# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:37:37 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,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
 NOY  NOY  (2R,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 PERFECT
;

data_comp_NOY
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
 NOY  O4    O  OH1   0  -0.690   1.7833  -2.7511   2.5519
 NOY  C4    C  CH1   0   0.072   1.4890  -1.6216   1.7635
 NOY  C3    C  CH1   0   0.001   2.7527  -0.7798   1.6536
 NOY  O3    O  OH1   0  -0.670   3.1416  -0.4051   2.9525
 NOY  C2    C  CH1   0   0.121   2.4924   0.4444   0.7664
 NOY  N     N  NH1   0  -0.588   2.0219   0.0813  -0.5534
 NOY  C7    C  CH2   0  -0.316   0.8104  -0.7166  -0.4714
 NOY  C5    C  CH1   0  -0.367   0.9581  -1.9852   0.3739
 NOY  C6    C  CH2   0  -0.156  -0.3866  -2.7035   0.4382
 NOY  O2    O  OH1   0  -0.662   3.6184   1.2748   0.7033
 NOY  O6    O  OH1   0  -0.666  -0.3549  -3.9220   1.1647
 NOY  H4    H  HOH1  0   0.442   1.0521  -3.3733   2.4339
 NOY  HA    H  HCH1  0   0.186   0.7199  -0.9976   2.2549
 NOY  H3    H  HCH1  0   0.197   3.5330  -1.3914   1.1646
 NOY  H5    H  HCH1  0   0.239   1.6878  -2.6395  -0.1234
 NOY  HB    H  HOH1  0   0.446   3.8849   0.2024   2.8749
 NOY  H     H  HNH1  0   0.342   2.7355  -0.4591  -1.0353
 NOY  H7C1  H  HCH2  0   0.254   0.4969  -0.9787  -1.4832
 NOY  H7C2  H  HCH2  0   0.229   0.0168  -0.0891  -0.0501
 NOY  H6C1  H  HCH2  0   0.227  -0.7610  -2.8701  -0.5785
 NOY  H6C2  H  HCH2  0   0.224  -1.1145  -2.0645   0.9459
 NOY  H6C3  H  HOH1  0   0.458   0.1268  -4.5713   0.6414
 NOY  H12   H  HCH1  0   0.227   1.7064   1.0481   1.2367
 NOY  H22   H  HOH1  0   0.448   4.3610   0.7789   0.3384

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
 NOY  O4  H4    single  0.850  0.020  0.980
 NOY  O4  C4    single  1.409  0.020  1.409
 NOY  C4  C5    single  1.531  0.020  1.531
 NOY  C4  HA    single  0.970  0.020  1.090
 NOY  C4  C3    single  1.522  0.020  1.522
 NOY  C3  C2    single  1.534  0.020  1.534
 NOY  C3  H3    single  0.970  0.020  1.090
 NOY  C3  O3    single  1.407  0.020  1.407
 NOY  O3  HB    single  0.850  0.020  0.980
 NOY  C2  N     single  1.447  0.020  1.447
 NOY  C2  O2    single  1.400  0.020  1.400
 NOY  C2  H12   single  0.970  0.020  1.090
 NOY  N   C7    single  1.453  0.020  1.453
 NOY  N   H     single  0.860  0.020  1.020
 NOY  C7  C5    single  1.532  0.020  1.532
 NOY  C7  H7C1  single  0.970  0.020  1.090
 NOY  C7  H7C2  single  0.970  0.020  1.090
 NOY  C5  C6    single  1.526  0.020  1.526
 NOY  C5  H5    single  0.970  0.020  1.090
 NOY  C6  H6C1  single  0.970  0.020  1.090
 NOY  C6  H6C2  single  0.970  0.020  1.090
 NOY  C6  O6    single  1.419  0.020  1.419
 NOY  O2  H22   single  0.850  0.020  0.980
 NOY  O6  H6C3  single  0.850  0.020  0.980

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
 NOY  H4    O4  C4    106.83  3.000
 NOY  HA    C4  C5    107.23  3.000
 NOY  HA    C4  C3    107.30  3.000
 NOY  C5    C4  C3    110.71  3.000
 NOY  C3    C4  O4    108.08  3.000
 NOY  HA    C4  O4    110.44  3.000
 NOY  C5    C4  O4    112.95  3.000
 NOY  H3    C3  C2    107.78  3.000
 NOY  H3    C3  O3    111.14  3.000
 NOY  C2    C3  O3    111.61  3.000
 NOY  O3    C3  C4    108.07  3.000
 NOY  H3    C3  C4    108.18  3.000
 NOY  C2    C3  C4    110.01  3.000
 NOY  HB    O3  C3    107.88  3.000
 NOY  H12   C2  O2    105.61  3.000
 NOY  H12   C2  N     107.22  3.000
 NOY  O2    C2  N     111.65  3.000
 NOY  H12   C2  C3    108.23  3.000
 NOY  O2    C2  C3    111.27  3.000
 NOY  N     C2  C3    112.47  3.000
 NOY  H     N   C7    108.67  3.000
 NOY  H     N   C2    109.72  3.000
 NOY  C7    N   C2    110.94  3.000
 NOY  H7C2  C7  H7C1  106.62  3.000
 NOY  H7C2  C7  C5    109.38  3.000
 NOY  H7C1  C7  C5    109.90  3.000
 NOY  H7C2  C7  N     108.12  3.000
 NOY  H7C1  C7  N     108.61  3.000
 NOY  C5    C7  N     113.93  3.000
 NOY  H5    C5  C6    108.90  3.000
 NOY  H5    C5  C7    107.90  3.000
 NOY  C6    C5  C7    109.16  3.000
 NOY  H5    C5  C4    108.77  3.000
 NOY  C6    C5  C4    112.27  3.000
 NOY  C7    C5  C4    109.73  3.000
 NOY  H6C2  C6  H6C1  106.98  3.000
 NOY  H6C2  C6  O6    106.20  3.000
 NOY  H6C1  C6  O6    110.61  3.000
 NOY  O6    C6  C5    113.96  3.000
 NOY  H6C2  C6  C5    109.33  3.000
 NOY  H6C1  C6  C5    109.47  3.000
 NOY  H22   O2  C2    109.34  3.000
 NOY  H6C3  O6  C6    108.18  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
 NOY  Var_01  C5  C7  N  C2  -56.46  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
 NOY  chir_01  C4  O4  C5  C3  positiv
 NOY  chir_02  C3  O3  C4  C2  negativ
 NOY  chir_03  C2  O2  N   C3  negativ
 NOY  chir_04  C5  C4  C7  C6  positiv

