# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:25:19 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2R)-2-[(cyclopentylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@H](NC(=O)CC1CCCC1)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
 J4P  J4P  (2R)-2-[(cyclopentylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide  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_J4P
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
 J4P  N    N  NH1   0  -0.649  -2.7056  -0.2002  -0.2842
 J4P  CA   C  CH1   0  -0.240  -1.8575  -1.1932   0.3207
 J4P  C    C  C     0   0.534  -2.0088  -2.5314  -0.4169
 J4P  O    O  O     0  -0.461  -2.1020  -2.6058  -1.6243
 J4P  CAG  C  CR16  0  -0.291   1.6819  -0.3319   1.3779
 J4P  CAH  C  CR16  0  -0.291   1.5276  -0.0776  -0.9977
 J4P  CAI  C  CR16  0  -0.299   0.3478  -0.7047   1.4220
 J4P  CAJ  C  CR16  0  -0.264   0.1955  -0.4516  -0.9541
 J4P  CAK  C  CR16  0  -0.487   4.6348  -0.1772   1.0016
 J4P  CAL  C  CR16  0  -0.488   4.1489   1.3332  -0.8078
 J4P  CAM  C  CH2   0  -0.451  -7.8438   2.6286   0.1703
 J4P  CAN  C  CH2   0  -0.442  -6.9652   2.6199   1.4397
 J4P  CAO  C  CH2   0  -0.423  -6.9200   2.1579  -0.9513
 J4P  CAP  C  CH2   0  -0.440  -5.7178   1.7835   1.0831
 J4P  CAT  C  C     0   0.578  -4.0333  -0.3915  -0.3826
 J4P  CAV  C  CR6   0   0.439   5.9566   0.2094   0.9495
 J4P  CAW  C  CR6   0   0.439   5.4773   1.6980  -0.8404
 J4P  CAX  C  CR6   0   0.088   2.2937  -0.0128   0.1669
 J4P  CAY  C  CR6   0   0.116   3.7135   0.3864   0.1190
 J4P  CAZ  C  CR6   0   0.087  -0.4103  -0.7686   0.2595
 J4P  CBA  C  CR6   0   0.256   6.3968   1.1469   0.0330
 J4P  CBB  C  CH1   0  -0.232  -6.0406   1.1189  -0.2602
 J4P  FAE  F  F     0  -0.299   5.9033   2.6083  -1.7164
 J4P  FAF  F  F     0  -0.294   7.6755   1.5139  -0.0052
 J4P  NAR  N  NH1   0  -0.371  -1.9159  -3.5866   0.4084
 J4P  OAA  O  O     0  -0.498  -4.5610  -1.4069   0.0503
 J4P  OAC  O  OH1   0  -0.541  -2.1068  -4.8432  -0.0803
 J4P  H1   H  HNH1  0   0.410  -2.2925   0.6521  -0.6264
 J4P  H2   H  HCH1  0   0.295  -2.1327  -1.3254   1.3725
 J4P  H3   H  HCR6  0   0.264   2.2396  -0.2656   2.3035
 J4P  H4   H  HCR6  0   0.263   1.9761   0.1422  -1.9581
 J4P  H5   H  HCR6  0   0.264  -0.1064  -0.9350   2.3778
 J4P  H6   H  HCR6  0   0.267  -0.3650  -0.5103  -1.8785
 J4P  H7   H  HCR6  0   0.294   4.3388  -0.9306   1.7197
 J4P  H8   H  HCR6  0   0.294   3.4601   1.8103  -1.4923
 J4P  H10  H  HCH2  0   0.229  -8.2878   3.6051  -0.0272
 J4P  H11  H  HCH2  0   0.226  -6.6802   3.6320   1.7292
 J4P  H12  H  HCH2  0   0.227  -7.5052   2.1962   2.2872
 J4P  H13  H  HCH2  0   0.231  -7.4581   1.7537  -1.8112
 J4P  H14  H  HCH2  0   0.212  -6.3031   2.9877  -1.3129
 J4P  H15  H  HCH2  0   0.219  -4.8481   2.4366   0.9626
 J4P  H16  H  HCH2  0   0.234  -5.4642   1.0556   1.8557
 J4P  H19  H  HCH1  0   0.231  -6.6514   0.2283  -0.0767
 J4P  H20  H  HNH1  0   0.416  -2.0453  -3.5012   1.4064
 J4P  H21  H  HOH1  0   0.480  -1.2255  -5.2070  -0.2348
 J4P  FAD  F  F     0  -0.299   6.8474  -0.3251   1.7854
 J4P  CAQ  C  CH2   0  -0.574  -4.8138   0.7085  -1.0610
 J4P  H9   H  HCH2  0   0.221  -8.6683   1.9204   0.2804
 J4P  H17  H  HCH2  0   0.246  -4.1811   1.5810  -1.2471
 J4P  H18  H  HCH2  0   0.275  -5.1190   0.3275  -2.0411

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
 J4P  CAM  CAN  single    1.544  0.020  1.544
 J4P  CAM  CAO  single    1.527  0.020  1.527
 J4P  CAN  CAP  single    1.544  0.020  1.544
 J4P  CAO  CBB  single    1.527  0.020  1.527
 J4P  CAP  CBB  single    1.533  0.020  1.533
 J4P  OAC  NAR  single    1.362  0.020  1.362
 J4P  CBB  CAQ  single    1.521  0.020  1.521
 J4P  NAR  C    single    1.343  0.020  1.343
 J4P  O    C    double    1.213  0.020  1.213
 J4P  C    CA   single    1.535  0.020  1.535
 J4P  CAQ  CAT  single    1.510  0.020  1.510
 J4P  CAT  N    single    1.345  0.020  1.345
 J4P  CAT  OAA  double    1.224  0.020  1.224
 J4P  N    CA   single    1.439  0.020  1.439
 J4P  CA   CAZ  single    1.509  0.020  1.509
 J4P  CAZ  CAI  aromatic  1.389  0.020  1.389
 J4P  CAZ  CAJ  aromatic  1.393  0.020  1.393
 J4P  CAI  CAG  aromatic  1.386  0.020  1.386
 J4P  CAJ  CAH  aromatic  1.384  0.020  1.384
 J4P  CAG  CAX  aromatic  1.394  0.020  1.394
 J4P  CAH  CAX  aromatic  1.396  0.020  1.396
 J4P  CAX  CAY  single    1.476  0.020  1.476
 J4P  CAY  CAL  aromatic  1.395  0.020  1.395
 J4P  CAY  CAK  aromatic  1.395  0.020  1.395
 J4P  CAL  CAW  aromatic  1.378  0.020  1.378
 J4P  CAK  CAV  aromatic  1.378  0.020  1.378
 J4P  CAW  FAE  single    1.333  0.020  1.333
 J4P  CAW  CBA  aromatic  1.383  0.020  1.383
 J4P  CAV  CBA  aromatic  1.383  0.020  1.383
 J4P  CAV  FAD  single    1.333  0.020  1.333
 J4P  CBA  FAF  single    1.331  0.020  1.331
 J4P  N    H1   single    0.860  0.020  1.020
 J4P  CA   H2   single    0.970  0.020  1.090
 J4P  CAG  H3   single    0.930  0.020  1.080
 J4P  CAH  H4   single    0.930  0.020  1.080
 J4P  CAI  H5   single    0.930  0.020  1.080
 J4P  CAJ  H6   single    0.930  0.020  1.080
 J4P  CAK  H7   single    0.930  0.020  1.080
 J4P  CAL  H8   single    0.930  0.020  1.080
 J4P  CAM  H9   single    0.970  0.020  1.090
 J4P  CAM  H10  single    0.970  0.020  1.090
 J4P  CAN  H11  single    0.970  0.020  1.090
 J4P  CAN  H12  single    0.970  0.020  1.090
 J4P  CAO  H13  single    0.970  0.020  1.090
 J4P  CAO  H14  single    0.970  0.020  1.090
 J4P  CAP  H15  single    0.970  0.020  1.090
 J4P  CAP  H16  single    0.970  0.020  1.090
 J4P  CAQ  H17  single    0.970  0.020  1.090
 J4P  CAQ  H18  single    0.970  0.020  1.090
 J4P  CBB  H19  single    0.970  0.020  1.090
 J4P  NAR  H20  single    0.890  0.020  1.040
 J4P  OAC  H21  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
 J4P  H1   N    CAT  120.03  3.000
 J4P  H1   N    CA   119.01  3.000
 J4P  CAT  N    CA   120.95  3.000
 J4P  H2   CA   CAZ  108.29  3.000
 J4P  H2   CA   C    109.35  3.000
 J4P  CAZ  CA   C    108.67  3.000
 J4P  H2   CA   N    109.81  3.000
 J4P  CAZ  CA   N    110.73  3.000
 J4P  C    CA   N    109.96  3.000
 J4P  NAR  C    O    124.66  3.000
 J4P  O    C    CA   122.62  3.000
 J4P  NAR  C    CA   112.51  3.000
 J4P  H3   CAG  CAX  120.18  3.000
 J4P  H3   CAG  CAI  119.02  3.000
 J4P  CAX  CAG  CAI  120.78  3.000
 J4P  H4   CAH  CAX  120.23  3.000
 J4P  H4   CAH  CAJ  118.78  3.000
 J4P  CAX  CAH  CAJ  120.97  3.000
 J4P  H5   CAI  CAZ  120.00  3.000
 J4P  H5   CAI  CAG  119.27  3.000
 J4P  CAZ  CAI  CAG  120.73  3.000
 J4P  H6   CAJ  CAZ  120.43  3.000
 J4P  H6   CAJ  CAH  119.07  3.000
 J4P  CAZ  CAJ  CAH  120.49  3.000
 J4P  H7   CAK  CAY  121.36  3.000
 J4P  H7   CAK  CAV  118.87  3.000
 J4P  CAY  CAK  CAV  119.76  3.000
 J4P  H8   CAL  CAY  121.40  3.000
 J4P  H8   CAL  CAW  118.82  3.000
 J4P  CAY  CAL  CAW  119.76  3.000
 J4P  H10  CAM  H9   106.95  3.000
 J4P  H10  CAM  CAO  112.90  3.000
 J4P  H9   CAM  CAO  109.31  3.000
 J4P  H10  CAM  CAN  112.68  3.000
 J4P  H9   CAM  CAN  110.06  3.000
 J4P  CAO  CAM  CAN  104.94  3.000
 J4P  H12  CAN  H11  106.48  3.000
 J4P  H12  CAN  CAP  111.66  3.000
 J4P  H11  CAN  CAP  110.67  3.000
 J4P  H12  CAN  CAM  111.06  3.000
 J4P  H11  CAN  CAM  111.21  3.000
 J4P  CAP  CAN  CAM  105.85  3.000
 J4P  H14  CAO  H13  107.34  3.000
 J4P  H14  CAO  CBB  109.91  3.000
 J4P  H13  CAO  CBB  112.86  3.000
 J4P  H14  CAO  CAM  110.47  3.000
 J4P  H13  CAO  CAM  113.22  3.000
 J4P  CBB  CAO  CAM  103.05  3.000
 J4P  H16  CAP  H15  106.94  3.000
 J4P  H16  CAP  CBB  112.34  3.000
 J4P  H15  CAP  CBB  109.24  3.000
 J4P  H16  CAP  CAN  112.69  3.000
 J4P  H15  CAP  CAN  110.14  3.000
 J4P  CBB  CAP  CAN  105.49  3.000
 J4P  OAA  CAT  CAQ  122.73  3.000
 J4P  OAA  CAT  N    121.20  3.000
 J4P  CAQ  CAT  N    116.08  3.000
 J4P  FAD  CAV  CBA  118.33  3.000
 J4P  FAD  CAV  CAK  120.30  3.000
 J4P  CBA  CAV  CAK  121.37  3.000
 J4P  FAE  CAW  CBA  118.34  3.000
 J4P  CBA  CAW  CAL  121.37  3.000
 J4P  FAE  CAW  CAL  120.29  3.000
 J4P  CAY  CAX  CAH  120.91  3.000
 J4P  CAY  CAX  CAG  120.83  3.000
 J4P  CAH  CAX  CAG  118.26  3.000
 J4P  CAX  CAY  CAL  120.37  3.000
 J4P  CAL  CAY  CAK  119.25  3.000
 J4P  CAX  CAY  CAK  120.38  3.000
 J4P  CAJ  CAZ  CAI  118.77  3.000
 J4P  CAJ  CAZ  CA   121.08  3.000
 J4P  CAI  CAZ  CA   120.14  3.000
 J4P  FAF  CBA  CAW  120.72  3.000
 J4P  FAF  CBA  CAV  120.78  3.000
 J4P  CAW  CBA  CAV  118.49  3.000
 J4P  H19  CBB  CAQ  108.57  3.000
 J4P  H19  CBB  CAP  108.85  3.000
 J4P  CAQ  CBB  CAP  114.10  3.000
 J4P  H19  CBB  CAO  107.94  3.000
 J4P  CAQ  CBB  CAO  114.20  3.000
 J4P  CAP  CBB  CAO  102.88  3.000
 J4P  H20  NAR  OAC  114.50  3.000
 J4P  H20  NAR  C    122.14  3.000
 J4P  OAC  NAR  C    119.66  3.000
 J4P  H21  OAC  NAR  106.09  3.000
 J4P  H18  CAQ  H17  106.65  3.000
 J4P  H18  CAQ  CBB  109.89  3.000
 J4P  H17  CAQ  CBB  109.93  3.000
 J4P  H18  CAQ  CAT  107.03  3.000
 J4P  H17  CAQ  CAT  111.02  3.000
 J4P  CBB  CAQ  CAT  112.14  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
 J4P  CONST_01  CAJ  CAZ  CAI  CAG     0.00   0.0  0
 J4P  CONST_02  CAJ  CAH  CAX  CAG     0.00   0.0  0
 J4P  CONST_05  CAI  CAZ  CAJ  CAH     0.00   0.0  0
 J4P  CONST_06  CAI  CAG  CAX  CAH     0.00   0.0  0
 J4P  CONST_09  CAY  CAX  CAG  CAI   180.00   0.0  0
 J4P  CONST_10  CAY  CAX  CAH  CAJ   180.00   0.0  0
 J4P  CONST_11  CAW  CAL  CAY  CAK     0.00   0.0  0
 J4P  CONST_12  CAW  CBA  CAV  CAK     0.00   0.0  0
 J4P  CONST_13  CAV  CAK  CAY  CAL     0.00   0.0  0
 J4P  CONST_14  CAV  CBA  CAW  CAL     0.00   0.0  0
 J4P  CONST_15  CAX  CAY  CAK  CAV   180.00   0.0  0
 J4P  CONST_16  CAX  CAY  CAL  CAW   180.00   0.0  0
 J4P  CONST_17  CAZ  CAI  CAG  CAX     0.00   0.0  0
 J4P  CONST_18  CAZ  CAJ  CAH  CAX     0.00   0.0  0
 J4P  CONST_19  CBA  CAW  CAL  CAY     0.00   0.0  0
 J4P  CONST_20  CBA  CAV  CAK  CAY     0.00   0.0  0
 J4P  CONST_21  CAG  CAI  CAZ  CA    180.00   0.0  0
 J4P  CONST_22  CAH  CAJ  CAZ  CA    180.00   0.0  0
 J4P  CONST_23  FAF  CBA  CAV  CAK   180.00   0.0  0
 J4P  CONST_24  FAF  CBA  CAW  CAL   180.00   0.0  0
 J4P  CONST_25  FAE  CAW  CBA  CAV   180.00   0.0  0
 J4P  CONST_26  FAD  CAV  CBA  CAW   180.00   0.0  0
 J4P  CONST_27  FAE  CAW  CAL  CAY   180.00   0.0  0
 J4P  CONST_28  FAD  CAV  CAK  CAY   180.00   0.0  0
 J4P  CONST_29  H4   CAH  CAX  CAG   180.00   0.0  0
 J4P  CONST_30  H3   CAG  CAX  CAH   180.00   0.0  0
 J4P  CONST_31  H6   CAJ  CAZ  CAI   180.00   0.0  0
 J4P  CONST_32  H5   CAI  CAZ  CAJ   180.00   0.0  0
 J4P  CONST_33  H8   CAL  CAY  CAK   180.00   0.0  0
 J4P  CONST_34  H7   CAK  CAY  CAL   180.00   0.0  0
 J4P  CONST_35  OAC  NAR  C    CA    180.00   0.0  0
 J4P  CONST_36  CAQ  CAT  N    CA    180.00   0.0  0
 J4P  CONST_37  OAA  CAT  N    CA      0.00   0.0  0
 J4P  CONST_38  OAC  NAR  C    O       0.00   0.0  0
 J4P  CONST_40  H1   N    CAT  CAQ     0.00   0.0  0
 J4P  Var_01    CBB  CAP  CAN  CAM   -10.75  30.0  1
 J4P  Var_02    CBB  CAO  CAM  CAN    35.94  30.0  1
 J4P  Var_03    CAP  CAN  CAM  CAO   -15.48  30.0  1
 J4P  Var_04    CBB  CAQ  CAT  N    -131.70  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
 J4P  chir_01  CA   C    N    CAZ  positiv
 J4P  chir_02  CBB  CAO  CAP  CAQ  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
 J4P  plan-1  CAK  0.020
 J4P  plan-1  CAL  0.020
 J4P  plan-1  CAV  0.020
 J4P  plan-1  CAW  0.020
 J4P  plan-1  CAX  0.020
 J4P  plan-1  CAY  0.020
 J4P  plan-1  CBA  0.020
 J4P  plan-1  FAE  0.020
 J4P  plan-1  FAF  0.020
 J4P  plan-1  H7   0.020
 J4P  plan-1  H8   0.020
 J4P  plan-1  FAD  0.020
 J4P  plan-2  CA   0.020
 J4P  plan-2  CAG  0.020
 J4P  plan-2  CAH  0.020
 J4P  plan-2  CAI  0.020
 J4P  plan-2  CAJ  0.020
 J4P  plan-2  CAX  0.020
 J4P  plan-2  CAY  0.020
 J4P  plan-2  CAZ  0.020
 J4P  plan-2  H3   0.020
 J4P  plan-2  H4   0.020
 J4P  plan-2  H5   0.020
 J4P  plan-2  H6   0.020
 J4P  plan-3  N    0.020
 J4P  plan-3  CA   0.020
 J4P  plan-3  CAT  0.020
 J4P  plan-3  OAA  0.020
 J4P  plan-3  H1   0.020
 J4P  plan-3  CAQ  0.020
 J4P  plan-4  CA   0.020
 J4P  plan-4  C    0.020
 J4P  plan-4  O    0.020
 J4P  plan-4  NAR  0.020
 J4P  plan-4  OAC  0.020
 J4P  plan-4  H20  0.020

