# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 08:37:21 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-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
 YJM  YJM  2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-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_YJM
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
 YJM  C01   C  CH1    0   0.253   0.9102   0.7962  -0.5006
 YJM  C02   C  CH1    0  -0.156   1.8343  -0.3346  -0.0292
 YJM  C03   C  CH1    0   0.048   1.2285  -1.6919  -0.3801
 YJM  C04   C  CH1    0  -0.011  -0.1986  -1.7730   0.1537
 YJM  C05   C  CH1    0  -0.019  -1.0221  -0.5881  -0.3571
 YJM  C06   C  CH2    0  -0.172  -2.4074  -0.5731   0.2501
 YJM  N07   N  NC1    0  -0.756   3.1797  -0.2348  -0.5600
 YJM  O08   O  OH1    0  -0.664   2.0342  -2.6977   0.1768
 YJM  O09   O  OH1    0  -0.675  -0.7393  -3.0042  -0.2769
 YJM  O10   O  O2     0  -0.500  -0.3888   0.6258   0.0008
 YJM  O11   O  OC2    0  -0.615  -3.1491   0.4626  -0.3761
 YJM  S12   S  S      0   1.504   4.2788   0.7655   0.2463
 YJM  O13   O  OS     0  -0.760   5.5118   0.5818  -0.5312
 YJM  O14   O  OS     0  -0.756   3.7834   2.1550   0.2146
 YJM  O15   O  OS    -1  -0.758   4.3284   0.2182   1.6094
 YJM  S16   S  S      0   1.578  -4.6907   0.7013   0.1375
 YJM  O17   O  OS     0  -0.746  -5.3693  -0.5865  -0.0302
 YJM  O18   O  OS    -1  -0.746  -4.5808   1.1309   1.5335
 YJM  O19   O  OS     0  -0.736  -5.1252   1.7438  -0.7888
 YJM  O20   O  OH1    0  -0.668   0.9403   0.8272  -1.8935
 YJM  H01   H  HCH1   0   0.239   1.2512   1.7443  -0.0773
 YJM  H02   H  HCH1   0   0.266   1.8940  -0.2720   1.0615
 YJM  H03   H  HCH1   0   0.207   1.1858  -1.7920  -1.4769
 YJM  H04   H  HCH1   0   0.224  -0.1558  -1.7253   1.2517
 YJM  H05   H  HCH1   0   0.227  -1.1179  -0.6746  -1.4485
 YJM  H06   H  HCH2   0   0.225  -2.8845  -1.5418   0.0798
 YJM  H06A  H  HCH2   0   0.222  -2.3362  -0.4106   1.3316
 YJM  HN07  H  HNC1   0   0.372   3.1760  -0.0191  -1.5522
 YJM  HO08  H  HOH1   0   0.446   1.6104  -3.5420  -0.0106
 YJM  HO09  H  HOH1   0   0.463  -1.3606  -3.3250   0.3824
 YJM  HO20  H  HOH1   0   0.465   0.6108   1.6790  -2.1985

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
 YJM  O10  C01   single  1.403  0.020  1.403
 YJM  C02  C01   single  1.535  0.020  1.535
 YJM  C01  O20   single  1.394  0.020  1.394
 YJM  C01  H01   single  0.970  0.020  1.090
 YJM  C03  C02   single  1.527  0.020  1.527
 YJM  C02  N07   single  1.450  0.020  1.450
 YJM  C02  H02   single  0.970  0.020  1.090
 YJM  C04  C03   single  1.526  0.020  1.526
 YJM  C03  O08   single  1.404  0.020  1.404
 YJM  C03  H03   single  0.970  0.020  1.090
 YJM  O09  C04   single  1.412  0.020  1.412
 YJM  C04  C05   single  1.531  0.020  1.531
 YJM  C04  H04   single  0.970  0.020  1.090
 YJM  C06  C05   single  1.513  0.020  1.513
 YJM  C05  O10   single  1.415  0.020  1.415
 YJM  C05  H05   single  0.970  0.020  1.090
 YJM  C06  O11   single  1.420  0.020  1.420
 YJM  C06  H06   single  0.970  0.020  1.090
 YJM  C06  H06A  single  0.970  0.020  1.090
 YJM  N07  S12   single  1.691  0.020  1.691
 YJM  N07  HN07  single  0.890  0.020  1.040
 YJM  O08  HO08  single  0.850  0.020  0.980
 YJM  O09  HO09  single  0.850  0.020  0.980
 YJM  S16  O11   single  1.642  0.020  1.642
 YJM  O13  S12   deloc   1.469  0.020  1.469
 YJM  O14  S12   deloc   1.476  0.020  1.476
 YJM  S12  O15   deloc   1.470  0.020  1.470
 YJM  O19  S16   deloc   1.461  0.020  1.461
 YJM  S16  O17   deloc   1.465  0.020  1.465
 YJM  S16  O18   deloc   1.465  0.020  1.465
 YJM  O20  HO20  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
 YJM  H01   C01  O20  111.16  3.000
 YJM  H01   C01  O10  104.82  3.000
 YJM  O20   C01  O10  112.33  3.000
 YJM  H01   C01  C02  109.42  3.000
 YJM  O20   C01  C02  108.09  3.000
 YJM  O10   C01  C02  111.00  3.000
 YJM  H02   C02  N07  108.08  3.000
 YJM  H02   C02  C03  107.55  3.000
 YJM  N07   C02  C03  110.19  3.000
 YJM  H02   C02  C01  107.27  3.000
 YJM  N07   C02  C01  113.31  3.000
 YJM  C03   C02  C01  110.21  3.000
 YJM  H03   C03  O08  110.61  3.000
 YJM  H03   C03  C04  107.88  3.000
 YJM  O08   C03  C04  111.09  3.000
 YJM  H03   C03  C02  108.95  3.000
 YJM  O08   C03  C02  108.54  3.000
 YJM  C04   C03  C02  109.75  3.000
 YJM  H04   C04  O09  110.93  3.000
 YJM  H04   C04  C05  108.69  3.000
 YJM  O09   C04  C05  111.54  3.000
 YJM  H04   C04  C03  108.10  3.000
 YJM  C05   C04  C03  110.20  3.000
 YJM  O09   C04  C03  107.33  3.000
 YJM  H05   C05  O10  110.96  3.000
 YJM  H05   C05  C06  108.63  3.000
 YJM  O10   C05  C06  107.45  3.000
 YJM  H05   C05  C04  108.51  3.000
 YJM  O10   C05  C04  109.81  3.000
 YJM  C06   C05  C04  111.49  3.000
 YJM  H06A  C06  H06  108.27  3.000
 YJM  H06A  C06  O11  111.17  3.000
 YJM  H06   C06  O11  110.47  3.000
 YJM  H06A  C06  C05  109.76  3.000
 YJM  H06   C06  C05  109.17  3.000
 YJM  O11   C06  C05  107.98  3.000
 YJM  HN07  N07  S12  110.04  3.000
 YJM  HN07  N07  C02  111.65  3.000
 YJM  S12   N07  C02  118.00  3.000
 YJM  HO08  O08  C03  107.36  3.000
 YJM  HO09  O09  C04  109.24  3.000
 YJM  C05   O10  C01  115.35  3.000
 YJM  S16   O11  C06  117.29  3.000
 YJM  O15   S12  O14  112.45  3.000
 YJM  O15   S12  O13  114.58  3.000
 YJM  O14   S12  O13  112.84  3.000
 YJM  O15   S12  N07  104.12  3.000
 YJM  O14   S12  N07  109.18  3.000
 YJM  O13   S12  N07  102.66  3.000
 YJM  O19   S16  O18  114.67  3.000
 YJM  O18   S16  O17  113.68  3.000
 YJM  O19   S16  O17  114.64  3.000
 YJM  O18   S16  O11  105.68  3.000
 YJM  O17   S16  O11  105.73  3.000
 YJM  O19   S16  O11  100.64  3.000
 YJM  HO20  O20  C01  109.21  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
 YJM  Var_01  O13  S12  N07  C02   178.17  30.0  3
 YJM  Var_02  O19  S16  O11  C06  -176.00  30.0  2
 YJM  Var_03  H06  C06  O11  S16    61.87  30.0  2

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
 YJM  chir_01  C01  O10  C02  O20  negativ
 YJM  chir_02  C02  N07  C03  C01  positiv
 YJM  chir_03  C03  O08  C02  C04  positiv
 YJM  chir_04  C04  O09  C05  C03  positiv
 YJM  chir_05  C05  O10  C04  C06  negativ

