# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:29:59 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-amino-2-deoxy-beta-D-glucopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)O[C@@H]([C@@H](O)[C@@H]1O)C(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
 N1L  N1L  '2-amino-2-deoxy-beta-D-glucopyranuronic acid'  D-saccharide  23  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N1L
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
 N1L  C1    C  CH1    0   0.306  15.7894  20.1075  42.1501
 N1L  C2    C  CH1    0  -0.168  15.8672  19.3396  43.4699
 N1L  C3    C  CH1    0   0.029  17.0697  18.3946  43.4226
 N1L  C4    C  CH1    0   0.028  17.0568  17.5348  42.1683
 N1L  C5    C  CH1    0  -0.159  16.9306  18.4481  40.9412
 N1L  C6    C  C      0   0.434  16.9207  17.6442  39.6247
 N1L  N2    N  NH2    0  -0.788  15.8926  20.2680  44.5858
 N1L  O3    O  OH1    0  -0.670  17.0530  17.6168  44.5986
 N1L  O4    O  OH1    0  -0.708  18.2310  16.7681  42.1254
 N1L  O5    O  O2     0  -0.491  15.7645  19.2244  41.0550
 N1L  O6B   O  OC    -1  -0.554  16.1115  17.9442  38.7459
 N1L  O6A   O  O      0  -0.614  17.7949  16.7363  39.5734
 N1L  O1    O  OH1    0  -0.651  14.6284  20.8524  42.1234
 N1L  H1    H  HCH1   0   0.168  16.6861  20.7520  42.0647
 N1L  H2    H  HCH1   0   0.233  14.9563  18.7333  43.5521
 N1L  HO1   H  HOH1   0   0.455  14.6829  21.4891  41.4028
 N1L  H3    H  HCH1   0   0.185  17.9818  19.0167  43.3853
 N1L  H21N  H  HNH2   0   0.347  15.9186  19.7449  45.4517
 N1L  H22N  H  HNH2   0   0.336  16.7562  20.8003  44.5635
 N1L  H4    H  HCH1   0   0.181  16.1582  16.8929  42.2022
 N1L  HO3   H  HOH1   0   0.447  17.8521  17.0807  44.6112
 N1L  H5    H  HCH1   0   0.215  17.8236  19.1006  40.9142
 N1L  HO4   H  HOH1   0   0.437  18.3104  16.5381  41.1678

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
 N1L  C1  C2    single  1.529  0.020  1.529
 N1L  C1  O5    single  1.407  0.020  1.407
 N1L  C1  O1    single  1.380  0.020  1.380
 N1L  C2  C3    single  1.530  0.020  1.530
 N1L  C2  N2    single  1.452  0.020  1.452
 N1L  C3  C4    single  1.521  0.020  1.521
 N1L  C3  O3    single  1.410  0.020  1.410
 N1L  C4  C5    single  1.535  0.020  1.535
 N1L  C4  O4    single  1.403  0.020  1.403
 N1L  C5  C6    single  1.543  0.020  1.543
 N1L  C5  O5    single  1.405  0.020  1.405
 N1L  C6  O6B   deloc   1.232  0.020  1.232
 N1L  C6  O6A   deloc   1.261  0.020  1.261
 N1L  C1  H1    single  0.970  0.020  1.090
 N1L  C2  H2    single  0.970  0.020  1.090
 N1L  O1  HO1   single  0.850  0.020  0.980
 N1L  C3  H3    single  0.970  0.020  1.090
 N1L  N2  H21N  single  0.890  0.020  1.040
 N1L  N2  H22N  single  0.890  0.020  1.040
 N1L  C4  H4    single  0.970  0.020  1.090
 N1L  O3  HO3   single  0.850  0.020  0.980
 N1L  C5  H5    single  0.970  0.020  1.090
 N1L  O4  HO4   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
 N1L  H1    C1  O1    111.45  3.000
 N1L  H1    C1  O5    108.64  3.000
 N1L  O1    C1  O5    108.00  3.000
 N1L  H1    C1  C2    108.52  3.000
 N1L  O1    C1  C2    109.31  3.000
 N1L  O5    C1  C2    110.95  3.000
 N1L  H2    C2  N2    108.08  3.000
 N1L  H2    C2  C3    108.27  3.000
 N1L  N2    C2  C3    113.89  3.000
 N1L  H2    C2  C1    107.45  3.000
 N1L  N2    C2  C1    110.07  3.000
 N1L  C3    C2  C1    108.87  3.000
 N1L  H3    C3  O3    110.40  3.000
 N1L  H3    C3  C4    107.31  3.000
 N1L  O3    C3  C4    112.09  3.000
 N1L  H3    C3  C2    107.58  3.000
 N1L  O3    C3  C2    107.79  3.000
 N1L  C4    C3  C2    111.59  3.000
 N1L  H4    C4  O4    111.35  3.000
 N1L  H4    C4  C5    107.66  3.000
 N1L  O4    C4  C5    111.69  3.000
 N1L  H4    C4  C3    108.06  3.000
 N1L  O4    C4  C3    109.09  3.000
 N1L  C5    C4  C3    108.89  3.000
 N1L  H5    C5  O5    110.24  3.000
 N1L  H5    C5  C6    106.96  3.000
 N1L  O5    C5  C6    110.59  3.000
 N1L  H5    C5  C4    107.71  3.000
 N1L  O5    C5  C4    109.40  3.000
 N1L  C6    C5  C4    111.88  3.000
 N1L  O6A   C6  O6B   126.98  3.000
 N1L  O6A   C6  C5    113.91  3.000
 N1L  O6B   C6  C5    119.09  3.000
 N1L  H22N  N2  H21N  105.55  3.000
 N1L  H22N  N2  C2    109.48  3.000
 N1L  H21N  N2  C2    109.12  3.000
 N1L  HO3   O3  C3    107.96  3.000
 N1L  HO4   O4  C4    102.95  3.000
 N1L  C5    O5  C1    113.27  3.000
 N1L  HO1   O1  C1    108.89  3.000

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
 N1L  chir_01  C1  C2  O5  O1  negativ
 N1L  chir_02  C2  N2  C3  C1  positiv
 N1L  chir_03  C3  O3  C2  C4  positiv
 N1L  chir_04  C4  O4  C3  C5  negativ
 N1L  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
 N1L  plan-1  C5   0.020
 N1L  plan-1  C6   0.020
 N1L  plan-1  O6B  0.020
 N1L  plan-1  O6A  0.020

