# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 08:23:46 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-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
 ERE  ERE  3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-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 PERFECT
;

data_comp_ERE
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
 ERE  C1    C  CH1   0   0.255  22.3595   9.4063  -6.4058
 ERE  C2    C  CH2   0  -0.458  20.9480   9.8863  -6.1049
 ERE  C3    C  CT    0   0.027  20.7564  10.5263  -4.7242
 ERE  C4    C  CH1   0   0.067  21.8943  11.5485  -4.5431
 ERE  C5    C  CH1   0   0.015  23.2727  10.9298  -4.8070
 ERE  O5    O  O2    0  -0.502  23.3127  10.3959  -6.1227
 ERE  C3A   C  CH3   0  -0.646  20.7379   9.4840  -3.6045
 ERE  N3    N  NH2   0  -0.789  19.4386  11.1596  -4.7281
 ERE  O4    O  OH1   0  -0.670  21.8135  12.0937  -3.2463
 ERE  C5A   C  CH3   0  -0.697  24.3942  11.9469  -4.7136
 ERE  O1    O  OH1   0  -0.662  22.6111   8.2191  -5.7153
 ERE  H1    H  HCH1  0   0.217  22.4560   9.2443  -7.4865
 ERE  H21   H  HCH2  0   0.236  20.7060  10.6373  -6.8644
 ERE  H22   H  HCH2  0   0.244  20.2374   9.0683  -6.2434
 ERE  HO1   H  HOH1  0   0.452  23.4516   7.8588  -6.0191
 ERE  H4    H  HCH1  0   0.202  21.7413  12.3318  -5.3046
 ERE  H31   H  HCH3  0   0.223  20.4700   9.9408  -2.6509
 ERE  H32   H  HCH3  0   0.224  19.9877   8.7244  -3.8275
 ERE  H33   H  HCH3  0   0.231  21.6918   8.9795  -3.4760
 ERE  HN31  H  HNH2  0   0.338  19.2914  11.6277  -3.8411
 ERE  HN32  H  HNH2  0   0.335  19.4130  11.8922  -5.4297
 ERE  H5    H  HCH1  0   0.210  23.4606  10.1413  -4.0658
 ERE  HO4   H  HOH1  0   0.453  22.2584  12.9457  -3.2391
 ERE  H51   H  HCH3  0   0.241  25.3525  11.4866  -4.9564
 ERE  H52   H  HCH3  0   0.225  24.2313  12.7819  -5.3981
 ERE  H53   H  HCH3  0   0.230  24.4773  12.3447  -3.7025

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
 ERE  C1   C2    single  1.521  0.020  1.521
 ERE  C1   O5    single  1.403  0.020  1.403
 ERE  C1   O1    single  1.396  0.020  1.396
 ERE  C2   C3    single  1.534  0.020  1.534
 ERE  C3   C4    single  1.540  0.020  1.540
 ERE  C3   C3A   single  1.530  0.020  1.530
 ERE  C3   N3    single  1.462  0.020  1.462
 ERE  C4   C5    single  1.534  0.020  1.534
 ERE  C4   O4    single  1.409  0.020  1.409
 ERE  C5   O5    single  1.420  0.020  1.420
 ERE  C5   C5A   single  1.517  0.020  1.517
 ERE  C1   H1    single  0.970  0.020  1.090
 ERE  C2   H21   single  0.970  0.020  1.090
 ERE  C2   H22   single  0.970  0.020  1.090
 ERE  O1   HO1   single  0.850  0.020  0.980
 ERE  C4   H4    single  0.970  0.020  1.090
 ERE  C3A  H31   single  0.970  0.020  1.090
 ERE  C3A  H32   single  0.970  0.020  1.090
 ERE  C3A  H33   single  0.970  0.020  1.090
 ERE  N3   HN31  single  0.890  0.020  1.040
 ERE  N3   HN32  single  0.890  0.020  1.040
 ERE  C5   H5    single  0.970  0.020  1.090
 ERE  O4   HO4   single  0.850  0.020  0.980
 ERE  C5A  H51   single  0.970  0.020  1.090
 ERE  C5A  H52   single  0.970  0.020  1.090
 ERE  C5A  H53   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
 ERE  H1    C1   O1    110.22  3.000
 ERE  H1    C1   O5    104.08  3.000
 ERE  O1    C1   O5    112.18  3.000
 ERE  H1    C1   C2    108.86  3.000
 ERE  O1    C1   C2    109.74  3.000
 ERE  O5    C1   C2    111.60  3.000
 ERE  H22   C2   H21   106.37  3.000
 ERE  H22   C2   C3    110.20  3.000
 ERE  H21   C2   C3    108.09  3.000
 ERE  H22   C2   C1    110.02  3.000
 ERE  H21   C2   C1    106.52  3.000
 ERE  C3    C2   C1    115.19  3.000
 ERE  N3    C3   C3A   106.63  3.000
 ERE  N3    C3   C4    112.25  3.000
 ERE  C3A   C3   C4    112.03  3.000
 ERE  N3    C3   C2    106.91  3.000
 ERE  C3A   C3   C2    112.09  3.000
 ERE  C4    C3   C2    106.89  3.000
 ERE  H4    C4   O4    110.65  3.000
 ERE  H4    C4   C5    106.99  3.000
 ERE  O4    C4   C5    111.47  3.000
 ERE  H4    C4   C3    106.72  3.000
 ERE  O4    C4   C3    108.82  3.000
 ERE  C5    C4   C3    112.08  3.000
 ERE  H5    C5   C5A   108.26  3.000
 ERE  H5    C5   O5    110.51  3.000
 ERE  C5A   C5   O5    106.75  3.000
 ERE  H5    C5   C4    109.10  3.000
 ERE  C5A   C5   C4    112.54  3.000
 ERE  O5    C5   C4    109.65  3.000
 ERE  C5    O5   C1    115.66  3.000
 ERE  H33   C3A  H32   107.73  3.000
 ERE  H33   C3A  H31   107.86  3.000
 ERE  H32   C3A  H31   107.55  3.000
 ERE  H33   C3A  C3    113.09  3.000
 ERE  H32   C3A  C3    109.46  3.000
 ERE  H31   C3A  C3    110.95  3.000
 ERE  HN32  N3   HN31  105.55  3.000
 ERE  HN32  N3   C3    109.71  3.000
 ERE  HN31  N3   C3    109.18  3.000
 ERE  HO4   O4   C4    108.86  3.000
 ERE  H53   C5A  H52   108.30  3.000
 ERE  H53   C5A  H51   107.07  3.000
 ERE  H52   C5A  H51   108.32  3.000
 ERE  H53   C5A  C5    111.00  3.000
 ERE  H52   C5A  C5    111.33  3.000
 ERE  H51   C5A  C5    110.67  3.000
 ERE  HO1   O1   C1    108.61  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
 ERE  chir_01  C1  C2   O5  O1   negativ
 ERE  chir_02  C3  C3A  C4  C2   negativ
 ERE  chir_03  C4  O4   C5  C3   negativ
 ERE  chir_04  C5  O5   C4  C5A  positiv

