# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 01:05:15 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: ethyl 3-O-[5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl]-1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCS[C@@H]1O[C@H](CO)[C@H](O)[C@H](O[C@@]2(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O2)[C@H](O)[C@H](O)CO)C(O)=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
 RMY  RMY  'ethyl 3-O-[5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl]-1-thio-beta-D-galactopyranoside'  ligand  66  34  .  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_RMY
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
 RMY  C1    C  CH1    0  -0.143   3.3073  -0.4400   0.5869
 RMY  C2    C  CH1    0   0.030   2.1035   0.2137   1.2885
 RMY  O1    O  OH1    0  -0.598   1.1804  -0.7574   1.7105
 RMY  C3    C  CH1    0  -0.007   1.4262   1.1290   0.2698
 RMY  O2    O  O2     0  -0.463   0.3193   1.7840   0.8612
 RMY  C4    C  CH1    0  -0.009   2.4264   2.1322  -0.2896
 RMY  O3    O  OH1    0  -0.665   2.8439   3.0065   0.7401
 RMY  C5    C  CH1    0   0.015   3.5834   1.3627  -0.9050
 RMY  O4    O  O2     0  -0.485   4.1904   0.4977   0.0414
 RMY  C6    C  CH2    0  -0.162   4.6467   2.2996  -1.4235
 RMY  O5    O  OH1    0  -0.693   5.5759   1.5636  -2.1801
 RMY  C7    C  CH3    0  -0.689   5.9967  -3.4754   1.5724
 RMY  S1    S  S2     0  -0.037   4.1957  -1.4447   1.7976
 RMY  C9    C  C      0   0.331  -0.8930   2.2986  -1.1934
 RMY  C10   C  CH1    0  -0.160  -3.4970   0.3081   0.5105
 RMY  C11   C  CH1    0   0.058  -2.3488  -0.2165  -0.3617
 RMY  C12   C  CH1    0   0.104  -3.3854   1.8241   0.6516
 RMY  C13   C  CT     0   0.372  -0.9218   1.6194   0.2205
 RMY  C14   C  CH2    0  -0.223  -0.8990  -3.6876  -1.2397
 RMY  C15   C  CH1    0  -0.020  -2.2306  -1.7427  -0.3290
 RMY  C16   C  CH1    0  -0.012  -1.3030  -2.2373  -1.4534
 RMY  C17   C  CH2    0  -0.543  -1.9894   2.2055   1.1363
 RMY  C19   C  CH3    0  -0.807  -7.0160  -0.9021  -0.2257
 RMY  O6    O  OC    -1  -0.429  -0.2381   1.7131  -2.0649
 RMY  O7    O  O      0  -0.565  -1.4874   3.3915  -1.2807
 RMY  O8    O  OH1    0  -0.668  -4.3918   2.2432   1.5477
 RMY  O10   O  OH1    0  -0.653  -1.8107  -2.1702   0.9428
 RMY  O11   O  OH1    0  -0.588  -1.9041  -2.0329  -2.7131
 RMY  O12   O  O2     0  -0.523  -1.1149   0.2362   0.1266
 RMY  O13   O  O      0  -0.407  -5.6663  -1.1002   1.7321
 RMY  H1    H  HCH1   0   0.192   2.9177  -1.1096  -0.1956
 RMY  H2    H  HCH1   0   0.227   2.4669   0.8020   2.1436
 RMY  H3    H  HCH1   0   0.225   1.0989   0.5126  -0.5731
 RMY  H4    H  HCH1   0   0.238   1.9366   2.6806  -1.1049
 RMY  HO4   H  HOH1   0   0.460   3.2165   3.7952   0.3355
 RMY  H5    H  HCH1   0   0.245   3.1832   0.7953  -1.7591
 RMY  H6    H  HCH2   0   0.225   4.1465   3.0653  -2.0324
 RMY  H6A   H  HCH2   0   0.179   5.1275   2.8129  -0.5818
 RMY  HO6   H  HOH1   0   0.457   6.2575   2.1686  -2.4842
 RMY  HAA   H  HCH3   0   0.223   6.5744  -4.1438   0.9347
 RMY  HAAA  H  HCH3   0   0.274   6.6982  -2.9088   2.1846
 RMY  HAAB  H  HCH3   0   0.241   5.3869  -4.0905   2.2346
 RMY  HAB   H  HCH2   0   0.288   5.7648  -1.9523   0.0608
 RMY  HABA  H  HCH2   0   0.292   4.4480  -3.1318   0.1003
 RMY  HAE   H  HCH1   0   0.229  -3.4297  -0.1441   1.5026
 RMY  HAF   H  HCH1   0   0.203  -2.5081   0.1110  -1.3979
 RMY  HAG   H  HCH1   0   0.213  -3.5474   2.2718  -0.3398
 RMY  HAI   H  HCH2   0   0.234  -0.4290  -3.7834  -0.2550
 RMY  HAIA  H  HCH2   0   0.179  -1.8033  -4.3176  -1.2216
 RMY  HAJ   H  HCH1   0   0.232  -3.2204  -2.1857  -0.4898
 RMY  HAK   H  HCH1   0   0.221  -0.3975  -1.6198  -1.4590
 RMY  HAL   H  HCH2   0   0.160  -1.8995   3.2934   1.1842
 RMY  HALA  H  HCH2   0   0.253  -1.8425   1.8106   2.1473
 RMY  HAN   H  HCH3   0   0.218  -7.2829  -1.9588  -0.2309
 RMY  HANA  H  HCH3   0   0.231  -7.8359  -0.3636   0.2511
 RMY  HANB  H  HCH3   0   0.269  -6.9366  -0.5607  -1.2571
 RMY  HOAQ  H  HOH1   0   0.450  -4.4181   3.2044   1.5387
 RMY  HOAR  H  HOH1   0   0.439   0.2753  -4.9679  -2.0943
 RMY  HOAS  H  HOH1   0   0.447  -1.0366  -1.6429   1.1834
 RMY  HOAT  H  HOH1   0   0.457  -2.6513  -2.6351  -2.7970
 RMY  HOAU  H  HOH1   0   0.450   1.6564  -1.4051   2.2452
 RMY  N1    N  NH1    0  -0.632  -4.7625  -0.0645  -0.0699
 RMY  C8    C  CH2    0  -0.566   5.1406  -2.5589   0.7168
 RMY  C18   C  C      0   0.504  -5.7521  -0.7059   0.5808
 RMY  HNAO  H  HNH1   0   0.399  -4.9513   0.2731  -0.9999
 RMY  O9    O  OH1    0  -0.718  -0.0206  -4.0715  -2.2735

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
 RMY  C1   S1    single  1.807  0.020  1.807
 RMY  C1   O4    single  1.399  0.020  1.399
 RMY  C1   C2    single  1.539  0.020  1.539
 RMY  C1   H1    single  0.970  0.020  1.090
 RMY  C2   H2    single  0.970  0.020  1.090
 RMY  O1   C2    single  1.405  0.020  1.405
 RMY  C3   C2    single  1.528  0.020  1.528
 RMY  C3   C4    single  1.523  0.020  1.523
 RMY  C3   O2    single  1.416  0.020  1.416
 RMY  C3   H3    single  0.970  0.020  1.090
 RMY  O2   C13   single  1.406  0.020  1.406
 RMY  C4   O3    single  1.414  0.020  1.414
 RMY  C4   H4    single  0.970  0.020  1.090
 RMY  O3   HO4   single  0.850  0.020  0.980
 RMY  C5   C4    single  1.520  0.020  1.520
 RMY  C5   C6    single  1.509  0.020  1.509
 RMY  C5   O4    single  1.419  0.020  1.419
 RMY  C5   H5    single  0.970  0.020  1.090
 RMY  C6   H6    single  0.970  0.020  1.090
 RMY  C6   H6A   single  0.970  0.020  1.090
 RMY  O5   C6    single  1.406  0.020  1.406
 RMY  O5   HO6   single  0.850  0.020  0.980
 RMY  C7   HAA   single  0.970  0.020  1.090
 RMY  C7   HAAA  single  0.970  0.020  1.090
 RMY  C7   HAAB  single  0.970  0.020  1.090
 RMY  C8   C7    single  1.518  0.020  1.518
 RMY  C8   HAB   single  0.970  0.020  1.090
 RMY  C8   HABA  single  0.970  0.020  1.090
 RMY  S1   C8    single  1.817  0.020  1.817
 RMY  C9   O6    deloc   1.237  0.020  1.237
 RMY  C9   C13   single  1.569  0.020  1.569
 RMY  C10  HAE   single  0.970  0.020  1.090
 RMY  C11  C10   single  1.534  0.020  1.534
 RMY  C11  C15   single  1.531  0.020  1.531
 RMY  C11  HAF   single  0.970  0.020  1.090
 RMY  C12  C10   single  1.527  0.020  1.527
 RMY  C12  O8    single  1.411  0.020  1.411
 RMY  C12  HAG   single  0.970  0.020  1.090
 RMY  C13  C17   single  1.524  0.020  1.524
 RMY  C13  O12   single  1.400  0.020  1.400
 RMY  C14  HAI   single  0.970  0.020  1.090
 RMY  C14  HAIA  single  0.970  0.020  1.090
 RMY  C15  C16   single  1.539  0.020  1.539
 RMY  C15  HAJ   single  0.970  0.020  1.090
 RMY  C16  C14   single  1.521  0.020  1.521
 RMY  C16  O11   single  1.411  0.020  1.411
 RMY  C16  HAK   single  0.970  0.020  1.090
 RMY  C17  C12   single  1.526  0.020  1.526
 RMY  C17  HAL   single  0.970  0.020  1.090
 RMY  C17  HALA  single  0.970  0.020  1.090
 RMY  C18  O13   double  1.220  0.020  1.220
 RMY  C18  C19   single  1.512  0.020  1.512
 RMY  C19  HAN   single  0.970  0.020  1.090
 RMY  C19  HANA  single  0.970  0.020  1.090
 RMY  C19  HANB  single  0.970  0.020  1.090
 RMY  N1   C10   single  1.441  0.020  1.441
 RMY  N1   C18   single  1.347  0.020  1.347
 RMY  N1   HNAO  single  0.860  0.020  1.020
 RMY  O7   C9    deloc   1.247  0.020  1.247
 RMY  O8   HOAQ  single  0.850  0.020  0.980
 RMY  O9   C14   single  1.410  0.020  1.410
 RMY  O9   HOAR  single  0.850  0.020  0.980
 RMY  O10  C15   single  1.406  0.020  1.406
 RMY  O10  HOAS  single  0.850  0.020  0.980
 RMY  O11  HOAT  single  0.850  0.020  0.980
 RMY  O12  C11   single  1.402  0.020  1.402
 RMY  O1   HOAU  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
 RMY  H1    C1   S1    108.18  3.000
 RMY  H1    C1   O4    110.72  3.000
 RMY  S1    C1   O4    108.89  3.000
 RMY  H1    C1   C2    107.79  3.000
 RMY  O4    C1   C2    112.76  3.000
 RMY  S1    C1   C2    108.38  3.000
 RMY  H2    C2   C3    110.15  3.000
 RMY  C3    C2   O1    108.86  3.000
 RMY  H2    C2   O1    110.70  3.000
 RMY  C3    C2   C1    107.29  3.000
 RMY  O1    C2   C1    110.94  3.000
 RMY  H2    C2   C1    108.85  3.000
 RMY  HOAU  O1   C2    107.83  3.000
 RMY  H3    C3   C4    106.53  3.000
 RMY  H3    C3   O2    110.40  3.000
 RMY  C4    C3   O2    111.23  3.000
 RMY  H3    C3   C2    107.98  3.000
 RMY  O2    C3   C2    110.20  3.000
 RMY  C4    C3   C2    110.39  3.000
 RMY  C13   O2   C3    116.46  3.000
 RMY  H4    C4   C5    106.97  3.000
 RMY  C5    C4   O3    112.54  3.000
 RMY  H4    C4   O3    111.33  3.000
 RMY  C5    C4   C3    108.37  3.000
 RMY  H4    C4   C3    107.99  3.000
 RMY  O3    C4   C3    109.49  3.000
 RMY  HO4   O3   C4    108.37  3.000
 RMY  H5    C5   C6    108.04  3.000
 RMY  H5    C5   O4    111.03  3.000
 RMY  C6    C5   O4    107.83  3.000
 RMY  H5    C5   C4    107.37  3.000
 RMY  O4    C5   C4    111.37  3.000
 RMY  C6    C5   C4    111.17  3.000
 RMY  C5    O4   C1    113.50  3.000
 RMY  H6A   C6   H6    107.38  3.000
 RMY  H6A   C6   O5    111.60  3.000
 RMY  H6    C6   O5    111.55  3.000
 RMY  O5    C6   C5    109.00  3.000
 RMY  H6A   C6   C5    109.62  3.000
 RMY  H6    C6   C5    107.60  3.000
 RMY  HO6   O5   C6    108.03  3.000
 RMY  HAAB  C7   HAAA  108.19  3.000
 RMY  HAAB  C7   HAA   107.81  3.000
 RMY  HAAA  C7   HAA   107.84  3.000
 RMY  HAAB  C7   C8    111.56  3.000
 RMY  HAAA  C7   C8    111.45  3.000
 RMY  HAA   C7   C8    109.85  3.000
 RMY  C8    S1   C1    101.43  3.000
 RMY  O7    C9   O6    128.14  3.000
 RMY  O7    C9   C13   115.70  3.000
 RMY  O6    C9   C13   116.08  3.000
 RMY  HAE   C10  N1    108.23  3.000
 RMY  N1    C10  C12   110.98  3.000
 RMY  HAE   C10  C12   108.82  3.000
 RMY  N1    C10  C11   109.86  3.000
 RMY  C12   C10  C11   109.72  3.000
 RMY  HAE   C10  C11   109.19  3.000
 RMY  HAF   C11  O12   111.09  3.000
 RMY  O12   C11  C15   104.27  3.000
 RMY  HAF   C11  C15   109.18  3.000
 RMY  O12   C11  C10   110.50  3.000
 RMY  HAF   C11  C10   109.02  3.000
 RMY  C15   C11  C10   112.73  3.000
 RMY  HAG   C12  O8    110.27  3.000
 RMY  HAG   C12  C17   108.62  3.000
 RMY  O8    C12  C17   112.12  3.000
 RMY  C17   C12  C10   110.14  3.000
 RMY  HAG   C12  C10   108.06  3.000
 RMY  O8    C12  C10   107.55  3.000
 RMY  O12   C13  C17   108.89  3.000
 RMY  O12   C13  C9    111.71  3.000
 RMY  C17   C13  C9    112.83  3.000
 RMY  O12   C13  O2    105.54  3.000
 RMY  C17   C13  O2    107.43  3.000
 RMY  C9    C13  O2    110.10  3.000
 RMY  HAIA  C14  HAI   106.69  3.000
 RMY  HAIA  C14  O9    111.56  3.000
 RMY  HAI   C14  O9    111.60  3.000
 RMY  O9    C14  C16   108.80  3.000
 RMY  HAIA  C14  C16   109.24  3.000
 RMY  HAI   C14  C16   108.89  3.000
 RMY  HAJ   C15  O10   106.23  3.000
 RMY  O10   C15  C16   112.53  3.000
 RMY  HAJ   C15  C16   107.89  3.000
 RMY  O10   C15  C11   110.21  3.000
 RMY  HAJ   C15  C11   109.26  3.000
 RMY  C16   C15  C11   110.56  3.000
 RMY  HAK   C16  O11   105.42  3.000
 RMY  HAK   C16  C15   108.70  3.000
 RMY  O11   C16  C15   110.43  3.000
 RMY  HAK   C16  C14   108.57  3.000
 RMY  O11   C16  C14   112.14  3.000
 RMY  C15   C16  C14   111.34  3.000
 RMY  HALA  C17  HAL   107.91  3.000
 RMY  HALA  C17  C13   108.79  3.000
 RMY  HAL   C17  C13   110.58  3.000
 RMY  HALA  C17  C12   109.01  3.000
 RMY  HAL   C17  C12   109.76  3.000
 RMY  C13   C17  C12   110.73  3.000
 RMY  HANB  C19  HANA  108.30  3.000
 RMY  HANB  C19  HAN   108.49  3.000
 RMY  HANA  C19  HAN   107.26  3.000
 RMY  HANB  C19  C18   113.79  3.000
 RMY  HANA  C19  C18   109.34  3.000
 RMY  HAN   C19  C18   109.45  3.000
 RMY  HOAQ  O8   C12   108.08  3.000
 RMY  HOAS  O10  C15   107.36  3.000
 RMY  HOAT  O11  C16   108.53  3.000
 RMY  C13   O12  C11   117.63  3.000
 RMY  HNAO  N1   C18   117.91  3.000
 RMY  HNAO  N1   C10   116.73  3.000
 RMY  C18   N1   C10   125.01  3.000
 RMY  HABA  C8   HAB   108.42  3.000
 RMY  HABA  C8   S1    109.16  3.000
 RMY  HAB   C8   S1    108.33  3.000
 RMY  S1    C8   C7    109.16  3.000
 RMY  HABA  C8   C7    111.09  3.000
 RMY  HAB   C8   C7    110.62  3.000
 RMY  O13   C18  N1    123.94  3.000
 RMY  N1    C18  C19   114.72  3.000
 RMY  O13   C18  C19   121.34  3.000
 RMY  HOAR  O9   C14   108.01  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
 RMY  CONST_01  O13   C18  N1   C10     0.00   0.0  0
 RMY  CONST_02  C19   C18  N1   C10   180.00   0.0  0
 RMY  CONST_03  HNAO  N1   C18  C19     0.00   0.0  0
 RMY  Var_01    C7    C8   S1   C1    178.49  30.0  3
 RMY  Var_02    HAA   C7   C8   S1   -179.57  30.0  3
 RMY  Var_03    HAN   C19  C18  N1    125.72  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
 RMY  chir_01  C1   S1   O4   C2   positiv
 RMY  chir_02  C2   O1   C1   C3   negativ
 RMY  chir_03  C3   O2   C4   C2   negativ
 RMY  chir_04  C4   O3   C5   C3   negativ
 RMY  chir_05  C5   O4   C6   C4   positiv
 RMY  chir_06  C10  C11  C12  N1   negativ
 RMY  chir_07  C11  O12  C15  C10  negativ
 RMY  chir_08  C12  O8   C10  C17  positiv
 RMY  chir_09  C13  O12  C9   C17  negativ
 RMY  chir_10  C15  O10  C11  C16  negativ
 RMY  chir_11  C16  O11  C15  C14  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
 RMY  plan-1  C10   0.020
 RMY  plan-1  C19   0.020
 RMY  plan-1  O13   0.020
 RMY  plan-1  N1    0.020
 RMY  plan-1  C18   0.020
 RMY  plan-1  HNAO  0.020
 RMY  plan-2  C9    0.020
 RMY  plan-2  C13   0.020
 RMY  plan-2  O6    0.020
 RMY  plan-2  O7    0.020

