# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:58:54 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-(acetylamino)-4-amino-2,6-anhydro-3,4,5-trideoxy-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)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
 4AM  4AM  '5-(acetylamino)-4-amino-2,6-anhydro-3,4,5-trideoxy-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  37  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_4AM
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
 4AM  C1    C  C      0   0.371  -3.3357   0.2453  -1.3425
 4AM  O1A   O  O      0  -0.592  -4.5005   0.1006  -0.9283
 4AM  O1B   O  OC    -1  -0.594  -2.9707   0.6156  -2.4700
 4AM  C2    C  C      0   0.170  -2.2255  -0.0687  -0.3449
 4AM  C3    C  C1     0  -0.366  -2.4491  -0.4854   0.9011
 4AM  C4    C  CH1    0  -0.071  -1.3580  -0.7415   1.8952
 4AM  N4    N  NH2    0  -0.799  -1.7283  -0.1984   3.1960
 4AM  C5    C  CH1    0  -0.103  -0.0755  -0.0767   1.3994
 4AM  N5    N  NH1    0  -0.638   1.0613  -0.5178   2.1690
 4AM  C10   C  C      0   0.503   1.8853   0.2876   2.8747
 4AM  O10   O  O      0  -0.487   1.7444   1.4976   2.9476
 4AM  C11   C  CH3    0  -0.788   3.0001  -0.4485   3.5800
 4AM  C6    C  CH1    0   0.037   0.1028  -0.3996  -0.0892
 4AM  O6    O  O2     0  -0.485  -0.9801   0.1180  -0.8446
 4AM  C7    C  CH1    0  -0.036   1.3704   0.1956  -0.6928
 4AM  O7    O  OH1    0  -0.659   1.4057   1.5942  -0.5398
 4AM  C8    C  CH1    0  -0.013   1.5623  -0.2113  -2.1673
 4AM  O8    O  OH1    0  -0.662   1.4475  -1.6068  -2.3347
 4AM  C9    C  CH2    0  -0.162   2.8887   0.3100  -2.6970
 4AM  O9    O  OH1    0  -0.671   2.9855  -0.0038  -4.0669
 4AM  H3    H  H      0   0.246  -3.4739  -0.6427   1.2093
 4AM  H4    H  HCH1   0   0.213  -1.1726  -1.8285   1.9440
 4AM  HN41  H  HNH2   0   0.348  -2.5782  -0.6524   3.5095
 4AM  HN42  H  HNH2   0   0.344  -1.0239  -0.4653   3.8742
 4AM  H5    H  HCH1   0   0.263  -0.1702   1.0020   1.5303
 4AM  H5N   H  HNH1   0   0.398   1.2530  -1.5086   2.1804
 4AM  H111  H  HCH3   0   0.260   3.6282   0.2486   4.1278
 4AM  H112  H  HCH3   0   0.265   2.5947  -1.1797   4.2805
 4AM  H113  H  HCH3   0   0.264   3.6196  -0.9933   2.8665
 4AM  H6    H  HCH1   0   0.232   0.1323  -1.4917  -0.2029
 4AM  H7    H  HCH1   0   0.241   2.2207  -0.1947  -0.1221
 4AM  H7O   H  HOH1   0   0.444   0.6235   1.9636  -0.9656
 4AM  H8    H  HCH1   0   0.234   0.7526   0.2248  -2.7628
 4AM  H8O   H  HOH1   0   0.444   2.1934  -2.0335  -1.8981
 4AM  H91   H  HCH2   0   0.208   2.9453   1.3897  -2.5251
 4AM  H92   H  HCH2   0   0.187   3.7077  -0.1471  -2.1191
 4AM  HO9   H  HOH1   0   0.454   3.8000   0.3810  -4.4019

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
 4AM  C1   O1A   deloc   1.245  0.020  1.245
 4AM  C1   O1B   deloc   1.242  0.020  1.242
 4AM  C1   C2    single  1.525  0.020  1.525
 4AM  C2   C3    double  1.333  0.020  1.333
 4AM  C2   O6    single  1.355  0.020  1.355
 4AM  C3   C4    single  1.498  0.020  1.498
 4AM  C3   H3    single  0.930  0.020  1.080
 4AM  C4   N4    single  1.457  0.020  1.457
 4AM  C4   C5    single  1.527  0.020  1.527
 4AM  C4   H4    single  0.970  0.020  1.090
 4AM  N4   HN41  single  0.890  0.020  1.040
 4AM  N4   HN42  single  0.890  0.020  1.040
 4AM  C5   N5    single  1.442  0.020  1.442
 4AM  C5   C6    single  1.534  0.020  1.534
 4AM  C5   H5    single  0.970  0.020  1.090
 4AM  N5   C10   single  1.351  0.020  1.351
 4AM  N5   H5N   single  0.860  0.020  1.020
 4AM  C10  O10   double  1.220  0.020  1.220
 4AM  C10  C11   single  1.511  0.020  1.511
 4AM  C11  H111  single  0.970  0.020  1.090
 4AM  C11  H112  single  0.970  0.020  1.090
 4AM  C11  H113  single  0.970  0.020  1.090
 4AM  C6   O6    single  1.418  0.020  1.418
 4AM  C6   C7    single  1.525  0.020  1.525
 4AM  C6   H6    single  0.970  0.020  1.090
 4AM  C7   O7    single  1.407  0.020  1.407
 4AM  C7   C8    single  1.542  0.020  1.542
 4AM  C7   H7    single  0.970  0.020  1.090
 4AM  O7   H7O   single  0.850  0.020  0.980
 4AM  C8   O8    single  1.410  0.020  1.410
 4AM  C8   C9    single  1.520  0.020  1.520
 4AM  C8   H8    single  0.970  0.020  1.090
 4AM  O8   H8O   single  0.850  0.020  0.980
 4AM  C9   O9    single  1.409  0.020  1.409
 4AM  C9   H91   single  0.970  0.020  1.090
 4AM  C9   H92   single  0.970  0.020  1.090
 4AM  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
 4AM  C2    C1   O1B   116.20  3.000
 4AM  C2    C1   O1A   116.07  3.000
 4AM  O1B   C1   O1A   127.73  3.000
 4AM  O6    C2   C3    122.83  3.000
 4AM  O6    C2   C1    113.54  3.000
 4AM  C3    C2   C1    123.63  3.000
 4AM  H3    C3   C4    118.44  3.000
 4AM  H3    C3   C2    118.08  3.000
 4AM  C4    C3   C2    123.48  3.000
 4AM  H4    C4   C5    107.58  3.000
 4AM  H4    C4   N4    111.73  3.000
 4AM  C5    C4   N4    109.93  3.000
 4AM  H4    C4   C3    108.66  3.000
 4AM  C5    C4   C3    108.77  3.000
 4AM  N4    C4   C3    110.09  3.000
 4AM  HN42  N4   HN41  104.94  3.000
 4AM  HN42  N4   C4    108.81  3.000
 4AM  HN41  N4   C4    108.80  3.000
 4AM  H5    C5   C6    109.56  3.000
 4AM  H5    C5   N5    107.88  3.000
 4AM  C6    C5   N5    111.22  3.000
 4AM  H5    C5   C4    108.58  3.000
 4AM  C6    C5   C4    108.73  3.000
 4AM  N5    C5   C4    110.83  3.000
 4AM  H5N   N5   C10   117.61  3.000
 4AM  H5N   N5   C5    117.14  3.000
 4AM  C10   N5   C5    125.25  3.000
 4AM  C11   C10  O10   122.71  3.000
 4AM  C11   C10  N5    113.79  3.000
 4AM  O10   C10  N5    123.49  3.000
 4AM  H113  C11  H112  107.24  3.000
 4AM  H113  C11  H111  108.78  3.000
 4AM  H112  C11  H111  108.73  3.000
 4AM  H113  C11  C10   110.92  3.000
 4AM  H112  C11  C10   110.63  3.000
 4AM  H111  C11  C10   110.45  3.000
 4AM  H6    C6   C7    108.95  3.000
 4AM  H6    C6   O6    109.17  3.000
 4AM  C7    C6   O6    106.34  3.000
 4AM  H6    C6   C5    108.24  3.000
 4AM  C7    C6   C5    113.49  3.000
 4AM  O6    C6   C5    110.57  3.000
 4AM  C6    O6   C2    117.07  3.000
 4AM  H7    C7   C8    107.91  3.000
 4AM  H7    C7   O7    106.13  3.000
 4AM  C8    C7   O7    111.29  3.000
 4AM  H7    C7   C6    107.44  3.000
 4AM  C8    C7   C6    112.28  3.000
 4AM  O7    C7   C6    111.45  3.000
 4AM  H7O   O7   C7    108.20  3.000
 4AM  H8    C8   C9    108.60  3.000
 4AM  H8    C8   O8    105.62  3.000
 4AM  C9    C8   O8    111.65  3.000
 4AM  H8    C8   C7    108.83  3.000
 4AM  C9    C8   C7    110.56  3.000
 4AM  O8    C8   C7    111.38  3.000
 4AM  H8O   O8   C8    108.75  3.000
 4AM  H92   C9   H91   106.77  3.000
 4AM  H92   C9   O9    111.50  3.000
 4AM  H91   C9   O9    111.64  3.000
 4AM  H92   C9   C8    108.88  3.000
 4AM  H91   C9   C8    109.18  3.000
 4AM  O9    C9   C8    108.80  3.000
 4AM  HO9   O9   C9    107.94  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
 4AM  CONST_01  O10   C10  N5   C5     0.00   0.0  0
 4AM  CONST_02  C11   C10  N5   C5   180.00   0.0  0
 4AM  CONST_03  H5N   N5   C10  O10  180.00   0.0  0
 4AM  Var_01    O6    C2   C3   C4     2.38  30.0  1
 4AM  Var_02    C3    C2   C1   O1A    0.50  30.0  2
 4AM  Var_03    H111  C11  C10  N5   179.93  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
 4AM  chir_01  C4  C3  N4  C5  positiv
 4AM  chir_02  C5  N5  C6  C4  negativ
 4AM  chir_03  C6  O6  C5  C7  positiv
 4AM  chir_04  C7  O7  C6  C8  negativ
 4AM  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
 4AM  plan-1  C5   0.020
 4AM  plan-1  N5   0.020
 4AM  plan-1  C10  0.020
 4AM  plan-1  O10  0.020
 4AM  plan-1  C11  0.020
 4AM  plan-1  H5N  0.020
 4AM  plan-2  C1   0.020
 4AM  plan-2  O1A  0.020
 4AM  plan-2  O1B  0.020
 4AM  plan-2  C2   0.020

