# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:40:10 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: propan-2-yl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 LVZ  LVZ  'propan-2-yl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside'  D-saccharide  40  23  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LVZ
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
 LVZ  C1A   C  CH1    0   0.040  -27.4277  27.3245  35.1766
 LVZ  C2A   C  CH3    0  -0.673  -27.1394  27.6023  33.7106
 LVZ  O1    O  O2     0  -0.497  -28.2044  28.3770  35.7474
 LVZ  C3A   C  CH3    0  -0.663  -28.1921  26.0261  35.3665
 LVZ  N9    N  NC1    0  -0.773  -29.5270  29.0112  38.1197
 LVZ  C1    C  CH1    0   0.289  -27.5537  29.2178  36.6289
 LVZ  S19   S  S      0   1.498  -29.0342  28.1719  39.5117
 LVZ  O1S   O  OS    -1  -0.752  -28.4756  29.1460  40.4666
 LVZ  C2    C  CH1    0  -0.129  -28.5837  29.9356  37.5119
 LVZ  S29   S  S      0   1.565  -24.0616  31.2029  33.3385
 LVZ  O2S   O  OS     0  -0.747  -28.0319  27.2053  39.0360
 LVZ  C3    C  CH1    0   0.011  -29.3605  30.9600  36.6907
 LVZ  O3    O  OH1    0  -0.666  -30.2063  31.6585  37.5737
 LVZ  O3S   O  OS     0  -0.754  -30.2904  27.5623  39.9678
 LVZ  C4    C  CH1    0   0.012  -28.4049  31.9018  35.9650
 LVZ  O4    O  OH1    0  -0.671  -29.1908  32.7544  35.1615
 LVZ  O4S   O  OS     0  -0.740  -23.8831  32.4721  32.6306
 LVZ  C5    C  CH1    0  -0.019  -27.4327  31.0672  35.1301
 LVZ  O5    O  O2     0  -0.502  -26.7456  30.1638  35.9752
 LVZ  O5S   O  OS    -1  -0.738  -23.4956  31.1944  34.6895
 LVZ  C6    C  CH2    0  -0.174  -26.3839  31.8951  34.4163
 LVZ  O6    O  OC2    0  -0.613  -25.6846  31.0318  33.5317
 LVZ  O6S   O  OS     0  -0.732  -23.7631  30.0147  32.5427
 LVZ  H1A   H  HCH1   0   0.205  -26.4733  27.2484  35.7132
 LVZ  H2A   H  HCH3   0   0.223  -26.5809  26.7729  33.2748
 LVZ  H2AA  H  HCH3   0   0.238  -26.5488  28.5078  33.5804
 LVZ  H2B   H  HCH3   0   0.218  -28.0675  27.7101  33.1458
 LVZ  H1    H  HCH1   0   0.230  -26.8564  28.6583  37.2609
 LVZ  H2    H  HCH1   0   0.242  -28.0073  30.4893  38.2676
 LVZ  H3A   H  HCH3   0   0.221  -27.6264  25.1890  34.9563
 LVZ  H3AA  H  HCH3   0   0.221  -29.1557  26.0607  34.8547
 LVZ  H3B   H  HCH3   0   0.228  -28.3703  25.8277  36.4235
 LVZ  H3    H  HCH1   0   0.218  -29.9542  30.4270  35.9318
 LVZ  H4    H  HCH1   0   0.223  -27.8384  32.4723  36.7152
 LVZ  H5    H  HCH1   0   0.225  -28.0155  30.5265  34.3707
 LVZ  H61   H  HCH2   0   0.226  -26.8609  32.6947  33.8438
 LVZ  H62   H  HCH2   0   0.223  -25.7175  32.3594  35.1505
 LVZ  HN9   H  HNC1   0   0.376  -30.3863  29.5005  38.3500
 LVZ  HO3   H  HOH1   0   0.452  -30.7874  32.2197  37.0503
 LVZ  HO4   H  HOH1   0   0.460  -28.7667  33.6149  35.1049

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
 LVZ  C2A   C1A  single  1.520  0.020  1.520
 LVZ  C1A   C3A  single  1.519  0.020  1.519
 LVZ  C1A   O1   single  1.427  0.020  1.427
 LVZ  C1A   H1A  single  0.970  0.020  1.090
 LVZ  H2AA  C2A  single  0.970  0.020  1.090
 LVZ  H2A   C2A  single  0.970  0.020  1.090
 LVZ  C2A   H2B  single  0.970  0.020  1.090
 LVZ  O1    C1   single  1.381  0.020  1.381
 LVZ  H3B   C3A  single  0.970  0.020  1.090
 LVZ  H3AA  C3A  single  0.970  0.020  1.090
 LVZ  C3A   H3A  single  0.970  0.020  1.090
 LVZ  HN9   N9   single  0.890  0.020  1.040
 LVZ  C2    N9   single  1.454  0.020  1.454
 LVZ  N9    S19  single  1.699  0.020  1.699
 LVZ  O5    C1   single  1.405  0.020  1.405
 LVZ  C1    H1   single  0.970  0.020  1.090
 LVZ  C1    C2   single  1.535  0.020  1.535
 LVZ  O2S   S19  deloc   1.471  0.020  1.471
 LVZ  S19   O3S  deloc   1.469  0.020  1.469
 LVZ  S19   O1S  deloc   1.474  0.020  1.474
 LVZ  C3    C2   single  1.525  0.020  1.525
 LVZ  C2    H2   single  0.970  0.020  1.090
 LVZ  O4S   S29  deloc   1.464  0.020  1.464
 LVZ  O6S   S29  deloc   1.461  0.020  1.461
 LVZ  O6    S29  single  1.643  0.020  1.643
 LVZ  S29   O5S  deloc   1.465  0.020  1.465
 LVZ  C4    C3   single  1.525  0.020  1.525
 LVZ  H3    C3   single  0.970  0.020  1.090
 LVZ  C3    O3   single  1.408  0.020  1.408
 LVZ  HO3   O3   single  0.850  0.020  0.980
 LVZ  C5    C4   single  1.529  0.020  1.529
 LVZ  O4    C4   single  1.411  0.020  1.411
 LVZ  C4    H4   single  0.970  0.020  1.090
 LVZ  O4    HO4  single  0.850  0.020  0.980
 LVZ  C6    C5   single  1.515  0.020  1.515
 LVZ  H5    C5   single  0.970  0.020  1.090
 LVZ  C5    O5   single  1.415  0.020  1.415
 LVZ  O6    C6   single  1.420  0.020  1.420
 LVZ  H61   C6   single  0.970  0.020  1.090
 LVZ  C6    H62  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
 LVZ  H1A   C1A  C3A   108.50  3.000
 LVZ  H1A   C1A  O1    109.20  3.000
 LVZ  C3A   C1A  O1    107.85  3.000
 LVZ  H1A   C1A  C2A   108.62  3.000
 LVZ  O1    C1A  C2A   110.75  3.000
 LVZ  C3A   C1A  C2A   111.87  3.000
 LVZ  H2B   C2A  H2AA  108.49  3.000
 LVZ  H2B   C2A  H2A   107.68  3.000
 LVZ  H2AA  C2A  H2A   107.87  3.000
 LVZ  H2B   C2A  C1A   110.84  3.000
 LVZ  H2A   C2A  C1A   110.09  3.000
 LVZ  H2AA  C2A  C1A   111.73  3.000
 LVZ  C1    O1   C1A   116.61  3.000
 LVZ  H3B   C3A  H3AA  108.43  3.000
 LVZ  H3AA  C3A  H3A   107.82  3.000
 LVZ  H3B   C3A  H3A   108.05  3.000
 LVZ  H3A   C3A  C1A   110.37  3.000
 LVZ  H3AA  C3A  C1A   111.01  3.000
 LVZ  H3B   C3A  C1A   111.04  3.000
 LVZ  HN9   N9   C2    109.73  3.000
 LVZ  C2    N9   S19   117.94  3.000
 LVZ  HN9   N9   S19   107.33  3.000
 LVZ  H1    C1   O5    104.26  3.000
 LVZ  H1    C1   C2    109.53  3.000
 LVZ  O5    C1   C2    109.80  3.000
 LVZ  C2    C1   O1    109.62  3.000
 LVZ  H1    C1   O1    110.94  3.000
 LVZ  O5    C1   O1    112.57  3.000
 LVZ  O3S   S19  O2S   114.22  3.000
 LVZ  O3S   S19  O1S   113.41  3.000
 LVZ  O2S   S19  O1S   112.67  3.000
 LVZ  O1S   S19  N9    108.32  3.000
 LVZ  O3S   S19  N9    102.20  3.000
 LVZ  O2S   S19  N9    104.91  3.000
 LVZ  H2    C2   C3    107.37  3.000
 LVZ  H2    C2   C1    106.20  3.000
 LVZ  C3    C2   C1    110.25  3.000
 LVZ  H2    C2   N9    111.89  3.000
 LVZ  C3    C2   N9    108.76  3.000
 LVZ  C1    C2   N9    112.25  3.000
 LVZ  O6S   S29  O6    100.44  3.000
 LVZ  O6    S29  O5S   105.82  3.000
 LVZ  O6S   S29  O5S   114.75  3.000
 LVZ  O5S   S29  O4S   113.82  3.000
 LVZ  O6    S29  O4S   105.52  3.000
 LVZ  O6S   S29  O4S   114.63  3.000
 LVZ  H3    C3   C4    107.98  3.000
 LVZ  H3    C3   O3    110.39  3.000
 LVZ  C4    C3   O3    111.61  3.000
 LVZ  O3    C3   C2    107.54  3.000
 LVZ  H3    C3   C2    108.70  3.000
 LVZ  C4    C3   C2    110.59  3.000
 LVZ  HO3   O3   C3    108.11  3.000
 LVZ  H4    C4   C5    109.15  3.000
 LVZ  H4    C4   O4    111.22  3.000
 LVZ  C5    C4   O4    111.90  3.000
 LVZ  H4    C4   C3    108.57  3.000
 LVZ  O4    C4   C3    107.17  3.000
 LVZ  C5    C4   C3    108.73  3.000
 LVZ  HO4   O4   C4    109.20  3.000
 LVZ  H5    C5   C6    108.08  3.000
 LVZ  H5    C5   O5    110.86  3.000
 LVZ  C6    C5   O5    107.11  3.000
 LVZ  O5    C5   C4    109.33  3.000
 LVZ  H5    C5   C4    107.96  3.000
 LVZ  C6    C5   C4    113.52  3.000
 LVZ  C5    O5   C1    115.36  3.000
 LVZ  H62   C6   H61   107.86  3.000
 LVZ  H62   C6   O6    112.07  3.000
 LVZ  H61   C6   O6    109.48  3.000
 LVZ  H62   C6   C5    109.70  3.000
 LVZ  H61   C6   C5    110.15  3.000
 LVZ  O6    C6   C5    107.58  3.000
 LVZ  C6    O6   S29   119.75  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
 LVZ  Var_01  C2    N9   S19  O1S    49.70  30.0  1
 LVZ  Var_02  C5    C6   O6   S29  -141.32  30.0  3
 LVZ  Var_03  O6S   S29  O6   C6    171.51  30.0  3
 LVZ  Var_04  H3B   C3A  C1A  C2A   178.61  30.0  3
 LVZ  Var_05  H2AA  C2A  C1A  O1     62.48  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
 LVZ  chir_01  C1  O1  O5  C2  negativ
 LVZ  chir_02  C2  N9  C3  C1  positiv
 LVZ  chir_03  C3  O3  C2  C4  positiv
 LVZ  chir_04  C4  O4  C3  C5  negativ
 LVZ  chir_05  C5  O5  C4  C6  negativ

