# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 10:43:34 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-O-alpha-L-arabinofuranosyl-beta-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](O[C@H]2[C@H](O)CO[C@@H](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
 KHO  KHO  3-O-alpha-L-arabinofuranosyl-beta-D-xylopyranose  ligand  37  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHO
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
 KHO  C1    C  CH1   0   0.270  -0.8007  -0.0176  -3.6251
 KHO  O4    O  OH1   0  -0.661  -1.8466  -0.6050  -4.3047
 KHO  C2    C  CH1   0   0.007  -0.8572  -0.4860  -2.1703
 KHO  O2    O  OH1   0  -0.678  -2.0243  -0.0003  -1.5440
 KHO  C3    C  CH1   0  -0.011   0.3513   0.0294  -1.3974
 KHO  O1'   O  O2    0  -0.499   0.3868  -0.5594  -0.1179
 KHO  C1'   C  CR15  0   0.286   0.2036   0.2616   0.9921
 KHO  C2'   C  CR15  0  -0.057  -1.1844   0.1237   1.6219
 KHO  C3'   C  CR15  0  -0.012  -0.8867   0.3963   3.0838
 KHO  O3'   O  OH1   0  -0.663  -1.8080  -0.1229   4.0015
 KHO  O2'   O  OH1   0  -0.687  -2.1414   0.9989   1.1041
 KHO  O4'   O  O     0  -0.500   1.1121  -0.1426   1.9804
 KHO  C4'   C  CR15  0   0.003   0.4639  -0.2976   3.2394
 KHO  C5'   C  CH2   0  -0.154   1.3066   0.2938   4.3425
 KHO  O5'   O  OH1   0  -0.671   2.4861  -0.4612   4.4809
 KHO  C4    C  CH1   0   0.017   1.6388  -0.2958  -2.1394
 KHO  O6    O  OH1   0  -0.661   2.6906   0.3598  -1.4785
 KHO  C5    C  CH2   0  -0.230   1.5238   0.1658  -3.5913
 KHO  O5    O  O2    0  -0.489   0.4081  -0.4256  -4.2179
 KHO  H1    H  HCH1  0   0.195  -0.8647   1.0847  -3.6512
 KHO  HO4   H  HOH1  0   0.468  -2.0589  -0.0842  -5.0862
 KHO  H2    H  HCH1  0   0.237  -0.8371  -1.5849  -2.1619
 KHO  HO2   H  HOH1  0   0.469  -2.7834  -0.4941  -1.8708
 KHO  H3    H  HCH1  0   0.238   0.2715   1.1249  -1.3201
 KHO  H1'   H  HCR5  0   0.197   0.3893   1.3112   0.7144
 KHO  H2'   H  HCR5  0   0.216  -1.4961  -0.9288   1.5255
 KHO  H3'   H  HCR5  0   0.221  -0.7549   1.4812   3.2214
 KHO  H6    H  HOH1  0   0.459  -2.6014   0.4207   3.9779
 KHO  H5    H  HOH1  0   0.459  -2.2771   0.7535   0.1748
 KHO  H4'   H  HCR5  0   0.227   0.2973  -1.3653   3.4422
 KHO  H5'1  H  HCH2  0   0.204   0.7072   0.2876   5.2627
 KHO  H5'2  H  HCH2  0   0.199   1.5177   1.3447   4.1033
 KHO  H5'   H  HOH1  0   0.457   3.0296  -0.0442   5.1552
 KHO  H4    H  HCH1  0   0.223   1.7781  -1.3861  -2.1307
 KHO  HO6   H  HOH1  0   0.458   3.5232  -0.0199  -1.7756
 KHO  H51   H  HCH2  0   0.253   2.4084  -0.1330  -4.1563
 KHO  H52   H  HCH2  0   0.215   1.4607   1.2634  -3.6256

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
 KHO  C1   O4    single  1.379  0.020  1.379
 KHO  C1   C2    single  1.529  0.020  1.529
 KHO  C1   O5    single  1.407  0.020  1.407
 KHO  C1   H1    single  0.970  0.020  1.090
 KHO  O4   HO4   single  0.850  0.020  0.980
 KHO  C2   O2    single  1.411  0.020  1.411
 KHO  C2   C3    single  1.524  0.020  1.524
 KHO  C2   H2    single  0.970  0.020  1.090
 KHO  O2   HO2   single  0.850  0.020  0.980
 KHO  C3   O1'   single  1.409  0.020  1.409
 KHO  C3   C4    single  1.521  0.020  1.521
 KHO  C3   H3    single  0.970  0.020  1.090
 KHO  O1'  C1'   single  1.393  0.020  1.393
 KHO  C1'  C2'   single  1.530  0.020  1.530
 KHO  C1'  O4'   single  1.402  0.020  1.402
 KHO  C1'  H1'   single  0.970  0.020  1.090
 KHO  C2'  C3'   single  1.517  0.020  1.517
 KHO  C2'  O2'   single  1.396  0.020  1.396
 KHO  C2'  H2'   single  0.970  0.020  1.090
 KHO  C3'  O3'   single  1.400  0.020  1.400
 KHO  C3'  C4'   single  1.526  0.020  1.526
 KHO  C3'  H3'   single  0.970  0.020  1.090
 KHO  O3'  H6    single  0.850  0.020  0.980
 KHO  O2'  H5    single  0.850  0.020  0.980
 KHO  O4'  C4'   single  1.425  0.020  1.425
 KHO  C4'  C5'   single  1.509  0.020  1.509
 KHO  C4'  H4'   single  0.970  0.020  1.090
 KHO  C5'  O5'   single  1.407  0.020  1.407
 KHO  C5'  H5'1  single  0.970  0.020  1.090
 KHO  C5'  H5'2  single  0.970  0.020  1.090
 KHO  O5'  H5'   single  0.850  0.020  0.980
 KHO  C4   O6    single  1.405  0.020  1.405
 KHO  C4   C5    single  1.528  0.020  1.528
 KHO  C4   H4    single  0.970  0.020  1.090
 KHO  O6   HO6   single  0.850  0.020  0.980
 KHO  C5   O5    single  1.410  0.020  1.410
 KHO  C5   H51   single  0.970  0.020  1.090
 KHO  C5   H52   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
 KHO  H1    C1   O5    109.23  3.000
 KHO  H1    C1   C2    109.03  3.000
 KHO  O5    C1   C2    110.10  3.000
 KHO  H1    C1   O4    111.69  3.000
 KHO  O5    C1   O4    108.70  3.000
 KHO  C2    C1   O4    108.08  3.000
 KHO  HO4   O4   C1    109.69  3.000
 KHO  H2    C2   C3    108.64  3.000
 KHO  H2    C2   O2    110.85  3.000
 KHO  C3    C2   O2    108.33  3.000
 KHO  H2    C2   C1    108.23  3.000
 KHO  C3    C2   C1    110.46  3.000
 KHO  O2    C2   C1    110.33  3.000
 KHO  HO2   O2   C2    108.97  3.000
 KHO  H3    C3   C4    107.95  3.000
 KHO  H3    C3   O1'   110.73  3.000
 KHO  C4    C3   O1'   109.41  3.000
 KHO  H3    C3   C2    108.33  3.000
 KHO  C4    C3   C2    110.57  3.000
 KHO  O1'   C3   C2    109.82  3.000
 KHO  C1'   O1'  C3    118.30  3.000
 KHO  H1'   C1'  O4'   110.07  3.000
 KHO  H1'   C1'  C2'   110.03  3.000
 KHO  O4'   C1'  C2'   105.76  3.000
 KHO  H1'   C1'  O1'   109.79  3.000
 KHO  O4'   C1'  O1'   107.85  3.000
 KHO  C2'   C1'  O1'   113.22  3.000
 KHO  H2'   C2'  O2'   111.85  3.000
 KHO  H2'   C2'  C3'   108.15  3.000
 KHO  O2'   C2'  C3'   112.29  3.000
 KHO  H2'   C2'  C1'   107.86  3.000
 KHO  O2'   C2'  C1'   114.36  3.000
 KHO  C3'   C2'  C1'   101.68  3.000
 KHO  H3'   C3'  C4'   109.21  3.000
 KHO  H3'   C3'  O3'   111.23  3.000
 KHO  C4'   C3'  O3'   110.29  3.000
 KHO  H3'   C3'  C2'   108.72  3.000
 KHO  C4'   C3'  C2'   100.97  3.000
 KHO  O3'   C3'  C2'   115.85  3.000
 KHO  H6    O3'  C3'   108.48  3.000
 KHO  H5    O2'  C2'   107.00  3.000
 KHO  C4'   O4'  C1'   111.07  3.000
 KHO  H4'   C4'  C5'   109.29  3.000
 KHO  H4'   C4'  O4'   109.73  3.000
 KHO  C5'   C4'  O4'   110.45  3.000
 KHO  H4'   C4'  C3'   109.04  3.000
 KHO  C5'   C4'  C3'   112.99  3.000
 KHO  O4'   C4'  C3'   105.25  3.000
 KHO  H5'2  C5'  H5'1  107.03  3.000
 KHO  H5'2  C5'  O5'   111.95  3.000
 KHO  H5'1  C5'  O5'   111.84  3.000
 KHO  H5'2  C5'  C4'   108.86  3.000
 KHO  H5'1  C5'  C4'   107.78  3.000
 KHO  O5'   C5'  C4'   109.25  3.000
 KHO  H5'   O5'  C5'   108.07  3.000
 KHO  H4    C4   C5    108.47  3.000
 KHO  H4    C4   O6    111.37  3.000
 KHO  C5    C4   O6    111.25  3.000
 KHO  H4    C4   C3    108.39  3.000
 KHO  C5    C4   C3    109.59  3.000
 KHO  O6    C4   C3    107.73  3.000
 KHO  HO6   O6   C4    108.57  3.000
 KHO  H52   C5   H51   107.68  3.000
 KHO  H52   C5   O5    111.06  3.000
 KHO  H51   C5   O5    107.24  3.000
 KHO  H52   C5   C4    109.60  3.000
 KHO  H51   C5   C4    110.38  3.000
 KHO  O5    C5   C4    110.80  3.000
 KHO  C5    O5   C1    111.78  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
 KHO  Var_01  C4  C5  O5  C1  64.05  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
 KHO  chir_01  C1   O4   C2   O5   negativ
 KHO  chir_02  C2   O2   C1   C3   negativ
 KHO  chir_03  C3   O1'  C4   C2   negativ
 KHO  chir_04  C1'  O1'  O4'  C2'  positiv
 KHO  chir_05  C2'  O2'  C1'  C3'  negativ
 KHO  chir_06  C3'  O3'  C4'  C2'  negativ
 KHO  chir_07  C4'  O4'  C3'  C5'  positiv
 KHO  chir_08  C4   O6   C3   C5   negativ

