# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:55:57 2019
#
#   Ligand name: methyl 2-(acetylamino)-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranoside
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H](C)C(N)=O)[C@H]1NC(C)=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
NM9        NM9 'methyl 2-(acetylamino)-3-O-[(2R)-1-amino-1-oxopropan-2-yl]-2-deoxy-beta-D-glucopyranoside' d-saccharide 43 21 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_NM9
#
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
NM9         C3A    C   CH1    0    .      -1.8205   -0.8797    1.8770
NM9         C1     C   CH1    0    .       1.4351    0.4963   -1.4457
NM9         N3A    N   NH2    0    .      -1.0944   -2.3489    3.8942
NM9         O4     O   OH1    0    .      -2.2903   -1.3296   -0.9744
NM9         O2B    O   O      0    .       1.8000    2.9426    1.2346
NM9         C1B    C   CH3    0    .       3.3248    1.2105   -2.6429
NM9         C3B    C   CH3    0    .      -3.2890   -0.6052    2.0648
NM9         C2     C   CH1    0    .       0.6636    0.7588   -0.1590
NM9         C3E    C   C      0    .      -1.1472   -1.0361    3.2504
NM9         C3     C   CH1    0    .      -0.4478   -0.2121    0.0343
NM9         C4     C   CH1    0    .      -1.3511   -0.2806   -1.1653
NM9         C5     C   CH1    0    .      -0.5749   -0.5412   -2.4542
NM9         C5A    C   CH2    0    .      -1.5215   -0.4410   -3.6230
NM9         C2A    C   C      0    .       2.1300    1.8800    1.6422
NM9         C2B    C   CH3    0    .       3.1443    1.7800    2.7988
NM9         N2A    N   NH1    0    .       1.6128    0.6561    1.0090
NM9         OCA    O   O      0    .      -0.6599   -0.0951    3.7821
NM9         O1A    O   O2     0    .       2.3351    1.4967   -1.6333
NM9         O3A    O   O2     0    .      -1.2295    0.1922    1.1854
NM9         O5A    O   OH1    0    .      -0.7865   -0.4649   -4.8282
NM9         O6     O   O2     0    .       0.5287    0.4256   -2.6447
NM9         H3A    H   HCH1   0    .      -1.6944   -1.7967    1.3028
NM9        H3B1    H   HCH3   0    .      -3.5294    0.3639    1.6511
NM9        H3B2    H   HCH3   0    .      -3.8650   -1.3649    1.5580
NM9        H3B3    H   HCH3   0    .      -3.5239   -0.6161    3.1100
NM9         H1     H   HCH1   0    .       1.9649   -0.4483   -1.3507
NM9         H2     H   HCH1   0    .       0.2524    1.7560   -0.1963
NM9        H3A1    H   HNH2   0    .      -0.7109   -2.4401    4.8145
NM9        H3A2    H   HNH2   0    .      -1.4373   -3.1570    3.4122
NM9         H4     H   HOH1   0    .      -3.1476   -1.0452   -1.2724
NM9         HA     H   HCH1   0    .      -1.8838    0.6652   -1.2611
NM9        H1B1    H   HCH3   0    .       3.6043    0.1652   -2.5881
NM9        H1B2    H   HCH3   0    .       4.2094    1.8342   -2.4741
NM9        H1B3    H   HCH3   0    .       2.9149    1.4229   -3.6215
NM9         H3     H   HCH1   0    .      -0.0282   -1.1934    0.2131
NM9         H2A    H   HNH1   0    .       1.7954   -0.2342    1.4249
NM9         H5     H   HCH1   0    .      -0.1610   -1.5390   -2.4156
NM9        H5A1    H   HCH2   0    .      -2.2092   -1.2761   -3.6032
NM9        H5A2    H   HCH2   0    .      -2.0811    0.4904   -3.5573
NM9         H5A    H   HOH1   0    .      -1.3825   -0.4500   -5.5615
NM9        H2B1    H   HCH3   0    .       4.0684    1.3164    2.4361
NM9        H2B2    H   HCH3   0    .       2.7216    1.1704    3.6025
NM9        H2B3    H   HCH3   0    .       3.3613    2.7717    3.1745
#
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
NM9   C3A     C3B   single        1.506 0.020     1.506
NM9   C3A     C3E   single        1.538 0.020     1.538
NM9   C3A     O3A   single        1.406 0.020     1.406
NM9   C1      C2    single        1.523 0.020     1.523
NM9   C1      O1A   single        1.359 0.020     1.359
NM9   C1      O6    single        1.505 0.020     1.505
NM9   N3A     C3E   single        1.463 0.020     1.463
NM9   O4      C4    single        1.421 0.020     1.421
NM9   O2B     C2A   double        1.185 0.020     1.185
NM9   C1B     O1A   single        1.442 0.020     1.442
NM9   C2      C3    single        1.488 0.020     1.488
NM9   C2      N2A   single        1.509 0.020     1.509
NM9   C3E     OCA   double        1.186 0.020     1.186
NM9   C3      C4    single        1.503 0.020     1.503
NM9   C3      O3A   single        1.449 0.020     1.449
NM9   C4      C5    single        1.527 0.020     1.527
NM9   C5      C5A   single        1.507 0.020     1.507
NM9   C5      O6    single        1.479 0.020     1.479
NM9   C5A     O5A   single        1.412 0.020     1.412
NM9   C2A     C2B   single        1.542 0.020     1.542
NM9   C2A     N2A   single        1.472 0.020     1.472
NM9   C3A     H3A   single        0.970 0.020     1.090
NM9   C3B    H3B1   single        0.970 0.020     1.090
NM9   C3B    H3B2   single        0.970 0.020     1.090
NM9   C3B    H3B3   single        0.970 0.020     1.090
NM9   C1      H1    single        0.970 0.020     1.090
NM9   C2      H2    single        0.970 0.020     1.090
NM9   N3A    H3A1   single        0.860 0.020     1.020
NM9   N3A    H3A2   single        0.860 0.020     1.020
NM9   O4      H4    single        0.850 0.020     0.980
NM9   C4      HA    single        0.970 0.020     1.090
NM9   C1B    H1B1   single        0.970 0.020     1.090
NM9   C1B    H1B2   single        0.970 0.020     1.090
NM9   C1B    H1B3   single        0.970 0.020     1.090
NM9   C3      H3    single        0.970 0.020     1.090
NM9   N2A     H2A   single        0.860 0.020     1.020
NM9   C5      H5    single        0.970 0.020     1.090
NM9   C5A    H5A1   single        0.970 0.020     1.090
NM9   C5A    H5A2   single        0.970 0.020     1.090
NM9   O5A     H5A   single        0.850 0.020     0.980
NM9   C2B    H2B1   single        0.970 0.020     1.090
NM9   C2B    H2B2   single        0.970 0.020     1.090
NM9   C2B    H2B3   single        0.970 0.020     1.090
#
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
NM9   H3A     C3A     O3A         109.50 3.000
NM9   H3A     C3A     C3E         109.54 3.000
NM9   O3A     C3A     C3E         109.44 3.000
NM9   H3A     C3A     C3B         109.40 3.000
NM9   O3A     C3A     C3B         109.41 3.000
NM9   C3E     C3A     C3B         109.53 3.000
NM9   H1      C1      O6          108.81 3.000
NM9   H1      C1      O1A         109.21 3.000
NM9   O6      C1      O1A         108.88 3.000
NM9   H1      C1      C2          108.83 3.000
NM9   O6      C1      C2          112.09 3.000
NM9   O1A     C1      C2          108.98 3.000
NM9  H3A2     N3A    H3A1         120.00 3.000
NM9  H3A2     N3A     C3E         120.00 3.000
NM9  H3A1     N3A     C3E         120.01 3.000
NM9   H4      O4      C4          109.45 3.000
NM9  H3B3     C3B    H3B2         109.50 3.000
NM9  H3B3     C3B    H3B1         109.50 3.000
NM9  H3B2     C3B    H3B1         109.43 3.000
NM9  H3B3     C3B     C3A         109.49 3.000
NM9  H3B2     C3B     C3A         109.48 3.000
NM9  H3B1     C3B     C3A         109.43 3.000
NM9   H2      C2      N2A         109.23 3.000
NM9   H2      C2      C3          108.83 3.000
NM9   N2A     C2      C3          108.96 3.000
NM9   H2      C2      C1          108.85 3.000
NM9   N2A     C2      C1          108.88 3.000
NM9   C3      C2      C1          112.06 3.000
NM9   OCA     C3E     N3A         120.00 3.000
NM9   OCA     C3E     C3A         119.99 3.000
NM9   N3A     C3E     C3A         120.01 3.000
NM9   H3      C3      O3A         109.32 3.000
NM9   H3      C3      C4          108.88 3.000
NM9   O3A     C3      C4          108.82 3.000
NM9   H3      C3      C2          108.87 3.000
NM9   O3A     C3      C2          108.91 3.000
NM9   C4      C3      C2          112.01 3.000
NM9   HA      C4      C5          108.81 3.000
NM9   HA      C4      C3          108.93 3.000
NM9   C5      C4      C3          112.08 3.000
NM9   HA      C4      O4          109.23 3.000
NM9   C5      C4      O4          108.87 3.000
NM9   C3      C4      O4          108.88 3.000
NM9   H5      C5      O6          108.80 3.000
NM9   H5      C5      C5A         109.24 3.000
NM9   O6      C5      C5A         108.97 3.000
NM9   H5      C5      C4          108.79 3.000
NM9   O6      C5      C4          112.11 3.000
NM9   C5A     C5      C4          108.90 3.000
NM9  H5A2     C5A    H5A1         109.43 3.000
NM9  H5A2     C5A     O5A         109.49 3.000
NM9  H5A1     C5A     O5A         109.47 3.000
NM9  H5A2     C5A     C5          109.45 3.000
NM9  H5A1     C5A     C5          109.49 3.000
NM9   O5A     C5A     C5          109.50 3.000
NM9  H2B3     C2B    H2B2         109.46 3.000
NM9  H2B3     C2B    H2B1         109.47 3.000
NM9  H2B2     C2B    H2B1         109.48 3.000
NM9  H2B3     C2B     C2A         109.44 3.000
NM9  H2B2     C2B     C2A         109.47 3.000
NM9  H2B1     C2B     C2A         109.51 3.000
NM9   H2A     N2A     C2A         119.83 3.000
NM9   H2A     N2A     C2          119.85 3.000
NM9   C2A     N2A     C2          119.84 3.000
NM9   C1B     O1A     C1          113.89 3.000
NM9   C3      O3A     C3A         113.88 3.000
NM9   H5A     O5A     C5A         109.50 3.000
NM9   C5      O6      C1          112.17 3.000
NM9  H1B3     C1B    H1B2         109.48 3.000
NM9  H1B3     C1B    H1B1         109.45 3.000
NM9  H1B2     C1B    H1B1         109.46 3.000
NM9  H1B3     C1B     O1A         109.52 3.000
NM9  H1B2     C1B     O1A         109.46 3.000
NM9  H1B1     C1B     O1A         109.46 3.000
NM9   N2A     C2A     C2B         120.00 3.000
NM9   N2A     C2A     O2B         119.98 3.000
NM9   C2B     C2A     O2B         119.97 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
NM9 CONST_01       C2      N2A     C2A     O2B           0.04   0.0 0
NM9 CONST_02       C2B     C2A     N2A     C2         -177.52   0.0 0
NM9 CONST_03      H3A1     N3A     C3E     C3A        -175.92   0.0 0
NM9 CONST_04      H3A2     N3A     C3E     C3A           4.41   0.0 0
NM9 CONST_05       H2A     N2A     C2A     O2B        -172.07   0.0 0
NM9 Var_01        H1B1     C1B     O1A     C1          -37.78  30.0 3
NM9 Var_02        H2B1     C2B     C2A     O2B        -114.11  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
NM9 chir_01   C3A     C3B     C3E     O3A   positiv
NM9 chir_02   C1      O1A     O6      C2    positiv
NM9 chir_03   C2      N2A     C3      C1    positiv
NM9 chir_04   C3      O3A     C4      C2    negativ
NM9 chir_05   C4      O4      C3      C5    negativ
NM9 chir_06   C5      O6      C4      C5A   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
NM9 plan-1    C3A 0.020
NM9 plan-1    N3A 0.020
NM9 plan-1    C3E 0.020
NM9 plan-1    OCA 0.020
NM9 plan-1   H3A1 0.020
NM9 plan-1   H3A2 0.020
NM9 plan-2    O2B 0.020
NM9 plan-2     C2 0.020
NM9 plan-2    C2B 0.020
NM9 plan-2    N2A 0.020
NM9 plan-2    H2A 0.020
NM9 plan-2    C2A 0.020
