# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:00:21 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1CO[C@H](CO)[C@@H](O)[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
 RTV  RTV  2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol  D-saccharide  29  14  .  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_RTV
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
 RTV  O4   O  OH1   0  -0.676  -4.9555  -1.0540  36.3084
 RTV  C4   C  CH1   0  -0.037  -4.4198  -1.1814  35.0094
 RTV  C3   C  CH1   0   0.037  -4.5512  -2.6562  34.6533
 RTV  O3   O  OH1   0  -0.665  -3.8799  -2.8515  33.4367
 RTV  C2   C  CH1   0  -0.103  -6.0470  -3.0452  34.5820
 RTV  N2   N  NH1   0  -0.654  -6.2294  -4.2496  33.7972
 RTV  C7   C  C     0   0.505  -6.2004  -5.4944  34.3202
 RTV  O7   O  O     0  -0.492  -5.9447  -5.7078  35.4957
 RTV  C8   C  CH3   0  -0.784  -6.4979  -6.5954  33.3318
 RTV  C5   C  CH1   0   0.011  -5.1576  -0.2974  33.9759
 RTV  C6   C  CH2   0  -0.175  -4.1910   0.3641  33.0171
 RTV  O6   O  OH1   0  -0.671  -4.9093   1.2282  32.1690
 RTV  O5   O  O2    0  -0.486  -6.1035  -1.0236  33.2224
 RTV  C1   C  CH2   0  -0.207  -6.8770  -1.8827  34.0221
 RTV  H4   H  HCH1  0   0.238  -3.3534  -0.9135  35.0120
 RTV  H3   H  HCH1  0   0.233  -4.0842  -3.2520  35.4496
 RTV  HO3  H  HOH1  0   0.449  -4.0382  -3.7565  33.1479
 RTV  H2   H  HCH1  0   0.268  -6.3898  -3.2601  35.5944
 RTV  HN2  H  HNH1  0   0.405  -6.4735  -4.1480  32.8239
 RTV  H82  H  HCH3  0   0.262  -6.5361  -7.5567  33.8372
 RTV  H83  H  HCH3  0   0.264  -7.4492  -6.4243  32.8271
 RTV  H81  H  HCH3  0   0.268  -5.7252  -6.6380  32.5628
 RTV  H5   H  HCH1  0   0.220  -5.6782   0.4983  34.5358
 RTV  H61  H  HCH2  0   0.201  -3.4511   0.9089  33.6179
 RTV  H62  H  HCH2  0   0.206  -3.6461  -0.4033  32.4546
 RTV  HO6  H  HOH1  0   0.456  -4.2832   1.6491  31.5734
 RTV  H11  H  HCH2  0   0.249  -7.6954  -2.2550  33.4024
 RTV  H12  H  HCH2  0   0.223  -7.3306  -1.3309  34.8540
 RTV  HO4  H  HOH1  0   0.455  -4.8980  -0.1322  36.5773

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
 RTV  O4  C4   single  1.411  0.020  1.411
 RTV  C4  C3   single  1.523  0.020  1.523
 RTV  C4  C5   single  1.547  0.020  1.547
 RTV  C3  C2   single  1.547  0.020  1.547
 RTV  C3  O3   single  1.403  0.020  1.403
 RTV  C2  N2   single  1.449  0.020  1.449
 RTV  C2  C1   single  1.534  0.020  1.534
 RTV  N2  C7   single  1.350  0.020  1.350
 RTV  C7  C8   single  1.509  0.020  1.509
 RTV  C7  O7   double  1.222  0.020  1.222
 RTV  C5  C6   single  1.514  0.020  1.514
 RTV  C5  O5   single  1.411  0.020  1.411
 RTV  C6  O6   single  1.408  0.020  1.408
 RTV  O5  C1   single  1.406  0.020  1.406
 RTV  C4  H4   single  0.970  0.020  1.090
 RTV  C3  H3   single  0.970  0.020  1.090
 RTV  O3  HO3  single  0.850  0.020  0.980
 RTV  C2  H2   single  0.970  0.020  1.090
 RTV  N2  HN2  single  0.860  0.020  1.020
 RTV  C8  H82  single  0.970  0.020  1.090
 RTV  C8  H83  single  0.970  0.020  1.090
 RTV  C8  H81  single  0.970  0.020  1.090
 RTV  C5  H5   single  0.970  0.020  1.090
 RTV  C6  H61  single  0.970  0.020  1.090
 RTV  C6  H62  single  0.970  0.020  1.090
 RTV  O6  HO6  single  0.850  0.020  0.980
 RTV  C1  H11  single  0.970  0.020  1.090
 RTV  C1  H12  single  0.970  0.020  1.090
 RTV  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
 RTV  HO4  O4  C4   108.73  3.000
 RTV  H4   C4  C5   108.96  3.000
 RTV  H4   C4  C3   108.68  3.000
 RTV  C5   C4  C3   110.85  3.000
 RTV  H4   C4  O4   110.12  3.000
 RTV  C5   C4  O4   112.48  3.000
 RTV  C3   C4  O4   105.66  3.000
 RTV  H3   C3  C2   107.94  3.000
 RTV  H3   C3  O3   110.47  3.000
 RTV  C2   C3  O3   112.80  3.000
 RTV  H3   C3  C4   108.60  3.000
 RTV  O3   C3  C4   107.23  3.000
 RTV  C2   C3  C4   109.74  3.000
 RTV  HO3  O3  C3   108.19  3.000
 RTV  H2   C2  C1   108.55  3.000
 RTV  H2   C2  N2   107.43  3.000
 RTV  C1   C2  N2   111.35  3.000
 RTV  H2   C2  C3   108.10  3.000
 RTV  C1   C2  C3   110.45  3.000
 RTV  N2   C2  C3   110.83  3.000
 RTV  HN2  N2  C7   118.15  3.000
 RTV  HN2  N2  C2   118.00  3.000
 RTV  C7   N2  C2   123.62  3.000
 RTV  C8   C7  O7   122.95  3.000
 RTV  O7   C7  N2   122.55  3.000
 RTV  C8   C7  N2   114.49  3.000
 RTV  H81  C8  H83  107.32  3.000
 RTV  H81  C8  H82  108.55  3.000
 RTV  H83  C8  H82  108.87  3.000
 RTV  H81  C8  C7   110.52  3.000
 RTV  H83  C8  C7   111.14  3.000
 RTV  H82  C8  C7   110.35  3.000
 RTV  H5   C5  O5   109.02  3.000
 RTV  H5   C5  C6   107.91  3.000
 RTV  O5   C5  C6   108.35  3.000
 RTV  H5   C5  C4   107.34  3.000
 RTV  O5   C5  C4   112.48  3.000
 RTV  C6   C5  C4   111.61  3.000
 RTV  H62  C6  H61  107.04  3.000
 RTV  H62  C6  O6   111.97  3.000
 RTV  H61  C6  O6   111.65  3.000
 RTV  H62  C6  C5   109.66  3.000
 RTV  H61  C6  C5   107.50  3.000
 RTV  O6   C6  C5   108.91  3.000
 RTV  HO6  O6  C6   108.05  3.000
 RTV  C1   O5  C5   112.32  3.000
 RTV  H12  C1  H11  106.99  3.000
 RTV  H12  C1  O5   110.59  3.000
 RTV  H11  C1  O5   107.33  3.000
 RTV  H12  C1  C2   109.16  3.000
 RTV  H11  C1  C2   110.75  3.000
 RTV  O5   C1  C2   111.90  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
 RTV  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 RTV  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 RTV  CONST_03  HN2  N2  C7  O7   180.00   0.0  0
 RTV  Var_01    H11  C1  O5  C5   169.42  30.0  1
 RTV  Var_02    H82  C8  C7  N2  -175.44  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
 RTV  chir_01  C4  O4  C3  C5  negativ
 RTV  chir_02  C3  O3  C4  C2  negativ
 RTV  chir_03  C2  N2  C3  C1  negativ
 RTV  chir_04  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
 RTV  plan-1  C2   0.020
 RTV  plan-1  N2   0.020
 RTV  plan-1  C7   0.020
 RTV  plan-1  O7   0.020
 RTV  plan-1  C8   0.020
 RTV  plan-1  HN2  0.020

