# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:40:42 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1R,2S,3S,4R,5S)-5-aminocyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[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
 25W  25W  (1R,2S,3S,4R,5S)-5-aminocyclohexane-1,2,3,4-tetrol  ligand  24  11  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_25W
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
 25W  O1   O  OH1   0  -0.680   2.3591  -1.1913  -0.1881
 25W  O2   O  OH1   0  -0.679  -0.0903  -2.4575   0.3546
 25W  O3   O  OH1   0  -0.679  -2.4160  -1.0442  -0.2515
 25W  C5   C  CH1   0   0.065  -1.2580  -0.4089   0.2399
 25W  C    C  CH1   0  -0.104  -1.2419   1.0223  -0.2806
 25W  N    N  NH2   0  -0.804  -2.4113   1.7346   0.2107
 25W  C4   C  CH1   0   0.002  -0.0016  -1.1592  -0.1898
 25W  C3   C  CH1   0   0.024   1.2591  -0.4422   0.2750
 25W  C2   C  CH1   0   0.030   1.2784   0.9882  -0.2460
 25W  O    O  OH1   0  -0.679   2.4576   1.5910   0.2457
 25W  C1   C  CH2   0  -0.493   0.0228   1.7237   0.2012
 25W  H1   H  HOH1  0   0.451   3.1642  -0.7691   0.1281
 25W  H2   H  HOH1  0   0.454   0.6244  -2.9900  -0.0077
 25W  H3   H  HOH1  0   0.449  -2.4120  -1.9556   0.0587
 25W  H4   H  HCH1  0   0.197  -1.2784  -0.3649   1.3413
 25W  H5   H  HCH1  0   0.206  -1.2087   0.9761  -1.3822
 25W  H6   H  HNH2  0   0.345  -2.3917   2.6837  -0.1417
 25W  H7   H  HNH2  0   0.345  -3.2490   1.3180  -0.1751
 25W  H9   H  HCH1  0   0.208   0.0131  -1.2028  -1.2911
 25W  H10  H  HCH1  0   0.204   1.2517  -0.4039   1.3770
 25W  H11  H  HCH1  0   0.206   1.2984   0.9532  -1.3457
 25W  H12  H  HOH1  0   0.455   2.6201   2.3969  -0.2534
 25W  H13  H  HCH2  0   0.248   0.0402   2.7483  -0.1819
 25W  H14  H  HCH2  0   0.229   0.0043   1.7931   1.2943

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
 25W  O1  C3   single  1.409  0.020  1.409
 25W  O   C2   single  1.413  0.020  1.413
 25W  C2  C3   single  1.522  0.020  1.522
 25W  C2  C1   single  1.522  0.020  1.522
 25W  C3  C4   single  1.523  0.020  1.523
 25W  C4  O2   single  1.411  0.020  1.411
 25W  C4  C5   single  1.525  0.020  1.525
 25W  C1  C    single  1.524  0.020  1.524
 25W  C   C5   single  1.523  0.020  1.523
 25W  C   N    single  1.455  0.020  1.455
 25W  O3  C5   single  1.409  0.020  1.409
 25W  O1  H1   single  0.850  0.020  0.980
 25W  O2  H2   single  0.850  0.020  0.980
 25W  O3  H3   single  0.850  0.020  0.980
 25W  C5  H4   single  0.970  0.020  1.090
 25W  C   H5   single  0.970  0.020  1.090
 25W  N   H6   single  0.890  0.020  1.040
 25W  N   H7   single  0.890  0.020  1.040
 25W  C4  H9   single  0.970  0.020  1.090
 25W  C3  H10  single  0.970  0.020  1.090
 25W  C2  H11  single  0.970  0.020  1.090
 25W  O   H12  single  0.850  0.020  0.980
 25W  C1  H13  single  0.970  0.020  1.090
 25W  C1  H14  single  0.970  0.020  1.090

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
 25W  H1   O1  C3   108.17  3.000
 25W  H2   O2  C4   108.51  3.000
 25W  H3   O3  C5   108.12  3.000
 25W  H4   C5  C4   108.44  3.000
 25W  H4   C5  C    107.71  3.000
 25W  C4   C5  C    110.94  3.000
 25W  H4   C5  O3   110.56  3.000
 25W  C    C5  O3   108.25  3.000
 25W  C4   C5  O3   110.91  3.000
 25W  H5   C   C1   108.05  3.000
 25W  H5   C   N    112.45  3.000
 25W  C1   C   N    109.57  3.000
 25W  H5   C   C5   107.60  3.000
 25W  N    C   C5   109.65  3.000
 25W  C1   C   C5   109.46  3.000
 25W  H7   N   H6   105.62  3.000
 25W  H7   N   C    109.58  3.000
 25W  H6   N   C    109.02  3.000
 25W  H9   C4  C3   108.21  3.000
 25W  H9   C4  C5   108.18  3.000
 25W  C3   C4  C5   111.36  3.000
 25W  H9   C4  O2   110.49  3.000
 25W  C5   C4  O2   107.00  3.000
 25W  C3   C4  O2   111.57  3.000
 25W  H10  C3  C2   108.03  3.000
 25W  H10  C3  C4   108.41  3.000
 25W  C2   C3  C4   110.39  3.000
 25W  H10  C3  O1   110.62  3.000
 25W  C4   C3  O1   107.19  3.000
 25W  C2   C3  O1   112.16  3.000
 25W  H11  C2  C1   108.90  3.000
 25W  H11  C2  O    110.26  3.000
 25W  C1   C2  O    112.34  3.000
 25W  H11  C2  C3   108.20  3.000
 25W  C1   C2  C3   110.06  3.000
 25W  O    C2  C3   107.00  3.000
 25W  H12  O   C2   108.54  3.000
 25W  H14  C1  H13  106.89  3.000
 25W  H14  C1  C2   109.73  3.000
 25W  H13  C1  C2   109.66  3.000
 25W  H14  C1  C    109.30  3.000
 25W  H13  C1  C    109.48  3.000
 25W  C2   C1  C    111.66  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
 25W  chir_01  C5  C4  C   O3  negativ
 25W  chir_02  C   N   C1  C5  negativ
 25W  chir_03  C4  O2  C5  C3  negativ
 25W  chir_04  C3  O1  C4  C2  positiv
 25W  chir_05  C2  O   C3  C1  negativ

