# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 03:40:24 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-[(1S,2R,3R,4R,5S)-2,3-dihydroxy-1-(hydroxymethyl)-6,8-dioxabicyclo[3.2.1]octan-4-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@]2(CO)CO[C@H]1O2
#
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
 ZPF  ZPF  'N-[(1S,2R,3R,4R,5S)-2,3-dihydroxy-1-(hydroxymethyl)-6,8-dioxabicyclo[3.2.1]octan-4-yl]acetamide (non-preferred name)'  ligand  31  16  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZPF
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
 ZPF  C4   C  CH1   0  -0.017   0.1927   1.2253   0.5520
 ZPF  C7   C  CH2   0  -0.175  -1.5951  -0.8774   1.4019
 ZPF  C6   C  CR5   0   0.068  -1.9215  -0.0855   0.1250
 ZPF  C9   C  CH2   0  -0.166  -3.3975  -0.0302  -0.2178
 ZPF  C8   C  CR15  0   0.238  -0.0184  -1.1397  -0.2210
 ZPF  O1   O  O     0  -0.497   3.3851  -0.0266  -1.5492
 ZPF  C2   C  C     0   0.509   3.3255  -0.2354  -0.3466
 ZPF  C1   C  CH3   0  -0.786   4.5383  -0.5791   0.4838
 ZPF  N    N  NH1   0  -0.628   2.1726  -0.1944   0.3525
 ZPF  C3   C  CH1   0  -0.092   0.8838   0.1006  -0.2168
 ZPF  O6   O  OH1   0  -0.663   0.8524   2.4340   0.2566
 ZPF  C5   C  CH1   0   0.051  -1.3032   1.3174   0.1872
 ZPF  O5   O  OH1   0  -0.670  -1.4750   1.9280  -1.0626
 ZPF  O4   O  OH1   0  -0.665  -3.9146  -1.3356  -0.2670
 ZPF  O3   O  O     0  -0.482  -1.2204  -0.8394  -0.8535
 ZPF  O2   O  O     0  -0.505  -0.3598  -1.5146   1.0949
 ZPF  H2   H  HCH1  0   0.241   0.2707   1.0106   1.6254
 ZPF  H9   H  HCH2  0   0.236  -1.4957  -0.2336   2.2802
 ZPF  H10  H  HCH2  0   0.249  -2.3532  -1.6324   1.6157
 ZPF  H11  H  HCH2  0   0.209  -3.8914   0.5803   0.5496
 ZPF  H12  H  HCH2  0   0.222  -3.5272   0.4896  -1.1733
 ZPF  H4   H  HCR5  0   0.262   0.4682  -1.9776  -0.7260
 ZPF  H5   H  HCH3  0   0.261   5.4467  -0.4439  -0.0973
 ZPF  H7   H  HCH3  0   0.261   4.5950   0.0404   1.3792
 ZPF  H6   H  HCH3  0   0.269   4.4872  -1.6190   0.8107
 ZPF  H8   H  HNH1  0   0.400   2.2102  -0.3911   1.3408
 ZPF  H1   H  HCH1  0   0.273   1.0379   0.4021  -1.2551
 ZPF  H15  H  HOH1  0   0.461   0.6875   3.0604   0.9689
 ZPF  H3   H  HCH1  0   0.226  -1.8133   1.8856   0.9822
 ZPF  H14  H  HOH1  0   0.449  -0.8593   2.6696  -1.1080
 ZPF  H13  H  HOH1  0   0.462  -4.8608  -1.2745  -0.4249

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
 ZPF  O1  C2   double  1.222  0.020  1.222
 ZPF  C1  C2   single  1.510  0.020  1.510
 ZPF  C2  N    single  1.349  0.020  1.349
 ZPF  N   C3   single  1.439  0.020  1.439
 ZPF  C3  C8   single  1.534  0.020  1.534
 ZPF  C3  C4   single  1.528  0.020  1.528
 ZPF  O6  C4   single  1.408  0.020  1.408
 ZPF  C8  O3   single  1.391  0.020  1.391
 ZPF  C8  O2   single  1.410  0.020  1.410
 ZPF  C4  C5   single  1.542  0.020  1.542
 ZPF  O5  C5   single  1.402  0.020  1.402
 ZPF  O3  C6   single  1.420  0.020  1.420
 ZPF  O2  C7   single  1.424  0.020  1.424
 ZPF  C5  C6   single  1.534  0.020  1.534
 ZPF  C6  C7   single  1.538  0.020  1.538
 ZPF  C6  C9   single  1.516  0.020  1.516
 ZPF  C9  O4   single  1.405  0.020  1.405
 ZPF  C4  H2   single  0.970  0.020  1.090
 ZPF  C7  H9   single  0.970  0.020  1.090
 ZPF  C7  H10  single  0.970  0.020  1.090
 ZPF  C9  H11  single  0.970  0.020  1.090
 ZPF  C9  H12  single  0.970  0.020  1.090
 ZPF  C8  H4   single  0.970  0.020  1.090
 ZPF  C1  H5   single  0.970  0.020  1.090
 ZPF  C1  H7   single  0.970  0.020  1.090
 ZPF  C1  H6   single  0.970  0.020  1.090
 ZPF  N   H8   single  0.860  0.020  1.020
 ZPF  C3  H1   single  0.970  0.020  1.090
 ZPF  O6  H15  single  0.850  0.020  0.980
 ZPF  C5  H3   single  0.970  0.020  1.090
 ZPF  O5  H14  single  0.850  0.020  0.980
 ZPF  O4  H13  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
 ZPF  H2   C4  C5   108.18  3.000
 ZPF  H2   C4  O6   109.87  3.000
 ZPF  C5   C4  O6   110.69  3.000
 ZPF  H2   C4  C3   108.42  3.000
 ZPF  C5   C4  C3   111.32  3.000
 ZPF  O6   C4  C3   108.32  3.000
 ZPF  H10  C7  H9   108.26  3.000
 ZPF  H10  C7  O2   109.60  3.000
 ZPF  H9   C7  O2   110.97  3.000
 ZPF  H10  C7  C6   111.81  3.000
 ZPF  H9   C7  C6   112.53  3.000
 ZPF  O2   C7  C6   103.63  3.000
 ZPF  O3   C6  C5   108.32  3.000
 ZPF  C5   C6  C9   111.60  3.000
 ZPF  O3   C6  C9   110.13  3.000
 ZPF  C9   C6  C7   114.40  3.000
 ZPF  C5   C6  C7   110.59  3.000
 ZPF  O3   C6  C7   101.19  3.000
 ZPF  H12  C9  H11  107.01  3.000
 ZPF  H12  C9  O4   111.51  3.000
 ZPF  H11  C9  O4   112.06  3.000
 ZPF  H12  C9  C6   109.25  3.000
 ZPF  H11  C9  C6   107.47  3.000
 ZPF  O4   C9  C6   109.41  3.000
 ZPF  H4   C8  O2   109.58  3.000
 ZPF  H4   C8  O3   109.89  3.000
 ZPF  O2   C8  O3   105.81  3.000
 ZPF  H4   C8  C3   111.07  3.000
 ZPF  O2   C8  C3   110.79  3.000
 ZPF  O3   C8  C3   109.57  3.000
 ZPF  N    C2  C1   114.11  3.000
 ZPF  N    C2  O1   123.13  3.000
 ZPF  C1   C2  O1   122.76  3.000
 ZPF  H6   C1  H7   107.33  3.000
 ZPF  H6   C1  H5   108.53  3.000
 ZPF  H7   C1  H5   108.96  3.000
 ZPF  H6   C1  C2   110.13  3.000
 ZPF  H7   C1  C2   111.36  3.000
 ZPF  H5   C1  C2   110.43  3.000
 ZPF  H8   N   C3   117.45  3.000
 ZPF  H8   N   C2   118.04  3.000
 ZPF  C3   N   C2   124.50  3.000
 ZPF  H1   C3  N    107.83  3.000
 ZPF  H1   C3  C8   107.68  3.000
 ZPF  N    C3  C8   111.23  3.000
 ZPF  H1   C3  C4   109.82  3.000
 ZPF  C8   C3  C4   109.31  3.000
 ZPF  N    C3  C4   110.90  3.000
 ZPF  H15  O6  C4   108.84  3.000
 ZPF  H3   C5  O5   111.21  3.000
 ZPF  H3   C5  C6   108.31  3.000
 ZPF  O5   C5  C6   108.23  3.000
 ZPF  H3   C5  C4   108.00  3.000
 ZPF  C6   C5  C4   110.23  3.000
 ZPF  O5   C5  C4   110.84  3.000
 ZPF  H14  O5  C5   107.37  3.000
 ZPF  H13  O4  C9   108.00  3.000
 ZPF  C8   O3  C6   103.17  3.000
 ZPF  C8   O2  C7   107.00  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
 ZPF  CONST_01  C3  N   C2  O1     0.00   0.0  0
 ZPF  CONST_02  C3  N   C2  C1   180.00   0.0  0
 ZPF  CONST_03  H8  N   C2  O1   180.00   0.0  0
 ZPF  Var_01    H9  C7  O2  C8  -121.48  30.0  3
 ZPF  Var_02    H5  C1  C2  O1     9.57  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
 ZPF  chir_01  C4  C3  O6  C5  negativ
 ZPF  chir_02  C6  C5  O3  C9  positiv
 ZPF  chir_03  C8  O2  O3  C3  negativ
 ZPF  chir_04  C3  N   C4  C8  positiv
 ZPF  chir_05  C5  O5  C6  C4  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
 ZPF  plan-1  O1  0.020
 ZPF  plan-1  C2  0.020
 ZPF  plan-1  C1  0.020
 ZPF  plan-1  N   0.020
 ZPF  plan-1  C3  0.020
 ZPF  plan-1  H8  0.020

