# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:41:44 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1NC[C@H](CO)[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
 IFG  IFG  N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)piperidin-2-yl]acetamide  ligand  30  14  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IFG
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
 IFG  N1    N  NH1   0  -0.613   1.2705  -0.4232   0.0540
 IFG  C2    C  CH1   0   0.080   0.1047   0.0549   0.7708
 IFG  C3    C  CH1   0   0.030  -1.1530  -0.4325   0.0433
 IFG  C4    C  CH1   0   0.004  -1.1647   0.0542  -1.4016
 IFG  C5    C  CH1   0  -0.304   0.1170  -0.3914  -2.0978
 IFG  C6    C  CH2   0  -0.132   0.1421   0.0636  -3.5477
 IFG  C8    C  CH3   0  -0.781   0.4014  -0.5483   4.5059
 IFG  C9    C  CH2   0  -0.273   1.3400   0.0713  -1.3132
 IFG  N2    N  NH1   0  -0.664   0.1157  -0.4727   2.1126
 IFG  O7    O  O     0  -0.495   0.4543   1.4702   3.2298
 IFG  O3    O  OH1   0  -0.670  -2.3258   0.0328   0.6628
 IFG  O4    O  OH1   0  -0.674  -1.2544   1.4600  -1.4702
 IFG  O6    O  OH1   0  -0.674   1.2394  -0.5463  -4.1941
 IFG  HN1   H  HNH1  0   0.358   2.1027  -0.1385   0.5560
 IFG  HC2   H  HCH1  0   0.229   0.0655   1.1475   0.8534
 IFG  HC3   H  HCH1  0   0.209  -1.1200  -1.5328   0.0255
 IFG  HC4   H  HCH1  0   0.228  -2.0225  -0.4105  -1.9118
 IFG  HC5   H  HCH1  0   0.242   0.1053  -1.4879  -2.0904
 IFG  HC61  H  HCH2  0   0.199  -0.8070  -0.2200  -4.0240
 IFG  HC62  H  HCH2  0   0.198   0.2111   1.1565  -3.5985
 IFG  HC81  H  HCH3  0   0.267  -0.2583  -0.1093   5.2531
 IFG  HC82  H  HCH3  0   0.250   0.1353  -1.5956   4.3775
 IFG  HC83  H  HCH3  0   0.270   1.4173  -0.4996   4.8999
 IFG  HC91  H  HCH2  0   0.200   1.4169   1.1677  -1.3672
 IFG  HC92  H  HCH2  0   0.242   2.2445  -0.3318  -1.7694
 IFG  HN2   H  HNH1  0   0.399   0.1085  -1.4785   2.1981
 IFG  HO3   H  HOH1  0   0.452  -2.2952  -0.2064   1.5955
 IFG  HO4   H  HOH1  0   0.450  -2.0162   1.7392  -0.9514
 IFG  HO6   H  HOH1  0   0.454   1.2975  -0.1886  -5.0843
 IFG  C7    C  C     0   0.520   0.3283   0.2554   3.2320

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
 IFG  N1  C2    single  1.450  0.020  1.450
 IFG  N1  C9    single  1.455  0.020  1.455
 IFG  N1  HN1   single  0.890  0.020  1.040
 IFG  C2  C3    single  1.532  0.020  1.532
 IFG  C2  N2    single  1.442  0.020  1.442
 IFG  C2  HC2   single  0.970  0.020  1.090
 IFG  C3  C4    single  1.525  0.020  1.525
 IFG  C3  O3    single  1.406  0.020  1.406
 IFG  C3  HC3   single  0.970  0.020  1.090
 IFG  C4  C5    single  1.525  0.020  1.525
 IFG  C4  O4    single  1.410  0.020  1.410
 IFG  C4  HC4   single  0.970  0.020  1.090
 IFG  C5  C6    single  1.520  0.020  1.520
 IFG  C5  C9    single  1.525  0.020  1.525
 IFG  C5  HC5   single  0.970  0.020  1.090
 IFG  C6  O6    single  1.412  0.020  1.412
 IFG  C6  HC61  single  0.970  0.020  1.090
 IFG  C6  HC62  single  0.970  0.020  1.090
 IFG  C7  C8    single  1.508  0.020  1.508
 IFG  C7  N2    single  1.352  0.020  1.352
 IFG  C7  O7    double  1.221  0.020  1.221
 IFG  C8  HC81  single  0.970  0.020  1.090
 IFG  C8  HC82  single  0.970  0.020  1.090
 IFG  C8  HC83  single  0.970  0.020  1.090
 IFG  C9  HC91  single  0.970  0.020  1.090
 IFG  C9  HC92  single  0.970  0.020  1.090
 IFG  N2  HN2   single  0.860  0.020  1.020
 IFG  O3  HO3   single  0.850  0.020  0.980
 IFG  O4  HO4   single  0.850  0.020  0.980
 IFG  O6  HO6   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
 IFG  HN1   N1  C9    109.32  3.000
 IFG  HN1   N1  C2    108.84  3.000
 IFG  C9    N1  C2    113.01  3.000
 IFG  HC2   C2  N2    107.14  3.000
 IFG  HC2   C2  C3    108.87  3.000
 IFG  N2    C2  C3    109.37  3.000
 IFG  HC2   C2  N1    113.24  3.000
 IFG  N2    C2  N1    109.48  3.000
 IFG  C3    C2  N1    108.69  3.000
 IFG  HC3   C3  O3    111.28  3.000
 IFG  HC3   C3  C4    107.69  3.000
 IFG  O3    C3  C4    107.79  3.000
 IFG  HC3   C3  C2    107.52  3.000
 IFG  O3    C3  C2    111.73  3.000
 IFG  C4    C3  C2    110.77  3.000
 IFG  HC4   C4  O4    110.40  3.000
 IFG  HC4   C4  C5    108.66  3.000
 IFG  O4    C4  C5    108.81  3.000
 IFG  HC4   C4  C3    108.08  3.000
 IFG  O4    C4  C3    111.39  3.000
 IFG  C5    C4  C3    109.45  3.000
 IFG  HC5   C5  C9    107.96  3.000
 IFG  HC5   C5  C6    107.82  3.000
 IFG  C9    C5  C6    112.76  3.000
 IFG  HC5   C5  C4    106.26  3.000
 IFG  C9    C5  C4    110.52  3.000
 IFG  C6    C5  C4    111.22  3.000
 IFG  HC62  C6  HC61  106.94  3.000
 IFG  HC62  C6  O6    111.13  3.000
 IFG  HC61  C6  O6    111.17  3.000
 IFG  HC62  C6  C5    110.10  3.000
 IFG  HC61  C6  C5    108.78  3.000
 IFG  O6    C6  C5    108.68  3.000
 IFG  HC83  C8  HC82  108.27  3.000
 IFG  HC83  C8  HC81  107.36  3.000
 IFG  HC82  C8  HC81  108.70  3.000
 IFG  HC83  C8  C7    109.06  3.000
 IFG  HC82  C8  C7    113.66  3.000
 IFG  HC81  C8  C7    109.60  3.000
 IFG  HC92  C9  HC91  106.85  3.000
 IFG  HC92  C9  C5    109.75  3.000
 IFG  HC91  C9  C5    109.45  3.000
 IFG  HC92  C9  N1    107.89  3.000
 IFG  HC91  C9  N1    112.82  3.000
 IFG  C5    C9  N1    109.99  3.000
 IFG  HN2   N2  C7    117.87  3.000
 IFG  HN2   N2  C2    116.32  3.000
 IFG  C7    N2  C2    125.07  3.000
 IFG  HO3   O3  C3    108.54  3.000
 IFG  HO4   O4  C4    108.24  3.000
 IFG  HO6   O6  C6    108.07  3.000
 IFG  O7    C7  N2    123.39  3.000
 IFG  O7    C7  C8    121.78  3.000
 IFG  N2    C7  C8    114.84  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
 IFG  CONST_01  C8    C7  N2  C2   180.00   0.0  0
 IFG  CONST_02  O7    C7  N2  C2     0.00   0.0  0
 IFG  CONST_03  HN2   N2  C7  C8     0.00   0.0  0
 IFG  Var_01    C5    C9  N1  C2   -60.63  30.0  1
 IFG  Var_02    HC81  C8  C7  N2  -129.94  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
 IFG  chir_01  C2  N1  C3  N2  negativ
 IFG  chir_02  C3  O3  C2  C4  positiv
 IFG  chir_03  C4  O4  C3  C5  positiv
 IFG  chir_04  C5  C4  C6  C9  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
 IFG  plan-1  C2   0.020
 IFG  plan-1  C8   0.020
 IFG  plan-1  N2   0.020
 IFG  plan-1  O7   0.020
 IFG  plan-1  HN2  0.020
 IFG  plan-1  C7   0.020

