# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 18:43:03 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R,2R,3S,5S,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@]2(O[C@H]([C@H](O)CO)[C@@H]1O2)C(O)=O
#
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
 SKD  SKD  '(1R,2R,3S,5S,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)'  ligand  36  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SKD
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
 SKD  C1    C  C      0   0.373  -2.6527  -0.1533  -1.0584
 SKD  C2    C  CT     0   0.384  -1.3026   0.2396  -0.4156
 SKD  C3    C  CH2    0  -0.505  -1.4759   1.1781   0.7782
 SKD  C4    C  CH1    0   0.033  -0.1380   1.5508   1.4247
 SKD  C5    C  CH1    0  -0.052   0.8072   0.3320   1.4557
 SKD  C6    C  CH1    0  -0.138   0.6911  -0.5035   0.1801
 SKD  C7    C  CH1    0   0.027   0.8820   0.2888  -1.1143
 SKD  C8    C  CH1    0  -0.020   1.3336  -0.6159  -2.2658
 SKD  C9    C  CH2    0  -0.163   1.2202   0.0933  -3.6036
 SKD  C11   C  CH3    0  -0.778   0.5567  -1.3449   4.8433
 SKD  N5    N  NH1    0  -0.635   0.5028  -0.5249   2.5805
 SKD  O1A   O  O      0  -0.582  -2.8404   0.1709  -2.2393
 SKD  O1B   O  OC    -1  -0.603  -3.4263  -0.7554  -0.2918
 SKD  O4    O  OH1    0  -0.665   0.5412   2.5884   0.7509
 SKD  O6    O  O2     0  -0.502  -0.6515  -0.9316   0.0347
 SKD  O7    O  O2     0  -0.512  -0.4136   0.8012  -1.3563
 SKD  O8    O  OH1    0  -0.662   2.6404  -1.0845  -2.0154
 SKD  O9    O  OH1    0  -0.672   1.6190  -0.7955  -4.6222
 SKD  O10   O  O      0  -0.505   1.7821   0.5698   4.0835
 SKD  H31   H  HCH2   0   0.247  -2.1051   0.6756   1.5151
 SKD  H32   H  HCH2   0   0.250  -2.0184   2.0826   0.4828
 SKD  H4    H  HCH1   0   0.228  -0.3329   1.8527   2.4624
 SKD  H5    H  HCH1   0   0.271   1.8356   0.6861   1.5593
 SKD  H6    H  HCH1   0   0.269   1.3428  -1.3771   0.2425
 SKD  H7    H  HCH1   0   0.240   1.5961   1.1119  -1.0006
 SKD  H8    H  HCH1   0   0.231   0.6949  -1.5061  -2.2869
 SKD  H91   H  HCH2   0   0.213   0.1855   0.4248  -3.7381
 SKD  H92   H  HCH2   0   0.185   1.8517   0.9958  -3.5865
 SKD  H111  H  HCH3   0   0.260   0.5533  -0.8958   5.8338
 SKD  H112  H  HCH3   0   0.251  -0.4320  -1.7512   4.6352
 SKD  H113  H  HCH3   0   0.271   1.2617  -2.1780   4.8566
 SKD  HN5   H  HNH1   0   0.399  -0.1968  -1.2387   2.4496
 SKD  HO4   H  HOH1   0   0.450  -0.1018   3.2503   0.4808
 SKD  HO8   H  HOH1   0   0.444   3.2463  -0.3355  -2.0460
 SKD  HO9   H  HOH1   0   0.454   1.4905  -0.3534  -5.4658
 SKD  C10   C  C      0   0.516   0.9998  -0.3324   3.8164

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
 SKD  C1   C2    single  1.546  0.020  1.546
 SKD  C1   O1A   deloc   1.239  0.020  1.239
 SKD  C1   O1B   deloc   1.244  0.020  1.244
 SKD  C2   C3    single  1.528  0.020  1.528
 SKD  C2   O6    single  1.414  0.020  1.414
 SKD  C2   O7    single  1.411  0.020  1.411
 SKD  C3   C4    single  1.532  0.020  1.532
 SKD  C3   H31   single  0.970  0.020  1.090
 SKD  C3   H32   single  0.970  0.020  1.090
 SKD  C4   C5    single  1.543  0.020  1.543
 SKD  C4   O4    single  1.411  0.020  1.411
 SKD  C4   H4    single  0.970  0.020  1.090
 SKD  C5   C6    single  1.529  0.020  1.529
 SKD  C5   N5    single  1.446  0.020  1.446
 SKD  C5   H5    single  0.970  0.020  1.090
 SKD  C6   C7    single  1.530  0.020  1.530
 SKD  C6   O6    single  1.417  0.020  1.417
 SKD  C6   H6    single  0.970  0.020  1.090
 SKD  C7   C8    single  1.532  0.020  1.532
 SKD  C7   O7    single  1.414  0.020  1.414
 SKD  C7   H7    single  0.970  0.020  1.090
 SKD  C8   C9    single  1.518  0.020  1.518
 SKD  C8   O8    single  1.411  0.020  1.411
 SKD  C8   H8    single  0.970  0.020  1.090
 SKD  C9   O9    single  1.410  0.020  1.410
 SKD  C9   H91   single  0.970  0.020  1.090
 SKD  C9   H92   single  0.970  0.020  1.090
 SKD  C10  C11   single  1.509  0.020  1.509
 SKD  C10  N5    single  1.346  0.020  1.346
 SKD  C10  O10   double  1.224  0.020  1.224
 SKD  C11  H111  single  0.970  0.020  1.090
 SKD  C11  H112  single  0.970  0.020  1.090
 SKD  C11  H113  single  0.970  0.020  1.090
 SKD  N5   HN5   single  0.860  0.020  1.020
 SKD  O4   HO4   single  0.850  0.020  0.980
 SKD  O8   HO8   single  0.850  0.020  0.980
 SKD  O9   HO9   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
 SKD  O1B   C1   O1A   128.28  3.000
 SKD  O1B   C1   C2    114.18  3.000
 SKD  O1A   C1   C2    117.53  3.000
 SKD  O7    C2   O6    104.59  3.000
 SKD  O7    C2   C3    110.36  3.000
 SKD  O6    C2   C3    108.19  3.000
 SKD  O7    C2   C1    111.97  3.000
 SKD  O6    C2   C1    108.91  3.000
 SKD  C3    C2   C1    112.44  3.000
 SKD  H32   C3   H31   106.07  3.000
 SKD  H32   C3   C4    110.21  3.000
 SKD  H31   C3   C4    109.30  3.000
 SKD  H32   C3   C2    110.65  3.000
 SKD  H31   C3   C2    108.06  3.000
 SKD  C4    C3   C2    112.33  3.000
 SKD  H4    C4   O4    109.54  3.000
 SKD  H4    C4   C5    107.87  3.000
 SKD  O4    C4   C5    107.19  3.000
 SKD  H4    C4   C3    108.10  3.000
 SKD  O4    C4   C3    113.44  3.000
 SKD  C5    C4   C3    110.57  3.000
 SKD  H5    C5   N5    108.44  3.000
 SKD  H5    C5   C6    109.13  3.000
 SKD  N5    C5   C6    107.99  3.000
 SKD  H5    C5   C4    108.82  3.000
 SKD  N5    C5   C4    110.78  3.000
 SKD  C6    C5   C4    111.61  3.000
 SKD  H6    C6   O6    109.26  3.000
 SKD  H6    C6   C7    112.84  3.000
 SKD  O6    C6   C7    100.83  3.000
 SKD  H6    C6   C5    110.13  3.000
 SKD  O6    C6   C5    108.83  3.000
 SKD  C7    C6   C5    114.42  3.000
 SKD  H7    C7   O7    110.04  3.000
 SKD  H7    C7   C8    109.24  3.000
 SKD  O7    C7   C8    110.81  3.000
 SKD  H7    C7   C6    112.49  3.000
 SKD  O7    C7   C6    102.60  3.000
 SKD  C8    C7   C6    111.53  3.000
 SKD  H8    C8   O8    105.87  3.000
 SKD  H8    C8   C9    108.60  3.000
 SKD  O8    C8   C9    112.38  3.000
 SKD  H8    C8   C7    108.80  3.000
 SKD  O8    C8   C7    109.62  3.000
 SKD  C9    C8   C7    111.36  3.000
 SKD  H92   C9   H91   107.20  3.000
 SKD  H92   C9   O9    111.45  3.000
 SKD  H91   C9   O9    111.69  3.000
 SKD  H92   C9   C8    109.04  3.000
 SKD  H91   C9   C8    108.68  3.000
 SKD  O9    C9   C8    108.73  3.000
 SKD  H113  C11  H112  107.70  3.000
 SKD  H113  C11  H111  107.82  3.000
 SKD  H112  C11  H111  108.99  3.000
 SKD  H113  C11  C10   109.32  3.000
 SKD  H112  C11  C10   112.77  3.000
 SKD  H111  C11  C10   110.10  3.000
 SKD  HN5   N5   C10   118.47  3.000
 SKD  HN5   N5   C5    117.69  3.000
 SKD  C10   N5   C5    123.48  3.000
 SKD  HO4   O4   C4    108.56  3.000
 SKD  C6    O6   C2    102.64  3.000
 SKD  C7    O7   C2    108.60  3.000
 SKD  HO8   O8   C8    108.57  3.000
 SKD  HO9   O9   C9    107.84  3.000
 SKD  O10   C10  N5    122.82  3.000
 SKD  O10   C10  C11   122.28  3.000
 SKD  N5    C10  C11   114.87  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
 SKD  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 SKD  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 SKD  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 SKD  Var_01    H111  C11  C10  N5   -151.64  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
 SKD  chir_01  C2  C3  O6  O7  positiv
 SKD  chir_02  C4  O4  C5  C3  positiv
 SKD  chir_03  C5  N5  C6  C4  negativ
 SKD  chir_04  C6  O6  C7  C5  negativ
 SKD  chir_05  C7  O7  C8  C6  positiv
 SKD  chir_06  C8  O8  C7  C9  negativ

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
 SKD  plan-1  C5   0.020
 SKD  plan-1  C11  0.020
 SKD  plan-1  N5   0.020
 SKD  plan-1  O10  0.020
 SKD  plan-1  HN5  0.020
 SKD  plan-1  C10  0.020
 SKD  plan-2  C1   0.020
 SKD  plan-2  C2   0.020
 SKD  plan-2  O1A  0.020
 SKD  plan-2  O1B  0.020

