# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 10:19:40 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{R},3~{S},4~{R},6~{S})-6-heptoxy-2-(hydroxymethyl)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@@H]1C[C@@H](O)[C@H](O)[C@@H](CO)O1
#
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
 6LS  6LS  (2~{R},3~{S},4~{R},6~{S})-6-heptoxy-2-(hydroxymethyl)oxane-3,4-diol  D-saccharide  44  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 PERFECT
;

data_comp_6LS
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
 6LS  O3   O  OH1   0  -0.677  -4.4483  -1.9717  -0.9960
 6LS  C4   C  CH1   0   0.039  -3.7256   0.2186  -0.4795
 6LS  C5   C  CH1   0  -0.010  -2.5484   1.0524   0.0309
 6LS  O4   O  OH1   0  -0.676  -4.1348   0.7519  -1.7156
 6LS  C6   C  CH2   0  -0.159  -2.9463   2.4905   0.2907
 6LS  O5   O  O2    0  -0.503  -2.0670   0.5248   1.2536
 6LS  O6   O  OH1   0  -0.670  -1.7963   3.2246   0.6406
 6LS  CAR  C  CH3   0  -0.662   8.1203   0.3297  -0.4243
 6LS  CAQ  C  CH2   0  -0.418   6.8423  -0.4307  -0.7497
 6LS  CAP  C  CH2   0  -0.406   5.6195   0.1293  -0.0329
 6LS  CAO  C  CH2   0  -0.410   4.3344  -0.6202  -0.3596
 6LS  CAN  C  CH2   0  -0.424   3.1143  -0.0642   0.3642
 6LS  CAM  C  CH2   0  -0.462   1.8316  -0.8121   0.0217
 6LS  CAL  C  CH2   0  -0.132   0.6375  -0.2626   0.7758
 6LS  O1   O  O2    0  -0.505  -0.5220  -0.9727   0.3782
 6LS  C1   C  CH1   0   0.267  -1.6286  -0.8065   1.2082
 6LS  C2   C  CH2   0  -0.517  -2.7336  -1.7269   0.7176
 6LS  C3   C  CH1   0   0.015  -3.3042  -1.2388  -0.6076
 6LS  H32  H  HOH1  0   0.457  -4.1640  -2.8215  -1.3459
 6LS  H41  H  HCH1  0   0.203  -4.5390   0.2756   0.2640
 6LS  H5   H  HCH1  0   0.222  -1.7580   1.0429  -0.7344
 6LS  H42  H  HOH1  0   0.452  -4.8258   0.1815  -2.0688
 6LS  H62  H  HCH2  0   0.210  -3.4175   2.8897  -0.6131
 6LS  H61  H  HCH2  0   0.193  -3.7032   2.5139   1.0874
 6LS  H63  H  HOH1  0   0.455  -2.0501   4.1479   0.7232
 6LS  HAR  H  HCH3  0   0.215   8.0358   1.3803  -0.7086
 6LS  HAS  H  HCH3  0   0.215   8.3386   0.2960   0.6447
 6LS  HAT  H  HCH3  0   0.226   8.9803  -0.0863  -0.9506
 6LS  HAQ  H  HCH2  0   0.210   6.6698  -0.4083  -1.8304
 6LS  HAU  H  HCH2  0   0.210   6.9646  -1.4855  -0.4848
 6LS  HAV  H  HCH2  0   0.206   5.7897   0.1025   1.0493
 6LS  HAP  H  HCH2  0   0.206   5.4993   1.1868  -0.2935
 6LS  HAO  H  HCH2  0   0.208   4.1617  -0.5867  -1.4409
 6LS  HAW  H  HCH2  0   0.209   4.4557  -1.6788  -0.1048
 6LS  HAX  H  HCH2  0   0.213   3.2837  -0.1059   1.4456
 6LS  HAN  H  HCH2  0   0.214   2.9964   0.9959   0.1153
 6LS  HAM  H  HCH2  0   0.222   1.6466  -0.7419  -1.0548
 6LS  HAY  H  HCH2  0   0.220   1.9518  -1.8747   0.2540
 6LS  HAZ  H  HCH2  0   0.198   0.7939  -0.3707   1.8580
 6LS  HAL  H  HCH2  0   0.207   0.5276   0.8097   0.5741
 6LS  H1   H  HCH1  0   0.229  -1.3629  -1.0444   2.2472
 6LS  H22  H  HCH2  0   0.251  -2.3550  -2.7480   0.6277
 6LS  H21  H  HCH2  0   0.244  -3.5266  -1.7430   1.4703
 6LS  H31  H  HCH1  0   0.215  -2.5312  -1.3009  -1.3857

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
 6LS  CAR  CAQ  single  1.522  0.020  1.522
 6LS  CAQ  CAP  single  1.524  0.020  1.524
 6LS  CAP  CAO  single  1.523  0.020  1.523
 6LS  CAO  CAN  single  1.524  0.020  1.524
 6LS  CAN  CAM  single  1.524  0.020  1.524
 6LS  CAM  CAL  single  1.515  0.020  1.515
 6LS  CAL  O1   single  1.417  0.020  1.417
 6LS  O1   C1   single  1.393  0.020  1.393
 6LS  C1   O5   single  1.402  0.020  1.402
 6LS  C1   C2   single  1.519  0.020  1.519
 6LS  O5   C5   single  1.416  0.020  1.416
 6LS  C5   C6   single  1.515  0.020  1.515
 6LS  C5   C4   single  1.530  0.020  1.530
 6LS  C2   C3   single  1.523  0.020  1.523
 6LS  C3   C4   single  1.523  0.020  1.523
 6LS  C3   O3   single  1.413  0.020  1.413
 6LS  C6   O6   single  1.408  0.020  1.408
 6LS  C4   O4   single  1.407  0.020  1.407
 6LS  O3   H32  single  0.850  0.020  0.980
 6LS  C4   H41  single  0.970  0.020  1.090
 6LS  C5   H5   single  0.970  0.020  1.090
 6LS  O4   H42  single  0.850  0.020  0.980
 6LS  C6   H62  single  0.970  0.020  1.090
 6LS  C6   H61  single  0.970  0.020  1.090
 6LS  O6   H63  single  0.850  0.020  0.980
 6LS  CAR  HAR  single  0.970  0.020  1.090
 6LS  CAR  HAS  single  0.970  0.020  1.090
 6LS  CAR  HAT  single  0.970  0.020  1.090
 6LS  CAQ  HAQ  single  0.970  0.020  1.090
 6LS  CAQ  HAU  single  0.970  0.020  1.090
 6LS  CAP  HAV  single  0.970  0.020  1.090
 6LS  CAP  HAP  single  0.970  0.020  1.090
 6LS  CAO  HAO  single  0.970  0.020  1.090
 6LS  CAO  HAW  single  0.970  0.020  1.090
 6LS  CAN  HAX  single  0.970  0.020  1.090
 6LS  CAN  HAN  single  0.970  0.020  1.090
 6LS  CAM  HAM  single  0.970  0.020  1.090
 6LS  CAM  HAY  single  0.970  0.020  1.090
 6LS  CAL  HAZ  single  0.970  0.020  1.090
 6LS  CAL  HAL  single  0.970  0.020  1.090
 6LS  C1   H1   single  0.970  0.020  1.090
 6LS  C2   H22  single  0.970  0.020  1.090
 6LS  C2   H21  single  0.970  0.020  1.090
 6LS  C3   H31  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
 6LS  H32  O3   C3   108.59  3.000
 6LS  H41  C4   C3   108.07  3.000
 6LS  H41  C4   O4   110.97  3.000
 6LS  C3   C4   O4   111.68  3.000
 6LS  H41  C4   C5   108.32  3.000
 6LS  O4   C4   C5   108.07  3.000
 6LS  C3   C4   C5   109.68  3.000
 6LS  H5   C5   O5   110.68  3.000
 6LS  H5   C5   C6   108.43  3.000
 6LS  O5   C5   C6   107.15  3.000
 6LS  H5   C5   C4   108.42  3.000
 6LS  C6   C5   C4   111.87  3.000
 6LS  O5   C5   C4   110.28  3.000
 6LS  H42  O4   C4   107.84  3.000
 6LS  H61  C6   H62  107.11  3.000
 6LS  H61  C6   O6   111.78  3.000
 6LS  H62  C6   O6   111.51  3.000
 6LS  H61  C6   C5   108.99  3.000
 6LS  H62  C6   C5   108.52  3.000
 6LS  O6   C6   C5   108.85  3.000
 6LS  C1   O5   C5   115.59  3.000
 6LS  H63  O6   C6   107.84  3.000
 6LS  HAT  CAR  HAS  107.64  3.000
 6LS  HAT  CAR  HAR  107.60  3.000
 6LS  HAS  CAR  HAR  107.47  3.000
 6LS  HAT  CAR  CAQ  111.61  3.000
 6LS  HAS  CAR  CAQ  111.21  3.000
 6LS  HAR  CAR  CAQ  111.11  3.000
 6LS  HAU  CAQ  HAQ  106.04  3.000
 6LS  HAU  CAQ  CAP  109.27  3.000
 6LS  HAQ  CAQ  CAP  109.29  3.000
 6LS  HAU  CAQ  CAR  109.63  3.000
 6LS  HAQ  CAQ  CAR  109.46  3.000
 6LS  CAP  CAQ  CAR  112.92  3.000
 6LS  HAP  CAP  HAV  105.99  3.000
 6LS  HAP  CAP  CAO  109.35  3.000
 6LS  HAV  CAP  CAO  109.31  3.000
 6LS  HAP  CAP  CAQ  109.32  3.000
 6LS  HAV  CAP  CAQ  109.33  3.000
 6LS  CAO  CAP  CAQ  113.28  3.000
 6LS  HAW  CAO  HAO  106.05  3.000
 6LS  HAW  CAO  CAN  109.32  3.000
 6LS  HAO  CAO  CAN  109.36  3.000
 6LS  HAW  CAO  CAP  109.40  3.000
 6LS  HAO  CAO  CAP  109.24  3.000
 6LS  CAN  CAO  CAP  113.21  3.000
 6LS  HAN  CAN  HAX  106.13  3.000
 6LS  HAN  CAN  CAM  109.47  3.000
 6LS  HAX  CAN  CAM  109.48  3.000
 6LS  HAN  CAN  CAO  109.36  3.000
 6LS  HAX  CAN  CAO  109.34  3.000
 6LS  CAM  CAN  CAO  112.84  3.000
 6LS  HAY  CAM  HAM  106.84  3.000
 6LS  HAY  CAM  CAL  109.45  3.000
 6LS  HAM  CAM  CAL  109.45  3.000
 6LS  HAY  CAM  CAN  109.65  3.000
 6LS  HAM  CAM  CAN  109.38  3.000
 6LS  CAL  CAM  CAN  111.93  3.000
 6LS  HAL  CAL  HAZ  106.95  3.000
 6LS  HAL  CAL  O1   110.88  3.000
 6LS  HAZ  CAL  O1   110.10  3.000
 6LS  HAL  CAL  CAM  110.00  3.000
 6LS  HAZ  CAL  CAM  110.02  3.000
 6LS  O1   CAL  CAM  108.88  3.000
 6LS  C1   O1   CAL  115.03  3.000
 6LS  H1   C1   C2   110.49  3.000
 6LS  H1   C1   O1   110.22  3.000
 6LS  C2   C1   O1   108.24  3.000
 6LS  H1   C1   O5   104.51  3.000
 6LS  C2   C1   O5   110.98  3.000
 6LS  O1   C1   O5   112.38  3.000
 6LS  H21  C2   H22  107.10  3.000
 6LS  H21  C2   C3   109.39  3.000
 6LS  H22  C2   C3   110.96  3.000
 6LS  H21  C2   C1   108.31  3.000
 6LS  H22  C2   C1   109.91  3.000
 6LS  C3   C2   C1   111.05  3.000
 6LS  H31  C3   C2   109.54  3.000
 6LS  H31  C3   C4   107.96  3.000
 6LS  C2   C3   C4   109.71  3.000
 6LS  H31  C3   O3   110.22  3.000
 6LS  C4   C3   O3   107.19  3.000
 6LS  C2   C3   O3   112.10  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
 6LS  Var_01  HAZ  CAL  O1   C1    44.45  30.0  1
 6LS  Var_02  CAO  CAP  CAQ  CAR  179.64  30.0  3
 6LS  Var_03  CAN  CAO  CAP  CAQ  179.66  30.0  3
 6LS  Var_04  CAM  CAN  CAO  CAP  179.48  30.0  3
 6LS  Var_05  CAL  CAM  CAN  CAO  178.72  30.0  3
 6LS  Var_06  O1   CAL  CAM  CAN  178.13  30.0  3
 6LS  Var_07  HAR  CAR  CAQ  CAP  -59.70  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
 6LS  chir_01  C4  C5  C3  O4  positiv
 6LS  chir_02  C5  O5  C4  C6  negativ
 6LS  chir_03  C1  O1  O5  C2  negativ
 6LS  chir_04  C3  O3  C2  C4  positiv

