# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 12:20:59 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-phenylprop-2-en-1-yl]-D-glycero-L-altro-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C(=C(O[C@H]1[C@@H](O)[C@H](O)CO)C(O)=O)C/C=C/c2ccccc2
#
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
 0LP  0LP  '5-(acetylamino)-2,6-anhydro-3,5-dideoxy-3-[(2E)-3-phenylprop-2-en-1-yl]-D-glycero-L-altro-non-2-enonic acid'  L-saccharide  54  29  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0LP
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
 0LP  C11   C  CH3   0  -0.788  -16.3933  27.1722   8.0497
 0LP  C10   C  C     0   0.531  -17.1081  26.5528   9.2245
 0LP  O10   O  O     0  -0.496  -16.9405  26.9541  10.3651
 0LP  N5    N  NH1   0  -0.633  -17.9605  25.5572   8.9031
 0LP  C5    C  CH1   0  -0.135  -18.7652  24.8405   9.8525
 0LP  C4    C  CH1   0   0.049  -18.3469  23.3700   9.8756
 0LP  O4    O  OH1   0  -0.652  -17.1237  23.3172  10.5718
 0LP  C6    C  CH1   0  -0.003  -20.2664  24.9177   9.5786
 0LP  C7    C  CH1   0  -0.023  -20.8845  26.3306   9.4913
 0LP  O7    O  OH1   0  -0.650  -20.0585  27.3651   9.9543
 0LP  C8    C  CH1   0  -0.016  -21.3695  26.7143   8.0838
 0LP  O8    O  OH1   0  -0.665  -22.3053  25.7689   7.6188
 0LP  C9    C  CH2   0  -0.160  -20.2751  26.8317   7.0431
 0LP  O9    O  OH1   0  -0.671  -20.8229  27.4434   5.8977
 0LP  O6    O  O2    0  -0.483  -20.9243  24.2664  10.6650
 0LP  C2    C  C     0   0.212  -20.5559  22.9897  10.9014
 0LP  C1    C  C     0   0.468  -21.6599  22.2768  11.6105
 0LP  O1B   O  OH1   0  -0.582  -21.2283  21.3164  12.4103
 0LP  O1A   O  O     0  -0.424  -22.8173  22.5840  11.4865
 0LP  C3    C  C     0   0.009  -19.3874  22.4708  10.5086
 0LP  CAQ   C  CH2   0  -0.607  -19.0159  21.0091  10.5679
 0LP  CAI   C  C1    0  -0.193  -18.1019  20.6545  11.7028
 0LP  CAJ   C  C1    0  -0.320  -16.9317  20.0329  11.5418
 0LP  CAX   C  CR6   0   0.150  -16.0007  19.6241  12.5978
 0LP  CAN   C  CR16  0  -0.330  -16.2313  19.8638  13.9565
 0LP  CAL   C  CR16  0  -0.233  -15.3165  19.4566  14.9132
 0LP  CAK   C  CR16  0  -0.271  -14.1485  18.8004  14.5383
 0LP  CAM   C  CR16  0  -0.241  -13.9062  18.5558  13.1942
 0LP  CAO   C  CR16  0  -0.318  -14.8239  18.9646  12.2365
 0LP  H111  H  HCH3  0   0.267  -15.3632  27.3974   8.3192
 0LP  H112  H  HCH3  0   0.249  -16.3936  26.5455   7.1596
 0LP  H113  H  HCH3  0   0.269  -16.8803  28.1156   7.7962
 0LP  HN5   H  HNH1  0   0.396  -17.9684  25.2312   7.9498
 0LP  H5    H  HCH1  0   0.275  -18.5701  25.2655  10.8389
 0LP  H4    H  HCH1  0   0.229  -18.2119  23.0338   8.8351
 0LP  HO4   H  HOH1  0   0.461  -16.7583  22.4285  10.5140
 0LP  H6    H  HCH1  0   0.252  -20.5040  24.3537   8.6657
 0LP  H7    H  HCH1  0   0.245  -21.7989  26.2819  10.1010
 0LP  HO7   H  HOH1  0   0.459  -19.9320  27.2750  10.9035
 0LP  H8    H  HCH1  0   0.233  -21.8357  27.7056   8.1837
 0LP  HO8   H  HOH1  0   0.454  -23.0941  25.8211   8.1678
 0LP  H91   H  HCH2  0   0.191  -19.8804  25.8347   6.8056
 0LP  H92   H  HCH2  0   0.209  -19.4492  27.4208   7.4558
 0LP  HO9   H  HOH1  0   0.455  -20.1596  27.4193   5.2027
 0LP  HO1B  H  HOH1  0   0.491  -21.9804  20.8635  12.8220
 0LP  H17   H  HCH2  0   0.278  -19.9091  20.3869  10.6250
 0LP  H18   H  HCH2  0   0.274  -18.5369  20.7456   9.6186
 0LP  H19   H  H     0   0.261  -18.4555  20.9184  12.6941
 0LP  H20   H  H     0   0.253  -16.6148  19.7891  10.5300
 0LP  H21   H  HCR6  0   0.252  -17.1336  20.3696  14.2763
 0LP  H22   H  HCR6  0   0.258  -15.5161  19.6515  15.9590
 0LP  H23   H  HCR6  0   0.257  -13.4361  18.4841  15.2892
 0LP  H24   H  HCR6  0   0.257  -13.0016  18.0467  12.8877
 0LP  H25   H  HCR6  0   0.253  -14.6239  18.7717  11.1890

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
 0LP  C11  C10   single    1.508  0.020  1.508
 0LP  O8   C8    single    1.409  0.020  1.409
 0LP  C9   O9    single    1.409  0.020  1.409
 0LP  C9   C8    single    1.515  0.020  1.515
 0LP  N5   C10   single    1.349  0.020  1.349
 0LP  N5   C5    single    1.436  0.020  1.436
 0LP  C10  O10   double    1.221  0.020  1.221
 0LP  C8   C7    single    1.537  0.020  1.537
 0LP  C6   C5    single    1.528  0.020  1.528
 0LP  C6   C7    single    1.545  0.020  1.545
 0LP  C6   O6    single    1.427  0.020  1.427
 0LP  C5   C4    single    1.529  0.020  1.529
 0LP  C4   O4    single    1.409  0.020  1.409
 0LP  C4   C3    single    1.514  0.020  1.514
 0LP  C7   O7    single    1.402  0.020  1.402
 0LP  O6   C2    single    1.350  0.020  1.350
 0LP  C3   CAQ   single    1.509  0.020  1.509
 0LP  C3   C2    double    1.337  0.020  1.337
 0LP  CAQ  CAI   single    1.500  0.020  1.500
 0LP  C2   C1    single    1.493  0.020  1.493
 0LP  O1A  C1    double    1.204  0.020  1.204
 0LP  C1   O1B   single    1.322  0.020  1.322
 0LP  CAJ  CAI   double    1.335  0.020  1.335
 0LP  CAJ  CAX   single    1.466  0.020  1.466
 0LP  CAX  CAO   aromatic  1.397  0.020  1.397
 0LP  CAX  CAN   aromatic  1.399  0.020  1.399
 0LP  CAO  CAM   aromatic  1.388  0.020  1.388
 0LP  CAN  CAL   aromatic  1.385  0.020  1.385
 0LP  CAM  CAK   aromatic  1.387  0.020  1.387
 0LP  CAL  CAK   aromatic  1.391  0.020  1.391
 0LP  C11  H111  single    0.970  0.020  1.090
 0LP  C11  H112  single    0.970  0.020  1.090
 0LP  C11  H113  single    0.970  0.020  1.090
 0LP  N5   HN5   single    0.860  0.020  1.020
 0LP  C5   H5    single    0.970  0.020  1.090
 0LP  C4   H4    single    0.970  0.020  1.090
 0LP  O4   HO4   single    0.850  0.020  0.980
 0LP  C6   H6    single    0.970  0.020  1.090
 0LP  C7   H7    single    0.970  0.020  1.090
 0LP  O7   HO7   single    0.850  0.020  0.980
 0LP  C8   H8    single    0.970  0.020  1.090
 0LP  O8   HO8   single    0.850  0.020  0.980
 0LP  C9   H91   single    0.970  0.020  1.090
 0LP  C9   H92   single    0.970  0.020  1.090
 0LP  O9   HO9   single    0.850  0.020  0.980
 0LP  O1B  HO1B  single    0.850  0.020  0.980
 0LP  CAQ  H17   single    0.970  0.020  1.090
 0LP  CAQ  H18   single    0.970  0.020  1.090
 0LP  CAI  H19   single    0.930  0.020  1.080
 0LP  CAJ  H20   single    0.930  0.020  1.080
 0LP  CAN  H21   single    0.930  0.020  1.080
 0LP  CAL  H22   single    0.930  0.020  1.080
 0LP  CAK  H23   single    0.930  0.020  1.080
 0LP  CAM  H24   single    0.930  0.020  1.080
 0LP  CAO  H25   single    0.930  0.020  1.080

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
 0LP  H113  C11  H112  107.91  3.000
 0LP  H113  C11  H111  107.52  3.000
 0LP  H112  C11  H111  108.78  3.000
 0LP  H113  C11  C10   108.93  3.000
 0LP  H112  C11  C10   113.60  3.000
 0LP  H111  C11  C10   109.92  3.000
 0LP  N5    C10  O10   123.49  3.000
 0LP  O10   C10  C11   121.85  3.000
 0LP  N5    C10  C11   114.64  3.000
 0LP  HN5   N5   C5    117.36  3.000
 0LP  HN5   N5   C10   117.97  3.000
 0LP  C5    N5   C10   124.38  3.000
 0LP  H5    C5   C6    108.53  3.000
 0LP  H5    C5   C4    108.18  3.000
 0LP  C6    C5   C4    108.67  3.000
 0LP  H5    C5   N5    107.63  3.000
 0LP  C4    C5   N5    109.67  3.000
 0LP  C6    C5   N5    114.01  3.000
 0LP  H4    C4   C3    107.33  3.000
 0LP  H4    C4   O4    110.42  3.000
 0LP  C3    C4   O4    111.59  3.000
 0LP  H4    C4   C5    108.23  3.000
 0LP  C3    C4   C5    112.93  3.000
 0LP  O4    C4   C5    106.33  3.000
 0LP  HO4   O4   C4    109.55  3.000
 0LP  H6    C6   O6    107.36  3.000
 0LP  H6    C6   C7    109.62  3.000
 0LP  O6    C6   C7    106.02  3.000
 0LP  H6    C6   C5    109.60  3.000
 0LP  O6    C6   C5    107.06  3.000
 0LP  C7    C6   C5    116.71  3.000
 0LP  H7    C7   C8    104.85  3.000
 0LP  H7    C7   O7    109.83  3.000
 0LP  C8    C7   O7    107.70  3.000
 0LP  H7    C7   C6    105.12  3.000
 0LP  O7    C7   C6    114.85  3.000
 0LP  C8    C7   C6    113.97  3.000
 0LP  HO7   O7   C7    109.52  3.000
 0LP  H8    C8   C9    107.38  3.000
 0LP  H8    C8   O8    110.68  3.000
 0LP  C9    C8   O8    107.76  3.000
 0LP  H8    C8   C7    105.99  3.000
 0LP  C9    C8   C7    114.86  3.000
 0LP  O8    C8   C7    110.14  3.000
 0LP  HO8   O8   C8    108.64  3.000
 0LP  H92   C9   H91   107.38  3.000
 0LP  H92   C9   O9    111.46  3.000
 0LP  H91   C9   O9    110.97  3.000
 0LP  H92   C9   C8    109.13  3.000
 0LP  H91   C9   C8    109.75  3.000
 0LP  O9    C9   C8    108.13  3.000
 0LP  HO9   O9   C9    107.97  3.000
 0LP  C2    O6   C6    116.05  3.000
 0LP  C3    C2   C1    126.88  3.000
 0LP  C1    C2   O6    109.45  3.000
 0LP  C3    C2   O6    123.65  3.000
 0LP  O1A   C1   O1B   124.16  3.000
 0LP  O1B   C1   C2    113.12  3.000
 0LP  O1A   C1   C2    122.68  3.000
 0LP  HO1B  O1B  C1    110.05  3.000
 0LP  CAQ   C3   C2    125.40  3.000
 0LP  C2    C3   C4    119.52  3.000
 0LP  CAQ   C3   C4    114.99  3.000
 0LP  H18   CAQ  H17   105.45  3.000
 0LP  H18   CAQ  CAI   109.42  3.000
 0LP  H17   CAQ  CAI   108.95  3.000
 0LP  H18   CAQ  C3    107.85  3.000
 0LP  H17   CAQ  C3    110.68  3.000
 0LP  CAI   CAQ  C3    114.12  3.000
 0LP  H19   CAI  CAJ   120.60  3.000
 0LP  H19   CAI  CAQ   115.81  3.000
 0LP  CAJ   CAI  CAQ   123.58  3.000
 0LP  H20   CAJ  CAX   114.99  3.000
 0LP  H20   CAJ  CAI   118.15  3.000
 0LP  CAX   CAJ  CAI   126.85  3.000
 0LP  CAO   CAX  CAN   118.11  3.000
 0LP  CAN   CAX  CAJ   123.18  3.000
 0LP  CAO   CAX  CAJ   118.71  3.000
 0LP  H21   CAN  CAL   118.93  3.000
 0LP  H21   CAN  CAX   120.29  3.000
 0LP  CAL   CAN  CAX   120.78  3.000
 0LP  H22   CAL  CAK   120.00  3.000
 0LP  H22   CAL  CAN   119.52  3.000
 0LP  CAK   CAL  CAN   120.47  3.000
 0LP  H23   CAK  CAM   120.37  3.000
 0LP  H23   CAK  CAL   120.24  3.000
 0LP  CAM   CAK  CAL   119.39  3.000
 0LP  H24   CAM  CAO   119.72  3.000
 0LP  H24   CAM  CAK   120.21  3.000
 0LP  CAO   CAM  CAK   120.07  3.000
 0LP  H25   CAO  CAM   119.51  3.000
 0LP  H25   CAO  CAX   119.32  3.000
 0LP  CAM   CAO  CAX   121.17  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
 0LP  CONST_01  CAK   CAM  CAO  CAX     0.00   0.0  0
 0LP  CONST_02  CAK   CAL  CAN  CAX     0.00   0.0  0
 0LP  CONST_03  CAM   CAO  CAX  CAN     0.00   0.0  0
 0LP  CONST_04  CAM   CAK  CAL  CAN     0.00   0.0  0
 0LP  CONST_05  CAO   CAX  CAN  CAL     0.00   0.0  0
 0LP  CONST_06  CAO   CAM  CAK  CAL     0.00   0.0  0
 0LP  CONST_07  CAM   CAO  CAX  CAJ   180.00   0.0  0
 0LP  CONST_08  CAL   CAN  CAX  CAJ   180.00   0.0  0
 0LP  CONST_09  H24   CAM  CAO  CAX   180.00   0.0  0
 0LP  CONST_10  H22   CAL  CAN  CAX   180.00   0.0  0
 0LP  CONST_11  H25   CAO  CAX  CAN   180.00   0.0  0
 0LP  CONST_12  H23   CAK  CAL  CAN   180.00   0.0  0
 0LP  CONST_13  H21   CAN  CAL  CAK   180.00   0.0  0
 0LP  CONST_14  C5    N5   C10  C11   180.00   0.0  0
 0LP  CONST_15  C5    N5   C10  O10     0.00   0.0  0
 0LP  CONST_16  HO1B  O1B  C1   C2    180.00   0.0  0
 0LP  CONST_17  HN5   N5   C10  C11     0.00   0.0  0
 0LP  Var_01    O6    C2   C3   C4      5.94  30.0  1
 0LP  Var_02    C3    C2   O6   C6     22.19  30.0  1
 0LP  Var_03    CAI   CAQ  C3   C4     80.63  30.0  3
 0LP  Var_04    O1A   C1   C2   O6     27.85  30.0  2
 0LP  Var_05    CAO   CAX  CAJ  CAI   179.18  30.0  2
 0LP  Var_06    CAX   CAJ  CAI  CAQ  -178.39   0.0  2
 0LP  Var_07    CAJ   CAI  CAQ  C3   -124.99  30.0  3
 0LP  Var_08    H111  C11  C10  O10    40.30  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
 0LP  chir_01  C5  N5  C6  C4  negativ
 0LP  chir_02  C4  O4  C5  C3  positiv
 0LP  chir_03  C6  O6  C5  C7  positiv
 0LP  chir_04  C7  O7  C6  C8  positiv
 0LP  chir_05  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
 0LP  plan-1  CAJ   0.020
 0LP  plan-1  CAX   0.020
 0LP  plan-1  CAN   0.020
 0LP  plan-1  CAL   0.020
 0LP  plan-1  CAK   0.020
 0LP  plan-1  CAM   0.020
 0LP  plan-1  CAO   0.020
 0LP  plan-1  H21   0.020
 0LP  plan-1  H22   0.020
 0LP  plan-1  H23   0.020
 0LP  plan-1  H24   0.020
 0LP  plan-1  H25   0.020
 0LP  plan-2  C11   0.020
 0LP  plan-2  C10   0.020
 0LP  plan-2  O10   0.020
 0LP  plan-2  N5    0.020
 0LP  plan-2  C5    0.020
 0LP  plan-2  HN5   0.020
 0LP  plan-3  C2    0.020
 0LP  plan-3  C1    0.020
 0LP  plan-3  O1B   0.020
 0LP  plan-3  O1A   0.020
 0LP  plan-3  HO1B  0.020
 0LP  plan-4  CAQ   0.020
 0LP  plan-4  CAI   0.020
 0LP  plan-4  CAJ   0.020
 0LP  plan-4  CAX   0.020
 0LP  plan-4  H19   0.020
 0LP  plan-4  H20   0.020

