# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:05:53 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCN=C1OC[C@@H]2[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)N12
#
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
 LGS  LGS  (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol  ligand  50  22  .  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_LGS
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
 LGS  O4    O  OH1   0  -0.670    4.5630   2.3884  -1.1341
 LGS  C4    C  CH1   0   0.054    3.9247   1.1430  -1.0497
 LGS  C5    C  CR15  0  -0.160    2.8394   1.2534  -0.0020
 LGS  C6    C  CH2   0  -0.161    1.6380   2.1280  -0.3214
 LGS  O6    O  O     0  -0.481    0.5658   1.4747   0.3760
 LGS  C3    C  CH1   0  -0.007    4.8769   0.0290  -0.6180
 LGS  O3    O  OH1   0  -0.670    5.8698  -0.0759  -1.6080
 LGS  C2    C  CH1   0  -0.002    4.1294  -1.2926  -0.4364
 LGS  O2    O  OH1   0  -0.670    5.0641  -2.2440   0.0062
 LGS  C1    C  CH1   0   0.200    2.9680  -1.1635   0.5524
 LGS  O1    O  OH1   0  -0.684    2.2268  -2.3356   0.5155
 LGS  N1    N  NR5   0  -0.571    2.1715  -0.0227   0.1367
 LGS  C7    C  CR5   0   0.782    0.9120   0.2006   0.6242
 LGS  N2    N  N     0  -0.559    0.2042  -0.6676   1.2152
 LGS  C8    C  CH2   0  -0.303   -1.1452  -0.3393   1.6256
 LGS  C9    C  CH2   0  -0.431   -2.1685  -0.5382   0.5104
 LGS  C10   C  CH2   0  -0.418   -3.5838  -0.2027   0.9621
 LGS  C11   C  CH2   0  -0.411   -4.6225  -0.3606  -0.1413
 LGS  C12   C  CH2   0  -0.411   -6.0258   0.0359   0.2998
 LGS  C13   C  CH2   0  -0.406   -7.0676  -0.0917  -0.8042
 LGS  C14   C  CH2   0  -0.420   -8.4628   0.3376  -0.3671
 LGS  C15   C  CH3   0  -0.661   -9.4958   0.2253  -1.4797
 LGS  H4    H  HOH1  0   0.456    5.2978   2.3125  -1.7520
 LGS  HA    H  HCH1  0   0.218    3.4633   0.8606  -2.0086
 LGS  H5    H  HCR5  0   0.267    3.2951   1.5671   0.9510
 LGS  H3    H  HCH1  0   0.218    5.3186   0.3176   0.3494
 LGS  H61C  H  HCH2  0   0.263    1.7249   3.1468   0.0467
 LGS  H62C  H  HCH2  0   0.249    1.4169   2.1430  -1.3916
 LGS  HB    H  HOH1  0   0.458    6.5747  -0.6422  -1.2792
 LGS  H2    H  HCH1  0   0.222    3.6962  -1.5774  -1.4070
 LGS  HC    H  HOH1  0   0.459    4.6896  -3.1226  -0.1099
 LGS  H81C  H  HCH2  0   0.223   -1.4051  -0.9944   2.4607
 LGS  H82C  H  HCH2  0   0.208   -1.2268   0.6855   2.0063
 LGS  H91C  H  HCH2  0   0.215   -1.8999   0.0917  -0.3435
 LGS  H92C  H  HCH2  0   0.215   -2.1231  -1.5734   0.1589
 LGS  H101  H  HCH2  0   0.210   -3.8590  -0.8356   1.8130
 LGS  H102  H  HCH2  0   0.209   -3.6081   0.8281   1.3329
 LGS  H111  H  HCH2  0   0.207   -4.3280   0.2483  -1.0033
 LGS  H112  H  HCH2  0   0.208   -4.6285  -1.3981  -0.4924
 LGS  H121  H  HCH2  0   0.207   -6.3267  -0.5780   1.1562
 LGS  H122  H  HCH2  0   0.206   -6.0092   1.0698   0.6623
 LGS  H131  H  HCH2  0   0.205   -6.7571   0.5098  -1.6662
 LGS  H132  H  HCH2  0   0.206   -7.1008  -1.1284  -1.1572
 LGS  H141  H  HCH2  0   0.210   -8.7769  -0.2686   0.4885
 LGS  H142  H  HCH2  0   0.210   -8.4250   1.3703  -0.0066
 LGS  H151  H  HCH3  0   0.215   -9.2177   0.8402  -2.3379
 LGS  H152  H  HCH3  0   0.215   -9.5884  -0.8040  -1.8313
 LGS  H153  H  HCH3  0   0.225  -10.4822   0.5498  -1.1466
 LGS  H154  H  HCH1  0   0.201    3.3694  -0.9714   1.5646
 LGS  H155  H  HOH1  0   0.454    1.3831  -2.1412   0.9739

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
 LGS  O4   C4    single  1.402  0.020  1.402
 LGS  C4   C5    single  1.513  0.020  1.513
 LGS  C5   C6    single  1.520  0.020  1.520
 LGS  C6   O6    single  1.436  0.020  1.436
 LGS  C4   C3    single  1.528  0.020  1.528
 LGS  C3   O3    single  1.406  0.020  1.406
 LGS  C3   C2    single  1.529  0.020  1.529
 LGS  C2   O2    single  1.405  0.020  1.405
 LGS  C2   C1    single  1.531  0.020  1.531
 LGS  C1   O1    single  1.387  0.020  1.387
 LGS  C5   N1    single  1.447  0.020  1.447
 LGS  C1   N1    single  1.452  0.020  1.452
 LGS  O6   C7    single  1.343  0.020  1.343
 LGS  N1   C7    single  1.369  0.020  1.369
 LGS  C7   N2    double  1.267  0.020  1.267
 LGS  N2   C8    single  1.448  0.020  1.448
 LGS  C8   C9    single  1.527  0.020  1.527
 LGS  C9   C10   single  1.523  0.020  1.523
 LGS  C10  C11   single  1.524  0.020  1.524
 LGS  C11  C12   single  1.524  0.020  1.524
 LGS  C12  C13   single  1.523  0.020  1.523
 LGS  C13  C14   single  1.524  0.020  1.524
 LGS  C14  C15   single  1.522  0.020  1.522
 LGS  O4   H4    single  0.850  0.020  0.980
 LGS  C4   HA    single  0.970  0.020  1.090
 LGS  C5   H5    single  0.970  0.020  1.090
 LGS  C3   H3    single  0.970  0.020  1.090
 LGS  C6   H61C  single  0.970  0.020  1.090
 LGS  C6   H62C  single  0.970  0.020  1.090
 LGS  O3   HB    single  0.850  0.020  0.980
 LGS  C2   H2    single  0.970  0.020  1.090
 LGS  O2   HC    single  0.850  0.020  0.980
 LGS  C8   H81C  single  0.970  0.020  1.090
 LGS  C8   H82C  single  0.970  0.020  1.090
 LGS  C9   H91C  single  0.970  0.020  1.090
 LGS  C9   H92C  single  0.970  0.020  1.090
 LGS  C10  H101  single  0.970  0.020  1.090
 LGS  C10  H102  single  0.970  0.020  1.090
 LGS  C11  H111  single  0.970  0.020  1.090
 LGS  C11  H112  single  0.970  0.020  1.090
 LGS  C12  H121  single  0.970  0.020  1.090
 LGS  C12  H122  single  0.970  0.020  1.090
 LGS  C13  H131  single  0.970  0.020  1.090
 LGS  C13  H132  single  0.970  0.020  1.090
 LGS  C14  H141  single  0.970  0.020  1.090
 LGS  C14  H142  single  0.970  0.020  1.090
 LGS  C15  H151  single  0.970  0.020  1.090
 LGS  C15  H152  single  0.970  0.020  1.090
 LGS  C15  H153  single  0.970  0.020  1.090
 LGS  C1   H154  single  0.970  0.020  1.090
 LGS  O1   H155  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
 LGS  H4    O4   C4    108.41  3.000
 LGS  HA    C4   C3    108.68  3.000
 LGS  HA    C4   C5    108.74  3.000
 LGS  C3    C4   C5    107.74  3.000
 LGS  HA    C4   O4    111.49  3.000
 LGS  C3    C4   O4    112.40  3.000
 LGS  C5    C4   O4    107.67  3.000
 LGS  H5    C5   N1    111.04  3.000
 LGS  H5    C5   C6    110.17  3.000
 LGS  N1    C5   C6     99.36  3.000
 LGS  H5    C5   C4    108.85  3.000
 LGS  N1    C5   C4    109.47  3.000
 LGS  C6    C5   C4    117.62  3.000
 LGS  H62C  C6   H61C  109.57  3.000
 LGS  H62C  C6   O6    109.31  3.000
 LGS  H61C  C6   O6    108.76  3.000
 LGS  H62C  C6   C5    111.94  3.000
 LGS  H61C  C6   C5    113.89  3.000
 LGS  O6    C6   C5    103.08  3.000
 LGS  C7    O6   C6    109.19  3.000
 LGS  H3    C3   C2    108.55  3.000
 LGS  H3    C3   O3    110.77  3.000
 LGS  C2    C3   O3    111.37  3.000
 LGS  H3    C3   C4    107.87  3.000
 LGS  C2    C3   C4    111.05  3.000
 LGS  O3    C3   C4    107.19  3.000
 LGS  HB    O3   C3    108.70  3.000
 LGS  H2    C2   C1    107.03  3.000
 LGS  H2    C2   O2    111.38  3.000
 LGS  C1    C2   O2    110.99  3.000
 LGS  H2    C2   C3    108.14  3.000
 LGS  C1    C2   C3    112.00  3.000
 LGS  O2    C2   C3    107.30  3.000
 LGS  HC    O2   C2    108.75  3.000
 LGS  H154  C1   N1    108.94  3.000
 LGS  H154  C1   O1    111.41  3.000
 LGS  N1    C1   O1    111.29  3.000
 LGS  H154  C1   C2    109.31  3.000
 LGS  N1    C1   C2    107.31  3.000
 LGS  O1    C1   C2    108.48  3.000
 LGS  H155  O1   C1    106.26  3.000
 LGS  C7    N1   C1    122.07  3.000
 LGS  C7    N1   C5    108.36  3.000
 LGS  C1    N1   C5    117.84  3.000
 LGS  N2    C7   N1    124.65  3.000
 LGS  N2    C7   O6    126.32  3.000
 LGS  N1    C7   O6    109.03  3.000
 LGS  C8    N2   C7    119.84  3.000
 LGS  H82C  C8   H81C  106.10  3.000
 LGS  H82C  C8   C9    109.00  3.000
 LGS  H81C  C8   C9    108.71  3.000
 LGS  H82C  C8   N2    112.31  3.000
 LGS  H81C  C8   N2    107.60  3.000
 LGS  C9    C8   N2    112.83  3.000
 LGS  H92C  C9   H91C  106.47  3.000
 LGS  H92C  C9   C10   110.02  3.000
 LGS  H91C  C9   C10   109.43  3.000
 LGS  H92C  C9   C8    109.28  3.000
 LGS  H91C  C9   C8    109.30  3.000
 LGS  C10   C9   C8    112.18  3.000
 LGS  H102  C10  H101  105.97  3.000
 LGS  H102  C10  C11   109.11  3.000
 LGS  H101  C10  C11   109.35  3.000
 LGS  H102  C10  C9    109.16  3.000
 LGS  H101  C10  C9    109.66  3.000
 LGS  C11   C10  C9    113.32  3.000
 LGS  H112  C11  H111  106.00  3.000
 LGS  H112  C11  C12   109.53  3.000
 LGS  H111  C11  C12   109.31  3.000
 LGS  H112  C11  C10   109.52  3.000
 LGS  H111  C11  C10   109.20  3.000
 LGS  C12   C11  C10   113.03  3.000
 LGS  H122  C12  H121  105.92  3.000
 LGS  H122  C12  C13   109.22  3.000
 LGS  H121  C12  C13   109.37  3.000
 LGS  H122  C12  C11   109.11  3.000
 LGS  H121  C12  C11   109.47  3.000
 LGS  C13   C12  C11   113.47  3.000
 LGS  H132  C13  H131  105.93  3.000
 LGS  H132  C13  C14   109.34  3.000
 LGS  H131  C13  C14   109.29  3.000
 LGS  H132  C13  C12   109.48  3.000
 LGS  H131  C13  C12   109.29  3.000
 LGS  C14   C13  C12   113.24  3.000
 LGS  H142  C14  H141  105.96  3.000
 LGS  H142  C14  C15   109.50  3.000
 LGS  H141  C14  C15   109.61  3.000
 LGS  H142  C14  C13   109.19  3.000
 LGS  H141  C14  C13   109.32  3.000
 LGS  C15   C14  C13   113.01  3.000
 LGS  H153  C15  H152  107.59  3.000
 LGS  H153  C15  H151  107.63  3.000
 LGS  H152  C15  H151  107.43  3.000
 LGS  H153  C15  C14   111.62  3.000
 LGS  H152  C15  C14   111.26  3.000
 LGS  H151  C15  C14   111.10  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
 LGS  CONST_05  C8    N2   C7   O6      0.00   0.0  0
 LGS  CONST_06  C8    N2   C7   N1    180.00   0.0  0
 LGS  Var_01    N1    C7   O6   C6      0.61  30.0  1
 LGS  Var_02    H61C  C6   O6   C7   -141.54  30.0  1
 LGS  Var_03    C9    C8   N2   C7     84.98  30.0  3
 LGS  Var_04    C10   C9   C8   N2    179.41  30.0  3
 LGS  Var_05    C11   C10  C9   C8    178.63  30.0  3
 LGS  Var_06    C12   C11  C10  C9   -177.44  30.0  3
 LGS  Var_07    C13   C12  C11  C10   178.85  30.0  3
 LGS  Var_08    C14   C13  C12  C11  -178.63  30.0  3
 LGS  Var_09    C15   C14  C13  C12   179.24  30.0  3
 LGS  Var_10    H151  C15  C14  C13   -59.12  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
 LGS  chir_01  C4  O4  C5  C3  positiv
 LGS  chir_02  C5  N1  C6  C4  positiv
 LGS  chir_03  C3  O3  C4  C2  negativ
 LGS  chir_04  C2  O2  C3  C1  positiv
 LGS  chir_05  C1  O1  N1  C2  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
 LGS  plan-1  C5  0.020
 LGS  plan-1  O6  0.020
 LGS  plan-1  C1  0.020
 LGS  plan-1  N1  0.020
 LGS  plan-1  C7  0.020
 LGS  plan-1  N2  0.020
 LGS  plan-1  C8  0.020

