# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 04:31:37 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (1R,2R,3S,4S,5r)-5-aminocyclopentane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)[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
 AOL  AOL  (1R,2R,3S,4S,5r)-5-aminocyclopentane-1,2,3,4-tetrol  ligand  21  10  .  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_AOL
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
 AOL  O4    O  OH1   0  -0.663   1.0068  -0.7928   1.1288
 AOL  C4    C  CH1   0  -0.020   1.0134  -0.7388  -0.2804
 AOL  C3    C  CH1   0  -0.012  -0.3110  -1.2343  -0.8603
 AOL  O3    O  OH1   0  -0.654  -0.7256  -2.4660  -0.3370
 AOL  C2    C  CH1   0  -0.070  -1.3167  -0.0843  -0.5987
 AOL  O2    O  OH1   0  -0.714  -2.0733  -0.4275   0.5402
 AOL  C1    C  CH1   0   0.016  -0.4388   1.1900  -0.3908
 AOL  O1    O  OH1   0  -0.646  -0.5700   1.7393   0.8940
 AOL  C5    C  CH1   0  -0.180   1.0024   0.7187  -0.7123
 AOL  N5    N  NH2   0  -0.776   2.0961   1.5025  -0.1830
 AOL  HO4   H  HOH1  0   0.439   0.7417  -1.6824   1.3886
 AOL  H4    H  HCH1  0   0.252   1.8720  -1.2855  -0.6924
 AOL  H3    H  HCH1  0   0.221  -0.1785  -1.3314  -1.9445
 AOL  HO3   H  HOH1  0   0.444  -1.4716  -2.2861   0.2514
 AOL  H2    H  HCH1  0   0.270  -1.9731   0.0414  -1.4646
 AOL  HO2   H  HOH1  0   0.445  -2.9120   0.0418   0.5167
 AOL  H1    H  HCH1  0   0.247  -0.7393   1.9848  -1.0784
 AOL  HO1   H  HOH1  0   0.459  -0.4510   1.0281   1.5343
 AOL  H5    H  HCH1  0   0.273   1.1044   0.7124  -1.8033
 AOL  HN51  H  HNH2  0   0.351   2.0987   2.4131  -0.6254
 AOL  HN52  H  HNH2  0   0.320   1.9456   1.6798   0.8022

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
 AOL  O4  C4    single  1.410  0.020  1.410
 AOL  O4  HO4   single  0.850  0.020  0.980
 AOL  C4  C3    single  1.528  0.020  1.528
 AOL  C4  C5    single  1.520  0.020  1.520
 AOL  C4  H4    single  0.970  0.020  1.090
 AOL  C3  O3    single  1.401  0.020  1.401
 AOL  C3  C2    single  1.550  0.020  1.550
 AOL  C3  H3    single  0.970  0.020  1.090
 AOL  O3  HO3   single  0.850  0.020  0.980
 AOL  C2  O2    single  1.410  0.020  1.410
 AOL  C2  C1    single  1.561  0.020  1.561
 AOL  C2  H2    single  0.970  0.020  1.090
 AOL  O2  HO2   single  0.850  0.020  0.980
 AOL  C1  O1    single  1.403  0.020  1.403
 AOL  C1  C5    single  1.550  0.020  1.550
 AOL  C1  H1    single  0.970  0.020  1.090
 AOL  O1  HO1   single  0.850  0.020  0.980
 AOL  C5  N5    single  1.446  0.020  1.446
 AOL  C5  H5    single  0.970  0.020  1.090
 AOL  N5  HN51  single  0.890  0.020  1.040
 AOL  N5  HN52  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
 AOL  HO4   O4  C4    107.82  3.000
 AOL  H4    C4  C5    112.11  3.000
 AOL  H4    C4  C3    111.95  3.000
 AOL  C5    C4  C3    101.35  3.000
 AOL  H4    C4  O4    111.07  3.000
 AOL  C5    C4  O4    108.70  3.000
 AOL  C3    C4  O4    111.26  3.000
 AOL  H3    C3  C2    108.12  3.000
 AOL  H3    C3  O3    109.10  3.000
 AOL  C2    C3  O3    113.41  3.000
 AOL  H3    C3  C4    107.40  3.000
 AOL  C2    C3  C4    104.94  3.000
 AOL  O3    C3  C4    113.56  3.000
 AOL  HO3   O3  C3    106.98  3.000
 AOL  H2    C2  C1    110.43  3.000
 AOL  H2    C2  O2    110.22  3.000
 AOL  C1    C2  O2    113.13  3.000
 AOL  H2    C2  C3    109.94  3.000
 AOL  C1    C2  C3    105.26  3.000
 AOL  O2    C2  C3    107.70  3.000
 AOL  HO2   O2  C2    109.25  3.000
 AOL  H1    C1  C5    110.26  3.000
 AOL  H1    C1  O1    105.40  3.000
 AOL  C5    C1  O1    113.32  3.000
 AOL  H1    C1  C2    110.80  3.000
 AOL  C5    C1  C2    104.30  3.000
 AOL  O1    C1  C2    112.88  3.000
 AOL  HO1   O1  C1    107.92  3.000
 AOL  H5    C5  N5    107.29  3.000
 AOL  H5    C5  C1    107.15  3.000
 AOL  N5    C5  C1    117.55  3.000
 AOL  H5    C5  C4    106.06  3.000
 AOL  N5    C5  C4    114.22  3.000
 AOL  C1    C5  C4    103.85  3.000
 AOL  HN52  N5  HN51  105.55  3.000
 AOL  HN52  N5  C5    109.80  3.000
 AOL  HN51  N5  C5    109.24  3.000

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
 AOL  chir_01  C4  O4  C3  C5  negativ
 AOL  chir_02  C3  O3  C4  C2  positiv
 AOL  chir_03  C2  O2  C3  C1  positiv
 AOL  chir_04  C1  O1  C2  C5  positiv
 AOL  chir_05  C5  N5  C4  C1  negativ

