# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:28:38 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: "2-[(1~{R},2~{S},6~{R},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]-~{N}-[[(1~{R},9~{R},10~{S})-10-oxidanyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-4-yl]methyl]ethanamide"
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H]2C[C@H]1Nc3ccc(CNC(=O)CN4C(=O)[C@@H]5[C@H]6CC[C@H](C6)[C@@H]5C4=O)cc23
#
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
 JVH  JVH  "2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide"
  ligand  58  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JVH
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
 JVH  C2   C  CR5   0   0.583  -4.6474  -1.3317   0.6167
 JVH  C4   C  CH2   0  -0.456  -2.4026  -0.4157   1.1725
 JVH  C5   C  C     0   0.553  -1.6210   0.0403  -0.0542
 JVH  C8   C  CH2   0  -0.348   0.6210   0.7678  -0.7928
 JVH  C11  C  CR6   0   0.066   4.2805   0.3908   0.1997
 JVH  C12  C  CR6   0   0.346   4.4559  -1.0008   0.1318
 JVH  N13  N  NH1   0  -0.687   5.6568  -1.5673   0.4606
 JVH  C16  C  CH2   0  -0.460   6.3769   0.4802   1.5015
 JVH  C17  C  CH1   0  -0.073   5.4578   1.2544   0.5692
 JVH  C21  C  CH1   0   0.041   7.5643  -0.3471  -0.5314
 JVH  C24  C  CR16  0  -0.341   3.3681  -1.7977  -0.2583
 JVH  C30  C  CR15  0  -0.397  -6.0421  -0.7879   0.4391
 JVH  C32  C  CH1   0  -0.248  -6.5641  -0.9012  -1.0050
 JVH  C34  C  CH2   0  -0.474  -5.8512   0.2700  -1.6907
 JVH  C35  C  CH1   0  -0.249  -6.3564   1.3222  -0.6966
 JVH  C37  C  CH2   0  -0.441  -7.8763   1.1203  -0.7838
 JVH  C38  C  CH2   0  -0.439  -8.0193  -0.4108  -0.9923
 JVH  O1   O  O     0  -0.427  -4.2876  -2.4771   0.4957
 JVH  N3   N  NR5   0  -0.509  -3.8144  -0.2871   0.9583
 JVH  O6   O  O     0  -0.481  -2.1222   0.0281  -1.1668
 JVH  N7   N  NH1   0  -0.624  -0.3594   0.3959   0.2105
 JVH  C9   C  CR6   0   0.068   1.9609   0.1584  -0.4887
 JVH  C10  C  CR16  0  -0.377   3.0417   0.9397  -0.1053
 JVH  C14  C  CH1   0  -0.157   6.8236  -0.7667   0.7496
 JVH  C20  C  CH2   0  -0.228   6.7083   0.6182  -1.3441
 JVH  O23  O  OH1   0  -0.673   8.7860   0.2235  -0.1177
 JVH  C25  C  CR16  0  -0.286   2.1512  -1.2227  -0.5627
 JVH  C26  C  CR5   0   0.588  -4.4394   0.9406   0.9349
 JVH  O27  O  O     0  -0.429  -3.8615   1.9852   1.1152
 JVH  C28  C  CR15  0  -0.394  -5.9030   0.7307   0.6508
 JVH  H1   H  HCH2  0   0.315  -2.1753  -1.4662   1.3602
 JVH  H2   H  HCH2  0   0.298  -2.1119   0.1412   2.0642
 JVH  H3   H  HCH2  0   0.262   0.2505   0.4312  -1.7609
 JVH  H4   H  HCH2  0   0.257   0.7085   1.8562  -0.8456
 JVH  H5   H  HNH1  0   0.383   5.8105  -2.5216   0.1797
 JVH  H6   H  HCH2  0   0.256   7.2366   1.0838   1.7918
 JVH  H7   H  HCH2  0   0.252   5.8452   0.2043   2.4150
 JVH  H8   H  HCH1  0   0.256   5.1068   2.1726   1.0459
 JVH  H9   H  HCH1  0   0.221   7.7367  -1.2395  -1.1511
 JVH  H10  H  HCR6  0   0.254   3.4899  -2.8728  -0.3233
 JVH  H11  H  HCR5  0   0.312  -6.7019  -1.2842   1.1539
 JVH  H12  H  HCH1  0   0.251  -6.4260  -1.8890  -1.4431
 JVH  H13  H  HCH2  0   0.257  -4.7635   0.1745  -1.7355
 JVH  H14  H  HCH2  0   0.253  -6.2144   0.4470  -2.7050
 JVH  H15  H  HCH1  0   0.251  -6.0311   2.3494  -0.8582
 JVH  H16  H  HCH2  0   0.238  -8.3909   1.4780   0.1095
 JVH  H17  H  HCH2  0   0.245  -8.2811   1.6724  -1.6331
 JVH  H18  H  HCH2  0   0.245  -8.5007  -0.6369  -1.9447
 JVH  H19  H  HCH2  0   0.237  -8.6078  -0.8923  -0.2096
 JVH  H20  H  HNH1  0   0.405  -0.0617   0.4352   1.1729
 JVH  H21  H  HCR6  0   0.244   2.9239   2.0171  -0.0384
 JVH  H22  H  HCH1  0   0.268   7.4981  -1.3680   1.3635
 JVH  H23  H  HCH2  0   0.249   7.3080   1.0699  -2.1390
 JVH  H24  H  HCH2  0   0.213   5.9096   0.0521  -1.8409
 JVH  H25  H  HOH1  0   0.452   9.2706   0.5105  -0.8978
 JVH  H26  H  HCR6  0   0.247   1.3284  -1.8633  -0.8607
 JVH  H27  H  HCR5  0   0.311  -6.4812   1.1235   1.4899
 JVH  O19  O  O2    0  -0.481   6.1827   1.6817  -0.5801

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
 JVH  O1   C2   double    1.207  0.020  1.207
 JVH  O6   C5   double    1.220  0.020  1.220
 JVH  C32  C34  single    1.533  0.020  1.533
 JVH  C32  C38  single    1.536  0.020  1.536
 JVH  C32  C30  single    1.540  0.020  1.540
 JVH  C8   N7   single    1.451  0.020  1.451
 JVH  C8   C9   single    1.503  0.020  1.503
 JVH  C5   N7   single    1.337  0.020  1.337
 JVH  C5   C4   single    1.524  0.020  1.524
 JVH  C2   C30  single    1.507  0.020  1.507
 JVH  C2   N3   single    1.379  0.020  1.379
 JVH  C34  C35  single    1.533  0.020  1.533
 JVH  C38  C37  single    1.552  0.020  1.552
 JVH  C4   N3   single    1.434  0.020  1.434
 JVH  C30  C28  single    1.540  0.020  1.540
 JVH  C10  C9   aromatic  1.388  0.020  1.388
 JVH  C10  C11  aromatic  1.389  0.020  1.389
 JVH  N3   C26  single    1.378  0.020  1.378
 JVH  C9   C25  aromatic  1.396  0.020  1.396
 JVH  C17  C11  single    1.506  0.020  1.506
 JVH  C17  C16  single    1.521  0.020  1.521
 JVH  C17  O19  single    1.424  0.020  1.424
 JVH  C11  C12  aromatic  1.404  0.020  1.404
 JVH  C35  C37  single    1.536  0.020  1.536
 JVH  C35  C28  single    1.540  0.020  1.540
 JVH  C26  C28  single    1.506  0.020  1.506
 JVH  C26  O27  double    1.207  0.020  1.207
 JVH  C25  C24  aromatic  1.380  0.020  1.380
 JVH  C16  C14  single    1.523  0.020  1.523
 JVH  O19  C20  single    1.411  0.020  1.411
 JVH  C12  C24  aromatic  1.404  0.020  1.404
 JVH  C12  N13  single    1.368  0.020  1.368
 JVH  C14  N13  single    1.444  0.020  1.444
 JVH  C14  C21  single    1.538  0.020  1.538
 JVH  C20  C21  single    1.525  0.020  1.525
 JVH  C21  O23  single    1.410  0.020  1.410
 JVH  C4   H1   single    0.970  0.020  1.090
 JVH  C4   H2   single    0.970  0.020  1.090
 JVH  C8   H3   single    0.970  0.020  1.090
 JVH  C8   H4   single    0.970  0.020  1.090
 JVH  N13  H5   single    0.890  0.020  1.040
 JVH  C16  H6   single    0.970  0.020  1.090
 JVH  C16  H7   single    0.970  0.020  1.090
 JVH  C17  H8   single    0.970  0.020  1.090
 JVH  C21  H9   single    0.970  0.020  1.090
 JVH  C24  H10  single    0.930  0.020  1.080
 JVH  C30  H11  single    0.970  0.020  1.090
 JVH  C32  H12  single    0.970  0.020  1.090
 JVH  C34  H13  single    0.970  0.020  1.090
 JVH  C34  H14  single    0.970  0.020  1.090
 JVH  C35  H15  single    0.970  0.020  1.090
 JVH  C37  H16  single    0.970  0.020  1.090
 JVH  C37  H17  single    0.970  0.020  1.090
 JVH  C38  H18  single    0.970  0.020  1.090
 JVH  C38  H19  single    0.970  0.020  1.090
 JVH  N7   H20  single    0.860  0.020  1.020
 JVH  C10  H21  single    0.930  0.020  1.080
 JVH  C14  H22  single    0.970  0.020  1.090
 JVH  C20  H23  single    0.970  0.020  1.090
 JVH  C20  H24  single    0.970  0.020  1.090
 JVH  O23  H25  single    0.850  0.020  0.980
 JVH  C25  H26  single    0.930  0.020  1.080
 JVH  C28  H27  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
 JVH  N3   C2   O1   124.32  3.000
 JVH  N3   C2   C30  108.35  3.000
 JVH  O1   C2   C30  127.33  3.000
 JVH  H2   C4   H1   107.18  3.000
 JVH  H2   C4   N3   109.81  3.000
 JVH  H1   C4   N3   108.49  3.000
 JVH  H2   C4   C5   111.62  3.000
 JVH  H1   C4   C5   108.64  3.000
 JVH  N3   C4   C5   110.97  3.000
 JVH  N7   C5   O6   124.79  3.000
 JVH  N7   C5   C4   113.83  3.000
 JVH  O6   C5   C4   121.34  3.000
 JVH  H4   C8   H3   106.96  3.000
 JVH  H4   C8   C9   110.01  3.000
 JVH  H3   C8   C9   110.95  3.000
 JVH  H4   C8   N7   110.03  3.000
 JVH  H3   C8   N7   107.78  3.000
 JVH  C9   C8   N7   111.01  3.000
 JVH  C10  C11  C17  121.63  3.000
 JVH  C17  C11  C12  118.85  3.000
 JVH  C10  C11  C12  119.50  3.000
 JVH  C24  C12  N13  120.80  3.000
 JVH  N13  C12  C11  120.56  3.000
 JVH  C24  C12  C11  118.63  3.000
 JVH  H5   N13  C14  117.26  3.000
 JVH  H5   N13  C12  117.36  3.000
 JVH  C14  N13  C12  121.86  3.000
 JVH  H7   C16  H6   107.52  3.000
 JVH  H7   C16  C14  110.42  3.000
 JVH  H6   C16  C14  110.70  3.000
 JVH  H7   C16  C17  110.31  3.000
 JVH  H6   C16  C17  110.98  3.000
 JVH  C14  C16  C17  106.94  3.000
 JVH  H8   C17  O19  105.27  3.000
 JVH  H8   C17  C16  110.77  3.000
 JVH  O19  C17  C16  109.86  3.000
 JVH  H8   C17  C11  109.75  3.000
 JVH  O19  C17  C11  111.83  3.000
 JVH  C16  C17  C11  109.32  3.000
 JVH  H9   C21  O23  110.96  3.000
 JVH  H9   C21  C20  107.53  3.000
 JVH  O23  C21  C20  112.74  3.000
 JVH  H9   C21  C14  108.86  3.000
 JVH  O23  C21  C14  106.45  3.000
 JVH  C20  C21  C14  110.26  3.000
 JVH  H10  C24  C25  119.95  3.000
 JVH  H10  C24  C12  119.51  3.000
 JVH  C25  C24  C12  120.54  3.000
 JVH  H11  C30  C28  114.39  3.000
 JVH  H11  C30  C32  112.06  3.000
 JVH  C28  C30  C32  103.42  3.000
 JVH  H11  C30  C2   108.54  3.000
 JVH  C28  C30  C2   104.84  3.000
 JVH  C32  C30  C2   113.43  3.000
 JVH  H12  C32  C38  114.39  3.000
 JVH  H12  C32  C34  117.00  3.000
 JVH  C38  C32  C34  101.56  3.000
 JVH  H12  C32  C30  113.63  3.000
 JVH  C38  C32  C30  106.86  3.000
 JVH  C34  C32  C30  101.87  3.000
 JVH  H14  C34  H13  107.89  3.000
 JVH  H14  C34  C35  112.43  3.000
 JVH  H13  C34  C35  114.49  3.000
 JVH  H14  C34  C32  112.63  3.000
 JVH  H13  C34  C32  114.48  3.000
 JVH  C35  C34  C32   94.65  3.000
 JVH  H15  C35  C28  113.82  3.000
 JVH  H15  C35  C37  114.27  3.000
 JVH  C28  C35  C37  106.89  3.000
 JVH  H15  C35  C34  116.90  3.000
 JVH  C28  C35  C34  101.93  3.000
 JVH  C37  C35  C34  101.49  3.000
 JVH  H17  C37  H16  107.24  3.000
 JVH  H17  C37  C38  111.13  3.000
 JVH  H16  C37  C38  112.95  3.000
 JVH  H17  C37  C35  110.18  3.000
 JVH  H16  C37  C35  112.16  3.000
 JVH  C38  C37  C35  103.21  3.000
 JVH  H19  C38  H18  107.27  3.000
 JVH  H19  C38  C37  112.87  3.000
 JVH  H18  C38  C37  111.25  3.000
 JVH  H19  C38  C32  112.09  3.000
 JVH  H18  C38  C32  110.17  3.000
 JVH  C37  C38  C32  103.22  3.000
 JVH  C26  N3   C4   121.94  3.000
 JVH  C26  N3   C2   113.37  3.000
 JVH  C4   N3   C2   124.33  3.000
 JVH  H20  N7   C8   116.77  3.000
 JVH  H20  N7   C5   118.55  3.000
 JVH  C8   N7   C5   124.66  3.000
 JVH  C25  C9   C10  117.74  3.000
 JVH  C25  C9   C8   120.79  3.000
 JVH  C10  C9   C8   121.47  3.000
 JVH  H21  C10  C9   119.42  3.000
 JVH  H21  C10  C11  118.38  3.000
 JVH  C9   C10  C11  122.20  3.000
 JVH  H22  C14  C21  108.72  3.000
 JVH  H22  C14  C16  110.75  3.000
 JVH  C21  C14  C16  109.21  3.000
 JVH  H22  C14  N13  107.83  3.000
 JVH  C21  C14  N13  111.94  3.000
 JVH  C16  C14  N13  108.40  3.000
 JVH  H24  C20  H23  106.44  3.000
 JVH  H24  C20  O19  111.27  3.000
 JVH  H23  C20  O19  106.65  3.000
 JVH  H24  C20  C21  108.85  3.000
 JVH  H23  C20  C21  109.95  3.000
 JVH  O19  C20  C21  113.43  3.000
 JVH  H25  O23  C21  108.61  3.000
 JVH  H26  C25  C9   119.70  3.000
 JVH  H26  C25  C24  118.91  3.000
 JVH  C9   C25  C24  121.38  3.000
 JVH  C28  C26  O27  127.88  3.000
 JVH  O27  C26  N3   123.45  3.000
 JVH  C28  C26  N3   108.66  3.000
 JVH  H27  C28  C26  108.63  3.000
 JVH  H27  C28  C35  112.23  3.000
 JVH  C26  C28  C35  113.45  3.000
 JVH  H27  C28  C30  114.37  3.000
 JVH  C26  C28  C30  104.55  3.000
 JVH  C35  C28  C30  103.41  3.000
 JVH  C20  O19  C17  113.60  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
 JVH  CONST_01  C25  C9   C10  C11     0.00   0.0  0
 JVH  CONST_02  C25  C24  C12  C11     0.00   0.0  0
 JVH  CONST_03  C9   C10  C11  C12     0.00   0.0  0
 JVH  CONST_04  C9   C25  C24  C12     0.00   0.0  0
 JVH  CONST_05  C10  C9   C25  C24     0.00   0.0  0
 JVH  CONST_06  C10  C11  C12  C24     0.00   0.0  0
 JVH  CONST_07  C26  N3   C2   C30     0.00   0.0  0
 JVH  CONST_08  C11  C10  C9   C8    180.00   0.0  0
 JVH  CONST_09  C24  C25  C9   C8    180.00   0.0  0
 JVH  CONST_10  C30  C2   N3   C4    180.00   0.0  0
 JVH  CONST_11  C26  N3   C2   O1    180.00   0.0  0
 JVH  CONST_12  H10  C24  C12  C11   180.00   0.0  0
 JVH  CONST_13  H21  C10  C11  C12   180.00   0.0  0
 JVH  CONST_14  H26  C25  C24  C12   180.00   0.0  0
 JVH  CONST_15  O1   C2   N3   C4      0.00   0.0  0
 JVH  CONST_16  C8   N7   C5   C4    180.00   0.0  0
 JVH  CONST_17  O6   C5   N7   C8      0.00   0.0  0
 JVH  CONST_18  H20  N7   C5   C4      0.00   0.0  0
 JVH  Var_01    C28  C26  N3   C2      4.93  30.0  1
 JVH  Var_02    C14  N13  C12  C11    -6.67  30.0  1
 JVH  Var_03    C21  C20  O19  C17   -54.07  30.0  3
 JVH  Var_04    C35  C37  C38  C32    -0.21  30.0  1
 JVH  Var_05    C5   C4   N3   C2    100.10  30.0  2
 JVH  Var_06    C10  C9   C8   N7   -111.54  30.0  2
 JVH  Var_07    C9   C8   N7   C5   -137.86  30.0  1
 JVH  Var_08    O6   C5   C4   N3    -24.48  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
 JVH  chir_01  C17  C11  C16  O19  negativ
 JVH  chir_02  C21  O23  C14  C20  negativ
 JVH  chir_03  C30  C32  C2   C28  negativ
 JVH  chir_04  C32  C34  C38  C30  positiv
 JVH  chir_05  C35  C28  C37  C34  positiv
 JVH  chir_06  C14  C16  N13  C21  negativ
 JVH  chir_07  C28  C30  C35  C26  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
 JVH  plan-1  C4   0.020
 JVH  plan-1  C5   0.020
 JVH  plan-1  C8   0.020
 JVH  plan-1  O6   0.020
 JVH  plan-1  N7   0.020
 JVH  plan-1  H20  0.020
 JVH  plan-2  C8   0.020
 JVH  plan-2  C11  0.020
 JVH  plan-2  C12  0.020
 JVH  plan-2  N13  0.020
 JVH  plan-2  C17  0.020
 JVH  plan-2  C24  0.020
 JVH  plan-2  C9   0.020
 JVH  plan-2  C10  0.020
 JVH  plan-2  C25  0.020
 JVH  plan-2  H10  0.020
 JVH  plan-2  H21  0.020
 JVH  plan-2  H26  0.020
 JVH  plan-3  N3   0.020
 JVH  plan-3  C26  0.020
 JVH  plan-3  O27  0.020
 JVH  plan-3  C28  0.020
 JVH  plan-4  C2   0.020
 JVH  plan-4  C4   0.020
 JVH  plan-4  C30  0.020
 JVH  plan-4  O1   0.020
 JVH  plan-4  N3   0.020
 JVH  plan-4  C26  0.020

