# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:07:15 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1R,2R,3R,4S,5R)-4-amino-5-methoxycyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](N)[C@@H](O)[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
 GOO  GOO  (1R,2R,3R,4S,5R)-4-amino-5-methoxycyclopentane-1,2,3-triol  ligand  24  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GOO
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
 GOO  C7    C  CH3   0  -0.404   3.1528  -0.6572  -0.5007
 GOO  O6    O  O2    0  -0.496   2.3072   0.1559   0.2760
 GOO  C1    C  CR15  0   0.079   0.9764   0.1736  -0.1698
 GOO  C2    C  CR15  0  -0.001   0.1822  -1.1270   0.0690
 GOO  O2    O  OH1   0  -0.668  -0.0238  -1.7770  -1.1599
 GOO  C3    C  CR15  0  -0.010  -1.1282  -0.6570   0.7467
 GOO  O3    O  OH1   0  -0.671  -2.2141  -1.4345   0.3122
 GOO  C4    C  CR15  0  -0.010  -1.2430   0.8300   0.4022
 GOO  O4    O  OH1   0  -0.669  -1.6538   1.0179  -0.9293
 GOO  C5    C  CR15  0  -0.132   0.2054   1.2684   0.5659
 GOO  N5    N  NH2   0  -0.804   0.4931   2.5904   0.0499
 GOO  H7    H  HCH3  0   0.234   4.1738  -0.5047  -0.1526
 GOO  H7A   H  HCH3  0   0.209   2.9167  -1.7226  -0.4044
 GOO  H7B   H  HCH3  0   0.205   3.1047  -0.3962  -1.5642
 GOO  H1    H  HCR5  0   0.209   0.9428   0.3910  -1.2476
 GOO  H2    H  HCR5  0   0.216   0.7309  -1.7773   0.7641
 GOO  HO2   H  HOH1  0   0.447  -0.6102  -2.5254  -1.0091
 GOO  H3    H  HCR5  0   0.231  -0.9925  -0.7391   1.8318
 GOO  HO3   H  HOH1  0   0.463  -2.9375  -1.3339   0.9387
 GOO  H4    H  HCR5  0   0.221  -1.9108   1.3586   1.0987
 GOO  HO4   H  HOH1  0   0.442  -2.3316   0.3581  -1.1154
 GOO  H5    H  HCR5  0   0.218   0.4340   1.1683   1.6404
 GOO  HN5   H  HNH2  0   0.346   0.0009   3.2817   0.6031
 GOO  HN5A  H  HNH2  0   0.345   1.4764   2.7880   0.1916

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
 GOO  C7  O6    single  1.407  0.020  1.407
 GOO  C7  H7    single  0.970  0.020  1.090
 GOO  C7  H7A   single  0.970  0.020  1.090
 GOO  C7  H7B   single  0.970  0.020  1.090
 GOO  O6  C1    single  1.404  0.020  1.404
 GOO  C2  C1    single  1.542  0.020  1.542
 GOO  C1  C5    single  1.528  0.020  1.528
 GOO  C1  H1    single  0.970  0.020  1.090
 GOO  O2  C2    single  1.405  0.020  1.405
 GOO  C2  C3    single  1.548  0.020  1.548
 GOO  C2  H2    single  0.970  0.020  1.090
 GOO  O2  HO2   single  0.850  0.020  0.980
 GOO  O3  C3    single  1.404  0.020  1.404
 GOO  C3  C4    single  1.531  0.020  1.531
 GOO  C3  H3    single  0.970  0.020  1.090
 GOO  O3  HO3   single  0.850  0.020  0.980
 GOO  C5  C4    single  1.522  0.020  1.522
 GOO  C4  O4    single  1.406  0.020  1.406
 GOO  C4  H4    single  0.970  0.020  1.090
 GOO  O4  HO4   single  0.850  0.020  0.980
 GOO  C5  N5    single  1.448  0.020  1.448
 GOO  C5  H5    single  0.970  0.020  1.090
 GOO  N5  HN5   single  0.890  0.020  1.040
 GOO  N5  HN5A  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
 GOO  H7B   C7  H7A  107.90  3.000
 GOO  H7B   C7  H7   108.53  3.000
 GOO  H7A   C7  H7   108.06  3.000
 GOO  H7B   C7  O6   111.82  3.000
 GOO  H7A   C7  O6   112.58  3.000
 GOO  H7    C7  O6   107.81  3.000
 GOO  C1    O6  C7   113.69  3.000
 GOO  H1    C1  C5   108.35  3.000
 GOO  H1    C1  C2   107.61  3.000
 GOO  C5    C1  C2   105.66  3.000
 GOO  H1    C1  O6   110.04  3.000
 GOO  C5    C1  O6   109.54  3.000
 GOO  C2    C1  O6   115.37  3.000
 GOO  H2    C2  C3   108.99  3.000
 GOO  H2    C2  O2   110.65  3.000
 GOO  C3    C2  O2   113.52  3.000
 GOO  H2    C2  C1   109.87  3.000
 GOO  C3    C2  C1   104.33  3.000
 GOO  O2    C2  C1   109.27  3.000
 GOO  HO2   O2  C2   108.17  3.000
 GOO  H3    C3  C4   107.74  3.000
 GOO  H3    C3  O3   111.12  3.000
 GOO  C4    C3  O3   114.21  3.000
 GOO  H3    C3  C2   107.80  3.000
 GOO  C4    C3  C2   105.06  3.000
 GOO  O3    C3  C2   110.55  3.000
 GOO  HO3   O3  C3   108.78  3.000
 GOO  H4    C4  C5   111.78  3.000
 GOO  H4    C4  O4   110.97  3.000
 GOO  C5    C4  O4   109.96  3.000
 GOO  H4    C4  C3   111.70  3.000
 GOO  O4    C4  C3   111.40  3.000
 GOO  C5    C4  C3   100.62  3.000
 GOO  HO4   O4  C4   107.27  3.000
 GOO  H5    C5  N5   112.88  3.000
 GOO  H5    C5  C4   106.01  3.000
 GOO  N5    C5  C4   114.43  3.000
 GOO  H5    C5  C1   107.43  3.000
 GOO  N5    C5  C1   112.48  3.000
 GOO  C4    C5  C1   102.82  3.000
 GOO  HN5A  N5  HN5  105.20  3.000
 GOO  HN5A  N5  C5   108.73  3.000
 GOO  HN5   N5  C5   109.38  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
 GOO  Var_01  H7  C7  O6  C1  173.02  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
 GOO  chir_01  C1  O6  C2  C5  negativ
 GOO  chir_02  C2  O2  C1  C3  negativ
 GOO  chir_03  C3  O3  C2  C4  negativ
 GOO  chir_04  C4  O4  C3  C5  negativ
 GOO  chir_05  C5  N5  C1  C4  positiv

