# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:41:22 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@H](NC(=O)C1CCCCC1)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
 J1V  J1V  N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide  ligand  50  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_J1V
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
 J1V  CAP  C  CH2   0  -0.414   6.1363  -0.9076  -0.6956
 J1V  CAN  C  CH2   0  -0.436   6.9039  -2.1852  -1.0196
 J1V  CAM  C  CH2   0  -0.430   7.0770  -3.0592   0.2178
 J1V  CAO  C  CH2   0  -0.435   5.7287  -3.3799   0.8532
 J1V  CAQ  C  CH2   0  -0.416   4.9503  -2.1092   1.1776
 J1V  CBB  C  CH1   0  -0.393   4.7802  -1.2293  -0.0708
 J1V  CAU  C  C     0   0.599   4.0251   0.0258   0.3072
 J1V  OAB  O  O     0  -0.495   4.5697   1.0305   0.7444
 J1V  N    N  NH1   0  -0.649   2.6866  -0.0384   0.1809
 J1V  CA   C  CH1   0  -0.244   1.8518   1.0455   0.6259
 J1V  C    C  C     0   0.536   2.1964   2.3252  -0.1487
 J1V  O    O  O     0  -0.460   2.4329   2.3257  -1.3383
 J1V  NAR  N  NH1   0  -0.371   2.0965   3.4284   0.6119
 J1V  OAC  O  OH1   0  -0.541   2.4484   4.6375   0.0923
 J1V  CAZ  C  CR6   0   0.090   0.3927   0.7307   0.4057
 J1V  CAJ  C  CR16  0  -0.298  -0.5073   0.8432   1.4583
 J1V  CAH  C  CR16  0  -0.289  -1.8549   0.5825   1.2686
 J1V  CAI  C  CR16  0  -0.268  -0.0830   0.3507  -0.8472
 J1V  CAG  C  CR16  0  -0.289  -1.4287   0.0860  -1.0356
 J1V  CAX  C  CR6   0   0.084  -2.3367   0.1996   0.0181
 J1V  CAY  C  CR6   0   0.112  -3.7713  -0.0781  -0.1859
 J1V  CAK  C  CR16  0  -0.484  -4.7360   0.6754   0.4826
 J1V  CAV  C  CR6   0   0.437  -6.0725   0.4059   0.2823
 J1V  FAD  F  F     0  -0.299  -7.0055   1.1246   0.9076
 J1V  CBA  C  CR6   0   0.256  -6.4838  -0.5991  -0.5742
 J1V  FAF  F  F     0  -0.294  -7.7786  -0.8454  -0.7606
 J1V  CAW  C  CR6   0   0.438  -5.5205  -1.3399  -1.2339
 J1V  FAE  F  F     0  -0.299  -5.9208  -2.3119  -2.0540
 J1V  CAL  C  CR16  0  -0.485  -4.1768  -1.0945  -1.0501
 J1V  H1   H  HCH2  0   0.219   6.7221  -0.3003   0.0005
 J1V  H2   H  HCH2  0   0.236   6.0016  -0.3101  -1.6009
 J1V  H3   H  HCH2  0   0.212   6.3647  -2.7491  -1.7888
 J1V  H4   H  HCH2  0   0.230   7.8776  -1.9322  -1.4454
 J1V  H5   H  HCH2  0   0.229   7.6025  -3.9817  -0.0406
 J1V  H6   H  HCH2  0   0.211   7.7045  -2.5345   0.9468
 J1V  H7   H  HCH2  0   0.214   5.1409  -3.9974   0.1654
 J1V  H8   H  HCH2  0   0.232   5.8650  -3.9689   1.7631
 J1V  H9   H  HCH2  0   0.239   3.9715  -2.3638   1.5920
 J1V  H10  H  HCH2  0   0.224   5.4824  -1.5390   1.9464
 J1V  H11  H  HCH1  0   0.249   4.1868  -1.7958  -0.7991
 J1V  H12  H  HNH1  0   0.409   2.2528  -0.8853  -0.1489
 J1V  H13  H  HCH1  0   0.294   2.0074   1.2168   1.6966
 J1V  H14  H  HNH1  0   0.416   2.1152   3.3856   1.6209
 J1V  H15  H  HOH1  0   0.480   1.6219   5.0712  -0.1557
 J1V  H16  H  HCR6  0   0.264  -0.1549   1.1268   2.4422
 J1V  H17  H  HCR6  0   0.264  -2.5285   0.6535   2.1128
 J1V  H18  H  HCR6  0   0.267   0.5923   0.2755  -1.6900
 J1V  H19  H  HCR6  0   0.264  -1.7760  -0.1868  -2.0239
 J1V  H20  H  HCR6  0   0.294  -4.4586   1.4887   1.1404
 J1V  H21  H  HCR6  0   0.294  -3.4562  -1.7129  -1.5689

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
 J1V  CAM  CAN  single    1.525  0.020  1.525
 J1V  CAM  CAO  single    1.525  0.020  1.525
 J1V  CAN  CAP  single    1.525  0.020  1.525
 J1V  CAO  CAQ  single    1.525  0.020  1.525
 J1V  OAC  NAR  single    1.362  0.020  1.362
 J1V  CAP  CBB  single    1.527  0.020  1.527
 J1V  NAR  C    single    1.344  0.020  1.344
 J1V  O    C    double    1.213  0.020  1.213
 J1V  CAQ  CBB  single    1.537  0.020  1.537
 J1V  CBB  CAU  single    1.513  0.020  1.513
 J1V  C    CA   single    1.535  0.020  1.535
 J1V  CAU  N    single    1.346  0.020  1.346
 J1V  CAU  OAB  double    1.224  0.020  1.224
 J1V  N    CA   single    1.439  0.020  1.439
 J1V  CA   CAZ  single    1.509  0.020  1.509
 J1V  CAZ  CAJ  aromatic  1.389  0.020  1.389
 J1V  CAZ  CAI  aromatic  1.393  0.020  1.393
 J1V  CAJ  CAH  aromatic  1.386  0.020  1.386
 J1V  CAI  CAG  aromatic  1.384  0.020  1.384
 J1V  CAH  CAX  aromatic  1.394  0.020  1.394
 J1V  CAG  CAX  aromatic  1.396  0.020  1.396
 J1V  CAX  CAY  single    1.475  0.020  1.475
 J1V  CAY  CAL  aromatic  1.394  0.020  1.394
 J1V  CAY  CAK  aromatic  1.395  0.020  1.395
 J1V  CAL  CAW  aromatic  1.378  0.020  1.378
 J1V  CAK  CAV  aromatic  1.378  0.020  1.378
 J1V  CAW  FAE  single    1.333  0.020  1.333
 J1V  CAW  CBA  aromatic  1.383  0.020  1.383
 J1V  CAV  CBA  aromatic  1.383  0.020  1.383
 J1V  CAV  FAD  single    1.333  0.020  1.333
 J1V  CBA  FAF  single    1.331  0.020  1.331
 J1V  CAP  H1   single    0.970  0.020  1.090
 J1V  CAP  H2   single    0.970  0.020  1.090
 J1V  CAN  H3   single    0.970  0.020  1.090
 J1V  CAN  H4   single    0.970  0.020  1.090
 J1V  CAM  H5   single    0.970  0.020  1.090
 J1V  CAM  H6   single    0.970  0.020  1.090
 J1V  CAO  H7   single    0.970  0.020  1.090
 J1V  CAO  H8   single    0.970  0.020  1.090
 J1V  CAQ  H9   single    0.970  0.020  1.090
 J1V  CAQ  H10  single    0.970  0.020  1.090
 J1V  CBB  H11  single    0.970  0.020  1.090
 J1V  N    H12  single    0.860  0.020  1.020
 J1V  CA   H13  single    0.970  0.020  1.090
 J1V  NAR  H14  single    0.890  0.020  1.040
 J1V  OAC  H15  single    0.850  0.020  0.980
 J1V  CAJ  H16  single    0.930  0.020  1.080
 J1V  CAH  H17  single    0.930  0.020  1.080
 J1V  CAI  H18  single    0.930  0.020  1.080
 J1V  CAG  H19  single    0.930  0.020  1.080
 J1V  CAK  H20  single    0.930  0.020  1.080
 J1V  CAL  H21  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
 J1V  H2   CAP  H1   106.83  3.000
 J1V  H2   CAP  CBB  110.15  3.000
 J1V  H1   CAP  CBB  109.39  3.000
 J1V  H2   CAP  CAN  110.12  3.000
 J1V  H1   CAP  CAN  109.31  3.000
 J1V  CBB  CAP  CAN  110.94  3.000
 J1V  H4   CAN  H3   106.51  3.000
 J1V  H4   CAN  CAM  110.36  3.000
 J1V  H3   CAN  CAM  109.31  3.000
 J1V  H4   CAN  CAP  109.71  3.000
 J1V  H3   CAN  CAP  109.43  3.000
 J1V  CAM  CAN  CAP  111.40  3.000
 J1V  H6   CAM  H5   106.63  3.000
 J1V  H6   CAM  CAO  109.27  3.000
 J1V  H5   CAM  CAO  110.26  3.000
 J1V  H6   CAM  CAN  109.30  3.000
 J1V  H5   CAM  CAN  110.27  3.000
 J1V  CAO  CAM  CAN  111.00  3.000
 J1V  H8   CAO  H7   106.61  3.000
 J1V  H8   CAO  CAQ  109.62  3.000
 J1V  H7   CAO  CAQ  109.23  3.000
 J1V  H8   CAO  CAM  110.50  3.000
 J1V  H7   CAO  CAM  109.36  3.000
 J1V  CAQ  CAO  CAM  111.40  3.000
 J1V  H10  CAQ  H9   106.88  3.000
 J1V  H10  CAQ  CBB  109.02  3.000
 J1V  H9   CAQ  CBB  110.01  3.000
 J1V  H10  CAQ  CAO  109.58  3.000
 J1V  H9   CAQ  CAO  110.10  3.000
 J1V  CBB  CAQ  CAO  111.15  3.000
 J1V  H11  CBB  CAU  108.93  3.000
 J1V  H11  CBB  CAQ  107.66  3.000
 J1V  CAU  CBB  CAQ  109.11  3.000
 J1V  H11  CBB  CAP  108.50  3.000
 J1V  CAU  CBB  CAP  111.76  3.000
 J1V  CAQ  CBB  CAP  110.77  3.000
 J1V  N    CAU  OAB  121.01  3.000
 J1V  OAB  CAU  CBB  123.26  3.000
 J1V  N    CAU  CBB  115.68  3.000
 J1V  H12  N    CA   119.01  3.000
 J1V  H12  N    CAU  119.95  3.000
 J1V  CA   N    CAU  120.80  3.000
 J1V  H13  CA   CAZ  108.22  3.000
 J1V  H13  CA   C    109.32  3.000
 J1V  CAZ  CA   C    108.51  3.000
 J1V  H13  CA   N    109.74  3.000
 J1V  CAZ  CA   N    111.03  3.000
 J1V  C    CA   N    109.98  3.000
 J1V  NAR  C    O    124.71  3.000
 J1V  O    C    CA   122.61  3.000
 J1V  NAR  C    CA   112.47  3.000
 J1V  H14  NAR  OAC  114.45  3.000
 J1V  H14  NAR  C    121.96  3.000
 J1V  OAC  NAR  C    119.57  3.000
 J1V  H15  OAC  NAR  105.99  3.000
 J1V  CAI  CAZ  CAJ  118.83  3.000
 J1V  CAI  CAZ  CA   121.23  3.000
 J1V  CAJ  CAZ  CA   119.93  3.000
 J1V  H16  CAJ  CAH  119.35  3.000
 J1V  H16  CAJ  CAZ  119.92  3.000
 J1V  CAH  CAJ  CAZ  120.73  3.000
 J1V  H17  CAH  CAX  120.18  3.000
 J1V  H17  CAH  CAJ  119.08  3.000
 J1V  CAX  CAH  CAJ  120.71  3.000
 J1V  H18  CAI  CAG  119.15  3.000
 J1V  H18  CAI  CAZ  120.41  3.000
 J1V  CAG  CAI  CAZ  120.43  3.000
 J1V  H19  CAG  CAX  120.08  3.000
 J1V  H19  CAG  CAI  118.96  3.000
 J1V  CAX  CAG  CAI  120.94  3.000
 J1V  CAY  CAX  CAG  120.86  3.000
 J1V  CAY  CAX  CAH  120.79  3.000
 J1V  CAG  CAX  CAH  118.35  3.000
 J1V  CAL  CAY  CAK  119.32  3.000
 J1V  CAK  CAY  CAX  120.30  3.000
 J1V  CAL  CAY  CAX  120.38  3.000
 J1V  H20  CAK  CAV  118.95  3.000
 J1V  H20  CAK  CAY  121.33  3.000
 J1V  CAV  CAK  CAY  119.70  3.000
 J1V  CBA  CAV  FAD  118.30  3.000
 J1V  FAD  CAV  CAK  120.33  3.000
 J1V  CBA  CAV  CAK  121.37  3.000
 J1V  CAW  CBA  FAF  120.78  3.000
 J1V  FAF  CBA  CAV  120.69  3.000
 J1V  CAW  CBA  CAV  118.53  3.000
 J1V  CAL  CAW  FAE  120.30  3.000
 J1V  FAE  CAW  CBA  118.35  3.000
 J1V  CAL  CAW  CBA  121.35  3.000
 J1V  H21  CAL  CAW  118.92  3.000
 J1V  H21  CAL  CAY  121.34  3.000
 J1V  CAW  CAL  CAY  119.73  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
 J1V  CONST_01  CAX  CAH  CAJ  CAZ    0.00   0.0  0
 J1V  CONST_02  CAX  CAG  CAI  CAZ    0.00   0.0  0
 J1V  CONST_03  CAG  CAI  CAZ  CAJ    0.00   0.0  0
 J1V  CONST_04  CAG  CAX  CAH  CAJ    0.00   0.0  0
 J1V  CONST_05  CAY  CAX  CAH  CAJ  180.00   0.0  0
 J1V  CONST_06  CAI  CAZ  CAJ  CAH    0.00   0.0  0
 J1V  CONST_07  CAI  CAG  CAX  CAH    0.00   0.0  0
 J1V  CONST_10  CAY  CAX  CAG  CAI  180.00   0.0  0
 J1V  CONST_13  CAW  CAL  CAY  CAX  180.00   0.0  0
 J1V  CONST_14  CAV  CAK  CAY  CAX  180.00   0.0  0
 J1V  CONST_15  CBA  CAW  CAL  CAY    0.00   0.0  0
 J1V  CONST_16  CBA  CAV  CAK  CAY    0.00   0.0  0
 J1V  CONST_17  CAW  CAL  CAY  CAK    0.00   0.0  0
 J1V  CONST_18  CAW  CBA  CAV  CAK    0.00   0.0  0
 J1V  CONST_19  CAL  CAY  CAK  CAV    0.00   0.0  0
 J1V  CONST_20  CAL  CAW  CBA  CAV    0.00   0.0  0
 J1V  CONST_21  CAH  CAJ  CAZ  CA   180.00   0.0  0
 J1V  CONST_22  CAG  CAI  CAZ  CA   180.00   0.0  0
 J1V  CONST_23  FAE  CAW  CAL  CAY  180.00   0.0  0
 J1V  CONST_24  FAD  CAV  CAK  CAY  180.00   0.0  0
 J1V  CONST_25  FAF  CBA  CAV  CAK  180.00   0.0  0
 J1V  CONST_26  FAE  CAW  CBA  CAV  180.00   0.0  0
 J1V  CONST_27  CAW  CBA  CAV  FAD  180.00   0.0  0
 J1V  CONST_28  CAL  CAW  CBA  FAF  180.00   0.0  0
 J1V  CONST_29  H17  CAH  CAJ  CAZ  180.00   0.0  0
 J1V  CONST_30  H19  CAG  CAI  CAZ  180.00   0.0  0
 J1V  CONST_31  H18  CAI  CAZ  CAJ  180.00   0.0  0
 J1V  CONST_32  H16  CAJ  CAZ  CAI  180.00   0.0  0
 J1V  CONST_33  H21  CAL  CAY  CAX    0.00   0.0  0
 J1V  CONST_34  H20  CAK  CAY  CAX    0.00   0.0  0
 J1V  CONST_35  CA   N    CAU  CBB  180.00   0.0  0
 J1V  CONST_36  H12  N    CAU  CBB    0.00   0.0  0
 J1V  CONST_37  CA   N    CAU  OAB    0.00   0.0  0
 J1V  CONST_38  OAC  NAR  C    CA   180.00   0.0  0
 J1V  CONST_39  OAC  NAR  C    O      0.00   0.0  0
 J1V  Var_01    CAO  CAM  CAN  CAP   55.84  30.0  1
 J1V  Var_02    CAQ  CAO  CAM  CAN  -55.40  30.0  1
 J1V  Var_03    CBB  CAP  CAN  CAM  -56.32  30.0  1
 J1V  Var_04    CBB  CAQ  CAO  CAM   55.43  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
 J1V  chir_01  CBB  CAP  CAQ  CAU  negativ
 J1V  chir_02  CA   N    CAZ  C    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
 J1V  plan-1  CA   0.020
 J1V  plan-1  CAZ  0.020
 J1V  plan-1  CAJ  0.020
 J1V  plan-1  CAH  0.020
 J1V  plan-1  CAI  0.020
 J1V  plan-1  CAG  0.020
 J1V  plan-1  CAX  0.020
 J1V  plan-1  CAY  0.020
 J1V  plan-1  H16  0.020
 J1V  plan-1  H17  0.020
 J1V  plan-1  H18  0.020
 J1V  plan-1  H19  0.020
 J1V  plan-2  CAX  0.020
 J1V  plan-2  CAY  0.020
 J1V  plan-2  CAK  0.020
 J1V  plan-2  CAV  0.020
 J1V  plan-2  FAD  0.020
 J1V  plan-2  CBA  0.020
 J1V  plan-2  FAF  0.020
 J1V  plan-2  CAW  0.020
 J1V  plan-2  FAE  0.020
 J1V  plan-2  CAL  0.020
 J1V  plan-2  H20  0.020
 J1V  plan-2  H21  0.020
 J1V  plan-3  CA   0.020
 J1V  plan-3  C    0.020
 J1V  plan-3  O    0.020
 J1V  plan-3  NAR  0.020
 J1V  plan-3  OAC  0.020
 J1V  plan-3  H14  0.020
 J1V  plan-4  CBB  0.020
 J1V  plan-4  CAU  0.020
 J1V  plan-4  OAB  0.020
 J1V  plan-4  N    0.020
 J1V  plan-4  CA   0.020
 J1V  plan-4  H12  0.020

