# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:28:22 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-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(=O)CO)[C@@H](O1)[C@H](O)[C@H](O)CO)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
 MN0  MN0  'methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  43  23  .  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_MN0
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
 MN0  C1    C  C      0   0.399  -2.0212  -2.0534  -1.2718
 MN0  C2    C  CT     0   0.414  -1.5009  -1.8798   0.1911
 MN0  O2    O  O2     0  -0.501  -2.5113  -2.3351   1.0264
 MN0  C3    C  CH2    0  -0.555  -0.1653  -2.5787   0.4581
 MN0  C4    C  CH1    0   0.077   1.0539  -1.8835  -0.1387
 MN0  O4    O  OH1    0  -0.668   2.2543  -2.4256   0.3720
 MN0  C5    C  CH1    0  -0.118   1.0346  -0.4054   0.2275
 MN0  N5    N  NH1    0  -0.642   2.1062   0.2987  -0.4343
 MN0  C6    C  CH1    0   0.045  -0.3174   0.2140  -0.1507
 MN0  O6    O  O2     0  -0.532  -1.3765  -0.4869   0.4583
 MN0  C7    C  CH1    0  -0.027  -0.4420   1.6596   0.3275
 MN0  O7    O  OH1    0  -0.663  -0.3351   1.7463   1.7300
 MN0  C8    C  CH1    0  -0.012  -1.7343   2.3314  -0.1739
 MN0  O8    O  OH1    0  -0.657  -1.8765   2.1918  -1.5690
 MN0  C9    C  CH2    0  -0.159  -1.7741   3.7915   0.2496
 MN0  O9    O  OH1    0  -0.671  -3.0038   4.3490  -0.1514
 MN0  C10   C  C      0   0.505   3.2018   0.7796   0.1816
 MN0  O10   O  O      0  -0.484   3.3670   0.7944   1.3875
 MN0  C11   C  CH2    0  -0.274   4.2419   1.3147  -0.7897
 MN0  O11   O  OH1    0  -0.658   5.2474   1.9621  -0.0678
 MN0  C12   C  CH3    0  -0.428  -2.2913  -2.3080   2.4216
 MN0  O1B   O  OC    -1  -0.593  -1.1442  -2.1115  -2.1570
 MN0  O1A   O  O      0  -0.590  -3.2487  -2.0826  -1.4332
 MN0  H3    H  HCH2   0   0.239   0.0044  -2.6260   1.5384
 MN0  H3A   H  HCH2   0   0.243  -0.2222  -3.6120   0.1038
 MN0  H4    H  HCH1   0   0.212   1.0247  -1.9716  -1.2286
 MN0  HO4   H  HOH1   0   0.449   2.3645  -3.3062   0.0008
 MN0  H5    H  HCH1   0   0.253   1.1863  -0.3040   1.3042
 MN0  HN5   H  HNH1   0   0.394   2.1013   0.2903  -1.4440
 MN0  H6    H  HCH1   0   0.223  -0.4123   0.1966  -1.2434
 MN0  H7    H  HCH1   0   0.237   0.4095   2.2194  -0.0775
 MN0  HO7   H  HOH1   0   0.441  -1.0000   1.1619   2.1121
 MN0  H8    H  HCH1   0   0.230  -2.5947   1.8151   0.2654
 MN0  HO8   H  HOH1   0   0.441  -1.1731   2.6883  -2.0015
 MN0  H9    H  HCH2   0   0.205  -1.6362   3.8564   1.3338
 MN0  H9A   H  HCH2   0   0.185  -0.9218   4.3175  -0.2100
 MN0  HO9   H  HOH1   0   0.454  -3.0208   5.2654   0.1375
 MN0  H11   H  HCH2   0   0.236   4.6239   0.4626  -1.3689
 MN0  H12   H  HCH3   0   0.236  -3.2703  -2.3756   2.8956
 MN0  H12A  H  HCH3   0   0.210  -1.6927  -3.1554   2.7694
 MN0  H12B  H  HCH3   0   0.212  -1.8133  -1.3873   2.7634
 MN0  H19   H  HCH2   0   0.230   3.7445   1.9785  -1.5096
 MN0  H20   H  HOH1   0   0.460   5.9150   2.2521  -0.6956

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
 MN0  C1   C2    single  1.562  0.020  1.562
 MN0  C2   O2    single  1.388  0.020  1.388
 MN0  O2   C12   single  1.413  0.020  1.413
 MN0  C3   C2    single  1.531  0.020  1.531
 MN0  C3   H3    single  0.970  0.020  1.090
 MN0  C3   H3A   single  0.970  0.020  1.090
 MN0  C4   C3    single  1.525  0.020  1.525
 MN0  C4   H4    single  0.970  0.020  1.090
 MN0  O4   C4    single  1.413  0.020  1.413
 MN0  O4   HO4   single  0.850  0.020  0.980
 MN0  C5   C4    single  1.523  0.020  1.523
 MN0  C5   C6    single  1.535  0.020  1.535
 MN0  C5   H5    single  0.970  0.020  1.090
 MN0  N5   C5    single  1.443  0.020  1.443
 MN0  N5   HN5   single  0.860  0.020  1.020
 MN0  C6   C7    single  1.528  0.020  1.528
 MN0  C6   O6    single  1.408  0.020  1.408
 MN0  C6   H6    single  0.970  0.020  1.090
 MN0  O6   C2    single  1.424  0.020  1.424
 MN0  C7   O7    single  1.409  0.020  1.409
 MN0  C7   C8    single  1.540  0.020  1.540
 MN0  C7   H7    single  0.970  0.020  1.090
 MN0  O7   HO7   single  0.850  0.020  0.980
 MN0  C8   H8    single  0.970  0.020  1.090
 MN0  O8   C8    single  1.409  0.020  1.409
 MN0  O8   HO8   single  0.850  0.020  0.980
 MN0  C9   C8    single  1.521  0.020  1.521
 MN0  C9   O9    single  1.408  0.020  1.408
 MN0  C9   H9    single  0.970  0.020  1.090
 MN0  C9   H9A   single  0.970  0.020  1.090
 MN0  O9   HO9   single  0.850  0.020  0.980
 MN0  C10  N5    single  1.346  0.020  1.346
 MN0  C10  O10   double  1.217  0.020  1.217
 MN0  C11  C10   single  1.520  0.020  1.520
 MN0  C11  H11   single  0.970  0.020  1.090
 MN0  O11  C11   single  1.397  0.020  1.397
 MN0  C12  H12   single  0.970  0.020  1.090
 MN0  C12  H12A  single  0.970  0.020  1.090
 MN0  C12  H12B  single  0.970  0.020  1.090
 MN0  O1B  C1    deloc   1.247  0.020  1.247
 MN0  O1A  C1    deloc   1.238  0.020  1.238
 MN0  C11  H19   single  0.970  0.020  1.090
 MN0  O11  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
 MN0  O1A   C1   O1B   127.10  3.000
 MN0  O1A   C1   C2    117.05  3.000
 MN0  O1B   C1   C2    115.81  3.000
 MN0  O6    C2   C3    109.74  3.000
 MN0  O6    C2   O2    105.76  3.000
 MN0  C3    C2   O2    112.36  3.000
 MN0  O6    C2   C1    108.27  3.000
 MN0  C3    C2   C1    113.77  3.000
 MN0  O2    C2   C1    106.53  3.000
 MN0  C12   O2   C2    118.34  3.000
 MN0  H3A   C3   H3    106.68  3.000
 MN0  H3A   C3   C4    110.21  3.000
 MN0  H3    C3   C4    106.37  3.000
 MN0  C4    C3   C2    114.90  3.000
 MN0  H3A   C3   C2    109.24  3.000
 MN0  H3    C3   C2    109.09  3.000
 MN0  H4    C4   C5    108.51  3.000
 MN0  C5    C4   O4    107.23  3.000
 MN0  H4    C4   O4    110.61  3.000
 MN0  C5    C4   C3    109.77  3.000
 MN0  O4    C4   C3    111.28  3.000
 MN0  H4    C4   C3    109.38  3.000
 MN0  HO4   O4   C4    108.00  3.000
 MN0  H5    C5   C6    109.14  3.000
 MN0  H5    C5   N5    107.68  3.000
 MN0  C6    C5   N5    110.14  3.000
 MN0  N5    C5   C4    110.73  3.000
 MN0  H5    C5   C4    108.99  3.000
 MN0  C6    C5   C4    110.10  3.000
 MN0  HN5   N5   C10   117.68  3.000
 MN0  C10   N5   C5    124.69  3.000
 MN0  HN5   N5   C5    116.80  3.000
 MN0  H6    C6   C7    108.65  3.000
 MN0  H6    C6   O6    110.96  3.000
 MN0  C7    C6   O6    105.91  3.000
 MN0  H6    C6   C5    108.38  3.000
 MN0  O6    C6   C5    110.80  3.000
 MN0  C7    C6   C5    112.13  3.000
 MN0  C6    O6   C2    118.12  3.000
 MN0  H7    C7   C8    107.97  3.000
 MN0  H7    C7   O7    106.10  3.000
 MN0  C8    C7   O7    111.15  3.000
 MN0  H7    C7   C6    107.71  3.000
 MN0  C8    C7   C6    112.28  3.000
 MN0  O7    C7   C6    111.32  3.000
 MN0  HO7   O7   C7    107.75  3.000
 MN0  H8    C8   C9    108.68  3.000
 MN0  C9    C8   O8    111.60  3.000
 MN0  H8    C8   O8    105.73  3.000
 MN0  C9    C8   C7    110.49  3.000
 MN0  O8    C8   C7    111.33  3.000
 MN0  H8    C8   C7    108.83  3.000
 MN0  HO8   O8   C8    108.64  3.000
 MN0  H9A   C9   H9    106.70  3.000
 MN0  H9A   C9   O9    111.57  3.000
 MN0  H9    C9   O9    111.62  3.000
 MN0  H9A   C9   C8    108.78  3.000
 MN0  H9    C9   C8    109.23  3.000
 MN0  O9    C9   C8    108.88  3.000
 MN0  HO9   O9   C9    107.90  3.000
 MN0  C11   C10  O10   122.40  3.000
 MN0  C11   C10  N5    112.98  3.000
 MN0  O10   C10  N5    124.62  3.000
 MN0  H19   C11  H11   106.30  3.000
 MN0  H19   C11  O11   112.63  3.000
 MN0  H11   C11  O11   112.43  3.000
 MN0  H19   C11  C10   108.76  3.000
 MN0  O11   C11  C10   108.99  3.000
 MN0  H11   C11  C10   107.55  3.000
 MN0  H20   O11  C11   107.59  3.000
 MN0  H12B  C12  H12A  108.30  3.000
 MN0  H12B  C12  H12   108.01  3.000
 MN0  H12A  C12  H12   107.76  3.000
 MN0  H12B  C12  O2    113.17  3.000
 MN0  H12A  C12  O2    112.60  3.000
 MN0  H12   C12  O2    106.77  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
 MN0  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 MN0  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 MN0  CONST_03  HN5  N5   C10  O10  180.00   0.0  0
 MN0  Var_01    H12  C12  O2   C2   161.52  30.0  3
 MN0  Var_02    O11  C11  C10  N5   171.57  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
 MN0  chir_01  C2  O2  C3  O6  positiv
 MN0  chir_02  C4  O4  C5  C3  positiv
 MN0  chir_03  C5  N5  C6  C4  negativ
 MN0  chir_04  C6  O6  C7  C5  negativ
 MN0  chir_05  C7  O7  C6  C8  negativ
 MN0  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
 MN0  plan-1  C5   0.020
 MN0  plan-1  N5   0.020
 MN0  plan-1  C10  0.020
 MN0  plan-1  O10  0.020
 MN0  plan-1  C11  0.020
 MN0  plan-1  HN5  0.020
 MN0  plan-2  C1   0.020
 MN0  plan-2  C2   0.020
 MN0  plan-2  O1B  0.020
 MN0  plan-2  O1A  0.020

