# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 03:35:46 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{R})-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@H](Oc2ccc(cc2)[N+]([O-])=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
 07Y  07Y  "(2S,3R,4R,5R)-2-(hydroxymethyl)-5-(4-nitrophenoxy)oxolane-3,4-diol"  saccharide  32  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_07Y
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
 07Y  C1   C  CR15   0   0.227  20.8713  -8.0789  28.0702
 07Y  C2   C  CR15   0  -0.038  22.1575  -8.1775  27.2481
 07Y  O2   O  OH1    0  -0.651  23.2681  -7.5097  27.7577
 07Y  C3   C  CR15   0  -0.021  21.6984  -7.5783  25.9251
 07Y  C4   C  CR15   0   0.019  20.2836  -8.1432  25.8213
 07Y  O4   O  O      0  -0.486  19.8438  -8.3301  27.1713
 07Y  C5   C  CH2    0  -0.172  19.2943  -7.3231  25.0282
 07Y  O5   O  OH1    0  -0.658  19.2398  -6.0062  25.5167
 07Y  C18  C  CR16   0  -0.338  18.7267  -5.6793  28.9984
 07Y  C19  C  CR16   0  -0.259  17.7034  -5.3418  29.8633
 07Y  C20  C  CR6    0   0.239  17.7097  -5.8572  31.1524
 07Y  N11  N  N      1   0.327  16.6398  -5.4990  32.0644
 07Y  O18  O  O     -1  -0.379  15.7997  -4.7202  31.6767
 07Y  O17  O  O      0  -0.379  16.6414  -5.9933  33.1679
 07Y  C21  C  CR16   0  -0.258  18.7217  -6.7015  31.5892
 07Y  C22  C  CR16   0  -0.325  19.7491  -7.0235  30.7230
 07Y  C17  C  CR6    0   0.392  19.7587  -6.5070  29.4291
 07Y  O1   O  O2     0  -0.497  20.7872  -6.7630  28.5888
 07Y  O3   O  OH1    0  -0.661  22.4453  -7.9594  24.8038
 07Y  H1   H  HCR5   0   0.248  20.8045  -8.8018  28.8905
 07Y  H2   H  HCR5   0   0.237  22.3579  -9.2473  27.0900
 07Y  H3   H  HOH1   0   0.458  23.6459  -8.0282  28.4747
 07Y  H4   H  HCR5   0   0.231  21.6682  -6.4857  26.0259
 07Y  H5   H  HCR5   0   0.238  20.3400  -9.1272  25.3377
 07Y  H6   H  HCH2   0   0.206  19.6168  -7.3583  23.9795
 07Y  H7   H  HCH2   0   0.218  18.3150  -7.8167  25.0725
 07Y  H8   H  HOH1   0   0.460  18.5868  -5.5204  25.0051
 07Y  H10  H  HCR6   0   0.297  16.9085  -4.6935  29.5246
 07Y  H11  H  HCR6   0   0.299  18.7258  -7.0984  32.5939
 07Y  H12  H  HCR6   0   0.287  20.5554  -7.6613  31.0617
 07Y  H13  H  HOH1   0   0.457  23.2613  -7.4499  24.7961
 07Y  H9   H  HCR6   0   0.282  18.7325  -5.3020  27.9852

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
 07Y  O3   C3   single    1.400  0.020  1.400
 07Y  C5   C4   single    1.510  0.020  1.510
 07Y  C5   O5   single    1.406  0.020  1.406
 07Y  C4   C3   single    1.527  0.020  1.527
 07Y  C4   O4   single    1.432  0.020  1.432
 07Y  C3   C2   single    1.523  0.020  1.523
 07Y  C2   O2   single    1.393  0.020  1.393
 07Y  C2   C1   single    1.530  0.020  1.530
 07Y  O4   C1   single    1.388  0.020  1.388
 07Y  C1   O1   single    1.417  0.020  1.417
 07Y  C18  C19  aromatic  1.382  0.020  1.382
 07Y  C18  C17  aromatic  1.391  0.020  1.391
 07Y  O1   C17  single    1.353  0.020  1.353
 07Y  C19  C20  aromatic  1.388  0.020  1.388
 07Y  C17  C22  aromatic  1.393  0.020  1.393
 07Y  O18  N11  single    1.209  0.020  1.209
 07Y  C20  N11  single    1.451  0.020  1.451
 07Y  C20  C21  aromatic  1.389  0.020  1.389
 07Y  C22  C21  aromatic  1.382  0.020  1.382
 07Y  N11  O17  double    1.209  0.020  1.209
 07Y  C1   H1   single    0.970  0.020  1.090
 07Y  C2   H2   single    0.970  0.020  1.090
 07Y  O2   H3   single    0.850  0.020  0.980
 07Y  C3   H4   single    0.970  0.020  1.090
 07Y  C4   H5   single    0.970  0.020  1.090
 07Y  C5   H6   single    0.970  0.020  1.090
 07Y  C5   H7   single    0.970  0.020  1.090
 07Y  O5   H8   single    0.850  0.020  0.980
 07Y  C18  H9   single    0.930  0.020  1.080
 07Y  C19  H10  single    0.930  0.020  1.080
 07Y  C21  H11  single    0.930  0.020  1.080
 07Y  C22  H12  single    0.930  0.020  1.080
 07Y  O3   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
 07Y  H1   C1   O1   109.58  3.000
 07Y  H1   C1   O4   108.69  3.000
 07Y  O1   C1   O4   111.17  3.000
 07Y  H1   C1   C2   114.28  3.000
 07Y  O1   C1   C2   107.84  3.000
 07Y  O4   C1   C2   105.23  3.000
 07Y  H2   C2   C3   108.23  3.000
 07Y  H2   C2   O2   111.95  3.000
 07Y  C3   C2   O2   111.69  3.000
 07Y  H2   C2   C1   107.05  3.000
 07Y  O2   C2   C1   116.30  3.000
 07Y  C3   C2   C1   100.84  3.000
 07Y  H3   O2   C2   109.11  3.000
 07Y  H4   C3   O3   111.05  3.000
 07Y  H4   C3   C4   110.43  3.000
 07Y  O3   C3   C4   109.82  3.000
 07Y  H4   C3   C2   108.67  3.000
 07Y  C4   C3   C2   101.11  3.000
 07Y  O3   C3   C2   115.32  3.000
 07Y  H5   C4   C5   106.80  3.000
 07Y  H5   C4   O4   108.31  3.000
 07Y  C5   C4   O4   111.40  3.000
 07Y  H5   C4   C3   108.30  3.000
 07Y  O4   C4   C3   105.59  3.000
 07Y  C5   C4   C3   116.21  3.000
 07Y  C4   O4   C1   111.07  3.000
 07Y  H7   C5   H6   106.63  3.000
 07Y  H7   C5   O5   111.88  3.000
 07Y  H6   C5   O5   111.93  3.000
 07Y  H7   C5   C4   108.60  3.000
 07Y  H6   C5   C4   106.97  3.000
 07Y  O5   C5   C4   110.59  3.000
 07Y  H8   O5   C5   108.35  3.000
 07Y  H9   C18  C17  119.59  3.000
 07Y  H9   C18  C19  120.35  3.000
 07Y  C17  C18  C19  120.06  3.000
 07Y  H10  C19  C20  121.15  3.000
 07Y  H10  C19  C18  119.69  3.000
 07Y  C20  C19  C18  119.16  3.000
 07Y  C21  C20  N11  119.34  3.000
 07Y  C21  C20  C19  121.41  3.000
 07Y  N11  C20  C19  119.26  3.000
 07Y  O17  N11  O18  123.83  3.000
 07Y  O17  N11  C20  118.15  3.000
 07Y  O18  N11  C20  118.02  3.000
 07Y  H11  C21  C22  119.64  3.000
 07Y  H11  C21  C20  121.25  3.000
 07Y  C22  C21  C20  119.11  3.000
 07Y  H12  C22  C17  120.26  3.000
 07Y  H12  C22  C21  119.67  3.000
 07Y  C17  C22  C21  120.06  3.000
 07Y  O1   C17  C22  120.80  3.000
 07Y  C22  C17  C18  120.20  3.000
 07Y  O1   C17  C18  118.97  3.000
 07Y  C17  O1   C1   116.63  3.000
 07Y  H13  O3   C3   108.34  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
 07Y  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 07Y  CONST_02  C21  C22  C17  C18     0.00   0.0  0
 07Y  CONST_03  C22  C17  C18  C19     0.00   0.0  0
 07Y  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 07Y  CONST_05  C17  C18  C19  C20     0.00   0.0  0
 07Y  CONST_06  C17  C22  C21  C20     0.00   0.0  0
 07Y  CONST_07  N11  C20  C19  C18   180.00   0.0  0
 07Y  CONST_08  O1   C17  C18  C19   180.00   0.0  0
 07Y  CONST_09  C22  C21  C20  N11   180.00   0.0  0
 07Y  CONST_10  O1   C17  C22  C21   180.00   0.0  0
 07Y  CONST_11  H12  C22  C17  C18   180.00   0.0  0
 07Y  CONST_12  H11  C21  C20  C19   180.00   0.0  0
 07Y  CONST_13  H9   C18  C19  C20   180.00   0.0  0
 07Y  CONST_14  H12  C22  C21  C20   180.00   0.0  0
 07Y  CONST_15  H10  C19  C20  C21   180.00   0.0  0
 07Y  CONST_16  H9   C18  C17  C22   180.00   0.0  0
 07Y  CONST_17  H10  C19  C18  C17   180.00   0.0  0
 07Y  CONST_18  H11  C21  C22  C17   180.00   0.0  0
 07Y  CONST_19  O18  N11  C20  C19     0.00   0.0  0
 07Y  CONST_20  O17  N11  C20  C19   180.00   0.0  0
 07Y  CONST_21  C21  C20  N11  O18   180.00   0.0  0
 07Y  CONST_22  C21  C20  N11  O17     0.00   0.0  0
 07Y  Var_01    C18  C17  O1   C1   -109.89  30.0  2
 07Y  Var_02    C22  C17  O1   C1     72.29  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
 07Y  chir_01  C1  C2  O4  O1  positiv
 07Y  chir_02  C2  O2  C3  C1  positiv
 07Y  chir_03  C3  O3  C2  C4  positiv
 07Y  chir_04  C4  O4  C3  C5  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
 07Y  plan-1  C18  0.020
 07Y  plan-1  C19  0.020
 07Y  plan-1  C20  0.020
 07Y  plan-1  N11  0.020
 07Y  plan-1  C21  0.020
 07Y  plan-1  C22  0.020
 07Y  plan-1  C17  0.020
 07Y  plan-1  O1   0.020
 07Y  plan-1  H10  0.020
 07Y  plan-1  H11  0.020
 07Y  plan-1  H12  0.020
 07Y  plan-1  H9   0.020
 07Y  plan-2  C20  0.020
 07Y  plan-2  N11  0.020
 07Y  plan-2  O18  0.020
 07Y  plan-2  O17  0.020

