# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:49:34 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclopentanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@H](NC(=O)C1CCCC1)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
 J1G  J1G  N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclopentanecarboxamide  ligand  47  28  .  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_J1G
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
 J1G  N    N  NH1   0  -0.646  -2.9439   0.1051   0.6678
 J1G  CA   C  CH1   0  -0.240  -2.1211  -1.0729   0.6406
 J1G  C    C  C     0   0.536  -2.5048  -1.9643  -0.5500
 J1G  O    O  O     0  -0.460  -2.8169  -1.5162  -1.6337
 J1G  CAG  C  CR16  0  -0.287   1.1142   0.4132  -0.6861
 J1G  CAH  C  CR16  0  -0.288   1.6170  -0.8869   1.2611
 J1G  CAI  C  CR16  0  -0.266  -0.2277   0.1014  -0.5523
 J1G  CAJ  C  CR16  0  -0.299   0.2724  -1.1940   1.3989
 J1G  CAK  C  CR16  0  -0.483   3.8766   1.5179  -0.3732
 J1G  CAL  C  CR16  0  -0.484   4.4650  -0.7003   0.3545
 J1G  CAM  C  CH2   0  -0.455  -7.0405   2.5606   0.3313
 J1G  CAN  C  CH2   0  -0.442  -6.4838   2.4463  -1.0917
 J1G  CAO  C  CH2   0  -0.419  -6.4411   1.3569   1.0495
 J1G  CAP  C  CH2   0  -0.439  -5.1081   1.7595  -0.9480
 J1G  CAT  C  C     0   0.587  -4.2884   0.0249   0.6863
 J1G  CAU  C  CR6   0   0.437   5.2157   1.8106  -0.5148
 J1G  CAV  C  CR6   0   0.437   5.7969  -0.3797   0.2050
 J1G  CAW  C  CR6   0   0.083   2.0585  -0.0779   0.2162
 J1G  CAX  C  CR6   0   0.110   3.4885   0.2519   0.0646
 J1G  CAY  C  CR6   0   0.085  -0.6638  -0.7055   0.4961
 J1G  CAZ  C  CR6   0   0.257   6.1912   0.8725  -0.2301
 J1G  CBA  C  CH1   0  -0.403  -5.0027   1.3458   0.5445
 J1G  FAE  F  F     0  -0.299   6.7403  -1.2841   0.4702
 J1G  FAF  F  F     0  -0.294   7.4813   1.1675  -0.3720
 J1G  NAQ  N  NH1   0  -0.370  -2.4084  -3.2716  -0.2640
 J1G  OAB  O  O     0  -0.492  -4.8594  -1.0533   0.7662
 J1G  OAC  O  OH1   0  -0.540  -2.4505  -4.1928  -1.2647
 J1G  H1   H  HNH1  0   0.408  -2.5008   1.0083   0.6187
 J1G  H2   H  HCH1  0   0.295  -2.2431  -1.6386   1.5711
 J1G  H3   H  HCR6  0   0.264   1.4297   1.0249  -1.5219
 J1G  H4   H  HCR6  0   0.264   2.3196  -1.2645   1.9932
 J1G  H5   H  HCR6  0   0.265  -0.9306   0.4827  -1.2822
 J1G  H6   H  HCR6  0   0.264  -0.0484  -1.8100   2.2303
 J1G  H7   H  HCR6  0   0.294   3.1457   2.2874  -0.5845
 J1G  H8   H  HCR6  0   0.295   4.1978  -1.6991   0.6734
 J1G  H9   H  HCH2  0   0.220  -6.6938   3.4842   0.8032
 J1G  H10  H  HCH2  0   0.234  -8.1309   2.5737   0.3602
 J1G  H11  H  HCH2  0   0.228  -7.1464   1.8278  -1.6994
 J1G  H12  H  HCH2  0   0.234  -6.4113   3.4143  -1.5884
 J1G  H13  H  HCH2  0   0.239  -6.5070   1.4228   2.1367
 J1G  H14  H  HCH2  0   0.225  -6.9528   0.4420   0.7411
 J1G  H15  H  HCH2  0   0.240  -5.0415   0.8863  -1.5996
 J1G  H16  H  HCH2  0   0.241  -4.2852   2.4189  -1.2235
 J1G  H17  H  HCH1  0   0.267  -4.4345   2.1137   1.0789
 J1G  H18  H  HNH1  0   0.416  -2.0403  -3.6123   0.6125
 J1G  H19  H  HOH1  0   0.480  -3.3557  -4.5299  -1.2820
 J1G  FAD  F  F     0  -0.299   5.6004   3.0206  -0.9221

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
 J1G  CAM  CAN  single    1.532  0.020  1.532
 J1G  CAM  CAO  single    1.524  0.020  1.524
 J1G  CAN  CAP  single    1.544  0.020  1.544
 J1G  OAC  NAQ  single    1.361  0.020  1.361
 J1G  CAO  CBA  single    1.524  0.020  1.524
 J1G  CAP  CBA  single    1.552  0.020  1.552
 J1G  NAQ  C    single    1.342  0.020  1.342
 J1G  O    C    double    1.213  0.020  1.213
 J1G  CBA  CAT  single    1.508  0.020  1.508
 J1G  C    CA   single    1.536  0.020  1.536
 J1G  CAT  N    single    1.347  0.020  1.347
 J1G  CAT  OAB  double    1.223  0.020  1.223
 J1G  N    CA   single    1.437  0.020  1.437
 J1G  CA   CAY  single    1.510  0.020  1.510
 J1G  CAY  CAJ  aromatic  1.389  0.020  1.389
 J1G  CAY  CAI  aromatic  1.393  0.020  1.393
 J1G  CAJ  CAH  aromatic  1.386  0.020  1.386
 J1G  CAI  CAG  aromatic  1.384  0.020  1.384
 J1G  CAH  CAW  aromatic  1.393  0.020  1.393
 J1G  CAG  CAW  aromatic  1.395  0.020  1.395
 J1G  CAW  CAX  single    1.475  0.020  1.475
 J1G  CAX  CAL  aromatic  1.394  0.020  1.394
 J1G  CAX  CAK  aromatic  1.395  0.020  1.395
 J1G  CAL  CAV  aromatic  1.378  0.020  1.378
 J1G  CAK  CAU  aromatic  1.378  0.020  1.378
 J1G  CAV  FAE  single    1.334  0.020  1.334
 J1G  CAV  CAZ  aromatic  1.383  0.020  1.383
 J1G  CAU  CAZ  aromatic  1.383  0.020  1.383
 J1G  CAU  FAD  single    1.333  0.020  1.333
 J1G  CAZ  FAF  single    1.331  0.020  1.331
 J1G  N    H1   single    0.860  0.020  1.020
 J1G  CA   H2   single    0.970  0.020  1.090
 J1G  CAG  H3   single    0.930  0.020  1.080
 J1G  CAH  H4   single    0.930  0.020  1.080
 J1G  CAI  H5   single    0.930  0.020  1.080
 J1G  CAJ  H6   single    0.930  0.020  1.080
 J1G  CAK  H7   single    0.930  0.020  1.080
 J1G  CAL  H8   single    0.930  0.020  1.080
 J1G  CAM  H9   single    0.970  0.020  1.090
 J1G  CAM  H10  single    0.970  0.020  1.090
 J1G  CAN  H11  single    0.970  0.020  1.090
 J1G  CAN  H12  single    0.970  0.020  1.090
 J1G  CAO  H13  single    0.970  0.020  1.090
 J1G  CAO  H14  single    0.970  0.020  1.090
 J1G  CAP  H15  single    0.970  0.020  1.090
 J1G  CAP  H16  single    0.970  0.020  1.090
 J1G  CBA  H17  single    0.970  0.020  1.090
 J1G  NAQ  H18  single    0.860  0.020  1.020
 J1G  OAC  H19  single    0.850  0.020  0.980

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
 J1G  H1   N    CAT  119.55  3.000
 J1G  H1   N    CA   118.82  3.000
 J1G  CAT  N    CA   121.53  3.000
 J1G  H2   CA   CAY  108.33  3.000
 J1G  H2   CA   C    109.32  3.000
 J1G  CAY  CA   C    107.94  3.000
 J1G  H2   CA   N    110.08  3.000
 J1G  CAY  CA   N    110.79  3.000
 J1G  C    CA   N    110.32  3.000
 J1G  NAQ  C    O    124.65  3.000
 J1G  O    C    CA   122.83  3.000
 J1G  NAQ  C    CA   112.48  3.000
 J1G  H3   CAG  CAW  120.05  3.000
 J1G  H3   CAG  CAI  118.97  3.000
 J1G  CAW  CAG  CAI  120.95  3.000
 J1G  H4   CAH  CAW  120.26  3.000
 J1G  H4   CAH  CAJ  119.02  3.000
 J1G  CAW  CAH  CAJ  120.71  3.000
 J1G  H5   CAI  CAY  120.54  3.000
 J1G  H5   CAI  CAG  119.00  3.000
 J1G  CAY  CAI  CAG  120.45  3.000
 J1G  H6   CAJ  CAY  119.94  3.000
 J1G  H6   CAJ  CAH  119.31  3.000
 J1G  CAY  CAJ  CAH  120.74  3.000
 J1G  H7   CAK  CAX  121.26  3.000
 J1G  H7   CAK  CAU  119.03  3.000
 J1G  CAX  CAK  CAU  119.70  3.000
 J1G  H8   CAL  CAX  121.25  3.000
 J1G  H8   CAL  CAV  119.04  3.000
 J1G  CAX  CAL  CAV  119.69  3.000
 J1G  H10  CAM  H9   107.18  3.000
 J1G  H10  CAM  CAO  112.96  3.000
 J1G  H9   CAM  CAO  109.81  3.000
 J1G  H10  CAM  CAN  112.87  3.000
 J1G  H9   CAM  CAN  110.40  3.000
 J1G  CAO  CAM  CAN  103.64  3.000
 J1G  H12  CAN  H11  106.85  3.000
 J1G  H12  CAN  CAP  112.20  3.000
 J1G  H11  CAN  CAP  109.91  3.000
 J1G  H12  CAN  CAM  112.40  3.000
 J1G  H11  CAN  CAM  109.81  3.000
 J1G  CAP  CAN  CAM  105.69  3.000
 J1G  H14  CAO  H13  107.67  3.000
 J1G  H14  CAO  CBA  110.01  3.000
 J1G  H13  CAO  CBA  112.80  3.000
 J1G  H14  CAO  CAM  110.12  3.000
 J1G  H13  CAO  CAM  113.45  3.000
 J1G  CBA  CAO  CAM  102.75  3.000
 J1G  H16  CAP  H15  106.68  3.000
 J1G  H16  CAP  CBA  110.67  3.000
 J1G  H15  CAP  CBA  110.89  3.000
 J1G  H16  CAP  CAN  112.34  3.000
 J1G  H15  CAP  CAN  110.77  3.000
 J1G  CBA  CAP  CAN  105.57  3.000
 J1G  OAB  CAT  CBA  123.86  3.000
 J1G  OAB  CAT  N    121.30  3.000
 J1G  CBA  CAT  N    114.79  3.000
 J1G  FAD  CAU  CAZ  118.36  3.000
 J1G  FAD  CAU  CAK  120.30  3.000
 J1G  CAZ  CAU  CAK  121.34  3.000
 J1G  FAE  CAV  CAZ  118.35  3.000
 J1G  CAZ  CAV  CAL  121.36  3.000
 J1G  FAE  CAV  CAL  120.29  3.000
 J1G  CAX  CAW  CAH  120.93  3.000
 J1G  CAX  CAW  CAG  120.72  3.000
 J1G  CAH  CAW  CAG  118.35  3.000
 J1G  CAW  CAX  CAL  120.31  3.000
 J1G  CAL  CAX  CAK  119.36  3.000
 J1G  CAW  CAX  CAK  120.32  3.000
 J1G  CAJ  CAY  CAI  118.80  3.000
 J1G  CAI  CAY  CA   121.01  3.000
 J1G  CAJ  CAY  CA   120.17  3.000
 J1G  FAF  CAZ  CAV  120.70  3.000
 J1G  FAF  CAZ  CAU  120.75  3.000
 J1G  CAV  CAZ  CAU  118.54  3.000
 J1G  H17  CBA  CAT  108.82  3.000
 J1G  H17  CBA  CAP  108.52  3.000
 J1G  CAT  CBA  CAP  110.85  3.000
 J1G  H17  CBA  CAO  108.84  3.000
 J1G  CAT  CBA  CAO  114.97  3.000
 J1G  CAP  CBA  CAO  104.62  3.000
 J1G  H18  NAQ  OAC  114.90  3.000
 J1G  H18  NAQ  C    122.68  3.000
 J1G  OAC  NAQ  C    120.04  3.000
 J1G  H19  OAC  NAQ  106.16  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
 J1G  CONST_01  CAJ  CAY  CAI  CAG    0.00   0.0  0
 J1G  CONST_02  CAJ  CAH  CAW  CAG    0.00   0.0  0
 J1G  CONST_05  CAI  CAY  CAJ  CAH    0.00   0.0  0
 J1G  CONST_06  CAI  CAG  CAW  CAH    0.00   0.0  0
 J1G  CONST_09  CAX  CAW  CAG  CAI  180.00   0.0  0
 J1G  CONST_10  CAX  CAW  CAH  CAJ  180.00   0.0  0
 J1G  CONST_11  CAV  CAL  CAX  CAK    0.00   0.0  0
 J1G  CONST_12  CAV  CAZ  CAU  CAK    0.00   0.0  0
 J1G  CONST_13  CAU  CAK  CAX  CAL    0.00   0.0  0
 J1G  CONST_14  CAU  CAZ  CAV  CAL    0.00   0.0  0
 J1G  CONST_15  CAW  CAX  CAK  CAU  180.00   0.0  0
 J1G  CONST_16  CAW  CAX  CAL  CAV  180.00   0.0  0
 J1G  CONST_17  CAY  CAJ  CAH  CAW    0.00   0.0  0
 J1G  CONST_18  CAY  CAI  CAG  CAW    0.00   0.0  0
 J1G  CONST_19  CAZ  CAV  CAL  CAX    0.00   0.0  0
 J1G  CONST_20  CAZ  CAU  CAK  CAX    0.00   0.0  0
 J1G  CONST_21  CAH  CAJ  CAY  CA   180.00   0.0  0
 J1G  CONST_22  CAG  CAI  CAY  CA   180.00   0.0  0
 J1G  CONST_23  FAF  CAZ  CAU  CAK  180.00   0.0  0
 J1G  CONST_24  FAF  CAZ  CAV  CAL  180.00   0.0  0
 J1G  CONST_25  FAE  CAV  CAZ  CAU  180.00   0.0  0
 J1G  CONST_26  FAD  CAU  CAZ  CAV  180.00   0.0  0
 J1G  CONST_27  FAE  CAV  CAL  CAX  180.00   0.0  0
 J1G  CONST_28  FAD  CAU  CAK  CAX  180.00   0.0  0
 J1G  CONST_29  H4   CAH  CAW  CAG  180.00   0.0  0
 J1G  CONST_30  H3   CAG  CAW  CAH  180.00   0.0  0
 J1G  CONST_31  H6   CAJ  CAY  CAI  180.00   0.0  0
 J1G  CONST_32  H5   CAI  CAY  CAJ  180.00   0.0  0
 J1G  CONST_33  H8   CAL  CAX  CAK  180.00   0.0  0
 J1G  CONST_34  H7   CAK  CAX  CAL  180.00   0.0  0
 J1G  CONST_35  CBA  CAT  N    CA   180.00   0.0  0
 J1G  CONST_36  H1   N    CAT  CBA    0.00   0.0  0
 J1G  CONST_37  OAC  NAQ  C    CA   180.00   0.0  0
 J1G  CONST_38  OAB  CAT  N    CA     0.00   0.0  0
 J1G  CONST_39  OAC  NAQ  C    O      0.00   0.0  0
 J1G  CONST_40  H18  NAQ  C    CA     0.00   0.0  0
 J1G  Var_01    CBA  CAP  CAN  CAM    6.78  30.0  1
 J1G  Var_02    CBA  CAO  CAM  CAN   42.12  30.0  1
 J1G  Var_03    CAP  CAN  CAM  CAO  -30.15  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
 J1G  chir_01  CA   C    N    CAY  positiv
 J1G  chir_02  CBA  CAT  CAP  CAO  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
 J1G  plan-1  CAK  0.020
 J1G  plan-1  CAL  0.020
 J1G  plan-1  CAU  0.020
 J1G  plan-1  CAV  0.020
 J1G  plan-1  CAW  0.020
 J1G  plan-1  CAX  0.020
 J1G  plan-1  CAZ  0.020
 J1G  plan-1  FAE  0.020
 J1G  plan-1  FAF  0.020
 J1G  plan-1  H7   0.020
 J1G  plan-1  H8   0.020
 J1G  plan-1  FAD  0.020
 J1G  plan-2  CA   0.020
 J1G  plan-2  CAG  0.020
 J1G  plan-2  CAH  0.020
 J1G  plan-2  CAI  0.020
 J1G  plan-2  CAJ  0.020
 J1G  plan-2  CAW  0.020
 J1G  plan-2  CAX  0.020
 J1G  plan-2  CAY  0.020
 J1G  plan-2  H3   0.020
 J1G  plan-2  H4   0.020
 J1G  plan-2  H5   0.020
 J1G  plan-2  H6   0.020
 J1G  plan-3  N    0.020
 J1G  plan-3  CA   0.020
 J1G  plan-3  CAT  0.020
 J1G  plan-3  CBA  0.020
 J1G  plan-3  OAB  0.020
 J1G  plan-3  H1   0.020
 J1G  plan-4  CA   0.020
 J1G  plan-4  C    0.020
 J1G  plan-4  O    0.020
 J1G  plan-4  NAQ  0.020
 J1G  plan-4  OAC  0.020
 J1G  plan-4  H18  0.020

