# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 22:26:10 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-amino-2,3,6-trideoxy-3-methyl-alpha-L-lyxo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)C[C@](C)(N)[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
 RER  RER  3-amino-2,3,6-trideoxy-3-methyl-alpha-L-lyxo-hexopyranose  L-saccharide  26  11  .  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_RER
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
 RER  C1    C  CH1   0   0.276  2.3536  14.4917  6.1385
 RER  C2    C  CH2   0  -0.507  2.4974  14.0563  7.5942
 RER  C3    C  CT    0   0.050  3.0799  12.6523  7.7895
 RER  N3    N  NH2   0  -0.796  3.3824  12.5078  9.2103
 RER  C3A   C  CH3   0  -0.665  2.0777  11.5486  7.4518
 RER  C4    C  CH1   0   0.056  4.3335  12.5201  6.8859
 RER  O4    O  OH1   0  -0.673  5.3929  13.3301  7.3466
 RER  C5    C  CH1   0   0.021  4.0203  12.9326  5.4502
 RER  O5    O  O2    0  -0.495  3.5115  14.2594  5.4039
 RER  C5A   C  CH3   0  -0.677  5.2265  12.8821  4.5334
 RER  O1    O  OH1   0  -0.667  1.2814  13.8737  5.4689
 RER  H1    H  HCH1  0   0.207  2.2210  15.5815  6.1126
 RER  H21C  H  HCH2  0   0.241  3.1608  14.7794  8.0781
 RER  H22C  H  HCH2  0   0.245  1.5357  14.1420  8.1092
 RER  HO1   H  HOH1  0   0.454  0.5693  13.7074  6.0941
 RER  H31N  H  HNH2  0   0.340  3.7917  11.5978  9.3931
 RER  H32N  H  HNH2  0   0.337  4.0598  13.1989  9.5094
 RER  H3A1  H  HCH3  0   0.233  1.7756  11.5411  6.4077
 RER  H3A2  H  HCH3  0   0.226  2.5071  10.5688  7.6753
 RER  H3A3  H  HCH3  0   0.233  1.1783  11.6610  8.0590
 RER  H4    H  HCH1  0   0.210  4.6341  11.4608  6.8666
 RER  HO4   H  HOH1  0   0.446  5.7883  12.9071  8.1138
 RER  H5    H  HCH1  0   0.220  3.2763  12.2299  5.0580
 RER  H5A1  H  HCH3  0   0.233  4.9378  13.1143  3.5079
 RER  H5A2  H  HCH3  0   0.229  6.0028  13.5824  4.8384
 RER  H5A3  H  HCH3  0   0.226  5.6542  11.8790  4.5361

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
 RER  C1   C2    single  1.526  0.020  1.526
 RER  C1   O5    single  1.391  0.020  1.391
 RER  C1   O1    single  1.407  0.020  1.407
 RER  C2   C3    single  1.533  0.020  1.533
 RER  C3   N3    single  1.460  0.020  1.460
 RER  C3   C3A   single  1.529  0.020  1.529
 RER  C3   C4    single  1.551  0.020  1.551
 RER  C4   O4    single  1.411  0.020  1.411
 RER  C4   C5    single  1.526  0.020  1.526
 RER  C5   O5    single  1.422  0.020  1.422
 RER  C5   C5A   single  1.516  0.020  1.516
 RER  C1   H1    single  0.970  0.020  1.090
 RER  C2   H21C  single  0.970  0.020  1.090
 RER  C2   H22C  single  0.970  0.020  1.090
 RER  O1   HO1   single  0.850  0.020  0.980
 RER  N3   H31N  single  0.890  0.020  1.040
 RER  N3   H32N  single  0.890  0.020  1.040
 RER  C3A  H3A1  single  0.970  0.020  1.090
 RER  C3A  H3A2  single  0.970  0.020  1.090
 RER  C3A  H3A3  single  0.970  0.020  1.090
 RER  C4   H4    single  0.970  0.020  1.090
 RER  O4   HO4   single  0.850  0.020  0.980
 RER  C5   H5    single  0.970  0.020  1.090
 RER  C5A  H5A1  single  0.970  0.020  1.090
 RER  C5A  H5A2  single  0.970  0.020  1.090
 RER  C5A  H5A3  single  0.970  0.020  1.090

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
 RER  H1    C1   O1    109.42  3.000
 RER  H1    C1   O5    104.70  3.000
 RER  O1    C1   O5    108.04  3.000
 RER  H1    C1   C2    108.49  3.000
 RER  O1    C1   C2    113.60  3.000
 RER  O5    C1   C2    112.19  3.000
 RER  H22C  C2   H21C  105.84  3.000
 RER  H22C  C2   C3    110.23  3.000
 RER  H21C  C2   C3    108.58  3.000
 RER  H22C  C2   C1    110.11  3.000
 RER  H21C  C2   C1    106.88  3.000
 RER  C3    C2   C1    114.76  3.000
 RER  C4    C3   C3A   109.86  3.000
 RER  C4    C3   N3    113.03  3.000
 RER  C3A   C3   N3    106.23  3.000
 RER  C4    C3   C2    108.12  3.000
 RER  C3A   C3   C2    112.59  3.000
 RER  N3    C3   C2    107.07  3.000
 RER  H32N  N3   H31N  106.80  3.000
 RER  H32N  N3   C3    111.00  3.000
 RER  H31N  N3   C3    110.35  3.000
 RER  H3A3  C3A  H3A2  107.60  3.000
 RER  H3A3  C3A  H3A1  107.83  3.000
 RER  H3A2  C3A  H3A1  107.43  3.000
 RER  H3A3  C3A  C3    110.07  3.000
 RER  H3A2  C3A  C3    110.16  3.000
 RER  H3A1  C3A  C3    113.55  3.000
 RER  H4    C4   C5    107.43  3.000
 RER  H4    C4   O4    110.67  3.000
 RER  C5    C4   O4    107.82  3.000
 RER  H4    C4   C3    108.23  3.000
 RER  C5    C4   C3    111.05  3.000
 RER  O4    C4   C3    111.57  3.000
 RER  HO4   O4   C4    108.47  3.000
 RER  H5    C5   C5A   107.60  3.000
 RER  H5    C5   O5    110.11  3.000
 RER  C5A   C5   O5    107.23  3.000
 RER  H5    C5   C4    107.61  3.000
 RER  C5A   C5   C4    113.37  3.000
 RER  O5    C5   C4    110.87  3.000
 RER  C5    O5   C1    115.89  3.000
 RER  H5A3  C5A  H5A2  108.13  3.000
 RER  H5A3  C5A  H5A1  107.58  3.000
 RER  H5A2  C5A  H5A1  108.37  3.000
 RER  H5A3  C5A  C5    109.95  3.000
 RER  H5A2  C5A  C5    112.11  3.000
 RER  H5A1  C5A  C5    110.55  3.000
 RER  HO1   O1   C1    109.31  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
 RER  chir_01  C1  C2  O5   O1   negativ
 RER  chir_02  C3  C4  C3A  C2   positiv
 RER  chir_03  C4  O4  C3   C5   negativ
 RER  chir_04  C5  O5  C4   C5A  positiv

