# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:58:08 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-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)CN)[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
 SIS  SIS  '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside'  ligand  68  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SIS
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
 SIS  C11  C  CR16  0   0.320  -3.7474   0.6959   0.0822
 SIS  C12  C  CH1   0  -0.103   0.8334  -2.0113   0.2747
 SIS  C13  C  CH1   0   0.244   2.6038   0.8345  -0.9097
 SIS  C21  C  CR16  0  -0.200  -4.3652   1.9637   0.6553
 SIS  C22  C  CH2   0  -0.466  -0.5129  -2.7183   0.1596
 SIS  C23  C  CH1   0   0.014   3.9943   0.2290  -1.1378
 SIS  C31  C  C     0  -0.459  -5.4032   2.4450  -0.3702
 SIS  C32  C  CH1   0  -0.096  -1.6505  -1.9712   0.8468
 SIS  C33  C  CH1   0  -0.099   4.8692   0.3957   0.1166
 SIS  C41  C  CR16  0  -0.396  -6.2291   1.2965  -0.8735
 SIS  C42  C  CH1   0   0.043  -1.7417  -0.5788   0.2348
 SIS  C43  C  CT    0   0.183   4.8836   1.8781   0.5389
 SIS  C51  C  CR6   0   0.376  -5.8837   0.0271  -0.6576
 SIS  C52  C  CH1   0   0.026  -0.4230   0.1781   0.3835
 SIS  C53  C  CH2   0  -0.188   3.4443   2.3789   0.6547
 SIS  C61  C  CH2   0  -0.368  -6.6680  -1.1885  -1.0380
 SIS  C62  C  CH1   0   0.059   0.7414  -0.5774  -0.2445
 SIS  C83  C  CH3   0  -0.678   5.5875   2.0632   1.8766
 SIS  N12  N  NH2   0  -0.805   1.9106  -2.7074  -0.4221
 SIS  N21  N  NH2   0  -0.789  -4.8844   1.7145   1.9885
 SIS  N33  N  NH1   0  -0.594   6.2190  -0.1102  -0.0348
 SIS  N61  N  NH2   0  -0.804  -5.8601  -2.0884  -1.8543
 SIS  O11  O  O2    0  -0.513  -2.7451   0.1985   0.8786
 SIS  O23  O  OH1   0  -0.706   3.8985  -1.0941  -1.5848
 SIS  O43  O  OH1   0  -0.683   5.5662   2.5766  -0.4894
 SIS  O51  O  O     0  -0.498  -4.7413  -0.3147  -0.0089
 SIS  O52  O  OH1   0  -0.664  -0.5093   1.4377  -0.2393
 SIS  O53  O  O2    0  -0.486   2.6917   2.1690  -0.5220
 SIS  O62  O  O2    0  -0.516   1.9513   0.0708   0.0638
 SIS  H1   H  HCR6  0   0.215  -3.3812   0.9074  -0.9344
 SIS  H2   H  HCH1  0   0.240   1.1147  -1.9590   1.3320
 SIS  H3   H  HCH1  0   0.229   2.0354   0.8273  -1.8474
 SIS  H4   H  HCR6  0   0.253  -3.5741   2.7135   0.7381
 SIS  H5   H  HCH2  0   0.225  -0.7696  -2.8490  -0.8985
 SIS  H6   H  HCH2  0   0.249  -0.4229  -3.7221   0.5842
 SIS  H7   H  HCH1  0   0.213   4.4624   0.7941  -1.9525
 SIS  H8   H  H     0   0.247  -6.0433   3.2004   0.0945
 SIS  H9   H  H     0   0.241  -4.9052   2.9512  -1.2040
 SIS  H10  H  HCH1  0   0.205  -1.3935  -1.8530   1.9132
 SIS  H11  H  HCH1  0   0.229   4.4020  -0.1621   0.9375
 SIS  H12  H  HCR6  0   0.241  -7.1446   1.4988  -1.4144
 SIS  H13  H  HCH1  0   0.223  -1.9774  -0.6929  -0.8330
 SIS  H14  H  HCH1  0   0.218  -0.2129   0.2846   1.4579
 SIS  H15  H  HCH2  0   0.208   2.9588   1.9123   1.5201
 SIS  H16  H  HCH2  0   0.234   3.4389   3.4581   0.8341
 SIS  H17  H  HCH2  0   0.215  -7.0452  -1.6580  -0.1170
 SIS  H18  H  HCH2  0   0.240  -7.5443  -0.8746  -1.6072
 SIS  H19  H  HCH1  0   0.218   0.5875  -0.6096  -1.3350
 SIS  H20  H  HCH3  0   0.222   5.0898   1.5063   2.6716
 SIS  H21  H  HCH3  0   0.242   6.6161   1.7130   1.8108
 SIS  H22  H  HCH3  0   0.225   5.5977   3.1160   2.1715
 SIS  H23  H  HCH3  0   0.216   6.1791  -1.6331   1.3902
 SIS  H24  H  HCH3  0   0.197   5.8293  -2.2216  -0.2367
 SIS  H25  H  HCH3  0   0.220   7.4726  -1.7528   0.2114
 SIS  H26  H  HNH2  0   0.367   2.1743  -3.5399   0.0903
 SIS  H27  H  HNH2  0   0.357   1.5757  -3.0316  -1.3238
 SIS  H29  H  HNH2  0   0.351  -5.1626   2.5960   2.4009
 SIS  H30  H  HNH2  0   0.344  -5.7320   1.1614   1.9365
 SIS  H35  H  HNH1  0   0.338   6.5532   0.0510  -0.9754
 SIS  H37  H  HNH2  0   0.340  -5.0678  -2.4117  -1.3108
 SIS  H38  H  HNH2  0   0.350  -6.4055  -2.9149  -2.0626
 SIS  H40  H  HOH1  0   0.463   3.2907  -1.6155  -1.0076
 SIS  H41  H  HOH1  0   0.444   5.6182   3.5062  -0.2435
 SIS  H42  H  HOH1  0   0.455  -0.7783   2.0899   0.4119
 SIS  N32  N  NH2   0  -0.799  -2.8885  -2.7074   0.6492
 SIS  C93  C  CH3   0  -0.517   6.4189  -1.4964   0.3338
 SIS  H32  H  HNH2  0   0.344  -2.8232  -3.5923   1.1377
 SIS  H33  H  HNH2  0   0.350  -3.6592  -2.2124   1.0773

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
 SIS  O43  C43  single  1.418  0.020  1.418
 SIS  C83  C43  single  1.523  0.020  1.523
 SIS  C43  C53  single  1.528  0.020  1.528
 SIS  C43  C33  single  1.542  0.020  1.542
 SIS  N33  C33  single  1.449  0.020  1.449
 SIS  N33  C93  single  1.448  0.020  1.448
 SIS  C53  O53  single  1.412  0.020  1.412
 SIS  C33  C23  single  1.538  0.020  1.538
 SIS  O53  C13  single  1.392  0.020  1.392
 SIS  C23  C13  single  1.534  0.020  1.534
 SIS  C23  O23  single  1.400  0.020  1.400
 SIS  C13  O62  single  1.399  0.020  1.399
 SIS  O62  C62  single  1.407  0.020  1.407
 SIS  O52  C52  single  1.408  0.020  1.408
 SIS  C62  C52  single  1.523  0.020  1.523
 SIS  C62  C12  single  1.528  0.020  1.528
 SIS  N12  C12  single  1.460  0.020  1.460
 SIS  C52  C42  single  1.528  0.020  1.528
 SIS  C12  C22  single  1.525  0.020  1.525
 SIS  C42  O11  single  1.423  0.020  1.423
 SIS  C42  C32  single  1.524  0.020  1.524
 SIS  C22  C32  single  1.525  0.020  1.525
 SIS  C11  O11  single  1.373  0.020  1.373
 SIS  C11  O51  single  1.420  0.020  1.420
 SIS  C11  C21  single  1.522  0.020  1.522
 SIS  N21  C21  single  1.452  0.020  1.452
 SIS  O51  C51  single  1.357  0.020  1.357
 SIS  C32  N32  single  1.454  0.020  1.454
 SIS  C21  C31  single  1.537  0.020  1.537
 SIS  C51  C61  single  1.496  0.020  1.496
 SIS  C51  C41  double  1.333  0.020  1.333
 SIS  N61  C61  single  1.459  0.020  1.459
 SIS  C31  C41  single  1.502  0.020  1.502
 SIS  C11  H1   single  0.970  0.020  1.090
 SIS  C12  H2   single  0.970  0.020  1.090
 SIS  C13  H3   single  0.970  0.020  1.090
 SIS  C21  H4   single  0.970  0.020  1.090
 SIS  C22  H5   single  0.970  0.020  1.090
 SIS  C22  H6   single  0.970  0.020  1.090
 SIS  C23  H7   single  0.970  0.020  1.090
 SIS  C31  H8   single  0.970  0.020  1.090
 SIS  C31  H9   single  0.970  0.020  1.090
 SIS  C32  H10  single  0.970  0.020  1.090
 SIS  C33  H11  single  0.970  0.020  1.090
 SIS  C41  H12  single  0.930  0.020  1.080
 SIS  C42  H13  single  0.970  0.020  1.090
 SIS  C52  H14  single  0.970  0.020  1.090
 SIS  C53  H15  single  0.970  0.020  1.090
 SIS  C53  H16  single  0.970  0.020  1.090
 SIS  C61  H17  single  0.970  0.020  1.090
 SIS  C61  H18  single  0.970  0.020  1.090
 SIS  C62  H19  single  0.970  0.020  1.090
 SIS  C83  H20  single  0.970  0.020  1.090
 SIS  C83  H21  single  0.970  0.020  1.090
 SIS  C83  H22  single  0.970  0.020  1.090
 SIS  C93  H23  single  0.970  0.020  1.090
 SIS  C93  H24  single  0.970  0.020  1.090
 SIS  C93  H25  single  0.970  0.020  1.090
 SIS  N12  H26  single  0.890  0.020  1.040
 SIS  N12  H27  single  0.890  0.020  1.040
 SIS  N21  H29  single  0.890  0.020  1.040
 SIS  N21  H30  single  0.890  0.020  1.040
 SIS  N32  H32  single  0.890  0.020  1.040
 SIS  N32  H33  single  0.890  0.020  1.040
 SIS  N33  H35  single  0.890  0.020  1.040
 SIS  N61  H37  single  0.890  0.020  1.040
 SIS  N61  H38  single  0.890  0.020  1.040
 SIS  O23  H40  single  0.850  0.020  0.980
 SIS  O43  H41  single  0.850  0.020  0.980
 SIS  O52  H42  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
 SIS  H1   C11  O51  108.07  3.000
 SIS  H1   C11  O11  111.24  3.000
 SIS  O51  C11  O11  106.87  3.000
 SIS  H1   C11  C21  108.82  3.000
 SIS  O51  C11  C21  109.44  3.000
 SIS  O11  C11  C21  112.30  3.000
 SIS  H2   C12  N12  107.10  3.000
 SIS  H2   C12  C62  107.38  3.000
 SIS  N12  C12  C62  109.26  3.000
 SIS  H2   C12  C22  108.76  3.000
 SIS  N12  C12  C22  113.23  3.000
 SIS  C62  C12  C22  110.87  3.000
 SIS  H3   C13  O62  110.47  3.000
 SIS  H3   C13  O53  106.09  3.000
 SIS  O62  C13  O53  111.03  3.000
 SIS  H3   C13  C23  109.89  3.000
 SIS  O62  C13  C23  108.11  3.000
 SIS  O53  C13  C23  111.26  3.000
 SIS  H4   C21  N21  107.88  3.000
 SIS  H4   C21  C31  108.94  3.000
 SIS  N21  C21  C31  115.15  3.000
 SIS  H4   C21  C11  107.82  3.000
 SIS  C31  C21  C11  106.48  3.000
 SIS  N21  C21  C11  110.35  3.000
 SIS  H6   C22  H5   106.53  3.000
 SIS  H6   C22  C32  109.65  3.000
 SIS  H5   C22  C32  108.59  3.000
 SIS  H6   C22  C12  108.87  3.000
 SIS  H5   C22  C12  109.55  3.000
 SIS  C32  C22  C12  113.42  3.000
 SIS  H7   C23  O23  106.20  3.000
 SIS  H7   C23  C33  107.89  3.000
 SIS  O23  C23  C33  113.68  3.000
 SIS  H7   C23  C13  107.11  3.000
 SIS  O23  C23  C13  111.02  3.000
 SIS  C33  C23  C13  110.58  3.000
 SIS  H9   C31  H8   105.69  3.000
 SIS  H9   C31  C41  110.39  3.000
 SIS  H8   C31  C41  110.41  3.000
 SIS  H9   C31  C21  110.23  3.000
 SIS  H8   C31  C21  109.15  3.000
 SIS  C41  C31  C21  110.84  3.000
 SIS  H10  C32  N32  112.58  3.000
 SIS  H10  C32  C42  107.71  3.000
 SIS  N32  C32  C42  110.93  3.000
 SIS  H10  C32  C22  108.32  3.000
 SIS  N32  C32  C22  109.02  3.000
 SIS  C42  C32  C22  108.14  3.000
 SIS  H11  C33  N33  107.30  3.000
 SIS  H11  C33  C43  106.73  3.000
 SIS  N33  C33  C43  110.83  3.000
 SIS  H11  C33  C23  108.23  3.000
 SIS  N33  C33  C23  114.00  3.000
 SIS  C43  C33  C23  109.44  3.000
 SIS  H12  C41  C51  118.56  3.000
 SIS  H12  C41  C31  119.32  3.000
 SIS  C51  C41  C31  122.11  3.000
 SIS  H13  C42  O11  110.17  3.000
 SIS  H13  C42  C52  109.33  3.000
 SIS  O11  C42  C52  107.10  3.000
 SIS  H13  C42  C32  107.94  3.000
 SIS  O11  C42  C32  111.08  3.000
 SIS  C52  C42  C32  111.22  3.000
 SIS  O43  C43  C83  110.76  3.000
 SIS  C83  C43  C53  109.21  3.000
 SIS  O43  C43  C53  110.29  3.000
 SIS  C53  C43  C33  109.09  3.000
 SIS  C83  C43  C33  111.21  3.000
 SIS  O43  C43  C33  106.23  3.000
 SIS  O51  C51  C61  110.99  3.000
 SIS  C61  C51  C41  126.64  3.000
 SIS  O51  C51  C41  122.36  3.000
 SIS  H14  C52  O52  110.93  3.000
 SIS  H14  C52  C62  107.74  3.000
 SIS  O52  C52  C62  107.95  3.000
 SIS  H14  C52  C42  107.93  3.000
 SIS  C62  C52  C42  111.96  3.000
 SIS  O52  C52  C42  110.32  3.000
 SIS  H16  C53  H15  106.74  3.000
 SIS  H16  C53  O53  106.30  3.000
 SIS  H15  C53  O53  111.00  3.000
 SIS  H16  C53  C43  109.89  3.000
 SIS  H15  C53  C43  109.71  3.000
 SIS  O53  C53  C43  112.95  3.000
 SIS  H18  C61  H17  106.51  3.000
 SIS  H18  C61  N61  109.29  3.000
 SIS  H17  C61  N61  113.26  3.000
 SIS  H18  C61  C51  108.66  3.000
 SIS  H17  C61  C51  108.28  3.000
 SIS  N61  C61  C51  110.68  3.000
 SIS  H19  C62  O62  110.52  3.000
 SIS  H19  C62  C52  108.40  3.000
 SIS  O62  C62  C52  109.79  3.000
 SIS  H19  C62  C12  108.50  3.000
 SIS  C52  C62  C12  111.80  3.000
 SIS  O62  C62  C12  107.83  3.000
 SIS  H22  C83  H21  108.50  3.000
 SIS  H22  C83  H20  107.42  3.000
 SIS  H21  C83  H20  108.11  3.000
 SIS  H22  C83  C43  110.99  3.000
 SIS  H21  C83  C43  110.16  3.000
 SIS  H20  C83  C43  111.54  3.000
 SIS  H27  N12  H26  105.83  3.000
 SIS  H27  N12  C12  109.44  3.000
 SIS  H26  N12  C12  110.05  3.000
 SIS  H30  N21  H29  105.44  3.000
 SIS  H30  N21  C21  110.22  3.000
 SIS  H29  N21  C21  108.84  3.000
 SIS  H35  N33  C93  110.10  3.000
 SIS  H35  N33  C33  110.45  3.000
 SIS  C93  N33  C33  115.85  3.000
 SIS  H38  N61  H37  105.72  3.000
 SIS  H38  N61  C61  108.69  3.000
 SIS  H37  N61  C61  109.24  3.000
 SIS  C42  O11  C11  116.75  3.000
 SIS  H40  O23  C23  110.77  3.000
 SIS  H41  O43  C43  108.44  3.000
 SIS  C51  O51  C11  116.13  3.000
 SIS  H42  O52  C52  108.96  3.000
 SIS  C53  O53  C13  114.08  3.000
 SIS  C62  O62  C13  120.02  3.000
 SIS  H33  N32  H32  105.82  3.000
 SIS  H33  N32  C32  110.11  3.000
 SIS  H32  N32  C32  108.78  3.000
 SIS  H25  C93  H24  107.81  3.000
 SIS  H25  C93  H23  106.93  3.000
 SIS  H24  C93  H23  107.63  3.000
 SIS  H25  C93  N33  109.24  3.000
 SIS  H24  C93  N33  115.27  3.000
 SIS  H23  C93  N33  109.62  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
 SIS  Var_01  C41  C51  O51  C11  -17.95  30.0  1
 SIS  Var_02  C43  C53  O53  C13   58.85  30.0  1
 SIS  Var_03  C51  C41  C31  C21  -13.28  30.0  1
 SIS  Var_04  O51  C51  C41  C31   -2.28  30.0  1
 SIS  Var_05  N61  C61  C51  C41  124.89  30.0  3
 SIS  Var_06  H23  C93  N33  C33  -61.20  30.0  3
 SIS  Var_07  H37  N61  C61  C51   62.84  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
 SIS  chir_01  C11  O11  O51  C21  negativ
 SIS  chir_02  C12  N12  C62  C22  negativ
 SIS  chir_03  C13  O53  O62  C23  positiv
 SIS  chir_04  C21  C11  N21  C31  positiv
 SIS  chir_05  C23  C33  C13  O23  positiv
 SIS  chir_06  C32  C42  C22  N32  positiv
 SIS  chir_07  C33  N33  C43  C23  negativ
 SIS  chir_08  C42  O11  C52  C32  negativ
 SIS  chir_09  C43  C83  C53  C33  positiv
 SIS  chir_10  C52  O52  C62  C42  positiv
 SIS  chir_11  C62  O62  C12  C52  negativ

