# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:41:34 2022
#   Inital geometry file: a 158 line input string
#   Ligand name: (1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1C[C@H](O)[C@@H](CN)O[C@@H]1O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[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
 R7Y  R7Y  '(1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside'  ligand  74  35  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R7Y
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
 R7Y  C01  C  CH3   0  -0.779  -13.2638  10.6300  20.7595
 R7Y  C02  C  C     0   0.515  -11.8762  11.1648  21.0136
 R7Y  C05  C  CH1   0  -0.135  -10.1264  12.6674  20.1298
 R7Y  C06  C  CH2   0  -0.494  -10.2716  14.1802  20.2486
 R7Y  C07  C  CH1   0   0.059   -8.8945  14.8349  20.2760
 R7Y  C09  C  CH1   0   0.018   -8.1060  14.4099  19.0428
 R7Y  C10  C  CH2   0  -0.304   -6.6738  14.9109  19.0369
 R7Y  C13  C  CH1   0   0.284   -9.2513  12.2996  18.9293
 R7Y  C15  C  CH1   0   0.039   -9.6325  11.7800  16.6208
 R7Y  C16  C  CH1   0  -0.121   -9.5668  12.6709  15.3772
 R7Y  C18  C  CH2   0  -0.453   -9.2520  11.7935  14.1724
 R7Y  C19  C  CH1   0  -0.089  -10.2663  10.6761  13.9763
 R7Y  C21  C  CH1   0   0.059  -10.3480   9.8124  15.2323
 R7Y  C23  C  CH1   0   0.254  -10.9598   7.5152  14.8988
 R7Y  C25  C  CH1   0  -0.003  -11.8742   6.7166  16.9424
 R7Y  C26  C  CH2   0  -0.203  -11.4209   6.1153  18.2550
 R7Y  C28  C  CH1   0   0.048  -12.9453   5.8980  16.2169
 R7Y  C30  C  CH1   0  -0.138  -13.3083   6.5850  14.9065
 R7Y  C32  C  CH1   0   0.017  -12.0302   6.7803  14.0940
 R7Y  C34  C  CH1   0   0.019  -10.6708  10.6644  16.4542
 R7Y  N04  N  NH1   0  -0.644  -11.4046  12.0008  20.0598
 R7Y  N11  N  NH2   0  -0.797   -5.9942  14.5299  17.8087
 R7Y  N17  N  NH2   0  -0.794   -8.6122  13.7601  15.4479
 R7Y  N20  N  NH2   0  -0.817   -9.8755   9.8552  12.8406
 R7Y  N31  N  NH2   0  -0.809  -14.2346   5.7564  14.1518
 R7Y  O03  O  O     0  -0.483  -11.2266  10.8337  21.9927
 R7Y  O08  O  OH1   0  -0.668   -8.9772  16.2402  20.2622
 R7Y  O12  O  O2    0  -0.503   -8.0393  12.9910  18.9764
 R7Y  O14  O  O2    0  -0.524   -9.9691  12.5581  17.7602
 R7Y  O22  O  O2    0  -0.514  -11.3623   8.8375  15.0665
 R7Y  O24  O  O2    0  -0.502  -10.7308   6.8597  16.1109
 R7Y  O27  O  OH1   0  -0.668  -10.9747   4.7943  18.0565
 R7Y  O29  O  OH1   0  -0.673  -14.1172   5.7900  16.9960
 R7Y  O33  O  OH1   0  -0.665  -12.2741   7.4938  12.9008
 R7Y  O35  O  OH1   0  -0.660  -10.7033   9.8226  17.5811
 R7Y  H1   H  HCH3  0   0.265  -13.8676  10.7354  21.6597
 R7Y  H2   H  HCH3  0   0.250  -13.7774  11.1191  19.9340
 R7Y  H3   H  HCH3  0   0.269  -13.1979   9.5645  20.5349
 R7Y  H4   H  HCH1  0   0.273   -9.6150  12.2923  21.0178
 R7Y  H5   H  HCH2  0   0.255  -10.8221  14.4211  21.1621
 R7Y  H6   H  HCH2  0   0.237  -10.8459  14.5779  19.4058
 R7Y  H7   H  HCH1  0   0.202   -8.3571  14.4804  21.1699
 R7Y  H8   H  HCH1  0   0.211   -8.6184  14.8103  18.1582
 R7Y  H9   H  HCH2  0   0.196   -6.1727  14.5603  19.9516
 R7Y  H10  H  HCH2  0   0.234   -6.6963  15.9997  19.0909
 R7Y  H11  H  HCH1  0   0.240   -8.9741  11.2418  18.9900
 R7Y  H12  H  HCH1  0   0.217   -8.6406  11.3228  16.7585
 R7Y  H13  H  HCH1  0   0.226  -10.5566  13.1180  15.2253
 R7Y  H14  H  HCH2  0   0.222   -8.2513  11.3586  14.2844
 R7Y  H15  H  HCH2  0   0.245   -9.2239  12.4186  13.2767
 R7Y  H16  H  HCH1  0   0.202  -11.2560  11.1428  13.8368
 R7Y  H17  H  HCH1  0   0.219   -9.3713   9.3300  15.3851
 R7Y  H18  H  HCH1  0   0.232  -10.0045   7.4684  14.3622
 R7Y  H19  H  HCH1  0   0.223  -12.2938   7.7004  17.1857
 R7Y  H20  H  HCH2  0   0.214  -10.6322   6.7559  18.6709
 R7Y  H21  H  HCH2  0   0.203  -12.2620   6.1634  18.9577
 R7Y  H22  H  HCH1  0   0.212  -12.5446   4.9045  15.9755
 R7Y  H23  H  HCH1  0   0.211  -13.7246   7.5770  15.1476
 R7Y  H24  H  HCH1  0   0.228  -11.6256   5.7845  13.8705
 R7Y  H25  H  HCH1  0   0.210  -11.6534  11.1361  16.2953
 R7Y  H26  H  HNH1  0   0.402  -12.0437  12.3135  19.3446
 R7Y  H27  H  HNH2  0   0.350   -5.0944  14.9901  17.7683
 R7Y  H28  H  HNH2  0   0.342   -5.7972  13.5380  17.8204
 R7Y  H30  H  HNH2  0   0.357   -8.8927  14.4256  16.1552
 R7Y  H31  H  HNH2  0   0.333   -7.7024  13.4172  15.7359
 R7Y  H33  H  HNH2  0   0.348  -10.6182   9.2029  12.6184
 R7Y  H34  H  HNH2  0   0.344   -9.7766  10.4458  12.0237
 R7Y  H36  H  HNH2  0   0.345  -15.0711   5.6095  14.7025
 R7Y  H37  H  HNH2  0   0.342  -14.5407   6.2595  13.3282
 R7Y  H39  H  HOH1  0   0.452   -9.4317  16.5256  21.0611
 R7Y  H40  H  HOH1  0   0.455  -10.7471   4.4226  18.9131
 R7Y  H41  H  HOH1  0   0.455  -14.0108   5.0617  17.6147
 R7Y  H42  H  HOH1  0   0.458  -12.3876   6.8656  12.1824
 R7Y  H43  H  HOH1  0   0.449  -11.1688  10.2767  18.2905

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
 R7Y  N20  C19  single  1.455  0.020  1.455
 R7Y  O33  C32  single  1.411  0.020  1.411
 R7Y  C32  C23  single  1.528  0.020  1.528
 R7Y  C32  C30  single  1.527  0.020  1.527
 R7Y  N31  C30  single  1.454  0.020  1.454
 R7Y  C19  C18  single  1.522  0.020  1.522
 R7Y  C19  C21  single  1.526  0.020  1.526
 R7Y  C18  C16  single  1.523  0.020  1.523
 R7Y  C23  O22  single  1.392  0.020  1.392
 R7Y  C23  O24  single  1.397  0.020  1.397
 R7Y  C30  C28  single  1.523  0.020  1.523
 R7Y  O22  C21  single  1.417  0.020  1.417
 R7Y  C21  C34  single  1.524  0.020  1.524
 R7Y  C16  N17  single  1.450  0.020  1.450
 R7Y  C16  C15  single  1.531  0.020  1.531
 R7Y  O24  C25  single  1.421  0.020  1.421
 R7Y  C28  C25  single  1.531  0.020  1.531
 R7Y  C28  O29  single  1.411  0.020  1.411
 R7Y  C34  C15  single  1.533  0.020  1.533
 R7Y  C34  O35  single  1.407  0.020  1.407
 R7Y  C25  C26  single  1.513  0.020  1.513
 R7Y  C15  O14  single  1.420  0.020  1.420
 R7Y  O27  C26  single  1.408  0.020  1.408
 R7Y  O14  C13  single  1.396  0.020  1.396
 R7Y  N11  C10  single  1.455  0.020  1.455
 R7Y  C09  O12  single  1.422  0.020  1.422
 R7Y  C09  C10  single  1.517  0.020  1.517
 R7Y  C09  C07  single  1.524  0.020  1.524
 R7Y  C13  O12  single  1.396  0.020  1.396
 R7Y  C13  C05  single  1.530  0.020  1.530
 R7Y  O08  C07  single  1.408  0.020  1.408
 R7Y  C06  C07  single  1.525  0.020  1.525
 R7Y  C06  C05  single  1.524  0.020  1.524
 R7Y  C05  N04  single  1.443  0.020  1.443
 R7Y  N04  C02  single  1.353  0.020  1.353
 R7Y  C02  C01  single  1.509  0.020  1.509
 R7Y  C02  O03  double  1.221  0.020  1.221
 R7Y  C01  H1   single  0.970  0.020  1.090
 R7Y  C01  H2   single  0.970  0.020  1.090
 R7Y  C01  H3   single  0.970  0.020  1.090
 R7Y  C05  H4   single  0.970  0.020  1.090
 R7Y  C06  H5   single  0.970  0.020  1.090
 R7Y  C06  H6   single  0.970  0.020  1.090
 R7Y  C07  H7   single  0.970  0.020  1.090
 R7Y  C09  H8   single  0.970  0.020  1.090
 R7Y  C10  H9   single  0.970  0.020  1.090
 R7Y  C10  H10  single  0.970  0.020  1.090
 R7Y  C13  H11  single  0.970  0.020  1.090
 R7Y  C15  H12  single  0.970  0.020  1.090
 R7Y  C16  H13  single  0.970  0.020  1.090
 R7Y  C18  H14  single  0.970  0.020  1.090
 R7Y  C18  H15  single  0.970  0.020  1.090
 R7Y  C19  H16  single  0.970  0.020  1.090
 R7Y  C21  H17  single  0.970  0.020  1.090
 R7Y  C23  H18  single  0.970  0.020  1.090
 R7Y  C25  H19  single  0.970  0.020  1.090
 R7Y  C26  H20  single  0.970  0.020  1.090
 R7Y  C26  H21  single  0.970  0.020  1.090
 R7Y  C28  H22  single  0.970  0.020  1.090
 R7Y  C30  H23  single  0.970  0.020  1.090
 R7Y  C32  H24  single  0.970  0.020  1.090
 R7Y  C34  H25  single  0.970  0.020  1.090
 R7Y  N04  H26  single  0.860  0.020  1.020
 R7Y  N11  H27  single  0.890  0.020  1.040
 R7Y  N11  H28  single  0.890  0.020  1.040
 R7Y  N17  H30  single  0.890  0.020  1.040
 R7Y  N17  H31  single  0.890  0.020  1.040
 R7Y  N20  H33  single  0.890  0.020  1.040
 R7Y  N20  H34  single  0.890  0.020  1.040
 R7Y  N31  H36  single  0.890  0.020  1.040
 R7Y  N31  H37  single  0.890  0.020  1.040
 R7Y  O08  H39  single  0.850  0.020  0.980
 R7Y  O27  H40  single  0.850  0.020  0.980
 R7Y  O29  H41  single  0.850  0.020  0.980
 R7Y  O33  H42  single  0.850  0.020  0.980
 R7Y  O35  H43  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
 R7Y  H3   C01  H2   108.13  3.000
 R7Y  H3   C01  H1   107.35  3.000
 R7Y  H2   C01  H1   108.77  3.000
 R7Y  H3   C01  C02  108.98  3.000
 R7Y  H2   C01  C02  113.74  3.000
 R7Y  H1   C01  C02  109.66  3.000
 R7Y  O03  C02  N04  123.19  3.000
 R7Y  O03  C02  C01  121.90  3.000
 R7Y  N04  C02  C01  114.89  3.000
 R7Y  H4   C05  N04  107.21  3.000
 R7Y  H4   C05  C13  106.72  3.000
 R7Y  N04  C05  C13  110.94  3.000
 R7Y  H4   C05  C06  108.81  3.000
 R7Y  N04  C05  C06  112.20  3.000
 R7Y  C13  C05  C06  110.73  3.000
 R7Y  H6   C06  H5   107.40  3.000
 R7Y  H6   C06  C07  109.37  3.000
 R7Y  H5   C06  C07  110.18  3.000
 R7Y  H6   C06  C05  110.52  3.000
 R7Y  H5   C06  C05  109.37  3.000
 R7Y  C07  C06  C05  109.97  3.000
 R7Y  H7   C07  O08  110.97  3.000
 R7Y  H7   C07  C09  108.32  3.000
 R7Y  O08  C07  C09  107.51  3.000
 R7Y  H7   C07  C06  108.48  3.000
 R7Y  O08  C07  C06  112.04  3.000
 R7Y  C09  C07  C06  109.44  3.000
 R7Y  H8   C09  O12  110.38  3.000
 R7Y  H8   C09  C10  108.48  3.000
 R7Y  O12  C09  C10  106.56  3.000
 R7Y  H8   C09  C07  107.98  3.000
 R7Y  C10  C09  C07  113.54  3.000
 R7Y  O12  C09  C07  109.89  3.000
 R7Y  H10  C10  H9   106.65  3.000
 R7Y  H10  C10  N11  108.24  3.000
 R7Y  H9   C10  N11  113.93  3.000
 R7Y  H10  C10  C09  108.06  3.000
 R7Y  H9   C10  C09  108.75  3.000
 R7Y  N11  C10  C09  110.97  3.000
 R7Y  H11  C13  O14  110.82  3.000
 R7Y  H11  C13  O12  104.87  3.000
 R7Y  O14  C13  O12  112.51  3.000
 R7Y  H11  C13  C05  109.47  3.000
 R7Y  O12  C13  C05  110.55  3.000
 R7Y  O14  C13  C05  108.57  3.000
 R7Y  H12  C15  O14  109.92  3.000
 R7Y  H12  C15  C34  108.76  3.000
 R7Y  O14  C15  C34  108.99  3.000
 R7Y  H12  C15  C16  107.73  3.000
 R7Y  O14  C15  C16  110.06  3.000
 R7Y  C34  C15  C16  111.36  3.000
 R7Y  H13  C16  N17  107.14  3.000
 R7Y  H13  C16  C18  108.17  3.000
 R7Y  N17  C16  C18  109.59  3.000
 R7Y  H13  C16  C15  108.11  3.000
 R7Y  N17  C16  C15  115.19  3.000
 R7Y  C18  C16  C15  108.43  3.000
 R7Y  H15  C18  H14  106.68  3.000
 R7Y  H15  C18  C19  109.36  3.000
 R7Y  H14  C18  C19  109.27  3.000
 R7Y  H15  C18  C16  108.92  3.000
 R7Y  H14  C18  C16  109.64  3.000
 R7Y  C19  C18  C16  112.78  3.000
 R7Y  H16  C19  N20  112.40  3.000
 R7Y  H16  C19  C21  107.18  3.000
 R7Y  N20  C19  C21  109.72  3.000
 R7Y  H16  C19  C18  107.68  3.000
 R7Y  C21  C19  C18  110.18  3.000
 R7Y  N20  C19  C18  109.63  3.000
 R7Y  H17  C21  O22  110.50  3.000
 R7Y  H17  C21  C34  108.77  3.000
 R7Y  O22  C21  C34  109.08  3.000
 R7Y  H17  C21  C19  108.36  3.000
 R7Y  C34  C21  C19  110.78  3.000
 R7Y  O22  C21  C19  109.35  3.000
 R7Y  H18  C23  O24  105.18  3.000
 R7Y  H18  C23  O22  110.56  3.000
 R7Y  O24  C23  O22  112.86  3.000
 R7Y  H18  C23  C32  109.39  3.000
 R7Y  O24  C23  C32  110.26  3.000
 R7Y  O22  C23  C32  108.52  3.000
 R7Y  H19  C25  O24  110.32  3.000
 R7Y  H19  C25  C28  108.49  3.000
 R7Y  O24  C25  C28  109.84  3.000
 R7Y  H19  C25  C26  106.18  3.000
 R7Y  C28  C25  C26  114.09  3.000
 R7Y  O24  C25  C26  107.85  3.000
 R7Y  H21  C26  H20  106.41  3.000
 R7Y  H21  C26  O27  111.98  3.000
 R7Y  H20  C26  O27  111.91  3.000
 R7Y  H21  C26  C25  107.97  3.000
 R7Y  H20  C26  C25  108.18  3.000
 R7Y  O27  C26  C25  110.21  3.000
 R7Y  H22  C28  O29  110.80  3.000
 R7Y  H22  C28  C30  107.81  3.000
 R7Y  O29  C28  C30  108.15  3.000
 R7Y  H22  C28  C25  109.43  3.000
 R7Y  O29  C28  C25  111.11  3.000
 R7Y  C30  C28  C25  109.46  3.000
 R7Y  H23  C30  N31  112.68  3.000
 R7Y  H23  C30  C32  108.50  3.000
 R7Y  N31  C30  C32  109.26  3.000
 R7Y  H23  C30  C28  107.92  3.000
 R7Y  N31  C30  C28  109.95  3.000
 R7Y  C32  C30  C28  108.42  3.000
 R7Y  H24  C32  O33  110.49  3.000
 R7Y  H24  C32  C30  107.50  3.000
 R7Y  O33  C32  C30  111.70  3.000
 R7Y  H24  C32  C23  106.58  3.000
 R7Y  C30  C32  C23  111.57  3.000
 R7Y  O33  C32  C23  108.86  3.000
 R7Y  H25  C34  O35  110.56  3.000
 R7Y  H25  C34  C21  108.22  3.000
 R7Y  O35  C34  C21  108.21  3.000
 R7Y  H25  C34  C15  107.95  3.000
 R7Y  O35  C34  C15  111.35  3.000
 R7Y  C21  C34  C15  110.51  3.000
 R7Y  H26  N04  C05  116.89  3.000
 R7Y  H26  N04  C02  118.06  3.000
 R7Y  C05  N04  C02  124.04  3.000
 R7Y  H28  N11  H27  105.87  3.000
 R7Y  H28  N11  C10  109.76  3.000
 R7Y  H27  N11  C10  109.28  3.000
 R7Y  H31  N17  H30  105.83  3.000
 R7Y  H31  N17  C16  110.52  3.000
 R7Y  H30  N17  C16  110.25  3.000
 R7Y  H34  N20  H33  105.67  3.000
 R7Y  H34  N20  C19  109.08  3.000
 R7Y  H33  N20  C19  109.73  3.000
 R7Y  H37  N31  H36  105.36  3.000
 R7Y  H37  N31  C30  109.37  3.000
 R7Y  H36  N31  C30  109.08  3.000
 R7Y  H39  O08  C07  108.40  3.000
 R7Y  C13  O12  C09  117.06  3.000
 R7Y  C15  O14  C13  116.66  3.000
 R7Y  C23  O22  C21  117.43  3.000
 R7Y  C25  O24  C23  115.03  3.000
 R7Y  H40  O27  C26  108.19  3.000
 R7Y  H41  O29  C28  108.74  3.000
 R7Y  H42  O33  C32  108.78  3.000
 R7Y  H43  O35  C34  108.62  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
 R7Y  CONST_01  C05  N04  C02  C01   180.00   0.0  0
 R7Y  CONST_02  O03  C02  N04  C05     0.00   0.0  0
 R7Y  CONST_03  H26  N04  C02  C01     0.00   0.0  0
 R7Y  Var_01    H27  N11  C10  C09   171.59  30.0  3
 R7Y  Var_02    H1   C01  C02  N04  -132.26  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
 R7Y  chir_01  C05  C13  C06  N04  negativ
 R7Y  chir_02  C07  O08  C06  C09  negativ
 R7Y  chir_03  C09  O12  C07  C10  negativ
 R7Y  chir_04  C13  O14  O12  C05  negativ
 R7Y  chir_05  C15  O14  C34  C16  negativ
 R7Y  chir_06  C16  N17  C18  C15  negativ
 R7Y  chir_07  C19  N20  C21  C18  negativ
 R7Y  chir_08  C21  O22  C34  C19  positiv
 R7Y  chir_09  C23  O22  O24  C32  negativ
 R7Y  chir_10  C25  O24  C26  C28  positiv
 R7Y  chir_11  C28  O29  C25  C30  positiv
 R7Y  chir_12  C30  N31  C28  C32  negativ
 R7Y  chir_13  C32  O33  C30  C23  positiv
 R7Y  chir_14  C34  O35  C21  C15  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
 R7Y  plan-1  C01  0.020
 R7Y  plan-1  C02  0.020
 R7Y  plan-1  C05  0.020
 R7Y  plan-1  N04  0.020
 R7Y  plan-1  O03  0.020
 R7Y  plan-1  H26  0.020

