# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:17:25 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-phenyl-1,6-dioxa-2-azaspiro[4.5]dec-2-ene-8,9,10-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(CC(=NO2)c3ccccc3)[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
 M08  M08  (5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-phenyl-1,6-dioxa-2-azaspiro[4.5]dec-2-ene-8,9,10-triol  ligand  38  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M08
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
 M08  C10  C  CR16  0  -0.270   3.8487   0.5694  -1.2409
 M08  C11  C  CR16  0  -0.190   5.1622   0.9906  -1.1333
 M08  C12  C  CR16  0  -0.296   5.7468   1.1536   0.1188
 M08  C13  C  CR16  0  -0.196   5.0074   0.8905   1.2622
 M08  C14  C  CR16  0  -0.289   3.6888   0.4689   1.1577
 M08  C9   C  CR6   0   0.021   3.0955   0.3041  -0.0929
 M08  C8   C  CR5   0   0.205   1.7050  -0.1390  -0.1829
 M08  C7   C  CH2   0  -0.583   0.8127  -0.4241   0.9811
 M08  N1   N  N     0  -0.148   1.1340  -0.3436  -1.3030
 M08  O7   O  O     0  -0.423  -0.1580  -0.7608  -1.0986
 M08  C1   C  CR5   0   0.465  -0.5234  -0.5747   0.2694
 M08  O5   O  O2    0  -0.474  -1.2226   0.6163   0.4198
 M08  C5   C  CH1   0  -0.042  -2.4729   0.7088  -0.2524
 M08  C6   C  CH2   0  -0.176  -3.0321   2.0825   0.0448
 M08  O6   O  OH1   0  -0.693  -2.1717   3.0548  -0.4962
 M08  C4   C  CH1   0   0.039  -3.4005  -0.4074   0.2340
 M08  O4   O  OH1   0  -0.679  -4.6121  -0.4281  -0.4866
 M08  C3   C  CH1   0  -0.012  -2.7243  -1.7569   0.0287
 M08  O3   O  OH1   0  -0.688  -3.4780  -2.8082   0.5808
 M08  C2   C  CH1   0   0.063  -1.3653  -1.7670   0.7177
 M08  O2   O  OH1   0  -0.648  -0.6383  -2.9350   0.4547
 M08  H10  H  HCR6  0   0.254   3.4037   0.4464  -2.2194
 M08  H11  H  HCR6  0   0.281   5.7338   1.1940  -2.0293
 M08  H12  H  HCR6  0   0.249   6.7738   1.4849   0.1999
 M08  H13  H  HCR6  0   0.275   5.4535   1.0160   2.2398
 M08  H14  H  HCR6  0   0.265   3.1257   0.2706   2.0605
 M08  H71  H  HCH2  0   0.282   1.1261  -1.3390   1.4894
 M08  H72  H  HCH2  0   0.311   0.7862   0.3767   1.7200
 M08  H5   H  HCH1  0   0.158  -2.3345   0.6087  -1.3377
 M08  H61  H  HCH2  0   0.194  -4.0354   2.1475  -0.3924
 M08  H62  H  HCH2  0   0.250  -3.1461   2.1948   1.1322
 M08  HO6  H  HOH1  0   0.454  -2.5728   3.9169  -0.3557
 M08  H4   H  HCH1  0   0.205  -3.5828  -0.2693   1.3100
 M08  HO4  H  HOH1  0   0.452  -5.2551   0.1276  -0.0380
 M08  H3   H  HCH1  0   0.248  -2.5775  -1.9092  -1.0521
 M08  HO3  H  HOH1  0   0.458  -4.3218  -2.8443   0.1185
 M08  H2   H  HCH1  0   0.206  -1.5340  -1.6381   1.7977
 M08  HO2  H  HOH1  0   0.474  -1.0521  -3.6614   0.9307

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
 M08  O3   C3   single    1.406  0.020  1.406
 M08  O4   C4   single    1.410  0.020  1.410
 M08  C3   C4   single    1.523  0.020  1.523
 M08  C3   C2   single    1.524  0.020  1.524
 M08  C4   C5   single    1.531  0.020  1.531
 M08  O2   C2   single    1.401  0.020  1.401
 M08  C2   C1   single    1.527  0.020  1.527
 M08  O6   C6   single    1.406  0.020  1.406
 M08  C5   C6   single    1.513  0.020  1.513
 M08  C5   O5   single    1.422  0.020  1.422
 M08  C1   O5   single    1.389  0.020  1.389
 M08  C1   O7   single    1.428  0.020  1.428
 M08  C1   C7   single    1.521  0.020  1.521
 M08  O7   N1   single    1.373  0.020  1.373
 M08  C7   C8   single    1.494  0.020  1.494
 M08  N1   C8   double    1.274  0.020  1.274
 M08  C8   C9   single    1.462  0.020  1.462
 M08  C10  C9   aromatic  1.398  0.020  1.398
 M08  C10  C11  aromatic  1.384  0.020  1.384
 M08  C9   C14  aromatic  1.394  0.020  1.394
 M08  C11  C12  aromatic  1.391  0.020  1.391
 M08  C14  C13  aromatic  1.388  0.020  1.388
 M08  C12  C13  aromatic  1.387  0.020  1.387
 M08  C10  H10  single    0.930  0.020  1.080
 M08  C11  H11  single    0.930  0.020  1.080
 M08  C12  H12  single    0.930  0.020  1.080
 M08  C13  H13  single    0.930  0.020  1.080
 M08  C14  H14  single    0.930  0.020  1.080
 M08  C7   H71  single    0.970  0.020  1.090
 M08  C7   H72  single    0.970  0.020  1.090
 M08  C5   H5   single    0.970  0.020  1.090
 M08  C6   H61  single    0.970  0.020  1.090
 M08  C6   H62  single    0.970  0.020  1.090
 M08  O6   HO6  single    0.850  0.020  0.980
 M08  C4   H4   single    0.970  0.020  1.090
 M08  O4   HO4  single    0.850  0.020  0.980
 M08  C3   H3   single    0.970  0.020  1.090
 M08  O3   HO3  single    0.850  0.020  0.980
 M08  C2   H2   single    0.970  0.020  1.090
 M08  O2   HO2  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
 M08  H10  C10  C9   119.95  3.000
 M08  H10  C10  C11  119.70  3.000
 M08  C9   C10  C11  120.35  3.000
 M08  H11  C11  C12  120.07  3.000
 M08  H11  C11  C10  119.63  3.000
 M08  C12  C11  C10  120.30  3.000
 M08  H12  C12  C13  120.16  3.000
 M08  H12  C12  C11  120.13  3.000
 M08  C13  C12  C11  119.71  3.000
 M08  H13  C13  C14  119.66  3.000
 M08  H13  C13  C12  120.20  3.000
 M08  C14  C13  C12  120.13  3.000
 M08  H14  C14  C9   120.34  3.000
 M08  H14  C14  C13  119.15  3.000
 M08  C9   C14  C13  120.51  3.000
 M08  C8   C9   C14  119.72  3.000
 M08  C14  C9   C10  119.00  3.000
 M08  C8   C9   C10  121.28  3.000
 M08  N1   C8   C7   112.75  3.000
 M08  N1   C8   C9   121.94  3.000
 M08  C7   C8   C9   125.30  3.000
 M08  H72  C7   H71  107.87  3.000
 M08  H72  C7   C1   111.63  3.000
 M08  H71  C7   C1   112.75  3.000
 M08  H72  C7   C8   113.73  3.000
 M08  H71  C7   C8   110.55  3.000
 M08  C1   C7   C8   100.30  3.000
 M08  O7   N1   C8   109.86  3.000
 M08  C1   O7   N1   110.10  3.000
 M08  C2   C1   O5   111.11  3.000
 M08  O5   C1   O7   110.13  3.000
 M08  C2   C1   O7   108.69  3.000
 M08  O7   C1   C7   103.67  3.000
 M08  O5   C1   C7   107.85  3.000
 M08  C2   C1   C7   115.10  3.000
 M08  C5   O5   C1   116.55  3.000
 M08  H5   C5   C4   108.90  3.000
 M08  H5   C5   C6   108.87  3.000
 M08  C4   C5   C6   112.07  3.000
 M08  H5   C5   O5   110.50  3.000
 M08  C6   C5   O5   106.92  3.000
 M08  C4   C5   O5   109.58  3.000
 M08  H62  C6   H61  107.07  3.000
 M08  H62  C6   O6   111.92  3.000
 M08  H61  C6   O6   111.43  3.000
 M08  H62  C6   C5   109.00  3.000
 M08  H61  C6   C5   108.29  3.000
 M08  O6   C6   C5   109.03  3.000
 M08  HO6  O6   C6   107.98  3.000
 M08  H4   C4   C3   108.46  3.000
 M08  H4   C4   O4   111.06  3.000
 M08  C3   C4   O4   107.43  3.000
 M08  H4   C4   C5   108.65  3.000
 M08  C3   C4   C5   109.52  3.000
 M08  O4   C4   C5   111.66  3.000
 M08  HO4  O4   C4   109.15  3.000
 M08  H3   C3   C2   108.90  3.000
 M08  H3   C3   O3   110.69  3.000
 M08  C2   C3   O3   107.19  3.000
 M08  H3   C3   C4   108.30  3.000
 M08  C2   C3   C4   109.93  3.000
 M08  O3   C3   C4   111.80  3.000
 M08  HO3  O3   C3   108.01  3.000
 M08  H2   C2   O2   111.19  3.000
 M08  H2   C2   C3   107.83  3.000
 M08  O2   C2   C3   112.55  3.000
 M08  H2   C2   C1   106.33  3.000
 M08  O2   C2   C1   108.05  3.000
 M08  C3   C2   C1   110.72  3.000
 M08  HO2  O2   C2   108.27  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
 M08  CONST_01  C13  C14  C9   C10     0.00   0.0  0
 M08  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 M08  CONST_03  C14  C9   C10  C11     0.00   0.0  0
 M08  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 M08  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 M08  CONST_06  C9   C14  C13  C12     0.00   0.0  0
 M08  CONST_07  C8   C9   C10  C11   180.00   0.0  0
 M08  CONST_08  C8   C9   C14  C13   180.00   0.0  0
 M08  CONST_09  H14  C14  C9   C10   180.00   0.0  0
 M08  CONST_10  H12  C12  C11  C10   180.00   0.0  0
 M08  CONST_11  H13  C13  C12  C11   180.00   0.0  0
 M08  CONST_12  H10  C10  C11  C12   180.00   0.0  0
 M08  CONST_13  H11  C11  C12  C13   180.00   0.0  0
 M08  Var_01    C7   C8   C9   C10  -178.88  30.0  3
 M08  Var_02    C1   C7   C8   C9    169.93  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
 M08  chir_01  C1  O5  O7  C7  negativ
 M08  chir_02  C5  O5  C6  C4  positiv
 M08  chir_03  C4  O4  C5  C3  positiv
 M08  chir_04  C3  O3  C4  C2  negativ
 M08  chir_05  C2  O2  C3  C1  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
 M08  plan-1  C10  0.020
 M08  plan-1  C11  0.020
 M08  plan-1  C12  0.020
 M08  plan-1  C13  0.020
 M08  plan-1  C14  0.020
 M08  plan-1  C9   0.020
 M08  plan-1  C8   0.020
 M08  plan-1  H10  0.020
 M08  plan-1  H11  0.020
 M08  plan-1  H12  0.020
 M08  plan-1  H13  0.020
 M08  plan-1  H14  0.020

