# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 04:07:27 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2Z,3R,4S,5R,6R)-2-[(2-aminoethyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN=C1N[C@H](CO)[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
 15A  15A  (2Z,3R,4S,5R,6R)-2-[(2-aminoethyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol  ligand  32  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_15A
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
 15A  O6    O  OH1   0  -0.673   0.1707   3.2833   0.0552
 15A  C6    C  CH2   0  -0.143  -0.8381   2.4732   0.6189
 15A  C5    C  CH1   0  -0.113  -0.9483   1.2107  -0.2195
 15A  C4    C  CH1   0   0.040  -2.0390   0.2854   0.3027
 15A  O4    O  OH1   0  -0.675  -3.2716   0.9253   0.0880
 15A  C3    C  CH1   0   0.012  -1.9592  -1.0365  -0.4479
 15A  O3    O  OH1   0  -0.673  -3.0502  -1.8268  -0.0458
 15A  C2    C  CH1   0  -0.065  -0.6241  -1.7165  -0.1860
 15A  O2    O  OH1   0  -0.660  -0.5856  -2.1345   1.1600
 15A  N5    N  NH1   0  -0.676   0.3379   0.5367  -0.2160
 15A  C1    C  C     0   0.444   0.5447  -0.7855  -0.4506
 15A  N1    N  N     0  -0.463   1.6533  -1.3456  -0.7545
 15A  C7    C  CH2   0  -0.359   2.8466  -0.5446  -0.8869
 15A  C8    C  CH2   0  -0.284   3.5291  -0.3005   0.4590
 15A  N2    N  NH2   0  -0.800   4.7519   0.4651   0.2711
 15A  H6    H  HOH1  0   0.462   0.3849   3.9807   0.6808
 15A  H6C1  H  HCH2  0   0.204  -0.5979   2.1895   1.6512
 15A  H6C2  H  HCH2  0   0.214  -1.8051   2.9869   0.6310
 15A  H5    H  HCH1  0   0.243  -1.2229   1.4949  -1.2463
 15A  H4    H  HCH1  0   0.216  -1.8716   0.1028   1.3749
 15A  HA    H  HNH1  0   0.393   1.1142   1.1589  -0.3850
 15A  HB    H  HOH1  0   0.452  -3.9681   0.2903   0.2887
 15A  H3    H  HCH1  0   0.232  -2.0103  -0.8165  -1.5249
 15A  HC    H  HOH1  0   0.460  -3.2288  -2.4822  -0.7268
 15A  H2    H  HCH1  0   0.235  -0.5169  -2.5703  -0.8663
 15A  HD    H  HOH1  0   0.452   0.2508  -2.5924   1.2947
 15A  H7C1  H  HCH2  0   0.228   3.5470  -1.0846  -1.5316
 15A  H7C2  H  HCH2  0   0.198   2.6790   0.4248  -1.3795
 15A  H8C1  H  HCH2  0   0.214   2.8626   0.2734   1.1088
 15A  H8C2  H  HCH2  0   0.197   3.6803  -1.2712   0.9503
 15A  H2N1  H  HNH2  0   0.349   5.1635   0.6689   1.1726
 15A  H2N2  H  HNH2  0   0.339   5.4331  -0.1054  -0.2148

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
 15A  O6  C6    single  1.411  0.020  1.411
 15A  C6  C5    single  1.520  0.020  1.520
 15A  C5  C4    single  1.523  0.020  1.523
 15A  C5  N5    single  1.452  0.020  1.452
 15A  C4  O4    single  1.405  0.020  1.405
 15A  C4  C3    single  1.522  0.020  1.522
 15A  C3  O3    single  1.406  0.020  1.406
 15A  C3  C2    single  1.521  0.020  1.521
 15A  C2  O2    single  1.410  0.020  1.410
 15A  C2  C1    single  1.518  0.020  1.518
 15A  N5  C1    single  1.359  0.020  1.359
 15A  C1  N1    double  1.279  0.020  1.279
 15A  N1  C7    single  1.443  0.020  1.443
 15A  C7  C8    single  1.529  0.020  1.529
 15A  C8  N2    single  1.455  0.020  1.455
 15A  O6  H6    single  0.850  0.020  0.980
 15A  C6  H6C1  single  0.970  0.020  1.090
 15A  C6  H6C2  single  0.970  0.020  1.090
 15A  C5  H5    single  0.970  0.020  1.090
 15A  C4  H4    single  0.970  0.020  1.090
 15A  N5  HA    single  0.890  0.020  1.040
 15A  O4  HB    single  0.850  0.020  0.980
 15A  C3  H3    single  0.970  0.020  1.090
 15A  O3  HC    single  0.850  0.020  0.980
 15A  C2  H2    single  0.970  0.020  1.090
 15A  O2  HD    single  0.850  0.020  0.980
 15A  C7  H7C1  single  0.970  0.020  1.090
 15A  C7  H7C2  single  0.970  0.020  1.090
 15A  C8  H8C1  single  0.970  0.020  1.090
 15A  C8  H8C2  single  0.970  0.020  1.090
 15A  N2  H2N1  single  0.890  0.020  1.040
 15A  N2  H2N2  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
 15A  H6    O6  C6    108.41  3.000
 15A  H6C2  C6  H6C1  107.71  3.000
 15A  H6C2  C6  C5    109.38  3.000
 15A  H6C1  C6  C5    108.68  3.000
 15A  H6C2  C6  O6    111.49  3.000
 15A  H6C1  C6  O6    111.58  3.000
 15A  C5    C6  O6    107.96  3.000
 15A  H5    C5  N5    110.07  3.000
 15A  H5    C5  C4    107.35  3.000
 15A  N5    C5  C4    110.58  3.000
 15A  H5    C5  C6    108.57  3.000
 15A  N5    C5  C6    108.67  3.000
 15A  C4    C5  C6    111.57  3.000
 15A  H4    C4  C3    109.17  3.000
 15A  H4    C4  O4    110.97  3.000
 15A  C3    C4  O4    111.47  3.000
 15A  H4    C4  C5    109.03  3.000
 15A  C3    C4  C5    108.73  3.000
 15A  O4    C4  C5    107.41  3.000
 15A  HB    O4  C4    107.59  3.000
 15A  H3    C3  C2    107.38  3.000
 15A  H3    C3  O3    110.87  3.000
 15A  C2    C3  O3    112.37  3.000
 15A  H3    C3  C4    107.85  3.000
 15A  C2    C3  C4    110.45  3.000
 15A  O3    C3  C4    107.84  3.000
 15A  HC    O3  C3    108.94  3.000
 15A  H2    C2  C1    107.11  3.000
 15A  H2    C2  O2    111.01  3.000
 15A  C1    C2  O2    109.11  3.000
 15A  H2    C2  C3    109.09  3.000
 15A  C1    C2  C3    111.82  3.000
 15A  O2    C2  C3    108.72  3.000
 15A  HD    O2  C2    107.35  3.000
 15A  HA    N5  C1    117.00  3.000
 15A  HA    N5  C5    113.25  3.000
 15A  C1    N5  C5    125.88  3.000
 15A  N1    C1  N5    126.82  3.000
 15A  N1    C1  C2    116.13  3.000
 15A  N5    C1  C2    116.72  3.000
 15A  C7    N1  C1    119.70  3.000
 15A  H7C2  C7  H7C1  105.58  3.000
 15A  H7C2  C7  C8    108.75  3.000
 15A  H7C1  C7  C8    108.16  3.000
 15A  H7C2  C7  N1    113.84  3.000
 15A  H7C1  C7  N1    108.02  3.000
 15A  C8    C7  N1    112.14  3.000
 15A  H8C2  C8  H8C1  106.37  3.000
 15A  H8C2  C8  N2    114.02  3.000
 15A  H8C1  C8  N2    108.23  3.000
 15A  H8C2  C8  C7    108.31  3.000
 15A  H8C1  C8  C7    109.57  3.000
 15A  N2    C8  C7    110.22  3.000
 15A  H2N2  N2  H2N1  105.50  3.000
 15A  H2N2  N2  C8    109.32  3.000
 15A  H2N1  N2  C8    109.45  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
 15A  CONST_03  HA    N5  C1  C2  180.00   0.0  0
 15A  CONST_04  C7    N1  C1  C2  180.00   0.0  0
 15A  CONST_05  C7    N1  C1  N5    0.00   0.0  0
 15A  Var_01    C8    C7  N1  C1   84.37  30.0  3
 15A  Var_02    N2    C8  C7  N1  177.80  30.0  3
 15A  Var_03    H2N1  N2  C8  C7  176.53  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
 15A  chir_01  C5  C6  C4  N5  positiv
 15A  chir_02  C4  O4  C5  C3  positiv
 15A  chir_03  C3  O3  C4  C2  negativ
 15A  chir_04  C2  O2  C3  C1  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
 15A  plan-1  C5  0.020
 15A  plan-1  C2  0.020
 15A  plan-1  N5  0.020
 15A  plan-1  C1  0.020
 15A  plan-1  N1  0.020
 15A  plan-1  C7  0.020
 15A  plan-1  HA  0.020

