# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 20:44:52 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: 5-cyclohexylpentyl 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](OCCCCCC3CCCCC3)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
 CM5  CM5  '5-cyclohexylpentyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'  ligand  76  34  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CM5
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
 CM5  C7    C  CH2   0  -0.414   9.8980   0.6693  -1.4257
 CM5  C8    C  CH2   0  -0.430  11.3344   0.3005  -1.0692
 CM5  C9    C  CH2   0  -0.428  11.6415   0.6145   0.3913
 CM5  C10   C  CH2   0  -0.428  10.6390  -0.0669   1.3157
 CM5  C11   C  CH2   0  -0.421   9.2031   0.3012   0.9519
 CM5  C6    C  CH1   0  -0.222   8.8778  -0.0095  -0.5105
 CM5  C5    C  CH2   0  -0.401   7.4562   0.4014  -0.8934
 CM5  C4    C  CH2   0  -0.422   6.3522  -0.3662  -0.1767
 CM5  C3    C  CH2   0  -0.423   4.9571   0.0515  -0.6253
 CM5  C2    C  CH2   0  -0.465   3.8550  -0.7580   0.0472
 CM5  C1    C  CH2   0  -0.142   2.4777  -0.3040  -0.3872
 CM5  O12   O  O2    0  -0.503   1.5066  -1.1646   0.1918
 CM5  C13   C  CH1   0   0.301   0.2030  -0.8964  -0.1549
 CM5  C18   C  CH1   0  -0.024  -0.6322  -2.1500   0.0858
 CM5  O22   O  OH1   0  -0.668  -0.2487  -3.2046  -0.7590
 CM5  C17   C  CH1   0   0.013  -2.0873  -1.8302  -0.2182
 CM5  O21   O  OH1   0  -0.671  -2.9381  -2.9054   0.1092
 CM5  O14   O  O2    0  -0.494  -0.2746   0.1442   0.6589
 CM5  C15   C  CH1   0  -0.010  -1.5843   0.5598   0.3331
 CM5  C19   C  CH2   0  -0.185  -1.9046   1.7645   1.1912
 CM5  O20   O  OH1   0  -0.670  -1.0168   2.8033   0.8474
 CM5  C16   C  CH1   0   0.021  -2.5567  -0.6071   0.5619
 CM5  O23   O  O2    0  -0.517  -3.8482  -0.2875   0.0966
 CM5  C24   C  CH1   0   0.214  -4.9128  -0.1943   1.0015
 CM5  O25   O  O2    0  -0.496  -5.3008   1.1282   1.2023
 CM5  C26   C  CH1   0  -0.012  -5.7734   1.8218   0.0561
 CM5  C30   C  CH2   0  -0.160  -6.1521   3.2157   0.5115
 CM5  O31   O  OH1   0  -0.664  -4.9950   3.8793   0.9613
 CM5  C27   C  CH1   0   0.031  -6.9622   1.0870  -0.5650
 CM5  O32   O  OH1   0  -0.673  -7.3119   1.7647  -1.7476
 CM5  C28   C  CH1   0  -0.010  -6.5947  -0.3670  -0.8339
 CM5  O33   O  OH1   0  -0.677  -7.7519  -1.0129  -1.3143
 CM5  C29   C  CH1   0  -0.005  -6.0865  -1.0088   0.4542
 CM5  O34   O  OH1   0  -0.691  -5.7844  -2.3689   0.2934
 CM5  H71   H  HCH2  0   0.221   9.6914   0.4080  -2.4678
 CM5  H72   H  HCH2  0   0.201   9.7728   1.7568  -1.3501
 CM5  H81   H  HCH2  0   0.206  11.4879  -0.7693  -1.2485
 CM5  H82   H  HCH2  0   0.222  12.0322   0.8261  -1.7262
 CM5  H91   H  HCH2  0   0.223  12.6597   0.3054   0.6408
 CM5  H92   H  HCH2  0   0.205  11.5988   1.6984   0.5461
 CM5  H101  H  HCH2  0   0.206  10.7626  -1.1534   1.2449
 CM5  H102  H  HCH2  0   0.223  10.8399   0.1985   2.3568
 CM5  H111  H  HCH2  0   0.201   9.0473   1.3733   1.1254
 CM5  H112  H  HCH2  0   0.227   8.5117  -0.2217   1.6171
 CM5  H6    H  HCH1  0   0.199   8.9675  -1.0960  -0.6545
 CM5  H51   H  HCH2  0   0.212   7.3320   0.2655  -1.9740
 CM5  H52   H  HCH2  0   0.203   7.3352   1.4759  -0.7090
 CM5  H41   H  HCH2  0   0.217   6.4342  -0.2255   0.9054
 CM5  H42   H  HCH2  0   0.209   6.4839  -1.4393  -0.3542
 CM5  H31A  H  HCH2  0   0.214   4.8767  -0.0585  -1.7122
 CM5  H32A  H  HCH2  0   0.215   4.8156   1.1172  -0.4161
 CM5  H21A  H  HCH2  0   0.225   3.9436  -0.6705   1.1345
 CM5  H22A  H  HCH2  0   0.223   3.9805  -1.8171  -0.1977
 CM5  H11   H  HCH2  0   0.207   2.3949  -0.3381  -1.4814
 CM5  H12   H  HCH2  0   0.211   2.3090   0.7343  -0.0810
 CM5  H13   H  HCH1  0   0.186   0.1269  -0.6024  -1.2194
 CM5  H18   H  HCH1  0   0.226  -0.5381  -2.4267   1.1470
 CM5  H22   H  HOH1  0   0.457   0.6269  -3.5049  -0.4956
 CM5  H17   H  HCH1  0   0.228  -2.1676  -1.5923  -1.2907
 CM5  H21   H  HOH1  0   0.466  -2.7318  -3.6485  -0.4686
 CM5  H15   H  HCH1  0   0.227  -1.6397   0.8521  -0.7285
 CM5  H191  H  HCH2  0   0.235  -2.9437   2.0590   1.0265
 CM5  H192  H  HCH2  0   0.195  -1.8106   1.4820   2.2496
 CM5  H20   H  HOH1  0   0.455  -1.2758   3.5868   1.3402
 CM5  H16   H  HCH1  0   0.239  -2.5784  -0.8476   1.6349
 CM5  H24   H  HCH1  0   0.255  -4.6133  -0.5725   1.9862
 CM5  H26   H  HCH1  0   0.228  -4.9773   1.9011  -0.6977
 CM5  H301  H  HCH2  0   0.196  -6.9107   3.1349   1.3021
 CM5  H302  H  HCH2  0   0.211  -6.6175   3.7404  -0.3294
 CM5  H31   H  HOH1  0   0.456  -5.2488   4.7648   1.2364
 CM5  H27   H  HCH1  0   0.211  -7.7957   1.1001   0.1565
 CM5  H32   H  HOH1  0   0.454  -8.0699   1.3162  -2.1363
 CM5  H28   H  HCH1  0   0.213  -5.7984  -0.3905  -1.5930
 CM5  H33   H  HOH1  0   0.454  -7.5071  -1.9028  -1.5873
 CM5  H29   H  HCH1  0   0.233  -6.8891  -0.9516   1.1992
 CM5  H34   H  HOH1  0   0.449  -4.8593  -2.4776   0.0199

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
 CM5  C7   C8    single  1.525  0.020  1.525
 CM5  C7   C6    single  1.529  0.020  1.529
 CM5  C7   H71   single  0.970  0.020  1.090
 CM5  C7   H72   single  0.970  0.020  1.090
 CM5  C8   C9    single  1.525  0.020  1.525
 CM5  C8   H81   single  0.970  0.020  1.090
 CM5  C8   H82   single  0.970  0.020  1.090
 CM5  C9   C10   single  1.524  0.020  1.524
 CM5  C9   H91   single  0.970  0.020  1.090
 CM5  C9   H92   single  0.970  0.020  1.090
 CM5  C10  C11   single  1.526  0.020  1.526
 CM5  C10  H101  single  0.970  0.020  1.090
 CM5  C10  H102  single  0.970  0.020  1.090
 CM5  C11  C6    single  1.530  0.020  1.530
 CM5  C11  H111  single  0.970  0.020  1.090
 CM5  C11  H112  single  0.970  0.020  1.090
 CM5  C6   C5    single  1.529  0.020  1.529
 CM5  C6   H6    single  0.970  0.020  1.090
 CM5  C5   C4    single  1.524  0.020  1.524
 CM5  C5   H51   single  0.970  0.020  1.090
 CM5  C5   H52   single  0.970  0.020  1.090
 CM5  C4   C3    single  1.524  0.020  1.524
 CM5  C4   H41   single  0.970  0.020  1.090
 CM5  C4   H42   single  0.970  0.020  1.090
 CM5  C3   C2    single  1.524  0.020  1.524
 CM5  C3   H31A  single  0.970  0.020  1.090
 CM5  C3   H32A  single  0.970  0.020  1.090
 CM5  C2   C1    single  1.514  0.020  1.514
 CM5  C2   H21A  single  0.970  0.020  1.090
 CM5  C2   H22A  single  0.970  0.020  1.090
 CM5  C1   O12   single  1.421  0.020  1.421
 CM5  C1   H11   single  0.970  0.020  1.090
 CM5  C1   H12   single  0.970  0.020  1.090
 CM5  O12  C13   single  1.375  0.020  1.375
 CM5  C13  C18   single  1.525  0.020  1.525
 CM5  C13  O14   single  1.405  0.020  1.405
 CM5  C13  H13   single  0.970  0.020  1.090
 CM5  C18  O22   single  1.405  0.020  1.405
 CM5  C18  C17   single  1.521  0.020  1.521
 CM5  C18  H18   single  0.970  0.020  1.090
 CM5  O22  H22   single  0.850  0.020  0.980
 CM5  C17  O21   single  1.410  0.020  1.410
 CM5  C17  C16   single  1.525  0.020  1.525
 CM5  C17  H17   single  0.970  0.020  1.090
 CM5  O21  H21   single  0.850  0.020  0.980
 CM5  O14  C15   single  1.412  0.020  1.412
 CM5  C15  C19   single  1.513  0.020  1.513
 CM5  C15  C16   single  1.536  0.020  1.536
 CM5  C15  H15   single  0.970  0.020  1.090
 CM5  C19  O20   single  1.409  0.020  1.409
 CM5  C19  H191  single  0.970  0.020  1.090
 CM5  C19  H192  single  0.970  0.020  1.090
 CM5  O20  H20   single  0.850  0.020  0.980
 CM5  C16  O23   single  1.409  0.020  1.409
 CM5  C16  H16   single  0.970  0.020  1.090
 CM5  O23  C24   single  1.400  0.020  1.400
 CM5  C24  O25   single  1.393  0.020  1.393
 CM5  C24  C29   single  1.530  0.020  1.530
 CM5  C24  H24   single  0.970  0.020  1.090
 CM5  O25  C26   single  1.421  0.020  1.421
 CM5  C26  C30   single  1.515  0.020  1.515
 CM5  C26  C27   single  1.529  0.020  1.529
 CM5  C26  H26   single  0.970  0.020  1.090
 CM5  C30  O31   single  1.408  0.020  1.408
 CM5  C30  H301  single  0.970  0.020  1.090
 CM5  C30  H302  single  0.970  0.020  1.090
 CM5  O31  H31   single  0.850  0.020  0.980
 CM5  C27  O32   single  1.407  0.020  1.407
 CM5  C27  C28   single  1.524  0.020  1.524
 CM5  C27  H27   single  0.970  0.020  1.090
 CM5  O32  H32   single  0.850  0.020  0.980
 CM5  C28  O33   single  1.410  0.020  1.410
 CM5  C28  C29   single  1.526  0.020  1.526
 CM5  C28  H28   single  0.970  0.020  1.090
 CM5  O33  H33   single  0.850  0.020  0.980
 CM5  C29  O34   single  1.402  0.020  1.402
 CM5  C29  H29   single  0.970  0.020  1.090
 CM5  O34  H34   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
 CM5  H72   C7   H71   106.31  3.000
 CM5  H72   C7   C6    108.81  3.000
 CM5  H71   C7   C6    109.76  3.000
 CM5  H72   C7   C8    109.33  3.000
 CM5  H71   C7   C8    110.04  3.000
 CM5  C6    C7   C8    112.40  3.000
 CM5  H82   C8   H81   106.37  3.000
 CM5  H82   C8   C9    110.37  3.000
 CM5  H81   C8   C9    109.24  3.000
 CM5  H82   C8   C7    110.15  3.000
 CM5  H81   C8   C7    109.26  3.000
 CM5  C9    C8   C7    111.32  3.000
 CM5  H92   C9   H91   106.49  3.000
 CM5  H92   C9   C10   109.32  3.000
 CM5  H91   C9   C10   110.36  3.000
 CM5  H92   C9   C8    109.34  3.000
 CM5  H91   C9   C8    110.36  3.000
 CM5  C10   C9   C8    110.87  3.000
 CM5  H102  C10  H101  106.35  3.000
 CM5  H102  C10  C11   109.97  3.000
 CM5  H101  C10  C11   109.26  3.000
 CM5  H102  C10  C9    110.38  3.000
 CM5  H101  C10  C9    109.25  3.000
 CM5  C11   C10  C9    111.49  3.000
 CM5  H112  C11  H111  106.35  3.000
 CM5  H112  C11  C6    110.50  3.000
 CM5  H111  C11  C6    108.62  3.000
 CM5  H112  C11  C10   109.56  3.000
 CM5  H111  C11  C10   109.36  3.000
 CM5  C6    C11  C10   112.26  3.000
 CM5  H6    C6   C5    107.98  3.000
 CM5  H6    C6   C11   107.97  3.000
 CM5  C5    C6   C11   112.50  3.000
 CM5  H6    C6   C7    107.80  3.000
 CM5  C5    C6   C7    110.56  3.000
 CM5  C11   C6   C7    109.88  3.000
 CM5  H52   C5   H51   105.95  3.000
 CM5  H52   C5   C4    109.54  3.000
 CM5  H51   C5   C4    108.61  3.000
 CM5  H52   C5   C6    108.89  3.000
 CM5  H51   C5   C6    108.60  3.000
 CM5  C4    C5   C6    114.87  3.000
 CM5  H42   C4   H41   106.09  3.000
 CM5  H42   C4   C3    109.32  3.000
 CM5  H41   C4   C3    108.94  3.000
 CM5  H42   C4   C5    109.27  3.000
 CM5  H41   C4   C5    110.25  3.000
 CM5  C3    C4   C5    112.75  3.000
 CM5  H32A  C3   H31A  106.13  3.000
 CM5  H32A  C3   C2    109.83  3.000
 CM5  H31A  C3   C2    109.36  3.000
 CM5  H32A  C3   C4    109.19  3.000
 CM5  H31A  C3   C4    109.38  3.000
 CM5  C2    C3   C4    112.74  3.000
 CM5  H22A  C2   H21A  106.89  3.000
 CM5  H22A  C2   C1    109.29  3.000
 CM5  H21A  C2   C1    109.56  3.000
 CM5  H22A  C2   C3    109.42  3.000
 CM5  H21A  C2   C3    109.72  3.000
 CM5  C1    C2   C3    111.84  3.000
 CM5  H12   C1   H11   107.24  3.000
 CM5  H12   C1   O12   110.79  3.000
 CM5  H11   C1   O12   109.62  3.000
 CM5  H12   C1   C2    110.13  3.000
 CM5  H11   C1   C2    110.20  3.000
 CM5  O12   C1   C2    108.86  3.000
 CM5  C13   O12  C1    115.28  3.000
 CM5  H13   C13  O14   109.69  3.000
 CM5  H13   C13  C18   109.41  3.000
 CM5  O14   C13  C18   109.34  3.000
 CM5  H13   C13  O12   111.06  3.000
 CM5  O14   C13  O12   108.71  3.000
 CM5  C18   C13  O12   108.60  3.000
 CM5  H18   C18  C17   109.11  3.000
 CM5  H18   C18  O22   111.58  3.000
 CM5  C17   C18  O22   107.39  3.000
 CM5  H18   C18  C13   108.18  3.000
 CM5  C17   C18  C13   108.64  3.000
 CM5  O22   C18  C13   111.88  3.000
 CM5  H22   O22  C18   108.54  3.000
 CM5  H17   C17  C16   107.61  3.000
 CM5  H17   C17  O21   110.30  3.000
 CM5  C16   C17  O21   107.89  3.000
 CM5  H17   C17  C18   108.05  3.000
 CM5  C16   C17  C18   111.16  3.000
 CM5  O21   C17  C18   111.76  3.000
 CM5  H21   O21  C17   108.64  3.000
 CM5  C15   O14  C13   113.56  3.000
 CM5  H15   C15  C16   108.25  3.000
 CM5  H15   C15  C19   108.93  3.000
 CM5  C16   C15  C19   112.72  3.000
 CM5  H15   C15  O14   110.29  3.000
 CM5  C16   C15  O14   109.22  3.000
 CM5  C19   C15  O14   107.44  3.000
 CM5  H192  C19  H191  107.19  3.000
 CM5  H192  C19  O20   111.75  3.000
 CM5  H191  C19  O20   111.33  3.000
 CM5  H192  C19  C15   108.86  3.000
 CM5  H191  C19  C15   109.29  3.000
 CM5  O20   C19  C15   108.37  3.000
 CM5  H20   O20  C19   107.83  3.000
 CM5  H16   C16  O23   110.71  3.000
 CM5  H16   C16  C15   108.90  3.000
 CM5  O23   C16  C15   111.01  3.000
 CM5  H16   C16  C17   109.26  3.000
 CM5  O23   C16  C17   107.16  3.000
 CM5  C15   C16  C17   109.77  3.000
 CM5  C24   O23  C16   119.89  3.000
 CM5  H24   C24  C29   110.32  3.000
 CM5  H24   C24  O25   105.91  3.000
 CM5  C29   C24  O25   110.09  3.000
 CM5  H24   C24  O23   110.46  3.000
 CM5  C29   C24  O23   108.46  3.000
 CM5  O25   C24  O23   111.61  3.000
 CM5  C26   O25  C24   116.09  3.000
 CM5  H26   C26  C27   108.61  3.000
 CM5  H26   C26  C30   108.72  3.000
 CM5  C27   C26  C30   111.72  3.000
 CM5  H26   C26  O25   110.34  3.000
 CM5  C27   C26  O25   110.59  3.000
 CM5  C30   C26  O25   106.85  3.000
 CM5  H302  C30  H301  107.12  3.000
 CM5  H302  C30  O31   111.65  3.000
 CM5  H301  C30  O31   111.86  3.000
 CM5  H302  C30  C26   108.44  3.000
 CM5  H301  C30  C26   108.74  3.000
 CM5  O31   C30  C26   108.93  3.000
 CM5  H31   O31  C30   107.98  3.000
 CM5  H27   C27  C28   108.01  3.000
 CM5  H27   C27  O32   110.87  3.000
 CM5  C28   C27  O32   111.79  3.000
 CM5  H27   C27  C26   108.43  3.000
 CM5  C28   C27  C26   110.04  3.000
 CM5  O32   C27  C26   107.64  3.000
 CM5  H32   O32  C27   108.10  3.000
 CM5  H28   C28  C29   109.41  3.000
 CM5  H28   C28  O33   110.44  3.000
 CM5  C29   C28  O33   111.61  3.000
 CM5  H28   C28  C27   108.46  3.000
 CM5  C29   C28  C27   109.43  3.000
 CM5  O33   C28  C27   107.42  3.000
 CM5  H33   O33  C28   108.16  3.000
 CM5  H29   C29  O34   106.63  3.000
 CM5  H29   C29  C28   107.92  3.000
 CM5  O34   C29  C28   112.51  3.000
 CM5  H29   C29  C24   106.90  3.000
 CM5  O34   C29  C24   113.08  3.000
 CM5  C28   C29  C24   109.48  3.000
 CM5  H34   O34  C29   110.25  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
 CM5  Var_01  C10  C9   C8   C7     55.01  30.0  1
 CM5  Var_02  C11  C10  C9   C8    -55.01  30.0  1
 CM5  Var_03  C6   C7   C8   C9    -55.65  30.0  1
 CM5  Var_04  C6   C11  C10  C9     55.49  30.0  1
 CM5  Var_05  C3   C4   C5   C6   -178.23  30.0  3
 CM5  Var_06  H11  C1   O12  C13   -57.31  30.0  2
 CM5  Var_07  C2   C3   C4   C5    177.51  30.0  3
 CM5  Var_08  C1   C2   C3   C4    178.61  30.0  3
 CM5  Var_09  O12  C1   C2   C3    175.44  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
 CM5  chir_01  C6   C7   C11  C5   negativ
 CM5  chir_02  C13  O12  C18  O14  negativ
 CM5  chir_03  C18  O22  C13  C17  negativ
 CM5  chir_04  C17  O21  C18  C16  positiv
 CM5  chir_05  C15  O14  C19  C16  positiv
 CM5  chir_06  C16  O23  C17  C15  negativ
 CM5  chir_07  C24  O23  O25  C29  negativ
 CM5  chir_08  C26  O25  C30  C27  positiv
 CM5  chir_09  C27  O32  C26  C28  positiv
 CM5  chir_10  C28  O33  C29  C27  positiv
 CM5  chir_11  C29  O34  C24  C28  negativ

