# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 11:09:53 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{(1R,3S,5S)-3-[(1R)-2-(2,6-dioxopiperidin-4-yl)-1-hydroxyethyl]-1,5-dimethyl-4-oxocyclohexyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@](C)(C[C@@H]([C@H](O)CC2CC(=O)NC(=O)C2)C1=O)NC(=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
 Z2V  Z2V  "N-[(1R,3S,4R,5S)-3-{(1R)-2-[(2R,4r,6S)-2,6-dihydroxypiperidin-4-yl]-1-hydroxyethyl}-4-hydroxy-1,5-dimethylcyclohexyl]benzamide"
  ligand  57  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z2V
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
 Z2V  C02  C  C     0   0.452  208.0424  175.5455  232.3419
 Z2V  C03  C  CH1   0  -0.406  208.9288  176.6638  232.8633
 Z2V  C04  C  CH1   0   0.060  210.1606  176.1519  233.6117
 Z2V  C06  C  CH2   0  -0.441  211.2222  177.2465  233.7307
 Z2V  C07  C  CH1   0  -0.286  212.4845  176.8399  234.4935
 Z2V  C08  C  CH2   0  -0.571  213.6734  177.6756  234.0312
 Z2V  C09  C  C     0   0.544  214.9410  177.3764  234.7799
 Z2V  C11  C  C     0   0.545  213.6073  176.7054  236.7528
 Z2V  C12  C  CH2   0  -0.566  212.3444  177.0169  236.0026
 Z2V  C15  C  CH2   0  -0.475  208.0871  177.6371  233.6976
 Z2V  C16  C  CT    0   0.152  206.8683  178.1946  232.9513
 Z2V  C19  C  CR6   0  -0.023  204.4154  180.2705  235.0169
 Z2V  C20  C  CR16  0  -0.297  204.6726  179.8161  236.3095
 Z2V  C21  C  CR16  0  -0.239  204.1355  180.4773  237.4051
 Z2V  C22  C  CR16  0  -0.251  203.3433  181.6019  237.2209
 Z2V  C23  C  CR16  0  -0.240  203.0774  182.0556  235.9350
 Z2V  C24  C  CR16  0  -0.271  203.6021  181.3878  234.8395
 Z2V  C26  C  CH3   0  -0.663  207.3010  179.1120  231.8056
 Z2V  C27  C  CH2   0  -0.411  206.0203  177.0141  232.4611
 Z2V  C28  C  CH1   0  -0.381  206.8054  176.0121  231.6034
 Z2V  C29  C  CH3   0  -0.651  205.9156  174.8669  231.1478
 Z2V  N10  N  NH1   0  -0.678  214.7875  176.9125  236.0692
 Z2V  N17  N  NH1   0  -0.688  206.1300  178.9641  233.9574
 Z2V  O01  O  O     0  -0.389  208.3134  174.3753  232.4785
 Z2V  O05  O  OH1   0  -0.672  209.7425  175.6464  234.8640
 Z2V  O13  O  O     0  -0.427  213.6295  176.3119  237.8974
 Z2V  O14  O  O     0  -0.427  216.0484  177.5339  234.3166
 Z2V  O25  O  O     0  -0.484  204.3212  179.6081  232.7447
 Z2V  H2   H  HCH1  0   0.283  209.2836  177.1969  231.9715
 Z2V  H3   H  HCH1  0   0.231  210.6017  175.3464  233.0115
 Z2V  H4   H  HCH2  0   0.245  211.5034  177.5217  232.7095
 Z2V  H5   H  HCH2  0   0.237  210.8107  178.1541  234.1845
 Z2V  H6   H  HCH1  0   0.256  212.7046  175.7869  234.2788
 Z2V  H7   H  HCH2  0   0.283  213.4516  178.7403  234.1746
 Z2V  H8   H  HCH2  0   0.286  213.8713  177.5373  232.9680
 Z2V  H11  H  HCH2  0   0.280  212.0869  178.0611  236.2190
 Z2V  H12  H  HCH2  0   0.284  211.5467  176.4095  236.4237
 Z2V  H13  H  HCH2  0   0.257  207.7356  177.1234  234.5967
 Z2V  H14  H  HCH2  0   0.262  208.7102  178.4720  234.0314
 Z2V  H15  H  HCR6  0   0.260  205.2709  178.9286  236.4765
 Z2V  H16  H  HCR6  0   0.262  204.3332  180.1091  238.4033
 Z2V  H17  H  HCR6  0   0.262  202.9289  182.1196  238.0762
 Z2V  H18  H  HCR6  0   0.260  202.4579  182.9302  235.7857
 Z2V  H19  H  HCR6  0   0.257  203.3859  181.7413  233.8399
 Z2V  H20  H  HCH3  0   0.235  207.8965  179.9407  232.1912
 Z2V  H21  H  HCH3  0   0.234  207.9082  178.5871  231.0686
 Z2V  H22  H  HCH3  0   0.246  206.4378  179.5211  231.2848
 Z2V  H23  H  HCH2  0   0.257  205.1671  177.3694  231.8835
 Z2V  H24  H  HCH2  0   0.237  205.6196  176.4904  233.3353
 Z2V  H25  H  HCH1  0   0.269  207.1721  176.5436  230.7156
 Z2V  H26  H  HCH3  0   0.235  206.4458  174.1704  230.4994
 Z2V  H27  H  HCH3  0   0.224  205.5241  174.3055  231.9971
 Z2V  H28  H  HCH3  0   0.233  205.0656  175.2568  230.5875
 Z2V  H29  H  HNH1  0   0.410  215.6418  176.7168  236.5796
 Z2V  H31  H  HNH1  0   0.407  206.6119  179.1209  234.8285
 Z2V  H33  H  HOH1  0   0.456  210.2925  174.8925  235.0930
 Z2V  C18  C  C     0   0.534  204.9473  179.5810  233.7956

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
 Z2V  C29  C28  single    1.520  0.020  1.520
 Z2V  C28  C27  single    1.535  0.020  1.535
 Z2V  C28  C02  single    1.514  0.020  1.514
 Z2V  O01  C02  double    1.209  0.020  1.209
 Z2V  C26  C16  single    1.530  0.020  1.530
 Z2V  C27  C16  single    1.534  0.020  1.534
 Z2V  C02  C03  single    1.519  0.020  1.519
 Z2V  O25  C18  double    1.224  0.020  1.224
 Z2V  C03  C04  single    1.530  0.020  1.530
 Z2V  C03  C15  single    1.534  0.020  1.534
 Z2V  C16  C15  single    1.534  0.020  1.534
 Z2V  C16  N17  single    1.466  0.020  1.466
 Z2V  O14  C09  double    1.211  0.020  1.211
 Z2V  C08  C09  single    1.502  0.020  1.502
 Z2V  C08  C07  single    1.525  0.020  1.525
 Z2V  C06  C04  single    1.530  0.020  1.530
 Z2V  C06  C07  single    1.530  0.020  1.530
 Z2V  C18  N17  single    1.344  0.020  1.344
 Z2V  C18  C19  single    1.500  0.020  1.500
 Z2V  C04  O05  single    1.414  0.020  1.414
 Z2V  C09  N10  single    1.379  0.020  1.379
 Z2V  C07  C12  single    1.526  0.020  1.526
 Z2V  C24  C19  aromatic  1.393  0.020  1.393
 Z2V  C24  C23  aromatic  1.386  0.020  1.386
 Z2V  C19  C20  aromatic  1.394  0.020  1.394
 Z2V  N10  C11  single    1.379  0.020  1.379
 Z2V  C12  C11  single    1.502  0.020  1.502
 Z2V  C23  C22  aromatic  1.389  0.020  1.389
 Z2V  C20  C21  aromatic  1.388  0.020  1.388
 Z2V  C11  O13  double    1.211  0.020  1.211
 Z2V  C22  C21  aromatic  1.388  0.020  1.388
 Z2V  C03  H2   single    0.970  0.020  1.090
 Z2V  C04  H3   single    0.970  0.020  1.090
 Z2V  C06  H4   single    0.970  0.020  1.090
 Z2V  C06  H5   single    0.970  0.020  1.090
 Z2V  C07  H6   single    0.970  0.020  1.090
 Z2V  C08  H7   single    0.970  0.020  1.090
 Z2V  C08  H8   single    0.970  0.020  1.090
 Z2V  C12  H11  single    0.970  0.020  1.090
 Z2V  C12  H12  single    0.970  0.020  1.090
 Z2V  C15  H13  single    0.970  0.020  1.090
 Z2V  C15  H14  single    0.970  0.020  1.090
 Z2V  C20  H15  single    0.930  0.020  1.080
 Z2V  C21  H16  single    0.930  0.020  1.080
 Z2V  C22  H17  single    0.930  0.020  1.080
 Z2V  C23  H18  single    0.930  0.020  1.080
 Z2V  C24  H19  single    0.930  0.020  1.080
 Z2V  C26  H20  single    0.970  0.020  1.090
 Z2V  C26  H21  single    0.970  0.020  1.090
 Z2V  C26  H22  single    0.970  0.020  1.090
 Z2V  C27  H23  single    0.970  0.020  1.090
 Z2V  C27  H24  single    0.970  0.020  1.090
 Z2V  C28  H25  single    0.970  0.020  1.090
 Z2V  C29  H26  single    0.970  0.020  1.090
 Z2V  C29  H27  single    0.970  0.020  1.090
 Z2V  C29  H28  single    0.970  0.020  1.090
 Z2V  N10  H29  single    0.860  0.020  1.020
 Z2V  N17  H31  single    0.860  0.020  1.020
 Z2V  O05  H33  single    0.850  0.020  0.980

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
 Z2V  O01  C02  C28  122.44  3.000
 Z2V  O01  C02  C03  122.88  3.000
 Z2V  C28  C02  C03  114.66  3.000
 Z2V  H2   C03  C15  108.12  3.000
 Z2V  H2   C03  C04  107.44  3.000
 Z2V  C15  C03  C04  112.84  3.000
 Z2V  H2   C03  C02  105.50  3.000
 Z2V  C15  C03  C02  109.49  3.000
 Z2V  C04  C03  C02  113.05  3.000
 Z2V  H3   C04  O05  109.94  3.000
 Z2V  H3   C04  C06  106.79  3.000
 Z2V  O05  C04  C06  113.09  3.000
 Z2V  H3   C04  C03  107.57  3.000
 Z2V  O05  C04  C03  108.36  3.000
 Z2V  C06  C04  C03  110.95  3.000
 Z2V  H5   C06  H4   105.96  3.000
 Z2V  H5   C06  C07  108.89  3.000
 Z2V  H4   C06  C07  108.67  3.000
 Z2V  H5   C06  C04  111.38  3.000
 Z2V  H4   C06  C04  106.60  3.000
 Z2V  C07  C06  C04  114.92  3.000
 Z2V  H6   C07  C12  108.87  3.000
 Z2V  H6   C07  C08  108.07  3.000
 Z2V  C12  C07  C08  107.93  3.000
 Z2V  H6   C07  C06  108.85  3.000
 Z2V  C12  C07  C06  112.74  3.000
 Z2V  C08  C07  C06  110.27  3.000
 Z2V  H8   C08  H7   106.69  3.000
 Z2V  H8   C08  C09  107.92  3.000
 Z2V  H7   C08  C09  107.39  3.000
 Z2V  H8   C08  C07  111.57  3.000
 Z2V  H7   C08  C07  109.55  3.000
 Z2V  C09  C08  C07  113.43  3.000
 Z2V  O14  C09  N10  120.23  3.000
 Z2V  N10  C09  C08  116.04  3.000
 Z2V  O14  C09  C08  123.72  3.000
 Z2V  O13  C11  N10  120.11  3.000
 Z2V  O13  C11  C12  123.72  3.000
 Z2V  N10  C11  C12  116.16  3.000
 Z2V  H12  C12  H11  106.45  3.000
 Z2V  H12  C12  C11  107.92  3.000
 Z2V  H11  C12  C11  107.24  3.000
 Z2V  H12  C12  C07  112.68  3.000
 Z2V  H11  C12  C07  109.09  3.000
 Z2V  C11  C12  C07  113.13  3.000
 Z2V  H14  C15  H13  106.91  3.000
 Z2V  H14  C15  C16  108.88  3.000
 Z2V  H13  C15  C16  108.38  3.000
 Z2V  H14  C15  C03  109.74  3.000
 Z2V  H13  C15  C03  109.00  3.000
 Z2V  C16  C15  C03  113.70  3.000
 Z2V  N17  C16  C27  110.17  3.000
 Z2V  N17  C16  C26  109.97  3.000
 Z2V  C27  C16  C26  112.24  3.000
 Z2V  N17  C16  C15  104.89  3.000
 Z2V  C27  C16  C15  108.36  3.000
 Z2V  C26  C16  C15  110.94  3.000
 Z2V  C24  C19  C20  119.15  3.000
 Z2V  C20  C19  C18  122.66  3.000
 Z2V  C24  C19  C18  118.16  3.000
 Z2V  H15  C20  C21  118.84  3.000
 Z2V  H15  C20  C19  120.79  3.000
 Z2V  C21  C20  C19  120.35  3.000
 Z2V  H16  C21  C22  120.16  3.000
 Z2V  H16  C21  C20  119.70  3.000
 Z2V  C22  C21  C20  120.15  3.000
 Z2V  H17  C22  C23  120.13  3.000
 Z2V  H17  C22  C21  120.08  3.000
 Z2V  C23  C22  C21  119.78  3.000
 Z2V  H18  C23  C24  119.80  3.000
 Z2V  H18  C23  C22  120.08  3.000
 Z2V  C24  C23  C22  120.12  3.000
 Z2V  H19  C24  C23  119.80  3.000
 Z2V  H19  C24  C19  119.76  3.000
 Z2V  C23  C24  C19  120.44  3.000
 Z2V  H22  C26  H21  107.43  3.000
 Z2V  H22  C26  H20  108.46  3.000
 Z2V  H21  C26  H20  107.51  3.000
 Z2V  H22  C26  C16  111.07  3.000
 Z2V  H21  C26  C16  112.04  3.000
 Z2V  H20  C26  C16  110.19  3.000
 Z2V  H24  C27  H23  107.01  3.000
 Z2V  H24  C27  C28  108.73  3.000
 Z2V  H23  C27  C28  108.48  3.000
 Z2V  H24  C27  C16  108.37  3.000
 Z2V  H23  C27  C16  110.56  3.000
 Z2V  C28  C27  C16  113.46  3.000
 Z2V  H25  C28  C29  108.53  3.000
 Z2V  H25  C28  C27  107.86  3.000
 Z2V  C29  C28  C27  111.09  3.000
 Z2V  H25  C28  C02  105.71  3.000
 Z2V  C27  C28  C02  110.27  3.000
 Z2V  C29  C28  C02  113.09  3.000
 Z2V  H28  C29  H27  107.73  3.000
 Z2V  H28  C29  H26  107.60  3.000
 Z2V  H27  C29  H26  108.00  3.000
 Z2V  H28  C29  C28  109.94  3.000
 Z2V  H27  C29  C28  111.37  3.000
 Z2V  H26  C29  C28  112.03  3.000
 Z2V  H29  N10  C11  116.25  3.000
 Z2V  H29  N10  C09  116.21  3.000
 Z2V  C11  N10  C09  127.53  3.000
 Z2V  H31  N17  C18  116.97  3.000
 Z2V  H31  N17  C16  115.72  3.000
 Z2V  C18  N17  C16  126.98  3.000
 Z2V  H33  O05  C04  108.81  3.000
 Z2V  O25  C18  N17  124.33  3.000
 Z2V  N17  C18  C19  115.16  3.000
 Z2V  O25  C18  C19  120.52  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
 Z2V  CONST_01  C22  C23  C24  C19     0.00   0.0  0
 Z2V  CONST_02  C22  C21  C20  C19     0.00   0.0  0
 Z2V  CONST_03  C23  C24  C19  C20     0.00   0.0  0
 Z2V  CONST_04  C23  C22  C21  C20     0.00   0.0  0
 Z2V  CONST_05  C24  C19  C20  C21     0.00   0.0  0
 Z2V  CONST_06  C24  C23  C22  C21     0.00   0.0  0
 Z2V  CONST_07  C11  N10  C09  C08     0.00   0.0  0
 Z2V  CONST_08  C23  C24  C19  C18   180.00   0.0  0
 Z2V  CONST_09  C21  C20  C19  C18   180.00   0.0  0
 Z2V  CONST_10  O14  C09  N10  C11   180.00   0.0  0
 Z2V  CONST_11  H18  C23  C24  C19   180.00   0.0  0
 Z2V  CONST_12  H16  C21  C20  C19   180.00   0.0  0
 Z2V  CONST_13  H19  C24  C19  C20   180.00   0.0  0
 Z2V  CONST_14  H17  C22  C21  C20   180.00   0.0  0
 Z2V  CONST_15  H18  C23  C22  C21   180.00   0.0  0
 Z2V  CONST_16  H19  C24  C23  C22   180.00   0.0  0
 Z2V  CONST_17  H15  C20  C21  C22   180.00   0.0  0
 Z2V  CONST_18  H16  C21  C22  C23   180.00   0.0  0
 Z2V  CONST_19  H15  C20  C19  C24   180.00   0.0  0
 Z2V  CONST_20  H17  C22  C23  C24   180.00   0.0  0
 Z2V  CONST_21  H29  N10  C09  C08   180.00   0.0  0
 Z2V  CONST_22  C19  C18  N17  C16   180.00   0.0  0
 Z2V  CONST_23  H29  N10  C09  O14     0.00   0.0  0
 Z2V  CONST_24  O25  C18  N17  C16     0.00   0.0  0
 Z2V  CONST_25  H31  N17  C18  C19     0.00   0.0  0
 Z2V  CONST_26  H31  N17  C18  O25   180.00   0.0  0
 Z2V  Var_01    N10  C09  C08  C07   -27.80  30.0  1
 Z2V  Var_02    N10  C11  C12  C07    28.65  30.0  1
 Z2V  Var_03    C12  C11  N10  C09     0.25  30.0  1
 Z2V  Var_04    O14  C09  C08  C07   152.95  30.0  1
 Z2V  Var_05    O13  C11  C12  C07  -152.37  30.0  1
 Z2V  Var_06    O13  C11  N10  C09  -178.77  30.0  1
 Z2V  Var_07    H29  N10  C11  C12   179.05  30.0  1
 Z2V  Var_08    H7   C08  C09  N10    93.39  30.0  1
 Z2V  Var_09    H8   C08  C09  N10  -151.94  30.0  1
 Z2V  Var_10    H11  C12  C11  N10   -91.67  30.0  1
 Z2V  Var_11    H12  C12  C11  N10   154.01  30.0  1
 Z2V  Var_12    O25  C18  C19  C20   149.35  30.0  2
 Z2V  Var_13    N17  C18  C19  C20   -31.01  30.0  2
 Z2V  Var_14    O25  C18  C19  C24   -28.83  30.0  2
 Z2V  Var_15    N17  C18  C19  C24   150.81  30.0  2
 Z2V  Var_16    H29  N10  C11  O13     0.02  30.0  1
 Z2V  Var_17    H11  C12  C11  O13    87.31  30.0  1
 Z2V  Var_18    H12  C12  C11  O13   -27.01  30.0  1
 Z2V  Var_19    H7   C08  C09  O14   -85.87  30.0  1
 Z2V  Var_20    H8   C08  C09  O14    28.81  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
 Z2V  chir_01  C03  C02  C04  C15  positiv
 Z2V  chir_02  C04  O05  C03  C06  negativ
 Z2V  chir_03  C07  C12  C06  C08  negativ
 Z2V  chir_04  C16  C15  C27  C26  positiv
 Z2V  chir_05  C28  C29  C27  C02  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
 Z2V  plan-1  C19  0.020
 Z2V  plan-1  C20  0.020
 Z2V  plan-1  C21  0.020
 Z2V  plan-1  C22  0.020
 Z2V  plan-1  C23  0.020
 Z2V  plan-1  C24  0.020
 Z2V  plan-1  H15  0.020
 Z2V  plan-1  H16  0.020
 Z2V  plan-1  H17  0.020
 Z2V  plan-1  H18  0.020
 Z2V  plan-1  H19  0.020
 Z2V  plan-1  C18  0.020
 Z2V  plan-2  C02  0.020
 Z2V  plan-2  C03  0.020
 Z2V  plan-2  C28  0.020
 Z2V  plan-2  O01  0.020
 Z2V  plan-3  C11  0.020
 Z2V  plan-3  C12  0.020
 Z2V  plan-3  N10  0.020
 Z2V  plan-3  O13  0.020
 Z2V  plan-4  C16  0.020
 Z2V  plan-4  C19  0.020
 Z2V  plan-4  N17  0.020
 Z2V  plan-4  O25  0.020
 Z2V  plan-4  H31  0.020
 Z2V  plan-4  C18  0.020
 Z2V  plan-5  C08  0.020
 Z2V  plan-5  C09  0.020
 Z2V  plan-5  C11  0.020
 Z2V  plan-5  N10  0.020
 Z2V  plan-5  O14  0.020
 Z2V  plan-5  H29  0.020

