# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:24:07 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](O[C@@H]2CCNC(=O)[C@H]2O)[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
 XIL  XIL  '(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside'  D-saccharide  35  18  .  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_XIL
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
 XIL  C1    C  CH1   0   0.292   0.0426   0.0812   0.8400
 XIL  C2    C  CH1   0  -0.016  -0.8060  -0.5268   1.9596
 XIL  O2    O  OH1   0  -0.662  -2.1715  -0.3079   1.7232
 XIL  C3    C  CH1   0   0.011  -0.4338   0.1276   3.2799
 XIL  O3    O  OH1   0  -0.667  -1.1468  -0.5078   4.3094
 XIL  C4    C  CH1   0  -0.004   1.0741   0.0375   3.4891
 XIL  O4    O  OH1   0  -0.670   1.3822   0.7669   4.6542
 XIL  C5    C  CH2   0  -0.230   1.8022   0.6034   2.2727
 XIL  O5    O  O2    0  -0.484   1.4114  -0.0785   1.1003
 XIL  N1'   N  NH1   0  -0.623  -0.4759   0.9834  -4.1732
 XIL  C2'   C  C     0   0.491   0.1725  -0.1746  -4.0207
 XIL  C3'   C  CH1   0  -0.048   0.1171  -0.8532  -2.6500
 XIL  O2'   O  O     0  -0.501   0.7599  -0.7426  -4.9342
 XIL  O3'   O  OH1   0  -0.661   1.2658  -1.6202  -2.4494
 XIL  C4'   C  CH1   0   0.023  -0.0582   0.1487  -1.5261
 XIL  O4'   O  O2    0  -0.512  -0.2554  -0.5866  -0.3309
 XIL  C5'   C  CH2   0  -0.511  -1.2591   1.0222  -1.8497
 XIL  C6'   C  CH2   0  -0.270  -0.9918   1.8249  -3.1079
 XIL  H1    H  HCH1  0   0.193  -0.1952   1.1584   0.7595
 XIL  H2    H  HCH1  0   0.221  -0.5712  -1.6013   2.0194
 XIL  HO2   H  HOH1  0   0.451  -2.4150  -0.7757   0.9177
 XIL  H3    H  HCH1  0   0.210  -0.7022   1.1963   3.2174
 XIL  HO3   H  HOH1  0   0.450  -0.9053  -0.0855   5.1403
 XIL  H4    H  HCH1  0   0.222   1.3453  -1.0218   3.6020
 XIL  HO4   H  HOH1  0   0.461   2.2493   0.4949   4.9693
 XIL  H51   H  HCH2  0   0.216   1.6001   1.6813   2.1901
 XIL  H52   H  HCH2  0   0.252   2.8809   0.4749   2.3752
 XIL  H3'   H  HCH1  0   0.242  -0.7882  -1.4852  -2.6731
 XIL  HO'   H  HOH1  0   0.447   1.5260  -1.9712  -3.3109
 XIL  H4'   H  HCH1  0   0.242   0.8462   0.7682  -1.4519
 XIL  H5'1  H  HCH2  0   0.252  -2.1449   0.3933  -1.9759
 XIL  H5'2  H  HCH2  0   0.268  -1.4670   1.7194  -1.0363
 XIL  H6'1  H  HCH2  0   0.266  -1.9097   2.2978  -3.4550
 XIL  H6'2  H  HCH2  0   0.248  -0.2762   2.6243  -2.8949
 XIL  HN'   H  HNH1  0   0.403  -0.4407   1.3915  -5.0966

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
 XIL  C1   C2    single  1.531  0.020  1.531
 XIL  C1   O5    single  1.403  0.020  1.403
 XIL  C1   O4'   single  1.381  0.020  1.381
 XIL  C1   H1    single  0.970  0.020  1.090
 XIL  C2   O2    single  1.403  0.020  1.403
 XIL  C2   C3    single  1.520  0.020  1.520
 XIL  C2   H2    single  0.970  0.020  1.090
 XIL  O2   HO2   single  0.850  0.020  0.980
 XIL  C3   O3    single  1.404  0.020  1.404
 XIL  C3   C4    single  1.525  0.020  1.525
 XIL  C3   H3    single  0.970  0.020  1.090
 XIL  O3   HO3   single  0.850  0.020  0.980
 XIL  C4   O4    single  1.409  0.020  1.409
 XIL  C4   C5    single  1.526  0.020  1.526
 XIL  C4   H4    single  0.970  0.020  1.090
 XIL  O4   HO4   single  0.850  0.020  0.980
 XIL  C5   O5    single  1.411  0.020  1.411
 XIL  C5   H51   single  0.970  0.020  1.090
 XIL  C5   H52   single  0.970  0.020  1.090
 XIL  N1'  C2'   single  1.336  0.020  1.336
 XIL  N1'  C6'   single  1.452  0.020  1.452
 XIL  N1'  HN'   single  0.860  0.020  1.020
 XIL  C2'  C3'   single  1.530  0.020  1.530
 XIL  C2'  O2'   double  1.226  0.020  1.226
 XIL  C3'  O3'   single  1.396  0.020  1.396
 XIL  C3'  C4'   single  1.516  0.020  1.516
 XIL  C3'  H3'   single  0.970  0.020  1.090
 XIL  O3'  HO'   single  0.850  0.020  0.980
 XIL  C4'  O4'   single  1.417  0.020  1.417
 XIL  C4'  C5'   single  1.520  0.020  1.520
 XIL  C4'  H4'   single  0.970  0.020  1.090
 XIL  C5'  C6'   single  1.516  0.020  1.516
 XIL  C5'  H5'1  single  0.970  0.020  1.090
 XIL  C5'  H5'2  single  0.970  0.020  1.090
 XIL  C6'  H6'1  single  0.970  0.020  1.090
 XIL  C6'  H6'2  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
 XIL  H1    C1   O4'   111.29  3.000
 XIL  H1    C1   O5    109.53  3.000
 XIL  O4'   C1   O5    108.24  3.000
 XIL  H1    C1   C2    108.72  3.000
 XIL  O4'   C1   C2    107.97  3.000
 XIL  O5    C1   C2    111.10  3.000
 XIL  H2    C2   C3    108.71  3.000
 XIL  H2    C2   O2    111.65  3.000
 XIL  C3    C2   O2    108.52  3.000
 XIL  H2    C2   C1    107.99  3.000
 XIL  C3    C2   C1    109.18  3.000
 XIL  O2    C2   C1    110.75  3.000
 XIL  HO2   O2   C2    108.14  3.000
 XIL  H3    C3   C4    107.79  3.000
 XIL  H3    C3   O3    110.87  3.000
 XIL  C4    C3   O3    112.01  3.000
 XIL  H3    C3   C2    107.95  3.000
 XIL  C4    C3   C2    109.63  3.000
 XIL  O3    C3   C2    108.52  3.000
 XIL  HO3   O3   C3    107.87  3.000
 XIL  H4    C4   C5    108.75  3.000
 XIL  H4    C4   O4    111.10  3.000
 XIL  C5    C4   O4    111.27  3.000
 XIL  H4    C4   C3    108.36  3.000
 XIL  C5    C4   C3    109.90  3.000
 XIL  O4    C4   C3    107.40  3.000
 XIL  HO4   O4   C4    108.76  3.000
 XIL  H52   C5   H51   107.71  3.000
 XIL  H52   C5   O5    107.15  3.000
 XIL  H51   C5   O5    111.12  3.000
 XIL  H52   C5   C4    110.67  3.000
 XIL  H51   C5   C4    109.60  3.000
 XIL  O5    C5   C4    110.53  3.000
 XIL  C5    O5   C1    111.67  3.000
 XIL  HN'   N1'  C6'   116.67  3.000
 XIL  HN'   N1'  C2'   115.95  3.000
 XIL  C6'   N1'  C2'   126.23  3.000
 XIL  O2'   C2'  C3'   118.65  3.000
 XIL  O2'   C2'  N1'   123.31  3.000
 XIL  C3'   C2'  N1'   117.97  3.000
 XIL  H3'   C3'  C4'   107.40  3.000
 XIL  H3'   C3'  O3'   111.30  3.000
 XIL  C4'   C3'  O3'   110.60  3.000
 XIL  H3'   C3'  C2'   105.35  3.000
 XIL  C4'   C3'  C2'   112.03  3.000
 XIL  O3'   C3'  C2'   110.03  3.000
 XIL  HO'   O3'  C3'   107.05  3.000
 XIL  H4'   C4'  C5'   109.92  3.000
 XIL  H4'   C4'  O4'   110.49  3.000
 XIL  C5'   C4'  O4'   111.58  3.000
 XIL  H4'   C4'  C3'   109.12  3.000
 XIL  C5'   C4'  C3'   108.26  3.000
 XIL  O4'   C4'  C3'   107.37  3.000
 XIL  C4'   O4'  C1    115.74  3.000
 XIL  H5'2  C5'  H5'1  107.40  3.000
 XIL  H5'2  C5'  C6'   108.29  3.000
 XIL  H5'1  C5'  C6'   110.58  3.000
 XIL  H5'2  C5'  C4'   111.04  3.000
 XIL  H5'1  C5'  C4'   109.52  3.000
 XIL  C6'   C5'  C4'   109.98  3.000
 XIL  H6'2  C6'  H6'1  107.22  3.000
 XIL  H6'2  C6'  C5'   109.92  3.000
 XIL  H6'1  C6'  C5'   110.23  3.000
 XIL  H6'2  C6'  N1'   109.50  3.000
 XIL  H6'1  C6'  N1'   108.49  3.000
 XIL  C5'   C6'  N1'   111.38  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
 XIL  CONST_01  C6'  N1'  C2'  C3'    0.00   0.0  0
 XIL  CONST_02  C6'  N1'  C2'  O2'  180.00   0.0  0
 XIL  CONST_03  HN'  N1'  C2'  C3'  180.00   0.0  0
 XIL  Var_01    C4   C5   O5   C1    62.27  30.0  1
 XIL  Var_02    C4'  C5'  C6'  N1'   48.31  30.0  1
 XIL  Var_03    C5'  C6'  N1'  C2'  -24.50  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
 XIL  chir_01  C1   C2   O5   O4'  negativ
 XIL  chir_02  C2   O2   C1   C3   negativ
 XIL  chir_03  C3   O3   C2   C4   positiv
 XIL  chir_04  C4   O4   C3   C5   negativ
 XIL  chir_05  C3'  O3'  C4'  C2'  negativ
 XIL  chir_06  C4'  O4'  C5'  C3'  positiv

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
 XIL  plan-1  N1'  0.020
 XIL  plan-1  C2'  0.020
 XIL  plan-1  C3'  0.020
 XIL  plan-1  O2'  0.020
 XIL  plan-1  C6'  0.020
 XIL  plan-1  HN'  0.020

