# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:39:36 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1N[S](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
 5KV  5KV  2-deoxy-6-O-sulfo-2-(sulfoamino)-beta-D-glucopyranose  D-saccharide  31  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5KV
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
 5KV  O13  O  OH1    0  -0.675   0.6902   3.0023  -0.1566
 5KV  C18  C  CH1    0   0.054  -1.2222   1.6208  -0.3192
 5KV  C19  C  CH1    0  -0.004   0.2007   1.7328   0.2193
 5KV  C20  C  CH1    0  -0.028   1.0528   0.5982  -0.3542
 5KV  C21  C  CH1    0  -0.141  -1.8032   0.2268  -0.0777
 5KV  C22  C  CH1    0   0.288  -0.8158  -0.8137  -0.6157
 5KV  O25  O  O2     0  -0.497   0.4519  -0.6333  -0.0257
 5KV  O28  O  OH1    0  -0.639  -1.2567  -2.0768  -0.3032
 5KV  N29  N  NC1    0  -0.767  -3.1062   0.1321  -0.7064
 5KV  O30  O  OH1    0  -0.659  -2.0672   2.5688   0.2739
 5KV  C31  C  CH2    0  -0.170   2.4563   0.6075   0.2069
 5KV  O32  O  OC2    0  -0.615   3.2078  -0.3875  -0.4704
 5KV  S33  S  S      0   1.578   4.7707  -0.5921  -0.0065
 5KV  S34  S  S      0   1.500  -4.4259  -0.4554   0.1674
 5KV  O35  O  OS     0  -0.752  -4.2686  -1.8985   0.4061
 5KV  O36  O  OS    -1  -0.758  -4.4018   0.3300   1.4096
 5KV  O37  O  OS     0  -0.768  -5.5558  -0.1517  -0.7245
 5KV  O38  O  OS     0  -0.746   5.4045   0.7196  -0.1620
 5KV  O39  O  OS    -1  -0.746   4.7131  -1.0568   1.3814
 5KV  O40  O  OS     0  -0.735   5.2086  -1.6000  -0.9686
 5KV  H1   H  HOH1   0   0.463   1.3240   3.3032   0.5003
 5KV  H2   H  HCH1   0   0.197  -1.1715   1.7706  -1.4123
 5KV  H3   H  HCH1   0   0.225   0.1706   1.6299   1.3138
 5KV  H4   H  HCH1   0   0.225   1.1063   0.7209  -1.4489
 5KV  H5   H  HCH1   0   0.258  -1.9056   0.0751   1.0017
 5KV  H6   H  HCH1   0   0.181  -0.7179  -0.6762  -1.7093
 5KV  H7   H  HOH1   0   0.462  -0.8209  -2.7139  -0.8789
 5KV  H8   H  HNC1   0   0.374  -3.0764  -0.2715  -1.6362
 5KV  H9   H  HOH1   0   0.445  -1.6869   3.4375   0.1061
 5KV  H10  H  HCH2   0   0.226   2.8961   1.5955   0.0481
 5KV  H11  H  HCH2   0   0.224   2.4250   0.4149   1.2853

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
 5KV  O30  C18  single  1.402  0.020  1.402
 5KV  O13  C19  single  1.412  0.020  1.412
 5KV  C18  C19  single  1.526  0.020  1.526
 5KV  C18  C21  single  1.529  0.020  1.529
 5KV  O37  S34  deloc   1.471  0.020  1.471
 5KV  C19  C20  single  1.530  0.020  1.530
 5KV  O35  S34  deloc   1.471  0.020  1.471
 5KV  N29  S34  single  1.688  0.020  1.688
 5KV  N29  C21  single  1.450  0.020  1.450
 5KV  S34  O36  deloc   1.470  0.020  1.470
 5KV  C21  C22  single  1.532  0.020  1.532
 5KV  C20  C31  single  1.512  0.020  1.512
 5KV  C20  O25  single  1.409  0.020  1.409
 5KV  C22  O25  single  1.410  0.020  1.410
 5KV  C22  O28  single  1.374  0.020  1.374
 5KV  C31  O32  single  1.419  0.020  1.419
 5KV  O32  S33  single  1.643  0.020  1.643
 5KV  O38  S33  deloc   1.465  0.020  1.465
 5KV  S33  O40  deloc   1.461  0.020  1.461
 5KV  S33  O39  deloc   1.465  0.020  1.465
 5KV  O13  H1   single  0.850  0.020  0.980
 5KV  C18  H2   single  0.970  0.020  1.090
 5KV  C19  H3   single  0.970  0.020  1.090
 5KV  C20  H4   single  0.970  0.020  1.090
 5KV  C21  H5   single  0.970  0.020  1.090
 5KV  C22  H6   single  0.970  0.020  1.090
 5KV  O28  H7   single  0.850  0.020  0.980
 5KV  N29  H8   single  0.890  0.020  1.040
 5KV  O30  H9   single  0.850  0.020  0.980
 5KV  C31  H10  single  0.970  0.020  1.090
 5KV  C31  H11  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
 5KV  H1   O13  C19  109.16  3.000
 5KV  H2   C18  O30  110.77  3.000
 5KV  H2   C18  C21  107.30  3.000
 5KV  O30  C18  C21  108.71  3.000
 5KV  H2   C18  C19  107.25  3.000
 5KV  C21  C18  C19  111.44  3.000
 5KV  O30  C18  C19  111.30  3.000
 5KV  H3   C19  C20  108.59  3.000
 5KV  H3   C19  C18  108.60  3.000
 5KV  C20  C19  C18  109.42  3.000
 5KV  H3   C19  O13  111.02  3.000
 5KV  C20  C19  O13  111.95  3.000
 5KV  C18  C19  O13  107.19  3.000
 5KV  H4   C20  C31  108.83  3.000
 5KV  H4   C20  O25  110.45  3.000
 5KV  C31  C20  O25  108.35  3.000
 5KV  H4   C20  C19  108.45  3.000
 5KV  O25  C20  C19  108.86  3.000
 5KV  C31  C20  C19  111.92  3.000
 5KV  H5   C21  N29  109.53  3.000
 5KV  H5   C21  C22  108.21  3.000
 5KV  N29  C21  C22  112.50  3.000
 5KV  H5   C21  C18  108.51  3.000
 5KV  C22  C21  C18  108.59  3.000
 5KV  N29  C21  C18  109.42  3.000
 5KV  H6   C22  O28  111.55  3.000
 5KV  H6   C22  O25  108.55  3.000
 5KV  O28  C22  O25  108.12  3.000
 5KV  H6   C22  C21  108.65  3.000
 5KV  O28  C22  C21  109.74  3.000
 5KV  O25  C22  C21  110.23  3.000
 5KV  C22  O25  C20  113.43  3.000
 5KV  H7   O28  C22  109.10  3.000
 5KV  H8   N29  S34  111.04  3.000
 5KV  H8   N29  C21  113.41  3.000
 5KV  S34  N29  C21  120.05  3.000
 5KV  H9   O30  C18  107.36  3.000
 5KV  H11  C31  H10  108.25  3.000
 5KV  H11  C31  O32  111.20  3.000
 5KV  H10  C31  O32  110.57  3.000
 5KV  H11  C31  C20  109.74  3.000
 5KV  H10  C31  C20  108.98  3.000
 5KV  O32  C31  C20  108.07  3.000
 5KV  S33  O32  C31  117.15  3.000
 5KV  O40  S33  O39  114.64  3.000
 5KV  O39  S33  O38  113.68  3.000
 5KV  O40  S33  O38  114.72  3.000
 5KV  O39  S33  O32  105.64  3.000
 5KV  O40  S33  O32  100.67  3.000
 5KV  O38  S33  O32  105.67  3.000
 5KV  O37  S34  O36  114.50  3.000
 5KV  O36  S34  O35  112.66  3.000
 5KV  O37  S34  O35  112.52  3.000
 5KV  O36  S34  N29  103.81  3.000
 5KV  O35  S34  N29  109.98  3.000
 5KV  O37  S34  N29  102.40  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
 5KV  Var_01  O37  S34  N29  C21  169.84  30.0  3
 5KV  Var_02  O38  S33  O32  C31  -56.63  30.0  3
 5KV  Var_03  H10  C31  O32  S33   62.12  30.0  1

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
 5KV  chir_01  C18  O30  C19  C21  negativ
 5KV  chir_02  C19  O13  C18  C20  negativ
 5KV  chir_03  C20  O25  C19  C31  negativ
 5KV  chir_04  C21  N29  C22  C18  negativ
 5KV  chir_05  C22  O25  O28  C21  negativ

