# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:40:41 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: methyl 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)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
 MNA  MNA  'methyl 5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  42  22  .  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_MNA
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
 MNA  C1    C  C      0   0.345   2.5743  -1.0963   0.5079
 MNA  C2    C  CT     0   0.433   2.0921   0.3755   0.2671
 MNA  C3    C  CH2    0  -0.519   2.1449   0.7731  -1.2015
 MNA  C4    C  CH1    0   0.062   1.1065   0.0040  -2.0048
 MNA  C5    C  CH1    0  -0.111  -0.2772   0.2160  -1.3994
 MNA  C6    C  CH1    0   0.030  -0.2568  -0.0961   0.1060
 MNA  C7    C  CH1    0  -0.007  -1.5412   0.3626   0.7985
 MNA  C8    C  CH1    0  -0.024  -1.6527  -0.2182   2.2208
 MNA  C9    C  CH2    0  -0.160  -2.8405   0.3685   2.9668
 MNA  C11   C  CH3    0  -0.789  -3.0286  -1.2637  -3.5370
 MNA  N5    N  NH1    0  -0.625  -1.2587  -0.6151  -2.0525
 MNA  O1A   O  O      0  -0.573   1.9684  -1.7671   1.3567
 MNA  O1B   O  OC    -1  -0.596   3.5636  -1.4394  -0.1675
 MNA  O2    O  O2     0  -0.511   2.9169   1.2687   0.9493
 MNA  O4    O  OH1    0  -0.666   1.0564   0.4220  -3.3493
 MNA  O6    O  O2     0  -0.520   0.7863   0.5927   0.7533
 MNA  O7    O  OH1    0  -0.668  -1.6389   1.7679   0.7858
 MNA  O8    O  OH1    0  -0.660  -1.7186  -1.6263   2.1688
 MNA  O9    O  OH1    0  -0.672  -2.8675  -0.1716   4.2690
 MNA  O10   O  O      0  -0.497  -2.4052   1.0169  -3.1245
 MNA  H31   H  HCH2   0   0.230   1.9416   1.8461  -1.2891
 MNA  H32   H  HCH2   0   0.244   3.1437   0.5861  -1.5979
 MNA  H4    H  HCH1   0   0.200   1.3434  -1.0702  -1.9527
 MNA  H5    H  HCH1   0   0.254  -0.5719   1.2575  -1.5469
 MNA  H6    H  HCH1   0   0.230  -0.1485  -1.1786   0.2401
 MNA  H7    H  HCH1   0   0.235  -2.3954  -0.0101   0.2211
 MNA  H8    H  HCH1   0   0.233  -0.7380   0.0165   2.7756
 MNA  H91   H  HCH2   0   0.206  -2.7540   1.4590   2.9868
 MNA  H92   H  HCH2   0   0.184  -3.7634   0.1309   2.4135
 MNA  H111  H  HCH3   0   0.258  -3.7864  -0.8382  -4.1895
 MNA  H112  H  HCH3   0   0.263  -2.3939  -1.9281  -4.1247
 MNA  H113  H  HCH3   0   0.263  -3.5219  -1.8735  -2.7790
 MNA  H121  H  HCH3   0   0.229   3.6828   1.8926   2.7039
 MNA  H122  H  HCH3   0   0.216   2.1708   0.9928   2.8858
 MNA  H123  H  HCH3   0   0.208   3.6830   0.1352   2.5354
 MNA  HN5   H  HNH1   0   0.395  -1.1390  -1.6135  -1.9702
 MNA  HO4   H  HOH1   0   0.450   1.8775   0.1551  -3.7739
 MNA  HO7   H  HOH1   0   0.442  -0.8050   2.1172   1.1224
 MNA  HO8   H  HOH1   0   0.441  -2.5616  -1.8765   1.7741
 MNA  HO9   H  HOH1   0   0.454  -3.5850   0.2519   4.7479
 MNA  C10   C  C      0   0.508  -2.2082  -0.1675  -2.8981
 MNA  C12   C  CH3    0  -0.415   3.1099   1.0444   2.3313

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
 MNA  C1   C2    single  1.567  0.020  1.567
 MNA  C1   O1A   deloc   1.240  0.020  1.240
 MNA  C1   O1B   deloc   1.246  0.020  1.246
 MNA  C2   C3    single  1.522  0.020  1.522
 MNA  C2   O2    single  1.394  0.020  1.394
 MNA  C2   O6    single  1.410  0.020  1.410
 MNA  C3   C4    single  1.522  0.020  1.522
 MNA  C3   H31   single  0.970  0.020  1.090
 MNA  C3   H32   single  0.970  0.020  1.090
 MNA  C4   C5    single  1.525  0.020  1.525
 MNA  C4   O4    single  1.409  0.020  1.409
 MNA  C4   H4    single  0.970  0.020  1.090
 MNA  C5   C6    single  1.538  0.020  1.538
 MNA  C5   N5    single  1.442  0.020  1.442
 MNA  C5   H5    single  0.970  0.020  1.090
 MNA  C6   C7    single  1.530  0.020  1.530
 MNA  C6   O6    single  1.408  0.020  1.408
 MNA  C6   H6    single  0.970  0.020  1.090
 MNA  C7   C8    single  1.540  0.020  1.540
 MNA  C7   O7    single  1.409  0.020  1.409
 MNA  C7   H7    single  0.970  0.020  1.090
 MNA  C8   C9    single  1.521  0.020  1.521
 MNA  C8   O8    single  1.411  0.020  1.411
 MNA  C8   H8    single  0.970  0.020  1.090
 MNA  C9   O9    single  1.410  0.020  1.410
 MNA  C9   H91   single  0.970  0.020  1.090
 MNA  C9   H92   single  0.970  0.020  1.090
 MNA  C10  C11   single  1.511  0.020  1.511
 MNA  C10  N5    single  1.348  0.020  1.348
 MNA  C10  O10   double  1.222  0.020  1.222
 MNA  C11  H111  single  0.970  0.020  1.090
 MNA  C11  H112  single  0.970  0.020  1.090
 MNA  C11  H113  single  0.970  0.020  1.090
 MNA  C12  O2    single  1.413  0.020  1.413
 MNA  C12  H121  single  0.970  0.020  1.090
 MNA  C12  H122  single  0.970  0.020  1.090
 MNA  C12  H123  single  0.970  0.020  1.090
 MNA  N5   HN5   single  0.860  0.020  1.020
 MNA  O4   HO4   single  0.850  0.020  0.980
 MNA  O7   HO7   single  0.850  0.020  0.980
 MNA  O8   HO8   single  0.850  0.020  0.980
 MNA  O9   HO9   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
 MNA  O1B   C1   O1A   127.59  3.000
 MNA  O1B   C1   C2    114.81  3.000
 MNA  O1A   C1   C2    117.57  3.000
 MNA  O6    C2   O2    106.28  3.000
 MNA  O6    C2   C3    108.94  3.000
 MNA  O2    C2   C3    106.51  3.000
 MNA  O6    C2   C1    112.12  3.000
 MNA  O2    C2   C1    110.14  3.000
 MNA  C3    C2   C1    112.50  3.000
 MNA  H32   C3   H31   107.99  3.000
 MNA  H32   C3   C4    110.27  3.000
 MNA  H31   C3   C4    109.04  3.000
 MNA  H32   C3   C2    109.73  3.000
 MNA  H31   C3   C2    109.05  3.000
 MNA  C4    C3   C2    110.71  3.000
 MNA  H4    C4   O4    110.01  3.000
 MNA  H4    C4   C5    108.18  3.000
 MNA  O4    C4   C5    107.77  3.000
 MNA  H4    C4   C3    108.74  3.000
 MNA  O4    C4   C3    112.22  3.000
 MNA  C5    C4   C3    109.84  3.000
 MNA  H5    C5   N5    107.74  3.000
 MNA  H5    C5   C6    109.23  3.000
 MNA  N5    C5   C6    109.60  3.000
 MNA  H5    C5   C4    108.88  3.000
 MNA  N5    C5   C4    110.95  3.000
 MNA  C6    C5   C4    110.39  3.000
 MNA  H6    C6   O6    110.72  3.000
 MNA  H6    C6   C7    108.89  3.000
 MNA  O6    C6   C7    105.51  3.000
 MNA  H6    C6   C5    108.76  3.000
 MNA  O6    C6   C5    111.15  3.000
 MNA  C7    C6   C5    111.79  3.000
 MNA  H7    C7   O7    106.28  3.000
 MNA  H7    C7   C8    107.56  3.000
 MNA  O7    C7   C8    112.30  3.000
 MNA  H7    C7   C6    108.30  3.000
 MNA  O7    C7   C6    110.69  3.000
 MNA  C8    C7   C6    111.45  3.000
 MNA  H8    C8   O8    105.76  3.000
 MNA  H8    C8   C9    108.73  3.000
 MNA  O8    C8   C9    111.51  3.000
 MNA  H8    C8   C7    109.06  3.000
 MNA  O8    C8   C7    110.23  3.000
 MNA  C9    C8   C7    111.35  3.000
 MNA  H92   C9   H91   106.88  3.000
 MNA  H92   C9   O9    111.42  3.000
 MNA  H91   C9   O9    111.50  3.000
 MNA  H92   C9   C8    108.94  3.000
 MNA  H91   C9   C8    109.38  3.000
 MNA  O9    C9   C8    108.68  3.000
 MNA  H113  C11  H112  107.28  3.000
 MNA  H113  C11  H111  108.71  3.000
 MNA  H112  C11  H111  108.71  3.000
 MNA  H113  C11  C10   110.94  3.000
 MNA  H112  C11  C10   110.72  3.000
 MNA  H111  C11  C10   110.39  3.000
 MNA  HN5   N5   C10   117.60  3.000
 MNA  HN5   N5   C5    116.90  3.000
 MNA  C10   N5   C5    124.89  3.000
 MNA  C12   O2   C2    117.23  3.000
 MNA  HO4   O4   C4    107.97  3.000
 MNA  C6    O6   C2    116.89  3.000
 MNA  HO7   O7   C7    107.34  3.000
 MNA  HO8   O8   C8    108.37  3.000
 MNA  HO9   O9   C9    107.80  3.000
 MNA  O10   C10  N5    123.48  3.000
 MNA  O10   C10  C11   122.50  3.000
 MNA  N5    C10  C11   114.01  3.000
 MNA  H123  C12  H122  108.46  3.000
 MNA  H123  C12  H121  107.93  3.000
 MNA  H122  C12  H121  108.39  3.000
 MNA  H123  C12  O2    112.70  3.000
 MNA  H122  C12  O2    112.75  3.000
 MNA  H121  C12  O2    106.42  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
 MNA  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 MNA  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 MNA  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 MNA  Var_01    H121  C12  O2   C2   -173.93  30.0  3
 MNA  Var_02    H111  C11  C10  N5    178.87  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
 MNA  chir_01  C2  C3  O2  O6  negativ
 MNA  chir_02  C4  O4  C5  C3  positiv
 MNA  chir_03  C5  N5  C6  C4  negativ
 MNA  chir_04  C6  O6  C7  C5  negativ
 MNA  chir_05  C7  O7  C6  C8  negativ
 MNA  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
 MNA  plan-1  C5   0.020
 MNA  plan-1  C11  0.020
 MNA  plan-1  N5   0.020
 MNA  plan-1  O10  0.020
 MNA  plan-1  HN5  0.020
 MNA  plan-1  C10  0.020
 MNA  plan-2  C1   0.020
 MNA  plan-2  C2   0.020
 MNA  plan-2  O1A  0.020
 MNA  plan-2  O1B  0.020

