# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 12:52:06 2019
#
#   Ligand name: 2-(acetylamino)-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P](O)(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
GN1        GN1 '2-(acetylamino)-2-deoxy-1-O-phosphono-alpha-D-glucopyranose' d-saccharide 33 19 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_GN1
#
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
GN1        C1'     C   CH1    0    .      -0.9082    0.5640   -0.4114
GN1         OP1    O   OP    -1    .      -2.8363    2.5894   -1.7986
GN1         P      P   P      0    .      -2.8664    1.1033   -2.0641
GN1         OP2    O   OP    -1    .      -3.9196    0.4582   -1.1956
GN1         OP3    O   O      0    .      -3.1935    0.8582   -3.5179
GN1        C2'     C   CH1    0    .       0.5814    0.5408   -0.4497
GN1        C3'     C   CH1    0    .       1.1744    0.5178    0.8797
GN1        C4'     C   CH1    0    .       0.6437   -0.5835    1.7177
GN1        C5'     C   CH1    0    .      -0.9083   -0.5566    1.8247
GN1        C6'     C   CH2    0    .      -1.3224    0.6003    2.5261
GN1        C8'     C   CH3    0    .       2.5625   -1.8688   -2.9408
GN1        O1'     O   O2     0    .      -1.3927    0.4528   -1.7153
GN1        O3'     O   OH1    0    .       0.8863    1.8054    1.5502
GN1        O4'     O   OH1    0    .       1.0428   -1.8287    1.1452
GN1        O5'     O   O2     0    .      -1.4689   -0.5305    0.3973
GN1        N2'     N   NH1    0    .       1.0334   -0.7110   -1.2108
GN1        C7'     C   C      0    .       2.1084   -0.6202   -2.1854
GN1        O6'     O   OH1    0    .      -2.6768    0.4826    2.8627
GN1        O7'     O   O      0    .       2.6349    0.4208   -2.3912
GN1        H1'     H   HCH1   0    .      -1.2313    1.5084    0.0084
GN1        H2'     H   HCH1   0    .       0.9314    1.4222   -0.9734
GN1        H3'     H   HCH1   0    .       2.2472    0.3980    0.7826
GN1        H4'     H   HCH1   0    .       1.0636   -0.4984    2.7125
GN1        H5'     H   HCH1   0    .      -1.2547   -1.4466    2.3371
GN1        H6'1    H   HCH2   0    .      -1.1805    1.4736    1.8988
GN1        H6'2    H   HCH2   0    .      -0.7321    0.7052    3.4316
GN1        H8'1    H   HCH3   0    .       1.7033   -2.3434   -3.4052
GN1        H8'2    H   HCH3   0    .       3.2796   -1.5876   -3.7077
GN1        H8'3    H   HCH3   0    .       3.0280   -2.5625   -2.2467
GN1        HO3'    H   HOH1   0    .       1.6868    2.2929    1.6514
GN1        HO4'    H   HOH1   0    .       1.4999   -2.3405    1.7929
GN1        HN2'    H   HNH1   0    .       0.6117   -1.5966   -1.0122
GN1        HO6'    H   HOH1   0    .      -2.8276    0.8810    3.7072
#
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
GN1  C1'     O1'    single        1.395 0.020     1.395
GN1  C1'     O5'    single        1.472 0.020     1.472
GN1  C1'     C2'    single        1.490 0.020     1.490
GN1  C1'     H1'    single        0.970 0.020     1.090
GN1   OP1     P     deloc         1.510 0.020     1.510
GN1   P       OP3   deloc         1.510 0.020     1.510
GN1   P       OP2   deloc         1.510 0.020     1.510
GN1   P      O1'    single        1.648 0.020     1.648
GN1  C2'     C3'    single        1.456 0.020     1.456
GN1  C2'     N2'    single        1.533 0.020     1.533
GN1  C2'     H2'    single        0.970 0.020     1.090
GN1  C3'     C4'    single        1.482 0.020     1.482
GN1  C3'     O3'    single        1.480 0.020     1.480
GN1  C3'     H3'    single        0.970 0.020     1.090
GN1  C4'     C5'    single        1.556 0.020     1.556
GN1  C4'     O4'    single        1.427 0.020     1.427
GN1  C4'     H4'    single        0.970 0.020     1.090
GN1  C5'     C6'    single        1.415 0.020     1.415
GN1  C5'     O5'    single        1.534 0.020     1.534
GN1  C5'     H5'    single        0.970 0.020     1.090
GN1  C6'     O6'    single        1.401 0.020     1.401
GN1  C6'     H6'1   single        0.970 0.020     1.090
GN1  C6'     H6'2   single        0.970 0.020     1.090
GN1  C8'     C7'    single        1.528 0.020     1.528
GN1  C8'     H8'1   single        0.970 0.020     1.090
GN1  C8'     H8'2   single        0.970 0.020     1.090
GN1  C8'     H8'3   single        0.970 0.020     1.090
GN1  O3'     HO3'   single        0.850 0.020     0.980
GN1  O4'     HO4'   single        0.850 0.020     0.980
GN1  N2'     C7'    single        1.454 0.020     1.454
GN1  N2'     HN2'   single        0.860 0.020     1.020
GN1  C7'     O7'    double        1.185 0.020     1.185
GN1  O6'     HO6'   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
GN1  H1'     C1'     O5'          108.77 3.000
GN1  H1'     C1'     O1'          109.16 3.000
GN1  O5'     C1'     O1'          108.77 3.000
GN1  H1'     C1'     C2'          108.77 3.000
GN1  O5'     C1'     C2'          112.54 3.000
GN1  O1'     C1'     C2'          108.77 3.000
GN1  O1'      P       OP3         109.47 3.000
GN1  O1'      P       OP2         109.47 3.000
GN1   OP3     P       OP2         109.47 3.000
GN1  O1'      P       OP1         109.47 3.000
GN1   OP2     P       OP1         109.47 3.000
GN1   OP3     P       OP1         109.47 3.000
GN1  H2'     C2'     N2'          109.21 3.000
GN1  H2'     C2'     C3'          108.83 3.000
GN1  N2'     C2'     C3'          108.68 3.000
GN1  H2'     C2'     C1'          108.83 3.000
GN1  N2'     C2'     C1'          108.67 3.000
GN1  C3'     C2'     C1'          112.58 3.000
GN1  H3'     C3'     O3'          109.23 3.000
GN1  H3'     C3'     C4'          108.85 3.000
GN1  O3'     C3'     C4'          108.70 3.000
GN1  H3'     C3'     C2'          108.85 3.000
GN1  O3'     C3'     C2'          108.70 3.000
GN1  C4'     C3'     C2'          112.47 3.000
GN1  H4'     C4'     O4'          109.18 3.000
GN1  H4'     C4'     C5'          108.79 3.000
GN1  O4'     C4'     C5'          108.75 3.000
GN1  H4'     C4'     C3'          108.79 3.000
GN1  O4'     C4'     C3'          108.75 3.000
GN1  C5'     C4'     C3'          112.53 3.000
GN1  H5'     C5'     O5'          109.70 3.000
GN1  H5'     C5'     C6'          110.09 3.000
GN1  O5'     C5'     C6'          109.90 3.000
GN1  H5'     C5'     C4'          109.70 3.000
GN1  O5'     C5'     C4'          107.51 3.000
GN1  C6'     C5'     C4'          109.89 3.000
GN1  H6'2    C6'     H6'1         109.47 3.000
GN1  H6'2    C6'     O6'          109.47 3.000
GN1  H6'1    C6'     O6'          109.47 3.000
GN1  H6'2    C6'     C5'          109.46 3.000
GN1  H6'1    C6'     C5'          109.47 3.000
GN1  O6'     C6'     C5'          109.48 3.000
GN1  H8'3    C8'     H8'2         109.47 3.000
GN1  H8'3    C8'     H8'1         109.47 3.000
GN1  H8'2    C8'     H8'1         109.47 3.000
GN1  H8'3    C8'     C7'          109.47 3.000
GN1  H8'2    C8'     C7'          109.47 3.000
GN1  H8'1    C8'     C7'          109.47 3.000
GN1   P      O1'     C1'          118.47 3.000
GN1  HO3'    O3'     C3'          109.47 3.000
GN1  HO4'    O4'     C4'          109.47 3.000
GN1  C5'     O5'     C1'          112.63 3.000
GN1  HN2'    N2'     C7'          119.99 3.000
GN1  HN2'    N2'     C2'          119.99 3.000
GN1  C7'     N2'     C2'          119.99 3.000
GN1  O7'     C7'     N2'          120.00 3.000
GN1  O7'     C7'     C8'          120.00 3.000
GN1  N2'     C7'     C8'          120.00 3.000
GN1  HO6'    O6'     C6'          109.48 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
GN1 CONST_01       C8'     C7'     N2'    C2'          179.79   0.0 0
GN1 CONST_02       O7'     C7'     N2'    C2'            0.00   0.0 0
GN1 CONST_03      HN2'     N2'     C7'     C8'           2.06   0.0 0
GN1 Var_01         OP1     P      O1'     C1'           60.46  30.0 2
GN1 Var_02        H8'1     C8'     C7'     N2'          52.92  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
GN1 chir_01  C1'     O1'     O5'     C2'    negativ
GN1 chir_02  C2'      N2'    C3'     C1'    positiv
GN1 chir_03  C3'     O3'     C2'     C4'    positiv
GN1 chir_04  C4'     O4'     C5'     C3'    positiv
GN1 chir_05  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
GN1 plan-1    C2' 0.020
GN1 plan-1    C8' 0.020
GN1 plan-1    N2' 0.020
GN1 plan-1    C7' 0.020
GN1 plan-1    O7' 0.020
GN1 plan-1   HN2' 0.020
