# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:05:09 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(cc1)C(=O)NC[C@H]2CN(C(=O)O2)c3ccc(cc3)N4CCOCC4=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
 RIV  RIV  5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide  ligand  47  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RIV
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
 RIV  C1    C   CH2   0  -0.289  10.2066  3.1592  19.1799
 RIV  N2    N   NT    0  -0.573   8.7621  2.9886  19.0734
 RIV  C3    C   CH2   0  -0.219  10.9200  1.9728  18.5761
 RIV  C4    C   C     0   0.485   8.1799  2.1384  18.2039
 RIV  O5    O   O2    0  -0.473  10.4327  1.7375  17.2764
 RIV  C6    C   CH2   0  -0.289   9.0962  1.3197  17.3127
 RIV  C7    C   CR6   0   0.380   6.3967  5.5116  21.4817
 RIV  C8    C   CR16  0  -0.338   6.6062  5.8089  20.1355
 RIV  C9    C   CR16  0  -0.292   6.9730  4.3575  22.0175
 RIV  C10   C   CR16  0  -0.261   7.3787  4.9766  19.3429
 RIV  C11   C   CR16  0  -0.264   7.7350  3.5284  21.2136
 RIV  C12   C   CR6   0   0.315   7.9456  3.8300  19.8760
 RIV  O13   O   O     0  -0.493   6.9702  1.9859  18.1295
 RIV  N14   N   NR5   0  -0.615   5.6683  6.4126  22.2632
 RIV  C15   C   CR5   0   0.695   5.0466  6.1430  23.4463
 RIV  C16   C   CH2   0  -0.353   5.4078  7.7865  21.8679
 RIV  O17   O   O     0  -0.467   4.5564  7.2823  23.9566
 RIV  C18   C   CR15  0  -0.010   5.0663  8.4032  23.2199
 RIV  O19   O   O     0  -0.463   4.9051  5.0830  24.0005
 RIV  C20   C   CH2   0  -0.325   6.2531  9.0014  23.9717
 RIV  N21   N   NH1   0  -0.660   7.2720  8.0238  24.2798
 RIV  C22   C   C     0   0.568   8.2514  7.6743  23.4259
 RIV  S23   S   S2    0   0.330  10.1664  5.9540  22.5842
 RIV  C24   C   CR5   0  -0.245  10.5008  4.5418  23.4910
 RIV  C25   C   CR5   0  -0.276   9.0032  6.4516  23.7505
 RIV  C26   C   CR15  0  -0.120   9.7612  4.4454  24.6315
 RIV  C27   C   CR15  0  -0.222   8.8924  5.5520  24.7731
 RIV  O28   O   O     0  -0.481   8.5123  8.2887  22.3996
 RIV  H11C  H   HCH2  0   0.257  10.5101  4.0876  18.6879
 RIV  H12C  H   HCH2  0   0.238  10.4764  3.2441  20.2341
 RIV  H31C  H   HCH2  0   0.261  11.9870  2.1823  18.5040
 RIV  H32C  H   HCH2  0   0.226  10.7916  1.0861  19.2116
 RIV  H61C  H   HCH2  0   0.250   9.0083  0.2743  17.6436
 RIV  H62C  H   HCH2  0   0.275   8.7024  1.3708  16.2963
 RIV  H8    H   HCR6  0   0.283   6.1692  6.6921  19.6898
 RIV  H9    H   HCR6  0   0.278   6.8474  4.1017  23.0570
 RIV  H10   H   HCR6  0   0.266   7.5381  5.2270  18.3020
 RIV  H11   H   HCR6  0   0.264   8.1806  2.6392  21.6416
 RIV  H161  H   HCH2  0   0.290   6.2754  8.2497  21.4048
 RIV  H162  H   HCH2  0   0.288   4.5674  7.8448  21.1715
 RIV  H18   H   HCR5  0   0.291   4.2786  9.1507  23.1386
 RIV  H201  H   HCH2  0   0.274   6.6726  9.8155  23.3808
 RIV  H202  H   HCH2  0   0.285   5.9047  9.4322  24.9102
 RIV  H21   H   HNH1  0   0.415   7.1644  7.5085  25.1378
 RIV  H26   H   HCR5  0   0.298   9.8274  3.6247  25.3297
 RIV  H27   H   HCR5  0   0.282   8.2122  5.6510  25.6078
 RIV  CL    CL  CL    0  -0.064  11.6606  3.4177  22.9413

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
 RIV  C1   N2    single    1.458  0.020  1.458
 RIV  C1   C3    single    1.510  0.020  1.510
 RIV  N2   C4    single    1.348  0.020  1.348
 RIV  N2   C12   single    1.421  0.020  1.421
 RIV  C3   O5    single    1.408  0.020  1.408
 RIV  C4   C6    single    1.518  0.020  1.518
 RIV  C4   O13   double    1.222  0.020  1.222
 RIV  O5   C6    single    1.401  0.020  1.401
 RIV  C7   C8    aromatic  1.395  0.020  1.395
 RIV  C7   C9    aromatic  1.397  0.020  1.397
 RIV  C7   N14   single    1.398  0.020  1.398
 RIV  C8   C10   aromatic  1.385  0.020  1.385
 RIV  C9   C11   aromatic  1.384  0.020  1.384
 RIV  C10  C12   aromatic  1.386  0.020  1.386
 RIV  C11  C12   aromatic  1.387  0.020  1.387
 RIV  N14  C15   single    1.363  0.020  1.363
 RIV  N14  C16   single    1.453  0.020  1.453
 RIV  C15  O17   single    1.341  0.020  1.341
 RIV  C15  O19   double    1.204  0.020  1.204
 RIV  C16  C18   single    1.525  0.020  1.525
 RIV  O17  C18   single    1.435  0.020  1.435
 RIV  C18  C20   single    1.527  0.020  1.527
 RIV  C20  N21   single    1.445  0.020  1.445
 RIV  N21  C22   single    1.346  0.020  1.346
 RIV  C22  C25   single    1.472  0.020  1.472
 RIV  C22  O28   double    1.224  0.020  1.224
 RIV  S23  C24   aromatic  1.711  0.020  1.711
 RIV  S23  C25   aromatic  1.721  0.020  1.721
 RIV  C24  C26   aromatic  1.363  0.020  1.363
 RIV  C24  CL    single    1.706  0.020  1.706
 RIV  C25  C27   aromatic  1.366  0.020  1.366
 RIV  C26  C27   aromatic  1.414  0.020  1.414
 RIV  C1   H11C  single    0.970  0.020  1.090
 RIV  C1   H12C  single    0.970  0.020  1.090
 RIV  C3   H31C  single    0.970  0.020  1.090
 RIV  C3   H32C  single    0.970  0.020  1.090
 RIV  C6   H61C  single    0.970  0.020  1.090
 RIV  C6   H62C  single    0.970  0.020  1.090
 RIV  C8   H8    single    0.930  0.020  1.080
 RIV  C9   H9    single    0.930  0.020  1.080
 RIV  C10  H10   single    0.930  0.020  1.080
 RIV  C11  H11   single    0.930  0.020  1.080
 RIV  C16  H161  single    0.970  0.020  1.090
 RIV  C16  H162  single    0.970  0.020  1.090
 RIV  C18  H18   single    0.970  0.020  1.090
 RIV  C20  H201  single    0.970  0.020  1.090
 RIV  C20  H202  single    0.970  0.020  1.090
 RIV  N21  H21   single    0.860  0.020  1.020
 RIV  C26  H26   single    0.930  0.020  1.080
 RIV  C27  H27   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
 RIV  H12C  C1   H11C  107.45  3.000
 RIV  H12C  C1   C3    109.30  3.000
 RIV  H11C  C1   C3    110.85  3.000
 RIV  H12C  C1   N2    108.93  3.000
 RIV  H11C  C1   N2    109.95  3.000
 RIV  C3    C1   N2    110.29  3.000
 RIV  C12   N2   C4    119.31  3.000
 RIV  C12   N2   C1    117.30  3.000
 RIV  C4    N2   C1    123.27  3.000
 RIV  H32C  C3   H31C  107.94  3.000
 RIV  H32C  C3   O5    111.02  3.000
 RIV  H31C  C3   O5    108.05  3.000
 RIV  H32C  C3   C1    110.34  3.000
 RIV  H31C  C3   C1    109.75  3.000
 RIV  O5    C3   C1    109.68  3.000
 RIV  O13   C4   C6    119.65  3.000
 RIV  O13   C4   N2    123.07  3.000
 RIV  C6    C4   N2    117.26  3.000
 RIV  C6    O5   C3    110.87  3.000
 RIV  H62C  C6   H61C  107.21  3.000
 RIV  H62C  C6   O5    107.83  3.000
 RIV  H61C  C6   O5    111.56  3.000
 RIV  H62C  C6   C4    107.69  3.000
 RIV  H61C  C6   C4    106.72  3.000
 RIV  O5    C6   C4    115.49  3.000
 RIV  N14   C7   C9    122.23  3.000
 RIV  N14   C7   C8    118.73  3.000
 RIV  C9    C7   C8    118.98  3.000
 RIV  H8    C8   C10   118.71  3.000
 RIV  H8    C8   C7    120.75  3.000
 RIV  C10   C8   C7    120.54  3.000
 RIV  H9    C9   C11   118.83  3.000
 RIV  H9    C9   C7    121.20  3.000
 RIV  C11   C9   C7    119.96  3.000
 RIV  H10   C10  C12   120.07  3.000
 RIV  H10   C10  C8    119.57  3.000
 RIV  C12   C10  C8    120.36  3.000
 RIV  H11   C11  C12   119.81  3.000
 RIV  H11   C11  C9    119.28  3.000
 RIV  C12   C11  C9    120.90  3.000
 RIV  C11   C12  C10   119.25  3.000
 RIV  C11   C12  N2    120.21  3.000
 RIV  C10   C12  N2    120.52  3.000
 RIV  C16   N14  C15   109.95  3.000
 RIV  C16   N14  C7    123.43  3.000
 RIV  C15   N14  C7    126.54  3.000
 RIV  O19   C15  O17   121.98  3.000
 RIV  O19   C15  N14   128.82  3.000
 RIV  O17   C15  N14   109.20  3.000
 RIV  H162  C16  H161  108.63  3.000
 RIV  H162  C16  C18   111.78  3.000
 RIV  H161  C16  C18   112.59  3.000
 RIV  H162  C16  N14   111.20  3.000
 RIV  H161  C16  N14   112.07  3.000
 RIV  C18   C16  N14   100.45  3.000
 RIV  C18   O17  C15   109.78  3.000
 RIV  H18   C18  C20   109.27  3.000
 RIV  H18   C18  O17   108.51  3.000
 RIV  C20   C18  O17   109.24  3.000
 RIV  H18   C18  C16   111.93  3.000
 RIV  C20   C18  C16   114.89  3.000
 RIV  O17   C18  C16   102.64  3.000
 RIV  H202  C20  H201  107.14  3.000
 RIV  H202  C20  N21   108.01  3.000
 RIV  H201  C20  N21   110.45  3.000
 RIV  H202  C20  C18   109.29  3.000
 RIV  H201  C20  C18   108.96  3.000
 RIV  N21   C20  C18   112.83  3.000
 RIV  H21   N21  C22   119.06  3.000
 RIV  H21   N21  C20   116.91  3.000
 RIV  C22   N21  C20   123.61  3.000
 RIV  O28   C22  C25   119.54  3.000
 RIV  O28   C22  N21   123.84  3.000
 RIV  C25   C22  N21   116.59  3.000
 RIV  C25   S23  C24    90.66  3.000
 RIV  CL    C24  C26   126.30  3.000
 RIV  CL    C24  S23   120.38  3.000
 RIV  C26   C24  S23   113.32  3.000
 RIV  C27   C25  S23   111.82  3.000
 RIV  C27   C25  C22   132.12  3.000
 RIV  S23   C25  C22   115.86  3.000
 RIV  H26   C26  C27   124.60  3.000
 RIV  H26   C26  C24   124.18  3.000
 RIV  C27   C26  C24   111.22  3.000
 RIV  H27   C27  C26   122.38  3.000
 RIV  H27   C27  C25   124.63  3.000
 RIV  C26   C27  C25   112.99  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
 RIV  CONST_01  C12  C10  C8   C7      0.00   0.0  0
 RIV  CONST_02  C12  C11  C9   C7      0.00   0.0  0
 RIV  CONST_03  C11  C9   C7   C8      0.00   0.0  0
 RIV  CONST_04  C11  C12  C10  C8      0.00   0.0  0
 RIV  CONST_05  C10  C8   C7   C9      0.00   0.0  0
 RIV  CONST_06  C10  C12  C11  C9      0.00   0.0  0
 RIV  CONST_07  C27  C26  C24  S23     0.00   0.0  0
 RIV  CONST_08  C26  C27  C25  S23     0.00   0.0  0
 RIV  CONST_09  C27  C25  S23  C24     0.00   0.0  0
 RIV  CONST_10  C25  C27  C26  C24     0.00   0.0  0
 RIV  CONST_11  C26  C24  S23  C25     0.00   0.0  0
 RIV  CONST_12  C8   C10  C12  N2    180.00   0.0  0
 RIV  CONST_13  C9   C11  C12  N2    180.00   0.0  0
 RIV  CONST_14  N14  C7   C8   C10   180.00   0.0  0
 RIV  CONST_15  N14  C7   C9   C11   180.00   0.0  0
 RIV  CONST_16  C6   C4   N2   C1      0.00   0.0  0
 RIV  CONST_17  C12  N2   C4   C6    180.00   0.0  0
 RIV  CONST_18  C24  S23  C25  C22   180.00   0.0  0
 RIV  CONST_19  C26  C27  C25  C22   180.00   0.0  0
 RIV  CONST_20  CL   C24  S23  C25   180.00   0.0  0
 RIV  CONST_21  CL   C24  C26  C27   180.00   0.0  0
 RIV  CONST_22  O13  C4   N2   C1    180.00   0.0  0
 RIV  CONST_23  O13  C4   N2   C12     0.00   0.0  0
 RIV  CONST_24  H10  C10  C12  N2      0.00   0.0  0
 RIV  CONST_25  H11  C11  C12  N2      0.00   0.0  0
 RIV  CONST_26  H9   C9   C7   C8    180.00   0.0  0
 RIV  CONST_27  H8   C8   C7   C9    180.00   0.0  0
 RIV  CONST_28  H26  C26  C24  S23   180.00   0.0  0
 RIV  CONST_29  H27  C27  C25  S23   180.00   0.0  0
 RIV  CONST_30  C25  C22  N21  C20   180.00   0.0  0
 RIV  CONST_31  H21  N21  C22  C25     0.00   0.0  0
 RIV  CONST_32  O28  C22  N21  C20     0.00   0.0  0
 RIV  Var_01    C10  C12  N2   C1     97.78  30.0  2
 RIV  Var_02    O5   C3   C1   N2     51.76  30.0  1
 RIV  Var_03    O5   C6   C4   N2    -13.42  30.0  1
 RIV  Var_04    C4   N2   C1   C3    -19.47  30.0  1
 RIV  Var_05    C4   C6   O5   C3     46.89  30.0  1
 RIV  Var_06    O17  C15  N14  C7    174.42  30.0  1
 RIV  Var_07    C18  C16  N14  C7   -160.45  30.0  1
 RIV  Var_08    C15  N14  C7   C8    160.03  30.0  2
 RIV  Var_09    S23  C25  C22  N21   175.37  30.0  2
 RIV  Var_10    C22  N21  C20  C18    85.27  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
 RIV  chir_01  C18  C16  O17  C20  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
 RIV  plan-1  C22  0.020
 RIV  plan-1  S23  0.020
 RIV  plan-1  C24  0.020
 RIV  plan-1  C25  0.020
 RIV  plan-1  C26  0.020
 RIV  plan-1  C27  0.020
 RIV  plan-1  H26  0.020
 RIV  plan-1  H27  0.020
 RIV  plan-1  CL   0.020
 RIV  plan-2  C20  0.020
 RIV  plan-2  N21  0.020
 RIV  plan-2  C22  0.020
 RIV  plan-2  C25  0.020
 RIV  plan-2  O28  0.020
 RIV  plan-2  H21  0.020
 RIV  plan-3  N2   0.020
 RIV  plan-3  C7   0.020
 RIV  plan-3  C8   0.020
 RIV  plan-3  C9   0.020
 RIV  plan-3  C10  0.020
 RIV  plan-3  C11  0.020
 RIV  plan-3  C12  0.020
 RIV  plan-3  N14  0.020
 RIV  plan-3  H8   0.020
 RIV  plan-3  H9   0.020
 RIV  plan-3  H10  0.020
 RIV  plan-3  H11  0.020
 RIV  plan-4  C1   0.020
 RIV  plan-4  N2   0.020
 RIV  plan-4  C4   0.020
 RIV  plan-4  C6   0.020
 RIV  plan-4  C12  0.020
 RIV  plan-4  O13  0.020
 RIV  plan-5  C7   0.020
 RIV  plan-5  N14  0.020
 RIV  plan-5  C15  0.020
 RIV  plan-5  C16  0.020
 RIV  plan-6  N14  0.020
 RIV  plan-6  C15  0.020
 RIV  plan-6  O17  0.020
 RIV  plan-6  O19  0.020

