# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 10:12:47 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: cyclotridecyl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@@H]([C@@H](O)[C@@H](O1)OC2CCCCCCCCCCCC2)N(C)C
#
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
 1D4  1D4  'cyclotridecyl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside'  ligand  66  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1D4
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
 1D4  O3    O  OH1   0  -0.662  -2.0755   1.4613  -1.2592
 1D4  C12   C  CH1   0   0.012  -2.6398   0.2583  -0.8068
 1D4  C5    C  CH1   0   0.309  -1.7066  -0.4608   0.1713
 1D4  O2    O  O2    0  -0.497  -2.2775  -1.6630   0.6088
 1D4  C6    C  CH1   0   0.040  -3.4662  -1.4563   1.3590
 1D4  C7    C  CH3   0  -0.678  -3.9439  -2.8047   1.8536
 1D4  C8    C  CH2   0  -0.459  -4.5051  -0.7413   0.5049
 1D4  C9    C  CH1   0  -0.117  -3.9482   0.5631  -0.0813
 1D4  N     N  NT    0  -0.409  -4.8674   1.3225  -0.9107
 1D4  C10   C  CH3   0  -0.536  -5.4031   0.6184  -2.0545
 1D4  C11   C  CH3   0  -0.521  -5.9116   1.9690  -0.1487
 1D4  O1    O  O2    0  -0.523  -0.5321  -0.7430  -0.4950
 1D4  C4    C  CH1   0   0.069   0.6033  -1.1020   0.2963
 1D4  C13   C  CH2   0  -0.480   1.6565  -1.6036  -0.6888
 1D4  C14   C  CH2   0  -0.457   2.7893  -2.3796  -0.0191
 1D4  C15   C  CH2   0  -0.428   3.9133  -2.8186  -0.9802
 1D4  C16   C  CH2   0  -0.436   5.2205  -2.0550  -0.7625
 1D4  C17   C  CH2   0  -0.440   5.1016  -0.5674  -1.0897
 1D4  C18   C  CH2   0  -0.427   6.0776   0.3548  -0.3522
 1D4  C19   C  CH2   0  -0.431   5.4763   1.7476  -0.1442
 1D4  C20   C  CH2   0  -0.439   4.3601   1.7251   0.9012
 1D4  C21   C  CH2   0  -0.436   3.3498   2.8700   0.8153
 1D4  C1    C  CH2   0  -0.430   1.9710   2.4673   1.3411
 1D4  C2    C  CH2   0  -0.448   1.2915   1.3894   0.4691
 1D4  C3    C  CH2   0  -0.510   1.0827   0.0540   1.1819
 1D4  H3    H  HOH1  0   0.450  -1.2440   1.2518  -1.6973
 1D4  H12   H  HCH1  0   0.207  -2.8308  -0.4345  -1.6414
 1D4  H5    H  HCH1  0   0.177  -1.5340   0.2021   1.0394
 1D4  H9    H  HCH1  0   0.232  -3.6903   1.2216   0.7597
 1D4  H6    H  HCH1  0   0.207  -3.2318  -0.8218   2.2289
 1D4  H71C  H  HCH3  0   0.238  -3.1803  -3.2995   2.4547
 1D4  H72C  H  HCH3  0   0.232  -4.8291  -2.6811   2.4770
 1D4  H73C  H  HCH3  0   0.226  -4.2070  -3.4596   1.0211
 1D4  H81C  H  HCH2  0   0.228  -4.8291  -1.4089  -0.3006
 1D4  H82C  H  HCH2  0   0.244  -5.3847  -0.5313   1.1182
 1D4  H101  H  HCH3  0   0.197  -6.1100  -0.1857  -1.8033
 1D4  H102  H  HCH3  0   0.235  -5.9347   1.3255  -2.6937
 1D4  H103  H  HCH3  0   0.237  -4.6052   0.1824  -2.6559
 1D4  H111  H  HCH3  0   0.230  -5.4760   2.5750   0.6478
 1D4  H112  H  HCH3  0   0.232  -6.4792   2.6365  -0.7993
 1D4  H113  H  HCH3  0   0.193  -6.6319   1.2775   0.3141
 1D4  H4    H  HCH1  0   0.219   0.3349  -1.9401   0.9537
 1D4  H131  H  HCH2  0   0.237   1.1648  -2.2614  -1.4115
 1D4  H132  H  HCH2  0   0.226   2.0574  -0.7645  -1.2652
 1D4  H31C  H  HCH2  0   0.240   0.3876   0.1980   2.0146
 1D4  H32C  H  HCH2  0   0.242   2.0162  -0.2656   1.6544
 1D4  H141  H  HCH2  0   0.223   3.2219  -1.7826   0.7899
 1D4  H142  H  HCH2  0   0.232   2.3579  -3.2581   0.4682
 1D4  H151  H  HCH2  0   0.228   4.1071  -3.8857  -0.8500
 1D4  H152  H  HCH2  0   0.217   3.5853  -2.7007  -2.0184
 1D4  H161  H  HCH2  0   0.210   5.5117  -2.1737   0.2870
 1D4  H162  H  HCH2  0   0.221   6.0232  -2.5100  -1.3497
 1D4  H171  H  HCH2  0   0.224   5.1940  -0.4149  -2.1692
 1D4  H172  H  HCH2  0   0.219   4.0873  -0.2466  -0.8474
 1D4  H181  H  HCH2  0   0.208   6.3218  -0.0731   0.6260
 1D4  H182  H  HCH2  0   0.224   7.0236   0.4222  -0.8959
 1D4  H191  H  HCH2  0   0.222   6.2507   2.4636   0.1444
 1D4  H192  H  HCH2  0   0.208   5.0753   2.1038  -1.0996
 1D4  H201  H  HCH2  0   0.220   3.8113   0.7851   0.8010
 1D4  H202  H  HCH2  0   0.224   4.7964   1.6893   1.9042
 1D4  H211  H  HCH2  0   0.221   3.7193   3.7463   1.3554
 1D4  H212  H  HCH2  0   0.210   3.2404   3.1856  -0.2282
 1D4  H11C  H  HCH2  0   0.217   2.0652   2.1149   2.3737
 1D4  H12C  H  HCH2  0   0.227   1.3361   3.3548   1.3901
 1D4  H21C  H  HCH2  0   0.230   0.3277   1.7635   0.1208
 1D4  H22C  H  HCH2  0   0.222   1.8859   1.2333  -0.4368

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
 1D4  O3   C12   single  1.404  0.020  1.404
 1D4  C12  C5    single  1.531  0.020  1.531
 1D4  C12  C9    single  1.527  0.020  1.527
 1D4  C5   O2    single  1.401  0.020  1.401
 1D4  C5   O1    single  1.380  0.020  1.380
 1D4  O2   C6    single  1.421  0.020  1.421
 1D4  C6   C7    single  1.514  0.020  1.514
 1D4  C6   C8    single  1.523  0.020  1.523
 1D4  C8   C9    single  1.535  0.020  1.535
 1D4  C9   N     single  1.453  0.020  1.453
 1D4  N    C10   single  1.446  0.020  1.446
 1D4  N    C11   single  1.445  0.020  1.445
 1D4  O1   C4    single  1.430  0.020  1.430
 1D4  C4   C13   single  1.527  0.020  1.527
 1D4  C4   C3    single  1.533  0.020  1.533
 1D4  C13  C14   single  1.528  0.020  1.528
 1D4  C14  C15   single  1.543  0.020  1.543
 1D4  C15  C16   single  1.529  0.020  1.529
 1D4  C16  C17   single  1.528  0.020  1.528
 1D4  C17  C18   single  1.532  0.020  1.532
 1D4  C18  C19   single  1.531  0.020  1.531
 1D4  C19  C20   single  1.529  0.020  1.529
 1D4  C20  C21   single  1.529  0.020  1.529
 1D4  C21  C1    single  1.530  0.020  1.530
 1D4  C1   C2    single  1.544  0.020  1.544
 1D4  C2   C3    single  1.528  0.020  1.528
 1D4  O3   H3    single  0.850  0.020  0.980
 1D4  C12  H12   single  0.970  0.020  1.090
 1D4  C5   H5    single  0.970  0.020  1.090
 1D4  C9   H9    single  0.970  0.020  1.090
 1D4  C6   H6    single  0.970  0.020  1.090
 1D4  C7   H71C  single  0.970  0.020  1.090
 1D4  C7   H72C  single  0.970  0.020  1.090
 1D4  C7   H73C  single  0.970  0.020  1.090
 1D4  C8   H81C  single  0.970  0.020  1.090
 1D4  C8   H82C  single  0.970  0.020  1.090
 1D4  C10  H101  single  0.970  0.020  1.090
 1D4  C10  H102  single  0.970  0.020  1.090
 1D4  C10  H103  single  0.970  0.020  1.090
 1D4  C11  H111  single  0.970  0.020  1.090
 1D4  C11  H112  single  0.970  0.020  1.090
 1D4  C11  H113  single  0.970  0.020  1.090
 1D4  C4   H4    single  0.970  0.020  1.090
 1D4  C13  H131  single  0.970  0.020  1.090
 1D4  C13  H132  single  0.970  0.020  1.090
 1D4  C3   H31C  single  0.970  0.020  1.090
 1D4  C3   H32C  single  0.970  0.020  1.090
 1D4  C14  H141  single  0.970  0.020  1.090
 1D4  C14  H142  single  0.970  0.020  1.090
 1D4  C15  H151  single  0.970  0.020  1.090
 1D4  C15  H152  single  0.970  0.020  1.090
 1D4  C16  H161  single  0.970  0.020  1.090
 1D4  C16  H162  single  0.970  0.020  1.090
 1D4  C17  H171  single  0.970  0.020  1.090
 1D4  C17  H172  single  0.970  0.020  1.090
 1D4  C18  H181  single  0.970  0.020  1.090
 1D4  C18  H182  single  0.970  0.020  1.090
 1D4  C19  H191  single  0.970  0.020  1.090
 1D4  C19  H192  single  0.970  0.020  1.090
 1D4  C20  H201  single  0.970  0.020  1.090
 1D4  C20  H202  single  0.970  0.020  1.090
 1D4  C21  H211  single  0.970  0.020  1.090
 1D4  C21  H212  single  0.970  0.020  1.090
 1D4  C1   H11C  single  0.970  0.020  1.090
 1D4  C1   H12C  single  0.970  0.020  1.090
 1D4  C2   H21C  single  0.970  0.020  1.090
 1D4  C2   H22C  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
 1D4  H3    O3   C12   107.90  3.000
 1D4  H12   C12  C9    109.69  3.000
 1D4  H12   C12  C5    107.12  3.000
 1D4  C9    C12  C5    108.21  3.000
 1D4  H12   C12  O3    111.38  3.000
 1D4  C9    C12  O3    109.06  3.000
 1D4  C5    C12  O3    111.31  3.000
 1D4  H5    C5   O1    111.65  3.000
 1D4  H5    C5   O2    109.44  3.000
 1D4  O1    C5   O2    108.80  3.000
 1D4  H5    C5   C12   108.36  3.000
 1D4  O1    C5   C12   107.84  3.000
 1D4  O2    C5   C12   110.74  3.000
 1D4  C6    O2   C5    112.39  3.000
 1D4  H6    C6   C8    108.51  3.000
 1D4  H6    C6   C7    108.79  3.000
 1D4  C8    C6   C7    112.71  3.000
 1D4  H6    C6   O2    108.83  3.000
 1D4  C8    C6   O2    110.05  3.000
 1D4  C7    C6   O2    107.88  3.000
 1D4  H73C  C7   H72C  107.97  3.000
 1D4  H73C  C7   H71C  108.48  3.000
 1D4  H72C  C7   H71C  107.76  3.000
 1D4  H73C  C7   C6    111.19  3.000
 1D4  H72C  C7   C6    110.02  3.000
 1D4  H71C  C7   C6    111.30  3.000
 1D4  H82C  C8   H81C  106.97  3.000
 1D4  H82C  C8   C9    110.07  3.000
 1D4  H81C  C8   C9    110.15  3.000
 1D4  H82C  C8   C6    108.94  3.000
 1D4  H81C  C8   C6    109.15  3.000
 1D4  C9    C8   C6    111.45  3.000
 1D4  H9    C9   N     105.79  3.000
 1D4  H9    C9   C8    107.59  3.000
 1D4  N     C9   C8    115.65  3.000
 1D4  H9    C9   C12   106.39  3.000
 1D4  N     C9   C12   112.05  3.000
 1D4  C8    C9   C12   108.83  3.000
 1D4  C11   N    C10   111.54  3.000
 1D4  C11   N    C9    112.95  3.000
 1D4  C10   N    C9    115.56  3.000
 1D4  H103  C10  H102  107.00  3.000
 1D4  H103  C10  H101  107.70  3.000
 1D4  H102  C10  H101  107.12  3.000
 1D4  H103  C10  N     111.10  3.000
 1D4  H102  C10  N     109.16  3.000
 1D4  H101  C10  N     114.43  3.000
 1D4  H113  C11  H112  107.13  3.000
 1D4  H113  C11  H111  107.65  3.000
 1D4  H112  C11  H111  107.63  3.000
 1D4  H113  C11  N     114.43  3.000
 1D4  H112  C11  N     109.57  3.000
 1D4  H111  C11  N     110.16  3.000
 1D4  C4    O1   C5    117.39  3.000
 1D4  H4    C4   C3    107.82  3.000
 1D4  H4    C4   C13   107.70  3.000
 1D4  C3    C4   C13   113.88  3.000
 1D4  H4    C4   O1    109.19  3.000
 1D4  C3    C4   O1    112.25  3.000
 1D4  C13   C4   O1    105.85  3.000
 1D4  H132  C13  H131  106.13  3.000
 1D4  H132  C13  C14   110.41  3.000
 1D4  H131  C13  C14   108.51  3.000
 1D4  H132  C13  C4    109.92  3.000
 1D4  H131  C13  C4    108.28  3.000
 1D4  C14   C13  C4    113.30  3.000
 1D4  H142  C14  H141  105.36  3.000
 1D4  H142  C14  C15   109.66  3.000
 1D4  H141  C14  C15   109.13  3.000
 1D4  H142  C14  C13   108.11  3.000
 1D4  H141  C14  C13   109.88  3.000
 1D4  C15   C14  C13   114.31  3.000
 1D4  H152  C15  H151  105.74  3.000
 1D4  H152  C15  C16   109.70  3.000
 1D4  H151  C15  C16   108.61  3.000
 1D4  H152  C15  C14   109.98  3.000
 1D4  H151  C15  C14   109.45  3.000
 1D4  C16   C15  C14   113.08  3.000
 1D4  H162  C16  H161  105.91  3.000
 1D4  H162  C16  C17   110.31  3.000
 1D4  H161  C16  C17   109.36  3.000
 1D4  H162  C16  C15   110.07  3.000
 1D4  H161  C16  C15   108.02  3.000
 1D4  C17   C16  C15   112.90  3.000
 1D4  H172  C17  H171  104.87  3.000
 1D4  H172  C17  C18   107.96  3.000
 1D4  H171  C17  C18   109.71  3.000
 1D4  H172  C17  C16   108.12  3.000
 1D4  H171  C17  C16   109.91  3.000
 1D4  C18   C17  C16   115.68  3.000
 1D4  H182  C18  H181  105.98  3.000
 1D4  H182  C18  C19   110.56  3.000
 1D4  H181  C18  C19   108.76  3.000
 1D4  H182  C18  C17   110.42  3.000
 1D4  H181  C18  C17   109.68  3.000
 1D4  C19   C18  C17   111.27  3.000
 1D4  H192  C19  H191  106.05  3.000
 1D4  H192  C19  C20   109.49  3.000
 1D4  H191  C19  C20   110.24  3.000
 1D4  H192  C19  C18   108.73  3.000
 1D4  H191  C19  C18   110.69  3.000
 1D4  C20   C19  C18   111.47  3.000
 1D4  H202  C20  H201  104.83  3.000
 1D4  H202  C20  C21   109.84  3.000
 1D4  H201  C20  C21   107.87  3.000
 1D4  H202  C20  C19   109.64  3.000
 1D4  H201  C20  C19   108.44  3.000
 1D4  C21   C20  C19   115.64  3.000
 1D4  H212  C21  H211  105.86  3.000
 1D4  H212  C21  C1    108.25  3.000
 1D4  H211  C21  C1    110.22  3.000
 1D4  H212  C21  C20   109.58  3.000
 1D4  H211  C21  C20   110.42  3.000
 1D4  C1    C21  C20   112.28  3.000
 1D4  H12C  C1   H11C  105.61  3.000
 1D4  H12C  C1   C2    109.68  3.000
 1D4  H11C  C1   C2    110.23  3.000
 1D4  H12C  C1   C21   108.99  3.000
 1D4  H11C  C1   C21   109.34  3.000
 1D4  C2    C1   C21   112.73  3.000
 1D4  H22C  C2   H21C  105.33  3.000
 1D4  H22C  C2   C3    109.61  3.000
 1D4  H21C  C2   C3    109.14  3.000
 1D4  H22C  C2   C1    109.15  3.000
 1D4  H21C  C2   C1    109.25  3.000
 1D4  C3    C2   C1    114.00  3.000
 1D4  H32C  C3   H31C  104.59  3.000
 1D4  H32C  C3   C2    109.89  3.000
 1D4  H31C  C3   C2    109.07  3.000
 1D4  H32C  C3   C4    107.22  3.000
 1D4  H31C  C3   C4    109.89  3.000
 1D4  C2    C3   C4    115.61  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
 1D4  Var_01  C15   C14  C13  C4   -176.23  30.0  1
 1D4  Var_02  C1    C2   C3   C4   -171.35  30.0  1
 1D4  Var_03  C16   C15  C14  C13   109.59  30.0  1
 1D4  Var_04  C17   C16  C15  C14   -65.39  30.0  1
 1D4  Var_05  C18   C17  C16  C15   153.80  30.0  1
 1D4  Var_06  C19   C18  C17  C16  -150.36  30.0  1
 1D4  Var_07  C20   C19  C18  C17    71.34  30.0  1
 1D4  Var_08  C21   C20  C19  C18  -157.36  30.0  1
 1D4  Var_09  C1    C21  C20  C19   151.42  30.0  1
 1D4  Var_10  C2    C1   C21  C20   -66.04  30.0  1
 1D4  Var_11  C3    C2   C1   C21   115.02  30.0  1
 1D4  Var_12  H101  C10  N    C9     69.74  30.0  3
 1D4  Var_13  H111  C11  N    C9     53.56  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
 1D4  chir_01  C12  O3  C5   C9   negativ
 1D4  chir_02  C5   O1  O2   C12  positiv
 1D4  chir_03  C6   O2  C7   C8   positiv
 1D4  chir_04  C9   N   C12  C8   positiv
 1D4  chir_05  C4   O1  C3   C13  positiv

