# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 20:50:29 2020
#   Inital geometry file: a 171 line input string
#   Ligand name: (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@@H](N)CO[C@H]1O[C@H](CO)[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
 N57  N57  '(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside'  ligand  82  33  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N57
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
 N57  C17  C  CH3   0  -0.662  15.8013   1.6291  -0.0592
 N57  C16  C  CH2   0  -0.419  14.6823   0.5970  -0.0560
 N57  C15  C  CH2   0  -0.406  13.2947   1.2269  -0.0305
 N57  C14  C  CH2   0  -0.411  12.1685   0.2013  -0.0267
 N57  C13  C  CH2   0  -0.411  10.7791   0.8266  -0.0021
 N57  C12  C  CH2   0  -0.411   9.6584  -0.2052   0.0028
 N57  C11  C  CH2   0  -0.412   8.2650   0.4110   0.0230
 N57  C10  C  CH2   0  -0.411   7.1520  -0.6290   0.0292
 N57  C9   C  CH2   0  -0.412   5.7535  -0.0243   0.0383
 N57  C8   C  CH2   0  -0.411   4.6500  -1.0744   0.0458
 N57  C7   C  CH2   0  -0.412   3.2454  -0.4840   0.0333
 N57  C6   C  CH2   0  -0.413   2.1547  -1.5469   0.0458
 N57  C5   C  CH2   0  -0.413   0.7433  -0.9748  -0.0090
 N57  C4   C  CH2   0  -0.445  -0.3209  -2.0639   0.0211
 N57  C3   C  CH1   0   0.000  -1.7518  -1.5460  -0.0884
 N57  O32  O  OH1   0  -0.660  -1.9681  -0.8559  -1.3010
 N57  C2   C  CH1   0  -0.023  -2.7713  -2.6847   0.0985
 N57  O1   O  OH1   0  -0.665  -2.6783  -3.2317   1.4003
 N57  C1   C  CH1   0  -0.136  -4.2267  -2.3269  -0.2661
 N57  N    N  NH2   0  -0.781  -5.1198  -3.4728  -0.1891
 N57  C    C  CH2   0  -0.147  -4.7671  -1.1923   0.5897
 N57  OC1  O  O2    0  -0.488  -6.0091  -0.7757   0.0630
 N57  CG1  C  CH1   0   0.251  -6.6945   0.1335   0.8542
 N57  OG   O  O2    0  -0.505  -6.0035   1.3420   1.0194
 N57  CG   C  CH1   0  -0.012  -5.7772   2.0662  -0.1803
 N57  CG5  C  CH2   0  -0.159  -4.9425   3.2811   0.1613
 N57  OG6  O  OH1   0  -0.667  -3.6630   2.8471   0.5593
 N57  CG4  C  CH1   0  -0.004  -7.0901   2.4289  -0.8593
 N57  OG5  O  OH1   0  -0.673  -7.7884   3.3455  -0.0518
 N57  CG3  C  CH1   0   0.004  -7.8925   1.1517  -1.0935
 N57  OG4  O  OH1   0  -0.678  -9.1327   1.5193  -1.6506
 N57  CG2  C  CH1   0  -0.017  -8.0633   0.3972   0.2189
 N57  OG3  O  OH1   0  -0.669  -8.7741  -0.7855  -0.0491
 N57  H1   H  HCH3  0   0.216  15.7339   2.2795  -0.9331
 N57  H2   H  HCH3  0   0.216  15.7530   2.2638   0.8276
 N57  H3   H  HCH3  0   0.225  16.7844   1.1570  -0.0739
 N57  H4   H  HCH2  0   0.210  14.7711  -0.0447  -0.9384
 N57  H5   H  HCH2  0   0.210  14.7940  -0.0644   0.8092
 N57  H6   H  HCH2  0   0.205  13.2048   1.8697   0.8526
 N57  H7   H  HCH2  0   0.205  13.1816   1.8888  -0.8966
 N57  H8   H  HCH2  0   0.206  12.2606  -0.4417  -0.9094
 N57  H9   H  HCH2  0   0.206  12.2831  -0.4600   0.8396
 N57  H10  H  HCH2  0   0.206  10.6854   1.4699   0.8802
 N57  H11  H  HCH2  0   0.206  10.6626   1.4865  -0.8692
 N57  H12  H  HCH2  0   0.206   9.7560  -0.8499  -0.8780
 N57  H13  H  HCH2  0   0.206   9.7757  -0.8636   0.8709
 N57  H14  H  HCH2  0   0.206   8.1652   1.0568   0.9027
 N57  H15  H  HCH2  0   0.206   8.1457   1.0670  -0.8467
 N57  H16  H  HCH2  0   0.206   7.2588  -1.2786  -0.8470
 N57  H17  H  HCH2  0   0.206   7.2701  -1.2812   0.9019
 N57  H18  H  HCH2  0   0.206   5.6436   0.6267   0.9129
 N57  H19  H  HCH2  0   0.206   5.6333   0.6246  -0.8366
 N57  H20  H  HCH2  0   0.206   4.7712  -1.7328  -0.8218
 N57  H21  H  HCH2  0   0.206   4.7657  -1.7157   0.9269
 N57  H22  H  HCH2  0   0.207   3.1202   0.1787   0.8968
 N57  H23  H  HCH2  0   0.206   3.1268   0.1502  -0.8525
 N57  H24  H  HCH2  0   0.207   2.2997  -2.2235  -0.8039
 N57  H25  H  HCH2  0   0.207   2.2618  -2.1666   0.9432
 N57  H26  H  HCH2  0   0.210   0.5927  -0.2936   0.8360
 N57  H27  H  HCH2  0   0.213   0.6358  -0.3682  -0.9129
 N57  H28  H  HCH2  0   0.215  -0.1431  -2.7766  -0.7949
 N57  H29  H  HCH2  0   0.228  -0.2222  -2.6394   0.9451
 N57  H30  H  HCH1  0   0.219  -1.9130  -0.7995   0.7006
 N57  H31  H  HOH1  0   0.442  -1.7514  -1.4508  -2.0275
 N57  H32  H  HCH1  0   0.226  -2.4826  -3.5024  -0.5759
 N57  H33  H  HOH1  0   0.445  -2.7417  -2.5197   2.0456
 N57  H34  H  HCH1  0   0.232  -4.2223  -1.9835  -1.3042
 N57  H35  H  HNH2  0   0.343  -4.8103  -4.1814  -0.8440
 N57  H36  H  HNH2  0   0.332  -5.0359  -3.8978   0.7277
 N57  H38  H  HCH2  0   0.195  -4.8958  -1.5239   1.6315
 N57  H39  H  HCH2  0   0.227  -4.0561  -0.3594   0.6011
 N57  H40  H  HCH1  0   0.225  -6.8194  -0.2602   1.8747
 N57  H41  H  HCH1  0   0.233  -5.2076   1.4578  -0.8969
 N57  H42  H  HCH2  0   0.199  -4.8947   3.9194  -0.7310
 N57  H43  H  HCH2  0   0.205  -5.4357   3.8638   0.9478
 N57  H44  H  HOH1  0   0.455  -3.1599   3.6199   0.8305
 N57  H45  H  HCH1  0   0.232  -6.8491   2.8695  -1.8386
 N57  H46  H  HOH1  0   0.451  -8.6593   3.4806  -0.4405
 N57  H47  H  HCH1  0   0.218  -7.3228   0.5240  -1.7942
 N57  H48  H  HOH1  0   0.453  -9.6993   0.7404  -1.6662
 N57  H49  H  HCH1  0   0.227  -8.6165   1.0394   0.9162
 N57  H50  H  HOH1  0   0.458  -9.1542  -1.1138   0.7712

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
 N57  C17  C16  single  1.522  0.020  1.522
 N57  C16  C15  single  1.524  0.020  1.524
 N57  C15  C14  single  1.523  0.020  1.523
 N57  C13  C14  single  1.524  0.020  1.524
 N57  C13  C12  single  1.523  0.020  1.523
 N57  C12  C11  single  1.524  0.020  1.524
 N57  C11  C10  single  1.523  0.020  1.523
 N57  C10  C9   single  1.524  0.020  1.524
 N57  C9   C8   single  1.523  0.020  1.523
 N57  C8   C7   single  1.524  0.020  1.524
 N57  C7   C6   single  1.523  0.020  1.523
 N57  C6   C5   single  1.524  0.020  1.524
 N57  O32  C3   single  1.412  0.020  1.412
 N57  C5   C4   single  1.523  0.020  1.523
 N57  C3   C4   single  1.526  0.020  1.526
 N57  C3   C2   single  1.540  0.020  1.540
 N57  C2   O1   single  1.415  0.020  1.415
 N57  C2   C1   single  1.542  0.020  1.542
 N57  OG3  CG2  single  1.406  0.020  1.406
 N57  OG4  CG3  single  1.408  0.020  1.408
 N57  N    C1   single  1.455  0.020  1.455
 N57  CG3  CG2  single  1.523  0.020  1.523
 N57  CG3  CG4  single  1.526  0.020  1.526
 N57  C1   C    single  1.520  0.020  1.520
 N57  CG2  CG1  single  1.532  0.020  1.532
 N57  OC1  C    single  1.412  0.020  1.412
 N57  OC1  CG1  single  1.387  0.020  1.387
 N57  CG1  OG   single  1.402  0.020  1.402
 N57  CG4  OG5  single  1.407  0.020  1.407
 N57  CG4  CG   single  1.522  0.020  1.522
 N57  CG   OG   single  1.419  0.020  1.419
 N57  CG   CG5  single  1.513  0.020  1.513
 N57  CG5  OG6  single  1.409  0.020  1.409
 N57  C17  H1   single  0.970  0.020  1.090
 N57  C17  H2   single  0.970  0.020  1.090
 N57  C17  H3   single  0.970  0.020  1.090
 N57  C16  H4   single  0.970  0.020  1.090
 N57  C16  H5   single  0.970  0.020  1.090
 N57  C15  H6   single  0.970  0.020  1.090
 N57  C15  H7   single  0.970  0.020  1.090
 N57  C14  H8   single  0.970  0.020  1.090
 N57  C14  H9   single  0.970  0.020  1.090
 N57  C13  H10  single  0.970  0.020  1.090
 N57  C13  H11  single  0.970  0.020  1.090
 N57  C12  H12  single  0.970  0.020  1.090
 N57  C12  H13  single  0.970  0.020  1.090
 N57  C11  H14  single  0.970  0.020  1.090
 N57  C11  H15  single  0.970  0.020  1.090
 N57  C10  H16  single  0.970  0.020  1.090
 N57  C10  H17  single  0.970  0.020  1.090
 N57  C9   H18  single  0.970  0.020  1.090
 N57  C9   H19  single  0.970  0.020  1.090
 N57  C8   H20  single  0.970  0.020  1.090
 N57  C8   H21  single  0.970  0.020  1.090
 N57  C7   H22  single  0.970  0.020  1.090
 N57  C7   H23  single  0.970  0.020  1.090
 N57  C6   H24  single  0.970  0.020  1.090
 N57  C6   H25  single  0.970  0.020  1.090
 N57  C5   H26  single  0.970  0.020  1.090
 N57  C5   H27  single  0.970  0.020  1.090
 N57  C4   H28  single  0.970  0.020  1.090
 N57  C4   H29  single  0.970  0.020  1.090
 N57  C3   H30  single  0.970  0.020  1.090
 N57  O32  H31  single  0.850  0.020  0.980
 N57  C2   H32  single  0.970  0.020  1.090
 N57  O1   H33  single  0.850  0.020  0.980
 N57  C1   H34  single  0.970  0.020  1.090
 N57  N    H35  single  0.890  0.020  1.040
 N57  N    H36  single  0.890  0.020  1.040
 N57  C    H38  single  0.970  0.020  1.090
 N57  C    H39  single  0.970  0.020  1.090
 N57  CG1  H40  single  0.970  0.020  1.090
 N57  CG   H41  single  0.970  0.020  1.090
 N57  CG5  H42  single  0.970  0.020  1.090
 N57  CG5  H43  single  0.970  0.020  1.090
 N57  OG6  H44  single  0.850  0.020  0.980
 N57  CG4  H45  single  0.970  0.020  1.090
 N57  OG5  H46  single  0.850  0.020  0.980
 N57  CG3  H47  single  0.970  0.020  1.090
 N57  OG4  H48  single  0.850  0.020  0.980
 N57  CG2  H49  single  0.970  0.020  1.090
 N57  OG3  H50  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
 N57  H3   C17  H2   107.61  3.000
 N57  H3   C17  H1   107.62  3.000
 N57  H2   C17  H1   107.53  3.000
 N57  H3   C17  C16  111.66  3.000
 N57  H2   C17  C16  111.10  3.000
 N57  H1   C17  C16  111.12  3.000
 N57  H5   C16  H4   105.94  3.000
 N57  H5   C16  C15  109.23  3.000
 N57  H4   C16  C15  109.25  3.000
 N57  H5   C16  C17  109.65  3.000
 N57  H4   C16  C17  109.64  3.000
 N57  C15  C16  C17  112.90  3.000
 N57  H7   C15  H6   105.91  3.000
 N57  H7   C15  C14  109.41  3.000
 N57  H6   C15  C14  109.41  3.000
 N57  H7   C15  C16  109.29  3.000
 N57  H6   C15  C16  109.30  3.000
 N57  C14  C15  C16  113.26  3.000
 N57  H9   C14  H8   105.90  3.000
 N57  H9   C14  C13  109.28  3.000
 N57  H8   C14  C13  109.30  3.000
 N57  H9   C14  C15  109.32  3.000
 N57  H8   C14  C15  109.32  3.000
 N57  C13  C14  C15  113.44  3.000
 N57  H11  C13  H10  105.93  3.000
 N57  H11  C13  C12  109.40  3.000
 N57  H10  C13  C12  109.40  3.000
 N57  H11  C13  C14  109.35  3.000
 N57  H10  C13  C14  109.39  3.000
 N57  C12  C13  C14  113.13  3.000
 N57  H13  C12  H12  105.88  3.000
 N57  H13  C12  C11  109.29  3.000
 N57  H12  C12  C11  109.27  3.000
 N57  H13  C12  C13  109.31  3.000
 N57  H12  C12  C13  109.29  3.000
 N57  C11  C12  C13  113.51  3.000
 N57  H15  C11  H14  105.93  3.000
 N57  H15  C11  C10  109.41  3.000
 N57  H14  C11  C10  109.42  3.000
 N57  H15  C11  C12  109.34  3.000
 N57  H14  C11  C12  109.41  3.000
 N57  C10  C11  C12  113.09  3.000
 N57  H17  C10  H16  105.87  3.000
 N57  H17  C10  C9   109.29  3.000
 N57  H16  C10  C9   109.24  3.000
 N57  H17  C10  C11  109.32  3.000
 N57  H16  C10  C11  109.29  3.000
 N57  C9   C10  C11  113.56  3.000
 N57  H19  C9   H18  105.93  3.000
 N57  H19  C9   C8   109.43  3.000
 N57  H18  C9   C8   109.45  3.000
 N57  H19  C9   C10  109.32  3.000
 N57  H18  C9   C10  109.42  3.000
 N57  C8   C9   C10  113.04  3.000
 N57  H21  C8   H20  105.86  3.000
 N57  H21  C8   C7   109.31  3.000
 N57  H20  C8   C7   109.16  3.000
 N57  H21  C8   C9   109.33  3.000
 N57  H20  C8   C9   109.28  3.000
 N57  C7   C8   C9   113.62  3.000
 N57  H23  C7   H22  105.94  3.000
 N57  H23  C7   C6   109.46  3.000
 N57  H22  C7   C6   109.50  3.000
 N57  H23  C7   C8   109.30  3.000
 N57  H22  C7   C8   109.46  3.000
 N57  C6   C7   C8   112.94  3.000
 N57  H25  C6   H24  105.84  3.000
 N57  H25  C6   C5   109.41  3.000
 N57  H24  C6   C5   109.06  3.000
 N57  H25  C6   C7   109.35  3.000
 N57  H24  C6   C7   109.25  3.000
 N57  C5   C6   C7   113.64  3.000
 N57  H27  C5   H26  106.20  3.000
 N57  H27  C5   C4   110.14  3.000
 N57  H26  C5   C4   109.47  3.000
 N57  H27  C5   C6   109.20  3.000
 N57  H26  C5   C6   109.45  3.000
 N57  C4   C5   C6   112.21  3.000
 N57  H29  C4   H28  105.77  3.000
 N57  H29  C4   C3   108.91  3.000
 N57  H28  C4   C3   108.59  3.000
 N57  H29  C4   C5   109.28  3.000
 N57  H28  C4   C5   109.65  3.000
 N57  C3   C4   C5   114.28  3.000
 N57  H30  C3   C2   108.56  3.000
 N57  H30  C3   O32  105.21  3.000
 N57  C2   C3   O32  111.36  3.000
 N57  H30  C3   C4   108.48  3.000
 N57  C2   C3   C4   111.18  3.000
 N57  O32  C3   C4   111.80  3.000
 N57  H31  O32  C3   108.13  3.000
 N57  H32  C2   C1   105.99  3.000
 N57  H32  C2   O1   105.05  3.000
 N57  C1   C2   O1   111.66  3.000
 N57  H32  C2   C3   107.57  3.000
 N57  C1   C2   C3   115.12  3.000
 N57  O1   C2   C3   110.73  3.000
 N57  H33  O1   C2   109.04  3.000
 N57  H34  C1   C    107.54  3.000
 N57  H34  C1   N    107.46  3.000
 N57  C    C1   N    109.86  3.000
 N57  H34  C1   C2   107.07  3.000
 N57  C    C1   C2   112.05  3.000
 N57  N    C1   C2   112.59  3.000
 N57  H36  N    H35  105.43  3.000
 N57  H36  N    C1   109.09  3.000
 N57  H35  N    C1   109.22  3.000
 N57  H39  C    H38  107.16  3.000
 N57  H39  C    OC1  110.52  3.000
 N57  H38  C    OC1  109.82  3.000
 N57  H39  C    C1   110.03  3.000
 N57  H38  C    C1   110.45  3.000
 N57  OC1  C    C1   108.84  3.000
 N57  CG1  OC1  C    114.55  3.000
 N57  H40  CG1  CG2  110.16  3.000
 N57  H40  CG1  OG   104.77  3.000
 N57  CG2  CG1  OG   109.93  3.000
 N57  H40  CG1  OC1  110.52  3.000
 N57  OG   CG1  OC1  112.88  3.000
 N57  CG2  CG1  OC1  108.54  3.000
 N57  CG   OG   CG1  114.76  3.000
 N57  H41  CG   CG4  106.74  3.000
 N57  H41  CG   CG5  107.80  3.000
 N57  CG4  CG   CG5  112.66  3.000
 N57  H41  CG   OG   110.57  3.000
 N57  CG5  CG   OG   107.87  3.000
 N57  CG4  CG   OG   111.17  3.000
 N57  H43  CG5  H42  107.08  3.000
 N57  H43  CG5  OG6  111.70  3.000
 N57  H42  CG5  OG6  111.66  3.000
 N57  H43  CG5  CG   109.92  3.000
 N57  H42  CG5  CG   107.89  3.000
 N57  OG6  CG5  CG   108.51  3.000
 N57  H44  OG6  CG5  107.90  3.000
 N57  H45  CG4  CG3  108.28  3.000
 N57  H45  CG4  OG5  111.01  3.000
 N57  CG3  CG4  OG5  111.86  3.000
 N57  H45  CG4  CG   107.66  3.000
 N57  OG5  CG4  CG   109.11  3.000
 N57  CG3  CG4  CG   108.81  3.000
 N57  H46  OG5  CG4  107.97  3.000
 N57  H47  CG3  CG2  108.92  3.000
 N57  H47  CG3  OG4  110.68  3.000
 N57  CG2  CG3  OG4  111.80  3.000
 N57  H47  CG3  CG4  107.64  3.000
 N57  CG2  CG3  CG4  109.95  3.000
 N57  OG4  CG3  CG4  107.77  3.000
 N57  H48  OG4  CG3  108.26  3.000
 N57  H49  CG2  OG3  111.01  3.000
 N57  H49  CG2  CG3  108.30  3.000
 N57  OG3  CG2  CG3  108.00  3.000
 N57  H49  CG2  CG1  106.72  3.000
 N57  CG3  CG2  CG1  110.02  3.000
 N57  OG3  CG2  CG1  112.71  3.000
 N57  H50  OG3  CG2  108.93  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
 N57  Var_01  H38  C    OC1  CG1    50.77  30.0  3
 N57  Var_02  C14  C15  C16  C17  -179.98  30.0  3
 N57  Var_03  C13  C14  C15  C16  -179.97  30.0  3
 N57  Var_04  C12  C13  C14  C15  -179.95  30.0  1
 N57  Var_05  C11  C12  C13  C14  -179.82  30.0  3
 N57  Var_06  C10  C11  C12  C13  -179.94  30.0  3
 N57  Var_07  C9   C10  C11  C12  -179.54  30.0  3
 N57  Var_08  C8   C9   C10  C11  -179.94  30.0  3
 N57  Var_09  C7   C8   C9   C10  -179.11  30.0  3
 N57  Var_10  C6   C7   C8   C9   -179.80  30.0  3
 N57  Var_11  C5   C6   C7   C8   -178.25  30.0  3
 N57  Var_12  C4   C5   C6   C7   -179.35  30.0  3
 N57  Var_13  C3   C4   C5   C6   -177.66  30.0  3
 N57  Var_14  H1   C17  C16  C15   -60.03  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
 N57  chir_01  C3   O32  C4   C2   positiv
 N57  chir_02  C2   O1   C3   C1   positiv
 N57  chir_03  C1   N    C2   C    positiv
 N57  chir_04  CG1  OC1  OG   CG2  negativ
 N57  chir_05  CG   OG   CG5  CG4  positiv
 N57  chir_06  CG4  OG5  CG   CG3  negativ
 N57  chir_07  CG3  OG4  CG2  CG4  positiv
 N57  chir_08  CG2  OG3  CG3  CG1  positiv

