# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 04:28:48 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 2-cyclohexylethyl 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](OCCC3CCCCC3)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
 MA5  MA5  '2-cyclohexylethyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'  ligand  67  31  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MA5
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
 MA5  C42   C  CH2   0  -0.415   7.4547   0.3622   0.8722
 MA5  C32   C  CH2   0  -0.432   8.6493   1.1634   0.3656
 MA5  C22   C  CH2   0  -0.430   9.1107   0.6686  -1.0005
 MA5  C12   C  CH2   0  -0.428   7.9627   0.6860  -2.0032
 MA5  C62   C  CH2   0  -0.421   6.7671  -0.1126  -1.4925
 MA5  C52   C  CH1   0  -0.236   6.2910   0.3691  -0.1201
 MA5  C61   C  CH2   0  -0.458   5.1254  -0.4677   0.4106
 MA5  C11   C  CH2   0  -0.147   3.8211  -0.1958  -0.3119
 MA5  O10   O  O2    0  -0.504   2.8451  -1.1221   0.1496
 MA5  C10   C  CH1   0   0.297   1.5495  -0.8375  -0.2163
 MA5  C20   C  CH1   0  -0.024   0.7358  -2.1273  -0.1771
 MA5  O20   O  OH1   0  -0.668   1.1663  -3.0457  -1.1485
 MA5  C30   C  CH1   0   0.012  -0.7203  -1.7997  -0.4709
 MA5  O30   O  OH1   0  -0.671  -1.5488  -2.9292  -0.3149
 MA5  O50   O  O2    0  -0.493   1.0231   0.0791   0.7097
 MA5  C50   C  CH1   0  -0.011  -0.2900   0.5012   0.4073
 MA5  C60   C  CH2   0  -0.184  -0.6642   1.5736   1.4069
 MA5  O60   O  OH1   0  -0.670   0.2164   2.6616   1.2469
 MA5  C40   C  CH1   0   0.021  -1.2299  -0.7116   0.4675
 MA5  O1    O  O2    0  -0.517  -2.5325  -0.3697   0.0516
 MA5  C1    C  CH1   0   0.215  -3.5906  -0.4329   0.9679
 MA5  O5    O  O2    0  -0.496  -4.0254   0.8379   1.3360
 MA5  C5    C  CH1   0  -0.015  -4.5439   1.6466   0.2881
 MA5  C6    C  CH2   0  -0.161  -4.9467   2.9679   0.9076
 MA5  O6    O  OH1   0  -0.663  -3.7985   3.6019   1.4180
 MA5  C4    C  CH1   0   0.033  -5.7258   0.9480  -0.3862
 MA5  O4    O  OH1   0  -0.673  -6.1452   1.7552  -1.4591
 MA5  C3    C  CH1   0  -0.009  -5.3036  -0.4407  -0.8502
 MA5  O3    O  OH1   0  -0.677  -6.4402  -1.0714  -1.3931
 MA5  C2    C  CH1   0  -0.008  -4.7395  -1.2199   0.3351
 MA5  O2    O  OH1   0  -0.691  -4.3822  -2.5324  -0.0071
 MA5  H421  H  HCH2  0   0.224   7.1195   0.7573   1.8355
 MA5  H422  H  HCH2  0   0.205   7.7630  -0.6745   1.0550
 MA5  H321  H  HCH2  0   0.207   8.3683   2.2198   0.2917
 MA5  H322  H  HCH2  0   0.225   9.4687   1.1110   1.0868
 MA5  H221  H  HCH2  0   0.225   9.9435   1.2761  -1.3641
 MA5  H222  H  HCH2  0   0.207   9.4916  -0.3546  -0.9050
 MA5  H121  H  HCH2  0   0.208   7.6560   1.7214  -2.1869
 MA5  H122  H  HCH2  0   0.225   8.2912   0.2873  -2.9663
 MA5  H621  H  HCH2  0   0.206   7.0486  -1.1698  -1.4135
 MA5  H622  H  HCH2  0   0.227   5.9547  -0.0641  -2.2219
 MA5  H52   H  HCH1  0   0.208   5.9505   1.4097  -0.2232
 MA5  H611  H  HCH2  0   0.231   4.9827  -0.2589   1.4755
 MA5  H612  H  HCH2  0   0.220   5.3780  -1.5306   0.3283
 MA5  H111  H  HCH2  0   0.211   3.9363  -0.3019  -1.3972
 MA5  H112  H  HCH2  0   0.213   3.5016   0.8337  -0.1166
 MA5  H10   H  HCH1  0   0.188   1.5043  -0.4077  -1.2346
 MA5  H20   H  HCH1  0   0.226   0.8081  -2.5463   0.8381
 MA5  H3    H  HOH1  0   0.458   2.0345  -3.3756  -0.8962
 MA5  H30   H  HCH1  0   0.229  -0.7871  -1.4147  -1.5007
 MA5  H2    H  HOH1  0   0.466  -1.3183  -3.5785  -0.9885
 MA5  H50   H  HCH1  0   0.227  -0.3298   0.9234  -0.6105
 MA5  H601  H  HCH2  0   0.237  -1.7011   1.8736   1.2407
 MA5  H602  H  HCH2  0   0.193  -0.6078   1.1483   2.4197
 MA5  H60   H  HOH1  0   0.455  -0.0984   3.3794   1.8032
 MA5  H40   H  HCH1  0   0.239  -1.2405  -1.0990   1.4970
 MA5  H1    H  HCH1  0   0.254  -3.2651  -0.9211   1.8942
 MA5  H5    H  HCH1  0   0.229  -3.7687   1.8309  -0.4688
 MA5  H61   H  HCH2  0   0.196  -5.6934   2.7782   1.6914
 MA5  H62   H  HCH2  0   0.212  -5.4354   3.5744   0.1384
 MA5  HO6   H  HOH1  0   0.456  -4.0628   4.4556   1.7726
 MA5  H7    H  HCH1  0   0.211  -6.5307   0.8307   0.3577
 MA5  HO4   H  HOH1  0   0.455  -6.8946   1.3253  -1.8837
 MA5  H6    H  HCH1  0   0.211  -4.5216  -0.3257  -1.6161
 MA5  HO3   H  HOH1  0   0.453  -6.1694  -1.9242  -1.7487
 MA5  H4    H  HCH1  0   0.234  -5.5270  -1.2980   1.0946
 MA5  HO2   H  HOH1  0   0.450  -3.4628  -2.5584  -0.3184

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
 MA5  C42  C32   single  1.525  0.020  1.525
 MA5  C42  C52   single  1.529  0.020  1.529
 MA5  C42  H421  single  0.970  0.020  1.090
 MA5  C42  H422  single  0.970  0.020  1.090
 MA5  C32  C22   single  1.524  0.020  1.524
 MA5  C32  H321  single  0.970  0.020  1.090
 MA5  C32  H322  single  0.970  0.020  1.090
 MA5  C22  C12   single  1.524  0.020  1.524
 MA5  C22  H221  single  0.970  0.020  1.090
 MA5  C22  H222  single  0.970  0.020  1.090
 MA5  C12  C62   single  1.526  0.020  1.526
 MA5  C12  H121  single  0.970  0.020  1.090
 MA5  C12  H122  single  0.970  0.020  1.090
 MA5  C62  C52   single  1.530  0.020  1.530
 MA5  C62  H621  single  0.970  0.020  1.090
 MA5  C62  H622  single  0.970  0.020  1.090
 MA5  C52  C61   single  1.530  0.020  1.530
 MA5  C52  H52   single  0.970  0.020  1.090
 MA5  C61  C11   single  1.516  0.020  1.516
 MA5  C61  H611  single  0.970  0.020  1.090
 MA5  C61  H612  single  0.970  0.020  1.090
 MA5  C11  O10   single  1.423  0.020  1.423
 MA5  C11  H111  single  0.970  0.020  1.090
 MA5  C11  H112  single  0.970  0.020  1.090
 MA5  O10  C10   single  1.376  0.020  1.376
 MA5  C10  C20   single  1.525  0.020  1.525
 MA5  C10  O50   single  1.405  0.020  1.405
 MA5  C10  H10   single  0.970  0.020  1.090
 MA5  C20  O20   single  1.404  0.020  1.404
 MA5  C20  C30   single  1.521  0.020  1.521
 MA5  C20  H20   single  0.970  0.020  1.090
 MA5  O20  H3    single  0.850  0.020  0.980
 MA5  C30  O30   single  1.409  0.020  1.409
 MA5  C30  C40   single  1.525  0.020  1.525
 MA5  C30  H30   single  0.970  0.020  1.090
 MA5  O30  H2    single  0.850  0.020  0.980
 MA5  O50  C50   single  1.412  0.020  1.412
 MA5  C50  C60   single  1.513  0.020  1.513
 MA5  C50  C40   single  1.535  0.020  1.535
 MA5  C50  H50   single  0.970  0.020  1.090
 MA5  C60  O60   single  1.409  0.020  1.409
 MA5  C60  H601  single  0.970  0.020  1.090
 MA5  C60  H602  single  0.970  0.020  1.090
 MA5  O60  H60   single  0.850  0.020  0.980
 MA5  C40  O1    single  1.409  0.020  1.409
 MA5  C40  H40   single  0.970  0.020  1.090
 MA5  O1   C1    single  1.401  0.020  1.401
 MA5  C1   O5    single  1.393  0.020  1.393
 MA5  C1   C2    single  1.530  0.020  1.530
 MA5  C1   H1    single  0.970  0.020  1.090
 MA5  O5   C5    single  1.422  0.020  1.422
 MA5  C5   C6    single  1.514  0.020  1.514
 MA5  C5   C4    single  1.529  0.020  1.529
 MA5  C5   H5    single  0.970  0.020  1.090
 MA5  C6   O6    single  1.408  0.020  1.408
 MA5  C6   H61   single  0.970  0.020  1.090
 MA5  C6   H62   single  0.970  0.020  1.090
 MA5  O6   HO6   single  0.850  0.020  0.980
 MA5  C4   O4    single  1.407  0.020  1.407
 MA5  C4   C3    single  1.524  0.020  1.524
 MA5  C4   H7    single  0.970  0.020  1.090
 MA5  O4   HO4   single  0.850  0.020  0.980
 MA5  C3   O3    single  1.409  0.020  1.409
 MA5  C3   C2    single  1.526  0.020  1.526
 MA5  C3   H6    single  0.970  0.020  1.090
 MA5  O3   HO3   single  0.850  0.020  0.980
 MA5  C2   O2    single  1.403  0.020  1.403
 MA5  C2   H4    single  0.970  0.020  1.090
 MA5  O2   HO2   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
 MA5  H422  C42  H421  106.30  3.000
 MA5  H422  C42  C52   109.04  3.000
 MA5  H421  C42  C52   109.67  3.000
 MA5  H422  C42  C32   109.37  3.000
 MA5  H421  C42  C32   110.05  3.000
 MA5  C52   C42  C32   112.22  3.000
 MA5  H322  C32  H321  106.45  3.000
 MA5  H322  C32  C22   110.42  3.000
 MA5  H321  C32  C22   109.27  3.000
 MA5  H322  C32  C42   110.06  3.000
 MA5  H321  C32  C42   109.15  3.000
 MA5  C22   C32  C42   111.36  3.000
 MA5  H222  C22  H221  106.44  3.000
 MA5  H222  C22  C12   109.25  3.000
 MA5  H221  C22  C12   110.41  3.000
 MA5  H222  C22  C32   109.27  3.000
 MA5  H221  C22  C32   110.38  3.000
 MA5  C12   C22  C32   110.97  3.000
 MA5  H122  C12  H121  106.33  3.000
 MA5  H122  C12  C62   109.85  3.000
 MA5  H121  C12  C62   109.36  3.000
 MA5  H122  C12  C22   110.43  3.000
 MA5  H121  C12  C22   109.38  3.000
 MA5  C62   C12  C22   111.35  3.000
 MA5  H622  C62  H621  106.35  3.000
 MA5  H622  C62  C52   110.69  3.000
 MA5  H621  C62  C52   108.58  3.000
 MA5  H622  C62  C12   109.63  3.000
 MA5  H621  C62  C12   109.12  3.000
 MA5  C52   C62  C12   112.29  3.000
 MA5  H52   C52  C61   108.31  3.000
 MA5  H52   C52  C62   108.07  3.000
 MA5  C61   C52  C62   112.08  3.000
 MA5  H52   C52  C42   107.49  3.000
 MA5  C61   C52  C42   110.62  3.000
 MA5  C62   C52  C42   110.10  3.000
 MA5  H612  C61  H611  106.75  3.000
 MA5  H612  C61  C11   109.67  3.000
 MA5  H611  C61  C11   108.51  3.000
 MA5  H612  C61  C52   109.21  3.000
 MA5  H611  C61  C52   109.42  3.000
 MA5  C11   C61  C52   113.09  3.000
 MA5  H112  C11  H111  107.34  3.000
 MA5  H112  C11  O10   110.73  3.000
 MA5  H111  C11  O10   109.28  3.000
 MA5  H112  C11  C61   109.55  3.000
 MA5  H111  C11  C61   111.35  3.000
 MA5  O10   C11  C61   108.60  3.000
 MA5  C10   O10  C11   115.16  3.000
 MA5  H10   C10  O50   109.75  3.000
 MA5  H10   C10  C20   109.30  3.000
 MA5  O50   C10  C20   109.56  3.000
 MA5  H10   C10  O10   111.32  3.000
 MA5  O50   C10  O10   108.20  3.000
 MA5  C20   C10  O10   108.69  3.000
 MA5  H20   C20  C30   108.84  3.000
 MA5  H20   C20  O20   111.65  3.000
 MA5  C30   C20  O20   107.50  3.000
 MA5  H20   C20  C10   108.09  3.000
 MA5  C30   C20  C10   108.88  3.000
 MA5  O20   C20  C10   111.82  3.000
 MA5  H3    O20  C20   108.62  3.000
 MA5  H30   C30  C40   107.80  3.000
 MA5  H30   C30  O30   110.36  3.000
 MA5  C40   C30  O30   107.90  3.000
 MA5  H30   C30  C20   108.29  3.000
 MA5  C40   C30  C20   110.78  3.000
 MA5  O30   C30  C20   111.64  3.000
 MA5  H2    O30  C30   108.78  3.000
 MA5  C50   O50  C10   113.71  3.000
 MA5  H50   C50  C40   108.45  3.000
 MA5  H50   C50  C60   109.24  3.000
 MA5  C40   C50  C60   112.49  3.000
 MA5  H50   C50  O50   110.23  3.000
 MA5  C40   C50  O50   108.95  3.000
 MA5  C60   C50  O50   107.48  3.000
 MA5  H602  C60  H601  107.16  3.000
 MA5  H602  C60  O60   111.78  3.000
 MA5  H601  C60  O60   111.35  3.000
 MA5  H602  C60  C50   108.76  3.000
 MA5  H601  C60  C50   109.21  3.000
 MA5  O60   C60  C50   108.53  3.000
 MA5  H60   O60  C60   107.83  3.000
 MA5  H40   C40  O1    110.65  3.000
 MA5  H40   C40  C50   108.71  3.000
 MA5  O1    C40  C50   111.26  3.000
 MA5  H40   C40  C30   109.14  3.000
 MA5  O1    C40  C30   107.48  3.000
 MA5  C50   C40  C30   109.57  3.000
 MA5  C1    O1   C40   119.60  3.000
 MA5  H1    C1   C2    110.08  3.000
 MA5  H1    C1   O5    106.00  3.000
 MA5  C2    C1   O5    110.14  3.000
 MA5  H1    C1   O1    110.39  3.000
 MA5  C2    C1   O1    108.65  3.000
 MA5  O5    C1   O1    111.56  3.000
 MA5  C5    O5   C1    115.98  3.000
 MA5  H5    C5   C4    108.55  3.000
 MA5  H5    C5   C6    108.85  3.000
 MA5  C4    C5   C6    111.93  3.000
 MA5  H5    C5   O5    110.23  3.000
 MA5  C4    C5   O5    110.31  3.000
 MA5  C6    C5   O5    106.97  3.000
 MA5  H62   C6   H61   107.06  3.000
 MA5  H62   C6   O6    111.68  3.000
 MA5  H61   C6   O6    111.92  3.000
 MA5  H62   C6   C5    108.35  3.000
 MA5  H61   C6   C5    108.78  3.000
 MA5  O6    C6   C5    108.94  3.000
 MA5  HO6   O6   C6    108.02  3.000
 MA5  H7    C4   C3    108.11  3.000
 MA5  H7    C4   O4    110.98  3.000
 MA5  C3    C4   O4    111.92  3.000
 MA5  H7    C4   C5    108.38  3.000
 MA5  C3    C4   C5    109.66  3.000
 MA5  O4    C4   C5    107.73  3.000
 MA5  HO4   O4   C4    108.20  3.000
 MA5  H6    C3   C2    109.34  3.000
 MA5  H6    C3   O3    110.60  3.000
 MA5  C2    C3   O3    111.65  3.000
 MA5  H6    C3   C4    108.27  3.000
 MA5  C2    C3   C4    109.34  3.000
 MA5  O3    C3   C4    107.57  3.000
 MA5  HO3   O3   C3    108.17  3.000
 MA5  H4    C2   O2    106.57  3.000
 MA5  H4    C2   C3    107.98  3.000
 MA5  O2    C2   C3    112.48  3.000
 MA5  H4    C2   C1    106.83  3.000
 MA5  O2    C2   C1    113.02  3.000
 MA5  C3    C2   C1    109.64  3.000
 MA5  HO2   O2   C2    110.15  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
 MA5  Var_01  C12  C22  C32  C42   55.24  30.0  1
 MA5  Var_02  C62  C12  C22  C32  -55.11  30.0  1
 MA5  Var_03  C52  C42  C32  C22  -55.57  30.0  1
 MA5  Var_04  C52  C62  C12  C22   55.35  30.0  1
 MA5  Var_05  O10  C11  C61  C52  173.57  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
 MA5  chir_01  C52  C42  C62  C61  negativ
 MA5  chir_02  C10  O10  O50  C20  positiv
 MA5  chir_03  C20  O20  C10  C30  negativ
 MA5  chir_04  C30  O30  C20  C40  positiv
 MA5  chir_05  C50  O50  C60  C40  positiv
 MA5  chir_06  C40  O1   C30  C50  negativ
 MA5  chir_07  C1   O1   O5   C2   negativ
 MA5  chir_08  C5   O5   C6   C4   positiv
 MA5  chir_09  C4   O4   C5   C3   positiv
 MA5  chir_10  C3   O3   C2   C4   positiv
 MA5  chir_11  C2   O2   C3   C1   positiv

