# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 16:07:33 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxane-3,4,5-triol
#   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](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
 Y9Y  Y9Y  "paranitrophenyl-alpha-L-galactopyranoside"
  ligand  36  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y9Y
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
 Y9Y  C1   C  CH1    0   0.218  103.1702  -39.8954  -85.1956
 Y9Y  C2   C  CH1    0  -0.009  103.1890  -40.8114  -86.4313
 Y9Y  O2   O  OH1    0  -0.655  104.3755  -40.6331  -87.1575
 Y9Y  C3   C  CH1    0   0.028  103.0713  -42.2701  -86.0114
 Y9Y  O3   O  OH1    0  -0.661  102.9945  -43.0531  -87.1723
 Y9Y  C4   C  CH1    0  -0.047  101.8527  -42.4471  -85.1015
 Y9Y  O4   O  OH1    0  -0.666  100.6915  -42.1995  -85.8558
 Y9Y  C5   C  CH1    0  -0.013  101.9874  -41.5033  -83.9087
 Y9Y  C6   C  CH2    0  -0.169  100.7927  -41.5657  -82.9825
 Y9Y  O6   O  OH1    0  -0.663  101.0756  -40.8267  -81.8194
 Y9Y  O5   O  O2     0  -0.477  102.1194  -40.1540  -84.3467
 Y9Y  O1   O  O2     0  -0.485  104.3739  -40.0774  -84.4566
 Y9Y  C1'  C  CR6    0   0.444  105.4457  -39.2937  -84.5768
 Y9Y  C2'  C  CR16   0  -0.366  105.5788  -38.2282  -85.4714
 Y9Y  C3'  C  CR16   0  -0.255  106.7375  -37.4759  -85.4797
 Y9Y  C4'  C  CR6    0   0.223  107.7715  -37.7816  -84.6062
 Y9Y  C5'  C  CR16   0  -0.251  107.6546  -38.8421  -83.7131
 Y9Y  C6'  C  CR16   0  -0.351  106.4984  -39.5880  -83.7010
 Y9Y  N1'  N  N      1   0.324  108.9809  -36.9936  -84.6267
 Y9Y  O2'  O  O      0  -0.387  109.0688  -36.0998  -85.4391
 Y9Y  O3'  O  O     -1  -0.387  109.8522  -37.2632  -83.8302
 Y9Y  H1   H  HCH1   0   0.265  103.0624  -38.8497  -85.4985
 Y9Y  H2   H  HCH1   0   0.243  102.3110  -40.5491  -87.0354
 Y9Y  H3   H  HOH1   0   0.460  104.2627  -39.8981  -87.7679
 Y9Y  H4   H  HCH1   0   0.223  103.9579  -42.5381  -85.4176
 Y9Y  H5   H  HOH1   0   0.450  103.0449  -43.9797  -86.9165
 Y9Y  H6   H  HCH1   0   0.243  101.8619  -43.4755  -84.7115
 Y9Y  H7   H  HOH1   0   0.458   99.9481  -42.6531  -85.4487
 Y9Y  H8   H  HCH1   0   0.235  102.8737  -41.8102  -83.3367
 Y9Y  H9   H  HCH2   0   0.203   99.9054  -41.1812  -83.5002
 Y9Y  H10  H  HCH2   0   0.206  100.6027  -42.6236  -82.7554
 Y9Y  H11  H  HOH1   0   0.455  100.2890  -40.8291  -81.2664
 Y9Y  H12  H  HCR6   0   0.289  104.8029  -37.9725  -86.1773
 Y9Y  H13  H  HCR6   0   0.298  106.8244  -36.6563  -86.1780
 Y9Y  H14  H  HCR6   0   0.295  108.4529  -39.0888  -83.0284
 Y9Y  H15  H  HCR6   0   0.282  106.3959  -40.4140  -83.0095

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
 Y9Y  O2   C2   single    1.402  0.020  1.402
 Y9Y  O3   C3   single    1.402  0.020  1.402
 Y9Y  C2   C3   single    1.523  0.020  1.523
 Y9Y  C2   C1   single    1.538  0.020  1.538
 Y9Y  O4   C4   single    1.407  0.020  1.407
 Y9Y  C3   C4   single    1.531  0.020  1.531
 Y9Y  C1   O5   single    1.375  0.020  1.375
 Y9Y  C1   O1   single    1.424  0.020  1.424
 Y9Y  C4   C5   single    1.527  0.020  1.527
 Y9Y  O3'  N1'  single    1.211  0.020  1.211
 Y9Y  O2'  N1'  double    1.211  0.020  1.211
 Y9Y  N1'  C4'  single    1.444  0.020  1.444
 Y9Y  C3'  C4'  aromatic  1.388  0.020  1.388
 Y9Y  C3'  C2'  aromatic  1.381  0.020  1.381
 Y9Y  C4'  C5'  aromatic  1.391  0.020  1.391
 Y9Y  C2'  C1'  aromatic  1.398  0.020  1.398
 Y9Y  O5   C5   single    1.425  0.020  1.425
 Y9Y  C5'  C6'  aromatic  1.376  0.020  1.376
 Y9Y  C1'  C6'  aromatic  1.401  0.020  1.401
 Y9Y  C1'  O1   single    1.333  0.020  1.333
 Y9Y  C5   C6   single    1.513  0.020  1.513
 Y9Y  C6   O6   single    1.407  0.020  1.407
 Y9Y  C1   H1   single    0.970  0.020  1.090
 Y9Y  C2   H2   single    0.970  0.020  1.090
 Y9Y  O2   H3   single    0.850  0.020  0.980
 Y9Y  C3   H4   single    0.970  0.020  1.090
 Y9Y  O3   H5   single    0.850  0.020  0.980
 Y9Y  C4   H6   single    0.970  0.020  1.090
 Y9Y  O4   H7   single    0.850  0.020  0.980
 Y9Y  C5   H8   single    0.970  0.020  1.090
 Y9Y  C6   H9   single    0.970  0.020  1.090
 Y9Y  C6   H10  single    0.970  0.020  1.090
 Y9Y  O6   H11  single    0.850  0.020  0.980
 Y9Y  C2'  H12  single    0.930  0.020  1.080
 Y9Y  C3'  H13  single    0.930  0.020  1.080
 Y9Y  C5'  H14  single    0.930  0.020  1.080
 Y9Y  C6'  H15  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
 Y9Y  H1   C1   O1   110.43  3.000
 Y9Y  H1   C1   O5   105.98  3.000
 Y9Y  O1   C1   O5   107.54  3.000
 Y9Y  H1   C1   C2   110.36  3.000
 Y9Y  O1   C1   C2   109.30  3.000
 Y9Y  O5   C1   C2   113.15  3.000
 Y9Y  H2   C2   C3   108.60  3.000
 Y9Y  H2   C2   O2   111.19  3.000
 Y9Y  C3   C2   O2   109.28  3.000
 Y9Y  H2   C2   C1   106.86  3.000
 Y9Y  C3   C2   C1   110.36  3.000
 Y9Y  O2   C2   C1   110.52  3.000
 Y9Y  H3   O2   C2   109.06  3.000
 Y9Y  H4   C3   C4   107.01  3.000
 Y9Y  H4   C3   O3   110.79  3.000
 Y9Y  C4   C3   O3   112.58  3.000
 Y9Y  H4   C3   C2   108.65  3.000
 Y9Y  C4   C3   C2   109.65  3.000
 Y9Y  O3   C3   C2   108.10  3.000
 Y9Y  H5   O3   C3   108.33  3.000
 Y9Y  H6   C4   C5   107.47  3.000
 Y9Y  H6   C4   O4   111.19  3.000
 Y9Y  C5   C4   O4   112.51  3.000
 Y9Y  H6   C4   C3   108.19  3.000
 Y9Y  C5   C4   C3   108.82  3.000
 Y9Y  O4   C4   C3   108.54  3.000
 Y9Y  H7   O4   C4   109.16  3.000
 Y9Y  H8   C5   O5   110.48  3.000
 Y9Y  H8   C5   C6   107.87  3.000
 Y9Y  O5   C5   C6   107.48  3.000
 Y9Y  H8   C5   C4   107.77  3.000
 Y9Y  C6   C5   C4   112.52  3.000
 Y9Y  O5   C5   C4   110.69  3.000
 Y9Y  H10  C6   H9   107.17  3.000
 Y9Y  H10  C6   O6   111.70  3.000
 Y9Y  H9   C6   O6   111.64  3.000
 Y9Y  H10  C6   C5   107.63  3.000
 Y9Y  H9   C6   C5   109.60  3.000
 Y9Y  O6   C6   C5   109.01  3.000
 Y9Y  H11  O6   C6   108.04  3.000
 Y9Y  C5   O5   C1   116.01  3.000
 Y9Y  C1'  O1   C1   123.89  3.000
 Y9Y  C6'  C1'  C2'  119.27  3.000
 Y9Y  C6'  C1'  O1   115.11  3.000
 Y9Y  C2'  C1'  O1   125.62  3.000
 Y9Y  H12  C2'  C3'  118.03  3.000
 Y9Y  H12  C2'  C1'  122.05  3.000
 Y9Y  C3'  C2'  C1'  119.92  3.000
 Y9Y  H13  C3'  C4'  120.94  3.000
 Y9Y  H13  C3'  C2'  118.98  3.000
 Y9Y  C4'  C3'  C2'  120.08  3.000
 Y9Y  N1'  C4'  C5'  119.71  3.000
 Y9Y  C5'  C4'  C3'  120.62  3.000
 Y9Y  N1'  C4'  C3'  119.67  3.000
 Y9Y  H14  C5'  C6'  119.44  3.000
 Y9Y  H14  C5'  C4'  121.25  3.000
 Y9Y  C6'  C5'  C4'  119.31  3.000
 Y9Y  H15  C6'  C5'  119.93  3.000
 Y9Y  H15  C6'  C1'  119.26  3.000
 Y9Y  C5'  C6'  C1'  120.80  3.000
 Y9Y  O3'  N1'  O2'  123.60  3.000
 Y9Y  O2'  N1'  C4'  118.24  3.000
 Y9Y  O3'  N1'  C4'  118.16  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
 Y9Y  CONST_01  C4'  C3'  C2'  C1'    0.00   0.0  0
 Y9Y  CONST_02  C4'  C5'  C6'  C1'    0.00   0.0  0
 Y9Y  CONST_03  C5'  C4'  C3'  C2'    0.00   0.0  0
 Y9Y  CONST_04  C5'  C6'  C1'  C2'    0.00   0.0  0
 Y9Y  CONST_05  C6'  C5'  C4'  C3'    0.00   0.0  0
 Y9Y  CONST_06  C6'  C1'  C2'  C3'    0.00   0.0  0
 Y9Y  CONST_07  C3'  C2'  C1'  O1   180.00   0.0  0
 Y9Y  CONST_08  C5'  C6'  C1'  O1   180.00   0.0  0
 Y9Y  CONST_09  N1'  C4'  C3'  C2'  180.00   0.0  0
 Y9Y  CONST_10  N1'  C4'  C5'  C6'  180.00   0.0  0
 Y9Y  CONST_11  H13  C3'  C2'  C1'  180.00   0.0  0
 Y9Y  CONST_12  H14  C5'  C6'  C1'  180.00   0.0  0
 Y9Y  CONST_13  H15  C6'  C1'  C2'  180.00   0.0  0
 Y9Y  CONST_14  H14  C5'  C4'  C3'  180.00   0.0  0
 Y9Y  CONST_15  H12  C2'  C3'  C4'  180.00   0.0  0
 Y9Y  CONST_16  H15  C6'  C5'  C4'  180.00   0.0  0
 Y9Y  CONST_17  H13  C3'  C4'  C5'  180.00   0.0  0
 Y9Y  CONST_18  H12  C2'  C1'  C6'  180.00   0.0  0
 Y9Y  CONST_19  O3'  N1'  C4'  C3'  180.00   0.0  0
 Y9Y  CONST_20  O2'  N1'  C4'  C3'    0.00   0.0  0
 Y9Y  CONST_21  O3'  N1'  C4'  C5'    0.00   0.0  0
 Y9Y  CONST_22  O2'  N1'  C4'  C5'  180.00   0.0  0
 Y9Y  Var_01    C2'  C1'  O1   C1    -3.03  30.0  3
 Y9Y  Var_02    C6'  C1'  O1   C1   176.14  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
 Y9Y  chir_01  C1  C2  O5  O1  negativ
 Y9Y  chir_02  C2  O2  C1  C3  positiv
 Y9Y  chir_03  C3  O3  C2  C4  negativ
 Y9Y  chir_04  C4  O4  C3  C5  negativ
 Y9Y  chir_05  C5  O5  C4  C6  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
 Y9Y  plan-1  O1   0.020
 Y9Y  plan-1  C1'  0.020
 Y9Y  plan-1  C2'  0.020
 Y9Y  plan-1  C3'  0.020
 Y9Y  plan-1  C4'  0.020
 Y9Y  plan-1  C5'  0.020
 Y9Y  plan-1  C6'  0.020
 Y9Y  plan-1  N1'  0.020
 Y9Y  plan-1  H12  0.020
 Y9Y  plan-1  H13  0.020
 Y9Y  plan-1  H14  0.020
 Y9Y  plan-1  H15  0.020
 Y9Y  plan-2  C4'  0.020
 Y9Y  plan-2  N1'  0.020
 Y9Y  plan-2  O2'  0.020
 Y9Y  plan-2  O3'  0.020

