# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 15:50:44 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (1R,2R,3R)-2-[4-(5-fluoropyrimidin-2-yl)phenyl]-N-hydroxy-3-phenylcyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@@H]1[C@@H]([C@H]1c2ccc(cc2)c3ncc(F)cn3)c4ccccc4
#
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
 9F4  9F4  (1R,2R,3R)-2-[4-(5-fluoropyrimidin-2-yl)phenyl]-N-hydroxy-3-phenylcyclopropanecarboxamide  ligand  42  26  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9F4
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
 9F4  F26  F  F     0  -0.288  -8.2210  -0.1721   0.2198
 9F4  C23  C  CR6   0   0.394  -6.8921  -0.1259   0.1306
 9F4  C22  C  CR16  0  -0.147  -6.1332   0.4209   1.1454
 9F4  N21  N  N     0  -0.408  -4.8153   0.4591   1.0521
 9F4  C24  C  CR16  0  -0.148  -6.2390  -0.6249  -0.9782
 9F4  N25  N  N     0  -0.408  -4.9204  -0.5798  -1.0576
 9F4  C20  C  CR6   0   0.404  -4.2489  -0.0423  -0.0424
 9F4  C12  C  CR6   0  -0.024  -2.7767  -0.0025  -0.1348
 9F4  C11  C  CR16  0  -0.265  -2.1172  -0.4937  -1.2602
 9F4  C10  C  CR16  0  -0.307  -0.7352  -0.4583  -1.3389
 9F4  C13  C  CR16  0  -0.258  -2.0098   0.5255   0.9051
 9F4  C14  C  CR16  0  -0.342  -0.6296   0.5571   0.8225
 9F4  C9   C  CR6   0   0.261   0.0339   0.0639  -0.3009
 9F4  C8   C  CH1   0  -0.393   1.5101   0.0677  -0.4210
 9F4  C15  C  CH1   0  -0.406   2.3348   1.1851   0.1650
 9F4  C16  C  C     0   0.577   3.4967   1.6858  -0.6207
 9F4  N18  N  NH1   0  -0.392   3.8995   2.9120  -0.2230
 9F4  O19  O  OH1   0  -0.542   5.0809   3.4079  -0.6873
 9F4  O17  O  O     0  -0.465   4.0156   1.0703  -1.5329
 9F4  C7   C  CH1   0  -0.252   2.3922  -0.2025   0.7543
 9F4  C6   C  CR6   0   0.126   3.6081  -1.0559   0.6540
 9F4  C1   C  CR16  0  -0.296   4.7231  -0.7576   1.4345
 9F4  C5   C  CR16  0  -0.310   3.6430  -2.1781  -0.1655
 9F4  C4   C  CR16  0  -0.241   4.7731  -2.9847  -0.2125
 9F4  C3   C  CR16  0  -0.269   5.8826  -2.6769   0.5626
 9F4  C2   C  CR16  0  -0.242   5.8538  -1.5601   1.3893
 9F4  H22  H  HCR6  0   0.299  -6.5947   0.8301   2.0374
 9F4  H24  H  HCR6  0   0.299  -6.7865  -1.0642  -1.8051
 9F4  H11  H  HCR6  0   0.255  -2.6860  -0.9077  -2.0813
 9F4  H13  H  HCR6  0   0.257  -2.4973   0.9156   1.7877
 9F4  H10  H  HCR6  0   0.257  -0.2452  -0.8471  -2.2232
 9F4  H14  H  HCR6  0   0.255  -0.0719   0.9751   1.6522
 9F4  H8   H  HCH1  0   0.276   1.8779  -0.3040  -1.3720
 9F4  H15  H  HCH1  0   0.293   1.8080   1.9250   0.7585
 9F4  H7   H  HCH1  0   0.298   1.8791  -0.2774   1.7094
 9F4  H18  H  HNH1  0   0.415   3.5980   3.3104   0.6553
 9F4  H1   H  HCR6  0   0.248   4.7058   0.1118   2.0813
 9F4  H5   H  HCR6  0   0.246   2.7819  -2.4265  -0.7743
 9F4  H2   H  HCR6  0   0.254   6.7134  -1.3136   1.9994
 9F4  H4   H  HCR6  0   0.255   4.7855  -3.8548  -0.8563
 9F4  H3   H  HCR6  0   0.254   6.7644  -3.3034   0.5241
 9F4  H19  H  HOH1  0   0.478   4.8516   4.0434  -1.3774

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
 9F4  F26  C23  single    1.333  0.020  1.333
 9F4  C23  C22  aromatic  1.380  0.020  1.380
 9F4  C23  C24  aromatic  1.380  0.020  1.380
 9F4  C22  N21  aromatic  1.322  0.020  1.322
 9F4  N21  C20  aromatic  1.330  0.020  1.330
 9F4  C24  N25  aromatic  1.322  0.020  1.322
 9F4  N25  C20  aromatic  1.331  0.020  1.331
 9F4  C20  C12  single    1.476  0.020  1.476
 9F4  C12  C11  aromatic  1.394  0.020  1.394
 9F4  C12  C13  aromatic  1.396  0.020  1.396
 9F4  C11  C10  aromatic  1.385  0.020  1.385
 9F4  C10  C9   aromatic  1.393  0.020  1.393
 9F4  C13  C14  aromatic  1.383  0.020  1.383
 9F4  C14  C9   aromatic  1.395  0.020  1.395
 9F4  C9   C8   single    1.481  0.020  1.481
 9F4  C8   C15  single    1.507  0.020  1.507
 9F4  C8   C7   single    1.494  0.020  1.494
 9F4  C15  C16  single    1.489  0.020  1.489
 9F4  C15  C7   single    1.509  0.020  1.509
 9F4  C16  N18  single    1.351  0.020  1.351
 9F4  C16  O17  double    1.217  0.020  1.217
 9F4  N18  O19  single    1.363  0.020  1.363
 9F4  C7   C6   single    1.489  0.020  1.489
 9F4  C6   C1   aromatic  1.393  0.020  1.393
 9F4  C6   C5   aromatic  1.390  0.020  1.390
 9F4  C1   C2   aromatic  1.387  0.020  1.387
 9F4  C5   C4   aromatic  1.389  0.020  1.389
 9F4  C4   C3   aromatic  1.388  0.020  1.388
 9F4  C3   C2   aromatic  1.390  0.020  1.390
 9F4  O19  H19  single    0.850  0.020  0.980
 9F4  C22  H22  single    0.930  0.020  1.080
 9F4  C24  H24  single    0.930  0.020  1.080
 9F4  C11  H11  single    0.930  0.020  1.080
 9F4  C13  H13  single    0.930  0.020  1.080
 9F4  C10  H10  single    0.930  0.020  1.080
 9F4  C14  H14  single    0.930  0.020  1.080
 9F4  C8   H8   single    0.970  0.020  1.090
 9F4  C15  H15  single    0.970  0.020  1.090
 9F4  C7   H7   single    0.970  0.020  1.090
 9F4  N18  H18  single    0.890  0.020  1.040
 9F4  C1   H1   single    0.930  0.020  1.080
 9F4  C5   H5   single    0.930  0.020  1.080
 9F4  C2   H2   single    0.930  0.020  1.080
 9F4  C4   H4   single    0.930  0.020  1.080
 9F4  C3   H3   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
 9F4  C24  C23  C22  118.28  3.000
 9F4  C24  C23  F26  120.87  3.000
 9F4  C22  C23  F26  120.85  3.000
 9F4  H22  C22  N21  118.12  3.000
 9F4  H22  C22  C23  121.36  3.000
 9F4  N21  C22  C23  120.52  3.000
 9F4  C20  N21  C22  118.14  3.000
 9F4  H24  C24  N25  118.14  3.000
 9F4  H24  C24  C23  121.34  3.000
 9F4  N25  C24  C23  120.53  3.000
 9F4  C20  N25  C24  118.12  3.000
 9F4  C12  C20  N25  117.81  3.000
 9F4  C12  C20  N21  117.78  3.000
 9F4  N25  C20  N21  124.41  3.000
 9F4  C13  C12  C11  118.35  3.000
 9F4  C13  C12  C20  120.78  3.000
 9F4  C11  C12  C20  120.87  3.000
 9F4  H11  C11  C10  119.45  3.000
 9F4  H11  C11  C12  119.94  3.000
 9F4  C10  C11  C12  120.60  3.000
 9F4  H10  C10  C9   119.54  3.000
 9F4  H10  C10  C11  119.25  3.000
 9F4  C9   C10  C11  121.20  3.000
 9F4  H13  C13  C14  119.38  3.000
 9F4  H13  C13  C12  119.80  3.000
 9F4  C14  C13  C12  120.83  3.000
 9F4  H14  C14  C9   120.55  3.000
 9F4  H14  C14  C13  118.47  3.000
 9F4  C9   C14  C13  120.98  3.000
 9F4  C8   C9   C14  122.58  3.000
 9F4  C8   C9   C10  119.38  3.000
 9F4  C14  C9   C10  118.03  3.000
 9F4  H8   C8   C7   115.29  3.000
 9F4  H8   C8   C15  114.15  3.000
 9F4  C7   C8   C15   60.35  3.000
 9F4  H8   C8   C9   114.08  3.000
 9F4  C7   C8   C9   121.61  3.000
 9F4  C15  C8   C9   121.04  3.000
 9F4  H15  C15  C7   115.59  3.000
 9F4  H15  C15  C16  115.98  3.000
 9F4  C7   C15  C16  119.06  3.000
 9F4  H15  C15  C8   116.91  3.000
 9F4  C7   C15  C8    59.39  3.000
 9F4  C16  C15  C8   118.10  3.000
 9F4  O17  C16  N18  123.57  3.000
 9F4  O17  C16  C15  123.93  3.000
 9F4  N18  C16  C15  112.49  3.000
 9F4  H18  N18  O19  114.29  3.000
 9F4  H18  N18  C16  121.67  3.000
 9F4  O19  N18  C16  119.24  3.000
 9F4  H19  O19  N18  106.09  3.000
 9F4  H7   C7   C6   113.91  3.000
 9F4  H7   C7   C15  112.88  3.000
 9F4  C6   C7   C15  122.13  3.000
 9F4  H7   C7   C8   115.15  3.000
 9F4  C6   C7   C8   122.19  3.000
 9F4  C15  C7   C8    60.26  3.000
 9F4  C5   C6   C1   118.88  3.000
 9F4  C5   C6   C7   121.53  3.000
 9F4  C1   C6   C7   119.54  3.000
 9F4  H1   C1   C2   119.77  3.000
 9F4  H1   C1   C6   119.56  3.000
 9F4  C2   C1   C6   120.67  3.000
 9F4  H5   C5   C4   119.63  3.000
 9F4  H5   C5   C6   119.76  3.000
 9F4  C4   C5   C6   120.61  3.000
 9F4  H4   C4   C3   120.08  3.000
 9F4  H4   C4   C5   119.75  3.000
 9F4  C3   C4   C5   120.17  3.000
 9F4  H3   C3   C2   120.21  3.000
 9F4  H3   C3   C4   120.20  3.000
 9F4  C2   C3   C4   119.59  3.000
 9F4  H2   C2   C3   120.11  3.000
 9F4  H2   C2   C1   119.81  3.000
 9F4  C3   C2   C1   120.08  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
 9F4  CONST_01  C20  N21  C22  C23    0.00   0.0  0
 9F4  CONST_02  C20  N25  C24  C23    0.00   0.0  0
 9F4  CONST_03  N25  C24  C23  C22    0.00   0.0  0
 9F4  CONST_04  N25  C20  N21  C22    0.00   0.0  0
 9F4  CONST_05  C12  C20  N21  C22  180.00   0.0  0
 9F4  CONST_06  C24  C23  C22  N21    0.00   0.0  0
 9F4  CONST_07  C24  N25  C20  N21    0.00   0.0  0
 9F4  CONST_08  C11  C12  C20  N21  180.00   0.0  0
 9F4  CONST_09  C13  C12  C20  N21    0.00   0.0  0
 9F4  CONST_10  C12  C20  N25  C24  180.00   0.0  0
 9F4  CONST_11  C11  C12  C20  N25    0.00   0.0  0
 9F4  CONST_12  C13  C12  C20  N25  180.00   0.0  0
 9F4  CONST_13  C10  C11  C12  C20  180.00   0.0  0
 9F4  CONST_14  C14  C13  C12  C20  180.00   0.0  0
 9F4  CONST_15  C9   C10  C11  C12    0.00   0.0  0
 9F4  CONST_16  C9   C14  C13  C12    0.00   0.0  0
 9F4  CONST_17  C14  C13  C12  C11    0.00   0.0  0
 9F4  CONST_18  C14  C9   C10  C11    0.00   0.0  0
 9F4  CONST_19  C13  C12  C11  C10    0.00   0.0  0
 9F4  CONST_20  C13  C14  C9   C10    0.00   0.0  0
 9F4  CONST_21  C3   C2   C1   C6     0.00   0.0  0
 9F4  CONST_22  C3   C4   C5   C6     0.00   0.0  0
 9F4  CONST_23  C4   C5   C6   C1     0.00   0.0  0
 9F4  CONST_24  C4   C3   C2   C1     0.00   0.0  0
 9F4  CONST_25  C2   C1   C6   C5     0.00   0.0  0
 9F4  CONST_26  C2   C3   C4   C5     0.00   0.0  0
 9F4  CONST_27  C8   C9   C10  C11  180.00   0.0  0
 9F4  CONST_28  C8   C9   C14  C13  180.00   0.0  0
 9F4  CONST_29  C2   C1   C6   C7   180.00   0.0  0
 9F4  CONST_30  C4   C5   C6   C7   180.00   0.0  0
 9F4  CONST_31  N21  C22  C23  F26  180.00   0.0  0
 9F4  CONST_32  N25  C24  C23  F26  180.00   0.0  0
 9F4  CONST_33  H24  C24  C23  C22  180.00   0.0  0
 9F4  CONST_34  H22  C22  C23  C24  180.00   0.0  0
 9F4  CONST_35  H11  C11  C12  C20    0.00   0.0  0
 9F4  CONST_36  H13  C13  C12  C20    0.00   0.0  0
 9F4  CONST_37  H10  C10  C11  C12  180.00   0.0  0
 9F4  CONST_38  H14  C14  C13  C12  180.00   0.0  0
 9F4  CONST_39  H1   C1   C6   C7     0.00   0.0  0
 9F4  CONST_40  H5   C5   C6   C7     0.00   0.0  0
 9F4  CONST_41  H2   C2   C1   C6   180.00   0.0  0
 9F4  CONST_42  H4   C4   C5   C6   180.00   0.0  0
 9F4  CONST_43  H3   C3   C2   C1   180.00   0.0  0
 9F4  CONST_44  O19  N18  C16  C15  180.00   0.0  0
 9F4  CONST_45  H18  N18  C16  C15    0.00   0.0  0
 9F4  CONST_46  O17  C16  N18  O19    0.00   0.0  0
 9F4  Var_01    C15  C8   C9   C10  145.65  30.0  2
 9F4  Var_02    C7   C15  C8   C9   111.18  30.0  1
 9F4  Var_03    C1   C6   C7   C8   146.18  30.0  2
 9F4  Var_04    N18  C16  C15  C8   160.98  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
 9F4  chir_01  C8   C9  C15  C7  both
 9F4  chir_02  C15  C7  C16  C8  both
 9F4  chir_03  C7   C8  C15  C6  both

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
 9F4  plan-1  F26  0.020
 9F4  plan-1  C23  0.020
 9F4  plan-1  C22  0.020
 9F4  plan-1  N21  0.020
 9F4  plan-1  C24  0.020
 9F4  plan-1  N25  0.020
 9F4  plan-1  C20  0.020
 9F4  plan-1  C12  0.020
 9F4  plan-1  H22  0.020
 9F4  plan-1  H24  0.020
 9F4  plan-2  C20  0.020
 9F4  plan-2  C12  0.020
 9F4  plan-2  C11  0.020
 9F4  plan-2  C10  0.020
 9F4  plan-2  C13  0.020
 9F4  plan-2  C14  0.020
 9F4  plan-2  C9   0.020
 9F4  plan-2  C8   0.020
 9F4  plan-2  H11  0.020
 9F4  plan-2  H13  0.020
 9F4  plan-2  H10  0.020
 9F4  plan-2  H14  0.020
 9F4  plan-3  C7   0.020
 9F4  plan-3  C6   0.020
 9F4  plan-3  C1   0.020
 9F4  plan-3  C5   0.020
 9F4  plan-3  C4   0.020
 9F4  plan-3  C3   0.020
 9F4  plan-3  C2   0.020
 9F4  plan-3  H1   0.020
 9F4  plan-3  H5   0.020
 9F4  plan-3  H2   0.020
 9F4  plan-3  H4   0.020
 9F4  plan-3  H3   0.020
 9F4  plan-4  C15  0.020
 9F4  plan-4  C16  0.020
 9F4  plan-4  N18  0.020
 9F4  plan-4  O19  0.020
 9F4  plan-4  O17  0.020
 9F4  plan-4  H18  0.020

