# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 15:08:29 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC[C@H]1CN(C(=O)O1)c2ccc(N3CCOCC3)c(F)c2
#
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
 ZLD  ZLD  N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide  ligand  44  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZLD
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
 ZLD  C2    C  CR6   0   0.379   0.0200  -0.1684  -0.4953
 ZLD  C5    C  CR16  0  -0.476   0.7161  -0.9648   0.4163
 ZLD  C9    C  CH2   0  -0.311  -4.1674   0.9481   0.2416
 ZLD  C1    C  CR16  0  -0.336   0.7300   0.7676  -1.2397
 ZLD  C3    C  CR16  0  -0.315   2.1004   0.9119  -1.0731
 ZLD  N4    N  NR5   0  -0.618  -1.3683  -0.2640  -0.6449
 ZLD  C6    C  CH2   0  -0.329  -2.1577   0.7684  -1.2877
 ZLD  C7    C  CR5   0   0.704  -2.1147  -1.3882  -0.4483
 ZLD  C8    C  CR15  0  -0.023  -3.5700   0.2766  -0.9866
 ZLD  O10   O  O     0  -0.464  -3.3945  -1.1237  -0.7362
 ZLD  C12   C  C     0   0.524  -6.5923   0.6948   0.0548
 ZLD  C13   C  CH3   0  -0.776  -7.8111   0.0009   0.6060
 ZLD  O14   O  O     0  -0.504  -6.6639   1.5092  -0.8558
 ZLD  O15   O  O     0  -0.469  -1.7509  -2.4773  -0.0843
 ZLD  C16   C  CR6   0   0.536   2.0786  -0.8175   0.5304
 ZLD  C17   C  CR6   0   0.152   2.8245   0.1210  -0.1852
 ZLD  F18   F  F     0  -0.313   2.7225  -1.6299   1.3849
 ZLD  N19   N  NT    0  -0.505   4.2123   0.1946  -0.0135
 ZLD  C20   C  CH2   0  -0.330   4.9683   0.8015  -1.0942
 ZLD  C21   C  CH2   0  -0.183   6.4469   0.5364  -0.8755
 ZLD  O22   O  O2    0  -0.484   6.8862   1.0293   0.3698
 ZLD  C23   C  CH2   0  -0.187   6.1528   0.4533   1.4273
 ZLD  C24   C  CH2   0  -0.327   4.6646   0.7028   1.2786
 ZLD  H5    H  HCR6  0   0.292   0.2218  -1.7058   1.0261
 ZLD  H9    H  HCH2  0   0.271  -3.4741   0.8757   1.0817
 ZLD  H9A   H  HCH2  0   0.268  -4.2946   2.0092   0.0219
 ZLD  H1    H  HCR6  0   0.282   0.2302   1.4051  -1.9566
 ZLD  H3    H  HCR6  0   0.279   2.6090   1.6617  -1.6640
 ZLD  H6    H  HCH2  0   0.283  -1.9585   1.7500  -0.8553
 ZLD  H6A   H  HCH2  0   0.282  -1.9593   0.8170  -2.3610
 ZLD  H8    H  HCR5  0   0.286  -4.2353   0.3813  -1.8421
 ZLD  HN11  H  HNH1  0   0.407  -5.4145  -0.3309   1.3595
 ZLD  H13   H  HCH3  0   0.269  -8.4606   0.7386   1.0782
 ZLD  H13A  H  HCH3  0   0.265  -8.3732  -0.4514  -0.2100
 ZLD  H13B  H  HCH3  0   0.250  -7.5819  -0.7706   1.3387
 ZLD  H20   H  HCH2  0   0.258   4.6683   0.3577  -2.0455
 ZLD  H20A  H  HCH2  0   0.217   4.7998   1.8872  -1.1666
 ZLD  H21   H  HCH2  0   0.205   6.6349  -0.5437  -0.9520
 ZLD  H21A  H  HCH2  0   0.241   7.0307   1.0358  -1.6500
 ZLD  H23   H  HCH2  0   0.205   6.3337  -0.6294   1.4779
 ZLD  H23A  H  HCH2  0   0.240   6.5120   0.8992   2.3558
 ZLD  H24   H  HCH2  0   0.221   4.4539   1.7790   1.3718
 ZLD  H24A  H  HCH2  0   0.258   4.1467   0.1998   2.0936
 ZLD  N11   N  NH1   0  -0.623  -5.4251   0.3750   0.6434

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
 ZLD  C2   C5    aromatic  1.396  0.020  1.396
 ZLD  C2   C1    aromatic  1.391  0.020  1.391
 ZLD  C2   N4    single    1.400  0.020  1.400
 ZLD  C5   C16   aromatic  1.375  0.020  1.375
 ZLD  C9   C8    single    1.522  0.020  1.522
 ZLD  C9   N11   single    1.439  0.020  1.439
 ZLD  C1   C3    aromatic  1.388  0.020  1.388
 ZLD  C3   C17   aromatic  1.392  0.020  1.392
 ZLD  N4   C6    single    1.450  0.020  1.450
 ZLD  N4   C7    single    1.364  0.020  1.364
 ZLD  C6   C8    single    1.526  0.020  1.526
 ZLD  C7   O10   single    1.338  0.020  1.338
 ZLD  C7   O15   double    1.205  0.020  1.205
 ZLD  C8   O10   single    1.433  0.020  1.433
 ZLD  N11  C12   single    1.346  0.020  1.346
 ZLD  C12  C13   single    1.507  0.020  1.507
 ZLD  C12  O14   double    1.224  0.020  1.224
 ZLD  C16  C17   aromatic  1.396  0.020  1.396
 ZLD  C16  F18   single    1.343  0.020  1.343
 ZLD  C17  N19   single    1.400  0.020  1.400
 ZLD  N19  C20   single    1.452  0.020  1.452
 ZLD  N19  C24   single    1.460  0.020  1.460
 ZLD  C20  C21   single    1.518  0.020  1.518
 ZLD  C21  O22   single    1.410  0.020  1.410
 ZLD  O22  C23   single    1.410  0.020  1.410
 ZLD  C23  C24   single    1.516  0.020  1.516
 ZLD  C5   H5    single    0.930  0.020  1.080
 ZLD  C9   H9    single    0.970  0.020  1.090
 ZLD  C9   H9A   single    0.970  0.020  1.090
 ZLD  C1   H1    single    0.930  0.020  1.080
 ZLD  C3   H3    single    0.930  0.020  1.080
 ZLD  C6   H6    single    0.970  0.020  1.090
 ZLD  C6   H6A   single    0.970  0.020  1.090
 ZLD  C8   H8    single    0.970  0.020  1.090
 ZLD  N11  HN11  single    0.860  0.020  1.020
 ZLD  C13  H13   single    0.970  0.020  1.090
 ZLD  C13  H13A  single    0.970  0.020  1.090
 ZLD  C13  H13B  single    0.970  0.020  1.090
 ZLD  C20  H20   single    0.970  0.020  1.090
 ZLD  C20  H20A  single    0.970  0.020  1.090
 ZLD  C21  H21   single    0.970  0.020  1.090
 ZLD  C21  H21A  single    0.970  0.020  1.090
 ZLD  C23  H23   single    0.970  0.020  1.090
 ZLD  C23  H23A  single    0.970  0.020  1.090
 ZLD  C24  H24   single    0.970  0.020  1.090
 ZLD  C24  H24A  single    0.970  0.020  1.090

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
 ZLD  N4    C2   C1    119.68  3.000
 ZLD  N4    C2   C5    121.69  3.000
 ZLD  C1    C2   C5    118.61  3.000
 ZLD  H5    C5   C16   118.71  3.000
 ZLD  H5    C5   C2    122.14  3.000
 ZLD  C16   C5   C2    119.14  3.000
 ZLD  H9A   C9   H9    107.07  3.000
 ZLD  H9A   C9   N11   109.97  3.000
 ZLD  H9    C9   N11   108.28  3.000
 ZLD  H9A   C9   C8    108.21  3.000
 ZLD  H9    C9   C8    110.03  3.000
 ZLD  N11   C9   C8    113.11  3.000
 ZLD  H1    C1   C3    118.32  3.000
 ZLD  H1    C1   C2    121.03  3.000
 ZLD  C3    C1   C2    120.64  3.000
 ZLD  H3    C3   C17   119.84  3.000
 ZLD  H3    C3   C1    118.09  3.000
 ZLD  C17   C3   C1    122.08  3.000
 ZLD  C7    N4   C6    110.67  3.000
 ZLD  C7    N4   C2    125.72  3.000
 ZLD  C6    N4   C2    122.60  3.000
 ZLD  H6A   C6   H6    108.43  3.000
 ZLD  H6A   C6   C8    112.11  3.000
 ZLD  H6    C6   C8    112.39  3.000
 ZLD  H6A   C6   N4    111.61  3.000
 ZLD  H6    C6   N4    111.44  3.000
 ZLD  C8    C6   N4    100.78  3.000
 ZLD  O15   C7   O10   122.18  3.000
 ZLD  O15   C7   N4    128.58  3.000
 ZLD  O10   C7   N4    109.24  3.000
 ZLD  H8    C8   O10   107.82  3.000
 ZLD  H8    C8   C6    112.31  3.000
 ZLD  O10   C8   C6    103.66  3.000
 ZLD  H8    C8   C9    110.60  3.000
 ZLD  O10   C8   C9    109.77  3.000
 ZLD  C6    C8   C9    112.36  3.000
 ZLD  C8    O10  C7    110.35  3.000
 ZLD  O14   C12  C13   122.09  3.000
 ZLD  O14   C12  N11   122.30  3.000
 ZLD  C13   C12  N11   115.60  3.000
 ZLD  H13B  C13  H13A  108.59  3.000
 ZLD  H13B  C13  H13   108.27  3.000
 ZLD  H13A  C13  H13   107.33  3.000
 ZLD  H13B  C13  C12   113.72  3.000
 ZLD  H13A  C13  C12   109.55  3.000
 ZLD  H13   C13  C12   109.18  3.000
 ZLD  F18   C16  C17   118.45  3.000
 ZLD  F18   C16  C5    117.58  3.000
 ZLD  C17   C16  C5    123.97  3.000
 ZLD  N19   C17  C16   120.13  3.000
 ZLD  N19   C17  C3    124.32  3.000
 ZLD  C16   C17  C3    115.52  3.000
 ZLD  C24   N19  C20   110.60  3.000
 ZLD  C24   N19  C17   115.70  3.000
 ZLD  C20   N19  C17   116.54  3.000
 ZLD  H20A  C20  H20   107.55  3.000
 ZLD  H20A  C20  C21   109.31  3.000
 ZLD  H20   C20  C21   108.80  3.000
 ZLD  H20A  C20  N19   112.42  3.000
 ZLD  H20   C20  N19   109.60  3.000
 ZLD  C21   C20  N19   109.09  3.000
 ZLD  H21A  C21  H21   107.99  3.000
 ZLD  H21A  C21  O22   107.48  3.000
 ZLD  H21   C21  O22   110.60  3.000
 ZLD  H21A  C21  C20   109.82  3.000
 ZLD  H21   C21  C20   109.17  3.000
 ZLD  O22   C21  C20   111.70  3.000
 ZLD  C23   O22  C21   110.96  3.000
 ZLD  H23A  C23  H23   108.02  3.000
 ZLD  H23A  C23  C24   109.84  3.000
 ZLD  H23   C23  C24   109.16  3.000
 ZLD  H23A  C23  O22   107.47  3.000
 ZLD  H23   C23  O22   110.58  3.000
 ZLD  C24   C23  O22   111.70  3.000
 ZLD  H24A  C24  H24   107.29  3.000
 ZLD  H24A  C24  C23   108.50  3.000
 ZLD  H24   C24  C23   109.91  3.000
 ZLD  H24A  C24  N19   110.75  3.000
 ZLD  H24   C24  N19   110.85  3.000
 ZLD  C23   C24  N19   109.48  3.000
 ZLD  HN11  N11  C12   119.17  3.000
 ZLD  HN11  N11  C9    117.97  3.000
 ZLD  C12   N11  C9    122.77  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
 ZLD  CONST_01  C17   C16  C5   C2      0.00   0.0  0
 ZLD  CONST_02  C17   C3   C1   C2      0.00   0.0  0
 ZLD  CONST_03  C3    C1   C2   C5      0.00   0.0  0
 ZLD  CONST_04  C3    C17  C16  C5      0.00   0.0  0
 ZLD  CONST_05  C16   C5   C2   C1      0.00   0.0  0
 ZLD  CONST_06  C16   C17  C3   C1      0.00   0.0  0
 ZLD  CONST_07  N19   C17  C16  C5    180.00   0.0  0
 ZLD  CONST_08  N19   C17  C3   C1    180.00   0.0  0
 ZLD  CONST_09  N4    C2   C1   C3    180.00   0.0  0
 ZLD  CONST_10  C16   C5   C2   N4    180.00   0.0  0
 ZLD  CONST_11  F18   C16  C5   C2    180.00   0.0  0
 ZLD  CONST_12  F18   C16  C17  C3    180.00   0.0  0
 ZLD  CONST_13  N19   C17  C16  F18     0.00   0.0  0
 ZLD  CONST_14  H3    C3   C1   C2    180.00   0.0  0
 ZLD  CONST_15  H1    C1   C2   C5    180.00   0.0  0
 ZLD  CONST_16  H5    C5   C2   C1    180.00   0.0  0
 ZLD  CONST_17  C13   C12  N11  C9    180.00   0.0  0
 ZLD  CONST_18  O14   C12  N11  C9      0.00   0.0  0
 ZLD  CONST_19  HN11  N11  C12  C13     0.00   0.0  0
 ZLD  Var_01    C8    C6   N4   C2   -171.51  30.0  1
 ZLD  Var_02    O10   C7   N4   C2   -177.43  30.0  1
 ZLD  Var_03    C6    N4   C2   C5    162.57  30.0  2
 ZLD  Var_04    C20   N19  C17  C3    -20.23  30.0  2
 ZLD  Var_05    C21   C20  N19  C17  -168.24  30.0  1
 ZLD  Var_06    C23   C24  N19  C17   168.18  30.0  1
 ZLD  Var_07    O22   C21  C20  N19   -57.64  30.0  1
 ZLD  Var_08    O22   C23  C24  N19    56.48  30.0  1
 ZLD  Var_09    C24   C23  O22  C21   -57.42  30.0  1
 ZLD  Var_10    C12   N11  C9   C8    -81.07  30.0  3
 ZLD  Var_11    H13   C13  C12  N11   113.97  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
 ZLD  chir_01  C8  C9  C6  O10  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
 ZLD  plan-1  C2    0.020
 ZLD  plan-1  C5    0.020
 ZLD  plan-1  C1    0.020
 ZLD  plan-1  C3    0.020
 ZLD  plan-1  N4    0.020
 ZLD  plan-1  C16   0.020
 ZLD  plan-1  C17   0.020
 ZLD  plan-1  F18   0.020
 ZLD  plan-1  N19   0.020
 ZLD  plan-1  H5    0.020
 ZLD  plan-1  H1    0.020
 ZLD  plan-1  H3    0.020
 ZLD  plan-2  C9    0.020
 ZLD  plan-2  C12   0.020
 ZLD  plan-2  C13   0.020
 ZLD  plan-2  O14   0.020
 ZLD  plan-2  HN11  0.020
 ZLD  plan-2  N11   0.020
 ZLD  plan-3  C2    0.020
 ZLD  plan-3  N4    0.020
 ZLD  plan-3  C6    0.020
 ZLD  plan-3  C7    0.020
 ZLD  plan-4  N4    0.020
 ZLD  plan-4  C7    0.020
 ZLD  plan-4  O10   0.020
 ZLD  plan-4  O15   0.020

