# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:39:01 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: 2,4-dinitrophenyl 2-deoxy-2-fluoro-4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](F)[C@@H](O[C@@H]2CO)Oc3ccc(cc3[N+]([O-])=O)[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
 DCB  DCB  '2,4-dinitrophenyl 2-deoxy-2-fluoro-4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside'  ligand  58  35  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DCB
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
 DCB  C1A   C  CH1    0   0.222   1.3753   0.5883   0.5188
 DCB  C2A   C  CH1    0   0.156   0.4735   1.8051   0.6064
 DCB  C3A   C  CH1    0  -0.043  -0.9061   1.3997   1.1121
 DCB  C4A   C  CH1    0   0.016  -1.4601   0.2462   0.2759
 DCB  C5A   C  CH1    0  -0.024  -0.4181  -0.8782   0.2155
 DCB  C6A   C  CH2    0  -0.163  -0.8172  -2.0431  -0.6622
 DCB  O1A   O  O2     0  -0.463   2.5835   0.9891  -0.0641
 DCB  F2A   F  F      0  -0.366   1.0266   2.7202   1.4911
 DCB  O3A   O  OH1    0  -0.648  -1.8047   2.4685   1.0490
 DCB  O4A   O  O2     0  -0.510  -2.6353  -0.2177   0.9035
 DCB  O5A   O  O2     0  -0.488   0.7852  -0.3469  -0.3192
 DCB  O6A   O  OH1    0  -0.663   0.1976  -3.0134  -0.5823
 DCB  C1B   C  CH1    0   0.287  -3.7423  -0.4150   0.0987
 DCB  C2B   C  CH1    0  -0.030  -4.7093  -1.3364   0.8386
 DCB  C3B   C  CH1    0  -0.011  -5.9664  -1.4954  -0.0056
 DCB  C4B   C  CH1    0   0.035  -6.5422  -0.1311  -0.3714
 DCB  C5B   C  CH1    0  -0.022  -5.4544   0.7299  -1.0180
 DCB  C6B   C  CH2    0  -0.152  -5.9391   2.1342  -1.3084
 DCB  O2B   O  OH1    0  -0.664  -4.1612  -2.6151   1.0406
 DCB  O3B   O  OH1    0  -0.672  -6.9726  -2.2115   0.6685
 DCB  O4B   O  OH1    0  -0.671  -7.6064  -0.2540  -1.2813
 DCB  O5B   O  O2     0  -0.479  -4.3487   0.8216  -0.1429
 DCB  O6B   O  OH1    0  -0.667  -4.9251   2.8329  -1.9881
 DCB  C1    C  CR6    0   0.439   3.6548   0.2028   0.0251
 DCB  C2    C  CR16   0  -0.361   3.6153  -1.1447   0.3888
 DCB  C3    C  CR16   0  -0.235   4.7786  -1.8777   0.4982
 DCB  C4    C  CR6    0   0.254   6.0024  -1.2741   0.2497
 DCB  C5    C  CR16   0  -0.296   6.0800   0.0581  -0.1084
 DCB  C6    C  CR6    0   0.166   4.9094   0.7762  -0.2342
 DCB  N4    N  N      1   0.329   7.2241  -2.0470   0.3643
 DCB  N6    N  N      1   0.338   5.0230   2.1665  -0.6433
 DCB  O41   O  O     -1  -0.371   7.1287  -3.2057   0.6908
 DCB  O42   O  O      0  -0.372   8.2702  -1.4909   0.1281
 DCB  O61   O  O     -1  -0.368   5.9501   2.7987  -0.1961
 DCB  O62   O  O      0  -0.356   4.2062   2.5959  -1.4177
 DCB  HC1A  H  HCH1   0   0.248   1.5606   0.1707   1.5230
 DCB  HC2A  H  HCH1   0   0.245   0.3980   2.2822  -0.3764
 DCB  HC3A  H  HCH1   0   0.239  -0.7903   1.0323   2.1442
 DCB  HC4A  H  HCH1   0   0.257  -1.6666   0.6052  -0.7411
 DCB  HC5A  H  HCH1   0   0.244  -0.2414  -1.2503   1.2375
 DCB  H6A1  H  HCH2   0   0.210  -1.7771  -2.4368  -0.3117
 DCB  HCA2  H  HCH2   0   0.207  -0.9666  -1.6860  -1.6904
 DCB  HO3A  H  HOH1   0   0.459  -1.5982   3.0901   1.7540
 DCB  HO6A  H  HOH1   0   0.460  -0.0800  -3.7775  -1.0954
 DCB  HC1B  H  HCH1   0   0.192  -3.4593  -0.8823  -0.8627
 DCB  HC2B  H  HCH1   0   0.229  -4.9766  -0.8573   1.7921
 DCB  HC3B  H  HCH1   0   0.217  -5.6869  -2.0048  -0.9423
 DCB  HC4B  H  HCH1   0   0.214  -6.8682   0.3681   0.5555
 DCB  HC5B  H  HCH1   0   0.223  -5.1504   0.2547  -1.9654
 DCB  H6B1  H  HCH2   0   0.195  -6.2082   2.6209  -0.3602
 DCB  H6B2  H  HCH2   0   0.212  -6.8544   2.0659  -1.9056
 DCB  HO2B  H  HOH1   0   0.459  -3.5151  -2.5640   1.7516
 DCB  HO3B  H  HOH1   0   0.457  -6.6998  -3.1314   0.7406
 DCB  HO4B  H  HOH1   0   0.455  -8.2819  -0.8098  -0.8790
 DCB  HO6B  H  HOH1   0   0.456  -5.2788   3.6870  -2.2511
 DCB  HC2   H  HCR6   0   0.325   2.6760  -1.6480   0.5631
 DCB  HC3   H  HCR6   0   0.319   4.7147  -2.9212   0.7699
 DCB  HC5   H  HCR6   0   0.334   7.0312   0.5327  -0.3019

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
 DCB  C1A  C2A   single    1.517  0.020  1.517
 DCB  C1A  O1A   single    1.400  0.020  1.400
 DCB  C1A  O5A   single    1.387  0.020  1.387
 DCB  C1A  HC1A  single    0.970  0.020  1.090
 DCB  C2A  C3A   single    1.524  0.020  1.524
 DCB  C2A  F2A   single    1.388  0.020  1.388
 DCB  C2A  HC2A  single    0.970  0.020  1.090
 DCB  C3A  C4A   single    1.529  0.020  1.529
 DCB  C3A  O3A   single    1.398  0.020  1.398
 DCB  C3A  HC3A  single    0.970  0.020  1.090
 DCB  C4A  C5A   single    1.534  0.020  1.534
 DCB  C4A  O4A   single    1.411  0.020  1.411
 DCB  C4A  HC4A  single    0.970  0.020  1.090
 DCB  C5A  C6A   single    1.512  0.020  1.512
 DCB  C5A  O5A   single    1.420  0.020  1.420
 DCB  C5A  HC5A  single    0.970  0.020  1.090
 DCB  C6A  O6A   single    1.406  0.020  1.406
 DCB  C6A  H6A1  single    0.970  0.020  1.090
 DCB  C6A  HCA2  single    0.970  0.020  1.090
 DCB  O1A  C1    single    1.332  0.020  1.332
 DCB  O3A  HO3A  single    0.850  0.020  0.980
 DCB  O4A  C1B   single    1.383  0.020  1.383
 DCB  O6A  HO6A  single    0.850  0.020  0.980
 DCB  C1B  C2B   single    1.527  0.020  1.527
 DCB  C1B  O5B   single    1.398  0.020  1.398
 DCB  C1B  HC1B  single    0.970  0.020  1.090
 DCB  C2B  C3B   single    1.523  0.020  1.523
 DCB  C2B  O2B   single    1.406  0.020  1.406
 DCB  C2B  HC2B  single    0.970  0.020  1.090
 DCB  C3B  C4B   single    1.525  0.020  1.525
 DCB  C3B  O3B   single    1.407  0.020  1.407
 DCB  C3B  HC3B  single    0.970  0.020  1.090
 DCB  C4B  C5B   single    1.531  0.020  1.531
 DCB  C4B  O4B   single    1.406  0.020  1.406
 DCB  C4B  HC4B  single    0.970  0.020  1.090
 DCB  C5B  C6B   single    1.514  0.020  1.514
 DCB  C5B  O5B   single    1.413  0.020  1.413
 DCB  C5B  HC5B  single    0.970  0.020  1.090
 DCB  C6B  O6B   single    1.407  0.020  1.407
 DCB  C6B  H6B1  single    0.970  0.020  1.090
 DCB  C6B  H6B2  single    0.970  0.020  1.090
 DCB  O2B  HO2B  single    0.850  0.020  0.980
 DCB  O3B  HO3B  single    0.850  0.020  0.980
 DCB  O4B  HO4B  single    0.850  0.020  0.980
 DCB  O6B  HO6B  single    0.850  0.020  0.980
 DCB  C1   C2    aromatic  1.396  0.020  1.396
 DCB  C1   C6    aromatic  1.404  0.020  1.404
 DCB  C2   C3    aromatic  1.379  0.020  1.379
 DCB  C2   HC2   single    0.930  0.020  1.080
 DCB  C3   C4    aromatic  1.387  0.020  1.387
 DCB  C3   HC3   single    0.930  0.020  1.080
 DCB  C4   C5    aromatic  1.382  0.020  1.382
 DCB  C4   N4    single    1.450  0.020  1.450
 DCB  C5   C6    aromatic  1.379  0.020  1.379
 DCB  C5   HC5   single    0.930  0.020  1.080
 DCB  C6   N6    single    1.454  0.020  1.454
 DCB  N4   O41   single    1.208  0.020  1.208
 DCB  N4   O42   double    1.208  0.020  1.208
 DCB  N6   O61   single    1.208  0.020  1.208
 DCB  N6   O62   double    1.205  0.020  1.205

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
 DCB  HC1A  C1A  O5A   111.47  3.000
 DCB  HC1A  C1A  O1A   110.02  3.000
 DCB  O5A   C1A  O1A   107.96  3.000
 DCB  HC1A  C1A  C2A   110.55  3.000
 DCB  O5A   C1A  C2A   108.83  3.000
 DCB  O1A   C1A  C2A   107.90  3.000
 DCB  HC2A  C2A  F2A   108.20  3.000
 DCB  HC2A  C2A  C3A   110.56  3.000
 DCB  F2A   C2A  C3A   108.94  3.000
 DCB  HC2A  C2A  C1A   109.79  3.000
 DCB  F2A   C2A  C1A   109.19  3.000
 DCB  C3A   C2A  C1A   110.11  3.000
 DCB  HC3A  C3A  O3A   111.40  3.000
 DCB  HC3A  C3A  C4A   107.39  3.000
 DCB  O3A   C3A  C4A   108.63  3.000
 DCB  HC3A  C3A  C2A   107.72  3.000
 DCB  O3A   C3A  C2A   111.32  3.000
 DCB  C4A   C3A  C2A   110.32  3.000
 DCB  HC4A  C4A  O4A   111.27  3.000
 DCB  HC4A  C4A  C5A   109.32  3.000
 DCB  O4A   C4A  C5A   110.02  3.000
 DCB  HC4A  C4A  C3A   109.15  3.000
 DCB  O4A   C4A  C3A   107.86  3.000
 DCB  C5A   C4A  C3A   109.18  3.000
 DCB  HC5A  C5A  O5A   109.86  3.000
 DCB  HC5A  C5A  C6A   108.69  3.000
 DCB  O5A   C5A  C6A   107.05  3.000
 DCB  HC5A  C5A  C4A   108.66  3.000
 DCB  O5A   C5A  C4A   108.43  3.000
 DCB  C6A   C5A  C4A   114.09  3.000
 DCB  HCA2  C6A  H6A1  107.29  3.000
 DCB  HCA2  C6A  O6A   112.07  3.000
 DCB  H6A1  C6A  O6A   111.49  3.000
 DCB  HCA2  C6A  C5A   109.19  3.000
 DCB  H6A1  C6A  C5A   108.81  3.000
 DCB  O6A   C6A  C5A   107.94  3.000
 DCB  C1    O1A  C1A   119.82  3.000
 DCB  HO3A  O3A  C3A   108.84  3.000
 DCB  C1B   O4A  C4A   117.06  3.000
 DCB  C5A   O5A  C1A   112.65  3.000
 DCB  HO6A  O6A  C6A   108.04  3.000
 DCB  HC1B  C1B  O5B   109.54  3.000
 DCB  HC1B  C1B  C2B   109.17  3.000
 DCB  O5B   C1B  C2B   110.04  3.000
 DCB  HC1B  C1B  O4A   111.19  3.000
 DCB  O5B   C1B  O4A   108.76  3.000
 DCB  C2B   C1B  O4A   108.13  3.000
 DCB  HC2B  C2B  O2B   111.49  3.000
 DCB  HC2B  C2B  C3B   108.99  3.000
 DCB  O2B   C2B  C3B   107.86  3.000
 DCB  HC2B  C2B  C1B   108.12  3.000
 DCB  O2B   C2B  C1B   111.81  3.000
 DCB  C3B   C2B  C1B   108.50  3.000
 DCB  HC3B  C3B  O3B   110.69  3.000
 DCB  HC3B  C3B  C4B   107.78  3.000
 DCB  O3B   C3B  C4B   107.47  3.000
 DCB  HC3B  C3B  C2B   108.06  3.000
 DCB  O3B   C3B  C2B   112.21  3.000
 DCB  C4B   C3B  C2B   110.56  3.000
 DCB  HC4B  C4B  O4B   111.11  3.000
 DCB  HC4B  C4B  C5B   108.10  3.000
 DCB  O4B   C4B  C5B   108.29  3.000
 DCB  HC4B  C4B  C3B   108.37  3.000
 DCB  O4B   C4B  C3B   111.28  3.000
 DCB  C5B   C4B  C3B   109.64  3.000
 DCB  HC5B  C5B  O5B   110.14  3.000
 DCB  HC5B  C5B  C6B   108.86  3.000
 DCB  O5B   C5B  C6B   108.01  3.000
 DCB  HC5B  C5B  C4B   108.45  3.000
 DCB  O5B   C5B  C4B   109.33  3.000
 DCB  C6B   C5B  C4B   112.04  3.000
 DCB  H6B2  C6B  H6B1  107.07  3.000
 DCB  H6B2  C6B  O6B   111.71  3.000
 DCB  H6B1  C6B  O6B   111.92  3.000
 DCB  H6B2  C6B  C5B   108.33  3.000
 DCB  H6B1  C6B  C5B   108.89  3.000
 DCB  O6B   C6B  C5B   108.82  3.000
 DCB  HO2B  O2B  C2B   108.65  3.000
 DCB  HO3B  O3B  C3B   108.64  3.000
 DCB  HO4B  O4B  C4B   108.12  3.000
 DCB  C5B   O5B  C1B   112.89  3.000
 DCB  HO6B  O6B  C6B   107.96  3.000
 DCB  C6    C1   C2    117.88  3.000
 DCB  C6    C1   O1A   117.74  3.000
 DCB  C2    C1   O1A   124.36  3.000
 DCB  HC2   C2   C3    118.24  3.000
 DCB  HC2   C2   C1    121.09  3.000
 DCB  C3    C2   C1    120.64  3.000
 DCB  HC3   C3   C4    121.18  3.000
 DCB  HC3   C3   C2    118.91  3.000
 DCB  C4    C3   C2    119.91  3.000
 DCB  N4    C4   C5    119.15  3.000
 DCB  N4    C4   C3    119.82  3.000
 DCB  C5    C4   C3    121.04  3.000
 DCB  HC5   C5   C6    120.15  3.000
 DCB  HC5   C5   C4    121.29  3.000
 DCB  C6    C5   C4    118.56  3.000
 DCB  N6    C6   C5    117.21  3.000
 DCB  N6    C6   C1    120.83  3.000
 DCB  C5    C6   C1    121.96  3.000
 DCB  O42   N4   O41   124.26  3.000
 DCB  O42   N4   C4    117.95  3.000
 DCB  O41   N4   C4    117.79  3.000
 DCB  O62   N6   O61   124.88  3.000
 DCB  O62   N6   C6    117.96  3.000
 DCB  O61   N6   C6    117.15  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
 DCB  CONST_01  C4   C3  C2   C1     0.00   0.0  0
 DCB  CONST_02  C4   C5  C6   C1     0.00   0.0  0
 DCB  CONST_03  C5   C6  C1   C2     0.00   0.0  0
 DCB  CONST_04  C5   C4  C3   C2     0.00   0.0  0
 DCB  CONST_05  C6   C1  C2   C3     0.00   0.0  0
 DCB  CONST_06  C6   C5  C4   C3     0.00   0.0  0
 DCB  CONST_07  C3   C2  C1   O1A  180.00   0.0  0
 DCB  CONST_08  C5   C6  C1   O1A  180.00   0.0  0
 DCB  CONST_09  N6   C6  C1   C2   180.00   0.0  0
 DCB  CONST_10  N4   C4  C3   C2   180.00   0.0  0
 DCB  CONST_11  N6   C6  C5   C4   180.00   0.0  0
 DCB  CONST_12  N4   C4  C5   C6   180.00   0.0  0
 DCB  CONST_13  HC3  C3  C2   C1   180.00   0.0  0
 DCB  CONST_14  HC5  C5  C6   C1   180.00   0.0  0
 DCB  CONST_15  HC2  C2  C3   C4   180.00   0.0  0
 DCB  CONST_18  O41  N4  C4   C3     0.00   0.0  0
 DCB  CONST_19  O42  N4  C4   C3   180.00   0.0  0
 DCB  CONST_20  O41  N4  C4   C5   180.00   0.0  0
 DCB  CONST_21  O42  N4  C4   C5     0.00   0.0  0
 DCB  Var_01    C2   C1  O1A  C1A   15.61  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
 DCB  chir_01  C1A  C2A  O1A  O5A  positiv
 DCB  chir_02  C2A  F2A  C1A  C3A  negativ
 DCB  chir_03  C3A  O3A  C2A  C4A  positiv
 DCB  chir_04  C4A  O4A  C5A  C3A  positiv
 DCB  chir_05  C5A  O5A  C4A  C6A  negativ
 DCB  chir_06  C1B  O4A  O5B  C2B  positiv
 DCB  chir_07  C2B  O2B  C1B  C3B  negativ
 DCB  chir_08  C3B  O3B  C2B  C4B  positiv
 DCB  chir_09  C4B  O4B  C3B  C5B  negativ
 DCB  chir_10  C5B  O5B  C4B  C6B  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
 DCB  plan-1  O1A  0.020
 DCB  plan-1  C1   0.020
 DCB  plan-1  C2   0.020
 DCB  plan-1  C3   0.020
 DCB  plan-1  C4   0.020
 DCB  plan-1  C5   0.020
 DCB  plan-1  C6   0.020
 DCB  plan-1  N4   0.020
 DCB  plan-1  N6   0.020
 DCB  plan-1  HC2  0.020
 DCB  plan-1  HC3  0.020
 DCB  plan-1  HC5  0.020
 DCB  plan-2  C6   0.020
 DCB  plan-2  N6   0.020
 DCB  plan-2  O61  0.020
 DCB  plan-2  O62  0.020
 DCB  plan-3  C4   0.020
 DCB  plan-3  N4   0.020
 DCB  plan-3  O41  0.020
 DCB  plan-3  O42  0.020

