# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 15:57:27 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-alpha-L-arabinopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[P](O)(=O)O[C@H]1[C@H](O)OC[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
 LAH  LAH  2-O-[(R)-hydroxy(propan-2-yloxy)phosphoryl]-alpha-L-arabinopyranose  L-saccharide  33  17  .  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 (reasonable std)
;

data_comp_LAH
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
 LAH  CAA  C  CH3    0  -0.659   3.7366   1.8891   0.1025
 LAH  CAL  C  CH1    0   0.037   3.5897   0.3839  -0.0280
 LAH  CAB  C  CH3    0  -0.666   4.6605  -0.3625   0.7521
 LAH  OAJ  O  O2     0  -0.611   2.2922   0.0364   0.4449
 LAH  PAQ  P  P      0   1.340   1.4810  -1.2009  -0.2600
 LAH  OAG  O  O      0  -0.805   1.2765  -0.9047  -1.7151
 LAH  OAC  O  OP    -1  -0.794   2.0723  -2.5096   0.1689
 LAH  OAK  O  O2     0  -0.626   0.0889  -1.0253   0.5877
 LAH  CBO  C  CH1    0   0.014  -1.0577  -0.4113   0.0486
 LAH  CBM  C  CH1    0   0.019  -1.5097   0.7229   0.9622
 LAH  O14  O  OH1    0  -0.653  -0.5096   1.7037   0.9743
 LAH  CBL  C  CH1    0  -0.022  -2.8690   1.2587   0.5111
 LAH  O10  O  OH1    0  -0.668  -2.6965   1.9159  -0.7217
 LAH  CBN  C  CH2    0  -0.234  -3.8447   0.0953   0.4103
 LAH  OAX  O  O2     0  -0.489  -3.3684  -0.8939  -0.4724
 LAH  C8   C  CH1    0   0.273  -2.1606  -1.4686  -0.0308
 LAH  OAH  O  OH1    0  -0.652  -1.7838  -2.4384  -0.9327
 LAH  H1   H  HCH3   0   0.218   4.7129   2.2100  -0.2622
 LAH  H2   H  HCH3   0   0.230   2.9721   2.4095  -0.4745
 LAH  H3   H  HCH3   0   0.217   3.6489   2.2024   1.1452
 LAH  H4   H  HCH1   0   0.198   3.6835   0.1225  -1.0896
 LAH  H5   H  HCH3   0   0.233   4.5552  -1.4395   0.6277
 LAH  H6   H  HCH3   0   0.217   5.6548  -0.0769   0.4064
 LAH  H7   H  HCH3   0   0.215   4.5966  -0.1328   1.8179
 LAH  H9   H  HCH1   0   0.232  -0.8669  -0.0236  -0.9580
 LAH  H10  H  HCH1   0   0.206  -1.6607   0.3022   1.9699
 LAH  H11  H  HOH1   0   0.447  -0.7539   2.3776   1.6164
 LAH  H12  H  HCH1   0   0.225  -3.2501   1.9487   1.2798
 LAH  H13  H  HOH1   0   0.452  -3.5428   2.2890  -0.9870
 LAH  H14  H  HCH2   0   0.212  -4.0235  -0.3185   1.4137
 LAH  H15  H  HCH2   0   0.253  -4.8101   0.4324   0.0273
 LAH  H16  H  HCH1   0   0.179  -2.3143  -1.8910   0.9795
 LAH  H17  H  HOH1   0   0.462  -2.2987  -3.2363  -0.7736

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
 LAH  CBN  OAX  single  1.409  0.020  1.409
 LAH  CBN  CBL  single  1.522  0.020  1.522
 LAH  OAX  C8   single  1.409  0.020  1.409
 LAH  C8   OAH  single  1.377  0.020  1.377
 LAH  C8   CBO  single  1.530  0.020  1.530
 LAH  CBL  O10  single  1.408  0.020  1.408
 LAH  CBL  CBM  single  1.529  0.020  1.529
 LAH  CBM  CBO  single  1.525  0.020  1.525
 LAH  CBM  O14  single  1.401  0.020  1.401
 LAH  CBO  OAK  single  1.408  0.020  1.408
 LAH  OAK  PAQ  single  1.639  0.020  1.639
 LAH  PAQ  OAG  deloc   1.499  0.020  1.499
 LAH  PAQ  OAC  deloc   1.499  0.020  1.499
 LAH  PAQ  OAJ  single  1.639  0.020  1.639
 LAH  OAJ  CAL  single  1.424  0.020  1.424
 LAH  CAA  CAL  single  1.518  0.020  1.518
 LAH  CAL  CAB  single  1.521  0.020  1.521
 LAH  CAA  H1   single  0.970  0.020  1.090
 LAH  CAA  H2   single  0.970  0.020  1.090
 LAH  CAA  H3   single  0.970  0.020  1.090
 LAH  CAL  H4   single  0.970  0.020  1.090
 LAH  CAB  H5   single  0.970  0.020  1.090
 LAH  CAB  H6   single  0.970  0.020  1.090
 LAH  CAB  H7   single  0.970  0.020  1.090
 LAH  CBO  H9   single  0.970  0.020  1.090
 LAH  CBM  H10  single  0.970  0.020  1.090
 LAH  O14  H11  single  0.850  0.020  0.980
 LAH  CBL  H12  single  0.970  0.020  1.090
 LAH  O10  H13  single  0.850  0.020  0.980
 LAH  CBN  H14  single  0.970  0.020  1.090
 LAH  CBN  H15  single  0.970  0.020  1.090
 LAH  C8   H16  single  0.970  0.020  1.090
 LAH  OAH  H17  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
 LAH  H3   CAA  H2   108.19  3.000
 LAH  H3   CAA  H1   107.86  3.000
 LAH  H2   CAA  H1   108.08  3.000
 LAH  H3   CAA  CAL  111.02  3.000
 LAH  H2   CAA  CAL  111.10  3.000
 LAH  H1   CAA  CAL  110.47  3.000
 LAH  H4   CAL  OAJ  109.94  3.000
 LAH  H4   CAL  CAB  108.61  3.000
 LAH  OAJ  CAL  CAB  110.58  3.000
 LAH  H4   CAL  CAA  108.12  3.000
 LAH  CAB  CAL  CAA  111.99  3.000
 LAH  OAJ  CAL  CAA  107.55  3.000
 LAH  H7   CAB  H6   107.91  3.000
 LAH  H7   CAB  H5   108.29  3.000
 LAH  H6   CAB  H5   108.11  3.000
 LAH  H7   CAB  CAL  110.87  3.000
 LAH  H6   CAB  CAL  110.53  3.000
 LAH  H5   CAB  CAL  111.01  3.000
 LAH  PAQ  OAJ  CAL  119.50  3.000
 LAH  OAK  PAQ  OAC  106.29  3.000
 LAH  OAC  PAQ  OAG  120.28  3.000
 LAH  OAK  PAQ  OAG  111.41  3.000
 LAH  OAC  PAQ  OAJ  109.93  3.000
 LAH  OAG  PAQ  OAJ  109.63  3.000
 LAH  OAK  PAQ  OAJ   96.72  3.000
 LAH  CBO  OAK  PAQ  122.70  3.000
 LAH  H9   CBO  C8   108.81  3.000
 LAH  H9   CBO  CBM  109.81  3.000
 LAH  C8   CBO  CBM  109.35  3.000
 LAH  H9   CBO  OAK  111.37  3.000
 LAH  CBM  CBO  OAK  109.65  3.000
 LAH  C8   CBO  OAK  107.79  3.000
 LAH  H10  CBM  CBL  106.36  3.000
 LAH  H10  CBM  O14  110.93  3.000
 LAH  CBL  CBM  O14  113.07  3.000
 LAH  H10  CBM  CBO  107.72  3.000
 LAH  O14  CBM  CBO  108.32  3.000
 LAH  CBL  CBM  CBO  110.32  3.000
 LAH  H11  O14  CBM  108.35  3.000
 LAH  H12  CBL  CBN  107.66  3.000
 LAH  H12  CBL  O10  111.18  3.000
 LAH  CBN  CBL  O10  112.18  3.000
 LAH  H12  CBL  CBM  108.74  3.000
 LAH  O10  CBL  CBM  108.24  3.000
 LAH  CBN  CBL  CBM  108.76  3.000
 LAH  H13  O10  CBL  108.34  3.000
 LAH  H15  CBN  H14  107.00  3.000
 LAH  H15  CBN  OAX  107.21  3.000
 LAH  H14  CBN  OAX  111.25  3.000
 LAH  H15  CBN  CBL  110.74  3.000
 LAH  H14  CBN  CBL  109.35  3.000
 LAH  OAX  CBN  CBL  111.20  3.000
 LAH  C8   OAX  CBN  112.34  3.000
 LAH  H16  C8   OAH  111.56  3.000
 LAH  H16  C8   OAX  108.85  3.000
 LAH  OAH  C8   OAX  108.47  3.000
 LAH  H16  C8   CBO  108.47  3.000
 LAH  OAH  C8   CBO  108.87  3.000
 LAH  OAX  C8   CBO  110.64  3.000
 LAH  H17  OAH  C8   109.21  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
 LAH  Var_01  H14  CBN  OAX  C8    -59.48  30.0  1
 LAH  Var_02  OAK  PAQ  OAJ  CAL  -175.46  30.0  1
 LAH  Var_03  H5   CAB  CAL  CAA  -178.60  30.0  3
 LAH  Var_04  H1   CAA  CAL  CAB    59.16  30.0  3
 LAH  Var_05  H4   CAL  OAJ  PAQ    28.12  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
 LAH  chir_02  CBO  C8   CBM  OAK  negativ
 LAH  chir_03  CBM  O14  CBO  CBL  positiv
 LAH  chir_04  CBL  O10  CBM  CBN  positiv
 LAH  chir_05  C8   OAX  OAH  CBO  negativ

