# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 18:39:26 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](NC(=O)c1[nH]c2cc(OC[C@@H]3CNC(=O)O3)c(Cl)cc2c1)c4ccc(cc4)C(O)=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
 ONV  ONV  '4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid'  ligand  53  33  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ONV
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
 ONV  C1   C   CR15  0  -0.043   5.9755   2.1505   0.4026
 ONV  C2   C   CH2   0  -0.303   6.0932   3.4951  -0.3271
 ONV  C3   C   CH2   0  -0.185   4.5890   1.5634   0.2634
 ONV  C4   C   CR6   0   0.449   3.4532  -0.4087   0.9171
 ONV  C5   C   CR6   0  -0.163   3.5198  -1.6524   1.5973
 ONV  C6   C   CR16  0  -0.466   2.2696  -0.0054   0.3299
 ONV  C7   C   CR56  0   0.400   1.1717  -0.8618   0.4359
 ONV  C8   C   CR56  0   0.032   1.2266  -2.0907   1.1211
 ONV  C9   C   CR16  0  -0.287   2.4359  -2.4856   1.7064
 ONV  C10  C   CR5   0   0.211  -0.8487  -1.8013   0.3283
 ONV  C11  C   CR15  0  -0.386  -0.0715  -2.6670   1.0469
 ONV  C12  C   C     0   0.531  -2.2664  -1.9974  -0.0260
 ONV  C13  C   CH1   0  -0.164  -4.1136  -1.3390  -1.4811
 ONV  C14  C   CR6   0   0.149  -5.0347  -0.5244  -0.5999
 ONV  C15  C   CR16  0  -0.288  -6.3675  -0.9072  -0.4764
 ONV  C16  C   CR16  0  -0.243  -7.2523  -0.1597   0.2795
 ONV  C17  C   CR6   0  -0.095  -6.8172   0.9902   0.9355
 ONV  O5   O   O     0  -0.441  -8.9639   1.4616   1.8409
 ONV  C20  C   C     0   0.531  -7.7973   1.7593   1.7382
 ONV  O4   O   OH1   0  -0.594  -7.2638   2.8147   2.3383
 ONV  C18  C   CR16  0  -0.246  -5.4822   1.3738   0.8188
 ONV  C19  C   CR16  0  -0.284  -4.6031   0.6232   0.0551
 ONV  C21  C   CH2   0  -0.169  -4.2143  -0.8988  -2.9363
 ONV  O6   O   OH1   0  -0.665  -3.7383   0.4204  -3.0366
 ONV  N2   N   NH1   0  -0.671  -2.7333  -1.2727  -1.0602
 ONV  O3   O   O     0  -0.474  -2.9579  -2.7929   0.5929
 ONV  CL   CL  CL    0  -0.115   5.0308  -2.1109   2.3087
 ONV  N11  N   NR15  0  -0.753  -0.0892  -0.7156  -0.0492
 ONV  O2   O   O2    0  -0.457   4.5899   0.3029   0.8975
 ONV  N    N   NR15  0  -0.651   6.7294   3.0656  -1.5473
 ONV  O1   O   O     0  -0.465   6.9339   1.3108  -0.2458
 ONV  C    C   CR5   0   0.676   7.3124   1.8585  -1.4180
 ONV  O    O   O     0  -0.489   8.0512   1.2866  -2.1818
 ONV  H1   H   HCR5  0   0.285   6.2474   2.2292   1.4552
 ONV  H2   H   HCH2  0   0.270   5.1208   3.9526  -0.5123
 ONV  H3   H   HCH2  0   0.271   6.7067   4.2071   0.2283
 ONV  H4   H   HCH2  0   0.251   3.8728   2.2424   0.7396
 ONV  H5   H   HCH2  0   0.242   4.3159   1.4739  -0.7954
 ONV  H6   H   HCR6  0   0.297   2.1833   0.9347  -0.1984
 ONV  H7   H   HCR6  0   0.277   2.5179  -3.4247   2.2378
 ONV  H8   H   HCR5  0   0.264  -0.3883  -3.6147   1.4513
 ONV  H9   H   HCH1  0   0.284  -4.4406  -2.3817  -1.4489
 ONV  H10  H   HCR6  0   0.259  -6.7170  -1.8046  -0.9731
 ONV  H11  H   HCR6  0   0.265  -8.2831  -0.4759   0.3653
 ONV  H12  H   HOH1  0   0.487  -7.9416   3.2813   2.8494
 ONV  H13  H   HCR6  0   0.266  -5.1158   2.2611   1.3160
 ONV  H14  H   HCR6  0   0.248  -3.5700   0.9360  -0.0165
 ONV  H15  H   HCH2  0   0.230  -3.6272  -1.5921  -3.5499
 ONV  H16  H   HCH2  0   0.224  -5.2608  -0.9892  -3.2507
 ONV  H17  H   HOH1  0   0.465  -3.6448   0.6413  -3.9677
 ONV  H18  H   HNH1  0   0.399  -2.1157  -0.6834  -1.5955
 ONV  H19  H   HNR5  0   0.414  -0.4325   0.1287  -0.4775
 ONV  H20  H   HNR5  0   0.416   7.0366   3.7122  -2.2554

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
 ONV  O    C    double    1.207  0.020  1.207
 ONV  N    C    single    1.347  0.020  1.347
 ONV  N    C2   single    1.442  0.020  1.442
 ONV  C    O1   single    1.348  0.020  1.348
 ONV  C2   C1   single    1.534  0.020  1.534
 ONV  O1   C1   single    1.430  0.020  1.430
 ONV  C1   C3   single    1.512  0.020  1.512
 ONV  C3   O2   single    1.411  0.020  1.411
 ONV  O2   C4   single    1.341  0.020  1.341
 ONV  C6   C4   aromatic  1.381  0.020  1.381
 ONV  C6   C7   aromatic  1.396  0.020  1.396
 ONV  C4   C5   aromatic  1.419  0.020  1.419
 ONV  C7   N11  aromatic  1.359  0.020  1.359
 ONV  C7   C8   aromatic  1.408  0.020  1.408
 ONV  N11  C10  aromatic  1.378  0.020  1.378
 ONV  C5   CL   single    1.732  0.020  1.732
 ONV  C5   C9   aromatic  1.372  0.020  1.372
 ONV  C8   C9   aromatic  1.400  0.020  1.400
 ONV  C8   C11  aromatic  1.422  0.020  1.422
 ONV  O3   C12  double    1.222  0.020  1.222
 ONV  C10  C12  single    1.474  0.020  1.474
 ONV  C10  C11  aromatic  1.367  0.020  1.367
 ONV  C12  N2   single    1.346  0.020  1.346
 ONV  N2   C13  single    1.445  0.020  1.445
 ONV  C13  C14  single    1.513  0.020  1.513
 ONV  C13  C21  single    1.524  0.020  1.524
 ONV  O6   C21  single    1.406  0.020  1.406
 ONV  C19  C14  aromatic  1.390  0.020  1.390
 ONV  C19  C18  aromatic  1.385  0.020  1.385
 ONV  C14  C15  aromatic  1.392  0.020  1.392
 ONV  C18  C17  aromatic  1.394  0.020  1.394
 ONV  C15  C16  aromatic  1.383  0.020  1.383
 ONV  C16  C17  aromatic  1.393  0.020  1.393
 ONV  C17  C20  single    1.482  0.020  1.482
 ONV  O5   C20  double    1.208  0.020  1.208
 ONV  C20  O4   single    1.326  0.020  1.326
 ONV  C1   H1   single    0.970  0.020  1.090
 ONV  C2   H2   single    0.970  0.020  1.090
 ONV  C2   H3   single    0.970  0.020  1.090
 ONV  C3   H4   single    0.970  0.020  1.090
 ONV  C3   H5   single    0.970  0.020  1.090
 ONV  C6   H6   single    0.930  0.020  1.080
 ONV  C9   H7   single    0.930  0.020  1.080
 ONV  C11  H8   single    0.930  0.020  1.080
 ONV  C13  H9   single    0.970  0.020  1.090
 ONV  C15  H10  single    0.930  0.020  1.080
 ONV  C16  H11  single    0.930  0.020  1.080
 ONV  O4   H12  single    0.850  0.020  0.980
 ONV  C18  H13  single    0.930  0.020  1.080
 ONV  C19  H14  single    0.930  0.020  1.080
 ONV  C21  H15  single    0.970  0.020  1.090
 ONV  C21  H16  single    0.970  0.020  1.090
 ONV  O6   H17  single    0.850  0.020  0.980
 ONV  N2   H18  single    0.860  0.020  1.020
 ONV  N11  H19  single    0.860  0.020  1.020
 ONV  N    H20  single    0.890  0.020  1.040

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
 ONV  H1   C1   O1   108.25  3.000
 ONV  H1   C1   C3   110.22  3.000
 ONV  O1   C1   C3   110.17  3.000
 ONV  H1   C1   C2   112.14  3.000
 ONV  C3   C1   C2   111.52  3.000
 ONV  O1   C1   C2   104.33  3.000
 ONV  H3   C2   H2   108.29  3.000
 ONV  H3   C2   N    112.14  3.000
 ONV  H2   C2   N    112.01  3.000
 ONV  H3   C2   C1   111.88  3.000
 ONV  H2   C2   C1   112.33  3.000
 ONV  N    C2   C1   100.10  3.000
 ONV  H5   C3   H4   107.89  3.000
 ONV  H5   C3   O2   111.16  3.000
 ONV  H4   C3   O2   111.02  3.000
 ONV  H5   C3   C1   110.41  3.000
 ONV  H4   C3   C1   108.58  3.000
 ONV  O2   C3   C1   107.75  3.000
 ONV  O2   C4   C6   124.40  3.000
 ONV  C6   C4   C5   119.99  3.000
 ONV  O2   C4   C5   115.61  3.000
 ONV  CL   C5   C9   119.73  3.000
 ONV  C9   C5   C4   122.24  3.000
 ONV  CL   C5   C4   118.03  3.000
 ONV  H6   C6   C7   120.49  3.000
 ONV  H6   C6   C4   121.98  3.000
 ONV  C7   C6   C4   117.53  3.000
 ONV  N11  C7   C8   107.69  3.000
 ONV  C8   C7   C6   122.79  3.000
 ONV  N11  C7   C6   129.52  3.000
 ONV  C11  C8   C9   134.08  3.000
 ONV  C11  C8   C7   107.02  3.000
 ONV  C9   C8   C7   118.90  3.000
 ONV  H7   C9   C8   121.03  3.000
 ONV  H7   C9   C5   120.42  3.000
 ONV  C8   C9   C5   118.55  3.000
 ONV  N11  C10  C12  124.68  3.000
 ONV  C12  C10  C11  126.06  3.000
 ONV  N11  C10  C11  109.24  3.000
 ONV  H8   C11  C10  125.92  3.000
 ONV  H8   C11  C8   127.23  3.000
 ONV  C10  C11  C8   106.84  3.000
 ONV  O3   C12  N2   122.89  3.000
 ONV  N2   C12  C10  116.51  3.000
 ONV  O3   C12  C10  120.59  3.000
 ONV  H9   C13  N2   108.72  3.000
 ONV  H9   C13  C21  106.49  3.000
 ONV  N2   C13  C21  109.15  3.000
 ONV  H9   C13  C14  108.32  3.000
 ONV  C21  C13  C14  111.13  3.000
 ONV  N2   C13  C14  112.79  3.000
 ONV  C19  C14  C15  118.85  3.000
 ONV  C15  C14  C13  119.11  3.000
 ONV  C19  C14  C13  122.00  3.000
 ONV  H10  C15  C16  119.46  3.000
 ONV  H10  C15  C14  119.72  3.000
 ONV  C16  C15  C14  120.82  3.000
 ONV  H11  C16  C17  120.10  3.000
 ONV  H11  C16  C15  119.67  3.000
 ONV  C17  C16  C15  120.23  3.000
 ONV  C18  C17  C20  122.41  3.000
 ONV  C20  C17  C16  118.47  3.000
 ONV  C18  C17  C16  119.13  3.000
 ONV  O4   C20  O5   123.09  3.000
 ONV  O4   C20  C17  113.08  3.000
 ONV  O5   C20  C17  123.83  3.000
 ONV  H12  O4   C20  109.91  3.000
 ONV  H13  C18  C19  118.89  3.000
 ONV  H13  C18  C17  120.79  3.000
 ONV  C19  C18  C17  120.32  3.000
 ONV  H14  C19  C18  119.07  3.000
 ONV  H14  C19  C14  120.27  3.000
 ONV  C18  C19  C14  120.66  3.000
 ONV  H16  C21  H15  107.37  3.000
 ONV  H16  C21  O6   112.34  3.000
 ONV  H15  C21  O6   111.85  3.000
 ONV  H16  C21  C13  108.24  3.000
 ONV  H15  C21  C13  108.45  3.000
 ONV  O6   C21  C13  108.47  3.000
 ONV  H17  O6   C21  108.51  3.000
 ONV  H18  N2   C13  117.24  3.000
 ONV  H18  N2   C12  120.69  3.000
 ONV  C13  N2   C12  122.03  3.000
 ONV  H19  N11  C10  126.11  3.000
 ONV  H19  N11  C7   123.94  3.000
 ONV  C10  N11  C7   109.20  3.000
 ONV  C4   O2   C3   118.69  3.000
 ONV  H20  N    C    120.73  3.000
 ONV  H20  N    C2   122.58  3.000
 ONV  C    N    C2   112.14  3.000
 ONV  C    O1   C1   110.11  3.000
 ONV  O    C    O1   121.98  3.000
 ONV  O1   C    N    109.03  3.000
 ONV  O    C    N    128.98  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
 ONV  CONST_01  N11  C7   C6   C4   180.00   0.0  0
 ONV  CONST_02  C8   C7   C6   C4     0.00   0.0  0
 ONV  CONST_03  C8   C9   C5   C4     0.00   0.0  0
 ONV  CONST_04  C7   C6   C4   C5     0.00   0.0  0
 ONV  CONST_05  C7   C8   C9   C5     0.00   0.0  0
 ONV  CONST_06  C11  C8   C9   C5   180.00   0.0  0
 ONV  CONST_07  C9   C5   C4   C6     0.00   0.0  0
 ONV  CONST_08  C10  N11  C7   C6   180.00   0.0  0
 ONV  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 ONV  CONST_10  C11  C8   C7   C6   180.00   0.0  0
 ONV  CONST_11  C11  C10  N11  C7     0.00   0.0  0
 ONV  CONST_12  C10  C11  C8   C7     0.00   0.0  0
 ONV  CONST_13  C10  N11  C7   C8     0.00   0.0  0
 ONV  CONST_14  N11  C10  C11  C8     0.00   0.0  0
 ONV  CONST_15  N11  C7   C8   C9   180.00   0.0  0
 ONV  CONST_16  C10  C11  C8   C9   180.00   0.0  0
 ONV  CONST_17  N11  C7   C8   C11    0.00   0.0  0
 ONV  CONST_18  C17  C18  C19  C14    0.00   0.0  0
 ONV  CONST_19  C17  C16  C15  C14    0.00   0.0  0
 ONV  CONST_20  C18  C19  C14  C15    0.00   0.0  0
 ONV  CONST_21  C18  C17  C16  C15    0.00   0.0  0
 ONV  CONST_22  C19  C14  C15  C16    0.00   0.0  0
 ONV  CONST_23  C19  C18  C17  C16    0.00   0.0  0
 ONV  CONST_24  CL   C5   C4   C6   180.00   0.0  0
 ONV  CONST_25  O2   C4   C6   C7   180.00   0.0  0
 ONV  CONST_26  C12  C10  N11  C7   180.00   0.0  0
 ONV  CONST_27  CL   C5   C9   C8   180.00   0.0  0
 ONV  CONST_28  C12  C10  C11  C8   180.00   0.0  0
 ONV  CONST_29  O2   C4   C5   C9   180.00   0.0  0
 ONV  CONST_30  C18  C19  C14  C13  180.00   0.0  0
 ONV  CONST_31  C16  C15  C14  C13  180.00   0.0  0
 ONV  CONST_32  C20  C17  C16  C15  180.00   0.0  0
 ONV  CONST_33  C19  C18  C17  C20  180.00   0.0  0
 ONV  CONST_34  H7   C9   C5   C4   180.00   0.0  0
 ONV  CONST_35  H6   C6   C4   C5   180.00   0.0  0
 ONV  CONST_36  H19  N11  C7   C6     0.00   0.0  0
 ONV  CONST_37  H8   C11  C8   C7   180.00   0.0  0
 ONV  CONST_38  H13  C18  C19  C14  180.00   0.0  0
 ONV  CONST_39  H11  C16  C15  C14  180.00   0.0  0
 ONV  CONST_40  H14  C19  C14  C15  180.00   0.0  0
 ONV  CONST_41  H10  C15  C16  C17  180.00   0.0  0
 ONV  CONST_42  C13  N2   C12  C10  180.00   0.0  0
 ONV  CONST_43  H18  N2   C12  C10    0.00   0.0  0
 ONV  CONST_44  H12  O4   C20  C17  180.00   0.0  0
 ONV  CONST_45  O3   C12  N2   C13    0.00   0.0  0
 ONV  Var_01    C    N    C2   C1   -18.67  30.0  1
 ONV  Var_02    N    C    O1   C1     4.23  30.0  1
 ONV  Var_03    O1   C    N    C2    10.22  30.0  1
 ONV  Var_04    C6   C4   O2   C3     1.40  30.0  2
 ONV  Var_05    O3   C12  C10  C11   19.48  30.0  2
 ONV  Var_06    O5   C20  C17  C16   -1.34  30.0  2
 ONV  Var_07    H4   C3   O2   C4    60.46  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
 ONV  chir_01  C1   C2  O1   C3   positiv
 ONV  chir_02  C13  N2  C14  C21  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
 ONV  plan-1  C13  0.020
 ONV  plan-1  C14  0.020
 ONV  plan-1  C15  0.020
 ONV  plan-1  C16  0.020
 ONV  plan-1  C17  0.020
 ONV  plan-1  C20  0.020
 ONV  plan-1  C18  0.020
 ONV  plan-1  C19  0.020
 ONV  plan-1  H10  0.020
 ONV  plan-1  H11  0.020
 ONV  plan-1  H13  0.020
 ONV  plan-1  H14  0.020
 ONV  plan-2  C4   0.020
 ONV  plan-2  C5   0.020
 ONV  plan-2  C6   0.020
 ONV  plan-2  C7   0.020
 ONV  plan-2  C8   0.020
 ONV  plan-2  C9   0.020
 ONV  plan-2  C10  0.020
 ONV  plan-2  C11  0.020
 ONV  plan-2  C12  0.020
 ONV  plan-2  CL   0.020
 ONV  plan-2  N11  0.020
 ONV  plan-2  O2   0.020
 ONV  plan-2  H6   0.020
 ONV  plan-2  H7   0.020
 ONV  plan-2  H8   0.020
 ONV  plan-2  H19  0.020
 ONV  plan-3  C10  0.020
 ONV  plan-3  C12  0.020
 ONV  plan-3  C13  0.020
 ONV  plan-3  N2   0.020
 ONV  plan-3  O3   0.020
 ONV  plan-3  H18  0.020
 ONV  plan-4  C2   0.020
 ONV  plan-4  N    0.020
 ONV  plan-4  C    0.020
 ONV  plan-4  H20  0.020
 ONV  plan-5  C17  0.020
 ONV  plan-5  O5   0.020
 ONV  plan-5  C20  0.020
 ONV  plan-5  O4   0.020
 ONV  plan-5  H12  0.020
 ONV  plan-6  N    0.020
 ONV  plan-6  O1   0.020
 ONV  plan-6  C    0.020
 ONV  plan-6  O    0.020

