# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:33:44 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: naphthalen-2-yl 1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Sc2ccc3ccccc3c2)[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
 GS9  GS9  'naphthalen-2-yl 1-thio-beta-D-galactopyranoside'  D-saccharide  40  22  .  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_GS9
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
 GS9  C1    C  CH1   0  -0.141  -1.3428   0.3651  -0.1965
 GS9  O5    O  O2    0  -0.469  -1.7354  -0.9146  -0.6014
 GS9  S1    S  S2    0   0.046  -0.1124   0.9878  -1.3687
 GS9  C2    C  CH1   0   0.018  -2.5451   1.3169  -0.1724
 GS9  O2    O  OH1   0  -0.663  -2.2039   2.5775   0.3438
 GS9  C3    C  CH1   0   0.011  -3.6107   0.7262   0.7495
 GS9  O3    O  OH1   0  -0.671  -4.8052   1.4646   0.7119
 GS9  C4    C  CH1   0   0.004  -3.9402  -0.7117   0.3551
 GS9  O4    O  OH1   0  -0.671  -4.5603  -0.7828  -0.9040
 GS9  C5    C  CH1   0  -0.015  -2.6447  -1.5095   0.3074
 GS9  C80   C  CR16  0  -0.236   1.5119  -1.0352  -0.3677
 GS9  C6    C  CH2   0  -0.157  -2.8434  -2.9510  -0.1050
 GS9  C90   C  CR16  0  -0.300   2.7013  -1.5206   0.0969
 GS9  C7    C  CR6   0  -0.146   1.3912   0.3369  -0.7011
 GS9  C8    C  CR16  0  -0.313   2.4683   1.1752  -0.5752
 GS9  C9    C  CR66  0   0.125   3.7146   0.6862  -0.1199
 GS9  C14   C  CR66  0   0.111   3.8347  -0.6834   0.2281
 GS9  C13   C  CR16  0  -0.309   5.0785  -1.1685   0.6928
 GS9  C12   C  CR16  0  -0.257   6.1534  -0.3291   0.8092
 GS9  C11   C  CR16  0  -0.256   6.0329   1.0343   0.4668
 GS9  C10   C  CR16  0  -0.310   4.8414   1.5311   0.0130
 GS9  H1    H  HCH1  0   0.263  -0.8778   0.3419   0.8009
 GS9  H2    H  HCH1  0   0.235  -2.9563   1.3921  -1.1889
 GS9  H5    H  HCH1  0   0.233  -2.2185  -1.4977   1.3233
 GS9  HA    H  HOH1  0   0.457  -1.7204   3.0717  -0.3260
 GS9  H3    H  HCH1  0   0.217  -3.1928   0.7007   1.7686
 GS9  H4    H  HCH1  0   0.236  -4.5777  -1.1459   1.1398
 GS9  HB    H  HOH1  0   0.453  -5.3248  -0.1967  -0.8965
 GS9  H90   H  HCR6  0   0.261   2.7892  -2.5683   0.3580
 GS9  H61C  H  HCH2  0   0.204  -3.6406  -3.3737   0.5204
 GS9  H62C  H  HCH2  0   0.210  -3.1887  -2.9978  -1.1438
 GS9  HC    H  HOH1  0   0.457  -1.7284  -4.5252  -0.2669
 GS9  H8    H  HCR6  0   0.267   2.3744   2.2272  -0.8170
 GS9  H10   H  HCR6  0   0.258   4.7480   2.5779  -0.2495
 GS9  H11   H  HCR6  0   0.261   6.8895   1.6882   0.5645
 GS9  H12   H  HCR6  0   0.261   7.1017  -0.7087   1.1659
 GS9  HD    H  HOH1  0   0.456  -4.5994   2.3926   0.8675
 GS9  H13   H  HCR6  0   0.258   5.1698  -2.2154   0.9559
 GS9  O6    O  OH1   0  -0.665  -1.6234  -3.6317   0.0718
 GS9  H80   H  HCR6  0   0.276   0.6632  -1.6980  -0.4744

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
 GS9  C1   O5    single    1.398  0.020  1.398
 GS9  C1   S1    single    1.810  0.020  1.810
 GS9  C1   C2    single    1.534  0.020  1.534
 GS9  O5   C5    single    1.417  0.020  1.417
 GS9  S1   C7    single    1.769  0.020  1.769
 GS9  C2   O2    single    1.404  0.020  1.404
 GS9  C2   C3    single    1.528  0.020  1.528
 GS9  C3   O3    single    1.405  0.020  1.405
 GS9  C3   C4    single    1.527  0.020  1.527
 GS9  C4   O4    single    1.405  0.020  1.405
 GS9  C4   C5    single    1.522  0.020  1.522
 GS9  C80  C90   aromatic  1.366  0.020  1.366
 GS9  C80  C7    aromatic  1.417  0.020  1.417
 GS9  C5   C6    single    1.512  0.020  1.512
 GS9  C90  C14   aromatic  1.415  0.020  1.415
 GS9  C13  C14   aromatic  1.414  0.020  1.414
 GS9  O6   C6    single    1.408  0.020  1.408
 GS9  C7   C8    aromatic  1.371  0.020  1.371
 GS9  C8   C9    aromatic  1.414  0.020  1.414
 GS9  C9   C10   aromatic  1.415  0.020  1.415
 GS9  C9   C14   aromatic  1.418  0.020  1.418
 GS9  C10  C11   aromatic  1.368  0.020  1.368
 GS9  C11  C12   aromatic  1.411  0.020  1.411
 GS9  C12  C13   aromatic  1.369  0.020  1.369
 GS9  C1   H1    single    0.970  0.020  1.090
 GS9  C2   H2    single    0.970  0.020  1.090
 GS9  C5   H5    single    0.970  0.020  1.090
 GS9  O3   HD    single    0.850  0.020  0.980
 GS9  O2   HA    single    0.850  0.020  0.980
 GS9  C3   H3    single    0.970  0.020  1.090
 GS9  C4   H4    single    0.970  0.020  1.090
 GS9  O4   HB    single    0.850  0.020  0.980
 GS9  C80  H80   single    0.930  0.020  1.080
 GS9  C90  H90   single    0.930  0.020  1.080
 GS9  C6   H61C  single    0.970  0.020  1.090
 GS9  C6   H62C  single    0.970  0.020  1.090
 GS9  O6   HC    single    0.850  0.020  0.980
 GS9  C8   H8    single    0.930  0.020  1.080
 GS9  C10  H10   single    0.930  0.020  1.080
 GS9  C11  H11   single    0.930  0.020  1.080
 GS9  C12  H12   single    0.930  0.020  1.080
 GS9  C13  H13   single    0.930  0.020  1.080

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
 GS9  H1    C1   C2    109.27  3.000
 GS9  H1    C1   S1    107.87  3.000
 GS9  C2    C1   S1    109.25  3.000
 GS9  H1    C1   O5    111.20  3.000
 GS9  C2    C1   O5    110.64  3.000
 GS9  S1    C1   O5    108.55  3.000
 GS9  C5    O5   C1    112.26  3.000
 GS9  C7    S1   C1    101.94  3.000
 GS9  H2    C2   C3    108.87  3.000
 GS9  H2    C2   O2    111.69  3.000
 GS9  C3    C2   O2    107.15  3.000
 GS9  H2    C2   C1    108.73  3.000
 GS9  C3    C2   C1    108.44  3.000
 GS9  O2    C2   C1    111.87  3.000
 GS9  HA    O2   C2    109.09  3.000
 GS9  H3    C3   C4    107.39  3.000
 GS9  H3    C3   O3    111.06  3.000
 GS9  C4    C3   O3    107.73  3.000
 GS9  H3    C3   C2    107.61  3.000
 GS9  C4    C3   C2    111.03  3.000
 GS9  O3    C3   C2    111.94  3.000
 GS9  HD    O3   C3    108.69  3.000
 GS9  H4    C4   C5    107.98  3.000
 GS9  H4    C4   O4    111.31  3.000
 GS9  C5    C4   O4    108.72  3.000
 GS9  H4    C4   C3    108.20  3.000
 GS9  C5    C4   C3    108.54  3.000
 GS9  O4    C4   C3    111.98  3.000
 GS9  HB    O4   C4    108.21  3.000
 GS9  H5    C5   C6    108.21  3.000
 GS9  H5    C5   C4    107.14  3.000
 GS9  C6    C5   C4    113.34  3.000
 GS9  H5    C5   O5    109.80  3.000
 GS9  C6    C5   O5    108.04  3.000
 GS9  C4    C5   O5    110.26  3.000
 GS9  H80   C80  C7    120.20  3.000
 GS9  H80   C80  C90   119.92  3.000
 GS9  C7    C80  C90   119.88  3.000
 GS9  H62C  C6   H61C  107.15  3.000
 GS9  H62C  C6   O6    111.80  3.000
 GS9  H61C  C6   O6    111.81  3.000
 GS9  H62C  C6   C5    109.92  3.000
 GS9  H61C  C6   C5    107.88  3.000
 GS9  O6    C6   C5    108.22  3.000
 GS9  H90   C90  C14   119.00  3.000
 GS9  H90   C90  C80   119.75  3.000
 GS9  C14   C90  C80   121.24  3.000
 GS9  C8    C7   C80   120.23  3.000
 GS9  C8    C7   S1    118.53  3.000
 GS9  C80   C7   S1    121.16  3.000
 GS9  H8    C8   C9    118.95  3.000
 GS9  H8    C8   C7    120.34  3.000
 GS9  C9    C8   C7    120.71  3.000
 GS9  C10   C9   C14   119.10  3.000
 GS9  C14   C9   C8    119.18  3.000
 GS9  C10   C9   C8    121.72  3.000
 GS9  C13   C14  C9    119.12  3.000
 GS9  C9    C14  C90   118.74  3.000
 GS9  C13   C14  C90   122.15  3.000
 GS9  H13   C13  C12   120.38  3.000
 GS9  H13   C13  C14   119.05  3.000
 GS9  C12   C13  C14   120.56  3.000
 GS9  H12   C12  C11   119.60  3.000
 GS9  H12   C12  C13   120.08  3.000
 GS9  C11   C12  C13   120.32  3.000
 GS9  H11   C11  C10   119.99  3.000
 GS9  H11   C11  C12   119.63  3.000
 GS9  C10   C11  C12   120.38  3.000
 GS9  H10   C10  C11   120.42  3.000
 GS9  H10   C10  C9    119.06  3.000
 GS9  C11   C10  C9    120.52  3.000
 GS9  HC    O6   C6    108.08  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
 GS9  CONST_01  C13  C14  C90  C80  180.00   0.0  0
 GS9  CONST_02  C9   C14  C90  C80    0.00   0.0  0
 GS9  CONST_03  C9   C8   C7   C80    0.00   0.0  0
 GS9  CONST_04  C8   C7   C80  C90    0.00   0.0  0
 GS9  CONST_05  C12  C13  C14  C90  180.00   0.0  0
 GS9  CONST_06  C8   C9   C14  C90    0.00   0.0  0
 GS9  CONST_07  C10  C9   C14  C90  180.00   0.0  0
 GS9  CONST_08  C14  C90  C80  C7     0.00   0.0  0
 GS9  CONST_09  C10  C9   C8   C7   180.00   0.0  0
 GS9  CONST_10  C14  C9   C8   C7     0.00   0.0  0
 GS9  CONST_11  C11  C10  C9   C8   180.00   0.0  0
 GS9  CONST_12  C13  C14  C9   C8   180.00   0.0  0
 GS9  CONST_13  C12  C11  C10  C9     0.00   0.0  0
 GS9  CONST_14  C12  C13  C14  C9     0.00   0.0  0
 GS9  CONST_15  C11  C12  C13  C14    0.00   0.0  0
 GS9  CONST_16  C11  C10  C9   C14    0.00   0.0  0
 GS9  CONST_17  C10  C9   C14  C13    0.00   0.0  0
 GS9  CONST_18  C10  C11  C12  C13    0.00   0.0  0
 GS9  CONST_19  C90  C80  C7   S1   180.00   0.0  0
 GS9  CONST_20  C9   C8   C7   S1   180.00   0.0  0
 GS9  CONST_21  H8   C8   C7   C80  180.00   0.0  0
 GS9  CONST_22  H13  C13  C14  C90    0.00   0.0  0
 GS9  CONST_23  H90  C90  C80  C7   180.00   0.0  0
 GS9  CONST_24  H80  C80  C7   C8   180.00   0.0  0
 GS9  CONST_25  H10  C10  C9   C8     0.00   0.0  0
 GS9  CONST_26  H11  C11  C10  C9   180.00   0.0  0
 GS9  CONST_27  H12  C12  C13  C14  180.00   0.0  0
 GS9  Var_01    C80  C7   S1   C1    50.33  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
 GS9  chir_01  C1  O5  S1  C2  negativ
 GS9  chir_02  C2  O2  C1  C3  negativ
 GS9  chir_03  C3  O3  C2  C4  positiv
 GS9  chir_04  C4  O4  C5  C3  negativ
 GS9  chir_05  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 GS9  plan-1  S1   0.020
 GS9  plan-1  C80  0.020
 GS9  plan-1  C90  0.020
 GS9  plan-1  C7   0.020
 GS9  plan-1  C8   0.020
 GS9  plan-1  C9   0.020
 GS9  plan-1  C14  0.020
 GS9  plan-1  C13  0.020
 GS9  plan-1  C12  0.020
 GS9  plan-1  C11  0.020
 GS9  plan-1  C10  0.020
 GS9  plan-1  H90  0.020
 GS9  plan-1  H8   0.020
 GS9  plan-1  H10  0.020
 GS9  plan-1  H11  0.020
 GS9  plan-1  H12  0.020
 GS9  plan-1  H13  0.020
 GS9  plan-1  H80  0.020

