# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:23:39 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: (2S)-({[(1R,3S,4S)-2-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl}-2-azabicyclo[2.2.1]heptan-3-yl]carbonyl}amino)(phenyl)acetic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](CC(=O)NO)C(=O)N1[C@@H]2CC[C@@H](C2)[C@H]1C(=O)N[C@H](C(O)=O)c3ccccc3
#
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
 E8P  E8P  '(2S)-({[(1R,3S,4S)-2-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl}-2-azabicyclo[2.2.1]heptan-3-yl]carbonyl}amino)(phenyl)acetic acid (non-preferred name)'  ligand  65  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E8P
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
 E8P  C17  C  CH1    0  -0.416   2.9455   0.2938  -0.5293
 E8P  C22  C  C      0   0.525   3.6192   1.7463   1.4390
 E8P  C28  C  C      0   0.604   1.4725   0.3931  -0.1467
 E8P  C01  C  CH3    0  -0.662   7.3270  -4.3795  -0.1339
 E8P  C05  C  CH2    0  -0.419   6.8743  -2.9763  -0.5130
 E8P  C08  C  CH2    0  -0.405   5.4309  -2.6922  -0.1145
 E8P  C11  C  CH2    0  -0.425   4.9658  -1.2884  -0.4814
 E8P  C14  C  CH2    0  -0.404   3.5312  -1.0287  -0.0338
 E8P  C19  C  CH2    0  -0.593   3.7425   1.5208  -0.0486
 E8P  O23  O  O      0  -0.466   2.6137   2.2011   1.9544
 E8P  N24  N  NH1    0  -0.372   4.7014   1.3547   2.1395
 E8P  O26  O  OH1    0  -0.544   4.7847   1.6210   3.4723
 E8P  O29  O  O      0  -0.508   0.9884  -0.3101   0.7322
 E8P  N30  N  NT     0  -0.450   0.7010   1.2539  -0.8273
 E8P  C31  C  CH1    0  -0.152   1.0415   2.2244  -1.8688
 E8P  C33  C  CH2    0  -0.429   0.9628   3.6259  -1.2410
 E8P  C36  C  CH2    0  -0.444  -0.5623   3.7975  -1.0068
 E8P  C39  C  CH1    0  -0.302  -1.1427   2.4699  -1.5198
 E8P  C41  C  CH2    0  -0.429  -0.2280   2.1832  -2.7148
 E8P  C44  C  CH1    0  -0.205  -0.7140   1.3662  -0.5287
 E8P  C46  C  C      0   0.607  -1.4667   0.0680  -0.7804
 E8P  O47  O  O      0  -0.500  -1.1499  -0.7217  -1.6563
 E8P  N48  N  NH1    0  -0.643  -2.5336  -0.1047   0.0123
 E8P  C50  C  CH1    0  -0.228  -3.5472  -1.0843  -0.3031
 E8P  C52  C  C      0   0.413  -4.2426  -0.8065  -1.6705
 E8P  O53  O  O      0  -0.585  -4.2273   0.3630  -2.0857
 E8P  O55  O  OC    -1  -0.602  -4.7891  -1.7980  -2.1868
 E8P  C56  C  CR6    0   0.104  -4.6004  -1.0985   0.7743
 E8P  C57  C  CR16   0  -0.295  -5.3157   0.0597   1.0799
 E8P  C59  C  CR16   0  -0.240  -6.2947   0.0472   2.0629
 E8P  C61  C  CR16   0  -0.270  -6.5819  -1.1267   2.7490
 E8P  C63  C  CR16   0  -0.240  -5.8820  -2.2860   2.4449
 E8P  C65  C  CR16   0  -0.330  -4.8969  -2.2688   1.4652
 E8P  H1   H  HCH1   0   0.278   3.0142   0.2975  -1.6222
 E8P  H2   H  HCH3   0   0.216   7.2434  -4.5431   0.9423
 E8P  H3   H  HCH3   0   0.216   6.7209  -5.1395  -0.6303
 E8P  H4   H  HCH3   0   0.226   8.3667  -4.5539  -0.4129
 E8P  H5   H  HCH2   0   0.210   7.5316  -2.2402  -0.0399
 E8P  H6   H  HCH2   0   0.211   6.9875  -2.8334  -1.5921
 E8P  H7   H  HCH2   0   0.210   4.7721  -3.4273  -0.5891
 E8P  H8   H  HCH2   0   0.209   5.3190  -2.8373   0.9658
 E8P  H9   H  HCH2   0   0.205   5.6511  -0.5662  -0.0273
 E8P  H10  H  HCH2   0   0.216   5.0490  -1.1463  -1.5647
 E8P  H11  H  HCH2   0   0.225   3.4733  -1.0855   1.0562
 E8P  H12  H  HCH2   0   0.233   2.9043  -1.8418  -0.4098
 E8P  H13  H  HCH2   0   0.275   4.7830   1.4019  -0.3547
 E8P  H14  H  HCH2   0   0.295   3.3846   2.4257  -0.5411
 E8P  H15  H  HNH1   0   0.415   5.5839   1.1443   1.6965
 E8P  H16  H  HOH1   0   0.478   4.4914   0.8204   3.9259
 E8P  H17  H  HCH1   0   0.265   1.9762   1.9869  -2.3706
 E8P  H18  H  HCH2   0   0.245   1.5420   3.6850  -0.3195
 E8P  H19  H  HCH2   0   0.241   1.3566   4.3757  -1.9290
 E8P  H20  H  HCH2   0   0.240  -0.8106   3.9781   0.0399
 E8P  H21  H  HCH2   0   0.247  -0.9606   4.6322  -1.5854
 E8P  H22  H  HCH1   0   0.263  -2.2152   2.4750  -1.7086
 E8P  H23  H  HCH2   0   0.249  -0.2590   2.9733  -3.4670
 E8P  H24  H  HCH2   0   0.257  -0.3979   1.2202  -3.1924
 E8P  H25  H  HCH1   0   0.273  -0.8791   1.6898   0.5048
 E8P  H26  H  HNH1   0   0.395  -2.7577   0.6229   0.6725
 E8P  H27  H  HCH1   0   0.249  -3.0829  -2.0726  -0.3469
 E8P  H29  H  HCR6   0   0.251  -5.1157   0.9759   0.5365
 E8P  H30  H  HCR6   0   0.254  -6.8399   0.9547   2.2893
 E8P  H31  H  HCR6   0   0.255  -7.3463  -1.1365   3.5150
 E8P  H32  H  HCR6   0   0.254  -6.0975  -3.2056   2.9741
 E8P  H33  H  HCR6   0   0.249  -4.3484  -3.1755   1.2392

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
 E8P  C59  C61  aromatic  1.390  0.020  1.390
 E8P  C59  C57  aromatic  1.387  0.020  1.387
 E8P  C61  C63  aromatic  1.388  0.020  1.388
 E8P  C57  C56  aromatic  1.395  0.020  1.395
 E8P  C63  C65  aromatic  1.389  0.020  1.389
 E8P  O53  C52  deloc     1.241  0.020  1.241
 E8P  C56  C65  aromatic  1.391  0.020  1.391
 E8P  C56  C50  single    1.507  0.020  1.507
 E8P  C52  C50  single    1.559  0.020  1.559
 E8P  C52  O55  deloc     1.244  0.020  1.244
 E8P  C50  N48  single    1.444  0.020  1.444
 E8P  N48  C46  single    1.340  0.020  1.340
 E8P  O47  C46  double    1.221  0.020  1.221
 E8P  C46  C44  single    1.522  0.020  1.522
 E8P  C44  C39  single    1.544  0.020  1.544
 E8P  C44  N30  single    1.451  0.020  1.451
 E8P  O29  C28  double    1.225  0.020  1.225
 E8P  C39  C41  single    1.532  0.020  1.532
 E8P  C39  C36  single    1.537  0.020  1.537
 E8P  N30  C28  single    1.341  0.020  1.341
 E8P  N30  C31  single    1.464  0.020  1.464
 E8P  C28  C17  single    1.525  0.020  1.525
 E8P  C41  C31  single    1.526  0.020  1.526
 E8P  C14  C11  single    1.525  0.020  1.525
 E8P  C14  C17  single    1.529  0.020  1.529
 E8P  C11  C08  single    1.524  0.020  1.524
 E8P  C05  C08  single    1.524  0.020  1.524
 E8P  C05  C01  single    1.522  0.020  1.522
 E8P  C31  C33  single    1.538  0.020  1.538
 E8P  C17  C19  single    1.540  0.020  1.540
 E8P  C36  C33  single    1.553  0.020  1.553
 E8P  C19  C22  single    1.510  0.020  1.510
 E8P  C22  N24  single    1.347  0.020  1.347
 E8P  C22  O23  double    1.218  0.020  1.218
 E8P  N24  O26  single    1.362  0.020  1.362
 E8P  C17  H1   single    0.970  0.020  1.090
 E8P  C01  H2   single    0.970  0.020  1.090
 E8P  C01  H3   single    0.970  0.020  1.090
 E8P  C01  H4   single    0.970  0.020  1.090
 E8P  C05  H5   single    0.970  0.020  1.090
 E8P  C05  H6   single    0.970  0.020  1.090
 E8P  C08  H7   single    0.970  0.020  1.090
 E8P  C08  H8   single    0.970  0.020  1.090
 E8P  C11  H9   single    0.970  0.020  1.090
 E8P  C11  H10  single    0.970  0.020  1.090
 E8P  C14  H11  single    0.970  0.020  1.090
 E8P  C14  H12  single    0.970  0.020  1.090
 E8P  C19  H13  single    0.970  0.020  1.090
 E8P  C19  H14  single    0.970  0.020  1.090
 E8P  N24  H15  single    0.890  0.020  1.040
 E8P  O26  H16  single    0.850  0.020  0.980
 E8P  C31  H17  single    0.970  0.020  1.090
 E8P  C33  H18  single    0.970  0.020  1.090
 E8P  C33  H19  single    0.970  0.020  1.090
 E8P  C36  H20  single    0.970  0.020  1.090
 E8P  C36  H21  single    0.970  0.020  1.090
 E8P  C39  H22  single    0.970  0.020  1.090
 E8P  C41  H23  single    0.970  0.020  1.090
 E8P  C41  H24  single    0.970  0.020  1.090
 E8P  C44  H25  single    0.970  0.020  1.090
 E8P  N48  H26  single    0.860  0.020  1.020
 E8P  C50  H27  single    0.970  0.020  1.090
 E8P  C57  H29  single    0.930  0.020  1.080
 E8P  C59  H30  single    0.930  0.020  1.080
 E8P  C61  H31  single    0.930  0.020  1.080
 E8P  C63  H32  single    0.930  0.020  1.080
 E8P  C65  H33  single    0.930  0.020  1.080

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
 E8P  H1   C17  C19  106.05  3.000
 E8P  H1   C17  C14  107.60  3.000
 E8P  C19  C17  C14  112.94  3.000
 E8P  H1   C17  C28  108.10  3.000
 E8P  C19  C17  C28  111.69  3.000
 E8P  C14  C17  C28  110.18  3.000
 E8P  N24  C22  O23  123.47  3.000
 E8P  O23  C22  C19  122.70  3.000
 E8P  N24  C22  C19  113.79  3.000
 E8P  N30  C28  O29  120.33  3.000
 E8P  N30  C28  C17  118.04  3.000
 E8P  O29  C28  C17  121.61  3.000
 E8P  H4   C01  H3   107.56  3.000
 E8P  H4   C01  H2   107.53  3.000
 E8P  H3   C01  H2   107.55  3.000
 E8P  H4   C01  C05  111.54  3.000
 E8P  H3   C01  C05  111.31  3.000
 E8P  H2   C01  C05  111.15  3.000
 E8P  H6   C05  H5   106.03  3.000
 E8P  H6   C05  C08  109.36  3.000
 E8P  H5   C05  C08  109.29  3.000
 E8P  H6   C05  C01  109.58  3.000
 E8P  H5   C05  C01  109.50  3.000
 E8P  C08  C05  C01  112.85  3.000
 E8P  H8   C08  H7   106.08  3.000
 E8P  H8   C08  C11  109.17  3.000
 E8P  H7   C08  C11  109.29  3.000
 E8P  H8   C08  C05  109.25  3.000
 E8P  H7   C08  C05  109.34  3.000
 E8P  C11  C08  C05  113.44  3.000
 E8P  H10  C11  H9   106.09  3.000
 E8P  H10  C11  C14  109.85  3.000
 E8P  H9   C11  C14  110.79  3.000
 E8P  H10  C11  C08  109.54  3.000
 E8P  H9   C11  C08  108.48  3.000
 E8P  C14  C11  C08  111.92  3.000
 E8P  H12  C14  H11  105.90  3.000
 E8P  H12  C14  C11  108.16  3.000
 E8P  H11  C14  C11  109.49  3.000
 E8P  H12  C14  C17  108.19  3.000
 E8P  H11  C14  C17  110.36  3.000
 E8P  C11  C14  C17  114.37  3.000
 E8P  H14  C19  H13  106.06  3.000
 E8P  H14  C19  C22  107.11  3.000
 E8P  H13  C19  C22  111.75  3.000
 E8P  H14  C19  C17  110.51  3.000
 E8P  H13  C19  C17  108.60  3.000
 E8P  C22  C19  C17  112.60  3.000
 E8P  H15  N24  O26  114.63  3.000
 E8P  H15  N24  C22  122.31  3.000
 E8P  O26  N24  C22  120.08  3.000
 E8P  H16  O26  N24  106.19  3.000
 E8P  C44  N30  C31  108.79  3.000
 E8P  C31  N30  C28  130.74  3.000
 E8P  C44  N30  C28  120.42  3.000
 E8P  H17  C31  C41  116.96  3.000
 E8P  H17  C31  C33  115.57  3.000
 E8P  C41  C31  C33  102.02  3.000
 E8P  H17  C31  N30  112.56  3.000
 E8P  C33  C31  N30  107.57  3.000
 E8P  C41  C31  N30  100.54  3.000
 E8P  H19  C33  H18  107.70  3.000
 E8P  H19  C33  C36  111.95  3.000
 E8P  H18  C33  C36  112.86  3.000
 E8P  H19  C33  C31  110.51  3.000
 E8P  H18  C33  C31  111.55  3.000
 E8P  C36  C33  C31  102.27  3.000
 E8P  H21  C36  H20  107.41  3.000
 E8P  H21  C36  C39  110.25  3.000
 E8P  H20  C36  C39  112.17  3.000
 E8P  H21  C36  C33  111.29  3.000
 E8P  H20  C36  C33  112.74  3.000
 E8P  C39  C36  C33  103.01  3.000
 E8P  H22  C39  C44  112.83  3.000
 E8P  H22  C39  C41  116.98  3.000
 E8P  C44  C39  C41  101.60  3.000
 E8P  H22  C39  C36  115.19  3.000
 E8P  C41  C39  C36  101.33  3.000
 E8P  C44  C39  C36  107.36  3.000
 E8P  H24  C41  H23  109.49  3.000
 E8P  H24  C41  C39  114.50  3.000
 E8P  H23  C41  C39  112.66  3.000
 E8P  H24  C41  C31  113.40  3.000
 E8P  H23  C41  C31  112.72  3.000
 E8P  C39  C41  C31   93.40  3.000
 E8P  H25  C44  C46  109.48  3.000
 E8P  H25  C44  C39  110.64  3.000
 E8P  C46  C44  C39  111.49  3.000
 E8P  H25  C44  N30  111.35  3.000
 E8P  C39  C44  N30  101.19  3.000
 E8P  C46  C44  N30  112.49  3.000
 E8P  N48  C46  O47  123.19  3.000
 E8P  O47  C46  C44  122.82  3.000
 E8P  N48  C46  C44  113.95  3.000
 E8P  H26  N48  C50  118.47  3.000
 E8P  H26  N48  C46  118.13  3.000
 E8P  C50  N48  C46  121.12  3.000
 E8P  H27  C50  C56  108.49  3.000
 E8P  H27  C50  C52  108.39  3.000
 E8P  C56  C50  C52  108.48  3.000
 E8P  H27  C50  N48  108.90  3.000
 E8P  C52  C50  N48  112.56  3.000
 E8P  C56  C50  N48  109.92  3.000
 E8P  O55  C52  O53  128.13  3.000
 E8P  O55  C52  C50  114.70  3.000
 E8P  O53  C52  C50  117.12  3.000
 E8P  C65  C56  C57  118.71  3.000
 E8P  C65  C56  C50  120.80  3.000
 E8P  C57  C56  C50  120.48  3.000
 E8P  H29  C57  C59  119.53  3.000
 E8P  H29  C57  C56  119.83  3.000
 E8P  C59  C57  C56  120.63  3.000
 E8P  H30  C59  C61  120.05  3.000
 E8P  H30  C59  C57  119.74  3.000
 E8P  C61  C59  C57  120.21  3.000
 E8P  H31  C61  C63  120.25  3.000
 E8P  H31  C61  C59  120.20  3.000
 E8P  C63  C61  C59  119.55  3.000
 E8P  H32  C63  C65  119.76  3.000
 E8P  H32  C63  C61  120.13  3.000
 E8P  C65  C63  C61  120.11  3.000
 E8P  H33  C65  C63  119.71  3.000
 E8P  H33  C65  C56  119.51  3.000
 E8P  C63  C65  C56  120.78  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
 E8P  CONST_01  C61  C59  C57  C56     0.00   0.0  0
 E8P  CONST_02  C61  C63  C65  C56     0.00   0.0  0
 E8P  CONST_03  C63  C61  C59  C57     0.00   0.0  0
 E8P  CONST_04  C63  C65  C56  C57     0.00   0.0  0
 E8P  CONST_05  C65  C63  C61  C59     0.00   0.0  0
 E8P  CONST_06  C65  C56  C57  C59     0.00   0.0  0
 E8P  CONST_07  C59  C57  C56  C50   180.00   0.0  0
 E8P  CONST_08  C63  C65  C56  C50   180.00   0.0  0
 E8P  CONST_09  H30  C59  C57  C56   180.00   0.0  0
 E8P  CONST_10  H32  C63  C65  C56   180.00   0.0  0
 E8P  CONST_11  H31  C61  C59  C57   180.00   0.0  0
 E8P  CONST_12  H33  C65  C56  C57   180.00   0.0  0
 E8P  CONST_13  H29  C57  C59  C61   180.00   0.0  0
 E8P  CONST_14  C44  N30  C28  C17   180.00   0.0  0
 E8P  CONST_15  C31  N30  C28  C17     0.00   0.0  0
 E8P  CONST_16  C44  N30  C28  O29     0.00   0.0  0
 E8P  CONST_17  C31  N30  C28  O29   180.00   0.0  0
 E8P  CONST_19  H26  N48  C46  C44     0.00   0.0  0
 E8P  CONST_20  O26  N24  C22  C19   180.00   0.0  0
 E8P  CONST_21  O26  N24  C22  O23     0.00   0.0  0
 E8P  CONST_22  C50  N48  C46  O47     0.00   0.0  0
 E8P  CONST_23  H15  N24  C22  C19     0.00   0.0  0
 E8P  Var_01    C39  C36  C33  C31     0.48  30.0  1
 E8P  Var_02    C08  C11  C14  C17  -172.53  30.0  3
 E8P  Var_03    N24  C22  C19  C17   103.09  30.0  3
 E8P  Var_04    C11  C08  C05  C01   179.71  30.0  3
 E8P  Var_05    C14  C11  C08  C05  -178.45  30.0  1
 E8P  Var_06    H2   C01  C05  C08   -59.02  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
 E8P  chir_01  C17  C28  C14  C19  positiv
 E8P  chir_02  C31  N30  C41  C33  negativ
 E8P  chir_03  C39  C36  C41  C44  negativ
 E8P  chir_04  C44  N30  C39  C46  negativ
 E8P  chir_05  C50  N48  C56  C52  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
 E8P  plan-1  C50  0.020
 E8P  plan-1  C56  0.020
 E8P  plan-1  C57  0.020
 E8P  plan-1  C59  0.020
 E8P  plan-1  C61  0.020
 E8P  plan-1  C63  0.020
 E8P  plan-1  C65  0.020
 E8P  plan-1  H29  0.020
 E8P  plan-1  H30  0.020
 E8P  plan-1  H31  0.020
 E8P  plan-1  H32  0.020
 E8P  plan-1  H33  0.020
 E8P  plan-2  C22  0.020
 E8P  plan-2  C19  0.020
 E8P  plan-2  O23  0.020
 E8P  plan-2  N24  0.020
 E8P  plan-2  O26  0.020
 E8P  plan-2  H15  0.020
 E8P  plan-3  C17  0.020
 E8P  plan-3  C28  0.020
 E8P  plan-3  O29  0.020
 E8P  plan-3  N30  0.020
 E8P  plan-3  C31  0.020
 E8P  plan-3  C44  0.020
 E8P  plan-4  C44  0.020
 E8P  plan-4  C46  0.020
 E8P  plan-4  O47  0.020
 E8P  plan-4  N48  0.020
 E8P  plan-4  C50  0.020
 E8P  plan-4  H26  0.020
 E8P  plan-5  C50  0.020
 E8P  plan-5  C52  0.020
 E8P  plan-5  O53  0.020
 E8P  plan-5  O55  0.020

