# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:18:51 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2R)-2-{[(1R,2S,3R,4R,5R)-4-(acetylamino)-2-hydroxy-6,8-dioxabicyclo[3.2.1]oct-3-yl]oxy}propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@H]1[C@H](O)[C@H]2CO[C@H](O2)[C@@H]1NC(C)=O)C(O)=O
#
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
 AH0  AH0  '(2R)-2-{[(1R,2S,3R,4R,5R)-4-(acetylamino)-2-hydroxy-6,8-dioxabicyclo[3.2.1]oct-3-yl]oxy}propanoic acid (non-preferred name)'  ligand  35  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AH0
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
 AH0  C1   C  CH1    0   0.265   1.0947   0.6337   1.3851
 AH0  C2   C  CH1    0  -0.156   0.8205  -0.2918   0.1921
 AH0  N2   N  NH1    0  -0.629   2.0726  -0.7517  -0.3620
 AH0  C7   C  C      0   0.523   2.6200  -1.9495  -0.0863
 AH0  O7   O  O      0  -0.506   2.0962  -2.7688   0.6570
 AH0  C8   C  CH3    0  -0.779   3.9438  -2.2184  -0.7567
 AH0  C3   C  CH1    0   0.016  -0.0118   0.4286  -0.8989
 AH0  O3   O  O2     0  -0.484  -1.3800   0.4546  -0.6128
 AH0  C4   C  CH1    0   0.061   0.4249   1.8965  -1.0423
 AH0  O4   O  OH1    0  -0.669   1.5716   1.8990  -1.8638
 AH0  C5   C  CH1    0  -0.156   0.7339   2.5143   0.3228
 AH0  O5   O  O2     0  -0.481   1.7750   1.7718   0.9412
 AH0  C6   C  CH2    0  -0.174  -0.3916   2.3570   1.3482
 AH0  O6   O  O2     0  -0.501  -0.0990   1.1014   1.9547
 AH0  CA   C  CH1    0  -0.073  -2.0919  -0.7614  -0.6905
 AH0  CB   C  CH3    0  -0.687  -2.2918  -1.2150  -2.1339
 AH0  C    C  C      0   0.382  -3.4557  -0.5828   0.0125
 AH0  O    O  O      0  -0.590  -3.7944   0.5590   0.3615
 AH0  OXT  O  OC    -1  -0.626  -4.1073  -1.6390   0.1496
 AH0  H1   H  HCH1   0   0.253   1.6975   0.1245   2.1427
 AH0  H2   H  HCH1   0   0.274   0.2789  -1.1696   0.5472
 AH0  HN2  H  HNH1   0   0.398   2.5812  -0.1126  -0.9531
 AH0  H81  H  HCH3   0   0.249   4.2154  -1.4713  -1.4999
 AH0  H82  H  HCH3   0   0.268   4.7296  -2.2522  -0.0015
 AH0  H83  H  HCH3   0   0.264   3.9147  -3.1947  -1.2390
 AH0  H3   H  HCH1   0   0.238   0.1887  -0.0734  -1.8564
 AH0  H4   H  HCH1   0   0.233  -0.3983   2.4575  -1.5046
 AH0  HO4  H  HOH1   0   0.458   1.9314   2.7915  -1.9025
 AH0  H5   H  HCH1   0   0.272   1.0563   3.5524   0.2138
 AH0  H61  H  HCH2   0   0.232  -0.3416   3.1492   2.0997
 AH0  H62  H  HCH2   0   0.247  -1.3894   2.3446   0.9120
 AH0  HA   H  HCH1   0   0.200  -1.5562  -1.5573  -0.1549
 AH0  HB1  H  HCH3   0   0.221  -2.8289  -0.4596  -2.7110
 AH0  HB2  H  HCH3   0   0.226  -1.3469  -1.4185  -2.6404
 AH0  HB3  H  HCH3   0   0.233  -2.8732  -2.1353  -2.1537

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
 AH0  C1  C2   single  1.535  0.020  1.535
 AH0  C1  O5   single  1.398  0.020  1.398
 AH0  C1  O6   single  1.403  0.020  1.403
 AH0  C1  H1   single  0.970  0.020  1.090
 AH0  C2  N2   single  1.444  0.020  1.444
 AH0  C2  C3   single  1.550  0.020  1.550
 AH0  C2  H2   single  0.970  0.020  1.090
 AH0  N2  C7   single  1.346  0.020  1.346
 AH0  N2  HN2  single  0.860  0.020  1.020
 AH0  C7  O7   double  1.224  0.020  1.224
 AH0  C7  C8   single  1.508  0.020  1.508
 AH0  C8  H81  single  0.970  0.020  1.090
 AH0  C8  H82  single  0.970  0.020  1.090
 AH0  C8  H83  single  0.970  0.020  1.090
 AH0  C3  O3   single  1.398  0.020  1.398
 AH0  C3  C4   single  1.538  0.020  1.538
 AH0  C3  H3   single  0.970  0.020  1.090
 AH0  O3  CA   single  1.411  0.020  1.411
 AH0  C4  O4   single  1.411  0.020  1.411
 AH0  C4  C5   single  1.530  0.020  1.530
 AH0  C4  H4   single  0.970  0.020  1.090
 AH0  O4  HO4  single  0.850  0.020  0.980
 AH0  C5  O5   single  1.420  0.020  1.420
 AH0  C5  C6   single  1.531  0.020  1.531
 AH0  C5  H5   single  0.970  0.020  1.090
 AH0  C6  O6   single  1.425  0.020  1.425
 AH0  C6  H61  single  0.970  0.020  1.090
 AH0  C6  H62  single  0.970  0.020  1.090
 AH0  CA  CB   single  1.526  0.020  1.526
 AH0  CA  C    single  1.545  0.020  1.545
 AH0  CA  HA   single  0.970  0.020  1.090
 AH0  CB  HB1  single  0.970  0.020  1.090
 AH0  CB  HB2  single  0.970  0.020  1.090
 AH0  CB  HB3  single  0.970  0.020  1.090
 AH0  C   O    deloc   1.241  0.020  1.241
 AH0  C   OXT  deloc   1.249  0.020  1.249

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
 AH0  H1   C1  O6   110.05  3.000
 AH0  H1   C1  O5   109.31  3.000
 AH0  O6   C1  O5   105.76  3.000
 AH0  H1   C1  C2   110.86  3.000
 AH0  O6   C1  C2   111.39  3.000
 AH0  O5   C1  C2   109.33  3.000
 AH0  H2   C2  C3   109.67  3.000
 AH0  H2   C2  N2   107.40  3.000
 AH0  C3   C2  N2   110.09  3.000
 AH0  H2   C2  C1   108.72  3.000
 AH0  C3   C2  C1   111.28  3.000
 AH0  N2   C2  C1   109.59  3.000
 AH0  HN2  N2  C7   118.64  3.000
 AH0  HN2  N2  C2   117.41  3.000
 AH0  C7   N2  C2   123.88  3.000
 AH0  C8   C7  O7   121.75  3.000
 AH0  C8   C7  N2   115.13  3.000
 AH0  O7   C7  N2   123.11  3.000
 AH0  H83  C8  H82  107.35  3.000
 AH0  H83  C8  H81  108.64  3.000
 AH0  H82  C8  H81  108.32  3.000
 AH0  H83  C8  C7   109.47  3.000
 AH0  H82  C8  C7   109.28  3.000
 AH0  H81  C8  C7   113.60  3.000
 AH0  H3   C3  C4   107.62  3.000
 AH0  H3   C3  O3   111.42  3.000
 AH0  C4   C3  O3   106.21  3.000
 AH0  H3   C3  C2   107.63  3.000
 AH0  C4   C3  C2   110.90  3.000
 AH0  O3   C3  C2   112.97  3.000
 AH0  CA   O3  C3   117.80  3.000
 AH0  H4   C4  C5   108.71  3.000
 AH0  H4   C4  O4   111.30  3.000
 AH0  C5   C4  O4   110.78  3.000
 AH0  H4   C4  C3   108.30  3.000
 AH0  C5   C4  C3   111.07  3.000
 AH0  O4   C4  C3   106.66  3.000
 AH0  HO4  O4  C4   109.19  3.000
 AH0  H5   C5  C6   112.43  3.000
 AH0  H5   C5  O5   108.90  3.000
 AH0  C6   C5  O5   101.16  3.000
 AH0  H5   C5  C4   110.75  3.000
 AH0  C6   C5  C4   114.06  3.000
 AH0  O5   C5  C4   108.99  3.000
 AH0  C5   O5  C1   101.95  3.000
 AH0  H62  C6  H61  109.00  3.000
 AH0  H62  C6  O6   110.40  3.000
 AH0  H61  C6  O6   109.67  3.000
 AH0  H62  C6  C5   113.99  3.000
 AH0  H61  C6  C5   110.64  3.000
 AH0  O6   C6  C5   102.99  3.000
 AH0  C6   O6  C1   107.20  3.000
 AH0  HA   CA  C    107.00  3.000
 AH0  HA   CA  CB   108.04  3.000
 AH0  C    CA  CB   110.44  3.000
 AH0  HA   CA  O3   110.57  3.000
 AH0  C    CA  O3   108.70  3.000
 AH0  CB   CA  O3   111.98  3.000
 AH0  HB3  CB  HB2  107.24  3.000
 AH0  HB3  CB  HB1  108.21  3.000
 AH0  HB2  CB  HB1  108.04  3.000
 AH0  HB3  CB  CA   109.77  3.000
 AH0  HB2  CB  CA   112.39  3.000
 AH0  HB1  CB  CA   111.02  3.000
 AH0  OXT  C   O    127.23  3.000
 AH0  OXT  C   CA   114.39  3.000
 AH0  O    C   CA   118.38  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
 AH0  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 AH0  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 AH0  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 AH0  Var_01    C5   C6  O6  C1    2.66  30.0  3
 AH0  Var_02    H81  C8  C7  N2   -8.91  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
 AH0  chir_01  C1  C2  O5  O6  negativ
 AH0  chir_02  C2  N2  C3  C1  positiv
 AH0  chir_03  C3  O3  C4  C2  negativ
 AH0  chir_04  C4  O4  C3  C5  negativ
 AH0  chir_05  C5  O5  C4  C6  negativ
 AH0  chir_06  CA  O3  C   CB  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
 AH0  plan-1  C2   0.020
 AH0  plan-1  N2   0.020
 AH0  plan-1  C7   0.020
 AH0  plan-1  O7   0.020
 AH0  plan-1  C8   0.020
 AH0  plan-1  HN2  0.020
 AH0  plan-2  CA   0.020
 AH0  plan-2  C    0.020
 AH0  plan-2  O    0.020
 AH0  plan-2  OXT  0.020

