# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:54:06 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]oxane-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@H](NC(=O)C1CCOCC1)c2ccc(cc2)c3cc(F)c(F)c(F)c3
#
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
 J2D  J2D  N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]oxane-4-carboxamide  ligand  48  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J2D
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
 J2D  CAO  C  CH2   0  -0.438  -6.2418  -0.9251  -1.0361
 J2D  CAM  C  CH2   0  -0.183  -6.9907  -2.2197  -0.7635
 J2D  OAS  O  O2    0  -0.483  -6.9846  -2.5580   0.6068
 J2D  CAN  C  CH2   0  -0.179  -5.6776  -2.7240   1.1089
 J2D  CAP  C  CH2   0  -0.441  -4.8380  -1.4659   0.9560
 J2D  CBB  C  CH1   0  -0.417  -4.8127  -1.0305  -0.5169
 J2D  CAU  C  C     0   0.607  -4.0484   0.2691  -0.6450
 J2D  OAB  O  O     0  -0.488  -4.5810   1.3690  -0.6575
 J2D  N    N  NH1   0  -0.656  -2.7100   0.1360  -0.6912
 J2D  CA   C  CH1   0  -0.228  -1.8388   1.2803  -0.6752
 J2D  C    C  C     0   0.529  -2.1899   2.1874   0.5145
 J2D  O    O  O     0  -0.454  -2.4248   1.7515   1.6207
 J2D  NAQ  N  NH1   0  -0.371  -2.0866   3.4928   0.2088
 J2D  OAC  O  OH1   0  -0.542  -2.4498   4.4241   1.1350
 J2D  CAZ  C  CR6   0   0.083  -0.3989   0.8542  -0.5257
 J2D  CAJ  C  CR16  0  -0.294   0.5740   1.3733  -1.3709
 J2D  CAH  C  CR16  0  -0.289   1.9048   1.0157  -1.2227
 J2D  CAI  C  CR16  0  -0.270  -0.0135  -0.0341   0.4754
 J2D  CAG  C  CR16  0  -0.288   1.3148  -0.3965   0.6192
 J2D  CAX  C  CR6   0   0.083   2.2956   0.1243  -0.2252
 J2D  CAY  C  CR6   0   0.111   3.7107  -0.2599  -0.0638
 J2D  CAK  C  CR16  0  -0.484   4.0496  -1.5631   0.2993
 J2D  CAV  C  CR6   0   0.437   5.3755  -1.9063   0.4519
 J2D  FAD  F  F     0  -0.299   5.7142  -3.1506   0.7910
 J2D  CBA  C  CR6   0   0.256   6.3854  -0.9833   0.2503
 J2D  FAF  F  F     0  -0.294   7.6622  -1.3282   0.4012
 J2D  CAW  C  CR6   0   0.437   6.0398   0.3062  -0.1110
 J2D  FAE  F  F     0  -0.299   7.0160   1.1962  -0.2926
 J2D  CAL  C  CR16  0  -0.484   4.7221   0.6777  -0.2689
 J2D  H1   H  HCH2  0   0.245  -6.2537  -0.7250  -2.1100
 J2D  H2   H  HCH2  0   0.233  -6.7550  -0.0943  -0.5464
 J2D  H3   H  HCH2  0   0.238  -8.0359  -2.1245  -1.0618
 J2D  H4   H  HCH2  0   0.197  -6.5525  -3.0338  -1.3606
 J2D  H5   H  HCH2  0   0.240  -5.7714  -2.9942   2.1619
 J2D  H6   H  HCH2  0   0.199  -5.1744  -3.5585   0.5980
 J2D  H7   H  HCH2  0   0.238  -5.2524  -0.6616   1.5709
 J2D  H8   H  HCH2  0   0.245  -3.8282  -1.6666   1.3216
 J2D  H9   H  HCH1  0   0.262  -4.2842  -1.8044  -1.0874
 J2D  H10  H  HNH1  0   0.408  -2.3012  -0.7838  -0.7356
 J2D  H11  H  HCH1  0   0.295  -1.9369   1.8456  -1.6090
 J2D  H12  H  HNH1  0   0.416  -2.1387   3.8163  -0.7469
 J2D  H13  H  HOH1  0   0.480  -1.6258   4.7709   1.5003
 J2D  H14  H  HCR6  0   0.263   0.2931   2.0540  -2.1653
 J2D  H15  H  HCR6  0   0.263   2.6374   1.4194  -1.9102
 J2D  H16  H  HCR6  0   0.265  -0.7461  -0.4416   1.1602
 J2D  H17  H  HCR6  0   0.263   1.5898  -1.0739   1.4179
 J2D  H18  H  HCR6  0   0.294   3.2909  -2.3212   0.4428
 J2D  H19  H  HCR6  0   0.294   4.4930   1.7031  -0.5275

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
 J2D  FAF  CBA  single    1.331  0.020  1.331
 J2D  FAD  CAV  single    1.333  0.020  1.333
 J2D  CBA  CAV  aromatic  1.383  0.020  1.383
 J2D  CBA  CAW  aromatic  1.383  0.020  1.383
 J2D  FAE  CAW  single    1.334  0.020  1.334
 J2D  CAV  CAK  aromatic  1.378  0.020  1.378
 J2D  CAW  CAL  aromatic  1.378  0.020  1.378
 J2D  CAK  CAY  aromatic  1.395  0.020  1.395
 J2D  CAL  CAY  aromatic  1.394  0.020  1.394
 J2D  CAY  CAX  single    1.475  0.020  1.475
 J2D  CAX  CAH  aromatic  1.394  0.020  1.394
 J2D  CAX  CAG  aromatic  1.395  0.020  1.395
 J2D  CAH  CAJ  aromatic  1.386  0.020  1.386
 J2D  CAG  CAI  aromatic  1.384  0.020  1.384
 J2D  CAJ  CAZ  aromatic  1.389  0.020  1.389
 J2D  CAI  CAZ  aromatic  1.393  0.020  1.393
 J2D  CAZ  CA   single    1.509  0.020  1.509
 J2D  CA   N    single    1.438  0.020  1.438
 J2D  CA   C    single    1.537  0.020  1.537
 J2D  OAB  CAU  double    1.222  0.020  1.222
 J2D  N    CAU  single    1.346  0.020  1.346
 J2D  CAU  CBB  single    1.513  0.020  1.513
 J2D  C    O    double    1.212  0.020  1.212
 J2D  C    NAQ  single    1.345  0.020  1.345
 J2D  CBB  CAO  single    1.524  0.020  1.524
 J2D  CBB  CAP  single    1.536  0.020  1.536
 J2D  CAO  CAM  single    1.520  0.020  1.520
 J2D  NAQ  OAC  single    1.363  0.020  1.363
 J2D  CAP  CAN  single    1.520  0.020  1.520
 J2D  CAM  OAS  single    1.412  0.020  1.412
 J2D  CAN  OAS  single    1.410  0.020  1.410
 J2D  CAO  H1   single    0.970  0.020  1.090
 J2D  CAO  H2   single    0.970  0.020  1.090
 J2D  CAM  H3   single    0.970  0.020  1.090
 J2D  CAM  H4   single    0.970  0.020  1.090
 J2D  CAN  H5   single    0.970  0.020  1.090
 J2D  CAN  H6   single    0.970  0.020  1.090
 J2D  CAP  H7   single    0.970  0.020  1.090
 J2D  CAP  H8   single    0.970  0.020  1.090
 J2D  CBB  H9   single    0.970  0.020  1.090
 J2D  N    H10  single    0.860  0.020  1.020
 J2D  CA   H11  single    0.970  0.020  1.090
 J2D  NAQ  H12  single    0.890  0.020  1.040
 J2D  OAC  H13  single    0.850  0.020  0.980
 J2D  CAJ  H14  single    0.930  0.020  1.080
 J2D  CAH  H15  single    0.930  0.020  1.080
 J2D  CAI  H16  single    0.930  0.020  1.080
 J2D  CAG  H17  single    0.930  0.020  1.080
 J2D  CAK  H18  single    0.930  0.020  1.080
 J2D  CAL  H19  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
 J2D  H2   CAO  H1   107.23  3.000
 J2D  H2   CAO  CBB  109.90  3.000
 J2D  H1   CAO  CBB  110.96  3.000
 J2D  H2   CAO  CAM  109.63  3.000
 J2D  H1   CAO  CAM  109.08  3.000
 J2D  CBB  CAO  CAM  109.99  3.000
 J2D  H4   CAM  H3   107.32  3.000
 J2D  H4   CAM  OAS  110.35  3.000
 J2D  H3   CAM  OAS  106.89  3.000
 J2D  H4   CAM  CAO  109.66  3.000
 J2D  H3   CAM  CAO  110.40  3.000
 J2D  OAS  CAM  CAO  112.09  3.000
 J2D  CAN  OAS  CAM  112.20  3.000
 J2D  H6   CAN  H5   107.43  3.000
 J2D  H6   CAN  CAP  109.17  3.000
 J2D  H5   CAN  CAP  110.45  3.000
 J2D  H6   CAN  OAS  110.36  3.000
 J2D  H5   CAN  OAS  107.04  3.000
 J2D  CAP  CAN  OAS  112.26  3.000
 J2D  H8   CAP  H7   107.28  3.000
 J2D  H8   CAP  CBB  110.96  3.000
 J2D  H7   CAP  CBB  109.68  3.000
 J2D  H8   CAP  CAN  108.95  3.000
 J2D  H7   CAP  CAN  110.04  3.000
 J2D  CBB  CAP  CAN  109.88  3.000
 J2D  H9   CBB  CAU  108.57  3.000
 J2D  H9   CBB  CAP  107.85  3.000
 J2D  CAU  CBB  CAP  109.45  3.000
 J2D  H9   CBB  CAO  108.86  3.000
 J2D  CAP  CBB  CAO  109.32  3.000
 J2D  CAU  CBB  CAO  112.67  3.000
 J2D  N    CAU  OAB  121.47  3.000
 J2D  N    CAU  CBB  114.86  3.000
 J2D  OAB  CAU  CBB  123.62  3.000
 J2D  H10  N    CA   118.75  3.000
 J2D  H10  N    CAU  119.69  3.000
 J2D  CA   N    CAU  121.56  3.000
 J2D  H11  CA   CAZ  108.39  3.000
 J2D  H11  CA   C    109.56  3.000
 J2D  CAZ  CA   C    107.94  3.000
 J2D  H11  CA   N    110.28  3.000
 J2D  C    CA   N    109.87  3.000
 J2D  CAZ  CA   N    110.76  3.000
 J2D  NAQ  C    O    124.86  3.000
 J2D  NAQ  C    CA   112.30  3.000
 J2D  O    C    CA   122.59  3.000
 J2D  H12  NAQ  OAC  114.23  3.000
 J2D  H12  NAQ  C    121.46  3.000
 J2D  OAC  NAQ  C    119.24  3.000
 J2D  H13  OAC  NAQ  105.96  3.000
 J2D  CAI  CAZ  CAJ  118.81  3.000
 J2D  CAI  CAZ  CA   121.02  3.000
 J2D  CAJ  CAZ  CA   120.16  3.000
 J2D  H14  CAJ  CAH  119.31  3.000
 J2D  H14  CAJ  CAZ  119.96  3.000
 J2D  CAH  CAJ  CAZ  120.72  3.000
 J2D  H15  CAH  CAX  120.22  3.000
 J2D  H15  CAH  CAJ  119.05  3.000
 J2D  CAX  CAH  CAJ  120.72  3.000
 J2D  H16  CAI  CAG  119.02  3.000
 J2D  H16  CAI  CAZ  120.50  3.000
 J2D  CAG  CAI  CAZ  120.47  3.000
 J2D  H17  CAG  CAX  120.10  3.000
 J2D  H17  CAG  CAI  118.95  3.000
 J2D  CAX  CAG  CAI  120.93  3.000
 J2D  CAY  CAX  CAG  120.73  3.000
 J2D  CAG  CAX  CAH  118.35  3.000
 J2D  CAY  CAX  CAH  120.92  3.000
 J2D  CAL  CAY  CAK  119.37  3.000
 J2D  CAL  CAY  CAX  120.30  3.000
 J2D  CAK  CAY  CAX  120.33  3.000
 J2D  H18  CAK  CAV  119.04  3.000
 J2D  H18  CAK  CAY  121.25  3.000
 J2D  CAV  CAK  CAY  119.70  3.000
 J2D  CBA  CAV  FAD  118.32  3.000
 J2D  CBA  CAV  CAK  121.35  3.000
 J2D  FAD  CAV  CAK  120.33  3.000
 J2D  CAW  CBA  FAF  120.73  3.000
 J2D  CAW  CBA  CAV  118.55  3.000
 J2D  FAF  CBA  CAV  120.73  3.000
 J2D  CAL  CAW  FAE  120.29  3.000
 J2D  CAL  CAW  CBA  121.35  3.000
 J2D  FAE  CAW  CBA  118.35  3.000
 J2D  H19  CAL  CAW  119.03  3.000
 J2D  H19  CAL  CAY  121.25  3.000
 J2D  CAW  CAL  CAY  119.70  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
 J2D  CONST_01  CAX  CAH  CAJ  CAZ    0.00   0.0  0
 J2D  CONST_02  CAX  CAG  CAI  CAZ    0.00   0.0  0
 J2D  CONST_03  CAY  CAX  CAH  CAJ  180.00   0.0  0
 J2D  CONST_04  CAG  CAX  CAH  CAJ    0.00   0.0  0
 J2D  CONST_05  CAG  CAI  CAZ  CAJ    0.00   0.0  0
 J2D  CONST_08  CAI  CAG  CAX  CAH    0.00   0.0  0
 J2D  CONST_09  CAI  CAZ  CAJ  CAH    0.00   0.0  0
 J2D  CONST_10  CAY  CAX  CAG  CAI  180.00   0.0  0
 J2D  CONST_13  CAV  CAK  CAY  CAX  180.00   0.0  0
 J2D  CONST_14  CAW  CAL  CAY  CAX  180.00   0.0  0
 J2D  CONST_15  CBA  CAV  CAK  CAY    0.00   0.0  0
 J2D  CONST_16  CBA  CAW  CAL  CAY    0.00   0.0  0
 J2D  CONST_17  CAW  CBA  CAV  CAK    0.00   0.0  0
 J2D  CONST_18  CAW  CAL  CAY  CAK    0.00   0.0  0
 J2D  CONST_19  CAL  CAW  CBA  CAV    0.00   0.0  0
 J2D  CONST_20  CAL  CAY  CAK  CAV    0.00   0.0  0
 J2D  CONST_21  CAH  CAJ  CAZ  CA   180.00   0.0  0
 J2D  CONST_22  CAG  CAI  CAZ  CA   180.00   0.0  0
 J2D  CONST_23  FAD  CAV  CAK  CAY  180.00   0.0  0
 J2D  CONST_24  FAE  CAW  CAL  CAY  180.00   0.0  0
 J2D  CONST_25  FAF  CBA  CAV  CAK  180.00   0.0  0
 J2D  CONST_26  FAE  CAW  CBA  CAV  180.00   0.0  0
 J2D  CONST_27  CAW  CBA  CAV  FAD  180.00   0.0  0
 J2D  CONST_28  CAL  CAW  CBA  FAF  180.00   0.0  0
 J2D  CONST_29  H15  CAH  CAJ  CAZ  180.00   0.0  0
 J2D  CONST_30  H17  CAG  CAI  CAZ  180.00   0.0  0
 J2D  CONST_31  H16  CAI  CAZ  CAJ  180.00   0.0  0
 J2D  CONST_32  H14  CAJ  CAZ  CAI  180.00   0.0  0
 J2D  CONST_33  H18  CAK  CAY  CAX    0.00   0.0  0
 J2D  CONST_34  H19  CAL  CAY  CAX    0.00   0.0  0
 J2D  CONST_35  CA   N    CAU  CBB  180.00   0.0  0
 J2D  CONST_36  H10  N    CAU  CBB    0.00   0.0  0
 J2D  CONST_37  CA   N    CAU  OAB    0.00   0.0  0
 J2D  CONST_38  OAC  NAQ  C    CA   180.00   0.0  0
 J2D  CONST_39  OAC  NAQ  C    O      0.00   0.0  0
 J2D  Var_01    CAP  CAN  OAS  CAM   59.36  30.0  1
 J2D  Var_02    CBB  CAO  CAM  OAS   56.56  30.0  1
 J2D  Var_03    CBB  CAP  CAN  OAS  -55.87  30.0  1
 J2D  Var_04    H3   CAM  OAS  CAN  179.36  30.0  1

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
 J2D  chir_01  CBB  CAU  CAO  CAP  positiv
 J2D  chir_02  CA   N    C    CAZ  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
 J2D  plan-1  CA   0.020
 J2D  plan-1  CAZ  0.020
 J2D  plan-1  CAJ  0.020
 J2D  plan-1  CAH  0.020
 J2D  plan-1  CAI  0.020
 J2D  plan-1  CAG  0.020
 J2D  plan-1  CAX  0.020
 J2D  plan-1  CAY  0.020
 J2D  plan-1  H14  0.020
 J2D  plan-1  H15  0.020
 J2D  plan-1  H16  0.020
 J2D  plan-1  H17  0.020
 J2D  plan-2  CAX  0.020
 J2D  plan-2  CAY  0.020
 J2D  plan-2  CAK  0.020
 J2D  plan-2  CAV  0.020
 J2D  plan-2  FAD  0.020
 J2D  plan-2  CBA  0.020
 J2D  plan-2  FAF  0.020
 J2D  plan-2  CAW  0.020
 J2D  plan-2  FAE  0.020
 J2D  plan-2  CAL  0.020
 J2D  plan-2  H18  0.020
 J2D  plan-2  H19  0.020
 J2D  plan-3  CA   0.020
 J2D  plan-3  C    0.020
 J2D  plan-3  O    0.020
 J2D  plan-3  NAQ  0.020
 J2D  plan-3  OAC  0.020
 J2D  plan-3  H12  0.020
 J2D  plan-4  CBB  0.020
 J2D  plan-4  CAU  0.020
 J2D  plan-4  OAB  0.020
 J2D  plan-4  N    0.020
 J2D  plan-4  CA   0.020
 J2D  plan-4  H10  0.020

