# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:08:08 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: 4-cyclohexylbutyl 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](OCCCCC3CCCCC3)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
 CVM  CVM  '4-cyclohexylbutyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'  ligand  73  33  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CVM
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
 CVM  C1    C  CH2   0  -0.142   -2.9709   0.4938  -0.2306
 CVM  C2    C  CH2   0  -0.463   -4.3086   1.0096   0.2553
 CVM  C3    C  CH2   0  -0.435   -5.4695   0.1943  -0.3026
 CVM  C4    C  CH2   0  -0.400   -6.8172   0.6809   0.2169
 CVM  C6    C  CH1   0  -0.222   -8.0339   0.0092  -0.4170
 CVM  C7    C  CH2   0  -0.414   -9.3240   0.6624   0.0807
 CVM  C8    C  CH2   0  -0.431  -10.5717   0.0235  -0.5192
 CVM  C9    C  CH2   0  -0.429  -10.6008  -1.4789  -0.2575
 CVM  C10   C  CH2   0  -0.429   -9.3247  -2.1428  -0.7621
 CVM  C11   C  CH2   0  -0.422   -8.0794  -1.4981  -0.1605
 CVM  O12   O  O2    0  -0.503   -1.9482   1.3612   0.2384
 CVM  C13   C  CH1   0   0.301   -0.6695   1.0205  -0.1374
 CVM  O14   O  O2    0  -0.494   -0.1883   0.0407   0.7469
 CVM  C15   C  CH1   0  -0.011    1.0988  -0.4371   0.4156
 CVM  C16   C  CH1   0   0.020    2.1045   0.7197   0.5123
 CVM  C17   C  CH1   0   0.013    1.6439   1.8744  -0.3708
 CVM  C18   C  CH1   0  -0.024    0.2097   2.2637  -0.0474
 CVM  C19   C  CH2   0  -0.185    1.4221  -1.5692   1.3662
 CVM  O20   O  OH1   0  -0.670    0.4879  -2.6043   1.1633
 CVM  O21   O  OH1   0  -0.671    2.5316   2.9514  -0.1748
 CVM  O22   O  OH1   0  -0.668   -0.1804   3.2462  -0.9721
 CVM  O23   O  O2    0  -0.517    3.3795   0.3297   0.0572
 CVM  C24   C  CH1   0   0.217    4.4489   0.2573   0.9594
 CVM  O25   O  O2    0  -0.496    4.8155  -1.0615   1.2140
 CVM  C26   C  CH1   0  -0.012    5.2710  -1.8094   0.0953
 CVM  C27   C  CH1   0   0.032    6.4753  -1.1246  -0.5517
 CVM  C28   C  CH1   0  -0.010    6.1330   0.3225  -0.8841
 CVM  C29   C  CH1   0  -0.007    5.6324   1.0292   0.3732
 CVM  C30   C  CH2   0  -0.161    5.6136  -3.1944   0.6031
 CVM  O31   O  OH1   0  -0.663    4.4386  -3.8073   1.0774
 CVM  O32   O  OH1   0  -0.673    6.8168  -1.8588  -1.7022
 CVM  O33   O  OH1   0  -0.677    7.3006   0.9280  -1.3896
 CVM  O34   O  OH1   0  -0.690    5.3455   2.3835   0.1508
 CVM  H11C  H  HCH2  0   0.211   -2.8081  -0.5287   0.1279
 CVM  H12C  H  HCH2  0   0.207   -2.9521   0.4613  -1.3278
 CVM  H21C  H  HCH2  0   0.225   -4.3342   0.9865   1.3491
 CVM  H22C  H  HCH2  0   0.223   -4.4234   2.0566  -0.0418
 CVM  H31C  H  HCH2  0   0.214   -5.4595   0.2520  -1.3966
 CVM  H32C  H  HCH2  0   0.221   -5.3275  -0.8608  -0.0510
 CVM  H41C  H  HCH2  0   0.206   -6.8577   0.5464   1.3045
 CVM  H42C  H  HCH2  0   0.214   -6.8902   1.7611   0.0462
 CVM  H6    H  HCH1  0   0.200   -7.9742   0.1631  -1.5042
 CVM  H71C  H  HCH2  0   0.202   -9.3653   0.5714   1.1733
 CVM  H72C  H  HCH2  0   0.221   -9.3036   1.7344  -0.1371
 CVM  H111  H  HCH2  0   0.228   -7.1859  -1.9819  -0.5636
 CVM  H112  H  HCH2  0   0.201   -8.0629  -1.6732   0.9227
 CVM  H81C  H  HCH2  0   0.223  -11.4686   0.4976  -0.1123
 CVM  H82C  H  HCH2  0   0.206  -10.5907   0.2025  -1.6001
 CVM  H91C  H  HCH2  0   0.206  -10.7030  -1.6563   0.8190
 CVM  H92C  H  HCH2  0   0.223  -11.4766  -1.9305  -0.7303
 CVM  H101  H  HCH2  0   0.224   -9.3381  -3.2130  -0.5408
 CVM  H102  H  HCH2  0   0.206   -9.2824  -2.0530  -1.8533
 CVM  H13   H  HCH1  0   0.186   -0.6487   0.6309  -1.1728
 CVM  H18   H  HCH1  0   0.226    0.1671   2.6399   0.9862
 CVM  H15   H  HCH1  0   0.227    1.1097  -0.8202  -0.6182
 CVM  H16   H  HCH1  0   0.239    2.1530   1.0623   1.5565
 CVM  H191  H  HCH2  0   0.236    2.4422  -1.9136   1.1813
 CVM  H192  H  HCH2  0   0.194    1.3899  -1.1858   2.3965
 CVM  H17   H  HCH1  0   0.229    1.6810   1.5317  -1.4168
 CVM  H21   H  HOH1  0   0.466    2.3304   3.6399  -0.8179
 CVM  H22   H  HOH1  0   0.457   -1.0339   3.5995  -0.7014
 CVM  H20   H  HOH1  0   0.455    0.7593  -3.3537   1.7003
 CVM  H24   H  HCH1  0   0.254    4.1620   0.6829   1.9285
 CVM  H29   H  HCH1  0   0.234    6.4347   0.9982   1.1202
 CVM  H26   H  HCH1  0   0.229    4.4734  -1.8983  -0.6557
 CVM  H27   H  HCH1  0   0.210    7.3063  -1.1209   0.1732
 CVM  H301  H  HCH2  0   0.211    6.0634  -3.7624  -0.2179
 CVM  H302  H  HCH2  0   0.196    6.3756  -3.1048   1.3898
 CVM  H28   H  HCH1  0   0.212    5.3375   0.3248  -1.6447
 CVM  H32   H  HOH1  0   0.455    7.5745  -1.4321  -2.1158
 CVM  H33   H  HOH1  0   0.454    7.0735   1.8144  -1.6889
 CVM  H34   H  HOH1  0   0.449    4.4332   2.4841  -0.1663
 CVM  H31   H  HOH1  0   0.456    4.6651  -4.6921   1.3776

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
 CVM  C1   C2    single  1.514  0.020  1.514
 CVM  C1   O12   single  1.421  0.020  1.421
 CVM  C2   C3    single  1.524  0.020  1.524
 CVM  C3   C4    single  1.524  0.020  1.524
 CVM  C4   C6    single  1.528  0.020  1.528
 CVM  C6   C7    single  1.529  0.020  1.529
 CVM  C6   C11   single  1.530  0.020  1.530
 CVM  C7   C8    single  1.525  0.020  1.525
 CVM  C8   C9    single  1.525  0.020  1.525
 CVM  C9   C10   single  1.524  0.020  1.524
 CVM  C10  C11   single  1.526  0.020  1.526
 CVM  O12  C13   single  1.376  0.020  1.376
 CVM  C13  O14   single  1.405  0.020  1.405
 CVM  C13  C18   single  1.525  0.020  1.525
 CVM  O14  C15   single  1.412  0.020  1.412
 CVM  C15  C16   single  1.536  0.020  1.536
 CVM  C15  C19   single  1.513  0.020  1.513
 CVM  C16  C17   single  1.525  0.020  1.525
 CVM  C16  O23   single  1.409  0.020  1.409
 CVM  C17  C18   single  1.521  0.020  1.521
 CVM  C17  O21   single  1.409  0.020  1.409
 CVM  C18  O22   single  1.405  0.020  1.405
 CVM  C19  O20   single  1.409  0.020  1.409
 CVM  O23  C24   single  1.401  0.020  1.401
 CVM  C24  O25   single  1.392  0.020  1.392
 CVM  C24  C29   single  1.530  0.020  1.530
 CVM  O25  C26   single  1.421  0.020  1.421
 CVM  C26  C27   single  1.529  0.020  1.529
 CVM  C26  C30   single  1.514  0.020  1.514
 CVM  C27  C28   single  1.524  0.020  1.524
 CVM  C27  O32   single  1.407  0.020  1.407
 CVM  C28  C29   single  1.527  0.020  1.527
 CVM  C28  O33   single  1.409  0.020  1.409
 CVM  C29  O34   single  1.402  0.020  1.402
 CVM  C30  O31   single  1.408  0.020  1.408
 CVM  C1   H11C  single  0.970  0.020  1.090
 CVM  C1   H12C  single  0.970  0.020  1.090
 CVM  C2   H21C  single  0.970  0.020  1.090
 CVM  C2   H22C  single  0.970  0.020  1.090
 CVM  C3   H31C  single  0.970  0.020  1.090
 CVM  C3   H32C  single  0.970  0.020  1.090
 CVM  C4   H41C  single  0.970  0.020  1.090
 CVM  C4   H42C  single  0.970  0.020  1.090
 CVM  C6   H6    single  0.970  0.020  1.090
 CVM  C7   H71C  single  0.970  0.020  1.090
 CVM  C7   H72C  single  0.970  0.020  1.090
 CVM  C11  H111  single  0.970  0.020  1.090
 CVM  C11  H112  single  0.970  0.020  1.090
 CVM  C8   H81C  single  0.970  0.020  1.090
 CVM  C8   H82C  single  0.970  0.020  1.090
 CVM  C9   H91C  single  0.970  0.020  1.090
 CVM  C9   H92C  single  0.970  0.020  1.090
 CVM  C10  H101  single  0.970  0.020  1.090
 CVM  C10  H102  single  0.970  0.020  1.090
 CVM  C13  H13   single  0.970  0.020  1.090
 CVM  C18  H18   single  0.970  0.020  1.090
 CVM  C15  H15   single  0.970  0.020  1.090
 CVM  C16  H16   single  0.970  0.020  1.090
 CVM  C19  H191  single  0.970  0.020  1.090
 CVM  C19  H192  single  0.970  0.020  1.090
 CVM  C17  H17   single  0.970  0.020  1.090
 CVM  O21  H21   single  0.850  0.020  0.980
 CVM  O22  H22   single  0.850  0.020  0.980
 CVM  O20  H20   single  0.850  0.020  0.980
 CVM  C24  H24   single  0.970  0.020  1.090
 CVM  C29  H29   single  0.970  0.020  1.090
 CVM  C26  H26   single  0.970  0.020  1.090
 CVM  C27  H27   single  0.970  0.020  1.090
 CVM  C30  H301  single  0.970  0.020  1.090
 CVM  C30  H302  single  0.970  0.020  1.090
 CVM  C28  H28   single  0.970  0.020  1.090
 CVM  O32  H32   single  0.850  0.020  0.980
 CVM  O33  H33   single  0.850  0.020  0.980
 CVM  O34  H34   single  0.850  0.020  0.980
 CVM  O31  H31   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
 CVM  H12C  C1   H11C  107.27  3.000
 CVM  H12C  C1   O12   109.61  3.000
 CVM  H11C  C1   O12   110.78  3.000
 CVM  H12C  C1   C2    110.25  3.000
 CVM  H11C  C1   C2    110.14  3.000
 CVM  O12   C1   C2    108.79  3.000
 CVM  H22C  C2   H21C  106.81  3.000
 CVM  H22C  C2   C3    109.41  3.000
 CVM  H21C  C2   C3    109.67  3.000
 CVM  H22C  C2   C1    109.37  3.000
 CVM  H21C  C2   C1    109.53  3.000
 CVM  C3    C2   C1    111.91  3.000
 CVM  H32C  C3   H31C  106.22  3.000
 CVM  H32C  C3   C4    110.14  3.000
 CVM  H31C  C3   C4    109.36  3.000
 CVM  H32C  C3   C2    109.44  3.000
 CVM  H31C  C3   C2    109.29  3.000
 CVM  C4    C3   C2    112.21  3.000
 CVM  H42C  C4   H41C  105.84  3.000
 CVM  H42C  C4   C6    108.41  3.000
 CVM  H41C  C4   C6    109.16  3.000
 CVM  H42C  C4   C3    108.69  3.000
 CVM  H41C  C4   C3    109.36  3.000
 CVM  C6    C4   C3    114.99  3.000
 CVM  H6    C6   C11   107.78  3.000
 CVM  H6    C6   C7    107.92  3.000
 CVM  C11   C6   C7    109.95  3.000
 CVM  H6    C6   C4    107.79  3.000
 CVM  C11   C6   C4    112.80  3.000
 CVM  C7    C6   C4    110.43  3.000
 CVM  H72C  C7   H71C  106.27  3.000
 CVM  H72C  C7   C8    110.34  3.000
 CVM  H71C  C7   C8    109.04  3.000
 CVM  H72C  C7   C6    109.76  3.000
 CVM  H71C  C7   C6    108.68  3.000
 CVM  C8    C7   C6    112.54  3.000
 CVM  H82C  C8   H81C  106.39  3.000
 CVM  H82C  C8   C9    109.26  3.000
 CVM  H81C  C8   C9    110.35  3.000
 CVM  H82C  C8   C7    109.50  3.000
 CVM  H81C  C8   C7    110.07  3.000
 CVM  C9    C8   C7    111.15  3.000
 CVM  H92C  C9   H91C  106.46  3.000
 CVM  H92C  C9   C10   110.34  3.000
 CVM  H91C  C9   C10   109.44  3.000
 CVM  H92C  C9   C8    110.37  3.000
 CVM  H91C  C9   C8    109.26  3.000
 CVM  C10   C9   C8    110.87  3.000
 CVM  H102  C10  H101  106.40  3.000
 CVM  H102  C10  C11   109.05  3.000
 CVM  H101  C10  C11   110.11  3.000
 CVM  H102  C10  C9    109.04  3.000
 CVM  H101  C10  C9    110.44  3.000
 CVM  C11   C10  C9    111.63  3.000
 CVM  H112  C11  H111  106.33  3.000
 CVM  H112  C11  C10   109.51  3.000
 CVM  H111  C11  C10   109.55  3.000
 CVM  H112  C11  C6    108.80  3.000
 CVM  H111  C11  C6    110.48  3.000
 CVM  C10   C11  C6    111.99  3.000
 CVM  C13   O12  C1    115.32  3.000
 CVM  H13   C13  C18   109.35  3.000
 CVM  H13   C13  O14   109.69  3.000
 CVM  C18   C13  O14   109.50  3.000
 CVM  H13   C13  O12   111.12  3.000
 CVM  C18   C13  O12   108.53  3.000
 CVM  O14   C13  O12   108.61  3.000
 CVM  C15   O14  C13   113.61  3.000
 CVM  H15   C15  C19   109.08  3.000
 CVM  H15   C15  C16   108.32  3.000
 CVM  C19   C15  C16   112.59  3.000
 CVM  H15   C15  O14   110.27  3.000
 CVM  C19   C15  O14   107.48  3.000
 CVM  C16   C15  O14   109.10  3.000
 CVM  H16   C16  O23   110.67  3.000
 CVM  H16   C16  C17   109.10  3.000
 CVM  O23   C16  C17   107.21  3.000
 CVM  H16   C16  C15   108.86  3.000
 CVM  O23   C16  C15   111.33  3.000
 CVM  C17   C16  C15   109.64  3.000
 CVM  H17   C17  O21   110.41  3.000
 CVM  H17   C17  C18   108.26  3.000
 CVM  O21   C17  C18   111.64  3.000
 CVM  H17   C17  C16   107.71  3.000
 CVM  O21   C17  C16   107.93  3.000
 CVM  C18   C17  C16   110.82  3.000
 CVM  H18   C18  O22   111.62  3.000
 CVM  H18   C18  C17   108.89  3.000
 CVM  O22   C18  C17   107.52  3.000
 CVM  H18   C18  C13   108.15  3.000
 CVM  O22   C18  C13   111.79  3.000
 CVM  C17   C18  C13   108.81  3.000
 CVM  H192  C19  H191  107.20  3.000
 CVM  H192  C19  O20   111.81  3.000
 CVM  H191  C19  O20   111.29  3.000
 CVM  H192  C19  C15   108.75  3.000
 CVM  H191  C19  C15   109.21  3.000
 CVM  O20   C19  C15   108.51  3.000
 CVM  H20   O20  C19   107.77  3.000
 CVM  H21   O21  C17   108.77  3.000
 CVM  H22   O22  C18   108.54  3.000
 CVM  C24   O23  C16   119.81  3.000
 CVM  H24   C24  C29   110.19  3.000
 CVM  H24   C24  O25   105.95  3.000
 CVM  C29   C24  O25   110.14  3.000
 CVM  H24   C24  O23   110.45  3.000
 CVM  C29   C24  O23   108.53  3.000
 CVM  O25   C24  O23   111.57  3.000
 CVM  C26   O25  C24   116.04  3.000
 CVM  H26   C26  C30   108.63  3.000
 CVM  H26   C26  C27   108.58  3.000
 CVM  C30   C26  C27   111.92  3.000
 CVM  H26   C26  O25   110.36  3.000
 CVM  C30   C26  O25   106.85  3.000
 CVM  C27   C26  O25   110.48  3.000
 CVM  H27   C27  O32   110.88  3.000
 CVM  H27   C27  C28   108.03  3.000
 CVM  O32   C27  C28   111.82  3.000
 CVM  H27   C27  C26   108.48  3.000
 CVM  O32   C27  C26   107.67  3.000
 CVM  C28   C27  C26   109.92  3.000
 CVM  H28   C28  O33   110.50  3.000
 CVM  H28   C28  C29   109.34  3.000
 CVM  O33   C28  C29   111.61  3.000
 CVM  H28   C28  C27   108.36  3.000
 CVM  O33   C28  C27   107.47  3.000
 CVM  C29   C28  C27   109.48  3.000
 CVM  H29   C29  O34   106.56  3.000
 CVM  H29   C29  C28   107.94  3.000
 CVM  O34   C29  C28   112.55  3.000
 CVM  H29   C29  C24   106.90  3.000
 CVM  O34   C29  C24   112.94  3.000
 CVM  C28   C29  C24   109.62  3.000
 CVM  H302  C30  H301  107.11  3.000
 CVM  H302  C30  O31   111.91  3.000
 CVM  H301  C30  O31   111.70  3.000
 CVM  H302  C30  C26   108.81  3.000
 CVM  H301  C30  C26   108.41  3.000
 CVM  O31   C30  C26   108.81  3.000
 CVM  H31   O31  C30   108.02  3.000
 CVM  H32   O32  C27   108.12  3.000
 CVM  H33   O33  C28   108.16  3.000
 CVM  H34   O34  C29   110.12  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
 CVM  Var_01  C9    C8   C7   C6    55.57  30.0  1
 CVM  Var_02  C9    C10  C11  C6   -55.61  30.0  1
 CVM  Var_03  C11   C10  C9   C8    55.22  30.0  1
 CVM  Var_04  C6    C4   C3   C2   173.65  30.0  3
 CVM  Var_05  H11C  C1   O12  C13   59.29  30.0  1
 CVM  Var_06  C4    C3   C2   C1   178.22  30.0  3
 CVM  Var_07  O12   C1   C2   C3   175.35  30.0  1

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
 CVM  chir_01  C6   C4   C7   C11  positiv
 CVM  chir_02  C13  O12  O14  C18  positiv
 CVM  chir_03  C15  O14  C16  C19  negativ
 CVM  chir_04  C16  O23  C17  C15  negativ
 CVM  chir_05  C17  O21  C16  C18  negativ
 CVM  chir_06  C18  O22  C17  C13  positiv
 CVM  chir_07  C24  O23  O25  C29  negativ
 CVM  chir_08  C26  O25  C30  C27  positiv
 CVM  chir_09  C27  O32  C26  C28  positiv
 CVM  chir_10  C28  O33  C29  C27  positiv
 CVM  chir_11  C29  O34  C28  C24  positiv

