021  -0.0128   1.6266
 7B6  C3   C  CH2    0  -0.425  -6.2087   1.2134   1.0533
 7B6  C7   C  C      0   0.407  -2.1998   3.1099  -1.3881
 7B6  C8   C  CH2    0  -0.470   6.0989  -0.3798   0.1872
 7B6  C10  C  CH1    0  -0.250   6.9279   0.7916  -0.3529
 7B6  C14  C  CH1    0  -0.240   1.2597  -0.5869   0.4485
 7B6  C15  C  C      0   0.572   2.4844   0.0551   1.0941
 7B6  C19  C  CH1    0  -0.265   5.2046   1.8208   0.6645
 7B6  C20  C  CH2    0  -0.443   4.9839   2.1539  -0.8143
 7B6  C21  C  CH2    0  -0.405   1.0757  -1.9923   1.0407
 7B6  C22  C  CH1    0  -0.231  -0.0479  -2.8119   0.4108
 7B6  C24  C  CH2    0  -0.429  -0.8612  -4.0475  -1.6457
 7B6  C27  C  CH2    0  -0.440   6.7338   1.8346   0.7547
 7B6  C26  C  CH2    0  -0.442   6.1599   1.4294  -1.5204
 7B6  C18  C  CH1    0  -0.042   4.9196   0.3246   0.9090
 7B6  N17  N  NH1    0  -0.648   3.6350  -0.1415   0.4370
 7B6  O16  O  O      0  -0.499   2.4073   0.6512   2.1594
 7B6  C23  C  CH2    0  -0.424   0.2389  -3.1749  -1.0472
 7B6  C25  C  CH2    0  -0.428  -1.0967  -5.3034  -0.8144
 7B6  C28  C  CH2    0  -0.431  -1.3984  -4.9449   0.6365
 7B6  C29  C  CH2    0  -0.412  -0.2919  -4.0801   1.2314
 7B6  N13  N  NH1    0  -0.676   0.1101   0.2485   0.6662
 7B6  O12  O  O      0  -0.550  -0.5781   0.3170  -1.5013
 7B6  N10  N  NH1    0  -0.665  -1.9287   1.1389   0.1283
 7B6  C6   C  CH1    0  -0.186  -2.8105   1.8163  -0.7934
 7B6  C5   C  CH2    0  -0.452  -4.1376   2.1207  -0.0971
 7B6  C4   C  CH2    0  -0.409  -4.8433   0.8898   0.4593
 7B6  N1   N  NH2    0  -0.801  -8.2027   0.3308   2.1857
 7B6  H1   H  HCH2   0   0.210  -7.0573  -0.7415   0.8256
 7B6  H2   H  HCH2   0   0.185  -6.2275  -0.4943   2.3500
 7B6  H3   H  HCH2   0   0.210  -6.8502   1.6653   0.2901
 7B6  H4   H  HCH2   0   0.209  -6.0912   1.9650   1.8426
 7B6  H7   H  HCH1   0   0.227   7.9579   0.5263  -0.5918
 7B6  H8   H  HCH1   0   0.271   1.4130  -0.6571  -0.6286
 7B6  H9   H  HCH1   0   0.229   4.6685   2.4732   1.3537
 7B6  H10  H  HCH2   0   0.229   4.0044   1.8409  -1.1793
 7B6  H11  H  HCH2   0   0.236   5.0438   3.2335  -0.9638
 7B6  H12  H  HCH2   0   0.228   2.0170  -2.5452   0.9499
 7B6  H13  H  HCH2   0   0.232   0.8872  -1.8848   2.1146
 7B6  H14  H  HCH1   0   0.215  -0.9703  -2.2171   0.4404
 7B6  H15  H  HCH2   0   0.207  -1.7905  -3.4690  -1.6961
 7B6  H16  H  HCH2   0   0.224  -0.6069  -4.3142  -2.6746
 7B6  H17  H  HCH2   0   0.235   7.1202   1.5138   1.7257
 7B6  H18  H  HCH2   0   0.236   7.1659   2.8087   0.5144
 7B6  H19  H  HCH2   0   0.234   6.7909   2.1361  -2.0626
 7B6  H20  H  HCH2   0   0.226   5.8242   0.6825  -2.2425
 7B6  H21  H  HCH1   0   0.260   4.9695   0.1302   1.9825
 7B6  H22  H  HNH1   0   0.395   3.5991  -0.5973  -0.4609
 7B6  H23  H  HCH2   0   0.234   0.3493  -2.2713  -1.6499
 7B6  H24  H  HCH2   0   0.201   1.1951  -3.7105  -1.0956
 7B6  H25  H  HCH2   0   0.223  -1.9129  -5.8931  -1.2395
 7B6  H26  H  HCH2   0   0.206  -0.2029  -5.9357  -0.8526
 7B6  H27  H  HCH2   0   0.207  -2.3480  -4.4002   0.6825
 7B6  H28  H  HCH2   0   0.224  -1.5296  -5.8501   1.2345
 7B6  H29  H  HCH2   0   0.204   0.6370  -4.6622   1.2736
 7B6  H30  H  HCH2   0   0.223  -0.5371  -3.8116   2.2631
 7B6  H31  H  HNH1   0   0.382  -0.1453   0.4157   1.6267
 7B6  H32  H  HNH1   0   0.373  -1.9218   1.5045   1.0686
 7B6  H33  H  HCH1   0   0.226  -3.0211   1.1325  -1.6204
 7B6  H35  H  HCH2   0   0.214  -3.9703   2.8437   0.7115
 7B6  H36  H  HCH2   0   0.230  -4.7879   2.6183  -0.8192
 7B6  H37  H  HCH2   0   0.213  -4.2202   0.4153   1.2225
 7B6  H38  H  HCH2   0   0.207  -4.9614   0.1482  -0.3389
 7B6  H39  H  HNH2   0   0.344  -8.6641  -0.5102   2.5081
 7B6  H40  H  HNH2   0   0.336  -8.0674   0.8987   3.0134
 7B6  O8   O  OC    -1  -0.622  -2.8502   3.6232  -2.3219
 7B6  C11  C  C      0   0.743  -0.7810   0.5645  -0.3164
 7B6  H5   H  HCH2   0   0.236   5.7641  -1.0499  -0.6092
 7B6  O9   O  O      0  -0.600  -1.1452   3.5368  -0.8863
 7B6  H6   H  HCH2   0   0.250   6.6731  -0.9858   0.8895

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
 7B6  C27  C19  single  1.532  0.020  1.532
 7B6  C27  C10  single  1.534  0.020  1.534
 7B6  C19  C18  single  1.543  0.020  1.543
 7B6  C19  C20  single  1.532  0.020  1.532
 7B6  O16  C15  double  1.223  0.020  1.223
 7B6  C18  C8   single  1.552  0.020  1.552
 7B6  C18  N17  single  1.446  0.020  1.446
 7B6  C10  C8   single  1.533  0.020  1.533
 7B6  C10  C26  single  1.536  0.020  1.536
 7B6  C20  C26  single  1.551  0.020  1.551
 7B6  C15  N17  single  1.340  0.020  1.340
 7B6  C15  C14  single  1.526  0.020  1.526
 7B6  C23  C24  single  1.526  0.020  1.526
 7B6  C23  C22  single  1.530  0.020  1.530
 7B6  C24  C25  single  1.524  0.020  1.524
 7B6  C14  C21  single  1.536  0.020  1.536
 7B6  C14  N13  single  1.438  0.020  1.438
 7B6  O12  C11  double  1.227  0.020  1.227
 7B6  C21  C22  single  1.527  0.020  1.527
 7B6  C22  C29  single  1.530  0.020  1.530
 7B6  O9   C7   deloc   1.243  0.020  1.243
 7B6  O8   C7   deloc   1.248  0.020  1.248
 7B6  C25  C28  single  1.525  0.020  1.525
 7B6  C11  N13  single  1.364  0.020  1.364
 7B6  C11  N10  single  1.358  0.020  1.358
 7B6  C7   C6   single  1.549  0.020  1.549
 7B6  C29  C28  single  1.525  0.020  1.525
 7B6  N10  C6   single  1.444  0.020  1.444
 7B6  C6   C5   single  1.529  0.020  1.529
 7B6  C5   C4   single  1.524  0.020  1.524
 7B6  C4   C3   single  1.524  0.020  1.524
 7B6  N1   C2   single  1.457  0.020  1.457
 7B6  C3   C2   single  1.521  0.020  1.521
 7B6  C2   H1   single  0.970  0.020  1.090
 7B6  C2   H2   single  0.970  0.020  1.090
 7B6  C3   H3   single  0.970  0.020  1.090
 7B6  C3   H4   single  0.970  0.020  1.090
 7B6  C8   H5   single  0.970  0.020  1.090
 7B6  C8   H6   single  0.970  0.020  1.090
 7B6  C10  H7   single  0.970  0.020  1.090
 7B6  C14  H8   single  0.970  0.020  1.090
 7B6  C19  H9   single  0.970  0.020  1.090
 7B6  C20  H10  single  0.970  0.020  1.090
 7B6  C20  H11  single  0.970  0.020  1.090
 7B6  C21  H12  single  0.970  0.020  1.090
 7B6  C21  H13  single  0.970  0.020  1.090
 7B6  C22  H14  single  0.970  0.020  1.090
 7B6  C24  H15  single  0.970  0.020  1.090
 7B6  C24  H16  single  0.970  0.020  1.090
 7B6  C27  H17  single  0.970  0.020  1.090
 7B6  C27  H18  single  0.970  0.020  1.090
 7B6  C26  H19  single  0.970  0.020  1.090
 7B6  C26  H20  single  0.970  0.020  1.090
 7B6  C18  H21  single  0.970  0.020  1.090
 7B6  N17  H22  single  0.860  0.020  1.020
 7B6  C23  H23  single  0.970  0.020  1.090
 7B6  C23  H24  single  0.970  0.020  1.090
 7B6  C25  H25  single  0.970  0.020  1.090
 7B6  C25  H26  single  0.970  0.020  1.090
 7B6  C28  H27  single  0.970  0.020  1.090
 7B6  C28  H28  single  0.970  0.020  1.090
 7B6  C29  H29  single  0.970  0.020  1.090
 7B6  C29  H30  single  0.970  0.020  1.090
 7B6  N13  H31  single  0.860  0.020  1.020
 7B6  N10  H32  single  0.890  0.020  1.040
 7B6  C6   H33  single  0.970  0.020  1.090
 7B6  C5   H35  single  0.970  0.020  1.090
 7B6  C5   H36  single  0.970  0.020  1.090
 7B6  C4   H37  single  0.970  0.020  1.090
 7B6  C4   H38  single  0.970  0.020  1.090
 7B6  N1   H39  single  0.890  0.020  1.040
 7B6  N1   H40  single  0.890  0.020  1.040

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
 7B6  H2   C2   H1   106.08  3.000
 7B6  H2   C2   N1   113.48  3.000
 7B6  H1   C2   N1   108.15  3.000
 7B6  H2   C2   C3   108.73  3.000
 7B6  H1   C2   C3   109.01  3.000
 7B6  N1   C2   C3   111.20  3.000
 7B6  H4   C3   H3   106.36  3.000
 7B6  H4   C3   C4   109.29  3.000
 7B6  H3   C3   C4   109.94  3.000
 7B6  H4   C3   C2   109.28  3.000
 7B6  H3   C3   C2   109.17  3.000
 7B6  C4   C3   C2   112.60  3.000
 7B6  O9   C7   O8   127.05  3.000
 7B6  O8   C7   C6   115.16  3.000
 7B6  O9   C7   C6   117.78  3.000
 7B6  H6   C8   H5   106.84  3.000
 7B6  H6   C8   C18  110.65  3.000
 7B6  H5   C8   C18  112.60  3.000
 7B6  H6   C8   C10  111.50  3.000
 7B6  H5   C8   C10  112.16  3.000
 7B6  C18  C8   C10  103.18  3.000
 7B6  H7   C10  C26  114.01  3.000
 7B6  H7   C10  C27  116.31  3.000
 7B6  C26  C10  C27  101.73  3.000
 7B6  H7   C10  C8   113.71  3.000
 7B6  C26  C10  C8   108.34  3.000
 7B6  C27  C10  C8   101.35  3.000
 7B6  H8   C14  N13  107.43  3.000
 7B6  H8   C14  C21  109.80  3.000
 7B6  N13  C14  C21  112.18  3.000
 7B6  H8   C14  C15  109.40  3.000
 7B6  N13  C14  C15  109.47  3.000
 7B6  C21  C14  C15  108.54  3.000
 7B6  O16  C15  N17  123.56  3.000
 7B6  N17  C15  C14  114.84  3.000
 7B6  O16  C15  C14  121.53  3.000
 7B6  H9   C19  C18  112.92  3.000
 7B6  H9   C19  C27  116.64  3.000
 7B6  C18  C19  C27  100.59  3.000
 7B6  H9   C19  C20  114.17  3.000
 7B6  C18  C19  C20  109.71  3.000
 7B6  C27  C19  C20  101.47  3.000
 7B6  H11  C20  H10  106.70  3.000
 7B6  H11  C20  C26  110.97  3.000
 7B6  H10  C20  C26  113.22  3.000
 7B6  H11  C20  C19  109.84  3.000
 7B6  H10  C20  C19  112.95  3.000
 7B6  C26  C20  C19  103.21  3.000
 7B6  H13  C21  H12  106.17  3.000
 7B6  H13  C21  C22  109.30  3.000
 7B6  H12  C21  C22  109.10  3.000
 7B6  H13  C21  C14  107.98  3.000
 7B6  H12  C21  C14  109.08  3.000
 7B6  C22  C21  C14  114.85  3.000
 7B6  H14  C22  C29  107.49  3.000
 7B6  H14  C22  C23  108.17  3.000
 7B6  C29  C22  C23  110.15  3.000
 7B6  H14  C22  C21  108.44  3.000
 7B6  C29  C22  C21  109.94  3.000
 7B6  C23  C22  C21  112.50  3.000
 7B6  H16  C24  H15  106.43  3.000
 7B6  H16  C24  C25  110.38  3.000
 7B6  H15  C24  C25  109.21  3.000
 7B6  H16  C24  C23  109.94  3.000
 7B6  H15  C24  C23  109.12  3.000
 7B6  C25  C24  C23  111.62  3.000
 7B6  H18  C27  H17  108.50  3.000
 7B6  H18  C27  C19  112.95  3.000
 7B6  H17  C27  C19  113.74  3.000
 7B6  H18  C27  C10  113.42  3.000
 7B6  H17  C27  C10  113.40  3.000
 7B6  C19  C27  C10   94.45  3.000
 7B6  H20  C26  H19  106.99  3.000
 7B6  H20  C26  C20  112.80  3.000
 7B6  H19  C26  C20  111.22  3.000
 7B6  H20  C26  C10  111.86  3.000
 7B6  H19  C26  C10  110.93  3.000
 7B6  C20  C26  C10  103.12  3.000
 7B6  H21  C18  N17  107.71  3.000
 7B6  H21  C18  C19  108.66  3.000
 7B6  N17  C18  C19  115.16  3.000
 7B6  H21  C18  C8   109.98  3.000
 7B6  N17  C18  C8   112.15  3.000
 7B6  C19  C18  C8   103.06  3.000
 7B6  H22  N17  C18  117.93  3.000
 7B6  H22  N17  C15  118.22  3.000
 7B6  C18  N17  C15  123.76  3.000
 7B6  H24  C23  H23  106.96  3.000
 7B6  H24  C23  C24  109.37  3.000
 7B6  H23  C23  C24  109.24  3.000
 7B6  H24  C23  C22  108.74  3.000
 7B6  H23  C23  C22  110.41  3.000
 7B6  C24  C23  C22  111.98  3.000
 7B6  H26  C25  H25  106.52  3.000
 7B6  H26  C25  C28  109.29  3.000
 7B6  H25  C25  C28  110.44  3.000
 7B6  H26  C25  C24  109.30  3.000
 7B6  H25  C25  C24  110.35  3.000
 7B6  C28  C25  C24  110.84  3.000
 7B6  H28  C28  H27  106.55  3.000
 7B6  H28  C28  C29  110.08  3.000
 7B6  H27  C28  C29  109.30  3.000
 7B6  H28  C28  C25  110.47  3.000
 7B6  H27  C28  C25  109.17  3.000
 7B6  C29  C28  C25  111.16  3.000
 7B6  H30  C29  H29  106.48  3.000
 7B6  H30  C29  C28  110.15  3.000
 7B6  H29  C29  C28  109.18  3.000
 7B6  H30  C29  C22  109.76  3.000
 7B6  H29  C29  C22  108.99  3.000
 7B6  C28  C29  C22  112.12  3.000
 7B6  H31  N13  C14  116.32  3.000
 7B6  H31  N13  C11  118.86  3.000
 7B6  C14  N13  C11  123.24  3.000
 7B6  H32  N10  C6   115.40  3.000
 7B6  H32  N10  C11  116.91  3.000
 7B6  C6   N10  C11  120.36  3.000
 7B6  H33  C6   C5   107.55  3.000
 7B6  H33  C6   N10  107.87  3.000
 7B6  C5   C6   N10  109.43  3.000
 7B6  H33  C6   C7   107.92  3.000
 7B6  C5   C6   C7   110.53  3.000
 7B6  N10  C6   C7   113.33  3.000
 7B6  H36  C5   H35  106.13  3.000
 7B6  H36  C5   C4   109.50  3.000
 7B6  H35  C5   C4   109.49  3.000
 7B6  H36  C5   C6   107.84  3.000
 7B6  H35  C5   C6   109.53  3.000
 7B6  C4   C5   C6   114.04  3.000
 7B6  H38  C4   H37  106.03  3.000
 7B6  H38  C4   C5   109.30  3.000
 7B6  H37  C4   C5   109.96  3.000
 7B6  H38  C4   C3   109.33  3.000
 7B6  H37  C4   C3   109.31  3.000
 7B6  C5   C4   C3   112.69  3.000
 7B6  H40  N1   H39  105.45  3.000
 7B6  H40  N1   C2   109.06  3.000
 7B6  H39  N1   C2   109.47  3.000
 7B6  N10  C11  O12  122.75  3.000
 7B6  N10  C11  N13  114.48  3.000
 7B6  O12  C11  N13  122.75  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
 7B6  CONST_01  C18  N17  C15  C14   180.00   0.0  0
 7B6  CONST_02  O16  C15  N17  C18     0.00   0.0  0
 7B6  CONST_03  O12  C11  N13  C14     0.00   0.0  0
 7B6  CONST_05  N10  C11  N13  C14   180.00   0.0  0
 7B6  CONST_07  H22  N17  C15  C14     0.00   0.0  0
 7B6  CONST_08  H31  N13  C11  O12   180.00   0.0  0
 7B6  CONST_09  H32  N10  C11  O12   180.00   0.0  0
 7B6  Var_01    C19  C20  C26  C10    -1.08  30.0  1
 7B6  Var_02    C25  C24  C23  C22   -55.27  30.0  1
 7B6  Var_03    C25  C28  C29  C22    56.02  30.0  1
 7B6  Var_04    C29  C28  C25  C24   -55.40  30.0  1
 7B6  Var_05    C28  C25  C24  C23    55.19  30.0  1
 7B6  Var_06    C5   C4   C3   C2   -179.14  30.0  1
 7B6  Var_07    C6   C5   C4   C3   -175.72  30.0  1
 7B6  Var_08    N1   C2   C3   C4    179.99  30.0  3
 7B6  Var_09    H39  N1   C2   C3    176.59  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
 7B6  chir_01  C10  C27  C8   C26  negativ
 7B6  chir_02  C14  N13  C15  C21  negativ
 7B6  chir_03  C19  C27  C18  C20  positiv
 7B6  chir_04  C22  C23  C21  C29  positiv
 7B6  chir_05  C18  N17  C19  C8   positiv
 7B6  chir_06  C6   C7   N10  C5   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
 7B6  plan-1  C14  0.020
 7B6  plan-1  C15  0.020
 7B6  plan-1  C18  0.020
 7B6  plan-1  N17  0.020
 7B6  plan-1  O16  0.020
 7B6  plan-1  H22  0.020
 7B6  plan-2  C14  0.020
 7B6  plan-2  N13  0.020
 7B6  plan-2  O12  0.020
 7B6  plan-2  N10  0.020
 7B6  plan-2  C6   0.020
 7B6  plan-2  H31  0.020
 7B6  plan-2  H32  0.020
 7B6  plan-2  C11  0.020
 7B6  plan-3  C7   0.020
 7B6  plan-3  C6   0.020
 7B6  plan-3  O8   0.020
 7B6  plan-3  O9   0.020

