# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:43:46 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[4-[3-(1-adamantylmethoxy)propyl]-1,2,3-triazol-1-yl]methyl]cyclohexane-1,2,3,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H](O)[C@H](Cn2cc(CCCOCC34CC5CC(CC(C5)C3)C4)nn2)[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
 RJR  RJR  (1~{S},2~{R},3~{R},4~{S},5~{S})-4-[[4-[3-(1-adamantylmethoxy)propyl]-1,2,3-triazol-1-yl]methyl]cyclohexane-1,2,3,5-tetrol  ligand  68  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJR
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
 RJR  C1   C  CH1   0   0.040   5.3170  -1.0058   0.4265
 RJR  C2   C  CH2   0  -0.517   6.4737  -1.0180   1.4207
 RJR  C3   C  CH1   0   0.043   7.8098  -0.7939   0.7271
 RJR  C4   C  CH1   0   0.023   7.7826   0.5309  -0.0208
 RJR  C5   C  CH1   0   0.066   6.6454   0.5632  -1.0382
 RJR  C6   C  CH1   0  -0.334   5.2993   0.3067  -0.3589
 RJR  C7   C  CH2   0  -0.275   4.1712   0.3518  -1.3927
 RJR  N8   N  NR5   0  -0.256   2.8667   0.1540  -0.7932
 RJR  N9   N  N     0  -0.099   2.2850  -1.0301  -0.7877
 RJR  N10  N  N     0  -0.331   1.1651  -0.9208  -0.1567
 RJR  C11  C  CR5   0   0.181   1.0058   0.3549   0.2615
 RJR  C12  C  CR15  0  -0.109   2.1093   1.0595  -0.1482
 RJR  C13  C  CH2   0  -0.512  -0.1963   0.8252   1.0072
 RJR  C14  C  CH2   0  -0.463  -1.5035   0.3359   0.3885
 RJR  C15  C  CH2   0  -0.121  -2.7101   0.9097   1.1039
 RJR  O16  O  O2    0  -0.489  -3.8762   0.3905   0.5179
 RJR  C17  C  CH2   0  -0.097  -5.0594   0.9096   1.0678
 RJR  C18  C  CT    0  -0.145  -6.2767   0.3037   0.3868
 RJR  C19  C  CH2   0  -0.399  -6.3199  -1.2205   0.5714
 RJR  C20  C  CH1   0  -0.246  -7.5807  -1.7987  -0.0749
 RJR  C21  C  CH2   0  -0.417  -8.8223  -1.1806   0.5703
 RJR  C22  C  CH1   0  -0.245  -8.7953   0.3376   0.3776
 RJR  C23  C  CH2   0  -0.416  -8.7912   0.6568  -1.1191
 RJR  C24  C  CH1   0  -0.246  -7.5502   0.0414  -1.7678
 RJR  C25  C  CH2   0  -0.398  -6.2906   0.6168  -1.1166
 RJR  C26  C  CH2   0  -0.419  -7.5741  -1.4774  -1.5713
 RJR  C27  C  CH2   0  -0.406  -7.5341   0.9115   1.0243
 RJR  O28  O  OH1   0  -0.668   5.4159  -2.0641  -0.5033
 RJR  O30  O  OH1   0  -0.682   8.8840  -0.7311   1.6447
 RJR  O31  O  OH1   0  -0.682   8.9774   0.7600  -0.7318
 RJR  O32  O  OH1   0  -0.677   6.5785   1.8201  -1.6740
 RJR  H1   H  HCH1  0   0.232   4.3802  -1.0783   0.9944
 RJR  H2   H  HCH2  0   0.235   6.3108  -0.2334   2.1664
 RJR  H3   H  HCH2  0   0.250   6.4822  -1.9687   1.9640
 RJR  H4   H  HCH1  0   0.209   7.9758  -1.5977  -0.0026
 RJR  H5   H  HCH1  0   0.201   7.6039   1.3343   0.7140
 RJR  H6   H  HCH1  0   0.212   6.8266  -0.2304  -1.7789
 RJR  H7   H  HCH1  0   0.260   5.1329   1.1108   0.3690
 RJR  H8   H  HCH2  0   0.284   4.1552   1.3158  -1.8969
 RJR  H9   H  HCH2  0   0.275   4.2992  -0.4191  -2.1498
 RJR  H10  H  HCR5  0   0.303   2.3928   2.0931  -0.0421
 RJR  H11  H  HCH2  0   0.249  -0.1402   0.4923   2.0484
 RJR  H12  H  HCH2  0   0.246  -0.1809   1.9171   1.0384
 RJR  H13  H  HCH2  0   0.231  -1.5401   0.6175  -0.6673
 RJR  H14  H  HCH2  0   0.233  -1.5407  -0.7552   0.4279
 RJR  H15  H  HCH2  0   0.191  -2.6693   0.6631   2.1758
 RJR  H16  H  HCH2  0   0.191  -2.6975   2.0080   1.0363
 RJR  H17  H  HCH2  0   0.194  -5.1054   0.7038   2.1497
 RJR  H18  H  HCH2  0   0.195  -5.0848   2.0059   0.9561
 RJR  H19  H  HCH2  0   0.224  -5.4326  -1.6780   0.1234
 RJR  H20  H  HCH2  0   0.214  -6.2975  -1.4671   1.6395
 RJR  H21  H  HCH1  0   0.220  -7.5943  -2.8840   0.0670
 RJR  H22  H  HCH2  0   0.220  -9.7275  -1.5982   0.1167
 RJR  H23  H  HCH2  0   0.219  -8.8597  -1.4262   1.6367
 RJR  H24  H  HCH1  0   0.221  -9.6775   0.7837   0.8469
 RJR  H25  H  HCH2  0   0.220  -9.6978   0.2598  -1.5888
 RJR  H26  H  HCH2  0   0.219  -8.8038   1.7406  -1.2749
 RJR  H27  H  HCH1  0   0.220  -7.5411   0.2726  -2.8375
 RJR  H28  H  HCH2  0   0.214  -6.2486   1.7019  -1.2682
 RJR  H29  H  HCH2  0   0.224  -5.4011   0.1965  -1.5956
 RJR  H30  H  HCH2  0   0.219  -6.7001  -1.9322  -2.0499
 RJR  H31  H  HCH2  0   0.219  -8.4607  -1.9042  -2.0525
 RJR  H32  H  HCH2  0   0.221  -7.5396   0.7112   2.1019
 RJR  H33  H  HCH2  0   0.221  -7.5181   2.0013   0.9086
 RJR  H34  H  HOH1  0   0.454   5.3386  -2.8954  -0.0252
 RJR  H35  H  HOH1  0   0.455   9.1058  -1.6263   1.9171
 RJR  H36  H  HOH1  0   0.452   9.7081   0.7386  -0.1055
 RJR  H37  H  HOH1  0   0.452   7.4119   1.9668  -2.1331

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
 RJR  O30  C3   single    1.414  0.020  1.414
 RJR  C2   C3   single    1.522  0.020  1.522
 RJR  C2   C1   single    1.525  0.020  1.525
 RJR  C26  C20  single    1.531  0.020  1.531
 RJR  C26  C24  single    1.532  0.020  1.532
 RJR  C3   C4   single    1.522  0.020  1.522
 RJR  C1   O28  single    1.412  0.020  1.412
 RJR  C1   C6   single    1.530  0.020  1.530
 RJR  C20  C19  single    1.530  0.020  1.530
 RJR  C20  C21  single    1.530  0.020  1.530
 RJR  C19  C18  single    1.536  0.020  1.536
 RJR  C24  C25  single    1.530  0.020  1.530
 RJR  C24  C23  single    1.530  0.020  1.530
 RJR  C25  C18  single    1.536  0.020  1.536
 RJR  C4   O31  single    1.409  0.020  1.409
 RJR  C4   C5   single    1.526  0.020  1.526
 RJR  C6   C7   single    1.531  0.020  1.531
 RJR  C6   C5   single    1.529  0.020  1.529
 RJR  C21  C22  single    1.531  0.020  1.531
 RJR  C18  C17  single    1.521  0.020  1.521
 RJR  C18  C27  single    1.535  0.020  1.535
 RJR  C17  O16  single    1.404  0.020  1.404
 RJR  C23  C22  single    1.530  0.020  1.530
 RJR  C7   N8   single    1.449  0.020  1.449
 RJR  C5   O32  single    1.410  0.020  1.410
 RJR  C22  C27  single    1.529  0.020  1.529
 RJR  C12  N8   aromatic  1.345  0.020  1.345
 RJR  C12  C11  aromatic  1.372  0.020  1.372
 RJR  N8   N9   aromatic  1.319  0.020  1.319
 RJR  O16  C15  single    1.405  0.020  1.405
 RJR  C15  C14  single    1.516  0.020  1.516
 RJR  C14  C13  single    1.527  0.020  1.527
 RJR  C11  C13  single    1.491  0.020  1.491
 RJR  C11  N10  aromatic  1.352  0.020  1.352
 RJR  N9   N10  aromatic  1.290  0.020  1.290
 RJR  C1   H1   single    0.970  0.020  1.090
 RJR  C2   H2   single    0.970  0.020  1.090
 RJR  C2   H3   single    0.970  0.020  1.090
 RJR  C3   H4   single    0.970  0.020  1.090
 RJR  C4   H5   single    0.970  0.020  1.090
 RJR  C5   H6   single    0.970  0.020  1.090
 RJR  C6   H7   single    0.970  0.020  1.090
 RJR  C7   H8   single    0.970  0.020  1.090
 RJR  C7   H9   single    0.970  0.020  1.090
 RJR  C12  H10  single    0.930  0.020  1.080
 RJR  C13  H11  single    0.970  0.020  1.090
 RJR  C13  H12  single    0.970  0.020  1.090
 RJR  C14  H13  single    0.970  0.020  1.090
 RJR  C14  H14  single    0.970  0.020  1.090
 RJR  C15  H15  single    0.970  0.020  1.090
 RJR  C15  H16  single    0.970  0.020  1.090
 RJR  C17  H17  single    0.970  0.020  1.090
 RJR  C17  H18  single    0.970  0.020  1.090
 RJR  C19  H19  single    0.970  0.020  1.090
 RJR  C19  H20  single    0.970  0.020  1.090
 RJR  C20  H21  single    0.970  0.020  1.090
 RJR  C21  H22  single    0.970  0.020  1.090
 RJR  C21  H23  single    0.970  0.020  1.090
 RJR  C22  H24  single    0.970  0.020  1.090
 RJR  C23  H25  single    0.970  0.020  1.090
 RJR  C23  H26  single    0.970  0.020  1.090
 RJR  C24  H27  single    0.970  0.020  1.090
 RJR  C25  H28  single    0.970  0.020  1.090
 RJR  C25  H29  single    0.970  0.020  1.090
 RJR  C26  H30  single    0.970  0.020  1.090
 RJR  C26  H31  single    0.970  0.020  1.090
 RJR  C27  H32  single    0.970  0.020  1.090
 RJR  C27  H33  single    0.970  0.020  1.090
 RJR  O28  H34  single    0.850  0.020  0.980
 RJR  O30  H35  single    0.850  0.020  0.980
 RJR  O31  H36  single    0.850  0.020  0.980
 RJR  O32  H37  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
 RJR  H1   C1   O28  110.54  3.000
 RJR  H1   C1   C6   108.21  3.000
 RJR  O28  C1   C6   107.80  3.000
 RJR  H1   C1   C2   108.02  3.000
 RJR  C6   C1   C2   110.50  3.000
 RJR  O28  C1   C2   111.72  3.000
 RJR  H3   C2   H2   106.58  3.000
 RJR  H3   C2   C3   110.32  3.000
 RJR  H2   C2   C3   109.61  3.000
 RJR  H3   C2   C1   109.64  3.000
 RJR  H2   C2   C1   108.99  3.000
 RJR  C3   C2   C1   111.56  3.000
 RJR  H4   C3   O30  110.41  3.000
 RJR  H4   C3   C4   108.27  3.000
 RJR  O30  C3   C4   107.08  3.000
 RJR  H4   C3   C2   109.13  3.000
 RJR  C4   C3   C2   109.67  3.000
 RJR  O30  C3   C2   112.19  3.000
 RJR  H5   C4   O31  110.79  3.000
 RJR  H5   C4   C5   107.93  3.000
 RJR  O31  C4   C5   106.97  3.000
 RJR  H5   C4   C3   108.04  3.000
 RJR  C5   C4   C3   111.06  3.000
 RJR  O31  C4   C3   111.99  3.000
 RJR  H6   C5   O32  110.31  3.000
 RJR  H6   C5   C6   108.84  3.000
 RJR  O32  C5   C6   107.94  3.000
 RJR  H6   C5   C4   108.10  3.000
 RJR  O32  C5   C4   110.78  3.000
 RJR  C6   C5   C4   110.86  3.000
 RJR  H7   C6   C7   108.34  3.000
 RJR  H7   C6   C5   107.77  3.000
 RJR  C7   C6   C5   110.10  3.000
 RJR  H7   C6   C1   106.85  3.000
 RJR  C5   C6   C1   111.21  3.000
 RJR  C7   C6   C1   112.37  3.000
 RJR  H9   C7   H8   107.88  3.000
 RJR  H9   C7   N8   107.28  3.000
 RJR  H8   C7   N8   107.42  3.000
 RJR  H9   C7   C6   111.24  3.000
 RJR  H8   C7   C6   110.48  3.000
 RJR  N8   C7   C6   112.33  3.000
 RJR  C12  N8   N9   110.72  3.000
 RJR  N9   N8   C7   121.41  3.000
 RJR  C12  N8   C7   127.83  3.000
 RJR  N10  N9   N8   107.99  3.000
 RJR  C11  N10  N9   109.48  3.000
 RJR  C13  C11  C12  129.49  3.000
 RJR  C13  C11  N10  123.19  3.000
 RJR  C12  C11  N10  107.31  3.000
 RJR  H10  C12  C11  132.47  3.000
 RJR  H10  C12  N8   123.02  3.000
 RJR  C11  C12  N8   104.50  3.000
 RJR  H12  C13  H11  106.02  3.000
 RJR  H12  C13  C14  110.12  3.000
 RJR  H11  C13  C14  109.38  3.000
 RJR  H12  C13  C11  108.56  3.000
 RJR  H11  C13  C11  109.79  3.000
 RJR  C14  C13  C11  112.75  3.000
 RJR  H14  C14  H13  106.91  3.000
 RJR  H14  C14  C15  109.51  3.000
 RJR  H13  C14  C15  109.37  3.000
 RJR  H14  C14  C13  109.55  3.000
 RJR  H13  C14  C13  109.72  3.000
 RJR  C15  C14  C13  111.66  3.000
 RJR  H16  C15  H15  106.44  3.000
 RJR  H16  C15  O16  110.66  3.000
 RJR  H15  C15  O16  110.75  3.000
 RJR  H16  C15  C14  109.86  3.000
 RJR  H15  C15  C14  110.21  3.000
 RJR  O16  C15  C14  108.91  3.000
 RJR  C17  O16  C15  113.55  3.000
 RJR  H18  C17  H17  106.51  3.000
 RJR  H18  C17  C18  109.42  3.000
 RJR  H17  C17  C18  109.37  3.000
 RJR  H18  C17  O16  110.33  3.000
 RJR  H17  C17  O16  110.52  3.000
 RJR  C18  C17  O16  110.60  3.000
 RJR  C27  C18  C25  108.57  3.000
 RJR  C27  C18  C19  108.66  3.000
 RJR  C25  C18  C19  108.65  3.000
 RJR  C27  C18  C17  108.17  3.000
 RJR  C25  C18  C17  111.37  3.000
 RJR  C19  C18  C17  111.35  3.000
 RJR  H20  C19  H19  106.75  3.000
 RJR  H20  C19  C20  110.08  3.000
 RJR  H19  C19  C20  109.71  3.000
 RJR  H20  C19  C18  109.86  3.000
 RJR  H19  C19  C18  110.06  3.000
 RJR  C20  C19  C18  110.33  3.000
 RJR  H21  C20  C26  109.57  3.000
 RJR  H21  C20  C21  109.63  3.000
 RJR  C26  C20  C21  109.33  3.000
 RJR  H21  C20  C19  109.27  3.000
 RJR  C21  C20  C19  109.75  3.000
 RJR  C26  C20  C19  109.27  3.000
 RJR  H23  C21  H22  106.83  3.000
 RJR  H23  C21  C22  110.22  3.000
 RJR  H22  C21  C22  109.91  3.000
 RJR  H23  C21  C20  110.36  3.000
 RJR  H22  C21  C20  110.01  3.000
 RJR  C22  C21  C20  109.48  3.000
 RJR  H24  C22  C27  109.30  3.000
 RJR  H24  C22  C23  109.67  3.000
 RJR  C27  C22  C23  109.46  3.000
 RJR  H24  C22  C21  109.64  3.000
 RJR  C27  C22  C21  109.48  3.000
 RJR  C23  C22  C21  109.27  3.000
 RJR  H26  C23  H25  106.74  3.000
 RJR  H26  C23  C24  110.32  3.000
 RJR  H25  C23  C24  110.11  3.000
 RJR  H26  C23  C22  110.22  3.000
 RJR  H25  C23  C22  109.97  3.000
 RJR  C24  C23  C22  109.46  3.000
 RJR  H27  C24  C26  109.57  3.000
 RJR  H27  C24  C25  109.25  3.000
 RJR  C26  C24  C25  109.34  3.000
 RJR  H27  C24  C23  109.65  3.000
 RJR  C25  C24  C23  109.64  3.000
 RJR  C26  C24  C23  109.38  3.000
 RJR  H29  C25  H28  106.77  3.000
 RJR  H29  C25  C24  109.78  3.000
 RJR  H28  C25  C24  110.17  3.000
 RJR  H29  C25  C18  110.05  3.000
 RJR  H28  C25  C18  109.68  3.000
 RJR  C24  C25  C18  110.32  3.000
 RJR  H31  C26  H30  106.99  3.000
 RJR  H31  C26  C24  110.04  3.000
 RJR  H30  C26  C24  110.07  3.000
 RJR  H31  C26  C20  110.13  3.000
 RJR  H30  C26  C20  110.09  3.000
 RJR  C24  C26  C20  109.49  3.000
 RJR  H33  C27  H32  106.59  3.000
 RJR  H33  C27  C22  109.91  3.000
 RJR  H32  C27  C22  110.06  3.000
 RJR  H33  C27  C18  109.75  3.000
 RJR  H32  C27  C18  109.88  3.000
 RJR  C22  C27  C18  110.57  3.000
 RJR  H34  O28  C1   108.34  3.000
 RJR  H35  O30  C3   108.52  3.000
 RJR  H36  O31  C4   108.16  3.000
 RJR  H37  O32  C5   108.04  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
 RJR  CONST_01  N10  C11  C12  N8      0.00   0.0  0
 RJR  CONST_02  C11  N10  N9   N8      0.00   0.0  0
 RJR  CONST_03  C11  C12  N8   N9      0.00   0.0  0
 RJR  CONST_04  C12  C11  N10  N9      0.00   0.0  0
 RJR  CONST_05  C12  N8   N9   N10     0.00   0.0  0
 RJR  CONST_06  C11  C12  N8   C7    180.00   0.0  0
 RJR  CONST_07  N10  N9   N8   C7    180.00   0.0  0
 RJR  CONST_08  C13  C11  C12  N8    180.00   0.0  0
 RJR  CONST_09  C13  C11  N10  N9    180.00   0.0  0
 RJR  CONST_10  H10  C12  N8   N9    180.00   0.0  0
 RJR  Var_01    C12  N8   C7   C6     80.38  30.0  2
 RJR  Var_02    C14  C13  C11  N10   -45.75  30.0  2
 RJR  Var_03    C15  C14  C13  C11  -175.84  30.0  1
 RJR  Var_04    C18  C17  O16  C15  -179.98  30.0  2
 RJR  Var_05    O16  C15  C14  C13  -178.13  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
 RJR  chir_01  C1   C2   O28  C6   positiv
 RJR  chir_02  C3   O30  C2   C4   negativ
 RJR  chir_03  C4   O31  C3   C5   positiv
 RJR  chir_04  C5   O32  C4   C6   negativ
 RJR  chir_05  C6   C5   C7   C1   negativ
 RJR  chir_06  C18  C19  C17  C27  positiv
 RJR  chir_07  C20  C21  C19  C26  positiv
 RJR  chir_08  C22  C21  C23  C27  positiv
 RJR  chir_09  C24  C26  C25  C23  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 RJR  plan-1  C7   0.020
 RJR  plan-1  N8   0.020
 RJR  plan-1  N9   0.020
 RJR  plan-1  N10  0.020
 RJR  plan-1  C11  0.020
 RJR  plan-1  C12  0.020
 RJR  plan-1  C13  0.020
 RJR  plan-1  H10  0.020

