# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:08:03 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)c2cccc(c2)c3ccc(F)cc3)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 JN2  JN2  3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide  ligand  47  27  .  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_JN2
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
 JN2  C2   C  C     0   0.557  -0.3042   0.3869   0.5363
 JN2  C4   C  CR16  0  -0.305   0.9392   2.2266  -0.6915
 JN2  C3   C  CR6   0  -0.021   0.9362   1.0028  -0.0262
 JN2  C9   C  CR6   0   0.075   4.5954   0.0749  -0.1591
 JN2  C8   C  CR16  0  -0.337   2.1339   0.3173   0.1517
 JN2  C13  C  CR16  0  -0.397   6.7466  -0.6564  -1.0038
 JN2  C14  C  CR16  0  -0.289   5.5621   0.0459  -1.1650
 JN2  C7   C  CR6   0   0.114   3.3341   0.8207  -0.3425
 JN2  C6   C  CR16  0  -0.304   3.3160   2.0454  -1.0122
 JN2  C10  C  CR16  0  -0.290   4.8500  -0.6204   1.0237
 JN2  C12  C  CR6   0   0.518   6.9581  -1.3334   0.1815
 JN2  C11  C  CR16  0  -0.397   6.0283  -1.3278   1.2031
 JN2  C5   C  CR16  0  -0.225   2.1300   2.7418  -1.1804
 JN2  C2'  C  CH1   0  -0.027  -3.8046   1.3886   0.3422
 JN2  C3'  C  CH1   0  -0.005  -5.1563   0.7820   0.6909
 JN2  O3'  O  OH1   0  -0.671  -6.2059   1.7080   0.5491
 JN2  C4'  C  CH1   0   0.033  -5.4593  -0.4010  -0.2211
 JN2  O4'  O  OH1   0  -0.671  -6.6302  -1.0677   0.1791
 JN2  C5'  C  CH1   0  -0.013  -4.3020  -1.4005  -0.1700
 JN2  C6'  C  CH2   0  -0.157  -4.5023  -2.5412  -1.1450
 JN2  O6'  O  OH1   0  -0.670  -3.4528  -3.4659  -0.9895
 JN2  O5'  O  O2    0  -0.488  -3.0937  -0.7501  -0.5082
 JN2  C1'  C  CH1   0   0.204  -2.7443   0.2858   0.3782
 JN2  N1   N  NH1   0  -0.712  -1.4731   0.8036  -0.0115
 JN2  F15  F  F     0  -0.313   8.1008  -2.0175   0.3463
 JN2  O2   O  O     0  -0.467  -0.2517  -0.4299   1.4390
 JN2  H1   H  HCR6  0   0.260   0.0317   2.8037  -0.8141
 JN2  H2   H  HCR6  0   0.262   2.1230  -0.6368   0.6629
 JN2  H3   H  HCR6  0   0.283   7.4865  -0.6827  -1.7925
 JN2  H4   H  HCR6  0   0.267   5.3869   0.5611  -2.1009
 JN2  H5   H  HCR6  0   0.265   4.2390   2.4720  -1.3841
 JN2  H6   H  HCR6  0   0.269   4.1303  -0.5981   1.8319
 JN2  H7   H  HCR6  0   0.283   6.2212  -1.8587   2.1261
 JN2  H8   H  HCR6  0   0.269   2.1349   3.6990  -1.6844
 JN2  H10  H  HCH1  0   0.226  -3.8518   1.7942  -0.6808
 JN2  H11  H  HCH1  0   0.217  -5.1039   0.4055   1.7254
 JN2  H12  H  HOH1  0   0.457  -6.1238   2.3728   1.2398
 JN2  H13  H  HCH1  0   0.214  -5.5487  -0.0287  -1.2547
 JN2  H14  H  HOH1  0   0.455  -7.3649  -0.4484   0.1183
 JN2  H15  H  HCH1  0   0.224  -4.2373  -1.8071   0.8529
 JN2  H16  H  HCH2  0   0.214  -5.4772  -2.9962  -0.9450
 JN2  H17  H  HCH2  0   0.196  -4.5404  -2.1325  -2.1647
 JN2  H18  H  HOH1  0   0.457  -3.6392  -4.2204  -1.5552
 JN2  H19  H  HCH1  0   0.235  -2.6600  -0.0962   1.4028
 JN2  H20  H  HNH1  0   0.411  -1.4426   1.3289  -0.8731
 JN2  O2'  O  OH1   0  -0.662  -3.5290   2.3947   1.2824
 JN2  H9   H  HOH1  0   0.456  -2.7623   2.8943   0.9847

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
 JN2  O3'  C3'  single    1.407  0.020  1.407
 JN2  O4'  C4'  single    1.406  0.020  1.406
 JN2  C3'  C4'  single    1.524  0.020  1.524
 JN2  C3'  C2'  single    1.522  0.020  1.522
 JN2  C4'  C5'  single    1.530  0.020  1.530
 JN2  O2'  C2'  single    1.404  0.020  1.404
 JN2  C2'  C1'  single    1.530  0.020  1.530
 JN2  O6'  C6'  single    1.407  0.020  1.407
 JN2  C5'  C6'  single    1.514  0.020  1.514
 JN2  C5'  O5'  single    1.413  0.020  1.413
 JN2  C1'  O5'  single    1.407  0.020  1.407
 JN2  C1'  N1   single    1.427  0.020  1.427
 JN2  N1   C2   single    1.356  0.020  1.356
 JN2  C2   O2   double    1.219  0.020  1.219
 JN2  C2   C3   single    1.495  0.020  1.495
 JN2  C4   C3   aromatic  1.393  0.020  1.393
 JN2  C4   C5   aromatic  1.387  0.020  1.387
 JN2  C3   C8   aromatic  1.391  0.020  1.391
 JN2  C5   C6   aromatic  1.386  0.020  1.386
 JN2  C8   C7   aromatic  1.392  0.020  1.392
 JN2  C6   C7   aromatic  1.396  0.020  1.396
 JN2  C7   C9   single    1.477  0.020  1.477
 JN2  C9   C14  aromatic  1.395  0.020  1.395
 JN2  C9   C10  aromatic  1.396  0.020  1.396
 JN2  C14  C13  aromatic  1.386  0.020  1.386
 JN2  C10  C11  aromatic  1.386  0.020  1.386
 JN2  C13  C12  aromatic  1.381  0.020  1.381
 JN2  C11  C12  aromatic  1.381  0.020  1.381
 JN2  C12  F15  single    1.342  0.020  1.342
 JN2  C4   H1   single    0.930  0.020  1.080
 JN2  C8   H2   single    0.930  0.020  1.080
 JN2  C13  H3   single    0.930  0.020  1.080
 JN2  C14  H4   single    0.930  0.020  1.080
 JN2  C6   H5   single    0.930  0.020  1.080
 JN2  C10  H6   single    0.930  0.020  1.080
 JN2  C11  H7   single    0.930  0.020  1.080
 JN2  C5   H8   single    0.930  0.020  1.080
 JN2  O2'  H9   single    0.850  0.020  0.980
 JN2  C2'  H10  single    0.970  0.020  1.090
 JN2  C3'  H11  single    0.970  0.020  1.090
 JN2  O3'  H12  single    0.850  0.020  0.980
 JN2  C4'  H13  single    0.970  0.020  1.090
 JN2  O4'  H14  single    0.850  0.020  0.980
 JN2  C5'  H15  single    0.970  0.020  1.090
 JN2  C6'  H16  single    0.970  0.020  1.090
 JN2  C6'  H17  single    0.970  0.020  1.090
 JN2  O6'  H18  single    0.850  0.020  0.980
 JN2  C1'  H19  single    0.970  0.020  1.090
 JN2  N1   H20  single    0.860  0.020  1.020

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
 JN2  O2   C2   N1   122.83  3.000
 JN2  O2   C2   C3   121.28  3.000
 JN2  N1   C2   C3   115.89  3.000
 JN2  H1   C4   C5   118.82  3.000
 JN2  H1   C4   C3   121.38  3.000
 JN2  C5   C4   C3   119.78  3.000
 JN2  C8   C3   C4   119.48  3.000
 JN2  C8   C3   C2   117.60  3.000
 JN2  C4   C3   C2   122.92  3.000
 JN2  C10  C9   C7   120.85  3.000
 JN2  C10  C9   C14  118.31  3.000
 JN2  C7   C9   C14  120.84  3.000
 JN2  H2   C8   C7   119.67  3.000
 JN2  H2   C8   C3   119.08  3.000
 JN2  C7   C8   C3   121.24  3.000
 JN2  H3   C13  C12  120.60  3.000
 JN2  H3   C13  C14  120.79  3.000
 JN2  C12  C13  C14  118.61  3.000
 JN2  H4   C14  C13  118.67  3.000
 JN2  H4   C14  C9   120.08  3.000
 JN2  C13  C14  C9   121.24  3.000
 JN2  C6   C7   C8   118.45  3.000
 JN2  C6   C7   C9   120.91  3.000
 JN2  C8   C7   C9   120.64  3.000
 JN2  H5   C6   C5   119.34  3.000
 JN2  H5   C6   C7   119.96  3.000
 JN2  C5   C6   C7   120.68  3.000
 JN2  H6   C10  C11  118.63  3.000
 JN2  H6   C10  C9   120.09  3.000
 JN2  C11  C10  C9   121.27  3.000
 JN2  F15  C12  C11  118.97  3.000
 JN2  F15  C12  C13  119.06  3.000
 JN2  C11  C12  C13  121.98  3.000
 JN2  H7   C11  C12  120.59  3.000
 JN2  H7   C11  C10  120.82  3.000
 JN2  C12  C11  C10  118.59  3.000
 JN2  H8   C5   C6   119.83  3.000
 JN2  H8   C5   C4   119.79  3.000
 JN2  C6   C5   C4   120.37  3.000
 JN2  H10  C2'  C1'  108.47  3.000
 JN2  H10  C2'  C3'  108.76  3.000
 JN2  C1'  C2'  C3'  108.83  3.000
 JN2  H10  C2'  O2'  111.50  3.000
 JN2  C1'  C2'  O2'  111.38  3.000
 JN2  C3'  C2'  O2'  107.84  3.000
 JN2  H11  C3'  C4'  107.82  3.000
 JN2  H11  C3'  O3'  110.79  3.000
 JN2  C4'  C3'  O3'  107.59  3.000
 JN2  H11  C3'  C2'  108.00  3.000
 JN2  C4'  C3'  C2'  110.41  3.000
 JN2  O3'  C3'  C2'  112.15  3.000
 JN2  H12  O3'  C3'  108.59  3.000
 JN2  H13  C4'  C5'  108.26  3.000
 JN2  H13  C4'  O4'  111.08  3.000
 JN2  C5'  C4'  O4'  108.10  3.000
 JN2  H13  C4'  C3'  108.37  3.000
 JN2  C5'  C4'  C3'  109.67  3.000
 JN2  O4'  C4'  C3'  111.31  3.000
 JN2  H14  O4'  C4'  108.21  3.000
 JN2  H15  C5'  O5'  109.98  3.000
 JN2  H15  C5'  C6'  109.11  3.000
 JN2  O5'  C5'  C6'  107.80  3.000
 JN2  H15  C5'  C4'  108.44  3.000
 JN2  O5'  C5'  C4'  109.76  3.000
 JN2  C6'  C5'  C4'  111.75  3.000
 JN2  H17  C6'  H16  107.06  3.000
 JN2  H17  C6'  O6'  111.87  3.000
 JN2  H16  C6'  O6'  111.77  3.000
 JN2  H17  C6'  C5'  108.78  3.000
 JN2  H16  C6'  C5'  108.27  3.000
 JN2  O6'  C6'  C5'  108.98  3.000
 JN2  H18  O6'  C6'  107.83  3.000
 JN2  C1'  O5'  C5'  113.59  3.000
 JN2  H19  C1'  N1   108.24  3.000
 JN2  H19  C1'  O5'  110.55  3.000
 JN2  N1   C1'  O5'  108.44  3.000
 JN2  H19  C1'  C2'  109.04  3.000
 JN2  N1   C1'  C2'  110.45  3.000
 JN2  O5'  C1'  C2'  110.10  3.000
 JN2  H20  N1   C1'  116.66  3.000
 JN2  H20  N1   C2   118.58  3.000
 JN2  C1'  N1   C2   123.10  3.000
 JN2  H9   O2'  C2'  108.73  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
 JN2  CONST_01  C7   C8   C3   C4     0.00   0.0  0
 JN2  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 JN2  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 JN2  CONST_04  C6   C7   C8   C3     0.00   0.0  0
 JN2  CONST_05  C9   C7   C8   C3   180.00   0.0  0
 JN2  CONST_06  C5   C6   C7   C9   180.00   0.0  0
 JN2  CONST_07  C12  C13  C14  C9     0.00   0.0  0
 JN2  CONST_08  C12  C11  C10  C9     0.00   0.0  0
 JN2  CONST_09  C5   C4   C3   C8     0.00   0.0  0
 JN2  CONST_10  C5   C6   C7   C8     0.00   0.0  0
 JN2  CONST_13  C7   C9   C14  C13  180.00   0.0  0
 JN2  CONST_14  C10  C9   C14  C13    0.00   0.0  0
 JN2  CONST_15  C10  C11  C12  C13    0.00   0.0  0
 JN2  CONST_17  C11  C10  C9   C14    0.00   0.0  0
 JN2  CONST_18  C11  C12  C13  C14    0.00   0.0  0
 JN2  CONST_19  C11  C10  C9   C7   180.00   0.0  0
 JN2  CONST_21  C5   C4   C3   C2   180.00   0.0  0
 JN2  CONST_22  C7   C8   C3   C2   180.00   0.0  0
 JN2  CONST_23  F15  C12  C13  C14  180.00   0.0  0
 JN2  CONST_24  F15  C12  C11  C10  180.00   0.0  0
 JN2  CONST_25  H2   C8   C3   C4   180.00   0.0  0
 JN2  CONST_26  H5   C6   C5   C4   180.00   0.0  0
 JN2  CONST_27  H8   C5   C4   C3   180.00   0.0  0
 JN2  CONST_28  H3   C13  C14  C9   180.00   0.0  0
 JN2  CONST_29  H7   C11  C10  C9   180.00   0.0  0
 JN2  CONST_30  H1   C4   C3   C8   180.00   0.0  0
 JN2  CONST_31  H6   C10  C9   C14  180.00   0.0  0
 JN2  CONST_32  H4   C14  C9   C7     0.00   0.0  0
 JN2  CONST_33  C1'  N1   C2   C3   180.00   0.0  0
 JN2  CONST_34  O2   C2   N1   C1'    0.00   0.0  0
 JN2  CONST_35  H20  N1   C2   C3     0.00   0.0  0
 JN2  Var_01    N1   C2   C3   C4    22.41  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
 JN2  chir_01  C2'  C3'  O2'  C1'  negativ
 JN2  chir_02  C3'  O3'  C2'  C4'  positiv
 JN2  chir_03  C4'  O4'  C5'  C3'  positiv
 JN2  chir_04  C5'  O5'  C4'  C6'  negativ
 JN2  chir_05  C1'  O5'  N1   C2'  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
 JN2  plan-1  C2   0.020
 JN2  plan-1  C4   0.020
 JN2  plan-1  C3   0.020
 JN2  plan-1  C9   0.020
 JN2  plan-1  C8   0.020
 JN2  plan-1  C7   0.020
 JN2  plan-1  C6   0.020
 JN2  plan-1  C5   0.020
 JN2  plan-1  H1   0.020
 JN2  plan-1  H2   0.020
 JN2  plan-1  H5   0.020
 JN2  plan-1  H8   0.020
 JN2  plan-2  C9   0.020
 JN2  plan-2  C13  0.020
 JN2  plan-2  C14  0.020
 JN2  plan-2  C7   0.020
 JN2  plan-2  C10  0.020
 JN2  plan-2  C12  0.020
 JN2  plan-2  C11  0.020
 JN2  plan-2  F15  0.020
 JN2  plan-2  H3   0.020
 JN2  plan-2  H4   0.020
 JN2  plan-2  H6   0.020
 JN2  plan-2  H7   0.020
 JN2  plan-3  C2   0.020
 JN2  plan-3  C3   0.020
 JN2  plan-3  C1'  0.020
 JN2  plan-3  N1   0.020
 JN2  plan-3  O2   0.020
 JN2  plan-3  H20  0.020

