# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 05:52:22 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-oxane-2,3,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](S[C@@H]2[C@@H](O)[C@H](O)O[C@H](CO)[C@H]2O)[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
 6BV  6BV  (2~{R},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-oxane-2,3,5-triol  ligand  45  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6BV
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
 6BV  O41  O  OH1   0  -0.695  26.0214  29.0031  34.4129
 6BV  C41  C  CH1   0   0.112  26.6597  29.6168  35.4976
 6BV  C51  C  CH1   0  -0.002  27.8438  30.4077  34.9310
 6BV  C61  C  CH2   0  -0.180  27.4452  31.4707  33.9297
 6BV  O61  O  OH1   0  -0.672  26.5397  32.3706  34.5217
 6BV  O01  O  O2    0  -0.498  28.5510  31.0266  35.9845
 6BV  C11  C  CH1   0   0.269  29.1329  30.0983  36.8621
 6BV  O11  O  OH1   0  -0.661  29.8530  30.7855  37.8173
 6BV  C21  C  CH1   0   0.043  28.0438  29.2962  37.5766
 6BV  O21  O  OH1   0  -0.654  28.6000  28.3158  38.4069
 6BV  C31  C  CH1   0  -0.511  27.1694  28.6085  36.5330
 6BV  S12  S  S2    0   0.046  25.7916  27.7736  37.3997
 6BV  C12  C  CH1   0  -0.141  25.5945  26.2644  36.4398
 6BV  O02  O  O2    0  -0.501  24.8625  26.5645  35.2723
 6BV  C52  C  CH1   0  -0.007  24.7388  25.4676  34.3746
 6BV  C62  C  CH2   0  -0.182  24.1252  25.9782  33.0898
 6BV  O62  O  OH1   0  -0.669  22.8242  26.4475  33.3401
 6BV  C42  C  CH1   0   0.043  23.9361  24.3664  35.0646
 6BV  O42  O  OH1   0  -0.673  23.8548  23.2744  34.1843
 6BV  C32  C  CH1   0  -0.036  24.6326  23.9862  36.3686
 6BV  O32  O  OH1   0  -0.676  23.8566  23.0395  37.0758
 6BV  C22  C  CH1   0   0.052  24.8374  25.2172  37.2511
 6BV  O22  O  OH1   0  -0.660  25.5835  24.9192  38.3977
 6BV  H1   H  HOH1  0   0.461  25.4592  28.2774  34.7244
 6BV  H2   H  HCH1  0   0.208  25.9874  30.3156  36.0165
 6BV  H3   H  HCH1  0   0.223  28.5003  29.7021  34.3963
 6BV  H4   H  HCH2  0   0.211  27.0172  30.9706  33.0546
 6BV  H5   H  HCH2  0   0.214  28.3585  31.9770  33.5895
 6BV  H6   H  HOH1  0   0.458  26.2488  32.9878  33.8450
 6BV  H7   H  HCH1  0   0.191  29.7735  29.4026  36.2916
 6BV  H8   H  HOH1  0   0.469  30.7202  31.0159  37.4673
 6BV  H9   H  HCH1  0   0.226  27.4282  30.0115  38.1457
 6BV  H10  H  HOH1  0   0.454  29.1052  28.7590  39.0964
 6BV  H11  H  HCH1  0   0.290  27.7607  27.8339  36.0290
 6BV  H12  H  HCH1  0   0.268  26.5945  25.8857  36.1807
 6BV  H13  H  HCH1  0   0.238  25.7378  25.0787  34.1242
 6BV  H14  H  HCH2  0   0.220  24.1399  25.1588  32.3633
 6BV  H15  H  HCH2  0   0.216  24.7745  26.7674  32.6875
 6BV  H16  H  HOH1  0   0.460  22.4211  26.6775  32.4987
 6BV  H17  H  HCH1  0   0.219  22.9371  24.7578  35.3040
 6BV  H18  H  HOH1  0   0.453  23.3151  22.5945  34.6008
 6BV  H19  H  HCH1  0   0.231  25.6203  23.5684  36.1259
 6BV  H20  H  HOH1  0   0.466  24.3365  22.2087  37.1179
 6BV  H21  H  HCH1  0   0.225  23.8495  25.6310  37.5091
 6BV  H22  H  HOH1  0   0.454  25.1235  24.2200  38.8751

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
 6BV  C62  O62  single  1.406  0.020  1.406
 6BV  C62  C52  single  1.513  0.020  1.513
 6BV  C61  O61  single  1.407  0.020  1.407
 6BV  C61  C51  single  1.514  0.020  1.514
 6BV  C52  C42  single  1.528  0.020  1.528
 6BV  C52  O02  single  1.423  0.020  1.423
 6BV  O42  C42  single  1.405  0.020  1.405
 6BV  O41  C41  single  1.400  0.020  1.400
 6BV  C42  C32  single  1.526  0.020  1.526
 6BV  O02  C12  single  1.410  0.020  1.410
 6BV  C51  C41  single  1.532  0.020  1.532
 6BV  C51  O01  single  1.412  0.020  1.412
 6BV  C41  C31  single  1.532  0.020  1.532
 6BV  O01  C11  single  1.404  0.020  1.404
 6BV  C12  C22  single  1.526  0.020  1.526
 6BV  C12  S12  single  1.799  0.020  1.799
 6BV  C32  O32  single  1.414  0.020  1.414
 6BV  C32  C22  single  1.528  0.020  1.528
 6BV  C31  S12  single  1.829  0.020  1.829
 6BV  C31  C21  single  1.525  0.020  1.525
 6BV  C11  C21  single  1.530  0.020  1.530
 6BV  C11  O11  single  1.380  0.020  1.380
 6BV  C22  O22  single  1.400  0.020  1.400
 6BV  C21  O21  single  1.400  0.020  1.400
 6BV  O41  H1   single  0.850  0.020  0.980
 6BV  C41  H2   single  0.970  0.020  1.090
 6BV  C51  H3   single  0.970  0.020  1.090
 6BV  C61  H4   single  0.970  0.020  1.090
 6BV  C61  H5   single  0.970  0.020  1.090
 6BV  O61  H6   single  0.850  0.020  0.980
 6BV  C11  H7   single  0.970  0.020  1.090
 6BV  O11  H8   single  0.850  0.020  0.980
 6BV  C21  H9   single  0.970  0.020  1.090
 6BV  O21  H10  single  0.850  0.020  0.980
 6BV  C31  H11  single  0.970  0.020  1.090
 6BV  C12  H12  single  0.970  0.020  1.090
 6BV  C52  H13  single  0.970  0.020  1.090
 6BV  C62  H14  single  0.970  0.020  1.090
 6BV  C62  H15  single  0.970  0.020  1.090
 6BV  O62  H16  single  0.850  0.020  0.980
 6BV  C42  H17  single  0.970  0.020  1.090
 6BV  O42  H18  single  0.850  0.020  0.980
 6BV  C32  H19  single  0.970  0.020  1.090
 6BV  O32  H20  single  0.850  0.020  0.980
 6BV  C22  H21  single  0.970  0.020  1.090
 6BV  O22  H22  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
 6BV  H1   O41  C41  110.10  3.000
 6BV  H2   C41  C31  107.61  3.000
 6BV  H2   C41  C51  108.59  3.000
 6BV  C31  C41  C51  109.42  3.000
 6BV  H2   C41  O41  111.43  3.000
 6BV  C31  C41  O41  112.74  3.000
 6BV  C51  C41  O41  106.98  3.000
 6BV  H3   C51  O01  110.14  3.000
 6BV  H3   C51  C61  106.59  3.000
 6BV  O01  C51  C61  108.52  3.000
 6BV  H3   C51  C41  108.01  3.000
 6BV  O01  C51  C41  109.72  3.000
 6BV  C61  C51  C41  113.80  3.000
 6BV  H5   C61  H4   106.74  3.000
 6BV  H5   C61  O61  111.76  3.000
 6BV  H4   C61  O61  112.13  3.000
 6BV  H5   C61  C51  108.04  3.000
 6BV  H4   C61  C51  108.10  3.000
 6BV  O61  C61  C51  109.89  3.000
 6BV  H6   O61  C61  108.02  3.000
 6BV  C11  O01  C51  112.60  3.000
 6BV  H7   C11  C21  108.90  3.000
 6BV  H7   C11  O11  111.63  3.000
 6BV  C21  C11  O11  108.03  3.000
 6BV  H7   C11  O01  109.51  3.000
 6BV  O11  C11  O01  108.66  3.000
 6BV  C21  C11  O01  110.10  3.000
 6BV  H8   O11  C11  109.73  3.000
 6BV  H9   C21  C31  109.01  3.000
 6BV  H9   C21  O21  111.73  3.000
 6BV  C31  C21  O21  108.53  3.000
 6BV  H9   C21  C11  107.37  3.000
 6BV  O21  C21  C11  111.18  3.000
 6BV  C31  C21  C11  108.96  3.000
 6BV  H10  O21  C21  108.12  3.000
 6BV  H11  C31  S12  107.54  3.000
 6BV  H11  C31  C21  108.89  3.000
 6BV  S12  C31  C21  108.26  3.000
 6BV  H11  C31  C41  109.48  3.000
 6BV  C21  C31  C41  110.87  3.000
 6BV  S12  C31  C41  111.71  3.000
 6BV  C12  S12  C31  102.27  3.000
 6BV  H12  C12  C22  109.88  3.000
 6BV  H12  C12  O02  110.50  3.000
 6BV  C22  C12  O02  109.19  3.000
 6BV  H12  C12  S12  108.34  3.000
 6BV  C22  C12  S12  110.26  3.000
 6BV  O02  C12  S12  108.66  3.000
 6BV  C52  O02  C12  113.79  3.000
 6BV  H13  C52  C42  108.96  3.000
 6BV  H13  C52  C62  107.11  3.000
 6BV  C42  C52  C62  114.45  3.000
 6BV  H13  C52  O02  109.69  3.000
 6BV  C42  C52  O02  108.45  3.000
 6BV  C62  C52  O02  108.12  3.000
 6BV  H15  C62  H14  106.67  3.000
 6BV  H15  C62  O62  111.87  3.000
 6BV  H14  C62  O62  112.36  3.000
 6BV  H15  C62  C52  108.29  3.000
 6BV  H14  C62  C52  107.79  3.000
 6BV  O62  C62  C52  109.69  3.000
 6BV  H16  O62  C62  108.19  3.000
 6BV  H17  C42  C32  108.50  3.000
 6BV  H17  C42  O42  111.14  3.000
 6BV  C32  C42  O42  111.60  3.000
 6BV  H17  C42  C52  108.62  3.000
 6BV  C32  C42  C52  109.01  3.000
 6BV  O42  C42  C52  107.92  3.000
 6BV  H18  O42  C42  108.08  3.000
 6BV  H19  C32  C22  108.25  3.000
 6BV  H19  C32  O32  110.43  3.000
 6BV  C22  C32  O32  108.91  3.000
 6BV  H19  C32  C42  108.42  3.000
 6BV  C22  C32  C42  110.72  3.000
 6BV  O32  C32  C42  110.10  3.000
 6BV  H20  O32  C32  109.08  3.000
 6BV  H21  C22  O22  111.47  3.000
 6BV  H21  C22  C32  108.52  3.000
 6BV  O22  C22  C32  111.89  3.000
 6BV  H21  C22  C12  108.16  3.000
 6BV  O22  C22  C12  108.49  3.000
 6BV  C32  C22  C12  108.19  3.000
 6BV  H22  O22  C22  107.81  3.000

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
 6BV  chir_01  C41  O41  C51  C31  positiv
 6BV  chir_02  C51  O01  C41  C61  negativ
 6BV  chir_03  C11  O01  O11  C21  negativ
 6BV  chir_04  C21  O21  C11  C31  negativ
 6BV  chir_05  C31  S12  C41  C21  negativ
 6BV  chir_06  C12  S12  O02  C22  positiv
 6BV  chir_07  C52  O02  C62  C42  positiv
 6BV  chir_08  C42  O42  C52  C32  positiv
 6BV  chir_09  C32  O32  C22  C42  positiv
 6BV  chir_10  C22  O22  C32  C12  positiv

