# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:04:35 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [(1S)-1-[(2-fluoro-6-phenyl-phenyl)carbonylamino]ethyl]-trihydroxy-boron
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1c(F)cccc1c2ccccc2)[B-](O)(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
 Z10  Z10  '[(1S)-1-[(2-fluoro-6-phenyl-phenyl)carbonylamino]ethyl]-trihydroxy-boron'  ligand  38  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z10
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
 Z10  F15   F  F      0  -0.307   1.8910  -2.8412  -0.1727
 Z10  C14   C  CR6    0   0.567   2.3128  -1.5876  -0.4105
 Z10  C13   C  CR16   0  -0.419   3.5525  -1.4079  -0.9901
 Z10  C12   C  CR16   0  -0.228   3.9853  -0.1089  -1.2049
 Z10  C11   C  CR16   0  -0.318   3.1889   0.9654  -0.8384
 Z10  C8    C  CR6    0   0.119   1.9401   0.7693  -0.2487
 Z10  C10   C  CR6    0   0.048   1.1248   1.9446   0.1321
 Z10  C21   C  CR16   0  -0.303   1.7165   3.0014   0.8257
 Z10  C20   C  CR16   0  -0.244   0.9772   4.1214   1.1777
 Z10  C19   C  CR16   0  -0.264  -0.3674   4.2037   0.8398
 Z10  C18   C  CR16   0  -0.256  -0.9630   3.1583   0.1464
 Z10  C17   C  CR16   0  -0.315  -0.2250   2.0385  -0.2075
 Z10  C7    C  CR6    0  -0.306   1.4889  -0.5399  -0.0380
 Z10  C5    C  C      0   0.472   0.1980  -0.8361   0.6826
 Z10  O6    O  O      0  -0.497   0.1081  -0.6264   1.8874
 Z10  N4    N  NH1    0  -0.596  -0.7694  -1.3067  -0.0953
 Z10  C3    C  CH1    0  -0.282  -2.1341  -1.6143   0.3178
 Z10  C16   C  CH3    0  -0.665  -2.2338  -3.0856   0.7142
 Z10  B     B  B     -1   0.471  -3.1996  -1.1772  -0.8788
 Z10  O1    O  OB     0  -0.748  -2.9610  -1.9192  -2.1323
 Z10  O2    O  OB     0  -0.740  -4.5715  -1.5459  -0.4959
 Z10  OXT   O  OB     0  -0.734  -3.0210   0.2790  -1.0629
 Z10  H13   H  HCR6   0   0.281   4.1608  -2.2607  -1.2614
 Z10  H12   H  HCR6   0   0.271   4.9481   0.0664  -1.6657
 Z10  H11   H  HCR6   0   0.261   3.5346   1.9730  -1.0285
 Z10  H21   H  HCR6   0   0.254   2.7603   2.9413   1.1091
 Z10  H17   H  HCR6   0   0.286  -0.7218   1.2451  -0.7492
 Z10  H20   H  HCR6   0   0.256   1.4520   4.9276   1.7219
 Z10  H19   H  HCR6   0   0.255  -0.9459   5.0754   1.1175
 Z10  H18   H  HCR6   0   0.251  -2.0097   3.2077  -0.1248
 Z10  H4    H  HNH1   0   0.379  -0.5535  -1.4242  -1.0730
 Z10  H3    H  HCH1   0   0.180  -2.3272  -1.0117   1.2123
 Z10  H161  H  HCH3   0   0.202  -3.2344  -3.3163   1.0839
 Z10  H162  H  HCH3   0   0.202  -2.0480  -3.7356  -0.1437
 Z10  H163  H  HCH3   0   0.204  -1.5219  -3.3586   1.4979
 Z10  H1    H  H      0   0.421  -2.2663  -1.4960  -2.6406
 Z10  H2    H  H      0   0.419  -4.7036  -1.3541   0.4351
 Z10  HXT   H  H      0   0.421  -3.6238   0.5899  -1.7447

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
 Z10  F15  C14   single    1.344  0.020  1.344
 Z10  C14  C13   aromatic  1.380  0.020  1.380
 Z10  C14  C7    aromatic  1.384  0.020  1.384
 Z10  C13  C12   aromatic  1.386  0.020  1.386
 Z10  C12  C11   aromatic  1.387  0.020  1.387
 Z10  C11  C8    aromatic  1.395  0.020  1.395
 Z10  C8   C10   single    1.480  0.020  1.480
 Z10  C8   C7    aromatic  1.401  0.020  1.401
 Z10  C10  C21   aromatic  1.396  0.020  1.396
 Z10  C10  C17   aromatic  1.395  0.020  1.395
 Z10  C21  C20   aromatic  1.387  0.020  1.387
 Z10  C20  C19   aromatic  1.389  0.020  1.389
 Z10  C19  C18   aromatic  1.389  0.020  1.389
 Z10  C18  C17   aromatic  1.387  0.020  1.387
 Z10  C7   C5    single    1.508  0.020  1.508
 Z10  C5   O6    double    1.226  0.020  1.226
 Z10  C5   N4    single    1.328  0.020  1.328
 Z10  N4   C3    single    1.459  0.020  1.459
 Z10  C3   C16   single    1.527  0.020  1.527
 Z10  C3   B     single    1.661  0.020  1.661
 Z10  B    O1    single    1.476  0.020  1.476
 Z10  B    O2    single    1.471  0.020  1.471
 Z10  B    OXT   single    1.479  0.020  1.479
 Z10  C13  H13   single    0.930  0.020  1.080
 Z10  C12  H12   single    0.930  0.020  1.080
 Z10  C11  H11   single    0.930  0.020  1.080
 Z10  C21  H21   single    0.930  0.020  1.080
 Z10  C17  H17   single    0.930  0.020  1.080
 Z10  C20  H20   single    0.930  0.020  1.080
 Z10  C19  H19   single    0.930  0.020  1.080
 Z10  C18  H18   single    0.930  0.020  1.080
 Z10  N4   H4    single    0.860  0.020  1.020
 Z10  C3   H3    single    0.970  0.020  1.090
 Z10  C16  H161  single    0.970  0.020  1.090
 Z10  C16  H162  single    0.970  0.020  1.090
 Z10  C16  H163  single    0.970  0.020  1.090
 Z10  O1   H1    single    0.850  0.020  0.980
 Z10  O2   H2    single    0.850  0.020  0.980
 Z10  OXT  HXT   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
 Z10  C7    C14  C13   123.31  3.000
 Z10  C7    C14  F15   118.15  3.000
 Z10  C13   C14  F15   118.53  3.000
 Z10  H13   C13  C12   121.62  3.000
 Z10  H13   C13  C14   120.51  3.000
 Z10  C12   C13  C14   117.87  3.000
 Z10  H12   C12  C11   119.89  3.000
 Z10  H12   C12  C13   119.72  3.000
 Z10  C11   C12  C13   120.39  3.000
 Z10  H11   C11  C8    119.41  3.000
 Z10  H11   C11  C12   119.44  3.000
 Z10  C8    C11  C12   121.14  3.000
 Z10  C7    C8   C10   121.74  3.000
 Z10  C7    C8   C11   118.90  3.000
 Z10  C10   C8   C11   119.36  3.000
 Z10  C17   C10  C21   118.70  3.000
 Z10  C17   C10  C8    121.58  3.000
 Z10  C21   C10  C8    119.70  3.000
 Z10  H21   C21  C20   119.46  3.000
 Z10  H21   C21  C10   119.77  3.000
 Z10  C20   C21  C10   120.76  3.000
 Z10  H20   C20  C19   120.19  3.000
 Z10  H20   C20  C21   119.68  3.000
 Z10  C19   C20  C21   120.13  3.000
 Z10  H19   C19  C18   120.34  3.000
 Z10  H19   C19  C20   120.18  3.000
 Z10  C18   C19  C20   119.48  3.000
 Z10  H18   C18  C17   119.17  3.000
 Z10  H18   C18  C19   120.37  3.000
 Z10  C17   C18  C19   120.46  3.000
 Z10  H17   C17  C18   118.40  3.000
 Z10  H17   C17  C10   121.13  3.000
 Z10  C18   C17  C10   120.47  3.000
 Z10  C5    C7   C8    122.09  3.000
 Z10  C5    C7   C14   119.32  3.000
 Z10  C8    C7   C14   118.38  3.000
 Z10  N4    C5   O6    125.65  3.000
 Z10  N4    C5   C7    114.42  3.000
 Z10  O6    C5   C7    119.92  3.000
 Z10  H4    N4   C3    116.77  3.000
 Z10  H4    N4   C5    116.97  3.000
 Z10  C3    N4   C5    126.20  3.000
 Z10  H3    C3   B     109.30  3.000
 Z10  H3    C3   C16   107.84  3.000
 Z10  B     C3   C16   113.50  3.000
 Z10  H3    C3   N4    106.26  3.000
 Z10  B     C3   N4    109.92  3.000
 Z10  C16   C3   N4    109.74  3.000
 Z10  H163  C16  H162  107.68  3.000
 Z10  H163  C16  H161  107.54  3.000
 Z10  H162  C16  H161  107.23  3.000
 Z10  H163  C16  C3    112.59  3.000
 Z10  H162  C16  C3    111.00  3.000
 Z10  H161  C16  C3    110.57  3.000
 Z10  OXT   B    O2    113.07  3.000
 Z10  OXT   B    O1    111.70  3.000
 Z10  O2    B    O1    104.23  3.000
 Z10  OXT   B    C3    105.75  3.000
 Z10  O2    B    C3    110.17  3.000
 Z10  O1    B    C3    112.08  3.000
 Z10  H1    O1   B     110.20  3.000
 Z10  H2    O2   B     109.31  3.000
 Z10  HXT   OXT  B     109.33  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
 Z10  CONST_01  C11  C12  C13  C14    0.00   0.0  0
 Z10  CONST_02  C11  C8   C7   C14    0.00   0.0  0
 Z10  CONST_03  C10  C8   C7   C14  180.00   0.0  0
 Z10  CONST_04  C8   C7   C14  C13    0.00   0.0  0
 Z10  CONST_05  C8   C11  C12  C13    0.00   0.0  0
 Z10  CONST_06  C7   C14  C13  C12    0.00   0.0  0
 Z10  CONST_07  C10  C8   C11  C12  180.00   0.0  0
 Z10  CONST_08  C7   C8   C11  C12    0.00   0.0  0
 Z10  CONST_11  C20  C21  C10  C8   180.00   0.0  0
 Z10  CONST_12  C18  C17  C10  C8   180.00   0.0  0
 Z10  CONST_13  C19  C20  C21  C10    0.00   0.0  0
 Z10  CONST_14  C19  C18  C17  C10    0.00   0.0  0
 Z10  CONST_16  C18  C17  C10  C21    0.00   0.0  0
 Z10  CONST_17  C18  C19  C20  C21    0.00   0.0  0
 Z10  CONST_18  C17  C10  C21  C20    0.00   0.0  0
 Z10  CONST_19  C17  C18  C19  C20    0.00   0.0  0
 Z10  CONST_21  C12  C13  C14  F15  180.00   0.0  0
 Z10  CONST_22  C8   C7   C14  F15  180.00   0.0  0
 Z10  CONST_23  C5   C7   C14  C13  180.00   0.0  0
 Z10  CONST_24  C5   C7   C8   C11  180.00   0.0  0
 Z10  CONST_25  C5   C7   C8   C10    0.00   0.0  0
 Z10  CONST_26  H12  C12  C13  C14  180.00   0.0  0
 Z10  CONST_27  H11  C11  C12  C13  180.00   0.0  0
 Z10  CONST_28  H13  C13  C12  C11  180.00   0.0  0
 Z10  CONST_29  H21  C21  C10  C8     0.00   0.0  0
 Z10  CONST_30  H17  C17  C10  C8     0.00   0.0  0
 Z10  CONST_31  H20  C20  C21  C10  180.00   0.0  0
 Z10  CONST_32  H18  C18  C17  C10  180.00   0.0  0
 Z10  CONST_33  H19  C19  C20  C21  180.00   0.0  0
 Z10  CONST_34  C3   N4   C5   C7   180.00   0.0  0
 Z10  CONST_35  H4   N4   C5   C7     0.00   0.0  0
 Z10  CONST_36  C3   N4   C5   O6     0.00   0.0  0
 Z10  Var_01    O6   C5   C7   C14  104.82  30.0  2

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
 Z10  chir_01  C3  N4  C16  B  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
 Z10  plan-1  F15  0.020
 Z10  plan-1  C14  0.020
 Z10  plan-1  C13  0.020
 Z10  plan-1  C12  0.020
 Z10  plan-1  C11  0.020
 Z10  plan-1  C8   0.020
 Z10  plan-1  C10  0.020
 Z10  plan-1  C7   0.020
 Z10  plan-1  C5   0.020
 Z10  plan-1  H13  0.020
 Z10  plan-1  H12  0.020
 Z10  plan-1  H11  0.020
 Z10  plan-2  C8   0.020
 Z10  plan-2  C10  0.020
 Z10  plan-2  C21  0.020
 Z10  plan-2  C20  0.020
 Z10  plan-2  C19  0.020
 Z10  plan-2  C18  0.020
 Z10  plan-2  C17  0.020
 Z10  plan-2  H21  0.020
 Z10  plan-2  H17  0.020
 Z10  plan-2  H20  0.020
 Z10  plan-2  H19  0.020
 Z10  plan-2  H18  0.020
 Z10  plan-3  C7   0.020
 Z10  plan-3  C5   0.020
 Z10  plan-3  O6   0.020
 Z10  plan-3  N4   0.020
 Z10  plan-3  C3   0.020
 Z10  plan-3  H4   0.020

