# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 19:14:42 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  39  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   0.556  -1.0701   0.1629   4.9424
 NAV  O1A   O  OH1   0  -0.596  -1.1640  -0.6538   5.9864
 NAV  O1B   O  O     0  -0.443  -1.5757   1.2572   4.9143
 NAV  C2    C  CH2   0  -0.585  -0.2613  -0.4494   3.8327
 NAV  C3    C  CH2   0  -0.575  -0.2012   0.4305   2.6013
 NAV  C4    C  C     0   0.434   0.6509  -0.1277   1.4973
 NAV  C5    C  CH1   0  -0.203   0.5604   0.5942   0.1474
 NAV  N2    N  NH1   0  -0.643   1.8759   0.9137  -0.3581
 NAV  C10   C  C     0   0.528   2.7416   0.1012  -1.0000
 NAV  C11   C  CH3   0  -0.774   4.1017   0.7092  -1.2472
 NAV  O10   O  O     0  -0.491   2.4753  -1.0306  -1.3735
 NAV  O6    O  OH1   0  -0.662  -1.5710  -0.4762  -0.1838
 NAV  C6    C  CH1   0   0.019  -0.3275  -0.2341  -0.8043
 NAV  C7    C  CH1   0  -0.039  -0.4855   0.4426  -2.1692
 NAV  O7    O  OH1   0  -0.665  -1.1204   1.6983  -2.0461
 NAV  C8    C  CH1   0  -0.030  -1.2052  -0.4633  -3.1830
 NAV  O8    O  OH1   0  -0.656  -0.6259  -1.7462  -3.2246
 NAV  C9    C  CH2   0  -0.152  -1.2332   0.1841  -4.5597
 NAV  O9    O  OH1   0  -0.670  -1.9939  -0.6264  -5.4232
 NAV  O4    O  O     0  -0.383   1.3966  -1.0637   1.6497
 NAV  HO1A  H  HOH1  0   0.480  -1.6840  -0.2355   6.6883
 NAV  HC21  H  HCH2  0   0.289  -0.6905  -1.4255   3.5920
 NAV  HC22  H  HCH2  0   0.291   0.7409  -0.6544   4.2184
 NAV  HC31  H  HCH2  0   0.291   0.2172   1.4151   2.8407
 NAV  HC32  H  HCH2  0   0.275  -1.1988   0.6375   2.2083
 NAV  HC5   H  HCH1  0   0.284   0.0673   1.5583   0.3055
 NAV  HN2   H  HNH1  0   0.409   2.2194   1.8220  -0.0929
 NAV  H111  H  HCH3  0   0.264   4.3903   0.5464  -2.2846
 NAV  H112  H  HCH3  0   0.250   4.1568   1.7746  -1.0320
 NAV  H113  H  HCH3  0   0.269   4.8354   0.1997  -0.6212
 NAV  HO6   H  HOH1  0   0.444  -2.0252   0.3604  -0.0314
 NAV  HC6   H  HCH1  0   0.266   0.1270  -1.2113  -0.9460
 NAV  HC7   H  HCH1  0   0.242   0.5142   0.6542  -2.5635
 NAV  HO7   H  HOH1  0   0.450  -2.0755   1.5760  -2.0182
 NAV  HC8   H  HCH1  0   0.232  -2.2375  -0.6184  -2.8472
 NAV  HO8   H  HOH1  0   0.443   0.2988  -1.6602  -3.4833
 NAV  HC91  H  HCH2  0   0.203  -1.6540   1.1924  -4.4784
 NAV  HC92  H  HCH2  0   0.192  -0.1981   0.3012  -4.9168
 NAV  HO9   H  HOH1  0   0.455  -2.0319  -0.1930  -6.2803

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   single  1.329  0.020  1.329
 NAV  C1   O1B   double  1.206  0.020  1.206
 NAV  C1   C2    single  1.504  0.020  1.504
 NAV  O1A  HO1A  single  0.850  0.020  0.980
 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  1.502  0.020  1.502
 NAV  C3   HC31  single  0.970  0.020  1.090
 NAV  C3   HC32  single  0.970  0.020  1.090
 NAV  C4   C5    single  1.533  0.020  1.533
 NAV  C4   O4    double  1.206  0.020  1.206
 NAV  C5   N2    single  1.445  0.020  1.445
 NAV  C5   C6    single  1.543  0.020  1.543
 NAV  C5   HC5   single  0.970  0.020  1.090
 NAV  N2   C10   single  1.350  0.020  1.350
 NAV  N2   HN2   single  0.860  0.020  1.020
 NAV  C10  C11   single  1.510  0.020  1.510
 NAV  C10  O10   double  1.221  0.020  1.221
 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  1.412  0.020  1.412
 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  1.522  0.020  1.522
 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   125.31  3.000
 NAV  C2    C1   O1A   111.56  3.000
 NAV  O1B   C1   O1A   123.12  3.000
 NAV  HO1A  O1A  C1    109.99  3.000
 NAV  HC22  C2   HC21  105.67  3.000
 NAV  HC22  C2   C3    111.06  3.000
 NAV  HC21  C2   C3    110.81  3.000
 NAV  HC22  C2   C1    108.01  3.000
 NAV  HC21  C2   C1    108.36  3.000
 NAV  C3    C2   C1    112.63  3.000
 NAV  HC32  C3   HC31  104.89  3.000
 NAV  HC32  C3   C4    108.92  3.000
 NAV  HC31  C3   C4    106.13  3.000
 NAV  HC32  C3   C2    111.49  3.000
 NAV  HC31  C3   C2    111.06  3.000
 NAV  C4    C3   C2    113.83  3.000
 NAV  O4    C4   C5    120.85  3.000
 NAV  O4    C4   C3    123.10  3.000
 NAV  C5    C4   C3    116.01  3.000
 NAV  HC5   C5   C6    107.62  3.000
 NAV  HC5   C5   N2    105.42  3.000
 NAV  C6    C5   N2    115.27  3.000
 NAV  HC5   C5   C4    108.31  3.000
 NAV  C6    C5   C4    108.92  3.000
 NAV  N2    C5   C4    110.99  3.000
 NAV  HN2   N2   C10   116.72  3.000
 NAV  HN2   N2   C5    114.71  3.000
 NAV  C10   N2   C5    128.11  3.000
 NAV  O10   C10  C11   121.29  3.000
 NAV  O10   C10  N2    124.30  3.000
 NAV  C11   C10  N2    114.40  3.000
 NAV  H113  C11  H112  108.04  3.000
 NAV  H113  C11  H111  107.37  3.000
 NAV  H112  C11  H111  108.74  3.000
 NAV  H113  C11  C10   108.89  3.000
 NAV  H112  C11  C10   114.04  3.000
 NAV  H111  C11  C10   109.54  3.000
 NAV  HO6   O6   C6    109.62  3.000
 NAV  HC6   C6   C7    108.92  3.000
 NAV  HC6   C6   O6    105.76  3.000
 NAV  C7    C6   O6    112.14  3.000
 NAV  HC6   C6   C5    108.81  3.000
 NAV  C7    C6   C5    111.84  3.000
 NAV  O6    C6   C5    109.15  3.000
 NAV  HC7   C7   C8    107.67  3.000
 NAV  HC7   C7   O7    105.66  3.000
 NAV  C8    C7   O7    111.76  3.000
 NAV  HC7   C7   C6    108.18  3.000
 NAV  C8    C7   C6    112.05  3.000
 NAV  O7    C7   C6    111.19  3.000
 NAV  HO7   O7   C7    109.59  3.000
 NAV  HC8   C8   C9    108.66  3.000
 NAV  HC8   C8   O8    105.50  3.000
 NAV  C9    C8   O8    111.62  3.000
 NAV  HC8   C8   C7    108.78  3.000
 NAV  C9    C8   C7    110.75  3.000
 NAV  O8    C8   C7    111.32  3.000
 NAV  HO8   O8   C8    108.73  3.000
 NAV  HC92  C9   HC91  106.69  3.000
 NAV  HC92  C9   O9    111.73  3.000
 NAV  HC91  C9   O9    111.59  3.000
 NAV  HC92  C9   C8    108.74  3.000
 NAV  HC91  C9   C8    109.36  3.000
 NAV  O9    C9   C8    108.67  3.000
 NAV  HO9   O9   C9    107.98  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
 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  CONST_04  HO1A  O1A  C1   O1B     0.00   0.0  0
 NAV  Var_01    C4    C3   C2   C1    177.43  30.0  3
 NAV  Var_02    C3    C2   C1   O1A   176.91  30.0  3
 NAV  Var_03    C5    C4   C3   C2    170.00  30.0  3
 NAV  Var_04    H111  C11  C10  N2   -132.06  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
 NAV  plan-3  HO1A  0.020

