# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:28:05 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: methyl 5-(acetylamino)-9-amino-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[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
 AMN  AMN  'methyl 5-(acetylamino)-9-amino-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  44  22  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AMN
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
 AMN  C1    C  C     0   0.470   2.6377  -1.1370   0.6172
 AMN  C2    C  CT    0   0.475   2.0880   0.2868   0.3477
 AMN  C3    C  CH2   0  -0.558   2.1876   0.6223  -1.1385
 AMN  C4    C  CH1   0   0.065   1.1717  -0.1608  -1.9597
 AMN  C5    C  CH1   0  -0.123  -0.2226   0.1237  -1.4154
 AMN  C6    C  CH1   0   0.035  -0.2889  -0.2095   0.0828
 AMN  C7    C  CH1   0  -0.018  -1.5659   0.3355   0.7246
 AMN  C8    C  CH1   0   0.008  -1.7336  -0.1236   2.1841
 AMN  C9    C  CH2   0  -0.298  -3.0386   0.3826   2.7852
 AMN  C11   C  CH3   0  -0.782  -3.0682  -1.1075  -3.5957
 AMN  N5    N  NH1   0  -0.635  -1.2233  -0.6387  -2.1169
 AMN  N9    N  NH2   0  -0.800  -3.1150   0.0432   4.1963
 AMN  O1A   O  O     0  -0.407   1.9689  -2.0774   0.9526
 AMN  O1B   O  OH1   0  -0.582   3.9427  -1.1878   0.4088
 AMN  O2    O  O2    0  -0.492   2.8491   1.2184   1.0287
 AMN  O4    O  OH1   0  -0.659   1.1957   0.2232  -3.3102
 AMN  O6    O  O2    0  -0.516   0.7772   0.3830   0.8064
 AMN  O7    O  OH1   0  -0.662  -1.6307   1.7377   0.6200
 AMN  O8    O  OH1   0  -0.662  -1.6379  -1.5298   2.2883
 AMN  O10   O  O     0  -0.499  -2.2892   1.0953  -3.1075
 AMN  H31   H  HCH2  0   0.268   1.9873   1.6924  -1.2510
 AMN  H32   H  HCH2  0   0.276   3.2006   0.4388  -1.5026
 AMN  H4    H  HCH1  0   0.214   1.3693  -1.2405  -1.8671
 AMN  H5    H  HCH1  0   0.268  -0.4463   1.1823  -1.5622
 AMN  H6    H  HCH1  0   0.242  -0.2728  -1.2975   0.1993
 AMN  H7    H  HCH1  0   0.240  -2.4142  -0.0526   0.1492
 AMN  H8    H  HCH1  0   0.228  -0.9073   0.2728   2.7840
 AMN  H91   H  HCH2  0   0.230  -3.0761   1.4683   2.6904
 AMN  H92   H  HCH2  0   0.189  -3.8774  -0.0107   2.1860
 AMN  H111  H  HCH3  0   0.266  -4.1030  -0.8874  -3.3344
 AMN  H112  H  HCH3  0   0.266  -2.9788  -1.0069  -4.6775
 AMN  H113  H  HCH3  0   0.248  -2.8581  -2.1411  -3.3277
 AMN  H121  H  HCH3  0   0.247   3.6147   1.8344   2.7898
 AMN  H122  H  HCH3  0   0.231   1.9088   1.3714   2.8913
 AMN  H123  H  HCH3  0   0.219   3.1697   0.1275   2.7969
 AMN  HN5   H  HNH1  0   0.398  -1.1627  -1.6435  -2.0599
 AMN  HN91  H  HNH2  0   0.348  -3.9633   0.4303   4.5882
 AMN  HN92  H  HNH2  0   0.338  -3.1962  -0.9600   4.3007
 AMN  HOB1  H  HOH1  0   0.487   4.2710  -2.0874   0.5622
 AMN  HO4   H  HOH1  0   0.455   2.0137  -0.0983  -3.7024
 AMN  HO7   H  HOH1  0   0.443  -0.8534   2.1058   1.0560
 AMN  HO8   H  HOH1  0   0.443  -2.3904  -1.9219   1.8305
 AMN  C10   C  C     0   0.526  -2.1602  -0.1063  -2.9259
 AMN  C12   C  CH3   0  -0.431   2.8713   1.1196   2.4438

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
 AMN  C1   C2    single  1.550  0.020  1.550
 AMN  C1   O1A   double  1.202  0.020  1.202
 AMN  C1   O1B   single  1.323  0.020  1.323
 AMN  C2   C3    single  1.527  0.020  1.527
 AMN  C2   O2    single  1.382  0.020  1.382
 AMN  C2   O6    single  1.392  0.020  1.392
 AMN  C3   C4    single  1.523  0.020  1.523
 AMN  C3   H31   single  0.970  0.020  1.090
 AMN  C3   H32   single  0.970  0.020  1.090
 AMN  C4   C5    single  1.523  0.020  1.523
 AMN  C4   O4    single  1.404  0.020  1.404
 AMN  C4   H4    single  0.970  0.020  1.090
 AMN  C5   C6    single  1.536  0.020  1.536
 AMN  C5   N5    single  1.440  0.020  1.440
 AMN  C5   H5    single  0.970  0.020  1.090
 AMN  C6   C7    single  1.530  0.020  1.530
 AMN  C6   O6    single  1.418  0.020  1.418
 AMN  C6   H6    single  0.970  0.020  1.090
 AMN  C7   C8    single  1.539  0.020  1.539
 AMN  C7   O7    single  1.408  0.020  1.408
 AMN  C7   H7    single  0.970  0.020  1.090
 AMN  C8   C9    single  1.523  0.020  1.523
 AMN  C8   O8    single  1.413  0.020  1.413
 AMN  C8   H8    single  0.970  0.020  1.090
 AMN  C9   N9    single  1.453  0.020  1.453
 AMN  C9   H91   single  0.970  0.020  1.090
 AMN  C9   H92   single  0.970  0.020  1.090
 AMN  C10  C11   single  1.508  0.020  1.508
 AMN  C10  N5    single  1.347  0.020  1.347
 AMN  C10  O10   double  1.222  0.020  1.222
 AMN  C11  H111  single  0.970  0.020  1.090
 AMN  C11  H112  single  0.970  0.020  1.090
 AMN  C11  H113  single  0.970  0.020  1.090
 AMN  C12  O2    single  1.419  0.020  1.419
 AMN  C12  H121  single  0.970  0.020  1.090
 AMN  C12  H122  single  0.970  0.020  1.090
 AMN  C12  H123  single  0.970  0.020  1.090
 AMN  N5   HN5   single  0.860  0.020  1.020
 AMN  N9   HN91  single  0.890  0.020  1.040
 AMN  N9   HN92  single  0.890  0.020  1.040
 AMN  O1B  HOB1  single  0.850  0.020  0.980
 AMN  O4   HO4   single  0.850  0.020  0.980
 AMN  O7   HO7   single  0.850  0.020  0.980
 AMN  O8   HO8   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
 AMN  O1B   C1   O1A   124.27  3.000
 AMN  O1B   C1   C2    110.97  3.000
 AMN  O1A   C1   C2    124.76  3.000
 AMN  O6    C2   O2    108.03  3.000
 AMN  O6    C2   C3    111.53  3.000
 AMN  O2    C2   C3    107.19  3.000
 AMN  O6    C2   C1    109.88  3.000
 AMN  O2    C2   C1    109.77  3.000
 AMN  C3    C2   C1    110.36  3.000
 AMN  H32   C3   H31   107.45  3.000
 AMN  H32   C3   C4    110.65  3.000
 AMN  H31   C3   C4    108.98  3.000
 AMN  H32   C3   C2    110.37  3.000
 AMN  H31   C3   C2    107.63  3.000
 AMN  C4    C3   C2    111.61  3.000
 AMN  H4    C4   O4    110.23  3.000
 AMN  H4    C4   C5    108.49  3.000
 AMN  O4    C4   C5    107.95  3.000
 AMN  H4    C4   C3    109.81  3.000
 AMN  O4    C4   C3    111.50  3.000
 AMN  C5    C4   C3    108.78  3.000
 AMN  H5    C5   N5    107.78  3.000
 AMN  H5    C5   C6    109.43  3.000
 AMN  N5    C5   C6    109.28  3.000
 AMN  H5    C5   C4    108.69  3.000
 AMN  N5    C5   C4    111.28  3.000
 AMN  C6    C5   C4    110.33  3.000
 AMN  H6    C6   O6    110.48  3.000
 AMN  H6    C6   C7    108.78  3.000
 AMN  O6    C6   C7    105.35  3.000
 AMN  H6    C6   C5    108.59  3.000
 AMN  O6    C6   C5    111.99  3.000
 AMN  C7    C6   C5    111.59  3.000
 AMN  H7    C7   O7    106.15  3.000
 AMN  H7    C7   C8    107.93  3.000
 AMN  O7    C7   C8    111.26  3.000
 AMN  H7    C7   C6    107.44  3.000
 AMN  O7    C7   C6    111.23  3.000
 AMN  C8    C7   C6    112.49  3.000
 AMN  H8    C8   O8    105.58  3.000
 AMN  H8    C8   C9    108.05  3.000
 AMN  O8    C8   C9    111.07  3.000
 AMN  H8    C8   C7    109.22  3.000
 AMN  O8    C8   C7    111.06  3.000
 AMN  C9    C8   C7    111.62  3.000
 AMN  H92   C9   H91   106.35  3.000
 AMN  H92   C9   N9    113.83  3.000
 AMN  H91   C9   N9    108.37  3.000
 AMN  H92   C9   C8    108.58  3.000
 AMN  H91   C9   C8    109.03  3.000
 AMN  N9    C9   C8    110.52  3.000
 AMN  H113  C11  H112  108.44  3.000
 AMN  H113  C11  H111  108.43  3.000
 AMN  H112  C11  H111  107.28  3.000
 AMN  H113  C11  C10   113.88  3.000
 AMN  H112  C11  C10   109.27  3.000
 AMN  H111  C11  C10   109.33  3.000
 AMN  HN5   N5   C10   118.00  3.000
 AMN  HN5   N5   C5    117.27  3.000
 AMN  C10   N5   C5    124.50  3.000
 AMN  HN92  N9   HN91  105.79  3.000
 AMN  HN92  N9   C9    109.63  3.000
 AMN  HN91  N9   C9    109.33  3.000
 AMN  HOB1  O1B  C1    110.16  3.000
 AMN  C12   O2   C2    116.94  3.000
 AMN  HO4   O4   C4    108.37  3.000
 AMN  C6    O6   C2    120.72  3.000
 AMN  HO7   O7   C7    108.03  3.000
 AMN  HO8   O8   C8    108.47  3.000
 AMN  O10   C10  N5    123.44  3.000
 AMN  O10   C10  C11   121.54  3.000
 AMN  N5    C10  C11   115.02  3.000
 AMN  H123  C12  H122  108.51  3.000
 AMN  H123  C12  H121  107.85  3.000
 AMN  H122  C12  H121  108.71  3.000
 AMN  H123  C12  O2    112.91  3.000
 AMN  H122  C12  O2    112.29  3.000
 AMN  H121  C12  O2    106.39  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
 AMN  CONST_01  C11   C10  N5   C5   180.00   0.0  0
 AMN  CONST_02  O10   C10  N5   C5     0.00   0.0  0
 AMN  CONST_03  HOB1  O1B  C1   C2   180.00   0.0  0
 AMN  CONST_04  HN5   N5   C10  C11    0.00   0.0  0
 AMN  Var_01    H121  C12  O2   C2   172.51  30.0  3
 AMN  Var_02    HN91  N9   C9   C8   176.97  30.0  3
 AMN  Var_03    H111  C11  C10  N5   122.24  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
 AMN  chir_01  C2  C3  O2  O6  negativ
 AMN  chir_02  C4  O4  C5  C3  positiv
 AMN  chir_03  C5  N5  C6  C4  negativ
 AMN  chir_04  C6  O6  C7  C5  negativ
 AMN  chir_05  C7  O7  C6  C8  negativ
 AMN  chir_06  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
 AMN  plan-1  C5    0.020
 AMN  plan-1  C11   0.020
 AMN  plan-1  N5    0.020
 AMN  plan-1  O10   0.020
 AMN  plan-1  HN5   0.020
 AMN  plan-1  C10   0.020
 AMN  plan-2  C1    0.020
 AMN  plan-2  C2    0.020
 AMN  plan-2  O1A   0.020
 AMN  plan-2  O1B   0.020
 AMN  plan-2  HOB1  0.020

