# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:54:19 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 2,6-diamino-1,5-anhydro-2,3,6-trideoxy-D-ribo-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1OC[C@H](N)C[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
 ADR  ADR  2,6-diamino-1,5-anhydro-2,3,6-trideoxy-D-ribo-hexitol  D-saccharide  24  10  .  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_ADR
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
 ADR  C    C  CH1   0   0.041   0.0173   0.1706   0.8771
 ADR  O    O  O2    0  -0.498   1.2226  -0.2915   0.2999
 ADR  C1   C  CH2   0  -0.168   1.4182   0.1569  -1.0207
 ADR  C2   C  CH1   0  -0.105   0.3289  -0.3600  -1.9508
 ADR  N2   N  NH2   0  -0.803   0.5300   0.2006  -3.2779
 ADR  C3   C  CH2   0  -0.494  -1.0212   0.0711  -1.3938
 ADR  C4   C  CH1   0   0.055  -1.1720  -0.3437   0.0662
 ADR  O4   O  OH1   0  -0.675  -2.3452   0.1851   0.6448
 ADR  C5   C  CH2   0  -0.302  -0.0022  -0.2939   2.3217
 ADR  N6   N  NH2   0  -0.803   1.0988   0.2905   3.0700
 ADR  HC   H  HCH1  0   0.198  -0.0030   1.2738   0.8583
 ADR  H11  H  HCH2  0   0.194   1.4332   1.2561  -1.0675
 ADR  H12  H  HCH2  0   0.235   2.4009  -0.2024  -1.3356
 ADR  H2   H  HCH1  0   0.206   0.3723  -1.4604  -1.9426
 ADR  H21  H  HNH2  0   0.345   1.3704  -0.1910  -3.6865
 ADR  H22  H  HNH2  0   0.348  -0.2257  -0.0971  -3.8831
 ADR  H31  H  HCH2  0   0.223  -1.1033   1.1618  -1.4680
 ADR  H32  H  HCH2  0   0.242  -1.8331  -0.3581  -1.9911
 ADR  H4   H  HCH1  0   0.196  -1.1722  -1.4435   0.1255
 ADR  HO4  H  HOH1  0   0.452  -3.1013  -0.1641   0.1630
 ADR  H51  H  HCH2  0   0.193  -0.0196  -1.3945   2.3385
 ADR  H52  H  HCH2  0   0.232  -0.9381   0.0378   2.7728
 ADR  H61  H  HNH2  0   0.349   1.0089   0.0395   4.0456
 ADR  H62  H  HNH2  0   0.340   1.9725  -0.1152   2.7616

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
 ADR  C   O    single  1.414  0.020  1.414
 ADR  C   C4   single  1.529  0.020  1.529
 ADR  C   C5   single  1.518  0.020  1.518
 ADR  C   HC   single  0.970  0.020  1.090
 ADR  O   C1   single  1.408  0.020  1.408
 ADR  C1  C2   single  1.523  0.020  1.523
 ADR  C1  H11  single  0.970  0.020  1.090
 ADR  C1  H12  single  0.970  0.020  1.090
 ADR  C2  N2   single  1.455  0.020  1.455
 ADR  C2  C3   single  1.523  0.020  1.523
 ADR  C2  H2   single  0.970  0.020  1.090
 ADR  N2  H21  single  0.890  0.020  1.040
 ADR  N2  H22  single  0.890  0.020  1.040
 ADR  C3  C4   single  1.525  0.020  1.525
 ADR  C3  H31  single  0.970  0.020  1.090
 ADR  C3  H32  single  0.970  0.020  1.090
 ADR  C4  O4   single  1.411  0.020  1.411
 ADR  C4  H4   single  0.970  0.020  1.090
 ADR  O4  HO4  single  0.850  0.020  0.980
 ADR  C5  N6   single  1.454  0.020  1.454
 ADR  C5  H51  single  0.970  0.020  1.090
 ADR  C5  H52  single  0.970  0.020  1.090
 ADR  N6  H61  single  0.890  0.020  1.040
 ADR  N6  H62  single  0.890  0.020  1.040

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
 ADR  HC   C   C5   108.79  3.000
 ADR  HC   C   C4   108.24  3.000
 ADR  C5   C   C4   113.08  3.000
 ADR  HC   C   O    109.60  3.000
 ADR  C5   C   O    107.43  3.000
 ADR  C4   C   O    109.67  3.000
 ADR  C1   O   C    113.40  3.000
 ADR  H12  C1  H11  107.70  3.000
 ADR  H12  C1  C2   110.83  3.000
 ADR  H11  C1  C2   108.83  3.000
 ADR  H12  C1  O    106.89  3.000
 ADR  H11  C1  O    111.09  3.000
 ADR  C2   C1  O    111.42  3.000
 ADR  H2   C2  C3   108.37  3.000
 ADR  H2   C2  N2   112.73  3.000
 ADR  C3   C2  N2   110.31  3.000
 ADR  H2   C2  C1   107.85  3.000
 ADR  C3   C2  C1   108.34  3.000
 ADR  N2   C2  C1   109.12  3.000
 ADR  H22  N2  H21  105.33  3.000
 ADR  H22  N2  C2   109.19  3.000
 ADR  H21  N2  C2   109.48  3.000
 ADR  H32  C3  H31  107.30  3.000
 ADR  H32  C3  C4   110.00  3.000
 ADR  H31  C3  C4   109.15  3.000
 ADR  H32  C3  C2   110.28  3.000
 ADR  H31  C3  C2   108.87  3.000
 ADR  C4   C3  C2   111.15  3.000
 ADR  H4   C4  O4   110.61  3.000
 ADR  H4   C4  C3   108.85  3.000
 ADR  O4   C4  C3   111.89  3.000
 ADR  H4   C4  C    107.91  3.000
 ADR  O4   C4  C    107.65  3.000
 ADR  C3   C4  C    109.84  3.000
 ADR  HO4  O4  C4   108.18  3.000
 ADR  H52  C5  H51  106.51  3.000
 ADR  H52  C5  N6   108.34  3.000
 ADR  H51  C5  N6   113.95  3.000
 ADR  H52  C5  C    108.16  3.000
 ADR  H51  C5  C    108.71  3.000
 ADR  N6   C5  C    110.92  3.000
 ADR  H62  N6  H61  105.74  3.000
 ADR  H62  N6  C5   109.63  3.000
 ADR  H61  N6  C5   109.24  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
 ADR  Var_01  C2   C1  O   C  -62.50  30.0  1
 ADR  Var_02  H61  N6  C5  C  174.40  30.0  3

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
 ADR  chir_01  C   O   C4  C5  negativ
 ADR  chir_02  C2  N2  C3  C1  positiv
 ADR  chir_03  C4  O4  C3  C   negativ

