# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:02:17 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
#   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]3OC(=CC[C@H]3N)CO)[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
 6HS  6HS  '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside'  ligand  67  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6HS
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
 6HS  C11  C  CR16  0   0.326   3.6496  -0.5118   0.1277
 6HS  C12  C  CH1   0  -0.106  -0.9017   2.2476   0.3507
 6HS  C13  C  CH1   0   0.223  -2.5454  -0.6049  -0.9719
 6HS  C21  C  CR16  0  -0.202   4.0715  -1.8045   0.8145
 6HS  C22  C  CH2   0  -0.464   0.4122   3.0109   0.2149
 6HS  C23  C  CH1   0   0.021  -3.9952  -0.1229  -1.0891
 6HS  C31  C  C     0  -0.459   4.9848  -2.5532  -0.1633
 6HS  C32  C  CH1   0  -0.098   1.5902   2.2936   0.8649
 6HS  C33  C  CH1   0  -0.100  -4.8052  -0.5078   0.1608
 6HS  C41  C  CR16  0  -0.387   5.9900  -1.6116  -0.7524
 6HS  C42  C  CH1   0   0.032   1.7332   0.9059   0.2510
 6HS  C43  C  CT    0   0.181  -4.6530  -2.0211   0.4131
 6HS  C51  C  CR6   0   0.343   5.8546  -0.2869  -0.6749
 6HS  C52  C  CH1   0   0.036   0.4448   0.1079   0.4077
 6HS  C53  C  CH2   0  -0.189  -3.1686  -2.3833   0.4460
 6HS  C61  C  CH2   0  -0.230   6.8769   0.6884  -1.1589
 6HS  C62  C  CH1   0   0.046  -0.7417   0.8402  -0.2150
 6HS  C83  C  CH3   0  -0.679  -5.2811  -2.4262   1.7400
 6HS  N12  N  NH2   0  -0.804  -2.0319   2.9040  -0.2970
 6HS  N21  N  NH2   0  -0.790   4.6632  -1.5222   2.1114
 6HS  N32  N  NH2   0  -0.803   2.8053   3.0570   0.6381
 6HS  N33  N  NH1   0  -0.594  -6.2055  -0.1414   0.0953
 6HS  O61  O  OH1   0  -0.670   6.3174   1.4793  -2.1844
 6HS  O11  O  O2    0  -0.509   2.7831   0.2160   0.9092
 6HS  O23  O  OH1   0  -0.703  -4.0366   1.2422  -1.3959
 6HS  O43  O  OH1   0  -0.682  -5.2959  -2.6688  -0.6713
 6HS  O51  O  O     0  -0.489   4.7824   0.3200  -0.1063
 6HS  O52  O  OH1   0  -0.668   0.6432  -1.1476  -0.1961
 6HS  O53  O  O2    0  -0.494  -2.4687  -1.9747  -0.7160
 6HS  O62  O  O2    0  -0.522  -1.9246   0.1187   0.0522
 6HS  H1   H  HCR6  0   0.217   3.2040  -0.7602  -0.8457
 6HS  H2   H  HCH1  0   0.241  -1.1498   2.1539   1.4135
 6HS  H3   H  HCH1  0   0.241  -2.0264  -0.4440  -1.9244
 6HS  H4   H  HCR6  0   0.254   3.1632  -2.3893   0.9783
 6HS  H5   H  HCH2  0   0.225   0.6364   3.1653  -0.8471
 6HS  H6   H  HCH2  0   0.250   0.2980   4.0042   0.6578
 6HS  H7   H  HCH1  0   0.217  -4.4362  -0.6449  -1.9463
 6HS  H8   H  H     0   0.248   5.4862  -3.3714   0.3607
 6HS  H9   H  H     0   0.242   4.3931  -3.0267  -0.9538
 6HS  H10  H  HCH1  0   0.209   1.3637   2.1617   1.9364
 6HS  H11  H  HCH1  0   0.231  -4.3739   0.0055   1.0288
 6HS  H12  H  HCR6  0   0.246   6.8717  -2.0094  -1.2378
 6HS  H13  H  HCH1  0   0.228   1.9652   1.0282  -0.8169
 6HS  H14  H  HCH1  0   0.208   0.2478  -0.0031   1.4860
 6HS  H15  H  HCH2  0   0.212  -2.7086  -1.9639   1.3486
 6HS  H16  H  HCH2  0   0.240  -3.0510  -3.4684   0.5043
 6HS  H17  H  HCH2  0   0.215   7.2057   1.3073  -0.3134
 6HS  H18  H  HCH2  0   0.212   7.7531   0.1264  -1.5025
 6HS  H19  H  HCH1  0   0.224  -0.5765   0.9106  -1.3016
 6HS  H20  H  HCH3  0   0.243  -6.3395  -2.1736   1.7496
 6HS  H21  H  HCH3  0   0.227  -5.1809  -3.5019   1.9076
 6HS  H22  H  HCH3  0   0.224  -4.8028  -1.9172   2.5779
 6HS  H23  H  HCH3  0   0.216  -6.2702   1.2900   1.6122
 6HS  H24  H  HCH3  0   0.199  -6.0620   2.0094   0.0147
 6HS  H25  H  HCH3  0   0.221  -7.6207   1.3296   0.4941
 6HS  H26  H  HNH2  0   0.368  -2.3102   3.7187   0.2363
 6HS  H27  H  HNH2  0   0.357  -1.7469   3.2536  -1.2064
 6HS  H29  H  HNH2  0   0.351   4.8302  -2.3988   2.5891
 6HS  H30  H  HNH2  0   0.343   5.5781  -1.1018   1.9960
 6HS  H32  H  HNH2  0   0.344   2.7528   3.9246   1.1577
 6HS  H33  H  HNH2  0   0.346   3.5996   2.5571   1.0169
 6HS  H35  H  HNH1  0   0.339  -6.5626  -0.2860  -0.8394
 6HS  H37  H  HOH1  0   0.457   6.9135   2.2159  -2.3464
 6HS  H38  H  HOH1  0   0.460  -3.4127   1.7532  -0.8280
 6HS  H39  H  HOH1  0   0.445  -5.2599  -3.6201  -0.5258
 6HS  H40  H  HOH1  0   0.451  -0.1183  -1.7077  -0.0105
 6HS  C93  C  CH3   0  -0.517  -6.5406   1.1893   0.5591

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
 6HS  N21  C21  single  1.453  0.020  1.453
 6HS  C21  C31  single  1.533  0.020  1.533
 6HS  C21  C11  single  1.523  0.020  1.523
 6HS  C31  C41  single  1.498  0.020  1.498
 6HS  C83  C43  single  1.523  0.020  1.523
 6HS  C11  O51  single  1.425  0.020  1.425
 6HS  C11  O11  single  1.375  0.020  1.375
 6HS  C41  C51  double  1.334  0.020  1.334
 6HS  O51  C51  single  1.357  0.020  1.357
 6HS  C53  C43  single  1.528  0.020  1.528
 6HS  C53  O53  single  1.417  0.020  1.417
 6HS  C51  C61  single  1.494  0.020  1.494
 6HS  O52  C52  single  1.407  0.020  1.407
 6HS  O43  C43  single  1.417  0.020  1.417
 6HS  C43  C33  single  1.542  0.020  1.542
 6HS  C61  O61  single  1.411  0.020  1.411
 6HS  O11  C42  single  1.418  0.020  1.418
 6HS  O53  C13  single  1.396  0.020  1.396
 6HS  C52  C42  single  1.524  0.020  1.524
 6HS  C52  C62  single  1.527  0.020  1.527
 6HS  C42  C32  single  1.524  0.020  1.524
 6HS  C33  N33  single  1.449  0.020  1.449
 6HS  C33  C23  single  1.538  0.020  1.538
 6HS  C13  O62  single  1.399  0.020  1.399
 6HS  C13  C23  single  1.532  0.020  1.532
 6HS  N33  C93  single  1.448  0.020  1.448
 6HS  O62  C62  single  1.411  0.020  1.411
 6HS  C62  C12  single  1.525  0.020  1.525
 6HS  C23  O23  single  1.400  0.020  1.400
 6HS  C32  N32  single  1.453  0.020  1.453
 6HS  C32  C22  single  1.525  0.020  1.525
 6HS  C12  C22  single  1.526  0.020  1.526
 6HS  C12  N12  single  1.459  0.020  1.459
 6HS  C11  H1   single  0.970  0.020  1.090
 6HS  C12  H2   single  0.970  0.020  1.090
 6HS  C13  H3   single  0.970  0.020  1.090
 6HS  C21  H4   single  0.970  0.020  1.090
 6HS  C22  H5   single  0.970  0.020  1.090
 6HS  C22  H6   single  0.970  0.020  1.090
 6HS  C23  H7   single  0.970  0.020  1.090
 6HS  C31  H8   single  0.970  0.020  1.090
 6HS  C31  H9   single  0.970  0.020  1.090
 6HS  C32  H10  single  0.970  0.020  1.090
 6HS  C33  H11  single  0.970  0.020  1.090
 6HS  C41  H12  single  0.930  0.020  1.080
 6HS  C42  H13  single  0.970  0.020  1.090
 6HS  C52  H14  single  0.970  0.020  1.090
 6HS  C53  H15  single  0.970  0.020  1.090
 6HS  C53  H16  single  0.970  0.020  1.090
 6HS  C61  H17  single  0.970  0.020  1.090
 6HS  C61  H18  single  0.970  0.020  1.090
 6HS  C62  H19  single  0.970  0.020  1.090
 6HS  C83  H20  single  0.970  0.020  1.090
 6HS  C83  H21  single  0.970  0.020  1.090
 6HS  C83  H22  single  0.970  0.020  1.090
 6HS  C93  H23  single  0.970  0.020  1.090
 6HS  C93  H24  single  0.970  0.020  1.090
 6HS  C93  H25  single  0.970  0.020  1.090
 6HS  N12  H26  single  0.890  0.020  1.040
 6HS  N12  H27  single  0.890  0.020  1.040
 6HS  N21  H29  single  0.890  0.020  1.040
 6HS  N21  H30  single  0.890  0.020  1.040
 6HS  N32  H32  single  0.890  0.020  1.040
 6HS  N32  H33  single  0.890  0.020  1.040
 6HS  N33  H35  single  0.890  0.020  1.040
 6HS  O61  H37  single  0.850  0.020  0.980
 6HS  O23  H38  single  0.850  0.020  0.980
 6HS  O43  H39  single  0.850  0.020  0.980
 6HS  O52  H40  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
 6HS  H1   C11  O51  107.99  3.000
 6HS  H1   C11  O11  111.56  3.000
 6HS  O51  C11  O11  106.58  3.000
 6HS  H1   C11  C21  108.65  3.000
 6HS  O11  C11  C21  111.56  3.000
 6HS  O51  C11  C21  110.44  3.000
 6HS  H2   C12  N12  107.08  3.000
 6HS  H2   C12  C62  107.74  3.000
 6HS  N12  C12  C62  109.38  3.000
 6HS  H2   C12  C22  108.92  3.000
 6HS  N12  C12  C22  113.74  3.000
 6HS  C62  C12  C22  109.78  3.000
 6HS  H3   C13  O62  110.48  3.000
 6HS  H3   C13  O53  106.10  3.000
 6HS  O62  C13  O53  110.43  3.000
 6HS  H3   C13  C23  109.58  3.000
 6HS  O62  C13  C23  108.24  3.000
 6HS  O53  C13  C23  112.01  3.000
 6HS  H4   C21  N21  107.98  3.000
 6HS  H4   C21  C31  109.24  3.000
 6HS  N21  C21  C31  114.93  3.000
 6HS  H4   C21  C11  106.95  3.000
 6HS  C31  C21  C11  106.96  3.000
 6HS  N21  C21  C11  110.50  3.000
 6HS  H6   C22  H5   106.61  3.000
 6HS  H6   C22  C32  109.59  3.000
 6HS  H5   C22  C32  108.74  3.000
 6HS  H6   C22  C12  109.17  3.000
 6HS  H5   C22  C12  109.44  3.000
 6HS  C32  C22  C12  113.08  3.000
 6HS  H7   C23  O23  106.32  3.000
 6HS  H7   C23  C33  107.72  3.000
 6HS  O23  C23  C33  113.99  3.000
 6HS  H7   C23  C13  106.90  3.000
 6HS  O23  C23  C13  110.58  3.000
 6HS  C33  C23  C13  110.94  3.000
 6HS  H9   C31  H8   105.67  3.000
 6HS  H9   C31  C41  110.52  3.000
 6HS  H8   C31  C41  110.55  3.000
 6HS  H9   C31  C21  110.47  3.000
 6HS  H8   C31  C21  109.44  3.000
 6HS  C41  C31  C21  110.10  3.000
 6HS  H10  C32  N32  112.72  3.000
 6HS  H10  C32  C42  107.55  3.000
 6HS  N32  C32  C42  109.70  3.000
 6HS  H10  C32  C22  108.16  3.000
 6HS  N32  C32  C22  109.41  3.000
 6HS  C42  C32  C22  109.21  3.000
 6HS  H11  C33  N33  107.31  3.000
 6HS  H11  C33  C43  106.92  3.000
 6HS  N33  C33  C43  110.55  3.000
 6HS  H11  C33  C23  108.59  3.000
 6HS  N33  C33  C23  114.14  3.000
 6HS  C43  C33  C23  109.06  3.000
 6HS  H12  C41  C51  118.28  3.000
 6HS  H12  C41  C31  119.48  3.000
 6HS  C51  C41  C31  122.23  3.000
 6HS  H13  C42  O11  110.40  3.000
 6HS  H13  C42  C52  109.66  3.000
 6HS  O11  C42  C52  108.87  3.000
 6HS  H13  C42  C32  108.04  3.000
 6HS  C52  C42  C32  110.87  3.000
 6HS  O11  C42  C32  108.99  3.000
 6HS  O43  C43  C83  110.97  3.000
 6HS  O43  C43  C53  110.41  3.000
 6HS  C83  C43  C53  108.59  3.000
 6HS  O43  C43  C33  106.18  3.000
 6HS  C53  C43  C33  109.39  3.000
 6HS  C83  C43  C33  111.28  3.000
 6HS  O51  C51  C61  112.62  3.000
 6HS  C61  C51  C41  124.07  3.000
 6HS  O51  C51  C41  123.28  3.000
 6HS  H14  C52  O52  110.81  3.000
 6HS  H14  C52  C62  107.96  3.000
 6HS  O52  C52  C62  111.25  3.000
 6HS  H14  C52  C42  107.74  3.000
 6HS  C62  C52  C42  111.34  3.000
 6HS  O52  C52  C42  107.70  3.000
 6HS  H16  C53  H15  106.90  3.000
 6HS  H16  C53  O53  106.08  3.000
 6HS  H15  C53  O53  110.95  3.000
 6HS  H16  C53  C43  109.93  3.000
 6HS  H15  C53  C43  109.55  3.000
 6HS  O53  C53  C43  113.19  3.000
 6HS  H18  C61  H17  106.92  3.000
 6HS  H18  C61  O61  112.13  3.000
 6HS  H17  C61  O61  111.25  3.000
 6HS  H18  C61  C51  108.29  3.000
 6HS  H17  C61  C51  108.87  3.000
 6HS  O61  C61  C51  109.28  3.000
 6HS  H19  C62  O62  110.20  3.000
 6HS  H19  C62  C52  108.44  3.000
 6HS  O62  C62  C52  109.21  3.000
 6HS  H19  C62  C12  108.82  3.000
 6HS  O62  C62  C12  108.28  3.000
 6HS  C52  C62  C12  111.89  3.000
 6HS  H22  C83  H21  107.53  3.000
 6HS  H22  C83  H20  108.14  3.000
 6HS  H21  C83  H20  108.43  3.000
 6HS  H22  C83  C43  111.36  3.000
 6HS  H21  C83  C43  110.95  3.000
 6HS  H20  C83  C43  110.31  3.000
 6HS  H27  N12  H26  105.78  3.000
 6HS  H27  N12  C12  109.58  3.000
 6HS  H26  N12  C12  109.95  3.000
 6HS  H30  N21  H29  105.31  3.000
 6HS  H30  N21  C21  110.28  3.000
 6HS  H29  N21  C21  108.67  3.000
 6HS  H33  N32  H32  105.77  3.000
 6HS  H33  N32  C32  109.78  3.000
 6HS  H32  N32  C32  109.06  3.000
 6HS  H35  N33  C93  110.22  3.000
 6HS  H35  N33  C33  110.30  3.000
 6HS  C93  N33  C33  116.19  3.000
 6HS  H37  O61  C61  107.83  3.000
 6HS  C42  O11  C11  117.40  3.000
 6HS  H38  O23  C23  111.12  3.000
 6HS  H39  O43  C43  108.60  3.000
 6HS  C51  O51  C11  115.84  3.000
 6HS  H40  O52  C52  108.94  3.000
 6HS  C53  O53  C13  113.98  3.000
 6HS  C62  O62  C13  119.85  3.000
 6HS  H25  C93  H24  107.87  3.000
 6HS  H25  C93  H23  106.90  3.000
 6HS  H24  C93  H23  107.60  3.000
 6HS  H25  C93  N33  109.15  3.000
 6HS  H24  C93  N33  115.34  3.000
 6HS  H23  C93  N33  109.65  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
 6HS  Var_01  C41  C51  O51  C11  -14.38  30.0  1
 6HS  Var_02  C43  C53  O53  C13   57.61  30.0  1
 6HS  Var_03  C51  C41  C31  C21  -15.46  30.0  1
 6HS  Var_04  O51  C51  C41  C31   -2.51  30.0  1
 6HS  Var_05  O61  C61  C51  C41  118.23  30.0  3
 6HS  Var_06  H23  C93  N33  C33  -61.14  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
 6HS  chir_01  C11  C21  O51  O11  positiv
 6HS  chir_02  C12  N12  C62  C22  negativ
 6HS  chir_03  C13  O53  O62  C23  positiv
 6HS  chir_04  C21  N21  C31  C11  positiv
 6HS  chir_05  C23  C33  C13  O23  positiv
 6HS  chir_06  C32  N32  C42  C22  positiv
 6HS  chir_07  C33  C43  N33  C23  positiv
 6HS  chir_08  C42  O11  C52  C32  negativ
 6HS  chir_09  C43  C53  O43  C33  positiv
 6HS  chir_10  C52  O52  C42  C62  negativ
 6HS  chir_11  C62  O62  C12  C52  negativ

