# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:58:23 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)COC(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
 MJJ  MJJ  'methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  47  25  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJJ
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
 MJJ  O4   O  OH1    0  -0.665   4.1212  -0.8721  -0.2942
 MJJ  C4   C  CH1    0   0.070   3.0051  -0.0992   0.0807
 MJJ  C5   C  CH1    0  -0.117   1.7554  -0.9277  -0.1917
 MJJ  N5   N  NH1    0  -0.631   1.7345  -2.1175   0.6235
 MJJ  C10  C  C      0   0.521   1.9180  -3.3691   0.1621
 MJJ  O10  O  O      0  -0.501   2.0438  -3.6399  -1.0236
 MJJ  C11  C  CH3    0  -0.783   1.9681  -4.4356   1.2290
 MJJ  C3   C  CH2    0  -0.541   2.9251   1.2092  -0.6922
 MJJ  C2   C  CT     0   0.415   1.6524   1.9699  -0.3345
 MJJ  O2   O  O2     0  -0.518   1.4595   3.1295  -1.0823
 MJJ  CM2  C  CH3    0  -0.423   1.5485   3.0353  -2.4910
 MJJ  C1   C  C      0   0.372   1.6501   2.4977   1.1412
 MJJ  O1   O  O      0  -0.580   0.5459   2.5623   1.7019
 MJJ  O3   O  OC    -1  -0.591   2.7567   2.8473   1.5896
 MJJ  O6   O  O2     0  -0.523   0.5391   1.1409  -0.5940
 MJJ  C6   C  CH1    0   0.027   0.5001  -0.0890   0.0891
 MJJ  C7   C  CH1    0  -0.009  -0.7777  -0.7829  -0.3857
 MJJ  O7   O  OH1    0  -0.665  -0.8268  -0.8461  -1.7901
 MJJ  C8   C  CH1    0  -0.042  -2.0257  -0.1093   0.2158
 MJJ  O8   O  OH1    0  -0.655  -2.0404  -0.2563   1.6155
 MJJ  C9   C  CH2    0  -0.180  -3.2942  -0.6570  -0.4171
 MJJ  O9   O  O2     0  -0.450  -4.3924   0.0355   0.1824
 MJJ  CA9  C  C      0   0.573  -5.6197  -0.3082  -0.1810
 MJJ  OA9  O  O      0  -0.463  -5.8578  -1.1747  -0.9871
 MJJ  CM9  C  CH3    0  -0.775  -6.6715   0.4999   0.5210
 MJJ  H1   H  HOH1   0   0.450   4.9149  -0.3745  -0.0740
 MJJ  H2   H  HCH1   0   0.201   3.0433   0.1254   1.1576
 MJJ  H3   H  HCH1   0   0.257   1.7584  -1.2391  -1.2383
 MJJ  H4   H  HNH1   0   0.396   1.6861  -1.9871   1.6224
 MJJ  H5   H  HCH3   0   0.248   1.5758  -4.1067   2.1896
 MJJ  H6   H  HCH3   0   0.262   1.4076  -5.3097   0.9022
 MJJ  H7   H  HCH3   0   0.269   3.0034  -4.7476   1.3752
 MJJ  H8   H  HCH2   0   0.246   3.7963   1.8297  -0.4762
 MJJ  H9   H  HCH2   0   0.241   2.9434   0.9709  -1.7604
 MJJ  H10  H  HCH3   0   0.214   2.5790   2.9189  -2.8378
 MJJ  H11  H  HCH3   0   0.215   0.9509   2.2177  -2.9010
 MJJ  H12  H  HCH3   0   0.239   1.1630   3.9716  -2.8922
 MJJ  H14  H  HCH1   0   0.230   0.4259   0.0760   1.1720
 MJJ  H15  H  HCH1   0   0.243  -0.7599  -1.8213  -0.0358
 MJJ  H16  H  HOH1   0   0.446  -0.6476   0.0385  -2.1305
 MJJ  H17  H  HCH1   0   0.245  -1.9755   0.9683   0.0304
 MJJ  H18  H  HOH1   0   0.444  -2.0979  -1.1947   1.8290
 MJJ  H19  H  HCH2   0   0.247  -3.2947  -0.4948  -1.4951
 MJJ  H20  H  HCH2   0   0.232  -3.3842  -1.7336  -0.2371
 MJJ  H21  H  HCH3   0   0.260  -6.2562   1.2234   1.2170
 MJJ  H22  H  HCH3   0   0.275  -7.2744   1.0263  -0.2188
 MJJ  H23  H  HCH3   0   0.274  -7.3399  -0.1703   1.0611

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
 MJJ  O4   C4   single  1.408  0.020  1.408
 MJJ  C3   C4   single  1.522  0.020  1.522
 MJJ  C3   C2   single  1.525  0.020  1.525
 MJJ  O2   C2   single  1.393  0.020  1.393
 MJJ  O2   CM2  single  1.415  0.020  1.415
 MJJ  C4   C5   single  1.524  0.020  1.524
 MJJ  O10  C10  double  1.223  0.020  1.223
 MJJ  C2   O6   single  1.412  0.020  1.412
 MJJ  C2   C1   single  1.567  0.020  1.567
 MJJ  C5   N5   single  1.442  0.020  1.442
 MJJ  C5   C6   single  1.536  0.020  1.536
 MJJ  C10  N5   single  1.346  0.020  1.346
 MJJ  C10  C11  single  1.509  0.020  1.509
 MJJ  O1   C1   deloc   1.240  0.020  1.240
 MJJ  O6   C6   single  1.407  0.020  1.407
 MJJ  C1   O3   deloc   1.244  0.020  1.244
 MJJ  C6   C7   single  1.530  0.020  1.530
 MJJ  O7   C7   single  1.407  0.020  1.407
 MJJ  C7   C8   single  1.541  0.020  1.541
 MJJ  C8   O8   single  1.407  0.020  1.407
 MJJ  C8   C9   single  1.520  0.020  1.520
 MJJ  C9   O9   single  1.430  0.020  1.430
 MJJ  O9   CA9  single  1.325  0.020  1.325
 MJJ  CA9  OA9  double  1.207  0.020  1.207
 MJJ  CA9  CM9  single  1.501  0.020  1.501
 MJJ  O4   H1   single  0.850  0.020  0.980
 MJJ  C4   H2   single  0.970  0.020  1.090
 MJJ  C5   H3   single  0.970  0.020  1.090
 MJJ  N5   H4   single  0.860  0.020  1.020
 MJJ  C11  H5   single  0.970  0.020  1.090
 MJJ  C11  H6   single  0.970  0.020  1.090
 MJJ  C11  H7   single  0.970  0.020  1.090
 MJJ  C3   H8   single  0.970  0.020  1.090
 MJJ  C3   H9   single  0.970  0.020  1.090
 MJJ  CM2  H10  single  0.970  0.020  1.090
 MJJ  CM2  H11  single  0.970  0.020  1.090
 MJJ  CM2  H12  single  0.970  0.020  1.090
 MJJ  C6   H14  single  0.970  0.020  1.090
 MJJ  C7   H15  single  0.970  0.020  1.090
 MJJ  O7   H16  single  0.850  0.020  0.980
 MJJ  C8   H17  single  0.970  0.020  1.090
 MJJ  O8   H18  single  0.850  0.020  0.980
 MJJ  C9   H19  single  0.970  0.020  1.090
 MJJ  C9   H20  single  0.970  0.020  1.090
 MJJ  CM9  H21  single  0.970  0.020  1.090
 MJJ  CM9  H22  single  0.970  0.020  1.090
 MJJ  CM9  H23  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
 MJJ  H1   O4   C4   108.00  3.000
 MJJ  H2   C4   C3   108.86  3.000
 MJJ  H2   C4   C5   108.32  3.000
 MJJ  C3   C4   C5   109.48  3.000
 MJJ  H2   C4   O4   110.18  3.000
 MJJ  C5   C4   O4   107.70  3.000
 MJJ  C3   C4   O4   112.23  3.000
 MJJ  H3   C5   C6   109.46  3.000
 MJJ  H3   C5   N5   107.84  3.000
 MJJ  C6   C5   N5   109.59  3.000
 MJJ  H3   C5   C4   108.91  3.000
 MJJ  C6   C5   C4   109.93  3.000
 MJJ  N5   C5   C4   111.06  3.000
 MJJ  H4   N5   C10  117.78  3.000
 MJJ  H4   N5   C5   116.98  3.000
 MJJ  C10  N5   C5   124.83  3.000
 MJJ  C11  C10  O10  121.71  3.000
 MJJ  C11  C10  N5   114.78  3.000
 MJJ  O10  C10  N5   123.51  3.000
 MJJ  H7   C11  H6   107.40  3.000
 MJJ  H7   C11  H5   108.07  3.000
 MJJ  H6   C11  H5   108.78  3.000
 MJJ  H7   C11  C10  109.16  3.000
 MJJ  H6   C11  C10  109.76  3.000
 MJJ  H5   C11  C10  113.48  3.000
 MJJ  H9   C3   H8   107.68  3.000
 MJJ  H9   C3   C2   110.57  3.000
 MJJ  H8   C3   C2   109.64  3.000
 MJJ  H9   C3   C4   107.91  3.000
 MJJ  H8   C3   C4   110.27  3.000
 MJJ  C2   C3   C4   110.71  3.000
 MJJ  O6   C2   C1   111.69  3.000
 MJJ  C1   C2   O2   103.00  3.000
 MJJ  O6   C2   O2   106.31  3.000
 MJJ  C1   C2   C3   112.95  3.000
 MJJ  O6   C2   C3   108.78  3.000
 MJJ  O2   C2   C3   113.88  3.000
 MJJ  CM2  O2   C2   118.06  3.000
 MJJ  H12  CM2  H11  108.15  3.000
 MJJ  H12  CM2  H10  107.96  3.000
 MJJ  H11  CM2  H10  108.47  3.000
 MJJ  H12  CM2  O2   106.70  3.000
 MJJ  H11  CM2  O2   112.89  3.000
 MJJ  H10  CM2  O2   112.47  3.000
 MJJ  O3   C1   O1   127.91  3.000
 MJJ  O3   C1   C2   115.63  3.000
 MJJ  O1   C1   C2   116.40  3.000
 MJJ  C6   O6   C2   116.47  3.000
 MJJ  H14  C6   C7   108.54  3.000
 MJJ  H14  C6   O6   110.44  3.000
 MJJ  C7   C6   O6   105.60  3.000
 MJJ  H14  C6   C5   108.52  3.000
 MJJ  C7   C6   C5   112.23  3.000
 MJJ  O6   C6   C5   111.46  3.000
 MJJ  H15  C7   C8   107.62  3.000
 MJJ  H15  C7   O7   106.07  3.000
 MJJ  C8   C7   O7   112.41  3.000
 MJJ  H15  C7   C6   108.49  3.000
 MJJ  C8   C7   C6   110.93  3.000
 MJJ  O7   C7   C6   111.07  3.000
 MJJ  H16  O7   C7   107.73  3.000
 MJJ  H17  C8   C9   108.82  3.000
 MJJ  H17  C8   O8   105.77  3.000
 MJJ  C9   C8   O8   111.58  3.000
 MJJ  H17  C8   C7   109.10  3.000
 MJJ  C9   C8   C7   110.86  3.000
 MJJ  O8   C8   C7   110.55  3.000
 MJJ  H18  O8   C8   108.82  3.000
 MJJ  H20  C9   H19  107.98  3.000
 MJJ  H20  C9   O9   110.12  3.000
 MJJ  H19  C9   O9   110.00  3.000
 MJJ  H20  C9   C8   110.76  3.000
 MJJ  H19  C9   C8   111.01  3.000
 MJJ  O9   C9   C8   106.97  3.000
 MJJ  CA9  O9   C9   118.08  3.000
 MJJ  CM9  CA9  OA9  124.10  3.000
 MJJ  CM9  CA9  O9   112.40  3.000
 MJJ  OA9  CA9  O9   123.50  3.000
 MJJ  H23  CM9  H22  107.10  3.000
 MJJ  H23  CM9  H21  109.05  3.000
 MJJ  H22  CM9  H21  108.94  3.000
 MJJ  H23  CM9  CA9  109.30  3.000
 MJJ  H22  CM9  CA9  109.29  3.000
 MJJ  H21  CM9  CA9  112.98  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
 MJJ  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 MJJ  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 MJJ  CONST_03  H4   N5   C10  O10  180.00   0.0  0
 MJJ  Var_01    H10  CM2  O2   C2   -73.71  30.0  3
 MJJ  Var_02    OA9  CA9  O9   C9     0.16  30.0  3
 MJJ  Var_03    H5   C11  C10  N5    16.30  30.0  3
 MJJ  Var_04    H21  CM9  CA9  O9    -0.63  30.0  3
 MJJ  Var_05    H19  C9   O9   CA9   61.62  30.0  1

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
 MJJ  chir_01  C4  O4  C3  C5  negativ
 MJJ  chir_02  C5  N5  C6  C4  negativ
 MJJ  chir_03  C2  O6  C1  C3  negativ
 MJJ  chir_04  C6  O6  C5  C7  positiv
 MJJ  chir_05  C7  O7  C6  C8  negativ
 MJJ  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
 MJJ  plan-1  C5   0.020
 MJJ  plan-1  N5   0.020
 MJJ  plan-1  C10  0.020
 MJJ  plan-1  O10  0.020
 MJJ  plan-1  C11  0.020
 MJJ  plan-1  H4   0.020
 MJJ  plan-2  C2   0.020
 MJJ  plan-2  C1   0.020
 MJJ  plan-2  O1   0.020
 MJJ  plan-2  O3   0.020
 MJJ  plan-3  O9   0.020
 MJJ  plan-3  CA9  0.020
 MJJ  plan-3  OA9  0.020
 MJJ  plan-3  CM9  0.020

