# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 26 22:36:11 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 3-cyclohexylpropyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](OCCCC3CCCCC3)O[C@@H]2CO)[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
 3CM  3CM  '3-cyclohexylpropyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'  D-saccharide  70  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_3CM
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
 3CM  C1    C  CH1   0   0.218  -3.8417   0.2987  -1.0987
 3CM  C2    C  CH1   0  -0.008  -5.0494   1.1667  -0.7401
 3CM  C3    C  CH1   0  -0.013  -5.7712   0.5708   0.4659
 3CM  C4    C  CH1   0   0.034  -6.1398  -0.8798   0.1789
 3CM  C5    C  CH1   0  -0.014  -4.8890  -1.6599  -0.2296
 3CM  C6    C  CH2   0  -0.160  -5.2209  -3.0668  -0.6798
 3CM  O2    O  OH1   0  -0.689  -4.7149   2.5156  -0.5528
 3CM  O3    O  OH1   0  -0.676  -6.9655   1.2635   0.7491
 3CM  O5    O  O2    0  -0.496  -4.2447  -1.0160  -1.3201
 3CM  O6    O  OH1   0  -0.663  -4.0210  -3.7633  -0.9202
 3CM  O1    O  O2    0  -0.518  -2.9052   0.3802  -0.0604
 3CM  O4    O  OH1   0  -0.673  -6.6927  -1.5111   1.3078
 3CM  C10   C  CH1   0   0.295   1.1300   0.9099   0.6026
 3CM  C20   C  CH1   0  -0.025   0.3176   2.1797   0.3687
 3CM  C30   C  CH1   0   0.013  -1.1604   1.8604   0.5352
 3CM  C40   C  CH1   0   0.021  -1.5633   0.6915  -0.3565
 3CM  C50   C  CH1   0  -0.010  -0.6343  -0.5008  -0.0842
 3CM  C60   C  CH2   0  -0.185  -0.8938  -1.6712  -1.0079
 3CM  O20   O  OH1   0  -0.669   0.6398   3.1846   1.2957
 3CM  O30   O  OH1   0  -0.670  -1.9698   2.9641   0.2014
 3CM  O50   O  O2    0  -0.492   0.7021  -0.0918  -0.2851
 3CM  O60   O  OH1   0  -0.669  -0.0338  -2.7257  -0.6421
 3CM  C21   C  CH2   0  -0.474   4.7209   0.4306   0.2370
 3CM  C31   C  CH2   0  -0.415   5.8029  -0.3895   0.9327
 3CM  C12   C  CH1   0  -0.224   7.0829  -0.5606   0.1176
 3CM  C22   C  CH2   0  -0.412   8.0781  -1.4578   0.8545
 3CM  C32   C  CH2   0  -0.430   9.3663  -1.6621   0.0635
 3CM  C42   C  CH2   0  -0.429  10.0110  -0.3269  -0.2940
 3CM  C52   C  CH2   0  -0.428   9.0288   0.5728  -1.0360
 3CM  C62   C  CH2   0  -0.423   7.7428   0.7723  -0.2384
 3CM  HO6   H  HOH1  0   0.456  -4.2455  -4.6662  -1.1625
 3CM  H61   H  HCH2  0   0.211  -5.8163  -3.5485   0.1026
 3CM  H62A  H  HCH2  0   0.196  -5.8507  -3.0140  -1.5791
 3CM  H5    H  HCH1  0   0.229  -4.2113  -1.7174   0.6338
 3CM  H1    H  HCH1  0   0.253  -3.3990   0.6400  -2.0420
 3CM  H40   H  HCH1  0   0.240  -1.4573   0.9874  -1.4110
 3CM  H30   H  HCH1  0   0.229  -1.3327   1.5595   1.5806
 3CM  HO30  H  HOH1  0   0.465  -1.8003   3.6728   0.8317
 3CM  H20   H  HCH1  0   0.226   0.4942   2.5115  -0.6659
 3CM  HO20  H  HOH1  0   0.458   1.5215   3.5149   1.0965
 3CM  H10   H  HCH1  0   0.188   0.9892   0.5705   1.6462
 3CM  H111  H  HCH2  0   0.209   3.4905   0.5408   2.0074
 3CM  H112  H  HCH2  0   0.214   3.0409  -0.7411   0.8770
 3CM  H211  H  HCH2  0   0.223   4.6107   0.0970  -0.7998
 3CM  H212  H  HCH2  0   0.230   5.0085   1.4847   0.2036
 3CM  H311  H  HCH2  0   0.213   6.0448   0.0706   1.8976
 3CM  H312  H  HCH2  0   0.218   5.4066  -1.3850   1.1646
 3CM  H12   H  HCH1  0   0.203   6.8142  -1.0617  -0.8235
 3CM  H6    H  HCH2  0   0.203   8.3171  -1.0019   1.8233
 3CM  H7    H  HCH2  0   0.223  10.0642  -2.2799   0.6346
 3CM  H421  H  HCH2  0   0.206  10.3336   0.1750   0.6250
 3CM  H422  H  HCH2  0   0.224  10.9107  -0.4860  -0.8937
 3CM  H8    H  HCH2  0   0.224   9.4890   1.5399  -1.2540
 3CM  H9    H  HCH2  0   0.230   7.0523   1.4011  -0.8067
 3CM  H50   H  HCH1  0   0.227  -0.7831  -0.8277   0.9584
 3CM  H601  H  HCH2  0   0.235  -1.9419  -1.9677  -0.9276
 3CM  H602  H  HCH2  0   0.193  -0.7243  -1.3490  -2.0455
 3CM  HO60  H  HOH1  0   0.455  -0.2675  -3.4919  -1.1731
 3CM  H2    H  HCH1  0   0.236  -5.7329   1.1320  -1.5965
 3CM  HO2   H  HOH1  0   0.449  -3.8728   2.5853  -0.0741
 3CM  H3    H  HCH1  0   0.213  -5.0987   0.5905   1.3376
 3CM  HO3   H  HOH1  0   0.454  -6.7354   2.1525   1.0375
 3CM  H4    H  HCH1  0   0.210  -6.8474  -0.8942  -0.6662
 3CM  HO4   H  HOH1  0   0.454  -7.4732  -1.0154   1.5760
 3CM  H22   H  HCH2  0   0.221   7.6126  -2.4230   1.0756
 3CM  H32   H  HCH2  0   0.206   9.1424  -2.2147  -0.8556
 3CM  H52   H  HCH2  0   0.207   8.7842   0.1215  -2.0040
 3CM  H62   H  HCH2  0   0.202   7.9702   1.3161   0.6873
 3CM  O10   O  O2    0  -0.503   2.4529   1.1799   0.3370
 3CM  C11   C  CH2   0  -0.142   3.3877   0.2958   0.9426

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
 3CM  C1   O5    single  1.393  0.020  1.393
 3CM  C1   H1    single  0.970  0.020  1.090
 3CM  C1   O1    single  1.401  0.020  1.401
 3CM  C1   C2    single  1.530  0.020  1.530
 3CM  C2   H2    single  0.970  0.020  1.090
 3CM  C2   O2    single  1.402  0.020  1.402
 3CM  C2   C3    single  1.527  0.020  1.527
 3CM  C3   H3    single  0.970  0.020  1.090
 3CM  C3   O3    single  1.409  0.020  1.409
 3CM  C3   C4    single  1.524  0.020  1.524
 3CM  C4   C5    single  1.530  0.020  1.530
 3CM  C4   H4    single  0.970  0.020  1.090
 3CM  C4   O4    single  1.407  0.020  1.407
 3CM  C5   C6    single  1.514  0.020  1.514
 3CM  C5   H5    single  0.970  0.020  1.090
 3CM  C5   O5    single  1.421  0.020  1.421
 3CM  C6   O6    single  1.408  0.020  1.408
 3CM  C6   H61   single  0.970  0.020  1.090
 3CM  C6   H62A  single  0.970  0.020  1.090
 3CM  O2   HO2   single  0.850  0.020  0.980
 3CM  O3   HO3   single  0.850  0.020  0.980
 3CM  O6   HO6   single  0.850  0.020  0.980
 3CM  O1   C40   single  1.409  0.020  1.409
 3CM  O4   HO4   single  0.850  0.020  0.980
 3CM  C10  C20   single  1.525  0.020  1.525
 3CM  C10  H10   single  0.970  0.020  1.090
 3CM  C10  O10   single  1.376  0.020  1.376
 3CM  C10  O50   single  1.405  0.020  1.405
 3CM  C20  C30   single  1.521  0.020  1.521
 3CM  C20  H20   single  0.970  0.020  1.090
 3CM  C20  O20   single  1.405  0.020  1.405
 3CM  C30  C40   single  1.524  0.020  1.524
 3CM  C30  H30   single  0.970  0.020  1.090
 3CM  C30  O30   single  1.409  0.020  1.409
 3CM  C40  H40   single  0.970  0.020  1.090
 3CM  C40  C50   single  1.536  0.020  1.536
 3CM  C50  O50   single  1.412  0.020  1.412
 3CM  C50  H50   single  0.970  0.020  1.090
 3CM  C50  C60   single  1.513  0.020  1.513
 3CM  C60  H601  single  0.970  0.020  1.090
 3CM  C60  H602  single  0.970  0.020  1.090
 3CM  C60  O60   single  1.409  0.020  1.409
 3CM  O10  C11   single  1.422  0.020  1.422
 3CM  O20  HO20  single  0.850  0.020  0.980
 3CM  O30  HO30  single  0.850  0.020  0.980
 3CM  O60  HO60  single  0.850  0.020  0.980
 3CM  C11  H111  single  0.970  0.020  1.090
 3CM  C11  H112  single  0.970  0.020  1.090
 3CM  C11  C21   single  1.514  0.020  1.514
 3CM  C21  H211  single  0.970  0.020  1.090
 3CM  C21  H212  single  0.970  0.020  1.090
 3CM  C21  C31   single  1.526  0.020  1.526
 3CM  C31  H311  single  0.970  0.020  1.090
 3CM  C31  H312  single  0.970  0.020  1.090
 3CM  C31  C12   single  1.527  0.020  1.527
 3CM  C12  H12   single  0.970  0.020  1.090
 3CM  C12  C22   single  1.529  0.020  1.529
 3CM  C12  C62   single  1.529  0.020  1.529
 3CM  C22  H6    single  0.970  0.020  1.090
 3CM  C22  C32   single  1.525  0.020  1.525
 3CM  C22  H22   single  0.970  0.020  1.090
 3CM  C32  H7    single  0.970  0.020  1.090
 3CM  C32  C42   single  1.525  0.020  1.525
 3CM  C32  H32   single  0.970  0.020  1.090
 3CM  C42  H421  single  0.970  0.020  1.090
 3CM  C42  H422  single  0.970  0.020  1.090
 3CM  C42  C52   single  1.525  0.020  1.525
 3CM  C52  H8    single  0.970  0.020  1.090
 3CM  C52  C62   single  1.526  0.020  1.526
 3CM  C52  H52   single  0.970  0.020  1.090
 3CM  C62  H9    single  0.970  0.020  1.090
 3CM  C62  H62   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
 3CM  H1    C1   O1    110.47  3.000
 3CM  O1    C1   O5    111.48  3.000
 3CM  H1    C1   O5    105.89  3.000
 3CM  O1    C1   C2    108.73  3.000
 3CM  H1    C1   C2    110.11  3.000
 3CM  O5    C1   C2    110.15  3.000
 3CM  H2    C2   O2    106.47  3.000
 3CM  O2    C2   C3    112.50  3.000
 3CM  H2    C2   C3    108.06  3.000
 3CM  C3    C2   C1    109.70  3.000
 3CM  O2    C2   C1    112.88  3.000
 3CM  H2    C2   C1    106.93  3.000
 3CM  H3    C3   O3    110.46  3.000
 3CM  O3    C3   C4    107.50  3.000
 3CM  H3    C3   C4    108.29  3.000
 3CM  C4    C3   C2    109.70  3.000
 3CM  O3    C3   C2    111.57  3.000
 3CM  H3    C3   C2    109.25  3.000
 3CM  H4    C4   O4    110.92  3.000
 3CM  O4    C4   C5    107.87  3.000
 3CM  H4    C4   C5    108.27  3.000
 3CM  O4    C4   C3    111.78  3.000
 3CM  H4    C4   C3    108.19  3.000
 3CM  C5    C4   C3    109.76  3.000
 3CM  H5    C5   O5    110.30  3.000
 3CM  O5    C5   C6    106.99  3.000
 3CM  H5    C5   C6    108.67  3.000
 3CM  O5    C5   C4    110.16  3.000
 3CM  H5    C5   C4    108.73  3.000
 3CM  C6    C5   C4    111.97  3.000
 3CM  H62A  C6   H61   107.11  3.000
 3CM  H62A  C6   O6    111.86  3.000
 3CM  H61   C6   O6    111.58  3.000
 3CM  H62A  C6   C5    108.92  3.000
 3CM  H61   C6   C5    108.40  3.000
 3CM  O6    C6   C5    108.89  3.000
 3CM  HO2   O2   C2    109.98  3.000
 3CM  HO3   O3   C3    108.15  3.000
 3CM  C5    O5   C1    115.91  3.000
 3CM  HO6   O6   C6    107.98  3.000
 3CM  C40   O1   C1    119.59  3.000
 3CM  HO4   O4   C4    108.13  3.000
 3CM  H10   C10  O50   109.78  3.000
 3CM  O50   C10  O10   108.10  3.000
 3CM  H10   C10  O10   111.38  3.000
 3CM  O50   C10  C20   109.54  3.000
 3CM  O10   C10  C20   108.60  3.000
 3CM  H10   C10  C20   109.40  3.000
 3CM  H20   C20  O20   111.58  3.000
 3CM  O20   C20  C30   107.50  3.000
 3CM  H20   C20  C30   108.78  3.000
 3CM  O20   C20  C10   111.85  3.000
 3CM  H20   C20  C10   108.04  3.000
 3CM  C30   C20  C10   109.02  3.000
 3CM  H30   C30  O30   110.43  3.000
 3CM  O30   C30  C40   108.07  3.000
 3CM  H30   C30  C40   107.72  3.000
 3CM  O30   C30  C20   111.58  3.000
 3CM  H30   C30  C20   108.26  3.000
 3CM  C40   C30  C20   110.71  3.000
 3CM  H40   C40  C50   108.68  3.000
 3CM  C50   C40  C30   109.37  3.000
 3CM  H40   C40  C30   109.20  3.000
 3CM  C50   C40  O1    111.55  3.000
 3CM  H40   C40  O1    110.65  3.000
 3CM  C30   C40  O1    107.35  3.000
 3CM  H50   C50  O50   110.38  3.000
 3CM  H50   C50  C60   108.94  3.000
 3CM  O50   C50  C60   107.42  3.000
 3CM  C60   C50  C40   112.85  3.000
 3CM  H50   C50  C40   108.43  3.000
 3CM  O50   C50  C40   108.81  3.000
 3CM  H602  C60  H601  107.27  3.000
 3CM  H602  C60  O60   111.73  3.000
 3CM  H601  C60  O60   111.31  3.000
 3CM  O60   C60  C50   108.40  3.000
 3CM  H602  C60  C50   108.84  3.000
 3CM  H601  C60  C50   109.25  3.000
 3CM  HO20  O20  C20   108.60  3.000
 3CM  HO30  O30  C30   108.67  3.000
 3CM  C50   O50  C10   113.88  3.000
 3CM  HO60  O60  C60   107.74  3.000
 3CM  H212  C21  H211  106.94  3.000
 3CM  H212  C21  C31   110.23  3.000
 3CM  H211  C21  C31   109.84  3.000
 3CM  C31   C21  C11   111.35  3.000
 3CM  H212  C21  C11   109.37  3.000
 3CM  H211  C21  C11   109.00  3.000
 3CM  H312  C31  H311  105.94  3.000
 3CM  H312  C31  C12   108.31  3.000
 3CM  H311  C31  C12   109.38  3.000
 3CM  C12   C31  C21   114.29  3.000
 3CM  H312  C31  C21   109.16  3.000
 3CM  H311  C31  C21   109.41  3.000
 3CM  H12   C12  C62   107.66  3.000
 3CM  C62   C12  C22   110.04  3.000
 3CM  H12   C12  C22   107.71  3.000
 3CM  C62   C12  C31   112.85  3.000
 3CM  C22   C12  C31   110.74  3.000
 3CM  H12   C12  C31   107.64  3.000
 3CM  H22   C22  H6    106.31  3.000
 3CM  H22   C22  C32   110.24  3.000
 3CM  H6    C22  C32   109.25  3.000
 3CM  H22   C22  C12   109.76  3.000
 3CM  C32   C22  C12   112.23  3.000
 3CM  H6    C22  C12   108.88  3.000
 3CM  H32   C32  H7    106.48  3.000
 3CM  H32   C32  C42   109.35  3.000
 3CM  H7    C32  C42   110.33  3.000
 3CM  H32   C32  C22   109.27  3.000
 3CM  C42   C32  C22   111.18  3.000
 3CM  H7    C32  C22   110.12  3.000
 3CM  H422  C42  H421  106.53  3.000
 3CM  H422  C42  C52   110.44  3.000
 3CM  H421  C42  C52   109.12  3.000
 3CM  C52   C42  C32   111.00  3.000
 3CM  H422  C42  C32   110.43  3.000
 3CM  H421  C42  C32   109.20  3.000
 3CM  H52   C52  H8    106.39  3.000
 3CM  H52   C52  C62   109.11  3.000
 3CM  H8    C52  C62   110.08  3.000
 3CM  H52   C52  C42   109.31  3.000
 3CM  C62   C52  C42   111.44  3.000
 3CM  H8    C52  C42   110.36  3.000
 3CM  H62   C62  H9    106.52  3.000
 3CM  H62   C62  C52   109.33  3.000
 3CM  H9    C62  C52   109.61  3.000
 3CM  H62   C62  C12   108.96  3.000
 3CM  H9    C62  C12   110.47  3.000
 3CM  C52   C62  C12   111.80  3.000
 3CM  C11   O10  C10   115.33  3.000
 3CM  H112  C11  H111  107.40  3.000
 3CM  H112  C11  C21   109.58  3.000
 3CM  H111  C11  C21   110.47  3.000
 3CM  C21   C11  O10   108.96  3.000
 3CM  H112  C11  O10   110.79  3.000
 3CM  H111  C11  O10   109.63  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
 3CM  Var_01  C42  C32  C22  C12   55.56  30.0  1
 3CM  Var_02  C42  C52  C62  C12  -55.84  30.0  1
 3CM  Var_03  C52  C42  C32  C22  -54.93  30.0  1
 3CM  Var_04  C62  C52  C42  C32   55.26  30.0  1
 3CM  Var_05  C21  C11  O10  C10  162.38  30.0  3
 3CM  Var_06  C12  C31  C21  C11  166.90  30.0  3
 3CM  Var_07  C31  C21  C11  O10  174.23  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
 3CM  chir_01  C1   O5   O1   C2   positiv
 3CM  chir_02  C2   O2   C1   C3   negativ
 3CM  chir_03  C3   O3   C2   C4   positiv
 3CM  chir_04  C4   O4   C5   C3   positiv
 3CM  chir_05  C5   O5   C4   C6   negativ
 3CM  chir_06  C10  C20  O10  O50  positiv
 3CM  chir_07  C20  O20  C10  C30  negativ
 3CM  chir_08  C30  O30  C20  C40  positiv
 3CM  chir_09  C40  O1   C50  C30  positiv
 3CM  chir_10  C50  O50  C40  C60  negativ
 3CM  chir_11  C12  C31  C22  C62  positiv

