# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 21 09:02:21 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2R,3S,4S,5S,6S)-2-[(2R,3S,4R,5R,6R)-6-(2,6-dimethylheptan-4-yloxy)-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(CC(C)C)O[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[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
 0BD  0BD  (2R,3S,4S,5S,6S)-2-[(2R,3S,4R,5R,6R)-6-(2,6-dimethylheptan-4-yloxy)-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol  D-saccharide  72  32  .  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_0BD
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
 0BD  C1    C  CH1   0  -0.026   1.4161   1.5237  -1.1523
 0BD  C2    C  CH1   0   0.017   0.0354   1.7312  -0.5502
 0BD  C3    C  CH1   0   0.009  -0.6441   0.3957  -0.2657
 0BD  C4    C  CH1   0  -0.017   0.2896  -0.4934   0.5675
 0BD  O5    O  O2    0  -0.479   1.5205  -0.6237  -0.1097
 0BD  C6    C  CH1   0   0.297   2.2146   0.5888  -0.2483
 0BD  O7    O  O2    0  -0.513  -1.8384   0.6720   0.4351
 0BD  O16   O  O2    0  -0.512   3.4259   0.3435  -0.8468
 0BD  C18   C  CH1   0   0.019   4.4899  -0.1334  -0.0152
 0BD  C19   C  CH2   0  -0.411   5.1836  -1.2742  -0.7470
 0BD  C22   C  CH1   0  -0.230   4.3437  -2.5239  -1.0177
 0BD  O49   O  OH1   0  -0.665   2.0193   2.7873  -1.2713
 0BD  O55   O  OH1   0  -0.673  -0.8017   2.4693  -1.4136
 0BD  C57   C  CH2   0  -0.170  -0.2608  -1.8864   0.7887
 0BD  O61   O  OH1   0  -0.665   0.5394  -2.5332   1.7520
 0BD  C10   C  CH1   0   0.284  -3.0466   0.2426  -0.0970
 0BD  C14   C  CH3   0  -0.654   5.1472  -3.4956  -1.8774
 0BD  C13   C  CH3   0  -0.669   3.8814  -3.2020   0.2686
 0BD  C     C  CH2   0  -0.395   5.4732   1.0006   0.2633
 0BD  C12   C  CH1   0  -0.258   4.9513   2.1926   1.0703
 0BD  C16   C  CH3   0  -0.658   4.5896   1.8061   2.5011
 0BD  C15   C  CH3   0  -0.648   5.9985   3.3028   1.0759
 0BD  O71   O  O2    0  -0.490  -3.5345  -0.7519   0.7559
 0BD  C17   C  CH1   0  -0.001  -4.0276   1.4143  -0.1393
 0BD  C181  C  CH1   0  -0.008  -4.7494  -1.3248   0.3127
 0BD  C191  C  CH1   0  -0.050  -5.4087   0.9192  -0.5743
 0BD  C20   C  CH1   0   0.012  -5.8518  -0.2732   0.2800
 0BD  H1    H  HCH1  0   0.228   1.3068   1.0352  -2.1330
 0BD  H2    H  HCH1  0   0.229   0.1538   2.2574   0.4103
 0BD  H3    H  HCH1  0   0.245  -0.8627  -0.1092  -1.2175
 0BD  H4    H  HCH1  0   0.223   0.4403  -0.0103   1.5474
 0BD  H6    H  HCH1  0   0.186   2.3332   1.0544   0.7485
 0BD  H18   H  HCH1  0   0.224   4.0753  -0.5140   0.9259
 0BD  H19   H  HCH2  0   0.220   5.5729  -0.8862  -1.6960
 0BD  H19A  H  HCH2  0   0.215   6.0630  -1.5638  -0.1610
 0BD  H22   H  HCH1  0   0.217   3.4544  -2.2256  -1.5813
 0BD  HO49  H  HOH1  0   0.458   2.8374   2.6882  -1.7690
 0BD  HO55  H  HOH1  0   0.468  -0.4427   3.3586  -1.5075
 0BD  H57   H  HCH2  0   0.221  -1.3026  -1.8214   1.1159
 0BD  H57A  H  HCH2  0   0.202  -0.2567  -2.4205  -0.1704
 0BD  HO61  H  HOH1  0   0.455   0.3620  -3.4761   1.7056
 0BD  H10   H  HCH1  0   0.195  -2.9012  -0.1604  -1.1139
 0BD  H14   H  HCH3  0   0.223   4.5734  -4.3964  -2.1025
 0BD  H14A  H  HCH3  0   0.222   5.4400  -3.0414  -2.8260
 0BD  H14B  H  HCH3  0   0.210   6.0609  -3.8070  -1.3649
 0BD  H13   H  HCH3  0   0.246   3.1812  -2.5850   0.8301
 0BD  H13A  H  HCH3  0   0.216   3.3700  -4.1406   0.0451
 0BD  H13B  H  HCH3  0   0.201   4.7317  -3.4394   0.9142
 0BD  H     H  HCH2  0   0.214   6.3376   0.5803   0.7901
 0BD  HA    H  HCH2  0   0.221   5.8521   1.3586  -0.7010
 0BD  H12   H  HCH1  0   0.215   4.0563   2.5882   0.5789
 0BD  H16   H  HCH3  0   0.217   5.4643   1.4215   3.0319
 0BD  H16A  H  HCH3  0   0.228   4.2195   2.6689   3.0577
 0BD  H16B  H  HCH3  0   0.222   3.8160   1.0385   2.5490
 0BD  H15   H  HCH3  0   0.224   6.2467   3.6219   0.0622
 0BD  H15A  H  HCH3  0   0.225   5.6463   4.1797   1.6219
 0BD  H15B  H  HCH3  0   0.213   6.9223   2.9661   1.5531
 0BD  O8    O  OH1   0  -0.700  -3.6345   2.4042  -1.0550
 0BD  H31   H  HCH1  0   0.215  -4.1105   1.8140   0.8822
 0BD  C21   C  CH2   0  -0.157  -5.0774  -2.4900   1.2212
 0BD  H32   H  HCH1  0   0.230  -4.6331  -1.7075  -0.7126
 0BD  O9    O  OH1   0  -0.673  -5.3946   0.4920  -1.9162
 0BD  H33   H  HCH1  0   0.234  -6.1332   1.7377  -0.4390
 0BD  O10   O  OH1   0  -0.671  -6.1249   0.1317   1.6000
 0BD  H34   H  HCH1  0   0.235  -6.7375  -0.7239  -0.1900
 0BD  H35   H  HCH2  0   0.200  -6.0773  -2.8563   0.9523
 0BD  O11   O  OH1   0  -0.666  -4.0947  -3.4839   1.0491
 0BD  H36   H  HCH2  0   0.206  -5.1297  -2.1466   2.2602
 0BD  H37   H  HOH1  0   0.456  -2.6681   2.5108  -1.0402
 0BD  H38   H  HOH1  0   0.450  -4.9529   1.1747  -2.4342
 0BD  H39   H  HOH1  0   0.457  -6.9081   0.6909   1.5925
 0BD  H40   H  HOH1  0   0.455  -4.2763  -4.1906   1.6749

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
 0BD  C1    C2    single  1.520  0.020  1.520
 0BD  C1    C6    single  1.526  0.020  1.526
 0BD  C1    O49   single  1.405  0.020  1.405
 0BD  C2    C3    single  1.525  0.020  1.525
 0BD  C2    O55   single  1.411  0.020  1.411
 0BD  C3    C4    single  1.535  0.020  1.535
 0BD  C3    O7    single  1.412  0.020  1.412
 0BD  C4    O5    single  1.411  0.020  1.411
 0BD  C4    C57   single  1.514  0.020  1.514
 0BD  O5    C6    single  1.404  0.020  1.404
 0BD  C6    O16   single  1.373  0.020  1.373
 0BD  O7    C10   single  1.388  0.020  1.388
 0BD  O16   C18   single  1.432  0.020  1.432
 0BD  C18   C19   single  1.523  0.020  1.523
 0BD  C18   C     single  1.527  0.020  1.527
 0BD  C19   C22   single  1.530  0.020  1.530
 0BD  C22   C14   single  1.526  0.020  1.526
 0BD  C22   C13   single  1.526  0.020  1.526
 0BD  C57   O61   single  1.409  0.020  1.409
 0BD  C     C12   single  1.531  0.020  1.531
 0BD  C12   C16   single  1.526  0.020  1.526
 0BD  C12   C15   single  1.526  0.020  1.526
 0BD  C10   O71   single  1.398  0.020  1.398
 0BD  C10   C17   single  1.529  0.020  1.529
 0BD  O71   C181  single  1.414  0.020  1.414
 0BD  C17   C191  single  1.530  0.020  1.530
 0BD  C181  C20   single  1.524  0.020  1.524
 0BD  C20   C191  single  1.532  0.020  1.532
 0BD  C1    H1    single  0.970  0.020  1.090
 0BD  C2    H2    single  0.970  0.020  1.090
 0BD  C3    H3    single  0.970  0.020  1.090
 0BD  C4    H4    single  0.970  0.020  1.090
 0BD  C6    H6    single  0.970  0.020  1.090
 0BD  C18   H18   single  0.970  0.020  1.090
 0BD  C19   H19   single  0.970  0.020  1.090
 0BD  C19   H19A  single  0.970  0.020  1.090
 0BD  C22   H22   single  0.970  0.020  1.090
 0BD  O49   HO49  single  0.850  0.020  0.980
 0BD  O55   HO55  single  0.850  0.020  0.980
 0BD  C57   H57   single  0.970  0.020  1.090
 0BD  C57   H57A  single  0.970  0.020  1.090
 0BD  O61   HO61  single  0.850  0.020  0.980
 0BD  C10   H10   single  0.970  0.020  1.090
 0BD  C14   H14   single  0.970  0.020  1.090
 0BD  C14   H14A  single  0.970  0.020  1.090
 0BD  C14   H14B  single  0.970  0.020  1.090
 0BD  C13   H13   single  0.970  0.020  1.090
 0BD  C13   H13A  single  0.970  0.020  1.090
 0BD  C13   H13B  single  0.970  0.020  1.090
 0BD  C     H     single  0.970  0.020  1.090
 0BD  C     HA    single  0.970  0.020  1.090
 0BD  C12   H12   single  0.970  0.020  1.090
 0BD  C16   H16   single  0.970  0.020  1.090
 0BD  C16   H16A  single  0.970  0.020  1.090
 0BD  C16   H16B  single  0.970  0.020  1.090
 0BD  C15   H15   single  0.970  0.020  1.090
 0BD  C15   H15A  single  0.970  0.020  1.090
 0BD  C15   H15B  single  0.970  0.020  1.090
 0BD  C17   O8    single  1.405  0.020  1.405
 0BD  C17   H31   single  0.970  0.020  1.090
 0BD  C181  C21   single  1.513  0.020  1.513
 0BD  C181  H32   single  0.970  0.020  1.090
 0BD  C191  O9    single  1.408  0.020  1.408
 0BD  C191  H33   single  0.970  0.020  1.090
 0BD  C20   O10   single  1.407  0.020  1.407
 0BD  C20   H34   single  0.970  0.020  1.090
 0BD  C21   H35   single  0.970  0.020  1.090
 0BD  C21   O11   single  1.408  0.020  1.408
 0BD  C21   H36   single  0.970  0.020  1.090
 0BD  O8    H37   single  0.850  0.020  0.980
 0BD  O9    H38   single  0.850  0.020  0.980
 0BD  O10   H39   single  0.850  0.020  0.980
 0BD  O11   H40   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
 0BD  H1    C1    O49   111.47  3.000
 0BD  H1    C1    C6    107.93  3.000
 0BD  O49   C1    C6    112.11  3.000
 0BD  H1    C1    C2    108.86  3.000
 0BD  O49   C1    C2    107.49  3.000
 0BD  C6    C1    C2    108.92  3.000
 0BD  H2    C2    O55   110.33  3.000
 0BD  H2    C2    C3    107.67  3.000
 0BD  O55   C2    C3    107.93  3.000
 0BD  H2    C2    C1    108.23  3.000
 0BD  O55   C2    C1    111.58  3.000
 0BD  C3    C2    C1    111.03  3.000
 0BD  H3    C3    O7    110.58  3.000
 0BD  H3    C3    C4    108.96  3.000
 0BD  O7    C3    C4    111.00  3.000
 0BD  H3    C3    C2    109.22  3.000
 0BD  O7    C3    C2    107.34  3.000
 0BD  C4    C3    C2    109.71  3.000
 0BD  H4    C4    C57   108.84  3.000
 0BD  H4    C4    O5    110.35  3.000
 0BD  C57   C4    O5    107.60  3.000
 0BD  H4    C4    C3    108.16  3.000
 0BD  C57   C4    C3    113.02  3.000
 0BD  O5    C4    C3    108.88  3.000
 0BD  C6    O5    C4    113.51  3.000
 0BD  H6    C6    O16   111.92  3.000
 0BD  H6    C6    O5    109.11  3.000
 0BD  O16   C6    O5    108.95  3.000
 0BD  H6    C6    C1    109.39  3.000
 0BD  O16   C6    C1    108.23  3.000
 0BD  O5    C6    C1    109.20  3.000
 0BD  C10   O7    C3    119.03  3.000
 0BD  C18   O16   C6    117.50  3.000
 0BD  H18   C18   C     110.17  3.000
 0BD  H18   C18   C19   108.95  3.000
 0BD  C     C18   C19   110.54  3.000
 0BD  H18   C18   O16   109.45  3.000
 0BD  C     C18   O16   109.70  3.000
 0BD  C19   C18   O16   107.99  3.000
 0BD  H19A  C19   H19   105.75  3.000
 0BD  H19A  C19   C22   108.63  3.000
 0BD  H19   C19   C22   109.32  3.000
 0BD  H19A  C19   C18   107.85  3.000
 0BD  H19   C19   C18   108.21  3.000
 0BD  C22   C19   C18   116.55  3.000
 0BD  H22   C22   C13   108.00  3.000
 0BD  H22   C22   C14   108.14  3.000
 0BD  C13   C22   C14   110.57  3.000
 0BD  H22   C22   C19   108.34  3.000
 0BD  C13   C22   C19   112.35  3.000
 0BD  C14   C22   C19   109.32  3.000
 0BD  HO49  O49   C1    108.43  3.000
 0BD  HO55  O55   C2    108.74  3.000
 0BD  H57A  C57   H57   107.09  3.000
 0BD  H57A  C57   O61   111.82  3.000
 0BD  H57   C57   O61   111.31  3.000
 0BD  H57A  C57   C4    108.58  3.000
 0BD  H57   C57   C4    109.59  3.000
 0BD  O61   C57   C4    108.40  3.000
 0BD  HO61  O61   C57   108.22  3.000
 0BD  H10   C10   C17   109.82  3.000
 0BD  H10   C10   O71   110.39  3.000
 0BD  C17   C10   O71   109.76  3.000
 0BD  H10   C10   O7    110.58  3.000
 0BD  C17   C10   O7    109.39  3.000
 0BD  O71   C10   O7    106.85  3.000
 0BD  H14B  C14   H14A  107.57  3.000
 0BD  H14B  C14   H14   107.52  3.000
 0BD  H14A  C14   H14   107.77  3.000
 0BD  H14B  C14   C22   110.94  3.000
 0BD  H14A  C14   C22   111.45  3.000
 0BD  H14   C14   C22   111.40  3.000
 0BD  H13B  C13   H13A  107.36  3.000
 0BD  H13B  C13   H13   108.57  3.000
 0BD  H13A  C13   H13   106.94  3.000
 0BD  H13B  C13   C22   111.01  3.000
 0BD  H13A  C13   C22   110.57  3.000
 0BD  H13   C13   C22   112.18  3.000
 0BD  HA    C     H     105.98  3.000
 0BD  HA    C     C12   109.10  3.000
 0BD  H     C     C12   108.30  3.000
 0BD  HA    C     C18   107.75  3.000
 0BD  H     C     C18   108.10  3.000
 0BD  C12   C     C18   117.06  3.000
 0BD  H12   C12   C15   107.44  3.000
 0BD  H12   C12   C16   108.58  3.000
 0BD  C15   C12   C16   110.09  3.000
 0BD  H12   C12   C     108.86  3.000
 0BD  C15   C12   C     109.54  3.000
 0BD  C16   C12   C     112.20  3.000
 0BD  H16B  C16   H16A  107.06  3.000
 0BD  H16B  C16   H16   107.37  3.000
 0BD  H16A  C16   H16   107.58  3.000
 0BD  H16B  C16   C12   112.80  3.000
 0BD  H16A  C16   C12   111.00  3.000
 0BD  H16   C16   C12   110.78  3.000
 0BD  H15B  C15   H15A  107.57  3.000
 0BD  H15B  C15   H15   107.66  3.000
 0BD  H15A  C15   H15   107.65  3.000
 0BD  H15B  C15   C12   110.95  3.000
 0BD  H15A  C15   C12   111.40  3.000
 0BD  H15   C15   C12   111.42  3.000
 0BD  C181  O71   C10   113.37  3.000
 0BD  H31   C17   O8    111.74  3.000
 0BD  H31   C17   C191  108.27  3.000
 0BD  O8    C17   C191  107.17  3.000
 0BD  H31   C17   C10   107.52  3.000
 0BD  O8    C17   C10   112.24  3.000
 0BD  C191  C17   C10   109.82  3.000
 0BD  H32   C181  C21   108.32  3.000
 0BD  H32   C181  C20   107.25  3.000
 0BD  C21   C181  C20   112.79  3.000
 0BD  H32   C181  O71   110.00  3.000
 0BD  C21   C181  O71   108.05  3.000
 0BD  C20   C181  O71   110.40  3.000
 0BD  H33   C191  O9    110.43  3.000
 0BD  H33   C191  C20   108.64  3.000
 0BD  O9    C191  C20   107.34  3.000
 0BD  H33   C191  C17   108.56  3.000
 0BD  O9    C191  C17   111.10  3.000
 0BD  C20   C191  C17   110.75  3.000
 0BD  H34   C20   O10   111.26  3.000
 0BD  H34   C20   C191  108.28  3.000
 0BD  O10   C20   C191  110.80  3.000
 0BD  H34   C20   C181  108.01  3.000
 0BD  O10   C20   C181  108.59  3.000
 0BD  C191  C20   C181  109.86  3.000
 0BD  H37   O8    C17   110.21  3.000
 0BD  H36   C21   O11   111.74  3.000
 0BD  H36   C21   H35   107.05  3.000
 0BD  O11   C21   H35   111.71  3.000
 0BD  H36   C21   C181  109.78  3.000
 0BD  O11   C21   C181  108.59  3.000
 0BD  H35   C21   C181  107.88  3.000
 0BD  H38   O9    C191  107.56  3.000
 0BD  H39   O10   C20   108.53  3.000
 0BD  H40   O11   C21   107.91  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
 0BD  Var_01  C19  C18  O16  C6    135.59  30.0  3
 0BD  Var_02  C22  C19  C18  O16   -63.72  30.0  3
 0BD  Var_03  C12  C    C18  O16    64.59  30.0  3
 0BD  Var_04  C14  C22  C19  C18   174.22  30.0  3
 0BD  Var_05  C16  C12  C    C18    65.52  30.0  3
 0BD  Var_06  H14  C14  C22  C19  -179.26  30.0  3
 0BD  Var_07  H13  C13  C22  C19    66.27  30.0  3
 0BD  Var_08  H16  C16  C12  C      60.60  30.0  3
 0BD  Var_09  H15  C15  C12  C      58.26  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
 0BD  chir_01  C1    C2   C6    O49   positiv
 0BD  chir_02  C2    O55  C1    C3    positiv
 0BD  chir_03  C3    O7   C4    C2    positiv
 0BD  chir_04  C4    O5   C3    C57   negativ
 0BD  chir_05  C6    O16  O5    C1    positiv
 0BD  chir_06  C10   O7   O71   C17   negativ
 0BD  chir_07  C17   O8   C10   C191  positiv
 0BD  chir_08  C181  O71  C20   C21   positiv
 0BD  chir_09  C191  O9   C20   C17   negativ
 0BD  chir_10  C20   O10  C181  C191  positiv

