# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:10:47 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2S)-2-{(5S)-5-[(3-chlorophenyl)methyl]-2-oxo-1,3-oxazolidin-3-yl}-4-methyl-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N1C[C@H](Cc2cccc(Cl)c2)OC1=O)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C=O
#
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
 V45  V45  (2S)-2-{(5S)-5-[(3-chlorophenyl)methyl]-2-oxo-1,3-oxazolidin-3-yl}-4-methyl-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}pentanamide  ligand  62  32  .  2021-08-24  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V45
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
 V45  C06  C   CR15  0  -0.002   2.1500   1.4490  -0.5946
 V45  C08  C   CR5   0   0.709   1.3413  -0.3068   0.6056
 V45  C10  C   CH1   0  -0.250  -0.8070  -0.7409  -0.5059
 V45  C11  C   CH2   0  -0.419  -0.7411  -2.2751  -0.5301
 V45  C12  C   CH1   0  -0.232   0.2604  -2.8493  -1.5330
 V45  C13  C   CH3   0  -0.653   0.2280  -4.3729  -1.4639
 V45  C14  C   CH3   0  -0.664  -0.0097  -2.3717  -2.9555
 V45  C15  C   C     0   0.595  -1.7255  -0.2183   0.6064
 V45  C17  C   CH1   0  -0.206  -3.9913  -0.3191   1.5129
 V45  C18  C   CH2   0  -0.466  -5.3935  -0.2227   0.9102
 V45  C19  C   CH1   0  -0.404  -5.4847   0.8612  -0.1522
 V45  C20  C   CH2   0  -0.472  -5.1588   2.2758   0.3240
 V45  C21  C   CH2   0  -0.258  -6.0167   3.1709  -0.5729
 V45  C23  C   C     0   0.570  -6.8874   0.9949  -0.7260
 V45  C25  C   C1    0   0.196  -3.9778  -1.3210   2.6451
 V45  C28  C   CH2   0  -0.310   0.7054   1.1936  -1.0186
 V45  N09  N   NR5   0  -0.489   0.4797  -0.1038  -0.4202
 V45  N16  N   NH1   0  -0.635  -3.0052  -0.6211   0.5148
 V45  N22  N   NH1   0  -0.629  -7.1266   2.3027  -0.9053
 V45  O07  O   O     0  -0.470   2.3003   0.6348   0.5744
 V45  O24  O   O     0  -0.495  -7.6481   0.0764  -0.9856
 V45  O27  O   O     0  -0.473  -1.3209   0.5335   1.4754
 V45  O29  O   O     0  -0.484   1.3378  -1.1828   1.4347
 V45  H1   H   HCR5  0   0.282   2.3177   2.4854  -0.3014
 V45  H3   H   HCH1  0   0.301  -1.2386  -0.4132  -1.4565
 V45  H4   H   HCH2  0   0.253  -0.5213  -2.6566   0.4674
 V45  H5   H   HCH2  0   0.232  -1.7354  -2.6506  -0.7917
 V45  H6   H   HCH1  0   0.224   1.2654  -2.5240  -1.2465
 V45  H7   H   HCH3  0   0.215  -0.7528  -4.7595  -1.7521
 V45  H8   H   HCH3  0   0.229   0.9672  -4.8104  -2.1367
 V45  H9   H   HCH3  0   0.227   0.4427  -4.7324  -0.4559
 V45  H10  H   HCH3  0   0.227   0.1123  -1.2927  -3.0638
 V45  H11  H   HCH3  0   0.233   0.6786  -2.8429  -3.6591
 V45  H12  H   HCH3  0   0.218  -1.0260  -2.6256  -3.2676
 V45  H13  H   HCH1  0   0.299  -3.7483   0.6468   1.9705
 V45  H14  H   HCH2  0   0.264  -5.6833  -1.1877   0.4856
 V45  H15  H   HCH2  0   0.263  -6.1005  -0.0069   1.7163
 V45  H16  H   HCH1  0   0.288  -4.8329   0.5977  -0.9946
 V45  H17  H   HCH2  0   0.250  -5.4649   2.3966   1.3665
 V45  H18  H   HCH2  0   0.259  -4.1005   2.5221   0.2550
 V45  H19  H   HCH2  0   0.253  -6.3606   4.0691  -0.0615
 V45  H20  H   HCH2  0   0.238  -5.4758   3.4820  -1.4710
 V45  H21  H   H     0   0.204  -4.7445  -1.1332   3.4175
 V45  H23  H   HCH2  0   0.266   0.0197   1.9484  -0.6231
 V45  H24  H   HCH2  0   0.269   0.5937   1.1599  -2.1029
 V45  H25  H   HNH1  0   0.407  -3.2529  -1.2987  -0.1902
 V45  H26  H   HNH1  0   0.398  -7.9540   2.6357  -1.3756
 V45  C1   C   CH2   0  -0.559   3.1577   1.0321  -1.6596
 V45  C2   C   CR16  0  -0.296   5.2595   2.3238  -1.1752
 V45  C3   C   CR16  0  -0.244   6.5542   2.4054  -0.6850
 V45  C4   C   CR16  0  -0.231   7.1906   1.2796  -0.1809
 V45  C5   C   CR6   0  -0.021   6.5032   0.0766  -0.1798
 V45  C6   C   CR16  0  -0.269   5.2078  -0.0193  -0.6630
 V45  C7   C   CR6   0   0.143   4.5741   1.1116  -1.1682
 V45  H2   H   HCH2  0   0.264   2.9274   0.0208  -2.0078
 V45  H22  H   HCH2  0   0.278   3.0203   1.6994  -2.5137
 V45  H27  H   HCR6  0   0.257   4.7781   3.2102  -1.5702
 V45  H28  H   HCR6  0   0.268   7.0785   3.3518  -0.6944
 V45  H29  H   HCR6  0   0.279   8.2008   1.3403   0.2001
 V45  H30  H   HCR6  0   0.268   4.6939  -0.9721  -0.6563
 V45  O26  O   O     0  -0.359  -3.2083  -2.2402   2.7300
 V45  CL1  CL  CL    0  -0.132   7.2786  -1.3442   0.4457

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
 V45  O24  C23  double    1.221  0.020  1.221
 V45  N22  C23  single    1.342  0.020  1.342
 V45  N22  C21  single    1.448  0.020  1.448
 V45  C23  C19  single    1.521  0.020  1.521
 V45  C21  C20  single    1.530  0.020  1.530
 V45  C19  C18  single    1.520  0.020  1.520
 V45  C19  C20  single    1.528  0.020  1.528
 V45  C18  C17  single    1.529  0.020  1.529
 V45  C25  C17  single    1.512  0.020  1.512
 V45  C25  O26  double    1.202  0.020  1.202
 V45  C17  N16  single    1.435  0.020  1.435
 V45  N16  C15  single    1.345  0.020  1.345
 V45  O29  C08  double    1.206  0.020  1.206
 V45  C15  O27  double    1.218  0.020  1.218
 V45  C15  C10  single    1.534  0.020  1.534
 V45  C08  O07  single    1.344  0.020  1.344
 V45  C08  N09  single    1.355  0.020  1.355
 V45  O07  C06  single    1.433  0.020  1.433
 V45  C10  N09  single    1.438  0.020  1.438
 V45  C10  C11  single    1.536  0.020  1.536
 V45  N09  C28  single    1.446  0.020  1.446
 V45  C06  C28  single    1.527  0.020  1.527
 V45  C11  C12  single    1.529  0.020  1.529
 V45  C13  C12  single    1.525  0.020  1.525
 V45  C12  C14  single    1.525  0.020  1.525
 V45  C06  H1   single    0.970  0.020  1.090
 V45  C10  H3   single    0.970  0.020  1.090
 V45  C11  H4   single    0.970  0.020  1.090
 V45  C11  H5   single    0.970  0.020  1.090
 V45  C12  H6   single    0.970  0.020  1.090
 V45  C13  H7   single    0.970  0.020  1.090
 V45  C13  H8   single    0.970  0.020  1.090
 V45  C13  H9   single    0.970  0.020  1.090
 V45  C14  H10  single    0.970  0.020  1.090
 V45  C14  H11  single    0.970  0.020  1.090
 V45  C14  H12  single    0.970  0.020  1.090
 V45  C17  H13  single    0.970  0.020  1.090
 V45  C18  H14  single    0.970  0.020  1.090
 V45  C18  H15  single    0.970  0.020  1.090
 V45  C19  H16  single    0.970  0.020  1.090
 V45  C20  H17  single    0.970  0.020  1.090
 V45  C20  H18  single    0.970  0.020  1.090
 V45  C21  H19  single    0.970  0.020  1.090
 V45  C21  H20  single    0.970  0.020  1.090
 V45  C25  H21  single    0.930  0.020  1.080
 V45  C28  H23  single    0.970  0.020  1.090
 V45  C28  H24  single    0.970  0.020  1.090
 V45  N16  H25  single    0.860  0.020  1.020
 V45  N22  H26  single    0.860  0.020  1.020
 V45  C06  C1   single    1.524  0.020  1.524
 V45  C2   C3   aromatic  1.387  0.020  1.387
 V45  C3   C4   aromatic  1.388  0.020  1.388
 V45  C4   C5   aromatic  1.386  0.020  1.386
 V45  C5   C6   aromatic  1.386  0.020  1.386
 V45  C6   C7   aromatic  1.391  0.020  1.391
 V45  C7   C2   aromatic  1.393  0.020  1.393
 V45  C7   C1   single    1.501  0.020  1.501
 V45  C5   CL1  single    1.735  0.020  1.735
 V45  C1   H2   single    0.970  0.020  1.090
 V45  C1   H22  single    0.970  0.020  1.090
 V45  C2   H27  single    0.930  0.020  1.080
 V45  C3   H28  single    0.930  0.020  1.080
 V45  C4   H29  single    0.930  0.020  1.080
 V45  C6   H30  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
 V45  C1   C06  H1   110.26  3.000
 V45  C1   C06  O07  110.20  3.000
 V45  H1   C06  O07  107.74  3.000
 V45  C1   C06  C28  112.69  3.000
 V45  H1   C06  C28  112.29  3.000
 V45  O07  C06  C28  103.34  3.000
 V45  O29  C08  O07  121.78  3.000
 V45  O07  C08  N09  109.34  3.000
 V45  O29  C08  N09  128.86  3.000
 V45  H3   C10  N09  105.78  3.000
 V45  H3   C10  C15  106.96  3.000
 V45  N09  C10  C15  109.97  3.000
 V45  H3   C10  C11  107.60  3.000
 V45  N09  C10  C11  113.89  3.000
 V45  C15  C10  C11  112.17  3.000
 V45  H5   C11  H4   106.36  3.000
 V45  H5   C11  C12  108.02  3.000
 V45  H4   C11  C12  109.67  3.000
 V45  H5   C11  C10  107.91  3.000
 V45  H4   C11  C10  110.10  3.000
 V45  C12  C11  C10  114.43  3.000
 V45  H6   C12  C14  108.28  3.000
 V45  H6   C12  C13  107.73  3.000
 V45  C14  C12  C13  110.57  3.000
 V45  H6   C12  C11  108.55  3.000
 V45  C14  C12  C11  112.23  3.000
 V45  C13  C12  C11  109.36  3.000
 V45  H9   C13  H8   107.71  3.000
 V45  H9   C13  H7   107.67  3.000
 V45  H8   C13  H7   107.67  3.000
 V45  H9   C13  C12  111.50  3.000
 V45  H8   C13  C12  110.99  3.000
 V45  H7   C13  C12  111.12  3.000
 V45  H12  C14  H11  107.58  3.000
 V45  H12  C14  H10  107.77  3.000
 V45  H11  C14  H10  107.01  3.000
 V45  H12  C14  C12  110.99  3.000
 V45  H11  C14  C12  110.77  3.000
 V45  H10  C14  C12  112.49  3.000
 V45  O27  C15  N16  123.33  3.000
 V45  O27  C15  C10  121.91  3.000
 V45  N16  C15  C10  114.73  3.000
 V45  H13  C17  N16  108.87  3.000
 V45  H13  C17  C25  105.62  3.000
 V45  N16  C17  C25  112.04  3.000
 V45  H13  C17  C18  108.20  3.000
 V45  N16  C17  C18  111.66  3.000
 V45  C25  C17  C18  110.19  3.000
 V45  H15  C18  H14  106.80  3.000
 V45  H15  C18  C19  109.60  3.000
 V45  H14  C18  C19  110.00  3.000
 V45  H15  C18  C17  108.34  3.000
 V45  H14  C18  C17  109.90  3.000
 V45  C19  C18  C17  112.05  3.000
 V45  H16  C19  C23  106.22  3.000
 V45  H16  C19  C20  109.56  3.000
 V45  C23  C19  C20  103.47  3.000
 V45  H16  C19  C18  109.25  3.000
 V45  C20  C19  C18  115.44  3.000
 V45  C23  C19  C18  112.43  3.000
 V45  H18  C20  H17  107.91  3.000
 V45  H18  C20  C21  112.06  3.000
 V45  H17  C20  C21  109.71  3.000
 V45  H18  C20  C19  113.40  3.000
 V45  H17  C20  C19  109.87  3.000
 V45  C21  C20  C19  103.85  3.000
 V45  H20  C21  H19  107.89  3.000
 V45  H20  C21  N22  111.18  3.000
 V45  H19  C21  N22  111.11  3.000
 V45  H20  C21  C20  111.74  3.000
 V45  H19  C21  C20  112.60  3.000
 V45  N22  C21  C20  102.33  3.000
 V45  O24  C23  N22  126.45  3.000
 V45  N22  C23  C19  107.48  3.000
 V45  O24  C23  C19  126.07  3.000
 V45  H21  C25  O26  121.69  3.000
 V45  H21  C25  C17  113.88  3.000
 V45  O26  C25  C17  124.43  3.000
 V45  H24  C28  H23  108.46  3.000
 V45  H24  C28  N09  111.57  3.000
 V45  H23  C28  N09  111.81  3.000
 V45  H24  C28  C06  112.22  3.000
 V45  H23  C28  C06  112.16  3.000
 V45  N09  C28  C06  100.53  3.000
 V45  C28  N09  C10  120.81  3.000
 V45  C28  N09  C08  110.39  3.000
 V45  C10  N09  C08  123.20  3.000
 V45  H25  N16  C17  117.30  3.000
 V45  H25  N16  C15  118.85  3.000
 V45  C17  N16  C15  122.92  3.000
 V45  H26  N22  C23  122.05  3.000
 V45  H26  N22  C21  122.55  3.000
 V45  C23  N22  C21  114.66  3.000
 V45  C08  O07  C06  110.01  3.000
 V45  H22  C1   H2   106.82  3.000
 V45  H22  C1   C7   110.01  3.000
 V45  H2   C1   C7   110.59  3.000
 V45  H22  C1   C06  107.22  3.000
 V45  H2   C1   C06  109.63  3.000
 V45  C7   C1   C06  112.37  3.000
 V45  H27  C2   C7   119.70  3.000
 V45  H27  C2   C3   119.71  3.000
 V45  C7   C2   C3   120.59  3.000
 V45  H28  C3   C4   119.37  3.000
 V45  H28  C3   C2   120.06  3.000
 V45  C4   C3   C2   120.58  3.000
 V45  H29  C4   C5   120.79  3.000
 V45  H29  C4   C3   120.72  3.000
 V45  C5   C4   C3   118.49  3.000
 V45  CL1  C5   C6   119.12  3.000
 V45  CL1  C5   C4   119.31  3.000
 V45  C6   C5   C4   121.57  3.000
 V45  H30  C6   C7   120.09  3.000
 V45  H30  C6   C5   120.16  3.000
 V45  C7   C6   C5   119.74  3.000
 V45  C6   C7   C2   119.03  3.000
 V45  C2   C7   C1   120.58  3.000
 V45  C6   C7   C1   120.37  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
 V45  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 V45  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 V45  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 V45  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 V45  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 V45  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 V45  CONST_07  C21  N22  C23  C19     0.00   0.0  0
 V45  CONST_08  C5   C6   C7   C1    180.00   0.0  0
 V45  CONST_09  C3   C2   C7   C1    180.00   0.0  0
 V45  CONST_10  CL1  C5   C4   C3    180.00   0.0  0
 V45  CONST_11  CL1  C5   C6   C7    180.00   0.0  0
 V45  CONST_12  O24  C23  N22  C21   180.00   0.0  0
 V45  CONST_13  H29  C4   C3   C2    180.00   0.0  0
 V45  CONST_14  H30  C6   C7   C2    180.00   0.0  0
 V45  CONST_15  H27  C2   C3   C4    180.00   0.0  0
 V45  CONST_16  H28  C3   C4   C5    180.00   0.0  0
 V45  CONST_17  H26  N22  C23  C19   180.00   0.0  0
 V45  CONST_18  C17  N16  C15  C10   180.00   0.0  0
 V45  CONST_19  O27  C15  N16  C17     0.00   0.0  0
 V45  CONST_20  H25  N16  C15  C10     0.00   0.0  0
 V45  Var_01    N09  C08  O07  C06    -5.18  30.0  1
 V45  Var_02    C08  N09  C28  C06    22.67  30.0  1
 V45  Var_03    N22  C21  C20  C19    27.48  30.0  1
 V45  Var_04    C23  N22  C21  C20   -19.36  30.0  1
 V45  Var_05    O07  C08  N09  C28   -12.21  30.0  1
 V45  Var_06    C6   C7   C1   C06    95.56  30.0  3
 V45  Var_07    C13  C12  C11  C10  -179.82  30.0  3
 V45  Var_08    H7   C13  C12  C11    62.86  30.0  3
 V45  Var_09    H10  C14  C12  C11    63.79  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
 V45  chir_01  C06  O07  C28  C1   positiv
 V45  chir_02  C10  N09  C15  C11  positiv
 V45  chir_03  C17  N16  C25  C18  positiv
 V45  chir_04  C19  C23  C18  C20  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
 V45  plan-1  C10  0.020
 V45  plan-1  C15  0.020
 V45  plan-1  C17  0.020
 V45  plan-1  N16  0.020
 V45  plan-1  O27  0.020
 V45  plan-1  H25  0.020
 V45  plan-2  C1   0.020
 V45  plan-2  C2   0.020
 V45  plan-2  C3   0.020
 V45  plan-2  C4   0.020
 V45  plan-2  C5   0.020
 V45  plan-2  C6   0.020
 V45  plan-2  C7   0.020
 V45  plan-2  H27  0.020
 V45  plan-2  H28  0.020
 V45  plan-2  H29  0.020
 V45  plan-2  H30  0.020
 V45  plan-2  CL1  0.020
 V45  plan-3  C08  0.020
 V45  plan-3  C10  0.020
 V45  plan-3  C28  0.020
 V45  plan-3  N09  0.020
 V45  plan-4  C19  0.020
 V45  plan-4  C21  0.020
 V45  plan-4  C23  0.020
 V45  plan-4  N22  0.020
 V45  plan-4  O24  0.020
 V45  plan-4  H26  0.020
 V45  plan-5  C08  0.020
 V45  plan-5  N09  0.020
 V45  plan-5  O07  0.020
 V45  plan-5  O29  0.020
 V45  plan-6  C17  0.020
 V45  plan-6  C25  0.020
 V45  plan-6  H21  0.020
 V45  plan-6  O26  0.020

