# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 10:08:34 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](S[C@@H]2O[C@H](CSCC#C)[C@@H](O)[C@H](O)[C@H]2O)[C@H](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
 QWJ  QWJ  '6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside'  ligand  50  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QWJ
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
 QWJ  C4    C  CH1   0  -0.003  61.6571  24.1844  10.9424
 QWJ  C3    C  CH1   0   0.008  63.1801  24.1127  11.0091
 QWJ  C5    C  CH1   0  -0.015  61.2531  24.7592   9.5914
 QWJ  C1    C  CH1   0  -0.120  63.2361  25.9892   9.3781
 QWJ  C2    C  CH1   0   0.028  63.7869  25.4789  10.7130
 QWJ  C6    C  CH2   0  -0.157  59.7542  24.9020   9.4418
 QWJ  C10   C  CH1   0   0.029  67.0695  27.8274   5.9051
 QWJ  C9    C  CH1   0   0.018  65.8131  28.6413   5.6282
 QWJ  C11   C  CH1   0   0.022  66.6906  26.5248   6.6315
 QWJ  C7    C  CH1   0  -0.153  64.7291  27.4707   7.5272
 QWJ  C8    C  CH1   0   0.008  64.9942  28.8398   6.9018
 QWJ  C12   C  CH2   0  -0.591  67.8881  25.7311   7.1418
 QWJ  C13   C  CH2   0  -0.717  70.2861  24.4231   6.6655
 QWJ  C14   C  CSP   0   0.296  71.0974  25.5613   7.0541
 QWJ  C15   C  CSP1  0  -0.501  71.7534  26.5120   7.3865
 QWJ  O5    O  O2    0  -0.471  61.8406  26.0344   9.3830
 QWJ  O2    O  OH1   0  -0.665  65.1792  25.3194  10.6632
 QWJ  O3    O  OH1   0  -0.672  63.5312  23.6364  12.2843
 QWJ  O4    O  OH1   0  -0.670  61.1228  24.9929  11.9604
 QWJ  O6    O  OH1   0  -0.670  59.4680  25.2296   8.1031
 QWJ  O11   O  O2    0  -0.469  65.9441  26.8253   7.7973
 QWJ  O8    O  OH1   0  -0.661  63.8042  29.4853   6.5318
 QWJ  O9    O  OH1   0  -0.664  66.1990  29.8718   5.0764
 QWJ  O10   O  OH1   0  -0.663  67.6849  27.5903   4.6666
 QWJ  S1    S  S2    0   0.013  63.8463  27.6778   9.0857
 QWJ  S12   S  S2    0  -0.011  68.7697  24.9052   5.7836
 QWJ  HC4   H  HCH1  0   0.237  61.2652  23.1577  10.9998
 QWJ  HC3   H  HCH1  0   0.216  63.5139  23.4181  10.2220
 QWJ  HC5   H  HCH1  0   0.232  61.6121  24.0542   8.8245
 QWJ  HC1   H  HCH1  0   0.265  63.6179  25.3532   8.5645
 QWJ  HC2   H  HCH1  0   0.226  63.4870  26.1816  11.5040
 QWJ  HC6B  H  HCH2  0   0.209  59.3820  25.6644  10.1356
 QWJ  HC6A  H  HCH2  0   0.205  59.2958  23.9485   9.7340
 QWJ  HC10  H  HCH1  0   0.217  67.7219  28.4078   6.5776
 QWJ  HC9   H  HCH1  0   0.216  65.1910  28.0665   4.9208
 QWJ  HC11  H  HCH1  0   0.239  66.0892  25.9025   5.9493
 QWJ  HC7   H  HCH1  0   0.272  64.1056  26.8701   6.8488
 QWJ  HC8   H  HCH1  0   0.240  65.5845  29.4412   7.6083
 QWJ  H12B  H  HCH2  0   0.299  67.5402  24.9717   7.8435
 QWJ  H12A  H  HCH2  0   0.281  68.5802  26.3951   7.6661
 QWJ  H13A  H  HCH2  0   0.327  70.8345  23.7742   5.9807
 QWJ  H13B  H  HCH2  0   0.313  70.0207  23.8227   7.5373
 QWJ  HC15  H  H     0   0.283  72.3362  27.3557   7.6774
 QWJ  HO2   H  HOH1  0   0.451  65.5781  26.1698  10.4423
 QWJ  HO3   H  HOH1  0   0.457  64.4881  23.6817  12.3825
 QWJ  HO4   H  HOH1  0   0.453  61.4717  24.6837  12.8034
 QWJ  HO6   H  HOH1  0   0.457  58.5153  25.3248   8.0171
 QWJ  HO8   H  HOH1  0   0.460  63.4102  29.8978   7.3064
 QWJ  HO9   H  HOH1  0   0.452  65.4001  30.3688   4.8715
 QWJ  HO10  H  HOH1  0   0.446  68.5045  27.1003   4.8103

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
 QWJ  C15  C14   triple  1.202  0.020  1.202
 QWJ  O10  C10   single  1.403  0.020  1.403
 QWJ  C14  C13   single  1.451  0.020  1.451
 QWJ  S12  C13   single  1.819  0.020  1.819
 QWJ  S12  C12   single  1.818  0.020  1.818
 QWJ  O9   C9    single  1.403  0.020  1.403
 QWJ  C10  C9    single  1.522  0.020  1.522
 QWJ  C10  C11   single  1.539  0.020  1.539
 QWJ  C9   C8    single  1.527  0.020  1.527
 QWJ  C11  C12   single  1.525  0.020  1.525
 QWJ  C11  O11   single  1.417  0.020  1.417
 QWJ  O6   C6    single  1.408  0.020  1.408
 QWJ  O8   C8    single  1.403  0.020  1.403
 QWJ  C8   C7    single  1.528  0.020  1.528
 QWJ  C6   C5    single  1.513  0.020  1.513
 QWJ  O11  C7    single  1.402  0.020  1.402
 QWJ  C7   S1    single  1.803  0.020  1.803
 QWJ  O5   C5    single  1.419  0.020  1.419
 QWJ  O5   C1    single  1.396  0.020  1.396
 QWJ  C5   C4    single  1.523  0.020  1.523
 QWJ  S1   C1    single  1.819  0.020  1.819
 QWJ  C1   C2    single  1.532  0.020  1.532
 QWJ  O4   C4    single  1.405  0.020  1.405
 QWJ  C4   C3    single  1.526  0.020  1.526
 QWJ  C2   C3    single  1.524  0.020  1.524
 QWJ  C2   O2    single  1.402  0.020  1.402
 QWJ  C3   O3    single  1.406  0.020  1.406
 QWJ  C4   HC4   single  0.939  0.020  1.096
 QWJ  C3   HC3   single  0.939  0.020  1.096
 QWJ  C5   HC5   single  0.939  0.020  1.096
 QWJ  C1   HC1   single  0.939  0.020  1.096
 QWJ  C2   HC2   single  0.939  0.020  1.096
 QWJ  C6   HC6B  single  0.939  0.020  1.096
 QWJ  C6   HC6A  single  0.939  0.020  1.096
 QWJ  C10  HC10  single  0.939  0.020  1.096
 QWJ  C9   HC9   single  0.939  0.020  1.096
 QWJ  C11  HC11  single  0.939  0.020  1.096
 QWJ  C7   HC7   single  0.939  0.020  1.096
 QWJ  C8   HC8   single  0.939  0.020  1.096
 QWJ  C12  H12B  single  0.939  0.020  1.096
 QWJ  C12  H12A  single  0.939  0.020  1.096
 QWJ  C13  H13A  single  0.939  0.020  1.096
 QWJ  C13  H13B  single  0.939  0.020  1.096
 QWJ  C15  HC15  single  0.913  0.020  1.066
 QWJ  O2   HO2   single  0.832  0.020  0.971
 QWJ  O3   HO3   single  0.832  0.020  0.971
 QWJ  O4   HO4   single  0.832  0.020  0.971
 QWJ  O6   HO6   single  0.832  0.020  0.971
 QWJ  O8   HO8   single  0.832  0.020  0.971
 QWJ  O9   HO9   single  0.832  0.020  0.971
 QWJ  O10  HO10  single  0.832  0.020  0.971

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
 QWJ  HC4   C4   O4    111.31  3.000
 QWJ  HC4   C4   C5    107.69  3.000
 QWJ  O4    C4   C5    108.94  3.000
 QWJ  HC4   C4   C3    108.01  3.000
 QWJ  O4    C4   C3    112.01  3.000
 QWJ  C5    C4   C3    108.74  3.000
 QWJ  HC3   C3   O3    111.03  3.000
 QWJ  HC3   C3   C2    107.81  3.000
 QWJ  O3    C3   C2    112.37  3.000
 QWJ  HC3   C3   C4    107.51  3.000
 QWJ  O3    C3   C4    107.74  3.000
 QWJ  C2    C3   C4    110.29  3.000
 QWJ  HC5   C5   O5    109.74  3.000
 QWJ  HC5   C5   C6    108.32  3.000
 QWJ  O5    C5   C6    108.10  3.000
 QWJ  HC5   C5   C4    106.83  3.000
 QWJ  O5    C5   C4    111.07  3.000
 QWJ  C6    C5   C4    112.72  3.000
 QWJ  HC1   C1   S1    107.53  3.000
 QWJ  HC1   C1   O5    111.58  3.000
 QWJ  S1    C1   O5    107.80  3.000
 QWJ  HC1   C1   C2    109.08  3.000
 QWJ  S1    C1   C2    109.19  3.000
 QWJ  O5    C1   C2    111.54  3.000
 QWJ  HC2   C2   O2    111.65  3.000
 QWJ  HC2   C2   C1    108.42  3.000
 QWJ  O2    C2   C1    111.34  3.000
 QWJ  HC2   C2   C3    108.94  3.000
 QWJ  O2    C2   C3    107.47  3.000
 QWJ  C1    C2   C3    108.96  3.000
 QWJ  HC6A  C6   HC6B  107.09  3.000
 QWJ  HC6A  C6   O6    111.75  3.000
 QWJ  HC6B  C6   O6    111.78  3.000
 QWJ  HC6A  C6   C5    107.78  3.000
 QWJ  HC6B  C6   C5    109.85  3.000
 QWJ  O6    C6   C5    108.51  3.000
 QWJ  HC10  C10  O10   111.59  3.000
 QWJ  HC10  C10  C11   107.66  3.000
 QWJ  O10   C10  C11   112.43  3.000
 QWJ  HC10  C10  C9    108.54  3.000
 QWJ  C11   C10  C9    109.58  3.000
 QWJ  O10   C10  C9    106.97  3.000
 QWJ  HC9   C9   O9    111.09  3.000
 QWJ  HC9   C9   C8    107.45  3.000
 QWJ  O9    C9   C8    111.20  3.000
 QWJ  HC9   C9   C10   107.66  3.000
 QWJ  C8    C9   C10   111.12  3.000
 QWJ  O9    C9   C10   108.27  3.000
 QWJ  HC11  C11  O11   109.98  3.000
 QWJ  HC11  C11  C12   110.00  3.000
 QWJ  O11   C11  C12   104.42  3.000
 QWJ  HC11  C11  C10   108.67  3.000
 QWJ  O11   C11  C10   109.79  3.000
 QWJ  C12   C11  C10   113.91  3.000
 QWJ  HC7   C7   S1    108.56  3.000
 QWJ  HC7   C7   O11   111.03  3.000
 QWJ  S1    C7   O11   108.10  3.000
 QWJ  HC7   C7   C8    109.58  3.000
 QWJ  S1    C7   C8    109.62  3.000
 QWJ  O11   C7   C8    109.93  3.000
 QWJ  HC8   C8   O8    111.90  3.000
 QWJ  HC8   C8   C7    108.67  3.000
 QWJ  O8    C8   C7    111.89  3.000
 QWJ  HC8   C8   C9    108.61  3.000
 QWJ  C7    C8   C9    108.53  3.000
 QWJ  O8    C8   C9    107.13  3.000
 QWJ  H12A  C12  H12B  108.43  3.000
 QWJ  H12A  C12  S12   109.11  3.000
 QWJ  H12B  C12  S12   108.60  3.000
 QWJ  H12A  C12  C11   109.98  3.000
 QWJ  H12B  C12  C11   109.10  3.000
 QWJ  S12   C12  C11   111.56  3.000
 QWJ  H13B  C13  H13A  107.24  3.000
 QWJ  H13B  C13  S12   109.29  3.000
 QWJ  H13A  C13  S12   105.80  3.000
 QWJ  H13B  C13  C14   110.71  3.000
 QWJ  H13A  C13  C14   110.71  3.000
 QWJ  S12   C13  C14   112.84  3.000
 QWJ  C15   C14  C13   180.00  3.000
 QWJ  HC15  C15  C14   180.00  3.000
 QWJ  C1    O5   C5    112.65  3.000
 QWJ  HO2   O2   C2    108.56  3.000
 QWJ  HO3   O3   C3    108.95  3.000
 QWJ  HO4   O4   C4    108.16  3.000
 QWJ  HO6   O6   C6    108.04  3.000
 QWJ  C7    O11  C11   113.31  3.000
 QWJ  HO8   O8   C8    109.40  3.000
 QWJ  HO9   O9   C9    107.96  3.000
 QWJ  HO10  O10  C10   109.06  3.000
 QWJ  C7    S1   C1    101.34  3.000
 QWJ  C13   S12  C12    99.35  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
 QWJ  Var_01  C14   C13  S12  C12  -67.47  30.0  3
 QWJ  Var_02  S12   C13  C14  C15   57.18  30.0  3
 QWJ  Var_03  H12B  C12  S12  C13  -72.43  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
 QWJ  chir_01  C4   C5   O4   C3   positiv
 QWJ  chir_02  C3   O3   C2   C4   positiv
 QWJ  chir_03  C5   O5   C4   C6   negativ
 QWJ  chir_04  C1   S1   O5   C2   positiv
 QWJ  chir_05  C2   O2   C1   C3   negativ
 QWJ  chir_06  C10  O10  C9   C11  negativ
 QWJ  chir_07  C9   O9   C10  C8   negativ
 QWJ  chir_08  C11  O11  C12  C10  positiv
 QWJ  chir_09  C7   S1   O11  C8   positiv
 QWJ  chir_10  C8   O8   C7   C9   negativ

