# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 15:41:06 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: methyl (2S,3R,4S)-3-ethenyl-2-(beta-D-glucopyranosyloxy)-4-(2-oxoethyl)-3,4-dihydro-2H-pyran-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](C=C)[C@@H]1CC=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
 SCG  SCG  'methyl (2S,3R,4S)-3-ethenyl-2-(beta-D-glucopyranosyloxy)-4-(2-oxoethyl)-3,4-dihydro-2H-pyran-5-carboxylate'  D-saccharide  51  27  .  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_SCG
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
 SCG  O16   O  O     0  -0.376  -3.5806  -1.6058   3.0480
 SCG  C10   C  C1    0   0.168  -3.7551  -1.8943   1.8891
 SCG  C9    C  CH2   0  -0.557  -3.8239  -0.8756   0.7848
 SCG  C1    C  CH1   0  -0.257  -2.4078  -0.4556   0.3364
 SCG  C6    C  CH1   0  -0.452  -1.5881  -1.6962  -0.0873
 SCG  C7    C  C1    0  -0.146  -2.3445  -2.6310  -0.9893
 SCG  C8    C  C2    0  -0.521  -2.4046  -3.9431  -0.8007
 SCG  C5    C  CH1   0   0.287  -0.3204  -1.2428  -0.7952
 SCG  O4    O  O2    0  -0.444  -0.6500  -0.5351  -1.9814
 SCG  C3    C  C1    0   0.054  -1.5904   0.4052  -1.8503
 SCG  C2    C  C     0  -0.145  -2.4209   0.5349  -0.8037
 SCG  C12   C  C     0   0.557  -3.2530   1.7538  -0.8144
 SCG  O14   O  O2    0  -0.456  -3.6297   2.1078   0.4077
 SCG  C15   C  CH3   0  -0.422  -4.4247   3.2853   0.5427
 SCG  O13   O  O     0  -0.461  -3.5323   2.3956  -1.8017
 SCG  O11   O  O2    0  -0.499   0.3866  -0.4119   0.0658
 SCG  C17   C  CH1   0   0.287   1.6877  -0.0800  -0.3017
 SCG  O22   O  O2    0  -0.488   2.5487  -0.9344   0.3912
 SCG  C21   C  CH1   0  -0.020   3.9108  -0.7250   0.0673
 SCG  C23   C  CH2   0  -0.158   4.7253  -1.7720   0.7962
 SCG  O24   O  OH1   0  -0.669   4.3367  -3.0471   0.3448
 SCG  C20   C  CH1   0   0.035   4.3181   0.6952   0.4660
 SCG  O25   O  OH1   0  -0.671   5.6552   0.8906   0.0817
 SCG  C19   C  CH1   0  -0.013   3.3952   1.7058  -0.2078
 SCG  O26   O  OH1   0  -0.671   3.7566   2.9837   0.2564
 SCG  C18   C  CH1   0  -0.032   1.9415   1.3716   0.0942
 SCG  O27   O  OH1   0  -0.662   1.1260   2.2484  -0.6410
 SCG  H10   H  H     0   0.200  -3.8626  -2.9488   1.5841
 SCG  H91   H  HCH2  0   0.289  -4.3616  -0.0081   1.1635
 SCG  H92   H  HCH2  0   0.263  -4.3860  -1.2849  -0.0566
 SCG  H1    H  HCH1  0   0.285  -1.9152  -0.0039   1.2034
 SCG  H6    H  HCH1  0   0.298  -1.2773  -2.2464   0.8061
 SCG  H7    H  H     0   0.267  -2.8550  -2.1990  -1.8454
 SCG  H81   H  H     0   0.245  -1.9158  -4.4234   0.0392
 SCG  H82   H  H     0   0.248  -2.9438  -4.5866  -1.4831
 SCG  H5    H  HCH1  0   0.274   0.2797  -2.0929  -1.1312
 SCG  H3    H  H     0   0.293  -1.6057   1.0859  -2.6927
 SCG  H151  H  HCH3  0   0.240  -3.8827   4.1699   0.2090
 SCG  H152  H  HCH3  0   0.240  -5.3582   3.2036  -0.0135
 SCG  H153  H  HCH3  0   0.253  -4.6431   3.3754   1.6025
 SCG  H17   H  HCH1  0   0.208   1.8355  -0.1903  -1.3892
 SCG  H21   H  HCH1  0   0.228   4.0606  -0.8422  -1.0186
 SCG  H231  H  HCH2  0   0.217   5.7850  -1.5800   0.6023
 SCG  H232  H  HCH2  0   0.196   4.5690  -1.6552   1.8782
 SCG  H24   H  HOH1  0   0.457   4.9652  -3.6869   0.6900
 SCG  H20   H  HCH1  0   0.215   4.2008   0.7921   1.5576
 SCG  H25   H  HOH1  0   0.455   5.9079   1.7871   0.3262
 SCG  H19   H  HCH1  0   0.219   3.5473   1.6292  -1.2965
 SCG  H26   H  HOH1  0   0.458   3.3517   3.6443  -0.3138
 SCG  H18   H  HCH1  0   0.231   1.7699   1.4693   1.1767
 SCG  H27   H  HOH1  0   0.454   0.2292   2.1964  -0.2959

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
 SCG  O16  C10   double  1.207  0.020  1.207
 SCG  C10  C9    single  1.504  0.020  1.504
 SCG  C10  H10   single  0.930  0.020  1.080
 SCG  C9   C1    single  1.544  0.020  1.544
 SCG  C9   H91   single  0.970  0.020  1.090
 SCG  C9   H92   single  0.970  0.020  1.090
 SCG  C1   C6    single  1.546  0.020  1.546
 SCG  C1   C2    single  1.510  0.020  1.510
 SCG  C1   H1    single  0.970  0.020  1.090
 SCG  C6   C7    single  1.503  0.020  1.503
 SCG  C6   C5    single  1.521  0.020  1.521
 SCG  C6   H6    single  0.970  0.020  1.090
 SCG  C7   C8    double  1.327  0.020  1.327
 SCG  C7   H7    single  0.930  0.020  1.080
 SCG  C8   H81   single  0.930  0.020  1.080
 SCG  C8   H82   single  0.930  0.020  1.080
 SCG  C5   O4    single  1.420  0.020  1.420
 SCG  C5   O11   single  1.390  0.020  1.390
 SCG  C5   H5    single  0.970  0.020  1.090
 SCG  O4   C3    single  1.336  0.020  1.336
 SCG  C3   C2    double  1.342  0.020  1.342
 SCG  C3   H3    single  0.930  0.020  1.080
 SCG  C2   C12   single  1.476  0.020  1.476
 SCG  C12  O14   single  1.327  0.020  1.327
 SCG  C12  O13   double  1.210  0.020  1.210
 SCG  O14  C15   single  1.427  0.020  1.427
 SCG  C15  H151  single  0.970  0.020  1.090
 SCG  C15  H152  single  0.970  0.020  1.090
 SCG  C15  H153  single  0.970  0.020  1.090
 SCG  O11  C17   single  1.392  0.020  1.392
 SCG  C17  O22   single  1.397  0.020  1.397
 SCG  C17  C18   single  1.526  0.020  1.526
 SCG  C17  H17   single  0.970  0.020  1.090
 SCG  O22  C21   single  1.416  0.020  1.416
 SCG  C21  C23   single  1.514  0.020  1.514
 SCG  C21  C20   single  1.530  0.020  1.530
 SCG  C21  H21   single  0.970  0.020  1.090
 SCG  C23  O24   single  1.407  0.020  1.407
 SCG  C23  H231  single  0.970  0.020  1.090
 SCG  C23  H232  single  0.970  0.020  1.090
 SCG  O24  H24   single  0.850  0.020  0.980
 SCG  C20  O25   single  1.405  0.020  1.405
 SCG  C20  C19   single  1.525  0.020  1.525
 SCG  C20  H20   single  0.970  0.020  1.090
 SCG  O25  H25   single  0.850  0.020  0.980
 SCG  C19  O26   single  1.407  0.020  1.407
 SCG  C19  C18   single  1.522  0.020  1.522
 SCG  C19  H19   single  0.970  0.020  1.090
 SCG  O26  H26   single  0.850  0.020  0.980
 SCG  C18  O27   single  1.405  0.020  1.405
 SCG  C18  H18   single  0.970  0.020  1.090
 SCG  O27  H27   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
 SCG  H10   C10  C9    116.11  3.000
 SCG  H10   C10  O16   120.54  3.000
 SCG  C9    C10  O16   123.35  3.000
 SCG  H92   C9   H91   108.22  3.000
 SCG  H92   C9   C1    110.52  3.000
 SCG  H91   C9   C1    109.72  3.000
 SCG  H92   C9   C10   109.61  3.000
 SCG  H91   C9   C10   107.87  3.000
 SCG  C1    C9   C10   110.83  3.000
 SCG  H1    C1   C2    109.34  3.000
 SCG  H1    C1   C6    108.03  3.000
 SCG  C2    C1   C6    108.90  3.000
 SCG  H1    C1   C9    107.16  3.000
 SCG  C2    C1   C9    112.94  3.000
 SCG  C6    C1   C9    110.34  3.000
 SCG  H6    C6   C5    107.04  3.000
 SCG  H6    C6   C7    108.67  3.000
 SCG  C5    C6   C7    108.99  3.000
 SCG  H6    C6   C1    109.29  3.000
 SCG  C5    C6   C1    109.28  3.000
 SCG  C7    C6   C1    113.37  3.000
 SCG  H7    C7   C8    118.94  3.000
 SCG  H7    C7   C6    117.52  3.000
 SCG  C8    C7   C6    123.54  3.000
 SCG  H82   C8   H81   116.74  3.000
 SCG  H82   C8   C7    121.40  3.000
 SCG  H81   C8   C7    121.86  3.000
 SCG  H5    C5   O11   112.08  3.000
 SCG  H5    C5   O4    104.96  3.000
 SCG  O11   C5   O4    109.73  3.000
 SCG  H5    C5   C6    111.64  3.000
 SCG  O11   C5   C6    108.29  3.000
 SCG  O4    C5   C6    110.11  3.000
 SCG  C3    O4   C5    115.60  3.000
 SCG  H3    C3   C2    122.47  3.000
 SCG  H3    C3   O4    112.08  3.000
 SCG  C2    C3   O4    125.44  3.000
 SCG  C12   C2   C3    115.02  3.000
 SCG  C12   C2   C1    123.50  3.000
 SCG  C3    C2   C1    121.32  3.000
 SCG  O13   C12  O14   122.98  3.000
 SCG  O13   C12  C2    125.03  3.000
 SCG  O14   C12  C2    111.95  3.000
 SCG  C15   O14  C12   117.73  3.000
 SCG  H153  C15  H152  109.39  3.000
 SCG  H153  C15  H151  109.36  3.000
 SCG  H152  C15  H151  109.30  3.000
 SCG  H153  C15  O14   105.84  3.000
 SCG  H152  C15  O14   111.54  3.000
 SCG  H151  C15  O14   111.33  3.000
 SCG  C17   O11  C5    117.03  3.000
 SCG  H17   C17  C18   109.19  3.000
 SCG  H17   C17  O22   110.20  3.000
 SCG  C18   C17  O22   110.53  3.000
 SCG  H17   C17  O11   111.20  3.000
 SCG  C18   C17  O11   108.28  3.000
 SCG  O22   C17  O11   107.41  3.000
 SCG  C21   O22  C17   112.89  3.000
 SCG  H21   C21  C20   108.61  3.000
 SCG  H21   C21  C23   109.12  3.000
 SCG  C20   C21  C23   111.92  3.000
 SCG  H21   C21  O22   109.90  3.000
 SCG  C20   C21  O22   109.50  3.000
 SCG  C23   C21  O22   107.77  3.000
 SCG  H232  C23  H231  107.06  3.000
 SCG  H232  C23  O24   111.88  3.000
 SCG  H231  C23  O24   111.69  3.000
 SCG  H232  C23  C21   108.90  3.000
 SCG  H231  C23  C21   108.33  3.000
 SCG  O24   C23  C21   108.89  3.000
 SCG  H24   O24  C23   107.90  3.000
 SCG  H20   C20  C19   108.35  3.000
 SCG  H20   C20  O25   111.10  3.000
 SCG  C19   C20  O25   111.28  3.000
 SCG  H20   C20  C21   108.14  3.000
 SCG  C19   C20  C21   109.80  3.000
 SCG  O25   C20  C21   108.13  3.000
 SCG  H25   O25  C20   108.05  3.000
 SCG  H19   C19  C18   108.22  3.000
 SCG  H19   C19  O26   110.71  3.000
 SCG  C18   C19  O26   112.29  3.000
 SCG  H19   C19  C20   107.87  3.000
 SCG  C18   C19  C20   110.17  3.000
 SCG  O26   C19  C20   107.50  3.000
 SCG  H26   O26  C19   108.67  3.000
 SCG  H18   C18  O27   111.64  3.000
 SCG  H18   C18  C19   108.95  3.000
 SCG  O27   C18  C19   108.27  3.000
 SCG  H18   C18  C17   108.29  3.000
 SCG  O27   C18  C17   111.18  3.000
 SCG  C19   C18  C17   108.44  3.000
 SCG  H27   O27  C18   108.63  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
 SCG  Var_01  O4    C3   C2   C1    -3.14  30.0  1
 SCG  Var_02  C2    C3   O4   C5   -14.89  30.0  1
 SCG  Var_03  O14   C12  C2   C1    20.57  30.0  2
 SCG  Var_04  C1    C9   C10  O16   81.59  30.0  3
 SCG  Var_05  H81   C8   C7   C6     1.01   0.0  2
 SCG  Var_06  H151  C15  O14  C12  -62.87  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
 SCG  chir_01  C1   C9   C6   C2   negativ
 SCG  chir_02  C6   C5   C7   C1   positiv
 SCG  chir_03  C5   O4   O11  C6   negativ
 SCG  chir_04  C17  O11  O22  C18  positiv
 SCG  chir_05  C21  O22  C23  C20  positiv
 SCG  chir_06  C20  O25  C21  C19  positiv
 SCG  chir_07  C19  O26  C18  C20  positiv
 SCG  chir_08  C18  O27  C17  C19  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
 SCG  plan-1  O16  0.020
 SCG  plan-1  C10  0.020
 SCG  plan-1  C9   0.020
 SCG  plan-1  H10  0.020
 SCG  plan-2  C6   0.020
 SCG  plan-2  C7   0.020
 SCG  plan-2  C8   0.020
 SCG  plan-2  H7   0.020
 SCG  plan-2  H81  0.020
 SCG  plan-2  H82  0.020
 SCG  plan-3  C2   0.020
 SCG  plan-3  C12  0.020
 SCG  plan-3  O14  0.020
 SCG  plan-3  O13  0.020

