# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 10:47:31 2019
#
#   Ligand name: 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
#   Random seed: 3628800
#   SMILES string: 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
GP1        GP1 '2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose' saccharide 28 16 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_GP1
#
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
GP1         C1B    C   CH1    0    .      -0.4651    0.2184   -0.9420
GP1         C2B    C   CH1    0    .       1.0570    0.2407   -1.0034
GP1         C3B    C   CH1    0    .       1.6691    0.2617    0.3491
GP1         C4B    C   CH1    0    .       1.1550   -0.8462    1.2156
GP1         C5B    C   CH1    0    .      -0.3746   -0.8689    1.2728
GP1         C6B    C   CH2    0    .      -0.8515    0.3515    1.9999
GP1         N2B    N   NH2    0    .       1.5282   -0.9784   -1.7274
GP1         O1B    O   O2     0    .      -0.9541    0.0533   -2.1996
GP1         O3B    O   OH1    0    .       1.3622    1.5341    0.9830
GP1         O4B    O   OH1    0    .       1.6159   -2.0937    0.6920
GP1         O5B    O   OH1    0    .      -2.2476    0.3001    2.1348
GP1         O6B    O   O2     0    .      -0.9795   -0.8916   -0.0704
GP1         O7B    O   OP    -1    .      -3.4883    0.0275   -1.7188
GP1         P4B    P   P      0    .      -2.4280    0.6966   -2.5598
GP1         O8B    O   O      0    .      -2.4152    2.1773   -2.2688
GP1         O9B    O   OP    -1    .      -2.7308    0.4737   -4.0225
GP1         H1     H   HCH1   0    .      -0.8134    1.1655   -0.5451
GP1         H2     H   HCH1   0    .       1.3738    1.1242   -1.5461
GP1         H3     H   HCH1   0    .       2.7437    0.1608    0.2501
GP1         H4     H   HCH1   0    .       1.5418   -0.7147    2.2196
GP1         H5     H   HCH1   0    .      -0.6911   -1.7526    1.8137
GP1         H61    H   HCH2   0    .      -0.5748    1.2374    1.4394
GP1         H62    H   HCH2   0    .      -0.3943    0.3883    2.9832
GP1        HN21    H   HNH2   0    .       2.5307   -1.0013   -1.7264
GP1        HN22    H   HNH2   0    .       1.1956   -0.9550   -2.6726
GP1         HO3    H   HOH1   0    .       2.1663    1.9793    1.2013
GP1         HO4    H   HOH1   0    .       1.9466   -2.6278    1.3965
GP1         HO5    H   HOH1   0    .      -2.4777    0.3399    3.0518
#
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
GP1   C1B     C2B   single        1.523 0.020     1.523
GP1   C1B     O1B   single        1.359 0.020     1.359
GP1   C1B     O6B   single        1.502 0.020     1.502
GP1   C1B     H1    single        0.970 0.020     1.090
GP1   C2B     C3B   single        1.485 0.020     1.485
GP1   C2B     N2B   single        1.494 0.020     1.494
GP1   C2B     H2    single        0.970 0.020     1.090
GP1   C3B     C4B   single        1.498 0.020     1.498
GP1   C3B     O3B   single        1.454 0.020     1.454
GP1   C3B     H3    single        0.970 0.020     1.090
GP1   C4B     C5B   single        1.531 0.020     1.531
GP1   C4B     O4B   single        1.429 0.020     1.429
GP1   C4B     H4    single        0.970 0.020     1.090
GP1   C5B     C6B   single        1.499 0.020     1.499
GP1   C5B     O6B   single        1.473 0.020     1.473
GP1   C5B     H5    single        0.970 0.020     1.090
GP1   C6B     O5B   single        1.404 0.020     1.404
GP1   C6B     H61   single        0.970 0.020     1.090
GP1   C6B     H62   single        0.970 0.020     1.090
GP1   N2B    HN21   single        0.890 0.020     1.040
GP1   N2B    HN22   single        0.890 0.020     1.040
GP1   O1B     P4B   single        1.648 0.020     1.648
GP1   O3B     HO3   single        0.850 0.020     0.980
GP1   O4B     HO4   single        0.850 0.020     0.980
GP1   O5B     HO5   single        0.850 0.020     0.980
GP1   O7B     P4B   deloc         1.510 0.020     1.510
GP1   P4B     O8B   deloc         1.509 0.020     1.509
GP1   P4B     O9B   deloc         1.510 0.020     1.510
#
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
GP1   H1      C1B     O6B         108.84 3.000
GP1   H1      C1B     O1B         109.22 3.000
GP1   O6B     C1B     O1B         108.90 3.000
GP1   H1      C1B     C2B         108.84 3.000
GP1   O6B     C1B     C2B         112.10 3.000
GP1   O1B     C1B     C2B         108.90 3.000
GP1   H2      C2B     N2B         109.28 3.000
GP1   H2      C2B     C3B         108.90 3.000
GP1   N2B     C2B     C3B         108.84 3.000
GP1   H2      C2B     C1B         108.91 3.000
GP1   N2B     C2B     C1B         108.83 3.000
GP1   C3B     C2B     C1B         112.05 3.000
GP1   H3      C3B     O3B         109.30 3.000
GP1   H3      C3B     C4B         108.92 3.000
GP1   O3B     C3B     C4B         108.82 3.000
GP1   H3      C3B     C2B         108.92 3.000
GP1   O3B     C3B     C2B         108.81 3.000
GP1   C4B     C3B     C2B         112.03 3.000
GP1   H4      C4B     O4B         109.28 3.000
GP1   H4      C4B     C5B         108.89 3.000
GP1   O4B     C4B     C5B         108.84 3.000
GP1   H4      C4B     C3B         108.89 3.000
GP1   O4B     C4B     C3B         108.85 3.000
GP1   C5B     C4B     C3B         112.06 3.000
GP1   H5      C5B     O6B         108.83 3.000
GP1   H5      C5B     C6B         109.21 3.000
GP1   O6B     C5B     C6B         108.92 3.000
GP1   H5      C5B     C4B         108.83 3.000
GP1   O6B     C5B     C4B         112.11 3.000
GP1   C6B     C5B     C4B         108.90 3.000
GP1   H62     C6B     H61         109.47 3.000
GP1   H62     C6B     O5B         109.47 3.000
GP1   H61     C6B     O5B         109.48 3.000
GP1   H62     C6B     C5B         109.47 3.000
GP1   H61     C6B     C5B         109.47 3.000
GP1   O5B     C6B     C5B         109.47 3.000
GP1  HN22     N2B    HN21         109.47 3.000
GP1  HN22     N2B     C2B         109.47 3.000
GP1  HN21     N2B     C2B         109.48 3.000
GP1   P4B     O1B     C1B         118.46 3.000
GP1   HO3     O3B     C3B         109.48 3.000
GP1   HO4     O4B     C4B         109.47 3.000
GP1   HO5     O5B     C6B         109.48 3.000
GP1   C5B     O6B     C1B         112.15 3.000
GP1   O9B     P4B     O8B         109.47 3.000
GP1   O9B     P4B     O7B         109.47 3.000
GP1   O8B     P4B     O7B         109.47 3.000
GP1   O9B     P4B     O1B         109.48 3.000
GP1   O8B     P4B     O1B         109.47 3.000
GP1   O7B     P4B     O1B         109.47 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
GP1 Var_01         O7B     P4B     O1B     C1B         -63.67  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
GP1 chir_01   C1B     C2B     O1B     O6B   negativ
GP1 chir_02   C2B     N2B     C3B     C1B   positiv
GP1 chir_03   C3B     O3B     C2B     C4B   positiv
GP1 chir_04   C4B     O4B     C5B     C3B   positiv
GP1 chir_05   C5B     O6B     C4B     C6B   negativ
