# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 19:16:52 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-(alpha-D-galactopyranosyloxy)-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)cc(c1)[N+]([O-])=O
#
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
 FNG  FNG  3-(alpha-D-galactopyranosyloxy)-5-nitrobenzamide  D-saccharide  40  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 PERFECT
;

data_comp_FNG
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
 FNG  C1    C  CH1    0   0.204  -1.5732   0.0085  -0.9080
 FNG  O1    O  O2     0  -0.491  -0.5721   0.8813  -0.4240
 FNG  C2    C  CH1    0  -0.013  -2.8262   0.8552  -1.1507
 FNG  O2    O  OH1    0  -0.665  -2.5586   1.9884  -1.9340
 FNG  C3    C  CH1    0   0.003  -3.4207   1.3137   0.1757
 FNG  O3    O  OH1    0  -0.674  -4.6519   1.9688  -0.0078
 FNG  C4    C  CH1    0  -0.007  -3.6660   0.1058   1.0766
 FNG  O4    O  OH1    0  -0.671  -4.6498  -0.7489   0.5490
 FNG  C5    C  CH1    0  -0.020  -2.3649  -0.6670   1.2313
 FNG  O5    O  O2     0  -0.490  -1.8305  -1.0360  -0.0359
 FNG  C6    C  CH2    0  -0.158  -2.5302  -1.9329   2.0437
 FNG  O6    O  OH1    0  -0.665  -1.2531  -2.4604   2.3121
 FNG  C7    C  CR6    0   0.430   0.7184   0.5005  -0.4338
 FNG  C12   C  CR16   0  -0.376   1.6456   1.5287  -0.2883
 FNG  C11   C  CR6    0   0.297   2.9906   1.2162  -0.2891
 FNG  C10   C  CR16   0  -0.338   3.4553  -0.0826  -0.4232
 FNG  C9    C  CR6    0  -0.011   2.5202  -1.0972  -0.5574
 FNG  C8    C  CR16   0  -0.366   1.1576  -0.8118  -0.5706
 FNG  N16   N  N      1   0.329   3.9584   2.3003  -0.1566
 FNG  O17   O  O      0  -0.371   5.1317   2.0165  -0.1871
 FNG  O18   O  O     -1  -0.370   3.5370   3.4235  -0.0221
 FNG  C13   C  C      0   0.504   2.9247  -2.5333  -0.7238
 FNG  N15   N  NH2    0  -0.809   4.1150  -2.8721  -0.2116
 FNG  O14   O  O      0  -0.471   2.1922  -3.3203  -1.3031
 FNG  H11   H  HCH1   0   0.270  -1.2374  -0.4506  -1.8454
 FNG  H21   H  HCH1   0   0.243  -3.5504   0.1952  -1.6438
 FNG  HO21  H  HOH1   0   0.463  -2.5652   1.7355  -2.8621
 FNG  H31   H  HCH1   0   0.224  -2.7023   1.9711   0.6868
 FNG  HO31  H  HOH1   0   0.455  -4.5381   2.6479  -0.6816
 FNG  H41   H  HCH1   0   0.239  -3.9524   0.4725   2.0737
 FNG  HO41  H  HOH1   0   0.453  -5.4299  -0.2183   0.3548
 FNG  H51   H  HCH1   0   0.244  -1.6634  -0.0122   1.7649
 FNG  H61   H  HCH2   0   0.203  -3.0643  -1.6687   2.9659
 FNG  H62   H  HCH2   0   0.208  -3.1587  -2.6467   1.4996
 FNG  HO61  H  HOH1   0   0.456  -1.3692  -3.2820   2.7975
 FNG  H121  H  HCR6   0   0.311   1.2991   2.5475  -0.1844
 FNG  H101  H  HCR6   0   0.298   4.5160  -0.2849  -0.4435
 FNG  H81   H  HCR6   0   0.305   0.4588  -1.6306  -0.6574
 FNG  H151  H  HNH2   0   0.411   4.4224  -3.8301  -0.2658
 FNG  H152  H  HNH2   0   0.417   4.6293  -2.2678   0.4058

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
 FNG  C1   O1    single    1.414  0.020  1.414
 FNG  C1   C2    single    1.532  0.020  1.532
 FNG  C1   O5    single    1.385  0.020  1.385
 FNG  C1   H11   single    0.970  0.020  1.090
 FNG  O1   C7    single    1.346  0.020  1.346
 FNG  C2   O2    single    1.403  0.020  1.403
 FNG  C2   C3    single    1.524  0.020  1.524
 FNG  C2   H21   single    0.970  0.020  1.090
 FNG  O2   HO21  single    0.850  0.020  0.980
 FNG  C3   O3    single    1.407  0.020  1.407
 FNG  C3   C4    single    1.527  0.020  1.527
 FNG  C3   H31   single    0.970  0.020  1.090
 FNG  O3   HO31  single    0.850  0.020  0.980
 FNG  C4   O4    single    1.406  0.020  1.406
 FNG  C4   C5    single    1.521  0.020  1.521
 FNG  C4   H41   single    0.970  0.020  1.090
 FNG  O4   HO41  single    0.850  0.020  0.980
 FNG  C5   O5    single    1.424  0.020  1.424
 FNG  C5   C6    single    1.513  0.020  1.513
 FNG  C5   H51   single    0.970  0.020  1.090
 FNG  C6   O6    single    1.408  0.020  1.408
 FNG  C6   H61   single    0.970  0.020  1.090
 FNG  C6   H62   single    0.970  0.020  1.090
 FNG  O6   HO61  single    0.850  0.020  0.980
 FNG  C7   C12   aromatic  1.392  0.020  1.392
 FNG  C7   C8    aromatic  1.391  0.020  1.391
 FNG  C12  C11   aromatic  1.381  0.020  1.381
 FNG  C12  H121  single    0.930  0.020  1.080
 FNG  C11  C10   aromatic  1.386  0.020  1.386
 FNG  C11  N16   single    1.459  0.020  1.459
 FNG  C10  C9    aromatic  1.386  0.020  1.386
 FNG  C10  H101  single    0.930  0.020  1.080
 FNG  C9   C8    aromatic  1.392  0.020  1.392
 FNG  C9   C13   single    1.501  0.020  1.501
 FNG  C8   H81   single    0.930  0.020  1.080
 FNG  N16  O17   double    1.207  0.020  1.207
 FNG  N16  O18   single    1.207  0.020  1.207
 FNG  C13  N15   single    1.339  0.020  1.339
 FNG  C13  O14   double    1.221  0.020  1.221
 FNG  N15  H151  single    0.860  0.020  1.020
 FNG  N15  H152  single    0.860  0.020  1.020

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
 FNG  H11   C1   O5    106.23  3.000
 FNG  H11   C1   C2    110.27  3.000
 FNG  O5    C1   C2    111.40  3.000
 FNG  H11   C1   O1    109.53  3.000
 FNG  O5    C1   O1    112.44  3.000
 FNG  C2    C1   O1    107.00  3.000
 FNG  C7    O1   C1    120.14  3.000
 FNG  H21   C2   C3    108.34  3.000
 FNG  H21   C2   O2    111.15  3.000
 FNG  C3    C2   O2    108.49  3.000
 FNG  H21   C2   C1    106.19  3.000
 FNG  C3    C2   C1    110.33  3.000
 FNG  O2    C2   C1    112.27  3.000
 FNG  HO21  O2   C2    108.96  3.000
 FNG  H31   C3   C4    107.67  3.000
 FNG  H31   C3   O3    110.73  3.000
 FNG  C4    C3   O3    107.75  3.000
 FNG  H31   C3   C2    109.24  3.000
 FNG  C4    C3   C2    109.77  3.000
 FNG  O3    C3   C2    111.59  3.000
 FNG  HO31  O3   C3    108.43  3.000
 FNG  H41   C4   C5    107.45  3.000
 FNG  H41   C4   O4    111.13  3.000
 FNG  C5    C4   O4    109.13  3.000
 FNG  H41   C4   C3    108.24  3.000
 FNG  C5    C4   C3    108.94  3.000
 FNG  O4    C4   C3    111.83  3.000
 FNG  HO41  O4   C4    107.91  3.000
 FNG  H51   C5   C6    107.93  3.000
 FNG  H51   C5   O5    110.32  3.000
 FNG  C6    C5   O5    107.58  3.000
 FNG  H51   C5   C4    107.03  3.000
 FNG  C6    C5   C4    112.71  3.000
 FNG  O5    C5   C4    111.23  3.000
 FNG  C5    O5   C1    115.76  3.000
 FNG  H62   C6   H61   107.14  3.000
 FNG  H62   C6   O6    111.77  3.000
 FNG  H61   C6   O6    111.80  3.000
 FNG  H62   C6   C5    109.94  3.000
 FNG  H61   C6   C5    107.63  3.000
 FNG  O6    C6   C5    108.47  3.000
 FNG  HO61  O6   C6    107.88  3.000
 FNG  C8    C7   C12   119.80  3.000
 FNG  C8    C7   O1    124.79  3.000
 FNG  C12   C7   O1    115.40  3.000
 FNG  H121  C12  C11   121.70  3.000
 FNG  H121  C12  C7    119.52  3.000
 FNG  C11   C12  C7    118.78  3.000
 FNG  N16   C11  C10   118.86  3.000
 FNG  N16   C11  C12   118.54  3.000
 FNG  C10   C11  C12   122.60  3.000
 FNG  H101  C10  C9    121.57  3.000
 FNG  H101  C10  C11   120.44  3.000
 FNG  C9    C10  C11   117.98  3.000
 FNG  C13   C9   C8    117.30  3.000
 FNG  C13   C9   C10   121.95  3.000
 FNG  C8    C9   C10   120.74  3.000
 FNG  H81   C8   C9    118.60  3.000
 FNG  H81   C8   C7    121.27  3.000
 FNG  C9    C8   C7    120.10  3.000
 FNG  O18   N16  O17   124.10  3.000
 FNG  O18   N16  C11   118.03  3.000
 FNG  O17   N16  C11   117.87  3.000
 FNG  O14   C13  N15   123.47  3.000
 FNG  O14   C13  C9    120.49  3.000
 FNG  N15   C13  C9    116.04  3.000
 FNG  H152  N15  H151  116.64  3.000
 FNG  H152  N15  C13   122.51  3.000
 FNG  H151  N15  C13   119.41  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
 FNG  CONST_01  C10   C11  C12  C7     0.00   0.0  0
 FNG  CONST_02  C10   C9   C8   C7     0.00   0.0  0
 FNG  CONST_03  C9    C8   C7   C12    0.00   0.0  0
 FNG  CONST_04  C9    C10  C11  C12    0.00   0.0  0
 FNG  CONST_05  C8    C7   C12  C11    0.00   0.0  0
 FNG  CONST_06  C8    C9   C10  C11    0.00   0.0  0
 FNG  CONST_07  C11   C12  C7   O1   180.00   0.0  0
 FNG  CONST_08  C9    C8   C7   O1   180.00   0.0  0
 FNG  CONST_09  N16   C11  C12  C7   180.00   0.0  0
 FNG  CONST_10  C13   C9   C8   C7   180.00   0.0  0
 FNG  CONST_11  C13   C9   C10  C11  180.00   0.0  0
 FNG  CONST_12  N16   C11  C10  C9   180.00   0.0  0
 FNG  CONST_13  H81   C8   C7   C12  180.00   0.0  0
 FNG  CONST_14  H101  C10  C11  C12  180.00   0.0  0
 FNG  CONST_15  H121  C12  C11  C10  180.00   0.0  0
 FNG  CONST_16  O17   N16  C11  C12  180.00   0.0  0
 FNG  CONST_17  O18   N16  C11  C12    0.00   0.0  0
 FNG  CONST_18  O17   N16  C11  C10    0.00   0.0  0
 FNG  CONST_19  O18   N16  C11  C10  180.00   0.0  0
 FNG  CONST_20  H151  N15  C13  C9   180.00   0.0  0
 FNG  CONST_21  H152  N15  C13  C9     0.00   0.0  0
 FNG  Var_01    C12   C7   O1   C1   163.26  30.0  2
 FNG  Var_02    N15   C13  C9   C10   26.27  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
 FNG  chir_01  C1  O1  C2  O5  positiv
 FNG  chir_02  C2  O2  C1  C3  negativ
 FNG  chir_03  C3  O3  C2  C4  positiv
 FNG  chir_04  C4  O4  C5  C3  negativ
 FNG  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
 FNG  plan-1  O1    0.020
 FNG  plan-1  C7    0.020
 FNG  plan-1  C12   0.020
 FNG  plan-1  C11   0.020
 FNG  plan-1  C10   0.020
 FNG  plan-1  C9    0.020
 FNG  plan-1  C8    0.020
 FNG  plan-1  N16   0.020
 FNG  plan-1  C13   0.020
 FNG  plan-1  H121  0.020
 FNG  plan-1  H101  0.020
 FNG  plan-1  H81   0.020
 FNG  plan-2  C11   0.020
 FNG  plan-2  N16   0.020
 FNG  plan-2  O17   0.020
 FNG  plan-2  O18   0.020
 FNG  plan-3  C9    0.020
 FNG  plan-3  C13   0.020
 FNG  plan-3  N15   0.020
 FNG  plan-3  O14   0.020
 FNG  plan-3  H151  0.020
 FNG  plan-3  H152  0.020

