# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 06:33:41 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  37  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   0.509  -2.6277  -0.1610  -1.0435
 SKD  C2    C  CR5   0   0.412  -1.3092   0.2310  -0.3841
 SKD  C3    C  CH2   0  -0.500  -1.5019   1.1882   0.7922
 SKD  C4    C  CH1   0   0.027  -0.1506   1.5745   1.4112
 SKD  C5    C  CH1   0  -0.051   0.7996   0.3587   1.4518
 SKD  C6    C  CR15  0  -0.143   0.6805  -0.4946   0.1894
 SKD  C7    C  CR15  0   0.015   0.8497   0.2782  -1.1203
 SKD  C8    C  CH1   0  -0.018   1.2920  -0.6337  -2.2688
 SKD  C9    C  CH2   0  -0.162   1.2175   0.0856  -3.6046
 SKD  C11   C  CH3   0  -0.784   0.5644  -1.2457   4.8699
 SKD  N5    N  NH1   0  -0.634   0.5136  -0.4828   2.5913
 SKD  O1A   O  O     0  -0.413  -2.9526   0.1852  -2.1455
 SKD  O1B   O  OH1   0  -0.583  -3.3582  -0.9006  -0.2304
 SKD  O4    O  OH1   0  -0.659   0.5124   2.5971   0.7068
 SKD  O6    O  O     0  -0.490  -0.6689  -0.9319   0.0673
 SKD  O7    O  O     0  -0.505  -0.4618   0.7795  -1.3529
 SKD  O8    O  OH1   0  -0.658   2.5816  -1.1330  -1.9993
 SKD  O9    O  OH1   0  -0.669   1.5968  -0.8126  -4.6199
 SKD  O10   O  O     0  -0.497   1.8219   0.6331   4.0517
 SKD  H31   H  HCH2  0   0.266  -2.1170   0.6980   1.5498
 SKD  H32   H  HCH2  0   0.274  -2.0492   2.0827   0.4801
 SKD  H4    H  HCH1  0   0.242  -0.3373   1.8914   2.4450
 SKD  H5    H  HCH1  0   0.282   1.8264   0.7217   1.5390
 SKD  H6    H  HCR5  0   0.286   1.3308  -1.3673   0.2551
 SKD  H7    H  HCR5  0   0.260   1.5485   1.1145  -1.0248
 SKD  H8    H  HCH1  0   0.237   0.6317  -1.5075  -2.3019
 SKD  H91   H  HCH2  0   0.212   0.1976   0.4564  -3.7528
 SKD  H92   H  HCH2  0   0.191   1.8788   0.9658  -3.5744
 SKD  H111  H  HCH3  0   0.261   0.9786  -0.9846   5.8405
 SKD  H112  H  HCH3  0   0.263  -0.5239  -1.2475   4.9419
 SKD  H113  H  HCH3  0   0.268   0.8756  -2.2599   4.6166
 SKD  HN5   H  HNH1  0   0.403  -0.1884  -1.1989   2.4866
 SKD  HOB1  H  HOH1  0   0.494  -4.2036  -1.1313  -0.6461
 SKD  HO4   H  HOH1  0   0.454  -0.1121   3.3076   0.5316
 SKD  HO8   H  HOH1  0   0.447   3.2123  -0.4056  -2.0471
 SKD  HO9   H  HOH1  0   0.456   1.5113  -0.3590  -5.4630
 SKD  C10   C  C     0   0.511   1.0309  -0.2687   3.8185

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  1.525  0.020  1.525
 SKD  C1   O1A   double  1.200  0.020  1.200
 SKD  C1   O1B   single  1.320  0.020  1.320
 SKD  C2   C3    single  1.529  0.020  1.529
 SKD  C2   O6    single  1.402  0.020  1.402
 SKD  C2   O7    single  1.399  0.020  1.399
 SKD  C3   C4    single  1.536  0.020  1.536
 SKD  C3   H31   single  0.970  0.020  1.090
 SKD  C3   H32   single  0.970  0.020  1.090
 SKD  C4   C5    single  1.544  0.020  1.544
 SKD  C4   O4    single  1.408  0.020  1.408
 SKD  C4   H4    single  0.970  0.020  1.090
 SKD  C5   C6    single  1.528  0.020  1.528
 SKD  C5   N5    single  1.445  0.020  1.445
 SKD  C5   H5    single  0.970  0.020  1.090
 SKD  C6   C7    single  1.530  0.020  1.530
 SKD  C6   O6    single  1.424  0.020  1.424
 SKD  C6   H6    single  0.970  0.020  1.090
 SKD  C7   C8    single  1.532  0.020  1.532
 SKD  C7   O7    single  1.423  0.020  1.423
 SKD  C7   H7    single  0.970  0.020  1.090
 SKD  C8   C9    single  1.519  0.020  1.519
 SKD  C8   O8    single  1.409  0.020  1.409
 SKD  C8   H8    single  0.970  0.020  1.090
 SKD  C9   O9    single  1.408  0.020  1.408
 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  1.349  0.020  1.349
 SKD  C10  O10   double  1.222  0.020  1.222
 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  O1B  HOB1  single  0.850  0.020  0.980
 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   125.29  3.000
 SKD  O1B   C1   C2    110.86  3.000
 SKD  O1A   C1   C2    123.84  3.000
 SKD  O7    C2   O6    105.75  3.000
 SKD  O7    C2   C3    111.32  3.000
 SKD  O6    C2   C3    109.22  3.000
 SKD  O7    C2   C1    108.96  3.000
 SKD  O6    C2   C1    108.71  3.000
 SKD  C3    C2   C1    112.61  3.000
 SKD  H32   C3   H31   106.45  3.000
 SKD  H32   C3   C4    110.46  3.000
 SKD  H31   C3   C4    109.20  3.000
 SKD  H32   C3   C2    110.83  3.000
 SKD  H31   C3   C2    108.89  3.000
 SKD  C4    C3   C2    110.90  3.000
 SKD  H4    C4   O4    109.99  3.000
 SKD  H4    C4   C5    107.90  3.000
 SKD  O4    C4   C5    107.18  3.000
 SKD  H4    C4   C3    107.62  3.000
 SKD  O4    C4   C3    113.29  3.000
 SKD  C5    C4   C3    110.74  3.000
 SKD  H5    C5   N5    108.46  3.000
 SKD  H5    C5   C6    108.94  3.000
 SKD  N5    C5   C6    108.10  3.000
 SKD  H5    C5   C4    108.60  3.000
 SKD  N5    C5   C4    110.95  3.000
 SKD  C6    C5   C4    111.72  3.000
 SKD  H6    C6   O6    108.94  3.000
 SKD  H6    C6   C7    112.95  3.000
 SKD  O6    C6   C7    100.75  3.000
 SKD  H6    C6   C5    110.52  3.000
 SKD  O6    C6   C5    108.43  3.000
 SKD  C7    C6   C5    114.61  3.000
 SKD  H7    C7   O7    109.49  3.000
 SKD  H7    C7   C8    109.64  3.000
 SKD  O7    C7   C8    110.69  3.000
 SKD  H7    C7   C6    112.46  3.000
 SKD  O7    C7   C6    102.47  3.000
 SKD  C8    C7   C6    111.90  3.000
 SKD  H8    C8   O8    105.95  3.000
 SKD  H8    C8   C9    108.76  3.000
 SKD  O8    C8   C9    112.39  3.000
 SKD  H8    C8   C7    108.87  3.000
 SKD  O8    C8   C7    109.38  3.000
 SKD  C9    C8   C7    111.30  3.000
 SKD  H92   C9   H91   107.00  3.000
 SKD  H92   C9   O9    111.59  3.000
 SKD  H91   C9   O9    111.68  3.000
 SKD  H92   C9   C8    108.96  3.000
 SKD  H91   C9   C8    108.97  3.000
 SKD  O9    C9   C8    108.59  3.000
 SKD  H113  C11  H112  107.37  3.000
 SKD  H113  C11  H111  108.78  3.000
 SKD  H112  C11  H111  108.76  3.000
 SKD  H113  C11  C10   110.61  3.000
 SKD  H112  C11  C10   110.82  3.000
 SKD  H111  C11  C10   110.42  3.000
 SKD  HN5   N5   C10   118.31  3.000
 SKD  HN5   N5   C5    118.00  3.000
 SKD  C10   N5   C5    123.30  3.000
 SKD  HOB1  O1B  C1    110.59  3.000
 SKD  HO4   O4   C4    108.78  3.000
 SKD  C6    O6   C2    101.87  3.000
 SKD  C7    O7   C2    107.87  3.000
 SKD  HO8   O8   C8    108.79  3.000
 SKD  HO9   O9   C9    107.91  3.000
 SKD  O10   C10  N5    122.62  3.000
 SKD  O10   C10  C11   123.02  3.000
 SKD  N5    C10  C11   114.37  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  HOB1  O1B  C1   C2    180.00   0.0  0
 SKD  CONST_04  HN5   N5   C10  C11     0.00   0.0  0
 SKD  Var_01    H111  C11  C10  N5   -177.11  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
 SKD  plan-2  HOB1  0.020

