# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:19:49 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(OC[C@@H]2CN(C(=O)O2)c3cccc(c3)C#Cc4cccnc4Cl)c1
#
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
 5TA  5TA  (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one  ligand  51  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5TA
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
 5TA  C1   C   CR5   0   0.706   1.0152  -1.0043   1.8247
 5TA  C4   C   CSP   0   0.170  -4.7060  -0.1488  -0.3611
 5TA  C5   C   CSP   0   0.167  -3.8634  -0.9911  -0.1712
 5TA  C6   C   CR6   0   0.398  -0.5835  -2.4882   0.6885
 5TA  C7   C   CR6   0   0.094  -5.4448   2.2028  -0.3883
 5TA  C8   C   CR15  0  -0.051   2.9855  -2.0287   1.3221
 5TA  C9   C   CH2   0  -0.342   1.8513  -2.9833   0.9562
 5TA  C10  C   CR6   0  -0.124  -5.6954   0.8382  -0.5848
 5TA  C13  C   CR16  0  -0.358  -1.5879  -1.5497   0.4644
 5TA  C17  C   CH2   0  -0.177   3.6614  -1.4657   0.0922
 5TA  C18  C   CR6   0   0.409   5.3547   0.1146  -0.4205
 5TA  C19  C   CR16  0  -0.396   6.2939   1.0272   0.0621
 5TA  C20  C   CR6   0   0.088   7.0881   1.7540  -0.8107
 5TA  C22  C   CR16  0  -0.328  -0.8541  -3.8400   0.4725
 5TA  C23  C   CR16  0  -0.236  -2.1139  -4.2448   0.0569
 5TA  C24  C   CR16  0  -0.228   6.0062   0.6570  -2.6610
 5TA  C25  C   CR16  0  -0.058  -7.5377   2.8150  -0.9969
 5TA  C26  C   CH2   0  -0.327   8.0852   2.7670  -0.3040
 5TA  C27  C   CR16  0  -0.194  -6.9794   0.5034  -1.0179
 5TA  C28  C   CR16  0  -0.309  -3.1232  -3.3228  -0.1506
 5TA  N12  N   N     0  -0.377  -6.3197   3.1533  -0.5828
 5TA  C31  C   CR16  0  -0.317  -7.9133   1.5019  -1.2274
 5TA  C14  C   CR6   0  -0.095  -2.8542  -1.9674   0.0528
 5TA  N2   N   NR5   0  -0.622   0.7036  -2.1066   1.0815
 5TA  O3   O   O     0  -0.459   2.3340  -0.9847   2.0520
 5TA  O11  O   O     0  -0.463   0.2788  -0.1531   2.2499
 5TA  O15  O   O2    0  -0.477   4.6352  -0.5426   0.5175
 5TA  C29  C   CR16  0  -0.396   5.2053  -0.0755  -1.7903
 5TA  C30  C   CR16  0  -0.325   6.9406   1.5591  -2.1855
 5TA  N21  N   NH2   0  -0.795   8.5198   2.4969   1.0532
 5TA  H1   H   HCR5  0   0.293   3.7166  -2.4963   1.9809
 5TA  H2   H   HCH2  0   0.289   1.9441  -3.3739  -0.0579
 5TA  H3   H   HCH2  0   0.288   1.7939  -3.8263   1.6481
 5TA  H4   H   HCR6  0   0.278  -1.4040  -0.4941   0.5899
 5TA  H5   H   HCH2  0   0.248   4.1132  -2.2971  -0.4606
 5TA  H6   H   HCH2  0   0.238   2.9212  -0.9914  -0.5648
 5TA  H7   H   HCR6  0   0.254   6.4051   1.1622   1.1309
 5TA  H8   H   HCR6  0   0.289  -0.0903  -4.5895   0.6268
 5TA  H9   H   HCR6  0   0.272  -2.3045  -5.2974  -0.1021
 5TA  H10  H   HCR6  0   0.257   5.8958   0.5058  -3.7273
 5TA  H11  H   HCR6  0   0.285  -8.2360   3.6279  -1.1497
 5TA  H12  H   HCH2  0   0.216   8.9062   2.8318  -1.0304
 5TA  H13  H   HCH2  0   0.244   7.6065   3.7513  -0.3123
 5TA  H14  H   HCR6  0   0.287  -7.2298  -0.5353  -1.1855
 5TA  H15  H   HCR6  0   0.266  -4.1052  -3.6402  -0.4730
 5TA  H16  H   HCR6  0   0.287  -8.9129   1.2675  -1.5635
 5TA  H17  H   HCR6  0   0.277   4.4911  -0.7790  -2.1967
 5TA  H18  H   HCR6  0   0.244   7.5625   2.1118  -2.8795
 5TA  H19  H   HNH2  0   0.345   9.1110   1.6750   1.0634
 5TA  H20  H   HNH2  0   0.356   9.0997   3.2613   1.3738
 5TA  CL1  CL  CL    0  -0.092  -3.8749   2.6937   0.1478

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
 5TA  C23  C28  aromatic  1.383  0.020  1.383
 5TA  C23  C22  aromatic  1.387  0.020  1.387
 5TA  C28  C14  aromatic  1.397  0.020  1.397
 5TA  C22  C6   aromatic  1.395  0.020  1.395
 5TA  C14  C5   single    1.422  0.020  1.422
 5TA  C14  C13  aromatic  1.396  0.020  1.396
 5TA  C5   C4   triple    1.206  0.020  1.206
 5TA  C27  C31  aromatic  1.383  0.020  1.383
 5TA  C27  C10  aromatic  1.396  0.020  1.396
 5TA  C4   C10  single    1.415  0.020  1.415
 5TA  C6   C13  aromatic  1.393  0.020  1.393
 5TA  C6   N2   single    1.399  0.020  1.399
 5TA  C31  C25  aromatic  1.385  0.020  1.385
 5TA  C10  C7   aromatic  1.401  0.020  1.401
 5TA  C25  N12  aromatic  1.330  0.020  1.330
 5TA  C7   N12  aromatic  1.306  0.020  1.306
 5TA  C7   CL1  single    1.730  0.020  1.730
 5TA  C9   N2   single    1.450  0.020  1.450
 5TA  C9   C8   single    1.527  0.020  1.527
 5TA  N2   C1   single    1.365  0.020  1.365
 5TA  C1   O11  double    1.203  0.020  1.203
 5TA  C1   O3   single    1.338  0.020  1.338
 5TA  C8   O3   single    1.431  0.020  1.431
 5TA  C8   C17  single    1.512  0.020  1.512
 5TA  C17  O15  single    1.408  0.020  1.408
 5TA  O15  C18  single    1.353  0.020  1.353
 5TA  C18  C19  aromatic  1.396  0.020  1.396
 5TA  C18  C29  aromatic  1.391  0.020  1.391
 5TA  C19  C20  aromatic  1.386  0.020  1.386
 5TA  C29  C24  aromatic  1.391  0.020  1.391
 5TA  N21  C26  single    1.451  0.020  1.451
 5TA  C20  C26  single    1.509  0.020  1.509
 5TA  C20  C30  aromatic  1.396  0.020  1.396
 5TA  C24  C30  aromatic  1.383  0.020  1.383
 5TA  C8   H1   single    0.970  0.020  1.090
 5TA  C9   H2   single    0.970  0.020  1.090
 5TA  C9   H3   single    0.970  0.020  1.090
 5TA  C13  H4   single    0.930  0.020  1.080
 5TA  C17  H5   single    0.970  0.020  1.090
 5TA  C17  H6   single    0.970  0.020  1.090
 5TA  C19  H7   single    0.930  0.020  1.080
 5TA  C22  H8   single    0.930  0.020  1.080
 5TA  C23  H9   single    0.930  0.020  1.080
 5TA  C24  H10  single    0.930  0.020  1.080
 5TA  C25  H11  single    0.930  0.020  1.080
 5TA  C26  H12  single    0.970  0.020  1.090
 5TA  C26  H13  single    0.970  0.020  1.090
 5TA  C27  H14  single    0.930  0.020  1.080
 5TA  C28  H15  single    0.930  0.020  1.080
 5TA  C31  H16  single    0.930  0.020  1.080
 5TA  C29  H17  single    0.930  0.020  1.080
 5TA  C30  H18  single    0.930  0.020  1.080
 5TA  N21  H19  single    0.890  0.020  1.040
 5TA  N21  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
 5TA  O11  C1   O3   122.19  3.000
 5TA  O3   C1   N2   109.22  3.000
 5TA  O11  C1   N2   128.59  3.000
 5TA  C10  C4   C5   180.00  3.000
 5TA  C14  C5   C4   180.00  3.000
 5TA  N2   C6   C22  119.09  3.000
 5TA  N2   C6   C13  121.66  3.000
 5TA  C22  C6   C13  119.21  3.000
 5TA  N12  C7   CL1  116.58  3.000
 5TA  CL1  C7   C10  118.82  3.000
 5TA  N12  C7   C10  124.60  3.000
 5TA  H1   C8   O3   108.07  3.000
 5TA  H1   C8   C17  110.59  3.000
 5TA  O3   C8   C17  110.29  3.000
 5TA  H1   C8   C9   112.02  3.000
 5TA  C17  C8   C9   111.71  3.000
 5TA  O3   C8   C9   103.90  3.000
 5TA  H3   C9   H2   108.49  3.000
 5TA  H3   C9   N2   111.74  3.000
 5TA  H2   C9   N2   111.36  3.000
 5TA  H3   C9   C8   111.70  3.000
 5TA  H2   C9   C8   112.55  3.000
 5TA  N2   C9   C8   100.91  3.000
 5TA  C27  C10  C7   116.21  3.000
 5TA  C7   C10  C4   122.14  3.000
 5TA  C27  C10  C4   121.65  3.000
 5TA  H4   C13  C14  118.80  3.000
 5TA  H4   C13  C6   121.18  3.000
 5TA  C14  C13  C6   120.01  3.000
 5TA  H6   C17  H5   107.70  3.000
 5TA  H6   C17  O15  111.35  3.000
 5TA  H5   C17  O15  111.39  3.000
 5TA  H6   C17  C8   110.26  3.000
 5TA  H5   C17  C8   108.18  3.000
 5TA  O15  C17  C8   107.92  3.000
 5TA  C29  C18  O15  124.02  3.000
 5TA  C29  C18  C19  120.15  3.000
 5TA  O15  C18  C19  115.84  3.000
 5TA  H7   C19  C20  119.82  3.000
 5TA  H7   C19  C18  119.47  3.000
 5TA  C20  C19  C18  120.71  3.000
 5TA  C30  C20  C26  119.61  3.000
 5TA  C30  C20  C19  119.10  3.000
 5TA  C26  C20  C19  121.28  3.000
 5TA  H8   C22  C23  118.83  3.000
 5TA  H8   C22  C6   120.83  3.000
 5TA  C23  C22  C6   120.35  3.000
 5TA  H9   C23  C28  119.89  3.000
 5TA  H9   C23  C22  119.22  3.000
 5TA  C28  C23  C22  120.89  3.000
 5TA  H10  C24  C30  119.91  3.000
 5TA  H10  C24  C29  118.96  3.000
 5TA  C30  C24  C29  121.14  3.000
 5TA  H11  C25  C31  120.90  3.000
 5TA  H11  C25  N12  116.34  3.000
 5TA  C31  C25  N12  122.76  3.000
 5TA  H13  C26  H12  105.60  3.000
 5TA  H13  C26  N21  107.79  3.000
 5TA  H12  C26  N21  113.94  3.000
 5TA  H13  C26  C20  108.19  3.000
 5TA  H12  C26  C20  108.15  3.000
 5TA  N21  C26  C20  112.78  3.000
 5TA  H14  C27  C31  120.90  3.000
 5TA  H14  C27  C10  119.44  3.000
 5TA  C31  C27  C10  119.66  3.000
 5TA  H15  C28  C14  120.21  3.000
 5TA  H15  C28  C23  120.80  3.000
 5TA  C14  C28  C23  118.99  3.000
 5TA  C25  N12  C7   118.33  3.000
 5TA  H16  C31  C27  121.01  3.000
 5TA  H16  C31  C25  120.55  3.000
 5TA  C27  C31  C25  118.43  3.000
 5TA  C28  C14  C13  120.54  3.000
 5TA  C13  C14  C5   119.01  3.000
 5TA  C28  C14  C5   120.44  3.000
 5TA  C9   N2   C6   122.63  3.000
 5TA  C9   N2   C1   110.77  3.000
 5TA  C6   N2   C1   125.67  3.000
 5TA  C8   O3   C1   110.57  3.000
 5TA  C18  O15  C17  118.49  3.000
 5TA  H17  C29  C24  119.16  3.000
 5TA  H17  C29  C18  121.99  3.000
 5TA  C24  C29  C18  118.85  3.000
 5TA  H18  C30  C24  120.02  3.000
 5TA  H18  C30  C20  119.92  3.000
 5TA  C24  C30  C20  120.06  3.000
 5TA  H20  N21  H19  105.99  3.000
 5TA  H20  N21  C26  109.12  3.000
 5TA  H19  N21  C26  109.61  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
 5TA  CONST_01  C28  C23  C22  C6      0.00   0.0  0
 5TA  CONST_02  C28  C14  C13  C6      0.00   0.0  0
 5TA  CONST_03  C31  C27  C10  C7      0.00   0.0  0
 5TA  CONST_04  C31  C25  N12  C7      0.00   0.0  0
 5TA  CONST_05  C25  C31  C27  C10     0.00   0.0  0
 5TA  CONST_06  C25  N12  C7   C10     0.00   0.0  0
 5TA  CONST_07  C23  C28  C14  C13     0.00   0.0  0
 5TA  CONST_08  C23  C22  C6   C13     0.00   0.0  0
 5TA  CONST_09  C30  C20  C19  C18     0.00   0.0  0
 5TA  CONST_10  C30  C24  C29  C18     0.00   0.0  0
 5TA  CONST_11  C24  C29  C18  C19     0.00   0.0  0
 5TA  CONST_12  C24  C30  C20  C19     0.00   0.0  0
 5TA  CONST_13  C29  C18  C19  C20     0.00   0.0  0
 5TA  CONST_14  C29  C24  C30  C20     0.00   0.0  0
 5TA  CONST_15  C14  C28  C23  C22     0.00   0.0  0
 5TA  CONST_16  C14  C13  C6   C22     0.00   0.0  0
 5TA  CONST_17  N12  C25  C31  C27     0.00   0.0  0
 5TA  CONST_18  N12  C7   C10  C27     0.00   0.0  0
 5TA  CONST_19  N2   C6   C22  C23   180.00   0.0  0
 5TA  CONST_20  N2   C6   C13  C14   180.00   0.0  0
 5TA  CONST_21  C31  C27  C10  C4    180.00   0.0  0
 5TA  CONST_22  N12  C7   C10  C4    180.00   0.0  0
 5TA  CONST_23  C23  C28  C14  C5    180.00   0.0  0
 5TA  CONST_24  C6   C13  C14  C5    180.00   0.0  0
 5TA  CONST_25  C26  C20  C19  C18   180.00   0.0  0
 5TA  CONST_26  O15  C18  C19  C20   180.00   0.0  0
 5TA  CONST_27  O15  C18  C29  C24   180.00   0.0  0
 5TA  CONST_28  C26  C20  C30  C24   180.00   0.0  0
 5TA  CONST_29  CL1  C7   N12  C25   180.00   0.0  0
 5TA  CONST_30  CL1  C7   C10  C27   180.00   0.0  0
 5TA  CONST_31  H9   C23  C22  C6    180.00   0.0  0
 5TA  CONST_32  H14  C27  C10  C7    180.00   0.0  0
 5TA  CONST_33  H11  C25  N12  C7    180.00   0.0  0
 5TA  CONST_34  H16  C31  C27  C10   180.00   0.0  0
 5TA  CONST_35  H15  C28  C14  C13   180.00   0.0  0
 5TA  CONST_36  H8   C22  C6   C13   180.00   0.0  0
 5TA  CONST_37  H10  C24  C29  C18   180.00   0.0  0
 5TA  CONST_38  H17  C29  C18  C19   180.00   0.0  0
 5TA  CONST_39  H18  C30  C20  C19   180.00   0.0  0
 5TA  CONST_40  H4   C13  C6   C22   180.00   0.0  0
 5TA  CONST_41  H7   C19  C18  C29   180.00   0.0  0
 5TA  Var_01    C22  C6   N2   C1   -152.04  30.0  2
 5TA  Var_02    C8   C9   N2   C1    -18.29  30.0  1
 5TA  Var_03    O3   C1   N2   C6    177.61  30.0  1
 5TA  Var_04    N2   C1   O3   C8      6.49  30.0  1
 5TA  Var_05    C19  C18  O15  C17   179.31  30.0  2
 5TA  Var_06    N21  C26  C20  C19    24.64  30.0  2
 5TA  Var_07    H5   C17  O15  C18    62.77  30.0  1
 5TA  Var_08    H19  N21  C26  C20    70.80  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
 5TA  chir_01  C8  C9  O3  C17  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
 5TA  plan-1  C18  0.020
 5TA  plan-1  C19  0.020
 5TA  plan-1  C20  0.020
 5TA  plan-1  C24  0.020
 5TA  plan-1  C26  0.020
 5TA  plan-1  O15  0.020
 5TA  plan-1  C29  0.020
 5TA  plan-1  C30  0.020
 5TA  plan-1  H7   0.020
 5TA  plan-1  H10  0.020
 5TA  plan-1  H17  0.020
 5TA  plan-1  H18  0.020
 5TA  plan-2  C1   0.020
 5TA  plan-2  C6   0.020
 5TA  plan-2  C9   0.020
 5TA  plan-2  N2   0.020
 5TA  plan-3  C4   0.020
 5TA  plan-3  C5   0.020
 5TA  plan-3  C6   0.020
 5TA  plan-3  C13  0.020
 5TA  plan-3  C22  0.020
 5TA  plan-3  C23  0.020
 5TA  plan-3  C28  0.020
 5TA  plan-3  C14  0.020
 5TA  plan-3  N2   0.020
 5TA  plan-3  H4   0.020
 5TA  plan-3  H8   0.020
 5TA  plan-3  H9   0.020
 5TA  plan-3  H15  0.020
 5TA  plan-4  C4   0.020
 5TA  plan-4  C5   0.020
 5TA  plan-4  C7   0.020
 5TA  plan-4  C10  0.020
 5TA  plan-4  C25  0.020
 5TA  plan-4  C27  0.020
 5TA  plan-4  N12  0.020
 5TA  plan-4  C31  0.020
 5TA  plan-4  H11  0.020
 5TA  plan-4  H14  0.020
 5TA  plan-4  H16  0.020
 5TA  plan-4  CL1  0.020
 5TA  plan-5  C1   0.020
 5TA  plan-5  N2   0.020
 5TA  plan-5  O3   0.020
 5TA  plan-5  O11  0.020

