# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:48:22 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](CCN1C=CC(=CC1=O)c2ccccc2)(C(=O)NO)[S](C)(=O)=O
#
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
 RFN  RFN  (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide  ligand  45  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RFN
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
 RFN  N1    N  NR6   0  -0.512   0.7513  -0.6137  -0.5869
 RFN  C4    C  CR16  0  -0.303   5.7543   0.1909  -1.0562
 RFN  C5    C  CR6   0   0.090   4.8494   0.3137  -0.0007
 RFN  C6    C  CR16  0  -0.303   5.3199   0.7470   1.2399
 RFN  C7    C  CR6   0   0.223   3.4238  -0.0129  -0.1939
 RFN  C8    C  CR16  0  -0.455   2.7849   0.2754  -1.4301
 RFN  C10   C  CR6   0   0.595   1.2988  -0.9133   0.6553
 RFN  C13   C  CH2   0  -0.442  -1.5164   0.2518  -0.2751
 RFN  C15   C  C     0   0.596  -3.6937   1.3293   0.1862
 RFN  C17   C  CH3   0  -0.721  -3.4237  -0.1800  -1.8975
 RFN  C1    C  CR16  0  -0.240   6.6617   1.0445   1.4216
 RFN  C2    C  CR16  0  -0.259   7.5558   0.9098   0.3672
 RFN  C3    C  CR16  0  -0.239   7.0978   0.4814  -0.8718
 RFN  C9    C  CR16  0   0.069   1.4751  -0.0336  -1.5757
 RFN  C11   C  CR16  0  -0.533   2.6902  -0.5953   0.8005
 RFN  O1    O  O     0  -0.516   0.6063  -1.4214   1.5370
 RFN  C12   C  CH2   0  -0.335  -0.6618  -0.8946  -0.8111
 RFN  C14   C  CT    0  -0.418  -3.0335   0.0942  -0.4459
 RFN  S1    S  S     0   1.219  -3.7016  -1.3284   0.5225
 RFN  C16   C  CH3   0  -0.808  -2.8852  -1.3557   2.1016
 RFN  O2    O  OS    0  -0.669  -5.1257  -1.0560   0.7231
 RFN  O3    O  OS    0  -0.665  -3.3409  -2.5601  -0.1827
 RFN  O4    O  O     0  -0.460  -3.4403   1.6551   1.3314
 RFN  N2    N  NH1   0  -0.367  -4.5087   2.0206  -0.6165
 RFN  O5    O  OH1   0  -0.533  -5.2267   3.0565  -0.1089
 RFN  H4    H  HCR6  0   0.260   5.4154  -0.1556  -2.0243
 RFN  H6    H  HCR6  0   0.260   4.6297   0.8741   2.0643
 RFN  H8    H  HCR6  0   0.276   3.3077   0.7524  -2.2452
 RFN  H13   H  HCH2  0   0.288  -1.2792   0.4287   0.7735
 RFN  H13A  H  HCH2  0   0.292  -1.2394   1.1658  -0.8096
 RFN  H17   H  HCH3  0   0.291  -2.9391  -1.0772  -2.2730
 RFN  H17A  H  HCH3  0   0.274  -4.4974  -0.3167  -2.0283
 RFN  H17B  H  HCH3  0   0.283  -3.0943   0.6471  -2.5268
 RFN  H1    H  HCR6  0   0.262   7.0084   1.3880   2.3872
 RFN  H2    H  HCR6  0   0.262   8.6035   1.1398   0.5100
 RFN  H3    H  HCR6  0   0.262   7.7883   0.3701  -1.6973
 RFN  H9    H  HCR6  0   0.311   0.9409   0.1720  -2.4928
 RFN  H11   H  HCR6  0   0.269   3.1416  -0.8568   1.7487
 RFN  H12   H  HCH2  0   0.281  -0.8031  -1.0218  -1.8825
 RFN  H12A  H  HCH2  0   0.278  -0.9015  -1.8457  -0.3434
 RFN  H16   H  HCH3  0   0.302  -3.0738  -0.4318   2.6380
 RFN  H16A  H  HCH3  0   0.316  -3.3225  -2.1988   2.6362
 RFN  H16B  H  HCH3  0   0.300  -1.8175  -1.5176   1.9715
 RFN  HN2   H  HNH1  0   0.436  -4.7977   1.7159  -1.5333
 RFN  HO5   H  HOH1  0   0.483  -4.7135   3.8561  -0.2870

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
 RFN  C10  N1    single    1.390  0.020  1.390
 RFN  C9   N1    single    1.356  0.020  1.356
 RFN  N1   C12   single    1.458  0.020  1.458
 RFN  C3   C4    aromatic  1.387  0.020  1.387
 RFN  C4   C5    aromatic  1.396  0.020  1.396
 RFN  C4   H4    single    0.930  0.020  1.080
 RFN  C5   C6    aromatic  1.396  0.020  1.396
 RFN  C5   C7    single    1.475  0.020  1.475
 RFN  C1   C6    aromatic  1.386  0.020  1.386
 RFN  C6   H6    single    0.930  0.020  1.080
 RFN  C7   C11   double    1.366  0.020  1.366
 RFN  C7   C8    single    1.421  0.020  1.421
 RFN  C8   C9    double    1.354  0.020  1.354
 RFN  C8   H8    single    0.930  0.020  1.080
 RFN  C11  C10   single    1.435  0.020  1.435
 RFN  C10  O1    double    1.231  0.020  1.231
 RFN  C13  C14   single    1.535  0.020  1.535
 RFN  C13  C12   single    1.527  0.020  1.527
 RFN  C13  H13   single    0.970  0.020  1.090
 RFN  C13  H13A  single    0.970  0.020  1.090
 RFN  C14  C15   single    1.537  0.020  1.537
 RFN  O4   C15   double    1.217  0.020  1.217
 RFN  C15  N2    single    1.337  0.020  1.337
 RFN  C14  C17   single    1.528  0.020  1.528
 RFN  C17  H17   single    0.970  0.020  1.090
 RFN  C17  H17A  single    0.970  0.020  1.090
 RFN  C17  H17B  single    0.970  0.020  1.090
 RFN  C2   C1    aromatic  1.389  0.020  1.389
 RFN  C1   H1    single    0.930  0.020  1.080
 RFN  C3   C2    aromatic  1.389  0.020  1.389
 RFN  C2   H2    single    0.930  0.020  1.080
 RFN  C3   H3    single    0.930  0.020  1.080
 RFN  C9   H9    single    0.930  0.020  1.080
 RFN  C11  H11   single    0.930  0.020  1.080
 RFN  C12  H12   single    0.970  0.020  1.090
 RFN  C12  H12A  single    0.970  0.020  1.090
 RFN  S1   C14   single    1.846  0.020  1.846
 RFN  O2   S1    double    1.464  0.020  1.464
 RFN  C16  S1    single    1.778  0.020  1.778
 RFN  S1   O3    double    1.464  0.020  1.464
 RFN  C16  H16   single    0.970  0.020  1.090
 RFN  C16  H16A  single    0.970  0.020  1.090
 RFN  C16  H16B  single    0.970  0.020  1.090
 RFN  N2   O5    single    1.359  0.020  1.359
 RFN  N2   HN2   single    0.860  0.020  1.020
 RFN  O5   HO5   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
 RFN  C12   N1   C9    119.19  3.000
 RFN  C12   N1   C10   118.53  3.000
 RFN  C9    N1   C10   122.25  3.000
 RFN  H4    C4   C3    119.29  3.000
 RFN  H4    C4   C5    120.10  3.000
 RFN  C3    C4   C5    120.60  3.000
 RFN  C7    C5   C6    120.72  3.000
 RFN  C7    C5   C4    120.53  3.000
 RFN  C6    C5   C4    118.75  3.000
 RFN  H6    C6   C1    119.47  3.000
 RFN  H6    C6   C5    119.89  3.000
 RFN  C1    C6   C5    120.62  3.000
 RFN  C11   C7   C8    118.58  3.000
 RFN  C8    C7   C5    120.23  3.000
 RFN  C11   C7   C5    121.20  3.000
 RFN  H8    C8   C9    119.23  3.000
 RFN  H8    C8   C7    121.92  3.000
 RFN  C9    C8   C7    118.84  3.000
 RFN  O1    C10  C11   124.38  3.000
 RFN  O1    C10  N1    120.49  3.000
 RFN  C11   C10  N1    115.13  3.000
 RFN  H13A  C13  H13   106.22  3.000
 RFN  H13A  C13  C14   106.35  3.000
 RFN  H13   C13  C14   109.81  3.000
 RFN  H13A  C13  C12   108.29  3.000
 RFN  H13   C13  C12   109.75  3.000
 RFN  C14   C13  C12   115.92  3.000
 RFN  N2    C15  O4    123.61  3.000
 RFN  N2    C15  C14   115.51  3.000
 RFN  O4    C15  C14   120.84  3.000
 RFN  H17B  C17  H17A  108.87  3.000
 RFN  H17B  C17  H17   106.99  3.000
 RFN  H17A  C17  H17   107.11  3.000
 RFN  H17B  C17  C14   109.58  3.000
 RFN  H17A  C17  C14   112.83  3.000
 RFN  H17   C17  C14   111.26  3.000
 RFN  H1    C1   C2    120.14  3.000
 RFN  H1    C1   C6    119.68  3.000
 RFN  C2    C1   C6    120.18  3.000
 RFN  H2    C2   C3    120.17  3.000
 RFN  H2    C2   C1    120.16  3.000
 RFN  C3    C2   C1    119.67  3.000
 RFN  H3    C3   C2    120.13  3.000
 RFN  H3    C3   C4    119.68  3.000
 RFN  C2    C3   C4    120.18  3.000
 RFN  H9    C9   C8    121.74  3.000
 RFN  H9    C9   N1    115.87  3.000
 RFN  C8    C9   N1    122.40  3.000
 RFN  H11   C11  C10   116.08  3.000
 RFN  H11   C11  C7    121.12  3.000
 RFN  C10   C11  C7    122.80  3.000
 RFN  H12A  C12  H12   107.03  3.000
 RFN  H12A  C12  C13   112.49  3.000
 RFN  H12   C12  C13   111.14  3.000
 RFN  H12A  C12  N1    108.44  3.000
 RFN  H12   C12  N1    107.44  3.000
 RFN  C13   C12  N1    110.11  3.000
 RFN  S1    C14  C17   105.53  3.000
 RFN  S1    C14  C15   104.37  3.000
 RFN  C17   C14  C15   115.17  3.000
 RFN  S1    C14  C13   112.24  3.000
 RFN  C17   C14  C13   112.12  3.000
 RFN  C15   C14  C13   107.24  3.000
 RFN  O3    S1   O2    117.52  3.000
 RFN  O3    S1   C16   107.56  3.000
 RFN  O2    S1   C16   109.14  3.000
 RFN  O3    S1   C14   107.84  3.000
 RFN  C16   S1   C14   108.16  3.000
 RFN  O2    S1   C14   106.30  3.000
 RFN  H16B  C16  H16A  109.72  3.000
 RFN  H16B  C16  H16   110.89  3.000
 RFN  H16A  C16  H16   110.27  3.000
 RFN  H16B  C16  S1    110.29  3.000
 RFN  H16A  C16  S1    105.27  3.000
 RFN  H16   C16  S1    110.25  3.000
 RFN  HN2   N2   O5    114.75  3.000
 RFN  HN2   N2   C15   124.36  3.000
 RFN  O5    N2   C15   119.48  3.000
 RFN  HO5   O5   N2    106.34  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
 RFN  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 RFN  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 RFN  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 RFN  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 RFN  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 RFN  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 RFN  CONST_07  C3   C4   C5   C7   180.00   0.0  0
 RFN  CONST_08  C1   C6   C5   C7   180.00   0.0  0
 RFN  CONST_09  C11  C10  N1   C9     0.00   0.0  0
 RFN  CONST_10  O1   C10  N1   C9   180.00   0.0  0
 RFN  CONST_11  C12  N1   C10  C11  180.00   0.0  0
 RFN  CONST_12  H2   C2   C3   C4   180.00   0.0  0
 RFN  CONST_13  H6   C6   C5   C4   180.00   0.0  0
 RFN  CONST_14  H3   C3   C4   C5   180.00   0.0  0
 RFN  CONST_15  H1   C1   C6   C5   180.00   0.0  0
 RFN  CONST_16  H4   C4   C5   C6   180.00   0.0  0
 RFN  CONST_17  C12  N1   C10  O1     0.00   0.0  0
 RFN  CONST_18  O5   N2   C15  C14  180.00   0.0  0
 RFN  CONST_19  O5   N2   C15  O4     0.00   0.0  0
 RFN  CONST_20  HN2  N2   C15  C14    0.00   0.0  0
 RFN  Var_01    C11  C7   C5   C4   144.26  30.0  2
 RFN  Var_02    C13  C12  N1   C10   83.35  30.0  3
 RFN  Var_03    C14  C13  C12  N1   179.87  30.0  1
 RFN  Var_04    H16  C16  S1   C14   60.29  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
 RFN  chir_01  C14  C15  C17  S1  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
 RFN  plan-1  N1   0.020
 RFN  plan-1  C5   0.020
 RFN  plan-1  C7   0.020
 RFN  plan-1  C8   0.020
 RFN  plan-1  C10  0.020
 RFN  plan-1  C9   0.020
 RFN  plan-1  C11  0.020
 RFN  plan-1  O1   0.020
 RFN  plan-1  C12  0.020
 RFN  plan-1  H8   0.020
 RFN  plan-1  H9   0.020
 RFN  plan-1  H11  0.020
 RFN  plan-2  C4   0.020
 RFN  plan-2  C5   0.020
 RFN  plan-2  C6   0.020
 RFN  plan-2  C7   0.020
 RFN  plan-2  C1   0.020
 RFN  plan-2  C2   0.020
 RFN  plan-2  C3   0.020
 RFN  plan-2  H4   0.020
 RFN  plan-2  H6   0.020
 RFN  plan-2  H1   0.020
 RFN  plan-2  H2   0.020
 RFN  plan-2  H3   0.020
 RFN  plan-3  C15  0.020
 RFN  plan-3  C14  0.020
 RFN  plan-3  O4   0.020
 RFN  plan-3  N2   0.020
 RFN  plan-3  O5   0.020
 RFN  plan-3  HN2  0.020

