# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 06:32:25 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: N-({(5S)-3-[2-fluoro-4'-({[(1H-1,2,3-triazol-4-yl)methyl]amino}methyl)[1,1'-biphenyl]-4-yl]-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(c(F)c2)c3ccc(CNCc4c[nH]nn4)cc3
#
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
 RD8  RD8  N-({(5S)-3-[2-fluoro-4'-({[(1H-1,2,3-triazol-4-yl)methyl]amino}methyl)[1,1'-biphenyl]-4-yl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide  ligand  55  32  .  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_RD8
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
 RD8  C02  C  CR6   0   0.551  246.0937  227.4297  208.2608
 RD8  C03  C  CR6   0  -0.160  245.9752  226.6854  209.4255
 RD8  C04  C  CR6   0   0.090  245.8001  227.3014  210.7548
 RD8  C05  C  CR16  0  -0.289  246.5795  226.8694  211.8306
 RD8  C06  C  CR16  0  -0.272  246.4209  227.4202  213.0911
 RD8  C07  C  CR16  0  -0.285  244.8537  228.2978  210.9850
 RD8  C08  C  CR16  0  -0.301  244.7014  228.8486  212.2498
 RD8  C09  C  CR6   0   0.095  245.4856  228.4278  213.3175
 RD8  C10  C  CH2   0  -0.337  245.3304  229.0394  214.6828
 RD8  C13  C  CR5   0   0.153  243.9485  229.5944  217.2832
 RD8  C14  C  CR15  0  -0.088  244.1029  230.9455  217.4658
 RD8  C18  C  CR16  0  -0.282  246.0505  225.3003  209.2686
 RD8  C19  C  CR16  0  -0.300  246.2231  224.6971  208.0364
 RD8  C20  C  CR6   0   0.392  246.3471  225.4849  206.8896
 RD8  C22  C  CH2   0  -0.333  246.2028  225.6468  204.3956
 RD8  C23  C  CR15  0  -0.012  246.2177  224.5001  203.3896
 RD8  C24  C  CH2   0  -0.320  244.8360  223.9357  203.0712
 RD8  C26  C  C     0   0.527  243.8788  222.9550  205.1230
 RD8  C27  C  CH3   0  -0.774  242.8273  223.1286  206.1890
 RD8  C30  C  CR5   0   0.707  247.1100  223.7397  205.3402
 RD8  C32  C  CR16  0  -0.497  246.2765  226.8705  207.0128
 RD8  F01  F  F     0  -0.306  246.0593  228.7690  208.3352
 RD8  N11  N  NH1   0  -0.574  245.0271  228.0253  215.6752
 RD8  N15  N  NR15  0  -0.399  242.8473  231.3988  217.5934
 RD8  N16  N  N     0  -0.095  241.9665  230.4239  217.4973
 RD8  N17  N  N     0  -0.321  242.6207  229.3297  217.3096
 RD8  N21  N  NR5   0  -0.620  246.4917  224.9269  205.6211
 RD8  N25  N  NH1   0  -0.630  243.9095  223.9124  204.1778
 RD8  O28  O  O     0  -0.498  244.6518  222.0073  205.1276
 RD8  O29  O  O     0  -0.461  247.0519  223.5208  204.0256
 RD8  H1   H  HCR6  0   0.254  247.3303  226.1040  211.6762
 RD8  H2   H  HCR6  0   0.248  247.0398  227.0704  213.9080
 RD8  H3   H  HCR6  0   0.249  244.2076  228.6338  210.1847
 RD8  H4   H  HCR6  0   0.252  243.9542  229.6180  212.4045
 RD8  H5   H  HCH2  0   0.239  246.2722  229.5158  214.9755
 RD8  H6   H  HCH2  0   0.221  244.5848  229.8457  214.6327
 RD8  H7   H  HCH2  0   0.260  244.7903  227.6887  217.7018
 RD8  H8   H  HCH2  0   0.245  245.9608  228.9273  217.2955
 RD8  H9   H  HCR5  0   0.305  244.9686  231.5831  217.5155
 RD8  H10  H  HCR6  0   0.270  245.9422  224.6694  210.1416
 RD8  H11  H  HCR6  0   0.277  246.2387  223.6204  207.9767
 RD8  H12  H  HCH2  0   0.284  246.9726  226.3909  204.1776
 RD8  H13  H  HCH2  0   0.279  245.2387  226.1522  204.4450
 RD8  H14  H  HCR5  0   0.288  246.7025  224.7806  202.4554
 RD8  H15  H  HCH2  0   0.276  244.3993  224.5716  202.3017
 RD8  H16  H  HCH2  0   0.273  244.9423  222.9398  202.6375
 RD8  H17  H  HCH3  0   0.269  242.1846  222.2489  206.2099
 RD8  H18  H  HCH3  0   0.263  243.3140  223.1968  207.1622
 RD8  H19  H  HCH3  0   0.251  242.2038  224.0104  206.0553
 RD8  H20  H  HCR6  0   0.299  246.3768  227.5262  206.1582
 RD8  H21  H  HNH1  0   0.347  244.1459  227.5805  215.4469
 RD8  H23  H  HNR5  0   0.436  242.5373  232.3478  217.7433
 RD8  H24  H  HNH1  0   0.408  243.2340  224.6559  204.2279
 RD8  O31  O  O     0  -0.467  247.6671  222.9886  206.0979
 RD8  C12  C  CH2   0  -0.389  244.9754  228.5337  217.0354

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
 RD8  C24  C23  single    1.526  0.020  1.526
 RD8  C24  N25  single    1.443  0.020  1.443
 RD8  C23  O29  single    1.435  0.020  1.435
 RD8  C23  C22  single    1.525  0.020  1.525
 RD8  O29  C30  single    1.334  0.020  1.334
 RD8  O28  C26  double    1.223  0.020  1.223
 RD8  N25  C26  single    1.346  0.020  1.346
 RD8  C26  C27  single    1.507  0.020  1.507
 RD8  C22  N21  single    1.450  0.020  1.450
 RD8  C30  N21  single    1.368  0.020  1.368
 RD8  C30  O31  double    1.204  0.020  1.204
 RD8  N21  C20  single    1.393  0.020  1.393
 RD8  C20  C32  aromatic  1.393  0.020  1.393
 RD8  C20  C19  aromatic  1.397  0.020  1.397
 RD8  C32  C02  aromatic  1.380  0.020  1.380
 RD8  C19  C18  aromatic  1.383  0.020  1.383
 RD8  C02  F01  single    1.342  0.020  1.342
 RD8  C02  C03  aromatic  1.387  0.020  1.387
 RD8  C18  C03  aromatic  1.396  0.020  1.396
 RD8  C03  C04  single    1.476  0.020  1.476
 RD8  C04  C07  aromatic  1.393  0.020  1.393
 RD8  C04  C05  aromatic  1.397  0.020  1.397
 RD8  C07  C08  aromatic  1.388  0.020  1.388
 RD8  C05  C06  aromatic  1.385  0.020  1.385
 RD8  C08  C09  aromatic  1.390  0.020  1.390
 RD8  C06  C09  aromatic  1.393  0.020  1.393
 RD8  C09  C10  single    1.504  0.020  1.504
 RD8  C10  N11  single    1.451  0.020  1.451
 RD8  N11  C12  single    1.453  0.020  1.453
 RD8  N15  N16  aromatic  1.317  0.020  1.317
 RD8  N15  C14  aromatic  1.341  0.020  1.341
 RD8  N16  N17  aromatic  1.289  0.020  1.289
 RD8  C14  C13  aromatic  1.372  0.020  1.372
 RD8  N17  C13  aromatic  1.354  0.020  1.354
 RD8  C13  C12  single    1.497  0.020  1.497
 RD8  C05  H1   single    0.930  0.020  1.080
 RD8  C06  H2   single    0.930  0.020  1.080
 RD8  C07  H3   single    0.930  0.020  1.080
 RD8  C08  H4   single    0.930  0.020  1.080
 RD8  C10  H5   single    0.970  0.020  1.090
 RD8  C10  H6   single    0.970  0.020  1.090
 RD8  C12  H7   single    0.970  0.020  1.090
 RD8  C12  H8   single    0.970  0.020  1.090
 RD8  C14  H9   single    0.930  0.020  1.080
 RD8  C18  H10  single    0.930  0.020  1.080
 RD8  C19  H11  single    0.930  0.020  1.080
 RD8  C22  H12  single    0.970  0.020  1.090
 RD8  C22  H13  single    0.970  0.020  1.090
 RD8  C23  H14  single    0.970  0.020  1.090
 RD8  C24  H15  single    0.970  0.020  1.090
 RD8  C24  H16  single    0.970  0.020  1.090
 RD8  C27  H17  single    0.970  0.020  1.090
 RD8  C27  H18  single    0.970  0.020  1.090
 RD8  C27  H19  single    0.970  0.020  1.090
 RD8  C32  H20  single    0.930  0.020  1.080
 RD8  N11  H21  single    0.890  0.020  1.040
 RD8  N15  H23  single    0.860  0.020  1.020
 RD8  N25  H24  single    0.860  0.020  1.020

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
 RD8  F01  C02  C32  117.27  3.000
 RD8  F01  C02  C03  119.13  3.000
 RD8  C32  C02  C03  123.59  3.000
 RD8  C18  C03  C04  121.46  3.000
 RD8  C04  C03  C02  122.85  3.000
 RD8  C18  C03  C02  115.68  3.000
 RD8  C07  C04  C05  118.22  3.000
 RD8  C05  C04  C03  119.90  3.000
 RD8  C07  C04  C03  121.87  3.000
 RD8  H1   C05  C06  119.35  3.000
 RD8  H1   C05  C04  119.70  3.000
 RD8  C06  C05  C04  120.94  3.000
 RD8  H2   C06  C09  119.64  3.000
 RD8  H2   C06  C05  119.52  3.000
 RD8  C09  C06  C05  120.83  3.000
 RD8  H3   C07  C08  119.03  3.000
 RD8  H3   C07  C04  120.36  3.000
 RD8  C08  C07  C04  120.59  3.000
 RD8  H4   C08  C09  119.62  3.000
 RD8  H4   C08  C07  119.18  3.000
 RD8  C09  C08  C07  121.20  3.000
 RD8  C10  C09  C08  121.06  3.000
 RD8  C10  C09  C06  120.72  3.000
 RD8  C08  C09  C06  118.22  3.000
 RD8  H6   C10  H5   106.04  3.000
 RD8  H6   C10  N11  113.71  3.000
 RD8  H5   C10  N11  107.52  3.000
 RD8  H6   C10  C09  109.08  3.000
 RD8  H5   C10  C09  109.31  3.000
 RD8  N11  C10  C09  111.00  3.000
 RD8  N17  C13  C14  107.47  3.000
 RD8  N17  C13  C12  122.50  3.000
 RD8  C14  C13  C12  129.98  3.000
 RD8  H9   C14  N15  123.26  3.000
 RD8  H9   C14  C13  132.84  3.000
 RD8  N15  C14  C13  103.90  3.000
 RD8  H10  C18  C19  118.48  3.000
 RD8  H10  C18  C03  118.83  3.000
 RD8  C19  C18  C03  122.66  3.000
 RD8  H11  C19  C20  121.08  3.000
 RD8  H11  C19  C18  119.12  3.000
 RD8  C20  C19  C18  119.78  3.000
 RD8  N21  C20  C32  118.96  3.000
 RD8  C32  C20  C19  118.94  3.000
 RD8  N21  C20  C19  122.06  3.000
 RD8  H13  C22  H12  108.45  3.000
 RD8  H13  C22  N21  111.60  3.000
 RD8  H12  C22  N21  111.49  3.000
 RD8  H13  C22  C23  112.78  3.000
 RD8  H12  C22  C23  111.93  3.000
 RD8  N21  C22  C23  100.50  3.000
 RD8  H14  C23  O29  107.28  3.000
 RD8  H14  C23  C24  108.62  3.000
 RD8  O29  C23  C24  111.49  3.000
 RD8  H14  C23  C22  112.11  3.000
 RD8  O29  C23  C22  103.08  3.000
 RD8  C24  C23  C22  114.00  3.000
 RD8  H16  C24  H15  106.92  3.000
 RD8  H16  C24  N25  110.64  3.000
 RD8  H15  C24  N25  107.07  3.000
 RD8  H16  C24  C23  109.40  3.000
 RD8  H15  C24  C23  107.12  3.000
 RD8  N25  C24  C23  115.29  3.000
 RD8  O28  C26  N25  122.65  3.000
 RD8  N25  C26  C27  115.51  3.000
 RD8  O28  C26  C27  121.83  3.000
 RD8  H19  C27  H18  108.34  3.000
 RD8  H19  C27  H17  108.59  3.000
 RD8  H18  C27  H17  107.26  3.000
 RD8  H19  C27  C26  113.96  3.000
 RD8  H18  C27  C26  109.09  3.000
 RD8  H17  C27  C26  109.39  3.000
 RD8  O31  C30  O29  122.56  3.000
 RD8  O31  C30  N21  128.44  3.000
 RD8  O29  C30  N21  108.97  3.000
 RD8  H20  C32  C20  121.90  3.000
 RD8  H20  C32  C02  118.76  3.000
 RD8  C20  C32  C02  119.34  3.000
 RD8  H21  N11  C12  109.49  3.000
 RD8  H21  N11  C10  109.54  3.000
 RD8  C12  N11  C10  113.78  3.000
 RD8  H23  N15  N16  120.08  3.000
 RD8  H23  N15  C14  128.28  3.000
 RD8  N16  N15  C14  111.65  3.000
 RD8  N17  N16  N15  107.43  3.000
 RD8  N16  N17  C13  109.55  3.000
 RD8  C30  N21  C22  110.32  3.000
 RD8  C30  N21  C20  125.56  3.000
 RD8  C22  N21  C20  123.36  3.000
 RD8  H24  N25  C26  118.40  3.000
 RD8  H24  N25  C24  117.22  3.000
 RD8  C26  N25  C24  124.37  3.000
 RD8  C30  O29  C23  110.49  3.000
 RD8  H8   C12  H7   106.64  3.000
 RD8  H8   C12  N11  108.47  3.000
 RD8  H7   C12  N11  107.85  3.000
 RD8  H8   C12  C13  108.91  3.000
 RD8  H7   C12  C13  109.33  3.000
 RD8  N11  C12  C13  115.30  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
 RD8  CONST_01  C19  C20  C32  C02     0.00   0.0  0
 RD8  CONST_02  C19  C18  C03  C02     0.00   0.0  0
 RD8  CONST_05  C20  C32  C02  C03     0.00   0.0  0
 RD8  CONST_06  C20  C19  C18  C03     0.00   0.0  0
 RD8  CONST_07  C08  C07  C04  C03   180.00   0.0  0
 RD8  CONST_08  C06  C05  C04  C03   180.00   0.0  0
 RD8  CONST_09  C32  C02  C03  C04   180.00   0.0  0
 RD8  CONST_10  C19  C18  C03  C04   180.00   0.0  0
 RD8  CONST_11  C09  C08  C07  C04     0.00   0.0  0
 RD8  CONST_12  C09  C06  C05  C04     0.00   0.0  0
 RD8  CONST_14  C08  C07  C04  C05     0.00   0.0  0
 RD8  CONST_15  C08  C09  C06  C05     0.00   0.0  0
 RD8  CONST_16  C07  C04  C05  C06     0.00   0.0  0
 RD8  CONST_17  C07  C08  C09  C06     0.00   0.0  0
 RD8  CONST_19  N16  N15  C14  C13     0.00   0.0  0
 RD8  CONST_20  N15  N16  N17  C13     0.00   0.0  0
 RD8  CONST_21  N17  N16  N15  C14     0.00   0.0  0
 RD8  CONST_22  N16  N17  C13  C14     0.00   0.0  0
 RD8  CONST_23  C32  C20  C19  C18     0.00   0.0  0
 RD8  CONST_24  C32  C02  C03  C18     0.00   0.0  0
 RD8  CONST_25  N17  C13  C14  N15     0.00   0.0  0
 RD8  CONST_26  N21  C20  C32  C02   180.00   0.0  0
 RD8  CONST_27  N21  C20  C19  C18   180.00   0.0  0
 RD8  CONST_28  F01  C02  C03  C04     0.00   0.0  0
 RD8  CONST_29  C10  C09  C06  C05   180.00   0.0  0
 RD8  CONST_30  C10  C09  C08  C07   180.00   0.0  0
 RD8  CONST_31  N15  C14  C13  C12   180.00   0.0  0
 RD8  CONST_32  N16  N17  C13  C12   180.00   0.0  0
 RD8  CONST_33  F01  C02  C03  C18   180.00   0.0  0
 RD8  CONST_34  F01  C02  C32  C20   180.00   0.0  0
 RD8  CONST_35  H10  C18  C03  C02   180.00   0.0  0
 RD8  CONST_36  H20  C32  C02  C03   180.00   0.0  0
 RD8  CONST_37  H11  C19  C18  C03   180.00   0.0  0
 RD8  CONST_38  H3   C07  C04  C03     0.00   0.0  0
 RD8  CONST_39  H1   C05  C04  C03     0.00   0.0  0
 RD8  CONST_40  H4   C08  C07  C04   180.00   0.0  0
 RD8  CONST_41  H2   C06  C05  C04   180.00   0.0  0
 RD8  CONST_42  H23  N15  C14  C13   180.00   0.0  0
 RD8  CONST_43  H9   C14  N15  N16   180.00   0.0  0
 RD8  CONST_44  O28  C26  N25  C24     0.00   0.0  0
 RD8  CONST_45  C27  C26  N25  C24   180.00   0.0  0
 RD8  CONST_46  H24  N25  C26  C27     0.00   0.0  0
 RD8  Var_01    C22  N21  C20  C19   159.75  30.0  2
 RD8  Var_02    C23  C22  N21  C20  -167.64  30.0  1
 RD8  Var_03    O29  C30  N21  C20   179.61  30.0  1
 RD8  Var_04    N21  C30  O29  C23    -7.65  30.0  1
 RD8  Var_05    N11  C10  C09  C06   -57.01  30.0  2
 RD8  Var_06    N11  C12  C13  C14  -105.97  30.0  2
 RD8  Var_07    C12  N11  C10  C09   175.10  30.0  3
 RD8  Var_08    C13  C12  N11  C10    60.23  30.0  3
 RD8  Var_09    C26  N25  C24  C23   -82.00  30.0  3
 RD8  Var_10    H17  C27  C26  N25   122.57  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
 RD8  chir_01  C23  C24  O29  C22  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
 RD8  plan-1  C13  0.020
 RD8  plan-1  C14  0.020
 RD8  plan-1  N15  0.020
 RD8  plan-1  N16  0.020
 RD8  plan-1  N17  0.020
 RD8  plan-1  H9   0.020
 RD8  plan-1  H23  0.020
 RD8  plan-1  C12  0.020
 RD8  plan-2  C03  0.020
 RD8  plan-2  C04  0.020
 RD8  plan-2  C05  0.020
 RD8  plan-2  C06  0.020
 RD8  plan-2  C07  0.020
 RD8  plan-2  C08  0.020
 RD8  plan-2  C09  0.020
 RD8  plan-2  C10  0.020
 RD8  plan-2  H1   0.020
 RD8  plan-2  H2   0.020
 RD8  plan-2  H3   0.020
 RD8  plan-2  H4   0.020
 RD8  plan-3  C02  0.020
 RD8  plan-3  C03  0.020
 RD8  plan-3  C04  0.020
 RD8  plan-3  C18  0.020
 RD8  plan-3  C19  0.020
 RD8  plan-3  C20  0.020
 RD8  plan-3  C32  0.020
 RD8  plan-3  F01  0.020
 RD8  plan-3  N21  0.020
 RD8  plan-3  H10  0.020
 RD8  plan-3  H11  0.020
 RD8  plan-3  H20  0.020
 RD8  plan-4  C24  0.020
 RD8  plan-4  C26  0.020
 RD8  plan-4  C27  0.020
 RD8  plan-4  N25  0.020
 RD8  plan-4  O28  0.020
 RD8  plan-4  H24  0.020
 RD8  plan-5  C20  0.020
 RD8  plan-5  C22  0.020
 RD8  plan-5  C30  0.020
 RD8  plan-5  N21  0.020
 RD8  plan-6  C30  0.020
 RD8  plan-6  N21  0.020
 RD8  plan-6  O29  0.020
 RD8  plan-6  O31  0.020

