# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:56:36 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5-(acetylamino)-4,9-diamino-2,6-anhydro-3,4,5,9-tetradeoxy-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](N)C=C(O[C@H]1[C@H](O)[C@H](O)CN)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
 49A  49A  '5-(acetylamino)-4,9-diamino-2,6-anhydro-3,4,5,9-tetradeoxy-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  38  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_49A
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
 49A  C1    C  C      0   0.371  -3.2249   0.2660  -1.6163
 49A  C2    C  C      0   0.169  -2.1964  -0.0460  -0.5343
 49A  C3    C  C1     0  -0.366  -2.5177  -0.4528   0.6936
 49A  C4    C  CH1    0  -0.070  -1.5080  -0.7069   1.7709
 49A  C5    C  CH1    0  -0.108  -0.1862  -0.0542   1.3705
 49A  C6    C  CH1    0   0.038   0.1032  -0.3845  -0.0984
 49A  C7    C  CH1    0  -0.029   1.4183   0.1979  -0.6076
 49A  C8    C  CH1    0   0.012   1.7239  -0.2133  -2.0600
 49A  C9    C  CH2    0  -0.298   3.0910   0.2914  -2.5036
 49A  C11   C  CH3    0  -0.783   2.7780  -0.4302   3.7039
 49A  N5    N  NH1    0  -0.641   0.8847  -0.5049   2.2253
 49A  O1A   O  O      0  -0.592  -4.4177   0.0972  -1.3027
 49A  O1B   O  OC    -1  -0.594  -2.7739   0.6593  -2.7042
 49A  N4    N  NH2    0  -0.799  -1.9711  -0.1505   3.0354
 49A  O6    O  O2     0  -0.485  -0.9157   0.1347  -0.9369
 49A  O7    O  OH1    0  -0.660   1.4537   1.5966  -0.4584
 49A  O8    O  OH1    0  -0.666   1.6196  -1.6138  -2.2274
 49A  N9    N  NH2    0  -0.801   3.3183  -0.0076  -3.9073
 49A  O10   O  O      0  -0.491   1.5434   1.5075   3.0328
 49A  H3    H  H      0   0.246  -3.5642  -0.6034   0.9218
 49A  H4    H  HCH1   0   0.213  -1.3342  -1.7946   1.8417
 49A  H5    H  HCH1   0   0.264  -0.2811   1.0256   1.4920
 49A  H6    H  HCH1   0   0.230   0.1329  -1.4778  -0.2039
 49A  H7    H  HCH1   0   0.237   2.2203  -0.1955   0.0276
 49A  H8    H  HCH1   0   0.228   0.9664   0.2170  -2.7235
 49A  H91   H  HCH2   0   0.230   3.1282   1.3735  -2.3724
 49A  H92   H  HCH2   0   0.189   3.8555  -0.1288  -1.8282
 49A  H111  H  HCH3   0   0.261   3.0148   0.0883   4.6302
 49A  H112  H  HCH3   0   0.251   2.5253  -1.4645   3.9323
 49A  H113  H  HCH3   0   0.270   3.6786  -0.4365   3.0869
 49A  HN5   H  HNH1   0   0.398   1.0714  -1.4960   2.2431
 49A  HN41  H  HNH2   0   0.348  -2.8442  -0.5973   3.2897
 49A  HN42  H  HNH2   0   0.344  -1.3194  -0.4136   3.7659
 49A  HO7   H  HOH1   0   0.443   0.7186   1.9710  -0.9573
 49A  HO8   H  HOH1   0   0.444   2.3108  -2.0373  -1.7055
 49A  HN91  H  HNH2   0   0.348   4.2086   0.3785  -4.1922
 49A  HN92  H  HNH2   0   0.338   3.3986  -1.0083  -4.0337
 49A  C10   C  C      0   0.512   1.6774   0.2956   2.9690

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
 49A  C1   C2    single  1.525  0.020  1.525
 49A  C1   O1A   deloc   1.245  0.020  1.245
 49A  C1   O1B   deloc   1.242  0.020  1.242
 49A  C2   C3    double  1.333  0.020  1.333
 49A  C2   O6    single  1.355  0.020  1.355
 49A  C3   C4    single  1.498  0.020  1.498
 49A  C3   H3    single  0.930  0.020  1.080
 49A  C4   C5    single  1.528  0.020  1.528
 49A  C4   N4    single  1.457  0.020  1.457
 49A  C4   H4    single  0.970  0.020  1.090
 49A  C5   C6    single  1.533  0.020  1.533
 49A  C5   N5    single  1.442  0.020  1.442
 49A  C5   H5    single  0.970  0.020  1.090
 49A  C6   C7    single  1.526  0.020  1.526
 49A  C6   O6    single  1.418  0.020  1.418
 49A  C6   H6    single  0.970  0.020  1.090
 49A  C7   C8    single  1.540  0.020  1.540
 49A  C7   O7    single  1.407  0.020  1.407
 49A  C7   H7    single  0.970  0.020  1.090
 49A  C8   C9    single  1.523  0.020  1.523
 49A  C8   O8    single  1.414  0.020  1.414
 49A  C8   H8    single  0.970  0.020  1.090
 49A  C9   N9    single  1.453  0.020  1.453
 49A  C9   H91   single  0.970  0.020  1.090
 49A  C9   H92   single  0.970  0.020  1.090
 49A  C10  C11   single  1.509  0.020  1.509
 49A  C10  N5    single  1.350  0.020  1.350
 49A  C10  O10   double  1.221  0.020  1.221
 49A  C11  H111  single  0.970  0.020  1.090
 49A  C11  H112  single  0.970  0.020  1.090
 49A  C11  H113  single  0.970  0.020  1.090
 49A  N5   HN5   single  0.860  0.020  1.020
 49A  N4   HN41  single  0.890  0.020  1.040
 49A  N4   HN42  single  0.890  0.020  1.040
 49A  O7   HO7   single  0.850  0.020  0.980
 49A  O8   HO8   single  0.850  0.020  0.980
 49A  N9   HN91  single  0.890  0.020  1.040
 49A  N9   HN92  single  0.890  0.020  1.040

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
 49A  O1B   C1   O1A   127.72  3.000
 49A  O1B   C1   C2    116.20  3.000
 49A  O1A   C1   C2    116.09  3.000
 49A  O6    C2   C3    122.85  3.000
 49A  O6    C2   C1    113.55  3.000
 49A  C3    C2   C1    123.60  3.000
 49A  H3    C3   C4    118.47  3.000
 49A  H3    C3   C2    118.05  3.000
 49A  C4    C3   C2    123.48  3.000
 49A  H4    C4   N4    111.76  3.000
 49A  H4    C4   C5    107.56  3.000
 49A  N4    C4   C5    109.83  3.000
 49A  H4    C4   C3    108.62  3.000
 49A  N4    C4   C3    110.18  3.000
 49A  C5    C4   C3    108.80  3.000
 49A  H5    C5   N5    107.93  3.000
 49A  H5    C5   C6    109.66  3.000
 49A  N5    C5   C6    111.12  3.000
 49A  H5    C5   C4    108.57  3.000
 49A  N5    C5   C4    110.70  3.000
 49A  C6    C5   C4    108.81  3.000
 49A  H6    C6   O6    109.09  3.000
 49A  H6    C6   C7    108.93  3.000
 49A  O6    C6   C7    106.39  3.000
 49A  H6    C6   C5    108.15  3.000
 49A  O6    C6   C5    110.61  3.000
 49A  C7    C6   C5    113.59  3.000
 49A  H7    C7   O7    106.07  3.000
 49A  H7    C7   C8    107.78  3.000
 49A  O7    C7   C8    111.12  3.000
 49A  H7    C7   C6    107.48  3.000
 49A  O7    C7   C6    111.46  3.000
 49A  C8    C7   C6    112.57  3.000
 49A  H8    C8   O8    105.45  3.000
 49A  H8    C8   C9    108.31  3.000
 49A  O8    C8   C9    111.09  3.000
 49A  H8    C8   C7    109.22  3.000
 49A  O8    C8   C7    111.19  3.000
 49A  C9    C8   C7    111.36  3.000
 49A  H92   C9   H91   106.30  3.000
 49A  H92   C9   N9    113.87  3.000
 49A  H91   C9   N9    108.36  3.000
 49A  H92   C9   C8    108.51  3.000
 49A  H91   C9   C8    108.92  3.000
 49A  N9    C9   C8    110.70  3.000
 49A  H113  C11  H112  107.73  3.000
 49A  H113  C11  H111  107.73  3.000
 49A  H112  C11  H111  108.94  3.000
 49A  H113  C11  C10   109.21  3.000
 49A  H112  C11  C10   112.93  3.000
 49A  H111  C11  C10   110.13  3.000
 49A  HN5   N5   C10   117.65  3.000
 49A  HN5   N5   C5    117.06  3.000
 49A  C10   N5   C5    125.26  3.000
 49A  HN42  N4   HN41  104.99  3.000
 49A  HN42  N4   C4    108.78  3.000
 49A  HN41  N4   C4    108.87  3.000
 49A  C6    O6   C2    117.05  3.000
 49A  HO7   O7   C7    108.17  3.000
 49A  HO8   O8   C8    108.55  3.000
 49A  HN92  N9   HN91  105.82  3.000
 49A  HN92  N9   C9    109.67  3.000
 49A  HN91  N9   C9    109.34  3.000
 49A  O10   C10  N5    123.56  3.000
 49A  O10   C10  C11   122.13  3.000
 49A  N5    C10  C11   114.29  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
 49A  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 49A  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 49A  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 49A  Var_01    O6    C2   C3   C4      2.22  30.0  1
 49A  Var_02    O1A   C1   C2   C3     -1.24  30.0  2
 49A  Var_03    HN91  N9   C9   C8    177.03  30.0  3
 49A  Var_04    H111  C11  C10  N5   -149.60  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
 49A  chir_01  C4  C3  C5  N4  negativ
 49A  chir_02  C5  N5  C6  C4  negativ
 49A  chir_03  C6  O6  C5  C7  positiv
 49A  chir_04  C7  O7  C6  C8  negativ
 49A  chir_05  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
 49A  plan-1  C5   0.020
 49A  plan-1  C11  0.020
 49A  plan-1  N5   0.020
 49A  plan-1  O10  0.020
 49A  plan-1  HN5  0.020
 49A  plan-1  C10  0.020
 49A  plan-2  C1   0.020
 49A  plan-2  C2   0.020
 49A  plan-2  O1A  0.020
 49A  plan-2  O1B  0.020

