# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:11:13 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-amino-2-deoxy-6-O-phosphono-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1O
#
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
 4R1  4R1  2-amino-2-deoxy-6-O-phosphono-beta-D-glucopyranose  D-saccharide  30  16  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4R1
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
 4R1  C2   C  CH1   0  -0.154  -3.1409   0.6120  -0.2690
 4R1  C4   C  CH1   0   0.034  -1.5525  -1.3360  -0.2075
 4R1  C5   C  CH1   0  -0.021  -0.4815  -0.3592   0.2788
 4R1  C6   C  CH2   0  -0.174   0.8899  -0.7685  -0.2061
 4R1  O1   O  OH1   0  -0.658  -2.1017   2.7380  -0.2623
 4R1  OAF  O  OH1   0  -0.731   3.9539   1.0947   0.9307
 4R1  PAP  P  P     0   1.457   3.3816  -0.0047  -0.0704
 4R1  OAG  O  OH1   0  -0.741   3.5051   0.5695  -1.5568
 4R1  OAB  O  O     0  -0.712   3.9611  -1.3599  -0.0195
 4R1  O6   O  O2    0  -0.589   1.8502   0.1303   0.3576
 4R1  O5   O  O2    0  -0.498  -0.7539   0.9284  -0.2178
 4R1  C1   C  CH1   0   0.300  -1.9793   1.4589   0.2391
 4R1  N2   N  NH2   0  -0.809  -4.3886   1.1248   0.2643
 4R1  C3   C  CH1   0   0.001  -2.9259  -0.8218   0.2081
 4R1  O3   O  OH1   0  -0.677  -3.9046  -1.6915  -0.3267
 4R1  O4   O  OH1   0  -0.673  -1.2837  -2.5958   0.3549
 4R1  H1   H  HCH1  0   0.219  -3.0971   0.6206  -1.3710
 4R1  H2   H  HCH1  0   0.213  -1.5097  -1.3767  -1.3080
 4R1  H3   H  HCH1  0   0.232  -0.4859  -0.3580   1.3815
 4R1  H4   H  HCH2  0   0.256   1.1012  -1.7905   0.1096
 4R1  H5   H  HCH2  0   0.238   0.9226  -0.7298  -1.2997
 4R1  H6   H  HOH1  0   0.465  -1.5550   3.3393   0.2546
 4R1  H7   H  HOH1  0   0.504   4.9186   1.1546   0.9407
 4R1  H8   H  HOH1  0   0.496   3.2095   1.4807  -1.6851
 4R1  H9   H  HCH1  0   0.186  -1.9871   1.4523   1.3429
 4R1  H10  H  HNH2  0   0.350  -4.5646   2.0472  -0.1126
 4R1  H11  H  HNH2  0   0.347  -5.1534   0.5495  -0.0659
 4R1  H13  H  HCH1  0   0.225  -2.9708  -0.8266   1.3068
 4R1  H14  H  HOH1  0   0.463  -4.5337  -1.9192   0.3623
 4R1  H15  H  HOH1  0   0.453  -1.9755  -3.2013   0.0675

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
 4R1  O1   C1   single  1.379  0.020  1.379
 4R1  N2   C2   single  1.451  0.020  1.451
 4R1  C1   O5   single  1.411  0.020  1.411
 4R1  C1   C2   single  1.525  0.020  1.525
 4R1  O5   C5   single  1.407  0.020  1.407
 4R1  C2   C3   single  1.526  0.020  1.526
 4R1  OAB  PAP  double  1.475  0.020  1.475
 4R1  O6   PAP  single  1.596  0.020  1.596
 4R1  O6   C6   single  1.431  0.020  1.431
 4R1  C5   C6   single  1.511  0.020  1.511
 4R1  C5   C4   single  1.529  0.020  1.529
 4R1  C3   O3   single  1.414  0.020  1.414
 4R1  C3   C4   single  1.524  0.020  1.524
 4R1  PAP  OAG  single  1.598  0.020  1.598
 4R1  PAP  OAF  single  1.593  0.020  1.593
 4R1  C4   O4   single  1.406  0.020  1.406
 4R1  C2   H1   single  0.970  0.020  1.090
 4R1  C4   H2   single  0.970  0.020  1.090
 4R1  C5   H3   single  0.970  0.020  1.090
 4R1  C6   H4   single  0.970  0.020  1.090
 4R1  C6   H5   single  0.970  0.020  1.090
 4R1  O1   H6   single  0.850  0.020  0.980
 4R1  OAF  H7   single  0.850  0.020  0.980
 4R1  OAG  H8   single  0.850  0.020  0.980
 4R1  C1   H9   single  0.970  0.020  1.090
 4R1  N2   H10  single  0.890  0.020  1.040
 4R1  N2   H11  single  0.890  0.020  1.040
 4R1  C3   H13  single  0.970  0.020  1.090
 4R1  O3   H14  single  0.850  0.020  0.980
 4R1  O4   H15  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
 4R1  H1   C2   C3   108.30  3.000
 4R1  H1   C2   N2   113.50  3.000
 4R1  C3   C2   N2   109.77  3.000
 4R1  H1   C2   C1   107.36  3.000
 4R1  C3   C2   C1   108.08  3.000
 4R1  N2   C2   C1   109.66  3.000
 4R1  H2   C4   O4   111.04  3.000
 4R1  H2   C4   C3   108.65  3.000
 4R1  O4   C4   C3   111.45  3.000
 4R1  H2   C4   C5   108.30  3.000
 4R1  O4   C4   C5   108.14  3.000
 4R1  C3   C4   C5   109.20  3.000
 4R1  H3   C5   O5   110.56  3.000
 4R1  H3   C5   C6   108.96  3.000
 4R1  O5   C5   C6   108.08  3.000
 4R1  H3   C5   C4   108.42  3.000
 4R1  C6   C5   C4   111.14  3.000
 4R1  O5   C5   C4   109.69  3.000
 4R1  H5   C6   H4   108.46  3.000
 4R1  H5   C6   O6   110.56  3.000
 4R1  H4   C6   O6   110.16  3.000
 4R1  H5   C6   C5   109.76  3.000
 4R1  H4   C6   C5   109.69  3.000
 4R1  O6   C6   C5   108.21  3.000
 4R1  H6   O1   C1   109.48  3.000
 4R1  H7   OAF  PAP  114.07  3.000
 4R1  O6   PAP  OAB  116.46  3.000
 4R1  O6   PAP  OAG  107.05  3.000
 4R1  OAB  PAP  OAG  109.38  3.000
 4R1  OAG  PAP  OAF  107.98  3.000
 4R1  O6   PAP  OAF   96.77  3.000
 4R1  OAB  PAP  OAF  118.11  3.000
 4R1  H8   OAG  PAP  116.01  3.000
 4R1  PAP  O6   C6   119.03  3.000
 4R1  C1   O5   C5   113.44  3.000
 4R1  H9   C1   O5   109.13  3.000
 4R1  H9   C1   O1   111.62  3.000
 4R1  O5   C1   O1   107.94  3.000
 4R1  H9   C1   C2   108.93  3.000
 4R1  O5   C1   C2   110.17  3.000
 4R1  O1   C1   C2   109.05  3.000
 4R1  H11  N2   H10  105.38  3.000
 4R1  H11  N2   C2   109.21  3.000
 4R1  H10  N2   C2   109.57  3.000
 4R1  H13  C3   O3   110.30  3.000
 4R1  H13  C3   C4   107.92  3.000
 4R1  O3   C3   C4   108.24  3.000
 4R1  H13  C3   C2   108.10  3.000
 4R1  C4   C3   C2   111.01  3.000
 4R1  O3   C3   C2   111.22  3.000
 4R1  H14  O3   C3   109.14  3.000
 4R1  H15  O4   C4   107.86  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
 4R1  Var_01  OAB  PAP  O6  C6   -48.76  30.0  3
 4R1  Var_02  H4   C6   O6  PAP   64.39  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
 4R1  chir_01  C2  N2  C1  C3  negativ
 4R1  chir_02  C4  O4  C3  C5  negativ
 4R1  chir_03  C5  O5  C4  C6  negativ
 4R1  chir_04  C1  O1  O5  C2  positiv
 4R1  chir_05  C3  O3  C4  C2  negativ

