# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:45:46 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-(acetylamino)-2,3,5-trideoxy-D-manno-non-4-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]([C@@H](O)[C@H](O)[C@H](O)CO)C(=O)CCC(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
 NAV  NAV  '5-(acetylamino)-2,3,5-trideoxy-D-manno-non-4-ulosonic acid'  ligand  38  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NAV
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
 NAV  C1    C  C      0   0.417  -1.1084   0.2228   5.0169
 NAV  O1A   O  OC    -1  -0.627  -1.4572  -0.5523   5.9309
 NAV  O1B   O  O      0  -0.608  -1.3173   1.4510   4.9682
 NAV  C2    C  CH2    0  -0.585  -0.3207  -0.4171   3.8586
 NAV  C3    C  CH2    0  -0.567  -0.2007   0.4521   2.6236
 NAV  C4    C  C      0   0.430   0.6257  -0.1223   1.5118
 NAV  C5    C  CH1    0  -0.200   0.5308   0.5973   0.1586
 NAV  N2    N  NH1    0  -0.643   1.8446   0.9223  -0.3505
 NAV  C10   C  C      0   0.527   2.7067   0.1185  -1.0061
 NAV  C11   C  CH3    0  -0.774   4.0553   0.7402  -1.2826
 NAV  O10   O  O      0  -0.493   2.4444  -1.0144  -1.3811
 NAV  O6    O  OH1    0  -0.662  -1.6023  -0.4653  -0.1720
 NAV  C6    C  CH1    0   0.018  -0.3544  -0.2354  -0.7895
 NAV  C7    C  CH1    0  -0.038  -0.5059   0.4278  -2.1622
 NAV  O7    O  OH1    0  -0.665  -1.1518   1.6795  -2.0554
 NAV  C8    C  CH1    0  -0.030  -1.2086  -0.4933  -3.1740
 NAV  O8    O  OH1    0  -0.656  -0.6070  -1.7661  -3.2094
 NAV  C9    C  CH2    0  -0.151  -1.2452   0.1473  -4.5536
 NAV  O9    O  OH1    0  -0.670  -1.9870  -0.6824  -5.4157
 NAV  O4    O  O      0  -0.392   1.3608  -1.0713   1.6459
 NAV  HC21  H  HCH2   0   0.226  -0.7858  -1.3724   3.6004
 NAV  HC22  H  HCH2   0   0.236   0.6757  -0.6730   4.2336
 NAV  HC31  H  HCH2   0   0.270   0.2551   1.4191   2.8698
 NAV  HC32  H  HCH2   0   0.252  -1.1842   0.7155   2.2253
 NAV  HC5   H  HCH1   0   0.279   0.0340   1.5597   0.3154
 NAV  HN2   H  HNH1   0   0.407   2.1860   1.8310  -0.0848
 NAV  H111  H  HCH3   0   0.264   4.2825   0.6515  -2.3443
 NAV  H112  H  HCH3   0   0.249   4.1289   1.7883  -0.9992
 NAV  H113  H  HCH3   0   0.268   4.8212   0.1866  -0.7386
 NAV  HO6   H  HOH1   0   0.443  -2.0478   0.3763  -0.0212
 NAV  HC6   H  HCH1   0   0.264   0.0950  -1.2167  -0.9195
 NAV  HC7   H  HCH1   0   0.241   0.4948   0.6457  -2.5501
 NAV  HO7   H  HOH1   0   0.449  -2.1053   1.5479  -2.0187
 NAV  HC8   H  HCH1   0   0.231  -2.2390  -0.6649  -2.8396
 NAV  HO8   H  HOH1   0   0.442   0.3219  -1.6626  -3.4457
 NAV  HC91  H  HCH2   0   0.203  -1.6868   1.1471  -4.4786
 NAV  HC92  H  HCH2   0   0.191  -0.2117   0.2834  -4.9084
 NAV  HO9   H  HOH1   0   0.455  -2.0303  -0.2540  -6.2750

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
 NAV  C1   O1A   deloc   1.248  0.020  1.248
 NAV  C1   O1B   deloc   1.247  0.020  1.247
 NAV  C1   C2    single  1.540  0.020  1.540
 NAV  C2   C3    single  1.515  0.020  1.515
 NAV  C2   HC21  single  0.970  0.020  1.090
 NAV  C2   HC22  single  0.970  0.020  1.090
 NAV  C3   C4    single  1.500  0.020  1.500
 NAV  C3   HC31  single  0.970  0.020  1.090
 NAV  C3   HC32  single  0.970  0.020  1.090
 NAV  C4   C5    single  1.536  0.020  1.536
 NAV  C4   O4    double  1.208  0.020  1.208
 NAV  C5   N2    single  1.446  0.020  1.446
 NAV  C5   C6    single  1.541  0.020  1.541
 NAV  C5   HC5   single  0.970  0.020  1.090
 NAV  N2   C10   single  1.349  0.020  1.349
 NAV  N2   HN2   single  0.860  0.020  1.020
 NAV  C10  C11   single  1.511  0.020  1.511
 NAV  C10  O10   double  1.222  0.020  1.222
 NAV  C11  H111  single  0.970  0.020  1.090
 NAV  C11  H112  single  0.970  0.020  1.090
 NAV  C11  H113  single  0.970  0.020  1.090
 NAV  O6   C6    single  1.411  0.020  1.411
 NAV  O6   HO6   single  0.850  0.020  0.980
 NAV  C6   C7    single  1.532  0.020  1.532
 NAV  C6   HC6   single  0.970  0.020  1.090
 NAV  C7   O7    single  1.413  0.020  1.413
 NAV  C7   C8    single  1.538  0.020  1.538
 NAV  C7   HC7   single  0.970  0.020  1.090
 NAV  O7   HO7   single  0.850  0.020  0.980
 NAV  C8   O8    single  1.408  0.020  1.408
 NAV  C8   C9    single  1.521  0.020  1.521
 NAV  C8   HC8   single  0.970  0.020  1.090
 NAV  O8   HO8   single  0.850  0.020  0.980
 NAV  C9   O9    single  1.408  0.020  1.408
 NAV  C9   HC91  single  0.970  0.020  1.090
 NAV  C9   HC92  single  0.970  0.020  1.090
 NAV  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
 NAV  C2    C1   O1B   117.75  3.000
 NAV  C2    C1   O1A   115.83  3.000
 NAV  O1B   C1   O1A   126.41  3.000
 NAV  HC22  C2   HC21  105.30  3.000
 NAV  HC22  C2   C3    109.95  3.000
 NAV  HC21  C2   C3    110.02  3.000
 NAV  HC22  C2   C1    107.76  3.000
 NAV  HC21  C2   C1    108.85  3.000
 NAV  C3    C2   C1    114.53  3.000
 NAV  HC32  C3   HC31  104.08  3.000
 NAV  HC32  C3   C4    108.53  3.000
 NAV  HC31  C3   C4    105.96  3.000
 NAV  HC32  C3   C2    111.35  3.000
 NAV  HC31  C3   C2    110.84  3.000
 NAV  C4    C3   C2    115.35  3.000
 NAV  O4    C4   C5    120.24  3.000
 NAV  O4    C4   C3    123.64  3.000
 NAV  C5    C4   C3    116.09  3.000
 NAV  HC5   C5   C6    107.60  3.000
 NAV  HC5   C5   N2    105.38  3.000
 NAV  C6    C5   N2    115.25  3.000
 NAV  HC5   C5   C4    108.30  3.000
 NAV  C6    C5   C4    108.93  3.000
 NAV  N2    C5   C4    111.07  3.000
 NAV  HN2   N2   C10   116.72  3.000
 NAV  HN2   N2   C5    114.72  3.000
 NAV  C10   N2   C5    128.16  3.000
 NAV  O10   C10  C11   121.14  3.000
 NAV  O10   C10  N2    124.37  3.000
 NAV  C11   C10  N2    114.48  3.000
 NAV  H113  C11  H112  108.16  3.000
 NAV  H113  C11  H111  107.37  3.000
 NAV  H112  C11  H111  108.55  3.000
 NAV  H113  C11  C10   109.07  3.000
 NAV  H112  C11  C10   114.15  3.000
 NAV  H111  C11  C10   109.33  3.000
 NAV  HO6   O6   C6    109.56  3.000
 NAV  HC6   C6   C7    108.93  3.000
 NAV  HC6   C6   O6    105.71  3.000
 NAV  C7    C6   O6    112.03  3.000
 NAV  HC6   C6   C5    108.89  3.000
 NAV  C7    C6   C5    111.97  3.000
 NAV  O6    C6   C5    109.07  3.000
 NAV  HC7   C7   C8    107.67  3.000
 NAV  HC7   C7   O7    105.56  3.000
 NAV  C8    C7   O7    111.80  3.000
 NAV  HC7   C7   C6    108.25  3.000
 NAV  C8    C7   C6    112.05  3.000
 NAV  O7    C7   C6    111.17  3.000
 NAV  HO7   O7   C7    109.53  3.000
 NAV  HC8   C8   C9    108.65  3.000
 NAV  HC8   C8   O8    105.52  3.000
 NAV  C9    C8   O8    111.59  3.000
 NAV  HC8   C8   C7    108.80  3.000
 NAV  C9    C8   C7    110.82  3.000
 NAV  O8    C8   C7    111.26  3.000
 NAV  HO8   O8   C8    108.71  3.000
 NAV  HC92  C9   HC91  106.71  3.000
 NAV  HC92  C9   O9    111.72  3.000
 NAV  HC91  C9   O9    111.55  3.000
 NAV  HC92  C9   C8    108.76  3.000
 NAV  HC91  C9   C8    109.38  3.000
 NAV  O9    C9   C8    108.66  3.000
 NAV  HO9   O9   C9    107.97  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
 NAV  CONST_01  C11   C10  N2   C5    180.00   0.0  0
 NAV  CONST_02  O10   C10  N2   C5      0.00   0.0  0
 NAV  CONST_03  HN2   N2   C10  C11     0.00   0.0  0
 NAV  Var_01    C4    C3   C2   C1    176.81  30.0  3
 NAV  Var_02    C3    C2   C1   O1A   165.99  30.0  3
 NAV  Var_03    C5    C4   C3   C2    168.06  30.0  3
 NAV  Var_04    H111  C11  C10  N2   -127.13  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
 NAV  chir_01  C5  C4  N2  C6  negativ
 NAV  chir_02  C6  O6  C5  C7  positiv
 NAV  chir_03  C7  O7  C6  C8  negativ
 NAV  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
 NAV  plan-1  C5   0.020
 NAV  plan-1  N2   0.020
 NAV  plan-1  C10  0.020
 NAV  plan-1  C11  0.020
 NAV  plan-1  O10  0.020
 NAV  plan-1  HN2  0.020
 NAV  plan-2  C3   0.020
 NAV  plan-2  C4   0.020
 NAV  plan-2  C5   0.020
 NAV  plan-2  O4   0.020
 NAV  plan-3  C1   0.020
 NAV  plan-3  O1A  0.020
 NAV  plan-3  O1B  0.020
 NAV  plan-3  C2   0.020

