# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:20:23 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  36  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   0.264   1.1047   0.6876   1.4028
 AH0  C2   C  CH1   0  -0.145   0.8131  -0.2921   0.2570
 AH0  N2   N  NH1   0  -0.630   2.0561  -0.7971  -0.2760
 AH0  C7   C  C     0   0.524   2.5818  -1.9903   0.0610
 AH0  O7   O  O     0  -0.503   2.0305  -2.7686   0.8271
 AH0  C8   C  CH3   0  -0.780   3.9175  -2.3011  -0.5650
 AH0  C3   C  CH1   0  -0.007  -0.0114   0.3902  -0.8602
 AH0  O3   O  O2    0  -0.486  -1.3842   0.4022  -0.5568
 AH0  C4   C  CH1   0   0.062   0.4227   1.8491  -1.0728
 AH0  O4   O  OH1   0  -0.667   1.5531   1.8008  -1.9133
 AH0  C5   C  CH1   0  -0.156   0.7634   2.5239   0.2576
 AH0  O5   O  O2    0  -0.479   1.7978   1.7914   0.8966
 AH0  C6   C  CH2   0  -0.172  -0.3505   2.4347   1.3018
 AH0  O6   O  O2    0  -0.498  -0.0800   1.1981   1.9535
 AH0  CA   C  CH1   0  -0.064  -2.0590  -0.8037  -0.7922
 AH0  CB   C  CH3   0  -0.675  -2.5411  -0.9055  -2.2381
 AH0  C    C  C     0   0.515  -3.2313  -0.8494   0.1680
 AH0  O    O  O     0  -0.423  -3.6091   0.0723   0.8397
 AH0  OXT  O  OH1   0  -0.595  -3.8069  -2.0447   0.1520
 AH0  H1   H  HCH1  0   0.257   1.7052   0.2078   2.1809
 AH0  H2   H  HCH1  0   0.278   0.2555  -1.1429   0.6528
 AH0  HN2  H  HNH1  0   0.400   2.5869  -0.1867  -0.8783
 AH0  H81  H  HCH3  0   0.250   4.1944  -1.6151  -1.3633
 AH0  H82  H  HCH3  0   0.269   4.6904  -2.2587   0.2034
 AH0  H83  H  HCH3  0   0.264   3.9083  -3.3149  -0.9624
 AH0  H3   H  HCH1  0   0.256   0.1720  -0.1529  -1.7982
 AH0  H4   H  HCH1  0   0.240  -0.4057   2.3942  -1.5445
 AH0  HO4  H  HOH1  0   0.460   1.9268   2.6849  -1.9936
 AH0  H5   H  HCH1  0   0.277   1.1022   3.5494   0.0950
 AH0  H61  H  HCH2  0   0.238  -0.2750   3.2558   2.0191
 AH0  H62  H  HCH2  0   0.242  -1.3536   2.4344   0.8770
 AH0  HA   H  HCH1  0   0.258  -1.4203  -1.6715  -0.5778
 AH0  HB1  H  HCH3  0   0.242  -3.2574  -0.1175  -2.4713
 AH0  HB2  H  HCH3  0   0.251  -1.6951  -0.8108  -2.9190
 AH0  HB3  H  HCH3  0   0.248  -3.0081  -1.8697  -2.4309
 AH0  HXT  H  HOH1  0   0.486  -4.5794  -2.0530   0.7371

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  1.547  0.020  1.547
 AH0  C2   H2   single  0.970  0.020  1.090
 AH0  N2   C7   single  1.347  0.020  1.347
 AH0  N2   HN2  single  0.860  0.020  1.020
 AH0  C7   O7   double  1.223  0.020  1.223
 AH0  C7   C8   single  1.507  0.020  1.507
 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  1.406  0.020  1.406
 AH0  C3   C4   single  1.537  0.020  1.537
 AH0  C3   H3   single  0.970  0.020  1.090
 AH0  O3   CA   single  1.402  0.020  1.402
 AH0  C4   O4   single  1.410  0.020  1.410
 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  1.529  0.020  1.529
 AH0  C5   H5   single  0.970  0.020  1.090
 AH0  C6   O6   single  1.424  0.020  1.424
 AH0  C6   H61  single  0.970  0.020  1.090
 AH0  C6   H62  single  0.970  0.020  1.090
 AH0  CA   CB   single  1.528  0.020  1.528
 AH0  CA   C    single  1.516  0.020  1.516
 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    double  1.201  0.020  1.201
 AH0  C    OXT  single  1.327  0.020  1.327
 AH0  OXT  HXT  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
 AH0  H1   C1   O6   110.13  3.000
 AH0  H1   C1   O5   109.37  3.000
 AH0  O6   C1   O5   105.87  3.000
 AH0  H1   C1   C2   110.81  3.000
 AH0  O6   C1   C2   111.39  3.000
 AH0  O5   C1   C2   109.13  3.000
 AH0  H2   C2   C3   109.47  3.000
 AH0  H2   C2   N2   107.52  3.000
 AH0  C3   C2   N2   110.28  3.000
 AH0  H2   C2   C1   108.89  3.000
 AH0  C3   C2   C1   111.02  3.000
 AH0  N2   C2   C1   109.58  3.000
 AH0  HN2  N2   C7   118.70  3.000
 AH0  HN2  N2   C2   117.51  3.000
 AH0  C7   N2   C2   123.62  3.000
 AH0  C8   C7   O7   121.88  3.000
 AH0  C8   C7   N2   115.13  3.000
 AH0  O7   C7   N2   122.99  3.000
 AH0  H83  C8   H82  107.41  3.000
 AH0  H83  C8   H81  108.74  3.000
 AH0  H82  C8   H81  108.18  3.000
 AH0  H83  C8   C7   109.63  3.000
 AH0  H82  C8   C7   109.11  3.000
 AH0  H81  C8   C7   113.58  3.000
 AH0  H3   C3   C4   107.69  3.000
 AH0  H3   C3   O3   110.56  3.000
 AH0  C4   C3   O3   107.31  3.000
 AH0  H3   C3   C2   108.02  3.000
 AH0  C4   C3   C2   111.60  3.000
 AH0  O3   C3   C2   111.61  3.000
 AH0  CA   O3   C3   115.24  3.000
 AH0  H4   C4   C5   108.82  3.000
 AH0  H4   C4   O4   111.46  3.000
 AH0  C5   C4   O4   110.79  3.000
 AH0  H4   C4   C3   108.52  3.000
 AH0  C5   C4   C3   111.17  3.000
 AH0  O4   C4   C3   106.05  3.000
 AH0  HO4  O4   C4   109.23  3.000
 AH0  H5   C5   C6   112.48  3.000
 AH0  H5   C5   O5   108.99  3.000
 AH0  C6   C5   O5   101.15  3.000
 AH0  H5   C5   C4   110.71  3.000
 AH0  C6   C5   C4   113.94  3.000
 AH0  O5   C5   C4   109.03  3.000
 AH0  C5   O5   C1   102.07  3.000
 AH0  H62  C6   H61  108.65  3.000
 AH0  H62  C6   O6   110.68  3.000
 AH0  H61  C6   O6   109.81  3.000
 AH0  H62  C6   C5   113.86  3.000
 AH0  H61  C6   C5   110.73  3.000
 AH0  O6   C6   C5   102.99  3.000
 AH0  C6   O6   C1   107.27  3.000
 AH0  HA   CA   C    107.59  3.000
 AH0  HA   CA   CB   108.40  3.000
 AH0  C    CA   CB   110.70  3.000
 AH0  HA   CA   O3   111.52  3.000
 AH0  C    CA   O3   106.96  3.000
 AH0  CB   CA   O3   111.61  3.000
 AH0  HB3  CB   HB2  107.41  3.000
 AH0  HB3  CB   HB1  108.69  3.000
 AH0  HB2  CB   HB1  108.27  3.000
 AH0  HB3  CB   CA   111.23  3.000
 AH0  HB2  CB   CA   109.91  3.000
 AH0  HB1  CB   CA   111.21  3.000
 AH0  OXT  C    O    124.16  3.000
 AH0  OXT  C    CA   110.79  3.000
 AH0  O    C    CA   125.04  3.000
 AH0  HXT  OXT  C    110.26  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  CONST_04  HXT  OXT  C   CA  180.00   0.0  0
 AH0  Var_01    C5   C6   O6  C1    3.52  30.0  3
 AH0  Var_02    H81  C8   C7  N2  -11.69  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
 AH0  plan-2  HXT  0.020

