# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 00:34:21 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (2~{R},3~{S},4~{S},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
 MBE  MBE  (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxane-3,4,5-triol  D-saccharide  36  21  .  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_MBE
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
 MBE  C1   C  CH1    0   0.269   1.1281   0.6818  -0.2743
 MBE  C2   C  CH1    0  -0.046   2.3551   1.5885  -0.1996
 MBE  C3   C  CH1    0  -0.001   3.5460   0.7703  -0.7011
 MBE  C4   C  CH1    0   0.040   3.6741  -0.5503   0.0569
 MBE  C5   C  CH1    0  -0.021   2.3413  -1.2983  -0.0066
 MBE  C6   C  CH2    0  -0.154   2.3447  -2.5675   0.8160
 MBE  C7   C  CR6    0   0.406  -1.2083   0.9227   0.0957
 MBE  C8   C  CR16   0  -0.340  -2.2225   1.7754   0.5386
 MBE  C9   C  CR16   0  -0.253  -3.5450   1.4172   0.4005
 MBE  C10  C  CR6    0   0.233  -3.8595   0.1965  -0.1871
 MBE  C11  C  CR16   0  -0.256  -2.8615  -0.6615  -0.6251
 MBE  C12  C  CR16   0  -0.347  -1.5333  -0.3069  -0.4789
 MBE  N1   N  N      1   0.328  -5.2456  -0.1847  -0.3392
 MBE  O1   O  O2     0  -0.489   0.0445   1.3798   0.2649
 MBE  O2   O  OH1    0  -0.661   2.6118   2.0078   1.1110
 MBE  O3   O  OH1    0  -0.668   4.7638   1.4578  -0.5700
 MBE  O4   O  OH1    0  -0.673   4.6571  -1.3709  -0.5235
 MBE  O5   O  O2     0  -0.491   1.3118  -0.4650   0.4931
 MBE  O6   O  OH1    0  -0.666   1.1190  -3.2302   0.6200
 MBE  O7   O  O     -1  -0.387  -5.4929  -1.2537  -0.8501
 MBE  O8   O  O      0  -0.387  -6.0955   0.5832   0.0519
 MBE  H1   H  HCH1   0   0.222   0.9287   0.4203  -1.3277
 MBE  H2   H  HCH1   0   0.243   2.1997   2.4391  -0.8792
 MBE  H3   H  HCH1   0   0.228   3.3484   0.5256  -1.7556
 MBE  H4   H  HCH1   0   0.219   3.9064  -0.3396   1.1114
 MBE  H5   H  HCH1   0   0.227   2.1343  -1.5575  -1.0582
 MBE  H6   H  HCH2   0   0.214   3.1944  -3.1808   0.4995
 MBE  H7   H  HCH2   0   0.199   2.5082  -2.3087   1.8716
 MBE  H8   H  HCR6   0   0.287  -1.9616   2.7244   0.9876
 MBE  H9   H  HCR6   0   0.299  -4.3169   2.0895   0.7452
 MBE  H10  H  HCR6   0   0.302  -3.1033  -1.6137  -1.0741
 MBE  H11  H  HCR6   0   0.302  -0.7766  -1.0073  -0.8001
 MBE  H12  H  HOH1   0   0.457   1.9358   2.6407   1.3722
 MBE  H13  H  HOH1   0   0.459   4.8456   2.0879  -1.2923
 MBE  H14  H  HOH1   0   0.454   5.4906  -0.8888  -0.5121
 MBE  H15  H  HOH1   0   0.457   1.1583  -4.0700   1.0862

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
 MBE  O7   N1   single    1.210  0.020  1.210
 MBE  O8   N1   double    1.210  0.020  1.210
 MBE  N1   C10  single    1.446  0.020  1.446
 MBE  C10  C11  aromatic  1.387  0.020  1.387
 MBE  C10  C9   aromatic  1.391  0.020  1.391
 MBE  C11  C12  aromatic  1.382  0.020  1.382
 MBE  C9   C8   aromatic  1.377  0.020  1.377
 MBE  C12  C7   aromatic  1.396  0.020  1.396
 MBE  C8   C7   aromatic  1.397  0.020  1.397
 MBE  C7   O1   single    1.344  0.020  1.344
 MBE  O1   C1   single    1.397  0.020  1.397
 MBE  C1   O5   single    1.392  0.020  1.392
 MBE  C1   C2   single    1.527  0.020  1.527
 MBE  O5   C5   single    1.416  0.020  1.416
 MBE  C2   O2   single    1.400  0.020  1.400
 MBE  C2   C3   single    1.529  0.020  1.529
 MBE  C5   C6   single    1.512  0.020  1.512
 MBE  C5   C4   single    1.530  0.020  1.530
 MBE  C3   C4   single    1.528  0.020  1.528
 MBE  C3   O3   single    1.405  0.020  1.405
 MBE  C6   O6   single    1.407  0.020  1.407
 MBE  C4   O4   single    1.406  0.020  1.406
 MBE  C1   H1   single    0.970  0.020  1.090
 MBE  C2   H2   single    0.970  0.020  1.090
 MBE  C3   H3   single    0.970  0.020  1.090
 MBE  C4   H4   single    0.970  0.020  1.090
 MBE  C5   H5   single    0.970  0.020  1.090
 MBE  C6   H6   single    0.970  0.020  1.090
 MBE  C6   H7   single    0.970  0.020  1.090
 MBE  C8   H8   single    0.930  0.020  1.080
 MBE  C9   H9   single    0.930  0.020  1.080
 MBE  C11  H10  single    0.930  0.020  1.080
 MBE  C12  H11  single    0.930  0.020  1.080
 MBE  O2   H12  single    0.850  0.020  0.980
 MBE  O3   H13  single    0.850  0.020  0.980
 MBE  O4   H14  single    0.850  0.020  0.980
 MBE  O6   H15  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
 MBE  H1   C1   O5   110.78  3.000
 MBE  H1   C1   O1   110.28  3.000
 MBE  O5   C1   O1   107.53  3.000
 MBE  H1   C1   C2   109.42  3.000
 MBE  O5   C1   C2   110.86  3.000
 MBE  O1   C1   C2   107.92  3.000
 MBE  H2   C2   O2   111.89  3.000
 MBE  H2   C2   C3   108.73  3.000
 MBE  O2   C2   C3   108.93  3.000
 MBE  H2   C2   C1   108.38  3.000
 MBE  C3   C2   C1   106.97  3.000
 MBE  O2   C2   C1   111.77  3.000
 MBE  H3   C3   O3   110.73  3.000
 MBE  H3   C3   C4   107.35  3.000
 MBE  O3   C3   C4   107.70  3.000
 MBE  H3   C3   C2   107.06  3.000
 MBE  O3   C3   C2   112.50  3.000
 MBE  C4   C3   C2   111.41  3.000
 MBE  H4   C4   O4   111.09  3.000
 MBE  H4   C4   C5   108.50  3.000
 MBE  O4   C4   C5   107.86  3.000
 MBE  H4   C4   C3   109.12  3.000
 MBE  O4   C4   C3   111.00  3.000
 MBE  C5   C4   C3   109.20  3.000
 MBE  H5   C5   O5   109.78  3.000
 MBE  H5   C5   C6   108.77  3.000
 MBE  O5   C5   C6   107.68  3.000
 MBE  H5   C5   C4   108.55  3.000
 MBE  C6   C5   C4   112.69  3.000
 MBE  O5   C5   C4   109.34  3.000
 MBE  H7   C6   H6   107.11  3.000
 MBE  H7   C6   O6   111.98  3.000
 MBE  H6   C6   O6   111.84  3.000
 MBE  H7   C6   C5   108.97  3.000
 MBE  H6   C6   C5   108.34  3.000
 MBE  O6   C6   C5   108.51  3.000
 MBE  O1   C7   C12  124.64  3.000
 MBE  O1   C7   C8   115.41  3.000
 MBE  C12  C7   C8   119.95  3.000
 MBE  H8   C8   C9   120.09  3.000
 MBE  H8   C8   C7   119.47  3.000
 MBE  C9   C8   C7   120.44  3.000
 MBE  H9   C9   C10  121.30  3.000
 MBE  H9   C9   C8   119.50  3.000
 MBE  C10  C9   C8   119.20  3.000
 MBE  N1   C10  C11  119.57  3.000
 MBE  C11  C10  C9   120.91  3.000
 MBE  N1   C10  C9   119.52  3.000
 MBE  H10  C11  C12  119.02  3.000
 MBE  H10  C11  C10  121.03  3.000
 MBE  C12  C11  C10  119.94  3.000
 MBE  H11  C12  C11  118.38  3.000
 MBE  H11  C12  C7   122.05  3.000
 MBE  C11  C12  C7   119.56  3.000
 MBE  O8   N1   O7   123.59  3.000
 MBE  O8   N1   C10  118.16  3.000
 MBE  O7   N1   C10  118.25  3.000
 MBE  C7   O1   C1   120.29  3.000
 MBE  H12  O2   C2   108.81  3.000
 MBE  H13  O3   C3   108.92  3.000
 MBE  H14  O4   C4   107.95  3.000
 MBE  C5   O5   C1   112.73  3.000
 MBE  H15  O6   C6   107.95  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
 MBE  CONST_01  C10  C11  C12  C7     0.00   0.0  0
 MBE  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 MBE  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 MBE  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 MBE  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 MBE  CONST_06  C12  C7   C8   C9     0.00   0.0  0
 MBE  CONST_07  N1   C10  C9   C8   180.00   0.0  0
 MBE  CONST_08  O1   C7   C8   C9   180.00   0.0  0
 MBE  CONST_09  O1   C7   C12  C11  180.00   0.0  0
 MBE  CONST_10  N1   C10  C11  C12  180.00   0.0  0
 MBE  CONST_11  H10  C11  C12  C7   180.00   0.0  0
 MBE  CONST_12  H9   C9   C8   C7   180.00   0.0  0
 MBE  CONST_13  H11  C12  C7   C8   180.00   0.0  0
 MBE  CONST_14  H8   C8   C9   C10  180.00   0.0  0
 MBE  CONST_15  O7   N1   C10  C9   180.00   0.0  0
 MBE  CONST_16  O8   N1   C10  C9     0.00   0.0  0
 MBE  CONST_17  O7   N1   C10  C11    0.00   0.0  0
 MBE  CONST_18  O8   N1   C10  C11  180.00   0.0  0
 MBE  Var_01    C12  C7   O1   C1     7.00  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
 MBE  chir_01  C1  O1  O5  C2  positiv
 MBE  chir_02  C2  O2  C1  C3  positiv
 MBE  chir_03  C3  O3  C2  C4  positiv
 MBE  chir_04  C4  O4  C3  C5  negativ
 MBE  chir_05  C5  O5  C4  C6  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
 MBE  plan-1  C7   0.020
 MBE  plan-1  C8   0.020
 MBE  plan-1  C9   0.020
 MBE  plan-1  C10  0.020
 MBE  plan-1  C11  0.020
 MBE  plan-1  C12  0.020
 MBE  plan-1  N1   0.020
 MBE  plan-1  O1   0.020
 MBE  plan-1  H8   0.020
 MBE  plan-1  H9   0.020
 MBE  plan-1  H10  0.020
 MBE  plan-1  H11  0.020
 MBE  plan-2  C10  0.020
 MBE  plan-2  N1   0.020
 MBE  plan-2  O7   0.020
 MBE  plan-2  O8   0.020

