# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:00:14 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3-nitrophenyl alpha-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2cccc(c2)[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
 GAA  GAA  '3-nitrophenyl alpha-D-galactopyranoside'  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_GAA
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
 GAA  C1   C  CH1    0   0.205  -1.2585  -0.4159   0.9050
 GAA  C2   C  CH1    0  -0.012  -2.4262  -1.2717   0.4034
 GAA  C3   C  CH1    0   0.003  -2.8723  -0.8025  -0.9756
 GAA  C4   C  CH1    0  -0.007  -3.1791   0.6933  -0.9399
 GAA  C5   C  CH1    0  -0.019  -1.9649   1.4366  -0.4015
 GAA  C6   C  CH2    0  -0.159  -2.2119   2.9220  -0.2505
 GAA  C7   C  CR6    0   0.411   1.0973  -0.3781   0.4997
 GAA  C8   C  CR16   0  -0.382   2.1388  -0.9779  -0.2018
 GAA  C9   C  CR6    0   0.269   3.4430  -0.6783   0.1481
 GAA  C10  C  CR16   0  -0.286   3.7551   0.1948   1.1796
 GAA  C11  C  CR16   0  -0.239   2.7047   0.7826   1.8615
 GAA  C12  C  CR16   0  -0.335   1.3829   0.5167   1.5295
 GAA  N1   N  N      1   0.329   4.5250  -1.3131  -0.5954
 GAA  O1   O  O2     0  -0.492  -0.1421  -0.7250   0.1000
 GAA  O2   O  OH1    0  -0.665  -2.0913  -2.6323   0.3230
 GAA  O3   O  OH1    0  -0.674  -4.0387  -1.4659  -1.3987
 GAA  O4   O  OH1    0  -0.672  -4.2896   0.9782  -0.1257
 GAA  O5   O  O2     0  -0.490  -1.5741   0.9331   0.8708
 GAA  O6   O  OH1    0  -0.666  -0.9855   3.5534   0.0301
 GAA  O7   O  O     -1  -0.375   5.6603  -1.0441  -0.2826
 GAA  O8   O  O      0  -0.376   4.2339  -2.0754  -1.4863
 GAA  H1   H  HCH1   0   0.265  -1.0376  -0.6525   1.9529
 GAA  H2   H  HCH1   0   0.241  -3.2512  -1.1083   1.1079
 GAA  H3   H  HCH1   0   0.224  -2.0548  -0.9603  -1.6939
 GAA  H4   H  HCH1   0   0.239  -3.3456   1.0360  -1.9722
 GAA  H5   H  HCH1   0   0.242  -1.1543   1.3004  -1.1296
 GAA  H61  H  HCH2   0   0.207  -2.9508   3.0987   0.5392
 GAA  H62  H  HCH2   0   0.204  -2.6498   3.2847  -1.1895
 GAA  H8   H  HCR6   0   0.304   1.9133  -1.6675  -1.0032
 GAA  H10  H  HCR6   0   0.296   4.7766   0.4161   1.4483
 GAA  H11  H  HCR6   0   0.282   2.9141   1.4739   2.6660
 GAA  H12  H  HCR6   0   0.301   0.5991   1.0269   2.0697
 GAA  HO2  H  HOH1   0   0.462  -2.1642  -3.0231   1.1987
 GAA  HO3  H  HOH1   0   0.456  -3.9020  -2.4152  -1.3084
 GAA  HO4  H  HOH1   0   0.453  -5.0143   0.4055  -0.3995
 GAA  HO6  H  HOH1   0   0.456  -1.1562   4.4923   0.1454

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
 GAA  C1   C2   single    1.532  0.020  1.532
 GAA  C1   O1   single    1.411  0.020  1.411
 GAA  C1   O5   single    1.386  0.020  1.386
 GAA  C1   H1   single    0.970  0.020  1.090
 GAA  C2   C3   single    1.523  0.020  1.523
 GAA  C2   O2   single    1.404  0.020  1.404
 GAA  C2   H2   single    0.970  0.020  1.090
 GAA  C3   C4   single    1.527  0.020  1.527
 GAA  C3   O3   single    1.407  0.020  1.407
 GAA  C3   H3   single    0.970  0.020  1.090
 GAA  C4   C5   single    1.522  0.020  1.522
 GAA  C4   O4   single    1.406  0.020  1.406
 GAA  C4   H4   single    0.970  0.020  1.090
 GAA  C5   C6   single    1.513  0.020  1.513
 GAA  C5   O5   single    1.423  0.020  1.423
 GAA  C5   H5   single    0.970  0.020  1.090
 GAA  C6   O6   single    1.408  0.020  1.408
 GAA  C6   H61  single    0.970  0.020  1.090
 GAA  C6   H62  single    0.970  0.020  1.090
 GAA  C7   C8   aromatic  1.392  0.020  1.392
 GAA  C7   C12  aromatic  1.394  0.020  1.394
 GAA  C7   O1   single    1.348  0.020  1.348
 GAA  C8   C9   aromatic  1.383  0.020  1.383
 GAA  C8   H8   single    0.930  0.020  1.080
 GAA  C9   C10  aromatic  1.387  0.020  1.387
 GAA  C9   N1   single    1.458  0.020  1.458
 GAA  C10  C11  aromatic  1.383  0.020  1.383
 GAA  C10  H10  single    0.930  0.020  1.080
 GAA  C11  C12  aromatic  1.389  0.020  1.389
 GAA  C11  H11  single    0.930  0.020  1.080
 GAA  C12  H12  single    0.930  0.020  1.080
 GAA  N1   O7   single    1.208  0.020  1.208
 GAA  N1   O8   double    1.208  0.020  1.208
 GAA  O2   HO2  single    0.850  0.020  0.980
 GAA  O3   HO3  single    0.850  0.020  0.980
 GAA  O4   HO4  single    0.850  0.020  0.980
 GAA  O6   HO6  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
 GAA  H1   C1   O5   106.23  3.000
 GAA  H1   C1   O1   109.79  3.000
 GAA  O5   C1   O1   112.30  3.000
 GAA  H1   C1   C2   110.23  3.000
 GAA  O5   C1   C2   111.23  3.000
 GAA  O1   C1   C2   107.10  3.000
 GAA  H2   C2   O2   111.14  3.000
 GAA  H2   C2   C3   108.37  3.000
 GAA  O2   C2   C3   108.46  3.000
 GAA  H2   C2   C1   106.24  3.000
 GAA  O2   C2   C1   112.23  3.000
 GAA  C3   C2   C1   110.33  3.000
 GAA  H3   C3   O3   110.63  3.000
 GAA  H3   C3   C4   107.77  3.000
 GAA  O3   C3   C4   107.60  3.000
 GAA  H3   C3   C2   109.23  3.000
 GAA  O3   C3   C2   111.70  3.000
 GAA  C4   C3   C2   109.83  3.000
 GAA  H4   C4   O4   111.14  3.000
 GAA  H4   C4   C5   107.49  3.000
 GAA  O4   C4   C5   109.05  3.000
 GAA  H4   C4   C3   108.26  3.000
 GAA  O4   C4   C3   111.75  3.000
 GAA  C5   C4   C3   109.05  3.000
 GAA  H5   C5   O5   110.25  3.000
 GAA  H5   C5   C6   107.96  3.000
 GAA  O5   C5   C6   107.64  3.000
 GAA  H5   C5   C4   107.08  3.000
 GAA  O5   C5   C4   111.26  3.000
 GAA  C6   C5   C4   112.61  3.000
 GAA  H62  C6   H61  107.11  3.000
 GAA  H62  C6   O6   111.71  3.000
 GAA  H61  C6   O6   111.81  3.000
 GAA  H62  C6   C5   107.70  3.000
 GAA  H61  C6   C5   109.89  3.000
 GAA  O6   C6   C5   108.54  3.000
 GAA  O1   C7   C12  124.95  3.000
 GAA  O1   C7   C8   115.33  3.000
 GAA  C12  C7   C8   119.72  3.000
 GAA  H8   C8   C9   121.49  3.000
 GAA  H8   C8   C7   119.51  3.000
 GAA  C9   C8   C7   119.00  3.000
 GAA  N1   C9   C10  119.10  3.000
 GAA  N1   C9   C8   118.45  3.000
 GAA  C10  C9   C8   122.45  3.000
 GAA  H10  C10  C11  120.59  3.000
 GAA  H10  C10  C9   121.82  3.000
 GAA  C11  C10  C9   117.60  3.000
 GAA  H11  C11  C12  118.99  3.000
 GAA  H11  C11  C10  119.43  3.000
 GAA  C12  C11  C10  121.57  3.000
 GAA  H12  C12  C11  118.73  3.000
 GAA  H12  C12  C7   121.61  3.000
 GAA  C11  C12  C7   119.65  3.000
 GAA  O8   N1   O7   123.91  3.000
 GAA  O8   N1   C9   118.16  3.000
 GAA  O7   N1   C9   117.93  3.000
 GAA  C7   O1   C1   120.14  3.000
 GAA  HO2  O2   C2   108.88  3.000
 GAA  HO3  O3   C3   108.59  3.000
 GAA  HO4  O4   C4   108.01  3.000
 GAA  C5   O5   C1   115.41  3.000
 GAA  HO6  O6   C6   107.89  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
 GAA  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 GAA  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 GAA  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 GAA  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 GAA  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 GAA  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 GAA  CONST_07  N1   C9   C8   C7   180.00   0.0  0
 GAA  CONST_08  O1   C7   C8   C9   180.00   0.0  0
 GAA  CONST_09  N1   C9   C10  C11  180.00   0.0  0
 GAA  CONST_10  O1   C7   C12  C11  180.00   0.0  0
 GAA  CONST_11  H11  C11  C12  C7   180.00   0.0  0
 GAA  CONST_12  H12  C12  C7   C8   180.00   0.0  0
 GAA  CONST_13  H10  C10  C9   C8   180.00   0.0  0
 GAA  CONST_14  H8   C8   C9   C10  180.00   0.0  0
 GAA  CONST_15  O7   N1   C9   C8   180.00   0.0  0
 GAA  CONST_16  O8   N1   C9   C8     0.00   0.0  0
 GAA  CONST_17  O7   N1   C9   C10    0.00   0.0  0
 GAA  CONST_18  O8   N1   C9   C10  180.00   0.0  0
 GAA  Var_01    C8   C7   O1   C1   166.35  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
 GAA  chir_01  C1  C2  O1  O5  negativ
 GAA  chir_02  C2  O2  C1  C3  negativ
 GAA  chir_03  C3  O3  C2  C4  positiv
 GAA  chir_04  C4  O4  C3  C5  positiv
 GAA  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
 GAA  plan-1  C7   0.020
 GAA  plan-1  C8   0.020
 GAA  plan-1  C9   0.020
 GAA  plan-1  C10  0.020
 GAA  plan-1  C11  0.020
 GAA  plan-1  C12  0.020
 GAA  plan-1  N1   0.020
 GAA  plan-1  O1   0.020
 GAA  plan-1  H8   0.020
 GAA  plan-1  H10  0.020
 GAA  plan-1  H11  0.020
 GAA  plan-1  H12  0.020
 GAA  plan-2  C9   0.020
 GAA  plan-2  N1   0.020
 GAA  plan-2  O7   0.020
 GAA  plan-2  O8   0.020

