# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:58:52 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-azido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1N=[N+]=[N-]
#
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
 C4W  C4W  ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-2-azido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  31  17  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C4W
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
 C4W  C2   C  CH1    0  -0.138   0.4673   0.4953  -0.1545
 C4W  C3   C  CH1    0   0.039  -0.5616   1.4962   0.3558
 C4W  C4   C  CH1    0  -0.000  -1.9487   1.1155  -0.1547
 C4W  C5   C  CH1    0  -0.030  -2.2602  -0.3424   0.2049
 C4W  C6   C  CH2    0  -0.159  -3.5798  -0.8009  -0.3751
 C4W  C8   C  CH3    0  -0.787   4.1242   1.2314   0.4569
 C4W  N2   N  NH1    0  -0.639   1.7735   0.7485   0.3896
 C4W  O3   O  OH1    0  -0.660  -0.1766   2.7745  -0.0680
 C4W  O4   O  OH1    0  -0.672  -2.8685   2.0021   0.4405
 C4W  O5   O  O2     0  -0.483  -1.2487  -1.1904  -0.3123
 C4W  O6   O  OH1    0  -0.668  -3.8484  -2.1061   0.0739
 C4W  C1   C  CH1    0   0.206   0.0110  -0.9222   0.2126
 C4W  O7   O  O      0  -0.483   2.8921   0.8756  -1.5730
 C4W  N1   N  N      0  -0.363   0.8830  -1.9117  -0.3986
 C4W  N3   N  N      1   0.355   1.8764  -2.2212   0.2350
 C4W  N4   N  N     -1  -0.208   2.8192  -2.5745   0.7315
 C4W  H2   H  HCH1   0   0.283   0.5341   0.5634  -1.2431
 C4W  H3   H  HCH1   0   0.213  -0.5851   1.4378   1.4579
 C4W  H4   H  HCH1   0   0.232  -1.9516   1.2154  -1.2497
 C4W  H5   H  HCH1   0   0.230  -2.2994  -0.4324   1.3026
 C4W  H61  H  HCH2   0   0.207  -4.3574  -0.0971  -0.0563
 C4W  H62  H  HCH2   0   0.203  -3.5251  -0.7473  -1.4715
 C4W  H81  H  HCH3   0   0.260   4.2448   0.5139   1.2687
 C4W  H82  H  HCH3   0   0.264   5.0078   1.2015  -0.1748
 C4W  H83  H  HCH3   0   0.272   4.0531   2.2225   0.9081
 C4W  HN2  H  HNH1   0   0.406   1.8478   0.8655   1.3893
 C4W  HO3  H  HOH1   0   0.453  -0.8263   3.4040   0.2630
 C4W  HO4  H  HOH1   0   0.465  -3.5895   2.1673  -0.1729
 C4W  HO6  H  HOH1   0   0.458  -4.6993  -2.3743  -0.2840
 C4W  H1   H  HCH1   0   0.240   0.0078  -1.0282   1.3112
 C4W  C7   C  C      0   0.506   2.8874   0.9374  -0.3549

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
 C4W  O3  C3   single  1.401  0.020  1.401
 C4W  O7  C7   double  1.220  0.020  1.220
 C4W  C8  C7   single  1.508  0.020  1.508
 C4W  C7  N2   single  1.353  0.020  1.353
 C4W  C3  C4   single  1.526  0.020  1.526
 C4W  C3  C2   single  1.523  0.020  1.523
 C4W  O4  C4   single  1.409  0.020  1.409
 C4W  N2  C2   single  1.437  0.020  1.437
 C4W  C4  C5   single  1.534  0.020  1.534
 C4W  C2  C1   single  1.534  0.020  1.534
 C4W  O6  C6   single  1.406  0.020  1.406
 C4W  C5  O5   single  1.418  0.020  1.418
 C4W  C5  C6   single  1.513  0.020  1.513
 C4W  C1  O5   single  1.391  0.020  1.391
 C4W  C1  N1   single  1.454  0.020  1.454
 C4W  N1  N3   double  1.218  0.020  1.218
 C4W  N3  N4   double  1.123  0.020  1.123
 C4W  C2  H2   single  0.970  0.020  1.090
 C4W  C3  H3   single  0.970  0.020  1.090
 C4W  C4  H4   single  0.970  0.020  1.090
 C4W  C5  H5   single  0.970  0.020  1.090
 C4W  C6  H61  single  0.970  0.020  1.090
 C4W  C6  H62  single  0.970  0.020  1.090
 C4W  C8  H81  single  0.970  0.020  1.090
 C4W  C8  H82  single  0.970  0.020  1.090
 C4W  C8  H83  single  0.970  0.020  1.090
 C4W  N2  HN2  single  0.860  0.020  1.020
 C4W  O3  HO3  single  0.850  0.020  0.980
 C4W  O4  HO4  single  0.850  0.020  0.980
 C4W  O6  HO6  single  0.850  0.020  0.980
 C4W  C1  H1   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
 C4W  H2   C2  C1   108.31  3.000
 C4W  H2   C2  N2   108.09  3.000
 C4W  C1   C2  N2   110.03  3.000
 C4W  H2   C2  C3   109.51  3.000
 C4W  C1   C2  C3   109.03  3.000
 C4W  N2   C2  C3   111.79  3.000
 C4W  H3   C3  O3   110.87  3.000
 C4W  H3   C3  C4   107.54  3.000
 C4W  O3   C3  C4   112.10  3.000
 C4W  H3   C3  C2   108.30  3.000
 C4W  C4   C3  C2   109.75  3.000
 C4W  O3   C3  C2   108.22  3.000
 C4W  H4   C4  O4   111.21  3.000
 C4W  H4   C4  C5   108.62  3.000
 C4W  O4   C4  C5   111.49  3.000
 C4W  H4   C4  C3   108.23  3.000
 C4W  C5   C4  C3   110.08  3.000
 C4W  O4   C4  C3   107.16  3.000
 C4W  H5   C5  O5   109.87  3.000
 C4W  H5   C5  C6   109.04  3.000
 C4W  O5   C5  C6   107.53  3.000
 C4W  H5   C5  C4   108.57  3.000
 C4W  C6   C5  C4   112.05  3.000
 C4W  O5   C5  C4   109.77  3.000
 C4W  H62  C6  H61  107.10  3.000
 C4W  H62  C6  O6   111.92  3.000
 C4W  H61  C6  O6   111.56  3.000
 C4W  H62  C6  C5   108.93  3.000
 C4W  H61  C6  C5   108.22  3.000
 C4W  O6   C6  C5   109.00  3.000
 C4W  H83  C8  H82  108.57  3.000
 C4W  H83  C8  H81  107.28  3.000
 C4W  H82  C8  H81  108.95  3.000
 C4W  H83  C8  C7   110.25  3.000
 C4W  H82  C8  C7   110.40  3.000
 C4W  H81  C8  C7   111.30  3.000
 C4W  HN2  N2  C7   117.92  3.000
 C4W  HN2  N2  C2   117.54  3.000
 C4W  C7   N2  C2   124.36  3.000
 C4W  HO3  O3  C3   107.89  3.000
 C4W  HO4  O4  C4   109.16  3.000
 C4W  C1   O5  C5   113.15  3.000
 C4W  HO6  O6  C6   108.01  3.000
 C4W  H1   C1  N1   110.78  3.000
 C4W  H1   C1  O5   110.76  3.000
 C4W  N1   C1  O5   104.68  3.000
 C4W  H1   C1  C2   109.14  3.000
 C4W  N1   C1  C2   110.49  3.000
 C4W  O5   C1  C2   110.94  3.000
 C4W  N3   N1  C1   116.32  3.000
 C4W  N4   N3  N1   174.18  3.000
 C4W  O7   C7  N2   123.07  3.000
 C4W  N2   C7  C8   113.96  3.000
 C4W  O7   C7  C8   122.97  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
 C4W  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 C4W  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 C4W  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 C4W  Var_01    H81  C8  C7  N2   49.05  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
 C4W  chir_01  C2  C3  N2  C1  negativ
 C4W  chir_02  C3  O3  C2  C4  positiv
 C4W  chir_03  C4  O4  C5  C3  positiv
 C4W  chir_04  C5  O5  C4  C6  negativ
 C4W  chir_05  C1  O5  N1  C2  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
 C4W  plan-1  C2   0.020
 C4W  plan-1  C8   0.020
 C4W  plan-1  N2   0.020
 C4W  plan-1  O7   0.020
 C4W  plan-1  HN2  0.020
 C4W  plan-1  C7   0.020
 C4W  plan-2  C2   0.020
 C4W  plan-2  O5   0.020
 C4W  plan-2  C1   0.020
 C4W  plan-2  N1   0.020
 C4W  plan-2  N3   0.020
 C4W  plan-2  N4   0.020
 C4W  plan-2  H1   0.020

