# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 01:39:18 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: "(2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol"
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)[C@@H](O)[C@H](O)[C@H]3N)[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
 JIA  JIA  "(2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol"
  ligand  72  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JIA
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
 JIA  C15  C  CH3   0  -0.686   5.5147   2.8450  -0.4908
 JIA  C16  C  CH3   0  -0.525   6.7776   0.5919   1.8198
 JIA  C17  C  CH2   0  -0.469  -0.4509  -2.5827   1.2394
 JIA  C18  C  CH1   0  -0.102  -1.4691  -1.5006   1.5693
 JIA  C19  C  CH1   0   0.058  -1.4777  -0.4545   0.4548
 JIA  C20  C  CH1   0   0.024  -0.0859   0.1598   0.3184
 JIA  C21  C  CT    0   0.150   5.0733   1.4976  -1.0504
 JIA  C22  C  CH2   0  -0.191   3.6389   1.6236  -1.5596
 JIA  C23  C  CH1   0   0.043   0.9601  -0.9227   0.0353
 JIA  C24  C  CH1   0  -0.083   5.1304   0.3853   0.0138
 JIA  C06  C  CH2   0  -0.300  -4.9262  -1.1642  -2.1969
 JIA  C07  C  CH1   0   0.201   3.0846  -0.6205  -1.0756
 JIA  C08  C  CH1   0  -0.098   0.9558  -2.0150   1.0981
 JIA  C09  C  CH1   0   0.286  -3.0724   1.2707  -0.1880
 JIA  C10  C  CH1   0  -0.144  -4.2063   2.0662   0.4608
 JIA  C11  C  CH1   0   0.025  -5.3034   1.1129   0.9135
 JIA  C12  C  CH1   0   0.071   4.4873  -0.8997  -0.5235
 JIA  C13  C  CH1   0   0.014  -5.7539   0.2333  -0.2516
 JIA  C14  C  CH1   0   0.002  -4.5616  -0.4619  -0.9027
 JIA  N01  N  NH2   0  -0.803  -3.7149   2.8520   1.5772
 JIA  N03  N  NH2   0  -0.797  -2.7845  -2.0995   1.7145
 JIA  N04  N  NH2   0  -0.818   1.9662  -3.0165   0.7791
 JIA  N05  N  NH1   0  -0.606   6.4740   0.1095   0.4903
 JIA  O25  O  OH1   0  -0.679  -6.6580  -0.7588   0.1909
 JIA  O26  O  OH1   0  -0.677  -6.3758   1.8885   1.4085
 JIA  O27  O  OH1   0  -0.717   4.4802  -1.8816   0.4735
 JIA  O28  O  O2    0  -0.524   2.2259  -0.2956  -0.0181
 JIA  O29  O  O2    0  -0.487   3.1109   0.3994  -2.0285
 JIA  O30  O  O2    0  -0.513  -3.5678   0.4998  -1.2398
 JIA  O31  O  OH1   0  -0.664  -0.1081   1.1031  -0.7248
 JIA  O32  O  O2    0  -0.524  -2.4524   0.5090   0.8115
 JIA  O33  O  OH1   0  -0.678   5.9337   1.0856  -2.1004
 JIA  H1   H  HCH3  0   0.233   4.8990   3.1488   0.3562
 JIA  H2   H  HCH3  0   0.244   6.5523   2.8138  -0.1597
 JIA  H3   H  HCH3  0   0.238   5.4341   3.6245  -1.2528
 JIA  H4   H  HCH3  0   0.192   6.6196   1.6678   1.9756
 JIA  H5   H  HCH3  0   0.221   6.1680   0.0639   2.5549
 JIA  H6   H  HCH3  0   0.226   7.8214   0.3780   2.0522
 JIA  H7   H  HCH2  0   0.252  -0.4541  -3.3440   2.0247
 JIA  H8   H  HCH2  0   0.227  -0.7470  -3.0838   0.3107
 JIA  H9   H  HCH1  0   0.205  -1.1376  -0.9977   2.4935
 JIA  H10  H  HCH1  0   0.228  -1.7506  -0.9531  -0.4853
 JIA  H11  H  HCH1  0   0.208   0.1709   0.6428   1.2745
 JIA  H12  H  HCH2  0   0.204   3.0118   2.0529  -0.7674
 JIA  H13  H  HCH2  0   0.243   3.6013   2.3172  -2.4037
 JIA  H14  H  HCH1  0   0.224   0.7186  -1.3767  -0.9387
 JIA  H15  H  HCH1  0   0.229   4.5246   0.7245   0.8632
 JIA  H16  H  HCH2  0   0.229  -5.7015  -1.8999  -1.9780
 JIA  H17  H  HCH2  0   0.191  -5.3761  -0.4295  -2.8831
 JIA  H18  H  HCH1  0   0.241   2.7099  -1.5044  -1.6061
 JIA  H19  H  HCH1  0   0.242   1.2475  -1.5622   2.0522
 JIA  H20  H  HCH1  0   0.234  -2.3607   1.9570  -0.6556
 JIA  H21  H  HCH1  0   0.219  -4.6235   2.6909  -0.3467
 JIA  H22  H  HCH1  0   0.210  -4.9022   0.4707   1.7099
 JIA  H23  H  HCH1  0   0.190   5.0850  -1.2437  -1.3808
 JIA  H24  H  HCH1  0   0.211  -6.2278   0.8828  -1.0024
 JIA  H25  H  HCH1  0   0.234  -4.1464  -1.2073  -0.2122
 JIA  H26  H  HNH2  0   0.344  -3.0394   3.5269   1.2388
 JIA  H27  H  HNH2  0   0.346  -4.4790   3.4009   1.9496
 JIA  H29  H  HNH2  0   0.347  -4.0495  -2.3550  -3.5829
 JIA  H30  H  HNH2  0   0.341  -3.0796  -1.1855  -3.0391
 JIA  H32  H  HNH2  0   0.349  -2.7492  -2.7922   2.4528
 JIA  H33  H  HNH2  0   0.353  -3.4413  -1.3980   2.0308
 JIA  H35  H  HNH2  0   0.374   2.0423  -3.6811   1.5406
 JIA  H36  H  HNH2  0   0.362   1.6805  -3.5539  -0.0329
 JIA  H38  H  HNH1  0   0.343   7.1598   0.4373  -0.1756
 JIA  H40  H  HOH1  0   0.458  -7.5558  -0.4446   0.0589
 JIA  H41  H  HOH1  0   0.452  -6.9542   1.3156   1.9206
 JIA  H42  H  HOH1  0   0.466   3.5810  -2.2852   0.5604
 JIA  H43  H  HOH1  0   0.453   0.7485   1.5412  -0.7527
 JIA  H44  H  HOH1  0   0.449   6.0473   1.8194  -2.7142
 JIA  N02  N  NH2   0  -0.797  -3.7738  -1.8599  -2.7448

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
 JIA  C16  N05  single  1.446  0.020  1.446
 JIA  N05  C24  single  1.452  0.020  1.452
 JIA  C24  C12  single  1.534  0.020  1.534
 JIA  C24  C21  single  1.540  0.020  1.540
 JIA  O33  C21  single  1.419  0.020  1.419
 JIA  C12  O27  single  1.399  0.020  1.399
 JIA  C12  C07  single  1.533  0.020  1.533
 JIA  C21  C15  single  1.524  0.020  1.524
 JIA  C21  C22  single  1.527  0.020  1.527
 JIA  O29  C07  single  1.396  0.020  1.396
 JIA  O29  C22  single  1.413  0.020  1.413
 JIA  C07  O28  single  1.400  0.020  1.400
 JIA  O28  C23  single  1.414  0.020  1.414
 JIA  N04  C08  single  1.458  0.020  1.458
 JIA  C23  C08  single  1.524  0.020  1.524
 JIA  C23  C20  single  1.532  0.020  1.532
 JIA  C08  C17  single  1.524  0.020  1.524
 JIA  O31  C20  single  1.407  0.020  1.407
 JIA  C20  C19  single  1.528  0.020  1.528
 JIA  C17  C18  single  1.522  0.020  1.522
 JIA  C19  C18  single  1.528  0.020  1.528
 JIA  C19  O32  single  1.416  0.020  1.416
 JIA  C18  N03  single  1.453  0.020  1.453
 JIA  O32  C09  single  1.401  0.020  1.401
 JIA  C09  O30  single  1.395  0.020  1.395
 JIA  C09  C10  single  1.530  0.020  1.530
 JIA  N01  C10  single  1.451  0.020  1.451
 JIA  O30  C14  single  1.423  0.020  1.423
 JIA  C10  C11  single  1.522  0.020  1.522
 JIA  C14  C06  single  1.517  0.020  1.517
 JIA  C14  C13  single  1.526  0.020  1.526
 JIA  N02  C06  single  1.453  0.020  1.453
 JIA  C11  C13  single  1.528  0.020  1.528
 JIA  C11  O26  single  1.413  0.020  1.413
 JIA  C13  O25  single  1.413  0.020  1.413
 JIA  C15  H1   single  0.970  0.020  1.090
 JIA  C15  H2   single  0.970  0.020  1.090
 JIA  C15  H3   single  0.970  0.020  1.090
 JIA  C16  H4   single  0.970  0.020  1.090
 JIA  C16  H5   single  0.970  0.020  1.090
 JIA  C16  H6   single  0.970  0.020  1.090
 JIA  C17  H7   single  0.970  0.020  1.090
 JIA  C17  H8   single  0.970  0.020  1.090
 JIA  C18  H9   single  0.970  0.020  1.090
 JIA  C19  H10  single  0.970  0.020  1.090
 JIA  C20  H11  single  0.970  0.020  1.090
 JIA  C22  H12  single  0.970  0.020  1.090
 JIA  C22  H13  single  0.970  0.020  1.090
 JIA  C23  H14  single  0.970  0.020  1.090
 JIA  C24  H15  single  0.970  0.020  1.090
 JIA  C06  H16  single  0.970  0.020  1.090
 JIA  C06  H17  single  0.970  0.020  1.090
 JIA  C07  H18  single  0.970  0.020  1.090
 JIA  C08  H19  single  0.970  0.020  1.090
 JIA  C09  H20  single  0.970  0.020  1.090
 JIA  C10  H21  single  0.970  0.020  1.090
 JIA  C11  H22  single  0.970  0.020  1.090
 JIA  C12  H23  single  0.970  0.020  1.090
 JIA  C13  H24  single  0.970  0.020  1.090
 JIA  C14  H25  single  0.970  0.020  1.090
 JIA  N01  H26  single  0.890  0.020  1.040
 JIA  N01  H27  single  0.890  0.020  1.040
 JIA  N02  H29  single  0.890  0.020  1.040
 JIA  N02  H30  single  0.890  0.020  1.040
 JIA  N03  H32  single  0.890  0.020  1.040
 JIA  N03  H33  single  0.890  0.020  1.040
 JIA  N04  H35  single  0.890  0.020  1.040
 JIA  N04  H36  single  0.890  0.020  1.040
 JIA  N05  H38  single  0.890  0.020  1.040
 JIA  O25  H40  single  0.850  0.020  0.980
 JIA  O26  H41  single  0.850  0.020  0.980
 JIA  O27  H42  single  0.850  0.020  0.980
 JIA  O31  H43  single  0.850  0.020  0.980
 JIA  O33  H44  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
 JIA  H3   C15  H2   107.61  3.000
 JIA  H3   C15  H1   107.53  3.000
 JIA  H2   C15  H1   108.04  3.000
 JIA  H3   C15  C21  110.68  3.000
 JIA  H2   C15  C21  111.22  3.000
 JIA  H1   C15  C21  111.59  3.000
 JIA  H6   C16  H5   107.23  3.000
 JIA  H6   C16  H4   107.43  3.000
 JIA  H5   C16  H4   107.34  3.000
 JIA  H6   C16  N05  109.35  3.000
 JIA  H5   C16  N05  109.91  3.000
 JIA  H4   C16  N05  115.27  3.000
 JIA  H8   C17  H7   106.82  3.000
 JIA  H8   C17  C08  109.95  3.000
 JIA  H7   C17  C08  109.19  3.000
 JIA  H8   C17  C18  109.15  3.000
 JIA  H7   C17  C18  109.71  3.000
 JIA  C08  C17  C18  111.89  3.000
 JIA  H9   C18  N03  112.11  3.000
 JIA  H9   C18  C19  107.49  3.000
 JIA  N03  C18  C19  110.49  3.000
 JIA  H9   C18  C17  107.74  3.000
 JIA  N03  C18  C17  109.53  3.000
 JIA  C19  C18  C17  109.41  3.000
 JIA  H10  C19  O32  110.69  3.000
 JIA  H10  C19  C20  109.41  3.000
 JIA  O32  C19  C20  112.08  3.000
 JIA  H10  C19  C18  108.35  3.000
 JIA  O32  C19  C18  106.61  3.000
 JIA  C20  C19  C18  109.59  3.000
 JIA  H11  C20  O31  110.69  3.000
 JIA  H11  C20  C23  108.12  3.000
 JIA  O31  C20  C23  110.35  3.000
 JIA  H11  C20  C19  108.13  3.000
 JIA  O31  C20  C19  108.76  3.000
 JIA  C23  C20  C19  110.76  3.000
 JIA  O33  C21  C24  106.21  3.000
 JIA  O33  C21  C22  110.30  3.000
 JIA  C24  C21  C22  108.95  3.000
 JIA  C22  C21  C15  108.74  3.000
 JIA  O33  C21  C15  110.66  3.000
 JIA  C24  C21  C15  111.96  3.000
 JIA  H13  C22  H12  106.82  3.000
 JIA  H13  C22  O29  106.30  3.000
 JIA  H12  C22  O29  111.39  3.000
 JIA  H13  C22  C21  110.01  3.000
 JIA  H12  C22  C21  109.16  3.000
 JIA  O29  C22  C21  112.95  3.000
 JIA  H14  C23  O28  110.24  3.000
 JIA  H14  C23  C08  108.70  3.000
 JIA  O28  C23  C08  110.29  3.000
 JIA  H14  C23  C20  107.75  3.000
 JIA  C08  C23  C20  112.07  3.000
 JIA  O28  C23  C20  107.75  3.000
 JIA  H15  C24  N05  108.40  3.000
 JIA  H15  C24  C12  107.38  3.000
 JIA  N05  C24  C12  110.10  3.000
 JIA  H15  C24  C21  106.93  3.000
 JIA  C12  C24  C21  110.32  3.000
 JIA  N05  C24  C21  113.47  3.000
 JIA  H17  C06  H16  106.54  3.000
 JIA  H17  C06  N02  114.10  3.000
 JIA  H16  C06  N02  108.44  3.000
 JIA  H17  C06  C14  108.72  3.000
 JIA  H16  C06  C14  108.17  3.000
 JIA  N02  C06  C14  110.65  3.000
 JIA  H18  C07  O29  105.38  3.000
 JIA  H18  C07  O28  110.05  3.000
 JIA  O29  C07  O28  110.95  3.000
 JIA  H18  C07  C12  109.87  3.000
 JIA  O28  C07  C12  109.35  3.000
 JIA  O29  C07  C12  111.20  3.000
 JIA  H19  C08  N04  106.85  3.000
 JIA  H19  C08  C23  108.07  3.000
 JIA  N04  C08  C23  109.74  3.000
 JIA  H19  C08  C17  108.61  3.000
 JIA  C23  C08  C17  109.54  3.000
 JIA  N04  C08  C17  113.84  3.000
 JIA  H20  C09  O32  110.99  3.000
 JIA  H20  C09  O30  104.80  3.000
 JIA  O32  C09  O30  113.24  3.000
 JIA  H20  C09  C10  109.72  3.000
 JIA  O30  C09  C10  110.12  3.000
 JIA  O32  C09  C10  107.95  3.000
 JIA  H21  C10  N01  112.63  3.000
 JIA  H21  C10  C11  107.45  3.000
 JIA  N01  C10  C11  110.76  3.000
 JIA  H21  C10  C09  105.33  3.000
 JIA  C11  C10  C09  109.55  3.000
 JIA  N01  C10  C09  110.91  3.000
 JIA  H22  C11  O26  110.12  3.000
 JIA  H22  C11  C13  108.90  3.000
 JIA  O26  C11  C13  111.06  3.000
 JIA  H22  C11  C10  108.56  3.000
 JIA  O26  C11  C10  107.90  3.000
 JIA  C13  C11  C10  110.26  3.000
 JIA  H23  C12  O27  109.79  3.000
 JIA  H23  C12  C07  105.87  3.000
 JIA  O27  C12  C07  112.31  3.000
 JIA  H23  C12  C24  107.88  3.000
 JIA  C07  C12  C24  110.93  3.000
 JIA  O27  C12  C24  109.90  3.000
 JIA  H24  C13  O25  110.64  3.000
 JIA  H24  C13  C14  108.32  3.000
 JIA  O25  C13  C14  108.27  3.000
 JIA  H24  C13  C11  107.92  3.000
 JIA  O25  C13  C11  110.73  3.000
 JIA  C14  C13  C11  110.93  3.000
 JIA  H25  C14  O30  110.10  3.000
 JIA  H25  C14  C13  109.66  3.000
 JIA  O30  C14  C13  109.80  3.000
 JIA  H25  C14  C06  108.26  3.000
 JIA  C13  C14  C06  112.78  3.000
 JIA  O30  C14  C06  106.17  3.000
 JIA  H27  N01  H26  105.37  3.000
 JIA  H27  N01  C10  108.73  3.000
 JIA  H26  N01  C10  109.24  3.000
 JIA  H33  N03  H32  105.60  3.000
 JIA  H33  N03  C18  109.47  3.000
 JIA  H32  N03  C18  108.86  3.000
 JIA  H36  N04  H35  105.96  3.000
 JIA  H36  N04  C08  110.10  3.000
 JIA  H35  N04  C08  109.76  3.000
 JIA  H38  N05  C24  110.49  3.000
 JIA  H38  N05  C16  110.80  3.000
 JIA  C24  N05  C16  115.62  3.000
 JIA  H40  O25  C13  108.99  3.000
 JIA  H41  O26  C11  108.42  3.000
 JIA  H42  O27  C12  110.70  3.000
 JIA  C07  O28  C23  118.33  3.000
 JIA  C07  O29  C22  114.42  3.000
 JIA  C14  O30  C09  116.28  3.000
 JIA  H43  O31  C20  108.22  3.000
 JIA  C09  O32  C19  119.65  3.000
 JIA  H44  O33  C21  108.78  3.000
 JIA  H30  N02  H29  105.80  3.000
 JIA  H30  N02  C06  109.56  3.000
 JIA  H29  N02  C06  109.30  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
 JIA  Var_01  H12  C22  O29  C07  -64.24  30.0  1
 JIA  Var_02  H4   C16  N05  C24  -55.90  30.0  3
 JIA  Var_03  H29  N02  C06  C14  177.42  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
 JIA  chir_01  C18  C17  C19  N03  negativ
 JIA  chir_02  C19  O32  C20  C18  negativ
 JIA  chir_03  C20  O31  C19  C23  negativ
 JIA  chir_04  C21  C24  C15  C22  positiv
 JIA  chir_05  C23  O28  C08  C20  negativ
 JIA  chir_06  C24  N05  C12  C21  positiv
 JIA  chir_07  C07  O29  O28  C12  positiv
 JIA  chir_08  C08  N04  C23  C17  negativ
 JIA  chir_09  C09  O30  O32  C10  positiv
 JIA  chir_10  C10  N01  C11  C09  positiv
 JIA  chir_11  C11  O26  C10  C13  positiv
 JIA  chir_12  C12  O27  C24  C07  positiv
 JIA  chir_13  C13  O25  C11  C14  negativ
 JIA  chir_14  C14  O30  C13  C06  negativ

