# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 17:26:45 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2R)-2-{[(1R,2S,3R,4R,5R)-4-(acetylamino)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-6,8-dioxabicyclo[3.2.1]oct-3-yl]oxy}propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@@H]1[C@@H](NC(C)=O)[C@@H]2OC[C@@H](O2)[C@H]1O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3NC(C)=O)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
 2YP  2YP  '(2R)-2-{[(1R,2S,3R,4R,5R)-4-(acetylamino)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-6,8-dioxabicyclo[3.2.1]oct-3-yl]oxy}propanoic acid (non-preferred name)'  ligand  62  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YP
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
 2YP  C1   C  CH1    0   0.345  -1.7147  -0.4669   0.8695
 2YP  O1   O  O2     0  -0.497  -0.7547   0.4945   0.6854
 2YP  C2   C  CH1    0  -0.162  -3.0182   0.0663   0.2713
 2YP  C3   C  CH1    0   0.036  -4.0953  -0.9945   0.4473
 2YP  O3   O  OH1    0  -0.662  -5.2723  -0.5413  -0.1641
 2YP  C4   C  CH1    0  -0.005  -3.6218  -2.3206  -0.1490
 2YP  OAC  O  O      0  -0.497  -2.5911   2.6557  -0.7778
 2YP  CAA  C  CH3    0  -0.782  -3.3779   3.7030   1.2179
 2YP  N2   N  NH1    0  -0.629  -3.3923   1.3195   0.8680
 2YP  O4   O  OH1    0  -0.672  -4.5942  -3.2910   0.1718
 2YP  C5   C  CH1    0  -0.016  -2.2439  -2.7055   0.4068
 2YP  C6   C  CH2    0  -0.154  -1.6798  -3.9292  -0.2818
 2YP  O6   O  OH1    0  -0.662  -0.5021  -4.3250   0.3758
 2YP  O5   O  O2     0  -0.486  -1.3387  -1.6404   0.2039
 2YP  CA4  C  CH1    0   0.034   0.5299   0.2598   1.2323
 2YP  CA3  C  CH1    0   0.024   1.5025   0.0325   0.0637
 2YP  OAH  O  O2     0  -0.487   2.6406  -0.6007   0.5717
 2YP  CAI  C  CH1    0  -0.069   3.3744  -1.3577  -0.3700
 2YP  CAJ  C  CH3    0  -0.680   2.7260  -2.7218  -0.5960
 2YP  CAL  C  C      0   0.377   4.8201  -1.5394   0.1317
 2YP  OAM  O  O      0  -0.591   5.0565  -1.3077   1.3278
 2YP  O    O  OC    -1  -0.629   5.6233  -1.9472  -0.7337
 2YP  CA5  C  CH1    0  -0.118   0.8919   1.5134   2.0264
 2YP  OA5  O  O2     0  -0.476   0.8284   2.6318   1.1523
 2YP  CA6  C  CH2    0  -0.172   2.3545   1.5724   2.4705
 2YP  OA6  O  O2     0  -0.499   3.0052   2.1760   1.3574
 2YP  CA1  C  CH1    0   0.258   2.0131   2.4975   0.4193
 2YP  CA2  C  CH1    0  -0.148   1.8390   1.3818  -0.6204
 2YP  NAD  N  NH1    0  -0.636   0.7947   1.7657  -1.5433
 2YP  CAE  C  C      0   0.520   0.9432   1.7759  -2.8804
 2YP  OAG  O  O      0  -0.507   2.0025   1.5291  -3.4428
 2YP  CAF  C  CH3    0  -0.791  -0.3004   2.1350  -3.6563
 2YP  H1   H  HCH1   0   0.186  -1.8537  -0.6850   1.9464
 2YP  H2   H  HCH1   0   0.270  -2.8501   0.2373  -0.7954
 2YP  H3   H  HCH1   0   0.210  -4.2531  -1.1548   1.5279
 2YP  H4   H  HOH1   0   0.452  -5.9484  -1.2162  -0.0399
 2YP  H5   H  HCH1   0   0.229  -3.5366  -2.1913  -1.2373
 2YP  H6   H  HCH3   0   0.263  -3.8678   4.4835   0.6382
 2YP  H7   H  HCH3   0   0.249  -4.0001   3.4616   2.0777
 2YP  H8   H  HCH3   0   0.268  -2.4348   4.1105   1.5853
 2YP  H9   H  HNH1   0   0.399  -3.7588   1.2990   1.8070
 2YP  H10  H  HOH1   0   0.463  -4.6968  -3.8947  -0.5686
 2YP  H11  H  HCH1   0   0.222  -2.3512  -2.9145   1.4843
 2YP  H12  H  HCH2   0   0.198  -2.4383  -4.7215  -0.2601
 2YP  H13  H  HCH2   0   0.203  -1.4980  -3.6854  -1.3368
 2YP  H14  H  HOH1   0   0.456  -0.0588  -4.9801  -0.1694
 2YP  H15  H  HCH1   0   0.257   0.5403  -0.6178   1.8889
 2YP  H16  H  HCH1   0   0.243   0.9943  -0.6006  -0.6739
 2YP  H17  H  HCH1   0   0.195   3.4131  -0.8255  -1.3317
 2YP  H18  H  HCH3   0   0.235   1.6750  -2.6373  -0.8782
 2YP  H19  H  HCH3   0   0.223   3.2420  -3.2585  -1.3914
 2YP  H20  H  HCH3   0   0.218   2.7712  -3.3292   0.3101
 2YP  H22  H  HCH1   0   0.265   0.1898   1.6622   2.8478
 2YP  H23  H  HCH2   0   0.231   2.4614   2.2113   3.3518
 2YP  H24  H  HCH2   0   0.245   2.7923   0.5986   2.6866
 2YP  H25  H  HCH1   0   0.253   2.2480   3.4498  -0.0649
 2YP  H26  H  HCH1   0   0.276   2.7609   1.2793  -1.1947
 2YP  H27  H  HNH1   0   0.407  -0.1277   1.9255  -1.1632
 2YP  H28  H  HCH3   0   0.253  -1.1918   2.2159  -3.0373
 2YP  H29  H  HCH3   0   0.265  -0.1467   3.0884  -4.1630
 2YP  H30  H  HCH3   0   0.261  -0.4756   1.3843  -4.4261
 2YP  CAB  C  C      0   0.544  -3.0801   2.5175   0.3353

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
 2YP  OAM  CAL  deloc   1.241  0.020  1.241
 2YP  CAL  O    deloc   1.249  0.020  1.249
 2YP  CAL  CAI  single  1.541  0.020  1.541
 2YP  CAJ  CAI  single  1.527  0.020  1.527
 2YP  CAI  OAH  single  1.414  0.020  1.414
 2YP  OAH  CA3  single  1.398  0.020  1.398
 2YP  O6   C6   single  1.406  0.020  1.406
 2YP  OAG  CAE  double  1.224  0.020  1.224
 2YP  CA3  CA2  single  1.550  0.020  1.550
 2YP  CA3  CA4  single  1.537  0.020  1.537
 2YP  C6   C5   single  1.513  0.020  1.513
 2YP  CAE  NAD  single  1.345  0.020  1.345
 2YP  CAE  CAF  single  1.509  0.020  1.509
 2YP  CA2  NAD  single  1.446  0.020  1.446
 2YP  CA2  CA1  single  1.535  0.020  1.535
 2YP  CA4  O1   single  1.416  0.020  1.416
 2YP  CA4  CA5  single  1.527  0.020  1.527
 2YP  O5   C5   single  1.412  0.020  1.412
 2YP  O5   C1   single  1.401  0.020  1.401
 2YP  O1   C1   single  1.371  0.020  1.371
 2YP  C5   C4   single  1.535  0.020  1.535
 2YP  OA6  CA6  single  1.424  0.020  1.424
 2YP  OA6  CA1  single  1.403  0.020  1.403
 2YP  CA6  CA5  single  1.530  0.020  1.530
 2YP  C1   C2   single  1.530  0.020  1.530
 2YP  CA1  OA5  single  1.400  0.020  1.400
 2YP  C4   O4   single  1.411  0.020  1.411
 2YP  C4   C3   single  1.529  0.020  1.529
 2YP  CA5  OA5  single  1.421  0.020  1.421
 2YP  OAC  CAB  double  1.224  0.020  1.224
 2YP  C2   C3   single  1.522  0.020  1.522
 2YP  C2   N2   single  1.437  0.020  1.437
 2YP  C3   O3   single  1.402  0.020  1.402
 2YP  CAB  N2   single  1.348  0.020  1.348
 2YP  CAB  CAA  single  1.508  0.020  1.508
 2YP  C1   H1   single  0.970  0.020  1.090
 2YP  C2   H2   single  0.970  0.020  1.090
 2YP  C3   H3   single  0.970  0.020  1.090
 2YP  O3   H4   single  0.850  0.020  0.980
 2YP  C4   H5   single  0.970  0.020  1.090
 2YP  CAA  H6   single  0.970  0.020  1.090
 2YP  CAA  H7   single  0.970  0.020  1.090
 2YP  CAA  H8   single  0.970  0.020  1.090
 2YP  N2   H9   single  0.860  0.020  1.020
 2YP  O4   H10  single  0.850  0.020  0.980
 2YP  C5   H11  single  0.970  0.020  1.090
 2YP  C6   H12  single  0.970  0.020  1.090
 2YP  C6   H13  single  0.970  0.020  1.090
 2YP  O6   H14  single  0.850  0.020  0.980
 2YP  CA4  H15  single  0.970  0.020  1.090
 2YP  CA3  H16  single  0.970  0.020  1.090
 2YP  CAI  H17  single  0.970  0.020  1.090
 2YP  CAJ  H18  single  0.970  0.020  1.090
 2YP  CAJ  H19  single  0.970  0.020  1.090
 2YP  CAJ  H20  single  0.970  0.020  1.090
 2YP  CA5  H22  single  0.970  0.020  1.090
 2YP  CA6  H23  single  0.970  0.020  1.090
 2YP  CA6  H24  single  0.970  0.020  1.090
 2YP  CA1  H25  single  0.970  0.020  1.090
 2YP  CA2  H26  single  0.970  0.020  1.090
 2YP  NAD  H27  single  0.860  0.020  1.020
 2YP  CAF  H28  single  0.970  0.020  1.090
 2YP  CAF  H29  single  0.970  0.020  1.090
 2YP  CAF  H30  single  0.970  0.020  1.090

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
 2YP  H1   C1   O5   109.32  3.000
 2YP  H1   C1   C2   109.99  3.000
 2YP  O5   C1   C2   109.57  3.000
 2YP  H1   C1   O1   110.89  3.000
 2YP  C2   C1   O1   107.44  3.000
 2YP  O5   C1   O1   109.61  3.000
 2YP  CA4  O1   C1   117.85  3.000
 2YP  H2   C2   N2   107.98  3.000
 2YP  H2   C2   C3   109.30  3.000
 2YP  N2   C2   C3   112.05  3.000
 2YP  H2   C2   C1   107.76  3.000
 2YP  N2   C2   C1   111.30  3.000
 2YP  C3   C2   C1   108.35  3.000
 2YP  H3   C3   C4   107.46  3.000
 2YP  H3   C3   O3   110.73  3.000
 2YP  C4   C3   O3   111.74  3.000
 2YP  H3   C3   C2   108.40  3.000
 2YP  O3   C3   C2   108.57  3.000
 2YP  C4   C3   C2   109.89  3.000
 2YP  H4   O3   C3   107.85  3.000
 2YP  H5   C4   C5   108.57  3.000
 2YP  H5   C4   O4   111.06  3.000
 2YP  C5   C4   O4   111.34  3.000
 2YP  H5   C4   C3   107.94  3.000
 2YP  O4   C4   C3   107.12  3.000
 2YP  C5   C4   C3   110.75  3.000
 2YP  H8   CAA  H7   108.12  3.000
 2YP  H8   CAA  H6   107.49  3.000
 2YP  H7   CAA  H6   108.81  3.000
 2YP  H8   CAA  CAB  108.66  3.000
 2YP  H7   CAA  CAB  113.64  3.000
 2YP  H6   CAA  CAB  109.93  3.000
 2YP  H9   N2   CAB  118.06  3.000
 2YP  H9   N2   C2   117.61  3.000
 2YP  CAB  N2   C2   123.41  3.000
 2YP  H10  O4   C4   109.31  3.000
 2YP  H11  C5   O5   110.22  3.000
 2YP  H11  C5   C6   109.13  3.000
 2YP  O5   C5   C6   107.79  3.000
 2YP  H11  C5   C4   108.30  3.000
 2YP  O5   C5   C4   109.52  3.000
 2YP  C6   C5   C4   111.88  3.000
 2YP  H13  C6   H12  107.09  3.000
 2YP  H13  C6   O6   111.92  3.000
 2YP  H12  C6   O6   111.50  3.000
 2YP  H13  C6   C5   108.63  3.000
 2YP  H12  C6   C5   108.50  3.000
 2YP  O6   C6   C5   109.10  3.000
 2YP  H14  O6   C6   108.25  3.000
 2YP  C5   O5   C1   113.05  3.000
 2YP  H15  CA4  CA5  110.09  3.000
 2YP  H15  CA4  CA3  109.33  3.000
 2YP  CA5  CA4  CA3  111.51  3.000
 2YP  H15  CA4  O1   111.88  3.000
 2YP  CA5  CA4  O1   106.25  3.000
 2YP  CA3  CA4  O1   107.75  3.000
 2YP  H16  CA3  CA2  107.84  3.000
 2YP  H16  CA3  OAH  111.11  3.000
 2YP  CA2  CA3  OAH  112.21  3.000
 2YP  H16  CA3  CA4  107.66  3.000
 2YP  CA2  CA3  CA4  110.13  3.000
 2YP  OAH  CA3  CA4  107.80  3.000
 2YP  CAI  OAH  CA3  115.02  3.000
 2YP  H17  CAI  CAL  107.99  3.000
 2YP  H17  CAI  CAJ  108.52  3.000
 2YP  CAL  CAI  CAJ  109.94  3.000
 2YP  H17  CAI  OAH  109.98  3.000
 2YP  CAJ  CAI  OAH  110.89  3.000
 2YP  CAL  CAI  OAH  109.46  3.000
 2YP  H20  CAJ  H19  108.20  3.000
 2YP  H20  CAJ  H18  107.31  3.000
 2YP  H19  CAJ  H18  107.78  3.000
 2YP  H20  CAJ  CAI  110.89  3.000
 2YP  H19  CAJ  CAI  110.30  3.000
 2YP  H18  CAJ  CAI  112.20  3.000
 2YP  O    CAL  OAM  127.31  3.000
 2YP  O    CAL  CAI  114.59  3.000
 2YP  OAM  CAL  CAI  118.07  3.000
 2YP  H22  CA5  CA6  113.05  3.000
 2YP  H22  CA5  OA5  109.10  3.000
 2YP  CA6  CA5  OA5  101.01  3.000
 2YP  H22  CA5  CA4  110.54  3.000
 2YP  OA5  CA5  CA4  108.40  3.000
 2YP  CA6  CA5  CA4  114.15  3.000
 2YP  CA1  OA5  CA5  102.06  3.000
 2YP  H24  CA6  H23  108.85  3.000
 2YP  H24  CA6  OA6  110.51  3.000
 2YP  H23  CA6  OA6  109.74  3.000
 2YP  H24  CA6  CA5  114.04  3.000
 2YP  H23  CA6  CA5  110.48  3.000
 2YP  OA6  CA6  CA5  103.08  3.000
 2YP  CA1  OA6  CA6  107.27  3.000
 2YP  H25  CA1  CA2  110.94  3.000
 2YP  H25  CA1  OA6  110.10  3.000
 2YP  CA2  CA1  OA6  111.51  3.000
 2YP  H25  CA1  OA5  109.27  3.000
 2YP  OA6  CA1  OA5  105.69  3.000
 2YP  CA2  CA1  OA5  109.18  3.000
 2YP  H26  CA2  NAD  107.42  3.000
 2YP  H26  CA2  CA1  109.21  3.000
 2YP  NAD  CA2  CA1  108.75  3.000
 2YP  H26  CA2  CA3  109.51  3.000
 2YP  CA1  CA2  CA3  111.01  3.000
 2YP  NAD  CA2  CA3  110.87  3.000
 2YP  H27  NAD  CAE  118.26  3.000
 2YP  H27  NAD  CA2  117.47  3.000
 2YP  CAE  NAD  CA2  123.84  3.000
 2YP  CAF  CAE  OAG  121.64  3.000
 2YP  CAF  CAE  NAD  114.95  3.000
 2YP  OAG  CAE  NAD  123.40  3.000
 2YP  H30  CAF  H29  107.26  3.000
 2YP  H30  CAF  H28  108.75  3.000
 2YP  H29  CAF  H28  108.35  3.000
 2YP  H30  CAF  CAE  109.38  3.000
 2YP  H29  CAF  CAE  109.32  3.000
 2YP  H28  CAF  CAE  113.59  3.000
 2YP  N2   CAB  CAA  114.95  3.000
 2YP  CAA  CAB  OAC  121.51  3.000
 2YP  N2   CAB  OAC  123.54  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
 2YP  CONST_01  OAC  CAB  N2   C2      0.00   0.0  0
 2YP  CONST_02  CAA  CAB  N2   C2    180.00   0.0  0
 2YP  CONST_03  OAG  CAE  NAD  CA2     0.00   0.0  0
 2YP  CONST_04  CAF  CAE  NAD  CA2   180.00   0.0  0
 2YP  CONST_05  H9   N2   CAB  OAC   180.00   0.0  0
 2YP  CONST_06  H27  NAD  CAE  OAG   180.00   0.0  0
 2YP  Var_01    H23  CA6  OA6  CA1  -114.58  30.0  3
 2YP  Var_02    H6   CAA  CAB  OAC    45.30  30.0  3
 2YP  Var_03    H28  CAF  CAE  NAD    -7.40  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
 2YP  chir_01  C1   O5   O1   C2   negativ
 2YP  chir_02  C2   N2   C3   C1   positiv
 2YP  chir_03  C3   O3   C2   C4   positiv
 2YP  chir_04  C4   O4   C3   C5   negativ
 2YP  chir_05  C5   O5   C4   C6   negativ
 2YP  chir_06  CA4  O1   CA3  CA5  negativ
 2YP  chir_07  CA3  OAH  CA2  CA4  positiv
 2YP  chir_08  CAI  OAH  CAJ  CAL  positiv
 2YP  chir_09  CA5  OA5  CA4  CA6  negativ
 2YP  chir_10  CA1  OA6  OA5  CA2  positiv
 2YP  chir_11  CA2  NAD  CA3  CA1  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
 2YP  plan-1  CA2  0.020
 2YP  plan-1  NAD  0.020
 2YP  plan-1  CAE  0.020
 2YP  plan-1  OAG  0.020
 2YP  plan-1  CAF  0.020
 2YP  plan-1  H27  0.020
 2YP  plan-2  C2   0.020
 2YP  plan-2  OAC  0.020
 2YP  plan-2  CAA  0.020
 2YP  plan-2  N2   0.020
 2YP  plan-2  H9   0.020
 2YP  plan-2  CAB  0.020
 2YP  plan-3  CAI  0.020
 2YP  plan-3  CAL  0.020
 2YP  plan-3  OAM  0.020
 2YP  plan-3  O    0.020

