# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 06:25:03 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: (1R)-4-(acetylamino)-3-amino-1,5-anhydro-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](N)C[C@H](O[C@H]1[C@H](O)[C@H](O)CO)[S](O)(=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
 E3M  E3M  (1R)-4-(acetylamino)-3-amino-1,5-anhydro-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol  D-saccharide  40  21  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E3M
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
 E3M  C1   C  CH1    0  -0.179   6.0541  23.8927   9.8061
 E3M  C8   C  CH2    0  -0.198   9.4437  19.6975  11.1908
 E3M  C2   C  CH2    0  -0.448   6.5292  25.3047   9.5310
 E3M  C3   C  CH1    0  -0.092   7.4949  25.7498  10.6209
 E3M  C4   C  CH1    0  -0.104   8.6139  24.7034  10.7732
 E3M  C10  C  CH3    0  -0.779  11.4304  25.7804  13.0772
 E3M  C5   C  CH1    0   0.057   8.0093  23.3038  10.9717
 E3M  C6   C  CH1    0   0.014   9.0615  22.2043  11.0390
 E3M  C7   C  CH1    0  -0.001   8.4445  20.8322  11.3538
 E3M  N3   N  NH2    0  -0.782   7.9613  27.0946  10.3477
 E3M  N4   N  NH1    0  -0.635   9.4706  25.0474  11.8817
 E3M  O9   O  O      0  -0.491  11.3970  25.3431  10.7278
 E3M  O6   O  OH1    0  -0.673   9.7608  22.1811   9.8163
 E3M  O7   O  OH1    0  -0.673   7.9494  20.9197  12.6750
 E3M  O5   O  O2     0  -0.494   7.1317  23.0034   9.9074
 E3M  S1   S  S      0   1.412   4.9753  23.2578   8.4840
 E3M  OS1  O  OS     0  -0.757   3.8933  24.2568   8.4045
 E3M  OS2  O  OS     0  -0.756   5.8155  23.1996   7.2740
 E3M  H1   H  HCH1   0   0.234   5.4485  23.8790  10.7262
 E3M  H19  H  HCH2   0   0.201   9.6463  19.5588  10.1221
 E3M  H3   H  HCH2   0   0.231   7.0319  25.3379   8.5588
 E3M  H2   H  HCH2   0   0.251   5.6813  25.9883   9.4923
 E3M  H4   H  HCH1   0   0.225   6.9428  25.7805  11.5696
 E3M  H8   H  HCH1   0   0.256   9.2193  24.7072   9.8649
 E3M  H12  H  HCH3   0   0.261  12.3926  25.2814  13.1806
 E3M  H10  H  HCH3   0   0.266  11.6229  26.8540  13.0498
 E3M  H11  H  HCH3   0   0.248  10.8293  25.5675  13.9593
 E3M  H13  H  HCH1   0   0.224   7.4563  23.3060  11.9246
 E3M  H14  H  HCH1   0   0.227   9.7293  22.4582  11.8712
 E3M  H16  H  HCH1   0   0.217   7.6338  20.6293  10.6410
 E3M  H5   H  HNH2   0   0.346   8.5793  27.4044  11.0876
 E3M  H6   H  HNH2   0   0.338   8.5155  27.0963   9.4982
 E3M  H9   H  HNH1   0   0.397   9.0367  25.1120  12.7900
 E3M  H15  H  HOH1   0   0.453  10.6490  21.8539   9.9853
 E3M  H17  H  HOH1   0   0.452   7.3710  20.1681  12.8347
 E3M  H20  H  HOH1   0   0.455  11.2469  19.2693  11.7652
 E3M  C9   C  C      0   0.511  10.7772  25.3649  11.7812
 E3M  O8   O  OH1    0  -0.671  10.6182  19.9805  11.9169
 E3M  H18  H  HCH2   0   0.211   8.9677  18.7684  11.5359
 E3M  OS3  O  OS    -1  -0.753   4.5235  21.9350   8.9504

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
 E3M  OS2  S1   deloc   1.474  0.020  1.474
 E3M  OS1  S1   deloc   1.475  0.020  1.475
 E3M  S1   OS3  deloc   1.474  0.020  1.474
 E3M  S1   C1   single  1.821  0.020  1.821
 E3M  C2   C1   single  1.515  0.020  1.515
 E3M  C2   C3   single  1.523  0.020  1.523
 E3M  O6   C6   single  1.409  0.020  1.409
 E3M  C1   O5   single  1.401  0.020  1.401
 E3M  O5   C5   single  1.412  0.020  1.412
 E3M  N3   C3   single  1.449  0.020  1.449
 E3M  C3   C4   single  1.540  0.020  1.540
 E3M  O9   C9   double  1.222  0.020  1.222
 E3M  C4   C5   single  1.537  0.020  1.537
 E3M  C4   N4   single  1.443  0.020  1.443
 E3M  C6   C5   single  1.523  0.020  1.523
 E3M  C6   C7   single  1.537  0.020  1.537
 E3M  C7   C8   single  1.521  0.020  1.521
 E3M  C7   O7   single  1.414  0.020  1.414
 E3M  C8   O8   single  1.410  0.020  1.410
 E3M  C9   N4   single  1.348  0.020  1.348
 E3M  C9   C10  single  1.510  0.020  1.510
 E3M  C1   H1   single  0.970  0.020  1.090
 E3M  C8   H18  single  0.970  0.020  1.090
 E3M  C8   H19  single  0.970  0.020  1.090
 E3M  C2   H3   single  0.970  0.020  1.090
 E3M  C2   H2   single  0.970  0.020  1.090
 E3M  C3   H4   single  0.970  0.020  1.090
 E3M  C4   H8   single  0.970  0.020  1.090
 E3M  C10  H12  single  0.970  0.020  1.090
 E3M  C10  H10  single  0.970  0.020  1.090
 E3M  C10  H11  single  0.970  0.020  1.090
 E3M  C5   H13  single  0.970  0.020  1.090
 E3M  C6   H14  single  0.970  0.020  1.090
 E3M  C7   H16  single  0.970  0.020  1.090
 E3M  N3   H5   single  0.890  0.020  1.040
 E3M  N3   H6   single  0.890  0.020  1.040
 E3M  N4   H9   single  0.860  0.020  1.020
 E3M  O6   H15  single  0.850  0.020  0.980
 E3M  O7   H17  single  0.850  0.020  0.980
 E3M  O8   H20  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
 E3M  H1   C1   S1   106.05  3.000
 E3M  H1   C1   O5   110.78  3.000
 E3M  S1   C1   O5   106.67  3.000
 E3M  H1   C1   C2   109.61  3.000
 E3M  O5   C1   C2   111.32  3.000
 E3M  S1   C1   C2   112.27  3.000
 E3M  H19  C8   H18  106.20  3.000
 E3M  H19  C8   O8   111.93  3.000
 E3M  H18  C8   O8   111.64  3.000
 E3M  H19  C8   C7   108.68  3.000
 E3M  H18  C8   C7   108.20  3.000
 E3M  O8   C8   C7   110.03  3.000
 E3M  H2   C2   H3   107.86  3.000
 E3M  H2   C2   C3   109.60  3.000
 E3M  H3   C2   C3   109.60  3.000
 E3M  H2   C2   C1   110.31  3.000
 E3M  H3   C2   C1   109.48  3.000
 E3M  C3   C2   C1   109.96  3.000
 E3M  H4   C3   N3   107.38  3.000
 E3M  H4   C3   C4   107.39  3.000
 E3M  N3   C3   C4   114.54  3.000
 E3M  H4   C3   C2   107.92  3.000
 E3M  C4   C3   C2   109.46  3.000
 E3M  N3   C3   C2   109.90  3.000
 E3M  H8   C4   N4   108.01  3.000
 E3M  H8   C4   C5   109.19  3.000
 E3M  N4   C4   C5   110.57  3.000
 E3M  H8   C4   C3   108.57  3.000
 E3M  N4   C4   C3   110.21  3.000
 E3M  C5   C4   C3   110.22  3.000
 E3M  H11  C10  H10  108.08  3.000
 E3M  H11  C10  H12  108.75  3.000
 E3M  H10  C10  H12  107.31  3.000
 E3M  H11  C10  C9   113.76  3.000
 E3M  H10  C10  C9   109.00  3.000
 E3M  H12  C10  C9   109.74  3.000
 E3M  H13  C5   O5   109.91  3.000
 E3M  H13  C5   C6   108.05  3.000
 E3M  O5   C5   C6   108.01  3.000
 E3M  H13  C5   C4   107.89  3.000
 E3M  C6   C5   C4   113.02  3.000
 E3M  O5   C5   C4   109.93  3.000
 E3M  H14  C6   O6   111.11  3.000
 E3M  H14  C6   C7   107.19  3.000
 E3M  O6   C6   C7   111.24  3.000
 E3M  H14  C6   C5   106.68  3.000
 E3M  C7   C6   C5   112.09  3.000
 E3M  O6   C6   C5   108.44  3.000
 E3M  H16  C7   O7   111.07  3.000
 E3M  H16  C7   C6   109.16  3.000
 E3M  O7   C7   C6   106.07  3.000
 E3M  H16  C7   C8   106.11  3.000
 E3M  O7   C7   C8   112.12  3.000
 E3M  C6   C7   C8   112.36  3.000
 E3M  H6   N3   H5   106.15  3.000
 E3M  H6   N3   C3   109.59  3.000
 E3M  H5   N3   C3   110.03  3.000
 E3M  H9   N4   C9   117.97  3.000
 E3M  H9   N4   C4   116.86  3.000
 E3M  C9   N4   C4   125.05  3.000
 E3M  H15  O6   C6   108.15  3.000
 E3M  H17  O7   C7   108.52  3.000
 E3M  C5   O5   C1   113.43  3.000
 E3M  OS2  S1   OS1  113.61  3.000
 E3M  OS1  S1   OS3  113.59  3.000
 E3M  OS2  S1   OS3  113.52  3.000
 E3M  OS3  S1   C1   105.36  3.000
 E3M  OS1  S1   C1   103.75  3.000
 E3M  OS2  S1   C1   105.79  3.000
 E3M  O9   C9   N4   123.47  3.000
 E3M  N4   C9   C10  114.84  3.000
 E3M  O9   C9   C10  121.69  3.000
 E3M  H20  O8   C8   108.37  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
 E3M  CONST_01  O9   C9   N4  C4     0.00   0.0  0
 E3M  CONST_02  C10  C9   N4  C4   180.00   0.0  0
 E3M  CONST_03  H9   N4   C9  C10    0.00   0.0  0
 E3M  Var_01    H12  C10  C9  N4   134.57  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
 E3M  chir_01  C1  S1  C2  O5  positiv
 E3M  chir_02  C3  N3  C4  C2  positiv
 E3M  chir_03  C4  N4  C5  C3  negativ
 E3M  chir_04  C5  O5  C6  C4  negativ
 E3M  chir_05  C6  O6  C5  C7  negativ
 E3M  chir_06  C7  O7  C6  C8  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
 E3M  plan-1  C4   0.020
 E3M  plan-1  C10  0.020
 E3M  plan-1  N4   0.020
 E3M  plan-1  O9   0.020
 E3M  plan-1  H9   0.020
 E3M  plan-1  C9   0.020

