# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:04:22 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2Z,3S,4S,5R)-3,4,5-trihydroxypiperidin-2-one oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O/N=C/1NC[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
 LOX  LOX  '(2Z,3S,4S,5R)-3,4,5-trihydroxypiperidin-2-one oxime'  D-saccharide  21  11  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LOX
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
 LOX  C1    C  C     0   0.414   1.1761  -0.0466  -0.2093
 LOX  C2    C  CH1   0  -0.004   0.0936   0.9840  -0.4276
 LOX  C3    C  CH1   0   0.027  -1.2150   0.5599   0.2371
 LOX  C4    C  CH1   0   0.024  -1.5804  -0.8242  -0.2692
 LOX  C5    C  CH2   0  -0.293  -0.4777  -1.8040   0.1258
 LOX  N1    N  NH1   0  -0.646   0.8237  -1.3532  -0.3291
 LOX  O22   O  OH1   0  -0.563   3.2999  -0.5600   0.1271
 LOX  N2    N  N     0  -0.254   2.3475   0.4260  -0.0330
 LOX  O2    O  OH1   0  -0.668   0.4739   2.2480   0.0351
 LOX  O3    O  OH1   0  -0.649  -2.2471   1.4525  -0.0806
 LOX  O4    O  OH1   0  -0.640  -2.8091  -1.2080   0.2914
 LOX  H2    H  HCH1  0   0.224  -0.0890   1.0189  -1.5141
 LOX  H3    H  HCH1  0   0.208  -1.0549   0.5100   1.3271
 LOX  H4    H  HCH1  0   0.212  -1.6435  -0.7876  -1.3664
 LOX  H51   H  HCH2  0   0.240  -0.6744  -2.7789  -0.3221
 LOX  H52   H  HCH2  0   0.226  -0.4990  -1.9372   1.2140
 LOX  HN1   H  HNH1  0   0.381   1.5687  -2.0152  -0.1812
 LOX  HO22  H  HOH1  0   0.454   4.1224  -0.0734   0.2102
 LOX  HO2   H  HOH1  0   0.440   1.4297   2.2182   0.1816
 LOX  HO3   H  HOH1  0   0.437  -2.0095   2.3155   0.2703
 LOX  HO4   H  HOH1  0   0.431  -3.1251  -1.9777  -0.1879

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
 LOX  C1   C2    single  1.510  0.020  1.510
 LOX  C1   N1    single  1.359  0.020  1.359
 LOX  C1   N2    double  1.275  0.020  1.275
 LOX  C2   C3    single  1.528  0.020  1.528
 LOX  C2   O2    single  1.399  0.020  1.399
 LOX  C2   H2    single  0.970  0.020  1.090
 LOX  C3   C4    single  1.518  0.020  1.518
 LOX  C3   O3    single  1.401  0.020  1.401
 LOX  C3   H3    single  0.970  0.020  1.090
 LOX  C4   C5    single  1.527  0.020  1.527
 LOX  C4   O4    single  1.404  0.020  1.404
 LOX  C4   H4    single  0.970  0.020  1.090
 LOX  C5   N1    single  1.450  0.020  1.450
 LOX  C5   H51   single  0.970  0.020  1.090
 LOX  C5   H52   single  0.970  0.020  1.090
 LOX  N1   HN1   single  0.890  0.020  1.040
 LOX  O22  N2    single  1.380  0.020  1.380
 LOX  O22  HO22  single  0.850  0.020  0.980
 LOX  O2   HO2   single  0.850  0.020  0.980
 LOX  O3   HO3   single  0.850  0.020  0.980
 LOX  O4   HO4   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
 LOX  N2    C1   N1   127.36  3.000
 LOX  N2    C1   C2   115.18  3.000
 LOX  N1    C1   C2   117.23  3.000
 LOX  H2    C2   O2   110.03  3.000
 LOX  H2    C2   C3   107.20  3.000
 LOX  O2    C2   C3   109.87  3.000
 LOX  H2    C2   C1   106.42  3.000
 LOX  O2    C2   C1   111.96  3.000
 LOX  C3    C2   C1   111.20  3.000
 LOX  H3    C3   O3   111.09  3.000
 LOX  H3    C3   C4   108.86  3.000
 LOX  O3    C3   C4   109.14  3.000
 LOX  H3    C3   C2   108.56  3.000
 LOX  O3    C3   C2   110.82  3.000
 LOX  C4    C3   C2   108.31  3.000
 LOX  H4    C4   O4   110.93  3.000
 LOX  H4    C4   C5   108.72  3.000
 LOX  O4    C4   C5   110.69  3.000
 LOX  H4    C4   C3   108.43  3.000
 LOX  O4    C4   C3   109.07  3.000
 LOX  C5    C4   C3   108.95  3.000
 LOX  H52   C5   H51  107.19  3.000
 LOX  H52   C5   N1   111.50  3.000
 LOX  H51   C5   N1   108.11  3.000
 LOX  H52   C5   C4   108.69  3.000
 LOX  H51   C5   C4   109.69  3.000
 LOX  N1    C5   C4   111.56  3.000
 LOX  HN1   N1   C5   114.41  3.000
 LOX  HN1   N1   C1   115.29  3.000
 LOX  C5    N1   C1   120.26  3.000
 LOX  HO22  O22  N2   103.85  3.000
 LOX  O22   N2   C1   112.65  3.000
 LOX  HO2   O2   C2   106.91  3.000
 LOX  HO3   O3   C3   107.88  3.000
 LOX  HO4   O4   C4   107.93  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
 LOX  CONST_03  HN1  N1  C1  C2  180.00   0.0  0
 LOX  CONST_04  O22  N2  C1  C2  180.00   0.0  0
 LOX  CONST_05  O22  N2  C1  N1    0.00   0.0  0
 LOX  Var_01    C4   C5  N1  C1   42.51  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
 LOX  chir_01  C2  C1  C3  O2  negativ
 LOX  chir_02  C3  O3  C2  C4  positiv
 LOX  chir_03  C4  O4  C3  C5  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
 LOX  plan-1  C1   0.020
 LOX  plan-1  C2   0.020
 LOX  plan-1  C5   0.020
 LOX  plan-1  N1   0.020
 LOX  plan-1  O22  0.020
 LOX  plan-1  N2   0.020
 LOX  plan-1  HN1  0.020

