# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 20:11:40 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: methyl (5R)-5-[(1R,2R)-2-hydroxy-1-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}propyl]-1-thio-beta-L-arabinopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H]1C[C@H](N(C)C1)C(=O)N[C@H]([C@@H](C)O)[C@H]2O[C@H](SC)[C@H](O)[C@@H](O)[C@H]2O
#
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
 3QB  3QB  'methyl (5R)-5-[(1R,2R)-2-hydroxy-1-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}propyl]-1-thio-beta-L-arabinopyranoside'  ligand  61  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3QB
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
 3QB  C4   C  CH1   0   0.021  -1.9417   0.0248  -0.1646
 3QB  C14  C  CH2   0  -0.254   4.9820  -1.3123   0.1434
 3QB  C5   C  CH1   0  -0.148  -4.2561   0.5283  -0.0903
 3QB  C6   C  CH3   0  -0.749  -4.3164   3.1164   0.8320
 3QB  C11  C  CH1   0  -0.172   2.7451  -0.7678   0.0090
 3QB  C7   C  CH1   0  -0.188  -0.7023   0.3741  -0.9887
 3QB  C8   C  CH1   0   0.098  -0.5487   1.8885  -1.2397
 3QB  C9   C  CH3   0  -0.703  -0.4399   2.7017   0.0361
 3QB  C12  C  CH2   0  -0.455   3.5046   0.5699   0.1728
 3QB  C13  C  CH1   0  -0.234   4.9893   0.2056  -0.0035
 3QB  N1   N  NH1   0  -0.638   0.4546  -0.1564  -0.3090
 3QB  N2   N  NT    0  -0.417   3.7328  -1.6958  -0.4798
 3QB  C3   C  CH1   0   0.039  -2.1699  -1.4752  -0.0290
 3QB  C18  C  CH3   0  -0.647   8.2968   1.3818   1.7030
 3QB  C16  C  CH2   0  -0.414   5.9153   0.9337   0.9584
 3QB  C15  C  CH3   0  -0.523   3.3716  -3.0797  -0.3112
 3QB  O8   O  OH1   0  -0.647   0.6249   2.1557  -1.9771
 3QB  O5   O  O2    0  -0.458  -3.0459   0.6567  -0.7738
 3QB  O7   O  OH1   0  -0.639  -2.2435  -2.0451  -1.3057
 3QB  C2   C  CH1   0   0.010  -3.4528  -1.6964   0.7656
 3QB  O6   O  OH1   0  -0.652  -3.6866  -3.0816   0.8078
 3QB  C1   C  CH1   0   0.013  -4.6097  -0.9512   0.1163
 3QB  O4   O  OH1   0  -0.632  -5.7326  -1.1450   0.9343
 3QB  S1   S  S2    0  -0.005  -4.2938   1.4342   1.4945
 3QB  H1   H  HCH1  0   0.222  -1.8085   0.4138   0.8579
 3QB  H2   H  HCH2  0   0.228   5.8263  -1.8017  -0.3480
 3QB  H3   H  HCH2  0   0.184   5.0222  -1.5925   1.2129
 3QB  H4   H  HCH1  0   0.260  -5.0044   0.9927  -0.7395
 3QB  H5   H  HCH3  0   0.259  -3.5111   3.2800   0.1193
 3QB  H6   H  HCH3  0   0.253  -5.2711   3.3372   0.3572
 3QB  H7   H  HCH3  0   0.264  -4.1818   3.7998   1.6674
 3QB  H8   H  HCH1  0   0.209   2.3680  -1.0839   1.0002
 3QB  H9   H  HCH1  0   0.290  -0.7747  -0.1335  -1.9542
 3QB  H10  H  HCH1  0   0.212  -1.4349   2.2212  -1.7936
 3QB  H11  H  HCH3  0   0.212   0.4451   2.4269   0.6130
 3QB  H12  H  HCH3  0   0.240  -0.3579   3.7637  -0.1973
 3QB  H13  H  HCH3  0   0.239  -1.3131   2.5806   0.6768
 3QB  H14  H  HCH2  0   0.262   3.1782   1.3193  -0.5493
 3QB  H15  H  HCH2  0   0.223   3.3167   0.9826   1.1656
 3QB  H16  H  HCH1  0   0.227   5.2914   0.4458  -1.0282
 3QB  H17  H  HNH1  0   0.361   0.5307   0.0375   0.6770
 3QB  H19  H  HCH1  0   0.217  -1.3349  -1.8929   0.5526
 3QB  H20  H  HCH3  0   0.211   8.1854   2.4546   1.5356
 3QB  H21  H  HCH3  0   0.214   8.0660   1.1884   2.7518
 3QB  H22  H  HCH3  0   0.223   9.3465   1.1323   1.5474
 3QB  H23  H  HCH2  0   0.208   7.6784   0.7558  -0.2609
 3QB  H24  H  HCH2  0   0.216   7.5370  -0.4855   0.9617
 3QB  H25  H  HCH2  0   0.217   5.7860   2.0136   0.8286
 3QB  H26  H  HCH2  0   0.205   5.6096   0.7152   1.9884
 3QB  H27  H  HCH3  0   0.246   2.4590  -3.3047  -0.8638
 3QB  H28  H  HCH3  0   0.220   4.1605  -3.7241  -0.7029
 3QB  H29  H  HCH3  0   0.188   3.2090  -3.3587   0.7422
 3QB  H30  H  HOH1  0   0.434   0.6842   1.5460  -2.7189
 3QB  H31  H  HOH1  0   0.435  -2.5165  -2.9616  -1.2030
 3QB  H32  H  HCH1  0   0.212  -3.2999  -1.2927   1.7789
 3QB  H33  H  HOH1  0   0.438  -4.5514  -3.2318   1.2004
 3QB  H34  H  HCH1  0   0.234  -4.7690  -1.3724  -0.8869
 3QB  H35  H  HOH1  0   0.432  -6.4969  -0.7154   0.5423
 3QB  C10  C  C     0   0.545   1.5673  -0.6027  -0.9392
 3QB  C17  C  CH2   0  -0.421   7.3878   0.5828   0.7801
 3QB  O9   O  O     0  -0.428   1.6409  -0.8094  -2.1315

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
 3QB  C6   S1   single  1.808  0.020  1.808
 3QB  S1   C5   single  1.826  0.020  1.826
 3QB  O8   C8   single  1.412  0.020  1.412
 3QB  O4   C1   single  1.403  0.020  1.403
 3QB  C5   O5   single  1.396  0.020  1.396
 3QB  C5   C1   single  1.535  0.020  1.535
 3QB  O5   C4   single  1.411  0.020  1.411
 3QB  C1   C2   single  1.522  0.020  1.522
 3QB  C8   C9   single  1.517  0.020  1.517
 3QB  C8   C7   single  1.543  0.020  1.543
 3QB  C4   C3   single  1.523  0.020  1.523
 3QB  C4   C7   single  1.529  0.020  1.529
 3QB  C2   C3   single  1.525  0.020  1.525
 3QB  C2   O6   single  1.405  0.020  1.405
 3QB  C3   O7   single  1.400  0.020  1.400
 3QB  C7   N1   single  1.443  0.020  1.443
 3QB  N1   C10  single  1.354  0.020  1.354
 3QB  C10  C11  single  1.521  0.020  1.521
 3QB  C10  O9   double  1.212  0.020  1.212
 3QB  C11  C12  single  1.547  0.020  1.547
 3QB  C11  N2   single  1.441  0.020  1.441
 3QB  C18  C17  single  1.522  0.020  1.522
 3QB  C15  N2   single  1.440  0.020  1.440
 3QB  C12  C13  single  1.539  0.020  1.539
 3QB  N2   C14  single  1.448  0.020  1.448
 3QB  C16  C13  single  1.521  0.020  1.521
 3QB  C16  C17  single  1.524  0.020  1.524
 3QB  C14  C13  single  1.525  0.020  1.525
 3QB  C4   H1   single  0.970  0.020  1.090
 3QB  C14  H2   single  0.970  0.020  1.090
 3QB  C14  H3   single  0.970  0.020  1.090
 3QB  C5   H4   single  0.970  0.020  1.090
 3QB  C6   H5   single  0.970  0.020  1.090
 3QB  C6   H6   single  0.970  0.020  1.090
 3QB  C6   H7   single  0.970  0.020  1.090
 3QB  C11  H8   single  0.970  0.020  1.090
 3QB  C7   H9   single  0.970  0.020  1.090
 3QB  C8   H10  single  0.970  0.020  1.090
 3QB  C9   H11  single  0.970  0.020  1.090
 3QB  C9   H12  single  0.970  0.020  1.090
 3QB  C9   H13  single  0.970  0.020  1.090
 3QB  C12  H14  single  0.970  0.020  1.090
 3QB  C12  H15  single  0.970  0.020  1.090
 3QB  C13  H16  single  0.970  0.020  1.090
 3QB  N1   H17  single  0.860  0.020  1.020
 3QB  C3   H19  single  0.970  0.020  1.090
 3QB  C18  H20  single  0.970  0.020  1.090
 3QB  C18  H21  single  0.970  0.020  1.090
 3QB  C18  H22  single  0.970  0.020  1.090
 3QB  C17  H23  single  0.970  0.020  1.090
 3QB  C17  H24  single  0.970  0.020  1.090
 3QB  C16  H25  single  0.970  0.020  1.090
 3QB  C16  H26  single  0.970  0.020  1.090
 3QB  C15  H27  single  0.970  0.020  1.090
 3QB  C15  H28  single  0.970  0.020  1.090
 3QB  C15  H29  single  0.970  0.020  1.090
 3QB  O8   H30  single  0.850  0.020  0.980
 3QB  O7   H31  single  0.850  0.020  0.980
 3QB  C2   H32  single  0.970  0.020  1.090
 3QB  O6   H33  single  0.850  0.020  0.980
 3QB  C1   H34  single  0.970  0.020  1.090
 3QB  O4   H35  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
 3QB  H1   C4   O5   109.71  3.000
 3QB  H1   C4   C3   106.44  3.000
 3QB  O5   C4   C3   111.24  3.000
 3QB  H1   C4   C7   108.75  3.000
 3QB  C3   C4   C7   113.23  3.000
 3QB  O5   C4   C7   107.42  3.000
 3QB  H3   C14  H2   107.05  3.000
 3QB  H3   C14  N2   112.36  3.000
 3QB  H2   C14  N2   110.77  3.000
 3QB  H3   C14  C13  110.19  3.000
 3QB  H2   C14  C13  113.50  3.000
 3QB  N2   C14  C13  103.08  3.000
 3QB  H4   C5   S1   106.88  3.000
 3QB  H4   C5   C1   109.35  3.000
 3QB  S1   C5   C1   110.89  3.000
 3QB  H4   C5   O5   105.27  3.000
 3QB  C1   C5   O5   110.75  3.000
 3QB  S1   C5   O5   113.41  3.000
 3QB  H7   C6   H6   108.42  3.000
 3QB  H7   C6   H5   108.49  3.000
 3QB  H6   C6   H5   109.44  3.000
 3QB  H7   C6   S1   107.55  3.000
 3QB  H6   C6   S1   111.07  3.000
 3QB  H5   C6   S1   111.76  3.000
 3QB  H8   C11  N2   110.70  3.000
 3QB  H8   C11  C12  108.63  3.000
 3QB  N2   C11  C12  104.85  3.000
 3QB  H8   C11  C10  109.00  3.000
 3QB  N2   C11  C10  112.91  3.000
 3QB  C12  C11  C10  110.63  3.000
 3QB  H9   C7   N1   107.37  3.000
 3QB  H9   C7   C8   108.58  3.000
 3QB  N1   C7   C8   110.96  3.000
 3QB  H9   C7   C4   108.44  3.000
 3QB  N1   C7   C4   108.18  3.000
 3QB  C8   C7   C4   113.12  3.000
 3QB  H10  C8   O8   110.52  3.000
 3QB  H10  C8   C9   108.67  3.000
 3QB  O8   C8   C9   106.16  3.000
 3QB  H10  C8   C7   107.43  3.000
 3QB  C9   C8   C7   113.36  3.000
 3QB  O8   C8   C7   110.71  3.000
 3QB  H13  C9   H12  107.12  3.000
 3QB  H13  C9   H11  108.12  3.000
 3QB  H12  C9   H11  107.30  3.000
 3QB  H13  C9   C8   112.18  3.000
 3QB  H12  C9   C8   110.33  3.000
 3QB  H11  C9   C8   111.57  3.000
 3QB  H15  C12  H14  106.91  3.000
 3QB  H15  C12  C13  111.09  3.000
 3QB  H14  C12  C13  112.06  3.000
 3QB  H15  C12  C11  109.80  3.000
 3QB  H14  C12  C11  112.16  3.000
 3QB  C13  C12  C11  104.88  3.000
 3QB  H16  C13  C16  108.60  3.000
 3QB  H16  C13  C12  108.75  3.000
 3QB  C16  C13  C12  113.68  3.000
 3QB  H16  C13  C14  108.05  3.000
 3QB  C16  C13  C14  114.74  3.000
 3QB  C12  C13  C14  102.70  3.000
 3QB  H17  N1   C10  117.17  3.000
 3QB  H17  N1   C7   116.79  3.000
 3QB  C10  N1   C7   124.10  3.000
 3QB  C15  N2   C11  114.04  3.000
 3QB  C15  N2   C14  114.87  3.000
 3QB  C11  N2   C14  105.95  3.000
 3QB  H19  C3   C2   107.94  3.000
 3QB  H19  C3   O7   111.56  3.000
 3QB  C2   C3   O7   111.83  3.000
 3QB  H19  C3   C4   107.89  3.000
 3QB  O7   C3   C4   109.11  3.000
 3QB  C2   C3   C4   108.37  3.000
 3QB  H22  C18  H21  107.48  3.000
 3QB  H22  C18  H20  107.54  3.000
 3QB  H21  C18  H20  107.46  3.000
 3QB  H22  C18  C17  111.61  3.000
 3QB  H21  C18  C17  111.31  3.000
 3QB  H20  C18  C17  111.22  3.000
 3QB  H26  C16  H25  105.96  3.000
 3QB  H26  C16  C17  109.48  3.000
 3QB  H25  C16  C17  109.09  3.000
 3QB  H26  C16  C13  109.21  3.000
 3QB  H25  C16  C13  108.97  3.000
 3QB  C17  C16  C13  113.83  3.000
 3QB  H29  C15  H28  107.48  3.000
 3QB  H29  C15  H27  107.98  3.000
 3QB  H28  C15  H27  107.53  3.000
 3QB  H29  C15  N2   113.10  3.000
 3QB  H28  C15  N2   110.13  3.000
 3QB  H27  C15  N2   110.42  3.000
 3QB  H30  O8   C8   109.51  3.000
 3QB  C5   O5   C4   115.22  3.000
 3QB  H31  O7   C3   107.78  3.000
 3QB  H32  C2   C1   108.57  3.000
 3QB  H32  C2   O6   110.90  3.000
 3QB  C1   C2   O6   111.66  3.000
 3QB  H32  C2   C3   108.02  3.000
 3QB  O6   C2   C3   107.37  3.000
 3QB  C1   C2   C3   110.26  3.000
 3QB  H33  O6   C2   108.41  3.000
 3QB  H34  C1   O4   111.29  3.000
 3QB  H34  C1   C2   108.17  3.000
 3QB  O4   C1   C2   106.99  3.000
 3QB  H34  C1   C5   106.25  3.000
 3QB  C2   C1   C5   110.75  3.000
 3QB  O4   C1   C5   113.33  3.000
 3QB  H35  O4   C1   109.71  3.000
 3QB  C6   S1   C5    98.27  3.000
 3QB  O9   C10  N1   124.31  3.000
 3QB  O9   C10  C11  123.20  3.000
 3QB  N1   C10  C11  112.45  3.000
 3QB  H24  C17  H23  106.02  3.000
 3QB  H24  C17  C16  109.71  3.000
 3QB  H23  C17  C16  109.35  3.000
 3QB  H24  C17  C18  109.31  3.000
 3QB  H23  C17  C18  109.59  3.000
 3QB  C16  C17  C18  112.66  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
 3QB  CONST_01  C7   N1   C10  C11   180.00   0.0  0
 3QB  CONST_02  H17  N1   C10  C11     0.00   0.0  0
 3QB  CONST_03  O9   C10  N1   C7      0.00   0.0  0
 3QB  Var_01    C13  C14  N2   C11   -44.56  30.0  1
 3QB  Var_02    H27  C15  N2   C14  -176.12  30.0  3
 3QB  Var_03    C18  C17  C16  C13   176.86  30.0  3
 3QB  Var_04    H5   C6   S1   C5    -52.25  30.0  3
 3QB  Var_05    H20  C18  C17  C16   -58.74  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
 3QB  chir_01  C4   O5   C3   C7   negativ
 3QB  chir_02  C5   S1   O5   C1   negativ
 3QB  chir_03  C11  N2   C10  C12  positiv
 3QB  chir_04  C7   N1   C8   C4   positiv
 3QB  chir_05  C8   O8   C7   C9   negativ
 3QB  chir_06  C13  C12  C16  C14  negativ
 3QB  chir_07  C3   C4   C2   O7   negativ
 3QB  chir_08  C2   O6   C3   C1   negativ
 3QB  chir_09  C1   O4   C2   C5   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
 3QB  plan-1  C11  0.020
 3QB  plan-1  C7   0.020
 3QB  plan-1  N1   0.020
 3QB  plan-1  H17  0.020
 3QB  plan-1  C10  0.020
 3QB  plan-1  O9   0.020

