# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 19:01:06 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[C@H](F)[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
 NFG  NFG  '2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside'  D-saccharide  37  24  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NFG
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
 NFG  C1    C  CH1    0   0.215  -1.3436  -0.2440  -0.2662
 NFG  O1    O  O2     0  -0.462  -0.1761  -0.8978   0.1465
 NFG  C2    C  CH1    0   0.163  -2.4793  -1.2518  -0.2282
 NFG  F     F  F      0  -0.365  -2.2453  -2.2342  -1.1792
 NFG  C3    C  CH1    0  -0.059  -3.7878  -0.5442  -0.5423
 NFG  O3    O  OH1    0  -0.667  -4.8935  -1.3923  -0.3669
 NFG  C4    C  CH1    0   0.033  -3.9742   0.6609   0.3805
 NFG  O4    O  OH1    0  -0.666  -5.0878   1.4210  -0.0033
 NFG  C5    C  CH1    0  -0.032  -2.7364   1.5543   0.3056
 NFG  C6    C  CH2    0  -0.153  -2.7892   2.7178   1.2693
 NFG  O6    O  OH1    0  -0.665  -1.6411   3.5063   1.0726
 NFG  O5    O  O2     0  -0.489  -1.5959   0.7762   0.6399
 NFG  C11   C  CR6    0   0.451   1.0139  -0.3474  -0.0774
 NFG  C12   C  CR6    0   0.161   2.1508  -1.1235   0.1964
 NFG  N1    N  N      1   0.337   2.0261  -2.4979   0.6571
 NFG  O11   O  O     -1  -0.369   2.8056  -2.8657   1.5038
 NFG  O12   O  O      0  -0.353   1.1782  -3.1898   0.1546
 NFG  C13   C  CR16   0  -0.293   3.4282  -0.6286   0.0379
 NFG  C14   C  CR6    0   0.251   3.5831   0.6575  -0.4428
 NFG  N2    N  N      1   0.329   4.9204   1.1793  -0.6456
 NFG  O21   O  O     -1  -0.371   5.0273   2.3039  -1.0725
 NFG  O22   O  O      0  -0.373   5.8552   0.4621  -0.3781
 NFG  C15   C  CR16   0  -0.235   2.4819   1.4538  -0.7219
 NFG  C16   C  CR16   0  -0.361   1.2093   0.9610  -0.5238
 NFG  H1    H  HCH1   0   0.245  -1.2181   0.1456  -1.2905
 NFG  H2    H  HCH1   0   0.243  -2.5221  -1.7295   0.7562
 NFG  H3    H  HCH1   0   0.241  -3.7369  -0.1697  -1.5755
 NFG  H3O1  H  HOH1   0   0.465  -5.0093  -1.9288  -1.1569
 NFG  H4    H  HCH1   0   0.226  -4.0754   0.2963   1.4150
 NFG  H4O1  H  HOH1   0   0.458  -5.8713   0.8659   0.0711
 NFG  H5    H  HCH1   0   0.241  -2.6362   1.9422  -0.7204
 NFG  H62   H  HCH2   0   0.218  -3.7085   3.2809   1.0797
 NFG  H61   H  HCH2   0   0.202  -2.8528   2.3298   2.2953
 NFG  H6    H  HOH1   0   0.458  -1.7188   4.2877   1.6273
 NFG  H13   H  HCR6   0   0.333   4.2835  -1.2497   0.2626
 NFG  H15   H  HCR6   0   0.319   2.6007   2.4663  -1.0790
 NFG  H16   H  HCR6   0   0.323   0.3745   1.6221  -0.7018

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
 NFG  C1   O1    single    1.400  0.020  1.400
 NFG  C1   C2    single    1.519  0.020  1.519
 NFG  C1   O5    single    1.388  0.020  1.388
 NFG  C1   H1    single    0.970  0.020  1.090
 NFG  O1   C11   single    1.330  0.020  1.330
 NFG  C2   F     single    1.387  0.020  1.387
 NFG  C2   C3    single    1.520  0.020  1.520
 NFG  C2   H2    single    0.970  0.020  1.090
 NFG  C3   O3    single    1.405  0.020  1.405
 NFG  C3   C4    single    1.529  0.020  1.529
 NFG  C3   H3    single    0.970  0.020  1.090
 NFG  O3   H3O1  single    0.850  0.020  0.980
 NFG  C4   O4    single    1.402  0.020  1.402
 NFG  C4   C5    single    1.528  0.020  1.528
 NFG  C4   H4    single    0.970  0.020  1.090
 NFG  O4   H4O1  single    0.850  0.020  0.980
 NFG  C5   C6    single    1.512  0.020  1.512
 NFG  C5   O5    single    1.421  0.020  1.421
 NFG  C5   H5    single    0.970  0.020  1.090
 NFG  C6   O6    single    1.407  0.020  1.407
 NFG  C6   H62   single    0.970  0.020  1.090
 NFG  C6   H61   single    0.970  0.020  1.090
 NFG  O6   H6    single    0.850  0.020  0.980
 NFG  C11  C12   aromatic  1.404  0.020  1.404
 NFG  C11  C16   aromatic  1.396  0.020  1.396
 NFG  C12  N1    single    1.455  0.020  1.455
 NFG  C12  C13   aromatic  1.379  0.020  1.379
 NFG  N1   O11   single    1.208  0.020  1.208
 NFG  N1   O12   double    1.204  0.020  1.204
 NFG  C13  C14   aromatic  1.382  0.020  1.382
 NFG  C13  H13   single    0.930  0.020  1.080
 NFG  C14  N2    single    1.450  0.020  1.450
 NFG  C14  C15   aromatic  1.387  0.020  1.387
 NFG  N2   O21   single    1.208  0.020  1.208
 NFG  N2   O22   double    1.208  0.020  1.208
 NFG  C15  C16   aromatic  1.379  0.020  1.379
 NFG  C15  H15   single    0.930  0.020  1.080
 NFG  C16  H16   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
 NFG  H1    C1   O5   111.56  3.000
 NFG  H1    C1   C2   110.04  3.000
 NFG  O5    C1   C2   109.61  3.000
 NFG  H1    C1   O1   110.11  3.000
 NFG  O5    C1   O1   107.60  3.000
 NFG  C2    C1   O1   107.83  3.000
 NFG  C11   O1   C1   120.20  3.000
 NFG  H2    C2   C3   110.80  3.000
 NFG  H2    C2   F    108.30  3.000
 NFG  C3    C2   F    109.46  3.000
 NFG  H2    C2   C1   109.95  3.000
 NFG  C3    C2   C1   109.24  3.000
 NFG  F     C2   C1   109.06  3.000
 NFG  H3    C3   C4   107.71  3.000
 NFG  H3    C3   O3   111.06  3.000
 NFG  C4    C3   O3   107.73  3.000
 NFG  H3    C3   C2   108.22  3.000
 NFG  C4    C3   C2   110.31  3.000
 NFG  O3    C3   C2   111.75  3.000
 NFG  H3O1  O3   C3   109.20  3.000
 NFG  H4    C4   C5   108.29  3.000
 NFG  H4    C4   O4   111.32  3.000
 NFG  C5    C4   O4   108.24  3.000
 NFG  H4    C4   C3   108.49  3.000
 NFG  C5    C4   C3   109.41  3.000
 NFG  O4    C4   C3   111.03  3.000
 NFG  H4O1  O4   C4   108.21  3.000
 NFG  H5    C5   O5   109.82  3.000
 NFG  H5    C5   C6   109.02  3.000
 NFG  O5    C5   C6   107.43  3.000
 NFG  H5    C5   C4   108.98  3.000
 NFG  O5    C5   C4   108.57  3.000
 NFG  C6    C5   C4   112.98  3.000
 NFG  H61   C6   H62  107.14  3.000
 NFG  H61   C6   O6   112.07  3.000
 NFG  H62   C6   O6   111.90  3.000
 NFG  H61   C6   C5   108.99  3.000
 NFG  H62   C6   C5   108.35  3.000
 NFG  O6    C6   C5   108.29  3.000
 NFG  H6    O6   C6   107.99  3.000
 NFG  C5    O5   C1   113.27  3.000
 NFG  C16   C11  C12  117.85  3.000
 NFG  C16   C11  O1   124.53  3.000
 NFG  C12   C11  O1   117.58  3.000
 NFG  C13   C12  N1   117.06  3.000
 NFG  C13   C12  C11  121.97  3.000
 NFG  N1    C12  C11  120.98  3.000
 NFG  O12   N1   O11  124.88  3.000
 NFG  O12   N1   C12  118.10  3.000
 NFG  O11   N1   C12  117.01  3.000
 NFG  H13   C13  C14  121.24  3.000
 NFG  H13   C13  C12  120.20  3.000
 NFG  C14   C13  C12  118.55  3.000
 NFG  C15   C14  N2   119.83  3.000
 NFG  C15   C14  C13  121.02  3.000
 NFG  N2    C14  C13  119.15  3.000
 NFG  O22   N2   O21  124.23  3.000
 NFG  O22   N2   C14  117.97  3.000
 NFG  O21   N2   C14  117.80  3.000
 NFG  H15   C15  C16  118.94  3.000
 NFG  H15   C15  C14  121.15  3.000
 NFG  C16   C15  C14  119.90  3.000
 NFG  H16   C16  C15  118.10  3.000
 NFG  H16   C16  C11  121.22  3.000
 NFG  C15   C16  C11  120.66  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
 NFG  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 NFG  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 NFG  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 NFG  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 NFG  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 NFG  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 NFG  CONST_07  C13  C12  C11  O1    180.00   0.0  0
 NFG  CONST_08  C15  C16  C11  O1    180.00   0.0  0
 NFG  CONST_09  N2   C14  C13  C12   180.00   0.0  0
 NFG  CONST_10  C16  C11  C12  N1    180.00   0.0  0
 NFG  CONST_11  C14  C13  C12  N1    180.00   0.0  0
 NFG  CONST_12  C16  C15  C14  N2    180.00   0.0  0
 NFG  CONST_13  H13  C13  C12  C11   180.00   0.0  0
 NFG  CONST_14  H15  C15  C16  C11   180.00   0.0  0
 NFG  CONST_15  H16  C16  C11  C12   180.00   0.0  0
 NFG  CONST_20  O21  N2   C14  C13   180.00   0.0  0
 NFG  CONST_21  O22  N2   C14  C13     0.00   0.0  0
 NFG  CONST_22  C15  C14  N2   O21     0.00   0.0  0
 NFG  CONST_23  C15  C14  N2   O22   180.00   0.0  0
 NFG  Var_01    C12  C11  O1   C1   -171.77  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
 NFG  chir_01  C1  O1  C2  O5  negativ
 NFG  chir_02  C2  F   C3  C1  positiv
 NFG  chir_03  C3  O3  C2  C4  positiv
 NFG  chir_04  C4  O4  C5  C3  positiv
 NFG  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
 NFG  plan-1  O1   0.020
 NFG  plan-1  C11  0.020
 NFG  plan-1  C12  0.020
 NFG  plan-1  N1   0.020
 NFG  plan-1  C13  0.020
 NFG  plan-1  C14  0.020
 NFG  plan-1  N2   0.020
 NFG  plan-1  C15  0.020
 NFG  plan-1  C16  0.020
 NFG  plan-1  H13  0.020
 NFG  plan-1  H15  0.020
 NFG  plan-1  H16  0.020
 NFG  plan-2  C12  0.020
 NFG  plan-2  N1   0.020
 NFG  plan-2  O11  0.020
 NFG  plan-2  O12  0.020
 NFG  plan-3  C14  0.020
 NFG  plan-3  N2   0.020
 NFG  plan-3  O21  0.020
 NFG  plan-3  O22  0.020

