# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:33:25 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-(acetylamino)-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@@H](O)[C@@H]1NC(C)=O)C(N)=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
 NM6  NM6  2-(acetylamino)-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranose  D-saccharide  40  20  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NM6
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
 NM6  O4    O  OH1   0  -0.666  -2.8333  23.4957  -13.4194
 NM6  C3A   C  CH1   0  -0.076  -2.0358  25.1895  -16.1202
 NM6  C1    C  CH1   0   0.306  -0.2535  26.2965  -11.8058
 NM6  C3B   C  CH3   0  -0.681  -1.9893  24.1556  -17.2250
 NM6  C2    C  CH1   0  -0.149  -0.0890  26.0155  -13.3016
 NM6  C3C   C  C     0   0.530  -1.7170  26.5846  -16.6710
 NM6  C3    C  CH1   0   0.033  -1.3118  25.2621  -13.8321
 NM6  C4    C  CH1   0   0.033  -1.6215  24.0479  -12.9659
 NM6  N3A   N  NH2   0  -0.805  -2.6025  27.5391  -16.3561
 NM6  O7    O  O     0  -0.488   2.1781  26.7777  -14.8357
 NM6  O3B   O  O     0  -0.487  -0.7149  26.7876  -17.3388
 NM6  O3    O  O2    0  -0.492  -1.0619  24.8519  -15.1553
 NM6  C5    C  CH1   0  -0.016  -1.7185  24.4851  -11.4987
 NM6  C6    C  CH2   0  -0.193  -2.0218  23.3533  -10.5407
 NM6  C7    C  C     0   0.507   1.2271  27.5367  -14.7343
 NM6  C8    C  CH3   0  -0.789   1.1985  28.9003  -15.3812
 NM6  N2    N  NH1   0  -0.622   0.1149  27.2375  -14.0298
 NM6  O6    O  OH1   0  -0.667  -1.0648  22.3317  -10.6865
 NM6  O5    O  O2    0  -0.496  -0.5044  25.0981  -11.1153
 NM6  O1    O  OH1   0  -0.648   0.9171  26.8420  -11.3298
 NM6  H4    H  HCH1  0   0.225  -0.7930  23.3358  -13.0716
 NM6  HAQ   H  HCH1  0   0.237  -3.0357  25.1839  -15.6707
 NM6  HAT1  H  HCH3  0   0.241  -2.2297  23.1709  -16.8252
 NM6  HAT2  H  HCH3  0   0.235  -2.7184  24.3921  -18.0001
 NM6  HAT3  H  HCH3  0   0.234  -1.0036  24.1146  -17.6875
 NM6  H1    H  HCH1  0   0.184  -1.1092  26.9815  -11.6601
 NM6  H2    H  HCH1  0   0.269   0.7969  25.3890  -13.4323
 NM6  HO1   H  HOH1  0   0.462   0.7450  27.2914  -10.4956
 NM6  H3    H  HCH1  0   0.227  -2.1813  25.9371  -13.7890
 NM6  HN2   H  HNH1  0   0.397  -0.6297  27.9179  -14.0036
 NM6  HAS1  H  HNH2  0   0.400  -2.4689  28.4873  -16.6709
 NM6  HAS2  H  HNH2  0   0.408  -3.4202  27.3465  -15.8036
 NM6  H5    H  HCH1  0   0.223  -2.5516  25.2021  -11.4059
 NM6  H61   H  HCH2  0   0.218  -2.0373  23.7592   -9.5207
 NM6  H62   H  HCH2  0   0.208  -3.0382  22.9986  -10.7495
 NM6  HO6   H  HOH1  0   0.457  -1.3229  21.5947  -10.1260
 NM6  H81   H  HCH3  0   0.256   2.1397  29.0971  -15.8877
 NM6  H82   H  HCH3  0   0.265   0.3904  28.9608  -16.1102
 NM6  H83   H  HCH3  0   0.257   1.0298  29.6803  -14.6378
 NM6  HO4   H  HOH1  0   0.458  -2.8486  22.5589  -13.2030

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
 NM6  O4   C4    single  1.407  0.020  1.407
 NM6  C3A  C3B   single  1.514  0.020  1.514
 NM6  C3A  C3C   single  1.533  0.020  1.533
 NM6  C3A  O3    single  1.412  0.020  1.412
 NM6  C1   C2    single  1.531  0.020  1.531
 NM6  C1   O5    single  1.406  0.020  1.406
 NM6  C1   O1    single  1.376  0.020  1.376
 NM6  C2   C3    single  1.531  0.020  1.531
 NM6  C2   N2    single  1.437  0.020  1.437
 NM6  C3C  N3A   single  1.340  0.020  1.340
 NM6  C3C  O3B   double  1.221  0.020  1.221
 NM6  C3   C4    single  1.523  0.020  1.523
 NM6  C3   O3    single  1.408  0.020  1.408
 NM6  C4   C5    single  1.534  0.020  1.534
 NM6  O7   C7    double  1.221  0.020  1.221
 NM6  C5   C6    single  1.514  0.020  1.514
 NM6  C5   O5    single  1.413  0.020  1.413
 NM6  C6   O6    single  1.407  0.020  1.407
 NM6  C7   C8    single  1.510  0.020  1.510
 NM6  C7   N2    single  1.350  0.020  1.350
 NM6  C4   H4    single  0.970  0.020  1.090
 NM6  C3A  HAQ   single  0.970  0.020  1.090
 NM6  C3B  HAT1  single  0.970  0.020  1.090
 NM6  C3B  HAT2  single  0.970  0.020  1.090
 NM6  C3B  HAT3  single  0.970  0.020  1.090
 NM6  C1   H1    single  0.970  0.020  1.090
 NM6  C2   H2    single  0.970  0.020  1.090
 NM6  O1   HO1   single  0.850  0.020  0.980
 NM6  C3   H3    single  0.970  0.020  1.090
 NM6  N2   HN2   single  0.860  0.020  1.020
 NM6  N3A  HAS1  single  0.860  0.020  1.020
 NM6  N3A  HAS2  single  0.860  0.020  1.020
 NM6  C5   H5    single  0.970  0.020  1.090
 NM6  C6   H61   single  0.970  0.020  1.090
 NM6  C6   H62   single  0.970  0.020  1.090
 NM6  O6   HO6   single  0.850  0.020  0.980
 NM6  C8   H81   single  0.970  0.020  1.090
 NM6  C8   H82   single  0.970  0.020  1.090
 NM6  C8   H83   single  0.970  0.020  1.090
 NM6  O4   HO4   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
 NM6  HO4   O4   C4    108.89  3.000
 NM6  HAQ   C3A  O3    110.35  3.000
 NM6  HAQ   C3A  C3C   109.97  3.000
 NM6  O3    C3A  C3C   108.64  3.000
 NM6  HAQ   C3A  C3B   108.89  3.000
 NM6  O3    C3A  C3B   108.32  3.000
 NM6  C3C   C3A  C3B   110.66  3.000
 NM6  H1    C1   O1    111.54  3.000
 NM6  H1    C1   O5    108.98  3.000
 NM6  O1    C1   O5    108.65  3.000
 NM6  H1    C1   C2    109.00  3.000
 NM6  O1    C1   C2    108.62  3.000
 NM6  O5    C1   C2    110.04  3.000
 NM6  HAT3  C3B  HAT2  108.14  3.000
 NM6  HAT3  C3B  HAT1  108.74  3.000
 NM6  HAT2  C3B  HAT1  108.02  3.000
 NM6  HAT3  C3B  C3A   111.31  3.000
 NM6  HAT2  C3B  C3A   110.50  3.000
 NM6  HAT1  C3B  C3A   110.04  3.000
 NM6  H2    C2   N2    108.17  3.000
 NM6  H2    C2   C3    108.89  3.000
 NM6  N2    C2   C3    110.87  3.000
 NM6  H2    C2   C1    108.00  3.000
 NM6  N2    C2   C1    110.75  3.000
 NM6  C3    C2   C1    110.07  3.000
 NM6  O3B   C3C  N3A   123.54  3.000
 NM6  O3B   C3C  C3A   121.22  3.000
 NM6  N3A   C3C  C3A   115.24  3.000
 NM6  H3    C3   O3    110.82  3.000
 NM6  H3    C3   C4    107.80  3.000
 NM6  O3    C3   C4    109.78  3.000
 NM6  H3    C3   C2    108.38  3.000
 NM6  O3    C3   C2    109.11  3.000
 NM6  C4    C3   C2    110.95  3.000
 NM6  H4    C4   C5    108.95  3.000
 NM6  H4    C4   C3    108.00  3.000
 NM6  C5    C4   C3    109.24  3.000
 NM6  H4    C4   O4    111.37  3.000
 NM6  C5    C4   O4    111.45  3.000
 NM6  C3    C4   O4    107.74  3.000
 NM6  HAS2  N3A  HAS1  117.37  3.000
 NM6  HAS2  N3A  C3C   122.02  3.000
 NM6  HAS1  N3A  C3C   120.61  3.000
 NM6  C3    O3   C3A   116.76  3.000
 NM6  H5    C5   O5    110.12  3.000
 NM6  H5    C5   C6    106.35  3.000
 NM6  O5    C5   C6    108.96  3.000
 NM6  H5    C5   C4    108.27  3.000
 NM6  O5    C5   C4    109.20  3.000
 NM6  C6    C5   C4    113.89  3.000
 NM6  H62   C6   H61   106.46  3.000
 NM6  H62   C6   O6    112.07  3.000
 NM6  H61   C6   O6    111.97  3.000
 NM6  H62   C6   C5    107.89  3.000
 NM6  H61   C6   C5    108.33  3.000
 NM6  O6    C6   C5    109.94  3.000
 NM6  N2    C7   C8    114.09  3.000
 NM6  N2    C7   O7    123.18  3.000
 NM6  C8    C7   O7    122.73  3.000
 NM6  H83   C8   H82   107.55  3.000
 NM6  H83   C8   H81   108.80  3.000
 NM6  H82   C8   H81   108.68  3.000
 NM6  H83   C8   C7    110.91  3.000
 NM6  H82   C8   C7    110.53  3.000
 NM6  H81   C8   C7    110.30  3.000
 NM6  HN2   N2   C7    118.17  3.000
 NM6  HN2   N2   C2    117.09  3.000
 NM6  C7    N2   C2    124.74  3.000
 NM6  HO6   O6   C6    108.27  3.000
 NM6  C5    O5   C1    112.95  3.000
 NM6  HO1   O1   C1    109.42  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
 NM6  CONST_01  O7    C7   N2   C2     0.00   0.0  0
 NM6  CONST_02  C8    C7   N2   C2   180.00   0.0  0
 NM6  CONST_03  HAS1  N3A  C3C  C3A  180.00   0.0  0
 NM6  CONST_04  HAS2  N3A  C3C  C3A    0.00   0.0  0
 NM6  CONST_05  HN2   N2   C7   O7   180.00   0.0  0
 NM6  Var_01    H81   C8   C7   O7    -2.46  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
 NM6  chir_01  C3A  C3B  C3C  O3  positiv
 NM6  chir_02  C1   O5   O1   C2  negativ
 NM6  chir_03  C2   N2   C3   C1  positiv
 NM6  chir_04  C3   O3   C4   C2  negativ
 NM6  chir_05  C4   O4   C5   C3  positiv
 NM6  chir_06  C5   O5   C4   C6  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
 NM6  plan-1  C3A   0.020
 NM6  plan-1  C3C   0.020
 NM6  plan-1  N3A   0.020
 NM6  plan-1  O3B   0.020
 NM6  plan-1  HAS1  0.020
 NM6  plan-1  HAS2  0.020
 NM6  plan-2  C2    0.020
 NM6  plan-2  O7    0.020
 NM6  plan-2  C7    0.020
 NM6  plan-2  C8    0.020
 NM6  plan-2  N2    0.020
 NM6  plan-2  HN2   0.020

