# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:14:26 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN[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
 NOZ  NOZ  (2S,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol  ligand  24  11  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NOZ
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
 NOZ  O4    O  OH1   0  -0.678  -0.2183   2.2790   0.1067
 NOZ  C4    C  CH1   0   0.050   0.0563   0.9283  -0.1975
 NOZ  C3    C  CH1   0   0.027   1.3608   0.4834   0.4600
 NOZ  O3    O  OH1   0  -0.676   2.3887   1.2939  -0.0595
 NOZ  C2    C  CH1   0   0.106   1.6130  -1.0073   0.2365
 NOZ  N     N  NH1   0  -0.625   0.4823  -1.7225   0.7519
 NOZ  C7    C  CH2   0  -0.271  -0.7736  -1.4073   0.0941
 NOZ  C5    C  CH1   0  -0.314  -1.1098   0.0699   0.2867
 NOZ  C6    C  CH2   0  -0.131  -2.3925   0.4474  -0.4390
 NOZ  O6    O  OH1   0  -0.674  -3.4520  -0.3414   0.0595
 NOZ  O2    O  OH1   0  -0.672   1.8736  -1.1959  -1.1407
 NOZ  H4    H  HOH1  0   0.447   0.5343   2.8038  -0.1853
 NOZ  HA    H  HCH1  0   0.198   0.1548   0.7955  -1.2868
 NOZ  H3    H  HCH1  0   0.214   1.2565   0.6266   1.5444
 NOZ  H5    H  HCH1  0   0.230  -1.2415   0.2539   1.3606
 NOZ  HB    H  HOH1  0   0.455   3.1591   1.2194   0.5114
 NOZ  H     H  HNH1  0   0.359   0.6505  -2.7199   0.7559
 NOZ  H7C1  H  HCH2  0   0.194  -0.7663  -1.6372  -0.9818
 NOZ  H7C2  H  HCH2  0   0.241  -1.5540  -2.0218   0.5417
 NOZ  H6C1  H  HCH2  0   0.210  -2.5953   1.5146  -0.2984
 NOZ  H6C2  H  HCH2  0   0.184  -2.2491   0.2870  -1.5175
 NOZ  H6    H  HOH1  0   0.454  -4.2503  -0.1032  -0.4196
 NOZ  H2    H  HOH1  0   0.448   2.1018  -2.1209  -1.2784
 NOZ  H8    H  HCH1  0   0.225   2.4867  -1.3169   0.8269

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
 NOZ  O4  C4    single  1.411  0.020  1.411
 NOZ  C4  C3    single  1.527  0.020  1.527
 NOZ  C4  C5    single  1.527  0.020  1.527
 NOZ  C3  O3    single  1.408  0.020  1.408
 NOZ  C3  C2    single  1.528  0.020  1.528
 NOZ  C2  N     single  1.434  0.020  1.434
 NOZ  C2  O2    single  1.414  0.020  1.414
 NOZ  O2  H2    single  0.850  0.020  0.980
 NOZ  N   C7    single  1.452  0.020  1.452
 NOZ  C7  C5    single  1.527  0.020  1.527
 NOZ  C5  C6    single  1.521  0.020  1.521
 NOZ  C6  O6    single  1.412  0.020  1.412
 NOZ  O4  H4    single  0.850  0.020  0.980
 NOZ  C4  HA    single  0.970  0.020  1.090
 NOZ  C3  H3    single  0.970  0.020  1.090
 NOZ  C5  H5    single  0.970  0.020  1.090
 NOZ  O3  HB    single  0.850  0.020  0.980
 NOZ  N   H     single  0.860  0.020  1.020
 NOZ  C7  H7C1  single  0.970  0.020  1.090
 NOZ  C7  H7C2  single  0.970  0.020  1.090
 NOZ  C6  H6C1  single  0.970  0.020  1.090
 NOZ  C6  H6C2  single  0.970  0.020  1.090
 NOZ  O6  H6    single  0.850  0.020  0.980
 NOZ  C2  H8    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
 NOZ  H4    O4  C4    107.71  3.000
 NOZ  HA    C4  C5    108.30  3.000
 NOZ  HA    C4  C3    108.31  3.000
 NOZ  C5    C4  C3    110.61  3.000
 NOZ  HA    C4  O4    110.23  3.000
 NOZ  C5    C4  O4    108.73  3.000
 NOZ  C3    C4  O4    110.63  3.000
 NOZ  H3    C3  C2    106.69  3.000
 NOZ  H3    C3  O3    111.00  3.000
 NOZ  C2    C3  O3    112.76  3.000
 NOZ  H3    C3  C4    107.81  3.000
 NOZ  C2    C3  C4    111.24  3.000
 NOZ  O3    C3  C4    107.28  3.000
 NOZ  HB    O3  C3    108.73  3.000
 NOZ  H8    C2  O2    109.82  3.000
 NOZ  H8    C2  N     107.06  3.000
 NOZ  O2    C2  N     115.40  3.000
 NOZ  H8    C2  C3    109.11  3.000
 NOZ  O2    C2  C3    107.63  3.000
 NOZ  N     C2  C3    107.68  3.000
 NOZ  H     N   C7    111.07  3.000
 NOZ  H     N   C2    111.23  3.000
 NOZ  C7    N   C2    114.26  3.000
 NOZ  H7C2  C7  H7C1  106.78  3.000
 NOZ  H7C2  C7  C5    109.64  3.000
 NOZ  H7C1  C7  C5    109.09  3.000
 NOZ  H7C2  C7  N     108.11  3.000
 NOZ  H7C1  C7  N     113.07  3.000
 NOZ  C5    C7  N     110.07  3.000
 NOZ  H5    C5  C6    108.90  3.000
 NOZ  H5    C5  C7    108.19  3.000
 NOZ  C6    C5  C7    111.44  3.000
 NOZ  H5    C5  C4    107.92  3.000
 NOZ  C6    C5  C4    110.68  3.000
 NOZ  C7    C5  C4    109.62  3.000
 NOZ  H6C2  C6  H6C1  106.98  3.000
 NOZ  H6C2  C6  O6    111.26  3.000
 NOZ  H6C1  C6  O6    111.11  3.000
 NOZ  H6C2  C6  C5    108.76  3.000
 NOZ  H6C1  C6  C5    109.67  3.000
 NOZ  O6    C6  C5    109.00  3.000
 NOZ  H6    O6  C6    107.99  3.000
 NOZ  H2    O2  C2    108.13  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
 NOZ  Var_01  C5  C7  N  C2  -61.81  30.0  1

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
 NOZ  chir_01  C4  O4  C3  C5  negativ
 NOZ  chir_02  C3  O3  C4  C2  negativ
 NOZ  chir_03  C2  O2  N   C3  positiv
 NOZ  chir_04  C5  C4  C7  C6  positiv

