# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 12:29:39 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: ~{N}-[(4~{S},5~{R})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1ON(CCc2c[nH]cn2)C(=O)[C@H]1NC(=O)c3cccc(O)c3O
#
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
 OPZ  OPZ  ~{N}-[(4~{S},5~{R})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide  ligand  43  25  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OPZ
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
 OPZ  CAJ  C  CR15  0  -0.126  -6.5300   1.0002  -0.3021
 OPZ  NAM  N  NR15  0  -0.561  -7.5487   1.0465   0.6049
 OPZ  CAI  C  CR15  0   0.086  -7.2340   0.2113   1.6120
 OPZ  NAO  N  N     0  -0.460  -6.0781  -0.3692   1.4096
 OPZ  CAT  C  CR5   0   0.137  -5.6241   0.1137   0.2113
 OPZ  CAK  C  CH2   0  -0.528  -4.3107  -0.2984  -0.3589
 OPZ  CAL  C  CH2   0  -0.284  -3.1498   0.2554   0.4695
 OPZ  NAY  N  NT    0  -0.183  -1.8681  -0.1273  -0.0528
 OPZ  C    C  C     0   0.537  -0.9473   0.6094  -0.6839
 OPZ  O    O  O     0  -0.468  -0.9761   1.8144  -0.8564
 OPZ  OG1  O  O2    0  -0.398  -1.5471  -1.4695   0.0415
 OPZ  CB   C  CH1   0   0.072  -0.5928  -1.6996  -1.0067
 OPZ  CG2  C  CH3   0  -0.695   0.2342  -2.9131  -0.6796
 OPZ  CA   C  CH1   0  -0.298   0.1438  -0.3653  -1.1252
 OPZ  N    N  NH1   0  -0.661   1.3070  -0.2161  -0.2900
 OPZ  CAQ  C  C     0   0.641   2.5580  -0.1923  -0.7773
 OPZ  OAB  O  O     0  -0.527   2.7747  -0.2488  -1.9935
 OPZ  CAV  C  CR6   0  -0.180   3.6767  -0.0805   0.1881
 OPZ  CAH  C  CR16  0  -0.329   3.5068  -0.2403   1.5717
 OPZ  CAF  C  CR16  0  -0.259   4.5761  -0.1124   2.4271
 OPZ  CAG  C  CR16  0  -0.371   5.8432   0.1784   1.9215
 OPZ  CAS  C  CR6   0   0.288   6.0402   0.3259   0.5638
 OPZ  OAD  O  OH1   0  -0.625   7.2336   0.5962   0.0007
 OPZ  CAU  C  CR6   0   0.286   4.9557   0.1828  -0.3238
 OPZ  OAE  O  OH1   0  -0.626   5.2224   0.3172  -1.6229
 OPZ  H1   H  HCR5  0   0.283  -6.5328   1.5817  -1.2085
 OPZ  H2   H  HNR5  0   0.420  -8.3883   1.5976   0.5291
 OPZ  H3   H  HCR5  0   0.276  -7.8808   0.0607   2.4627
 OPZ  H5   H  HCH2  0   0.253  -4.2451  -1.3884  -0.3915
 OPZ  H6   H  HCH2  0   0.253  -4.2223   0.0605  -1.3860
 OPZ  H7   H  HCH2  0   0.269  -3.1680   1.3446   0.4701
 OPZ  H8   H  HCH2  0   0.266  -3.2276  -0.0709   1.5087
 OPZ  H9   H  HCH1  0   0.259  -1.1420  -1.8533  -1.9435
 OPZ  H10  H  HCH3  0   0.261  -0.3899  -3.8045  -0.6256
 OPZ  H11  H  HCH3  0   0.251   0.9688  -3.0710  -1.4692
 OPZ  H12  H  HCH3  0   0.237   0.7663  -2.8046   0.2646
 OPZ  H13  H  HCH1  0   0.322   0.4246  -0.1642  -2.1571
 OPZ  H14  H  HNH1  0   0.425   1.1669  -0.1174   0.7024
 OPZ  H15  H  HCR6  0   0.254   2.5418  -0.4916   1.9916
 OPZ  H16  H  HCR6  0   0.266   4.4408  -0.2410   3.4918
 OPZ  H17  H  HCR6  0   0.280   6.6836   0.2805   2.5988
 OPZ  H18  H  HOH1  0   0.477   7.9099   0.6787   0.6823
 OPZ  H19  H  HOH1  0   0.478   4.3843   0.1159  -2.1033

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
 OPZ  NAM  CAJ  aromatic  1.365  0.020  1.365
 OPZ  NAM  CAI  aromatic  1.346  0.020  1.346
 OPZ  CAJ  CAT  aromatic  1.367  0.020  1.367
 OPZ  CAI  NAO  aromatic  1.309  0.020  1.309
 OPZ  CAT  NAO  aromatic  1.369  0.020  1.369
 OPZ  CAT  CAK  single    1.490  0.020  1.490
 OPZ  OAB  CAQ  double    1.237  0.020  1.237
 OPZ  CAK  CAL  single    1.530  0.020  1.530
 OPZ  OG1  CB   single    1.436  0.020  1.436
 OPZ  OG1  NAY  single    1.383  0.020  1.383
 OPZ  CA   CB   single    1.529  0.020  1.529
 OPZ  CA   C    single    1.528  0.020  1.528
 OPZ  CA   N    single    1.440  0.020  1.440
 OPZ  CB   CG2  single    1.504  0.020  1.504
 OPZ  CAQ  N    single    1.343  0.020  1.343
 OPZ  CAQ  CAV  single    1.482  0.020  1.482
 OPZ  NAY  C    single    1.338  0.020  1.338
 OPZ  NAY  CAL  single    1.436  0.020  1.436
 OPZ  C    O    double    1.218  0.020  1.218
 OPZ  CAH  CAV  aromatic  1.403  0.020  1.403
 OPZ  CAH  CAF  aromatic  1.375  0.020  1.375
 OPZ  CAV  CAU  aromatic  1.403  0.020  1.403
 OPZ  CAF  CAG  aromatic  1.395  0.020  1.395
 OPZ  CAU  OAE  single    1.333  0.020  1.333
 OPZ  CAU  CAS  aromatic  1.409  0.020  1.409
 OPZ  CAG  CAS  aromatic  1.380  0.020  1.380
 OPZ  CAS  OAD  single    1.347  0.020  1.347
 OPZ  CAJ  H1   single    0.930  0.020  1.080
 OPZ  NAM  H2   single    0.860  0.020  1.020
 OPZ  CAI  H3   single    0.930  0.020  1.080
 OPZ  CAK  H5   single    0.970  0.020  1.090
 OPZ  CAK  H6   single    0.970  0.020  1.090
 OPZ  CAL  H7   single    0.970  0.020  1.090
 OPZ  CAL  H8   single    0.970  0.020  1.090
 OPZ  CB   H9   single    0.970  0.020  1.090
 OPZ  CG2  H10  single    0.970  0.020  1.090
 OPZ  CG2  H11  single    0.970  0.020  1.090
 OPZ  CG2  H12  single    0.970  0.020  1.090
 OPZ  CA   H13  single    0.970  0.020  1.090
 OPZ  N    H14  single    0.860  0.020  1.020
 OPZ  CAH  H15  single    0.930  0.020  1.080
 OPZ  CAF  H16  single    0.930  0.020  1.080
 OPZ  CAG  H17  single    0.930  0.020  1.080
 OPZ  OAD  H18  single    0.850  0.020  0.980
 OPZ  OAE  H19  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
 OPZ  H1   CAJ  CAT  131.90  3.000
 OPZ  H1   CAJ  NAM  122.62  3.000
 OPZ  CAT  CAJ  NAM  105.48  3.000
 OPZ  H2   NAM  CAI  126.22  3.000
 OPZ  H2   NAM  CAJ  126.21  3.000
 OPZ  CAI  NAM  CAJ  107.56  3.000
 OPZ  H3   CAI  NAO  126.10  3.000
 OPZ  H3   CAI  NAM  122.44  3.000
 OPZ  NAO  CAI  NAM  111.47  3.000
 OPZ  CAT  NAO  CAI  105.76  3.000
 OPZ  CAK  CAT  NAO  121.98  3.000
 OPZ  CAK  CAT  CAJ  128.28  3.000
 OPZ  NAO  CAT  CAJ  109.72  3.000
 OPZ  H6   CAK  H5   107.16  3.000
 OPZ  H6   CAK  CAL  109.21  3.000
 OPZ  H5   CAK  CAL  109.37  3.000
 OPZ  H6   CAK  CAT  109.92  3.000
 OPZ  H5   CAK  CAT  109.90  3.000
 OPZ  CAL  CAK  CAT  111.20  3.000
 OPZ  H8   CAL  H7   107.28  3.000
 OPZ  H8   CAL  NAY  109.28  3.000
 OPZ  H7   CAL  NAY  106.35  3.000
 OPZ  H8   CAL  CAK  110.68  3.000
 OPZ  H7   CAL  CAK  110.46  3.000
 OPZ  NAY  CAL  CAK  112.57  3.000
 OPZ  OG1  NAY  C    114.01  3.000
 OPZ  C    NAY  CAL  129.74  3.000
 OPZ  OG1  NAY  CAL  116.16  3.000
 OPZ  CA   C    O    127.39  3.000
 OPZ  O    C    NAY  126.55  3.000
 OPZ  CA   C    NAY  106.05  3.000
 OPZ  CB   OG1  NAY  105.06  3.000
 OPZ  H9   CB   CA   107.30  3.000
 OPZ  H9   CB   CG2  110.36  3.000
 OPZ  CA   CB   CG2  117.13  3.000
 OPZ  H9   CB   OG1  108.25  3.000
 OPZ  CG2  CB   OG1  109.62  3.000
 OPZ  CA   CB   OG1  103.71  3.000
 OPZ  H12  CG2  H11  108.25  3.000
 OPZ  H12  CG2  H10  108.56  3.000
 OPZ  H11  CG2  H10  107.66  3.000
 OPZ  H12  CG2  CB   112.12  3.000
 OPZ  H11  CG2  CB   109.26  3.000
 OPZ  H10  CG2  CB   110.84  3.000
 OPZ  H13  CA   N    108.81  3.000
 OPZ  H13  CA   CB   111.05  3.000
 OPZ  N    CA   CB   115.77  3.000
 OPZ  H13  CA   C    109.89  3.000
 OPZ  N    CA   C    110.07  3.000
 OPZ  CB   CA   C    100.97  3.000
 OPZ  H14  N    CAQ  119.05  3.000
 OPZ  H14  N    CA   117.99  3.000
 OPZ  CAQ  N    CA   122.96  3.000
 OPZ  CAV  CAQ  OAB  120.79  3.000
 OPZ  CAV  CAQ  N    117.92  3.000
 OPZ  OAB  CAQ  N    121.28  3.000
 OPZ  CAU  CAV  CAH  119.45  3.000
 OPZ  CAU  CAV  CAQ  117.70  3.000
 OPZ  CAH  CAV  CAQ  122.85  3.000
 OPZ  H15  CAH  CAF  118.28  3.000
 OPZ  H15  CAH  CAV  121.14  3.000
 OPZ  CAF  CAH  CAV  120.57  3.000
 OPZ  H16  CAF  CAG  119.71  3.000
 OPZ  H16  CAF  CAH  120.28  3.000
 OPZ  CAG  CAF  CAH  120.01  3.000
 OPZ  H17  CAG  CAS  119.60  3.000
 OPZ  H17  CAG  CAF  119.82  3.000
 OPZ  CAS  CAG  CAF  120.57  3.000
 OPZ  CAU  CAS  OAD  116.04  3.000
 OPZ  OAD  CAS  CAG  124.00  3.000
 OPZ  CAU  CAS  CAG  119.95  3.000
 OPZ  H18  OAD  CAS  110.08  3.000
 OPZ  OAE  CAU  CAS  116.73  3.000
 OPZ  CAS  CAU  CAV  119.42  3.000
 OPZ  OAE  CAU  CAV  123.85  3.000
 OPZ  H19  OAE  CAU  106.50  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
 OPZ  CONST_01  NAO  CAI  NAM  CAJ    0.00   0.0  0
 OPZ  CONST_02  CAI  NAO  CAT  CAJ    0.00   0.0  0
 OPZ  CONST_03  NAO  CAT  CAJ  NAM    0.00   0.0  0
 OPZ  CONST_04  CAT  NAO  CAI  NAM    0.00   0.0  0
 OPZ  CONST_05  CAT  CAJ  NAM  CAI    0.00   0.0  0
 OPZ  CONST_06  CAG  CAF  CAH  CAV    0.00   0.0  0
 OPZ  CONST_07  CAG  CAS  CAU  CAV    0.00   0.0  0
 OPZ  CONST_08  CAS  CAU  CAV  CAH    0.00   0.0  0
 OPZ  CONST_09  CAS  CAG  CAF  CAH    0.00   0.0  0
 OPZ  CONST_10  CAU  CAV  CAH  CAF    0.00   0.0  0
 OPZ  CONST_11  CAU  CAS  CAG  CAF    0.00   0.0  0
 OPZ  CONST_12  CA   C    NAY  OG1    0.00   0.0  0
 OPZ  CONST_13  CAK  CAT  CAJ  NAM  180.00   0.0  0
 OPZ  CONST_14  CAK  CAT  NAO  CAI  180.00   0.0  0
 OPZ  CONST_15  CAF  CAH  CAV  CAQ  180.00   0.0  0
 OPZ  CONST_16  CAS  CAU  CAV  CAQ  180.00   0.0  0
 OPZ  CONST_17  OAD  CAS  CAU  CAV  180.00   0.0  0
 OPZ  CONST_18  OAE  CAU  CAV  CAH  180.00   0.0  0
 OPZ  CONST_19  OAD  CAS  CAG  CAF  180.00   0.0  0
 OPZ  CONST_20  OAE  CAU  CAS  CAG  180.00   0.0  0
 OPZ  CONST_21  CA   C    NAY  CAL  180.00   0.0  0
 OPZ  CONST_22  OG1  NAY  C    O    180.00   0.0  0
 OPZ  CONST_23  H3   CAI  NAM  CAJ  180.00   0.0  0
 OPZ  CONST_24  H1   CAJ  NAM  CAI  180.00   0.0  0
 OPZ  CONST_25  H2   NAM  CAI  NAO  180.00   0.0  0
 OPZ  CONST_26  H16  CAF  CAH  CAV  180.00   0.0  0
 OPZ  CONST_27  H17  CAG  CAF  CAH  180.00   0.0  0
 OPZ  CONST_28  H15  CAH  CAF  CAG  180.00   0.0  0
 OPZ  CONST_29  CAV  CAQ  N    CA   180.00   0.0  0
 OPZ  CONST_30  O    C    NAY  CAL    0.00   0.0  0
 OPZ  CONST_31  OAB  CAQ  N    CA     0.00   0.0  0
 OPZ  CONST_32  H14  N    CAQ  CAV    0.00   0.0  0
 OPZ  Var_01    CAL  CAK  CAT  CAJ  109.75  30.0  2
 OPZ  Var_02    NAY  CAL  CAK  CAT  179.85  30.0  3
 OPZ  Var_03    OG1  NAY  CAL  CAK  -68.23  30.0  1
 OPZ  Var_04    CAH  CAV  CAQ  N     11.79  30.0  2

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
 OPZ  chir_01  CB  OG1  CA  CG2  negativ
 OPZ  chir_02  CA  N    CB  C    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
 OPZ  plan-1  CAJ  0.020
 OPZ  plan-1  NAM  0.020
 OPZ  plan-1  CAI  0.020
 OPZ  plan-1  NAO  0.020
 OPZ  plan-1  CAT  0.020
 OPZ  plan-1  CAK  0.020
 OPZ  plan-1  H1   0.020
 OPZ  plan-1  H2   0.020
 OPZ  plan-1  H3   0.020
 OPZ  plan-2  CAQ  0.020
 OPZ  plan-2  CAV  0.020
 OPZ  plan-2  CAH  0.020
 OPZ  plan-2  CAF  0.020
 OPZ  plan-2  CAG  0.020
 OPZ  plan-2  CAS  0.020
 OPZ  plan-2  OAD  0.020
 OPZ  plan-2  CAU  0.020
 OPZ  plan-2  OAE  0.020
 OPZ  plan-2  H15  0.020
 OPZ  plan-2  H16  0.020
 OPZ  plan-2  H17  0.020
 OPZ  plan-3  CA   0.020
 OPZ  plan-3  N    0.020
 OPZ  plan-3  CAQ  0.020
 OPZ  plan-3  OAB  0.020
 OPZ  plan-3  CAV  0.020
 OPZ  plan-3  H14  0.020
 OPZ  plan-4  CAL  0.020
 OPZ  plan-4  NAY  0.020
 OPZ  plan-4  C    0.020
 OPZ  plan-4  O    0.020
 OPZ  plan-4  OG1  0.020
 OPZ  plan-4  CA   0.020

