# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:06:39 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-(acetylamino)-3,4,5-trideoxy-D-manno-non-2-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](CCC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 NAY  NAY  '5-(acetylamino)-3,4,5-trideoxy-D-manno-non-2-ulosonic acid'  ligand  38  20  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NAY
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
 NAY  C1    C  C      0   0.346  -0.2424   0.2272   5.1541
 NAY  O1A   O  OC    -1  -0.583  -0.7552  -0.2798   6.1610
 NAY  O1B   O  O      0  -0.579   0.5753   1.1606   5.0835
 NAY  C2    C  C      0   0.235  -0.6801  -0.3893   3.7913
 NAY  O2    O  O      0  -0.399  -1.4167  -1.3479   3.7609
 NAY  C3    C  CH2    0  -0.551  -0.1461   0.2549   2.5408
 NAY  C4    C  CH2    0  -0.415  -0.6372  -0.3806   1.2515
 NAY  C5    C  CH1    0  -0.114  -0.2153   0.4187   0.0150
 NAY  N     N  NH1    0  -0.640   1.2054   0.7281  -0.0074
 NAY  C10   C  C      0   0.522   2.2071  -0.1674  -0.0358
 NAY  C11   C  CH3    0  -0.772   3.5972   0.4211  -0.0050
 NAY  O10   O  O      0  -0.501   2.0287  -1.3779  -0.0825
 NAY  O6    O  OH1    0  -0.669  -2.0678  -0.4927  -1.2700
 NAY  C6    C  CH1    0   0.033  -0.6764  -0.2481  -1.2960
 NAY  C7    C  CH1    0  -0.019  -0.2872   0.5726  -2.5324
 NAY  O7    O  OH1    0  -0.668  -0.9155   1.8385  -2.5278
 NAY  C8    C  CH1    0  -0.029  -0.5554  -0.1873  -3.8426
 NAY  O8    O  OH1    0  -0.659   0.0623  -1.4542  -3.8279
 NAY  C9    C  CH2    0  -0.156  -0.1202   0.6326  -5.0484
 NAY  O9    O  OH1    0  -0.671  -0.4342  -0.0820  -6.2211
 NAY  HC31  H  HCH2   0   0.260   0.9458   0.2394   2.6055
 NAY  HC32  H  HCH2   0   0.256  -0.4023   1.3197   2.5757
 NAY  HC41  H  HCH2   0   0.234  -1.7269  -0.4279   1.2643
 NAY  HC42  H  HCH2   0   0.232  -0.2840  -1.4097   1.1731
 NAY  HC5   H  HCH1   0   0.251  -0.7033   1.3966   0.0781
 NAY  HN    H  HNH1   0   0.403   1.4527   1.7024   0.0321
 NAY  H111  H  HCH3   0   0.266   4.1192   0.0639   0.8827
 NAY  H112  H  HCH3   0   0.264   4.1564   0.0707  -0.8724
 NAY  H113  H  HCH3   0   0.248   3.6174   1.5092   0.0011
 NAY  HO6   H  HOH1   0   0.443  -2.5257   0.3105  -0.9995
 NAY  HC6   H  HCH1   0   0.239  -0.2029  -1.2272  -1.3716
 NAY  HC7   H  HCH1   0   0.231   0.7880   0.7777  -2.4813
 NAY  HO7   H  HOH1   0   0.444  -1.8455   1.7282  -2.7543
 NAY  HC8   H  HCH1   0   0.228  -1.6309  -0.3841  -3.9245
 NAY  HO8   H  HOH1   0   0.444   1.0179  -1.3295  -3.8213
 NAY  HC91  H  HCH2   0   0.205  -0.6206   1.6060  -5.0240
 NAY  HC92  H  HCH2   0   0.188   0.9610   0.8294  -4.9726
 NAY  HO9   H  HOH1   0   0.455  -0.2368   0.4836  -6.9725

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
 NAY  C1   O1A   deloc   1.238  0.020  1.238
 NAY  C1   O1B   deloc   1.243  0.020  1.243
 NAY  C1   C2    single  1.558  0.020  1.558
 NAY  C2   O2    double  1.209  0.020  1.209
 NAY  C2   C3    single  1.505  0.020  1.505
 NAY  C3   C4    single  1.519  0.020  1.519
 NAY  C3   HC31  single  0.970  0.020  1.090
 NAY  C3   HC32  single  0.970  0.020  1.090
 NAY  C4   C5    single  1.532  0.020  1.532
 NAY  C4   HC41  single  0.970  0.020  1.090
 NAY  C4   HC42  single  0.970  0.020  1.090
 NAY  C5   N     single  1.454  0.020  1.454
 NAY  C5   C6    single  1.541  0.020  1.541
 NAY  C5   HC5   single  0.970  0.020  1.090
 NAY  N    C10   single  1.344  0.020  1.344
 NAY  N    HN    single  0.860  0.020  1.020
 NAY  C10  C11   single  1.510  0.020  1.510
 NAY  C10  O10   double  1.224  0.020  1.224
 NAY  C11  H111  single  0.970  0.020  1.090
 NAY  C11  H112  single  0.970  0.020  1.090
 NAY  C11  H113  single  0.970  0.020  1.090
 NAY  O6   C6    single  1.413  0.020  1.413
 NAY  O6   HO6   single  0.850  0.020  0.980
 NAY  C6   C7    single  1.534  0.020  1.534
 NAY  C6   HC6   single  0.970  0.020  1.090
 NAY  C7   O7    single  1.413  0.020  1.413
 NAY  C7   C8    single  1.538  0.020  1.538
 NAY  C7   HC7   single  0.970  0.020  1.090
 NAY  O7   HO7   single  0.850  0.020  0.980
 NAY  C8   O8    single  1.410  0.020  1.410
 NAY  C8   C9    single  1.522  0.020  1.522
 NAY  C8   HC8   single  0.970  0.020  1.090
 NAY  O8   HO8   single  0.850  0.020  0.980
 NAY  C9   O9    single  1.409  0.020  1.409
 NAY  C9   HC91  single  0.970  0.020  1.090
 NAY  C9   HC92  single  0.970  0.020  1.090
 NAY  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
 NAY  C2    C1   O1B   115.60  3.000
 NAY  C2    C1   O1A   115.64  3.000
 NAY  O1B   C1   O1A   128.76  3.000
 NAY  C3    C2   O2    122.32  3.000
 NAY  C3    C2   C1    117.24  3.000
 NAY  O2    C2   C1    120.43  3.000
 NAY  HC32  C3   HC31  104.20  3.000
 NAY  HC32  C3   C4    110.98  3.000
 NAY  HC31  C3   C4    111.53  3.000
 NAY  HC32  C3   C2    107.85  3.000
 NAY  HC31  C3   C2    107.40  3.000
 NAY  C4    C3   C2    114.30  3.000
 NAY  HC42  C4   HC41  106.46  3.000
 NAY  HC42  C4   C5    110.19  3.000
 NAY  HC41  C4   C5    107.89  3.000
 NAY  HC42  C4   C3    110.55  3.000
 NAY  HC41  C4   C3    109.35  3.000
 NAY  C5    C4   C3    112.20  3.000
 NAY  HC5   C5   C6    107.59  3.000
 NAY  HC5   C5   N     104.26  3.000
 NAY  C6    C5   N     111.79  3.000
 NAY  HC5   C5   C4    107.27  3.000
 NAY  C6    C5   C4    112.24  3.000
 NAY  N     C5   C4    113.12  3.000
 NAY  HN    N    C10   117.57  3.000
 NAY  HN    N    C5    116.47  3.000
 NAY  C10   N    C5    125.93  3.000
 NAY  O10   C10  C11   121.35  3.000
 NAY  O10   C10  N     123.43  3.000
 NAY  C11   C10  N     115.22  3.000
 NAY  H113  C11  H112  108.44  3.000
 NAY  H113  C11  H111  108.31  3.000
 NAY  H112  C11  H111  107.29  3.000
 NAY  H113  C11  C10   114.00  3.000
 NAY  H112  C11  C10   109.32  3.000
 NAY  H111  C11  C10   109.26  3.000
 NAY  HO6   O6   C6    109.20  3.000
 NAY  HC6   C6   C7    108.32  3.000
 NAY  HC6   C6   O6    105.87  3.000
 NAY  C7    C6   O6    110.93  3.000
 NAY  HC6   C6   C5    108.52  3.000
 NAY  C7    C6   C5    112.22  3.000
 NAY  O6    C6   C5    110.72  3.000
 NAY  HC7   C7   C8    107.66  3.000
 NAY  HC7   C7   O7    105.57  3.000
 NAY  C8    C7   O7    111.58  3.000
 NAY  HC7   C7   C6    108.15  3.000
 NAY  C8    C7   C6    112.21  3.000
 NAY  O7    C7   C6    111.33  3.000
 NAY  HO7   O7   C7    109.01  3.000
 NAY  HC8   C8   C9    108.54  3.000
 NAY  HC8   C8   O8    105.63  3.000
 NAY  C9    C8   O8    111.54  3.000
 NAY  HC8   C8   C7    108.87  3.000
 NAY  C9    C8   C7    111.03  3.000
 NAY  O8    C8   C7    111.02  3.000
 NAY  HO8   O8   C8    108.56  3.000
 NAY  HC92  C9   HC91  106.75  3.000
 NAY  HC92  C9   O9    111.51  3.000
 NAY  HC91  C9   O9    111.58  3.000
 NAY  HC92  C9   C8    108.81  3.000
 NAY  HC91  C9   C8    109.31  3.000
 NAY  O9    C9   C8    108.82  3.000
 NAY  HO9   O9   C9    107.85  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
 NAY  CONST_01  C11   C10  N    C5    180.00   0.0  0
 NAY  CONST_02  O10   C10  N    C5      0.00   0.0  0
 NAY  CONST_03  HN    N    C10  C11     0.00   0.0  0
 NAY  Var_01    C4    C3   C2   C1   -178.80  30.0  3
 NAY  Var_02    O2    C2   C1   O1A    -3.90  30.0  2
 NAY  Var_03    C5    C4   C3   C2    172.53  30.0  3
 NAY  Var_04    H111  C11  C10  N     119.27  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
 NAY  chir_01  C5  C4  N   C6  negativ
 NAY  chir_02  C6  O6  C5  C7  positiv
 NAY  chir_03  C7  O7  C6  C8  negativ
 NAY  chir_04  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
 NAY  plan-1  C5   0.020
 NAY  plan-1  N    0.020
 NAY  plan-1  C10  0.020
 NAY  plan-1  C11  0.020
 NAY  plan-1  O10  0.020
 NAY  plan-1  HN   0.020
 NAY  plan-2  C1   0.020
 NAY  plan-2  C2   0.020
 NAY  plan-2  O2   0.020
 NAY  plan-2  C3   0.020
 NAY  plan-3  C1   0.020
 NAY  plan-3  O1A  0.020
 NAY  plan-3  O1B  0.020
 NAY  plan-3  C2   0.020

