# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:47:20 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: ~{N}-[(4~{S},5~{S})-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
 OPV  OPV  ~{N}-[(4~{S},5~{S})-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_OPV
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
 OPV  CAJ  C  CR15  0  -0.126   6.4474   0.9781   0.5048
 OPV  NAM  N  NR15  0  -0.561   7.4565   1.2547  -0.3713
 OPV  CAI  C  CR15  0   0.086   7.1331   0.6969  -1.5523
 OPV  NAO  N  N     0  -0.460   5.9809   0.0785  -1.4911
 OPV  CAT  C  CR5   0   0.141   5.5382   0.2442  -0.2060
 OPV  CAK  C  CH2   0  -0.532   4.2272  -0.2950   0.2527
 OPV  CAL  C  CH2   0  -0.290   3.0655   0.4326  -0.4274
 OPV  NAY  N  NT    0  -0.173   1.7840  -0.0867  -0.0392
 OPV  C    C  C     0   0.498   0.9177   0.3788   0.8638
 OPV  O    O  O     0  -0.467   0.9886   1.4424   1.4545
 OPV  OG1  O  O2    0  -0.391   1.4362  -1.3121  -0.5753
 OPV  CB   C  CH1   0   0.015   0.5128  -1.8941   0.3619
 OPV  CG2  C  CH3   0  -0.676   1.2416  -2.7440   1.3809
 OPV  CA   C  CH1   0  -0.231  -0.1718  -0.6824   0.9948
 OPV  N    N  NH1   0  -0.646  -1.3665  -0.2307   0.3268
 OPV  CAQ  C  C     0   0.539  -2.5516  -0.8402   0.5363
 OPV  OAB  O  O     0  -0.472  -2.6747  -1.7770   1.3073
 OPV  CAV  C  CR6   0  -0.161  -3.6833  -0.2915  -0.2676
 OPV  CAH  C  CR16  0  -0.292  -3.5386  -0.1085  -1.6452
 OPV  CAF  C  CR16  0  -0.264  -4.5963   0.3556  -2.4035
 OPV  CAG  C  CR16  0  -0.368  -5.8088   0.6551  -1.7918
 OPV  CAS  C  CR6   0   0.269  -5.9608   0.4841  -0.4272
 OPV  OAD  O  OH1   0  -0.644  -7.0974   0.7551   0.2512
 OPV  CAU  C  CR6   0   0.285  -4.8961   0.0012   0.3486
 OPV  OAE  O  OH1   0  -0.615  -5.0240  -0.1518   1.6777
 OPV  H1   H  HCR5  0   0.284   6.4589   1.3128   1.5284
 OPV  H2   H  HNR5  0   0.420   8.2942   1.7767  -0.1697
 OPV  H3   H  HCR5  0   0.277   7.7699   0.7702  -2.4204
 OPV  H5   H  HCH2  0   0.252   4.1612  -1.3638   0.0342
 OPV  H6   H  HCH2  0   0.254   4.1393  -0.1819   1.3350
 OPV  H7   H  HCH2  0   0.270   3.0697   1.4894  -0.1626
 OPV  H8   H  HCH2  0   0.270   3.1542   0.3717  -1.5135
 OPV  H9   H  HCH1  0   0.280  -0.1744  -2.4995  -0.2286
 OPV  H10  H  HCH3  0   0.235   1.8990  -2.1501   2.0190
 OPV  H11  H  HCH3  0   0.248   0.5177  -3.2454   2.0234
 OPV  H12  H  HCH3  0   0.254   1.8412  -3.5088   0.8886
 OPV  H13  H  HCH1  0   0.307  -0.3860  -0.8575   2.0510
 OPV  H14  H  HNH1  0   0.417  -1.3258   0.5682  -0.2862
 OPV  H15  H  HCR6  0   0.263  -2.5991  -0.3538  -2.1239
 OPV  H16  H  HCR6  0   0.263  -4.4874   0.4848  -3.4714
 OPV  H17  H  HCR6  0   0.280  -6.6407   1.0237  -2.3812
 OPV  H18  H  HOH1  0   0.484  -7.7604   1.1506  -0.3253
 OPV  H19  H  HOH1  0   0.477  -5.8853   0.1715   1.9701

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
 OPV  NAO  CAI  aromatic  1.309  0.020  1.309
 OPV  NAO  CAT  aromatic  1.369  0.020  1.369
 OPV  CAI  NAM  aromatic  1.346  0.020  1.346
 OPV  CAL  CAK  single    1.530  0.020  1.530
 OPV  CAL  NAY  single    1.436  0.020  1.436
 OPV  CAT  CAK  single    1.490  0.020  1.490
 OPV  CAT  CAJ  aromatic  1.368  0.020  1.368
 OPV  NAM  CAJ  aromatic  1.365  0.020  1.365
 OPV  O    C    double    1.219  0.020  1.219
 OPV  OAD  CAS  single    1.351  0.020  1.351
 OPV  NAY  C    single    1.335  0.020  1.335
 OPV  NAY  OG1  single    1.382  0.020  1.382
 OPV  OAE  CAU  single    1.344  0.020  1.344
 OPV  C    CA   single    1.527  0.020  1.527
 OPV  CAS  CAU  aromatic  1.403  0.020  1.403
 OPV  CAS  CAG  aromatic  1.384  0.020  1.384
 OPV  CAU  CAV  aromatic  1.391  0.020  1.391
 OPV  OG1  CB   single    1.439  0.020  1.439
 OPV  N    CA   single    1.441  0.020  1.441
 OPV  N    CAQ  single    1.349  0.020  1.349
 OPV  CA   CB   single    1.529  0.020  1.529
 OPV  CAG  CAF  aromatic  1.391  0.020  1.391
 OPV  CAV  CAQ  single    1.493  0.020  1.493
 OPV  CAV  CAH  aromatic  1.397  0.020  1.397
 OPV  CAQ  OAB  double    1.220  0.020  1.220
 OPV  CB   CG2  single    1.514  0.020  1.514
 OPV  CAF  CAH  aromatic  1.382  0.020  1.382
 OPV  CAJ  H1   single    0.930  0.020  1.080
 OPV  NAM  H2   single    0.860  0.020  1.020
 OPV  CAI  H3   single    0.930  0.020  1.080
 OPV  CAK  H5   single    0.970  0.020  1.090
 OPV  CAK  H6   single    0.970  0.020  1.090
 OPV  CAL  H7   single    0.970  0.020  1.090
 OPV  CAL  H8   single    0.970  0.020  1.090
 OPV  CB   H9   single    0.970  0.020  1.090
 OPV  CG2  H10  single    0.970  0.020  1.090
 OPV  CG2  H11  single    0.970  0.020  1.090
 OPV  CG2  H12  single    0.970  0.020  1.090
 OPV  CA   H13  single    0.970  0.020  1.090
 OPV  N    H14  single    0.860  0.020  1.020
 OPV  CAH  H15  single    0.930  0.020  1.080
 OPV  CAF  H16  single    0.930  0.020  1.080
 OPV  CAG  H17  single    0.930  0.020  1.080
 OPV  OAD  H18  single    0.850  0.020  0.980
 OPV  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
 OPV  H1   CAJ  CAT  131.90  3.000
 OPV  H1   CAJ  NAM  122.63  3.000
 OPV  CAT  CAJ  NAM  105.47  3.000
 OPV  H2   NAM  CAI  126.18  3.000
 OPV  H2   NAM  CAJ  126.26  3.000
 OPV  CAI  NAM  CAJ  107.56  3.000
 OPV  H3   CAI  NAO  126.09  3.000
 OPV  H3   CAI  NAM  122.42  3.000
 OPV  NAO  CAI  NAM  111.49  3.000
 OPV  CAT  NAO  CAI  105.74  3.000
 OPV  CAK  CAT  NAO  121.98  3.000
 OPV  CAK  CAT  CAJ  128.25  3.000
 OPV  NAO  CAT  CAJ  109.74  3.000
 OPV  H6   CAK  H5   107.14  3.000
 OPV  H6   CAK  CAL  109.28  3.000
 OPV  H5   CAK  CAL  109.29  3.000
 OPV  H6   CAK  CAT  109.79  3.000
 OPV  H5   CAK  CAT  110.21  3.000
 OPV  CAL  CAK  CAT  111.05  3.000
 OPV  H8   CAL  H7   107.20  3.000
 OPV  H8   CAL  NAY  108.74  3.000
 OPV  H7   CAL  NAY  106.77  3.000
 OPV  H8   CAL  CAK  110.74  3.000
 OPV  H7   CAL  CAK  110.51  3.000
 OPV  NAY  CAL  CAK  112.67  3.000
 OPV  OG1  NAY  C    114.10  3.000
 OPV  OG1  NAY  CAL  116.12  3.000
 OPV  C    NAY  CAL  129.47  3.000
 OPV  CA   C    O    127.35  3.000
 OPV  CA   C    NAY  106.18  3.000
 OPV  O    C    NAY  126.47  3.000
 OPV  CB   OG1  NAY  105.52  3.000
 OPV  H9   CB   CA   112.47  3.000
 OPV  H9   CB   CG2  110.88  3.000
 OPV  CA   CB   CG2  112.45  3.000
 OPV  H9   CB   OG1  106.05  3.000
 OPV  CG2  CB   OG1  110.89  3.000
 OPV  CA   CB   OG1  103.68  3.000
 OPV  H12  CG2  H11  108.00  3.000
 OPV  H12  CG2  H10  108.34  3.000
 OPV  H11  CG2  H10  107.80  3.000
 OPV  H12  CG2  CB   110.78  3.000
 OPV  H11  CG2  CB   109.58  3.000
 OPV  H10  CG2  CB   112.20  3.000
 OPV  H13  CA   N    109.63  3.000
 OPV  H13  CA   CB   111.17  3.000
 OPV  N    CA   CB   115.32  3.000
 OPV  H13  CA   C    109.54  3.000
 OPV  CB   CA   C    101.29  3.000
 OPV  N    CA   C    109.51  3.000
 OPV  H14  N    CAQ  119.21  3.000
 OPV  H14  N    CA   119.79  3.000
 OPV  CAQ  N    CA   120.97  3.000
 OPV  CAV  CAQ  OAB  123.12  3.000
 OPV  OAB  CAQ  N    122.27  3.000
 OPV  CAV  CAQ  N    114.60  3.000
 OPV  CAU  CAV  CAH  119.96  3.000
 OPV  CAH  CAV  CAQ  120.04  3.000
 OPV  CAU  CAV  CAQ  119.98  3.000
 OPV  H15  CAH  CAF  119.85  3.000
 OPV  H15  CAH  CAV  119.75  3.000
 OPV  CAF  CAH  CAV  120.38  3.000
 OPV  H16  CAF  CAG  119.77  3.000
 OPV  H16  CAF  CAH  120.33  3.000
 OPV  CAG  CAF  CAH  119.89  3.000
 OPV  H17  CAG  CAS  119.60  3.000
 OPV  H17  CAG  CAF  120.20  3.000
 OPV  CAS  CAG  CAF  120.20  3.000
 OPV  CAU  CAS  OAD  115.45  3.000
 OPV  CAU  CAS  CAG  120.30  3.000
 OPV  OAD  CAS  CAG  124.25  3.000
 OPV  H18  OAD  CAS  111.15  3.000
 OPV  OAE  CAU  CAS  120.92  3.000
 OPV  CAS  CAU  CAV  119.27  3.000
 OPV  OAE  CAU  CAV  119.79  3.000
 OPV  H19  OAE  CAU  110.26  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
 OPV  CONST_01  CAI  NAO  CAT  CAJ     0.00   0.0  0
 OPV  CONST_02  NAO  CAI  NAM  CAJ     0.00   0.0  0
 OPV  CONST_03  CAT  NAO  CAI  NAM     0.00   0.0  0
 OPV  CONST_04  NAO  CAT  CAJ  NAM     0.00   0.0  0
 OPV  CONST_05  CAT  CAJ  NAM  CAI     0.00   0.0  0
 OPV  CONST_06  CAG  CAS  CAU  CAV     0.00   0.0  0
 OPV  CONST_07  CAG  CAF  CAH  CAV     0.00   0.0  0
 OPV  CONST_08  CAS  CAU  CAV  CAH     0.00   0.0  0
 OPV  CONST_09  CAS  CAG  CAF  CAH     0.00   0.0  0
 OPV  CONST_10  CAU  CAS  CAG  CAF     0.00   0.0  0
 OPV  CONST_11  CAU  CAV  CAH  CAF     0.00   0.0  0
 OPV  CONST_12  CA   C    NAY  OG1     0.00   0.0  0
 OPV  CONST_13  CAK  CAT  CAJ  NAM   180.00   0.0  0
 OPV  CONST_14  CAK  CAT  NAO  CAI   180.00   0.0  0
 OPV  CONST_15  CAS  CAU  CAV  CAQ   180.00   0.0  0
 OPV  CONST_16  CAF  CAH  CAV  CAQ   180.00   0.0  0
 OPV  CONST_17  OAD  CAS  CAU  CAV   180.00   0.0  0
 OPV  CONST_18  OAE  CAU  CAV  CAH   180.00   0.0  0
 OPV  CONST_19  OAD  CAS  CAG  CAF   180.00   0.0  0
 OPV  CONST_20  OAE  CAU  CAS  CAG   180.00   0.0  0
 OPV  CONST_21  CA   C    NAY  CAL   180.00   0.0  0
 OPV  CONST_22  OG1  NAY  C    O     180.00   0.0  0
 OPV  CONST_23  H3   CAI  NAM  CAJ   180.00   0.0  0
 OPV  CONST_24  H1   CAJ  NAM  CAI   180.00   0.0  0
 OPV  CONST_25  H2   NAM  CAI  NAO   180.00   0.0  0
 OPV  CONST_26  H16  CAF  CAH  CAV   180.00   0.0  0
 OPV  CONST_27  H17  CAG  CAF  CAH   180.00   0.0  0
 OPV  CONST_28  H15  CAH  CAF  CAG   180.00   0.0  0
 OPV  CONST_29  CAV  CAQ  N    CA    180.00   0.0  0
 OPV  CONST_30  O    C    NAY  CAL     0.00   0.0  0
 OPV  CONST_31  OAB  CAQ  N    CA      0.00   0.0  0
 OPV  CONST_32  H14  N    CAQ  CAV     0.00   0.0  0
 OPV  Var_01    CAL  CAK  CAT  CAJ   110.63  30.0  2
 OPV  Var_02    NAY  CAL  CAK  CAT   178.29  30.0  1
 OPV  Var_03    C    NAY  CAL  CAK    99.11  30.0  3
 OPV  Var_04    CAU  CAV  CAQ  N    -132.43  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
 OPV  chir_01  CB  OG1  CA  CG2  positiv
 OPV  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
 OPV  plan-1  CAJ  0.020
 OPV  plan-1  NAM  0.020
 OPV  plan-1  CAI  0.020
 OPV  plan-1  NAO  0.020
 OPV  plan-1  CAT  0.020
 OPV  plan-1  CAK  0.020
 OPV  plan-1  H1   0.020
 OPV  plan-1  H2   0.020
 OPV  plan-1  H3   0.020
 OPV  plan-2  CAQ  0.020
 OPV  plan-2  CAV  0.020
 OPV  plan-2  CAH  0.020
 OPV  plan-2  CAF  0.020
 OPV  plan-2  CAG  0.020
 OPV  plan-2  CAS  0.020
 OPV  plan-2  OAD  0.020
 OPV  plan-2  CAU  0.020
 OPV  plan-2  OAE  0.020
 OPV  plan-2  H15  0.020
 OPV  plan-2  H16  0.020
 OPV  plan-2  H17  0.020
 OPV  plan-3  CA   0.020
 OPV  plan-3  N    0.020
 OPV  plan-3  CAQ  0.020
 OPV  plan-3  OAB  0.020
 OPV  plan-3  CAV  0.020
 OPV  plan-3  H14  0.020
 OPV  plan-4  CAL  0.020
 OPV  plan-4  NAY  0.020
 OPV  plan-4  C    0.020
 OPV  plan-4  O    0.020
 OPV  plan-4  OG1  0.020
 OPV  plan-4  CA   0.020

