# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:39:54 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,7-dideoxy-D-glycero-alpha-D-gluco-heptopyranoside
#   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]([C@@H](C)O)[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
 GET  GET  '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,7-dideoxy-D-glycero-alpha-D-gluco-heptopyranoside'  ligand  74  34  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GET
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
 GET  C11   C  CH1   0   0.270   1.2382  -0.2884  -2.8641
 GET  O11   O  O2    0  -0.523   0.5782   0.7764  -2.2407
 GET  C21   C  CH1   0  -0.147   2.2436   0.2787  -3.8605
 GET  N21   N  NH2   0  -0.810   3.1358   1.2324  -3.2236
 GET  C31   C  CH1   0   0.005   1.4921   0.9339  -5.0097
 GET  O31   O  OH1   0  -0.681   2.3735   1.3677  -6.0302
 GET  C41   C  CH1   0   0.047   0.5080  -0.0382  -5.6588
 GET  O41   O  OH1   0  -0.672  -0.2940   0.6471  -6.5903
 GET  C51   C  CH1   0  -0.014  -0.3998  -0.6639  -4.5979
 GET  O51   O  O2    0  -0.510   0.3706  -1.1674  -3.5149
 GET  C61   C  CH1   0   0.016  -1.2091  -1.8846  -5.0665
 GET  O61   O  OH1   0  -0.660  -1.8274  -1.6951  -6.3173
 GET  C71   C  CH3   0  -0.687  -2.2260  -2.2908  -4.0067
 GET  C12   C  CH1   0  -0.100  -2.0123   1.1297   1.1189
 GET  N12   N  NH2   0  -0.815  -3.0346   0.8078   2.1074
 GET  C22   C  CH2   0  -0.472  -2.5480   1.2791  -0.3006
 GET  C32   C  CH1   0  -0.100  -1.4387   1.5991  -1.2932
 GET  N32   N  NH2   0  -0.787  -1.9998   1.7573  -2.6234
 GET  C42   C  CH1   0   0.059  -0.4115   0.4681  -1.2761
 GET  C52   C  CH1   0   0.026   0.1821   0.3394   0.1258
 GET  O52   O  OH1   0  -0.664   1.1230  -0.7055   0.1284
 GET  C62   C  CH1   0   0.044  -0.9229   0.0641   1.1486
 GET  O62   O  O2    0  -0.523  -0.3308   0.0152   2.4310
 GET  C13   C  CH1   0   0.199  -0.6337  -1.0682   3.2648
 GET  C23   C  CH1   0   0.072  -0.9547  -0.5469   4.6700
 GET  O23   O  OH1   0  -0.716  -1.9743   0.4122   4.6596
 GET  C33   C  CH1   0  -0.081   0.3002   0.0232   5.3440
 GET  N33   N  NH1   0  -0.605  -0.0133   0.4670   6.6898
 GET  C93   C  CH3   0  -0.524   0.3962   1.8140   7.0179
 GET  C43   C  CT    0   0.148   1.4475  -1.0038   5.2904
 GET  O43   O  OH1   0  -0.678   1.0560  -2.0795   6.1280
 GET  C83   C  CH3   0  -0.684   2.7683  -0.4075   5.7642
 GET  C53   C  CH2   0  -0.192   1.6151  -1.4855   3.8510
 GET  O53   O  O2    0  -0.488   0.4169  -1.9873   3.2940
 GET  H111  H  HCH1  0   0.242   1.7565  -0.9098  -2.1289
 GET  H21   H  HCH1  0   0.224   2.7784  -0.5976  -4.2599
 GET  H211  H  HNH2  0   0.349   3.4814   0.8472  -2.3528
 GET  H212  H  HNH2  0   0.348   3.9554   1.3583  -3.8033
 GET  H311  H  HCH1  0   0.216   0.9247   1.7882  -4.6168
 GET  H31   H  HOH1  0   0.458   2.6820   2.2523  -5.8154
 GET  H411  H  HCH1  0   0.199   1.0896  -0.8396  -6.1450
 GET  H41   H  HOH1  0   0.446   0.2964   1.1433  -7.1678
 GET  H511  H  HCH1  0   0.233  -1.1004   0.1048  -4.2427
 GET  H611  H  HCH1  0   0.220  -0.4999  -2.7051  -5.2189
 GET  H61   H  HOH1  0   0.440  -2.4074  -0.9285  -6.2656
 GET  H711  H  HCH3  0   0.234  -2.7616  -3.1891  -4.3161
 GET  H712  H  HCH3  0   0.233  -1.7528  -2.4980  -3.0483
 GET  H713  H  HCH3  0   0.219  -2.9585  -1.4945  -3.8499
 GET  H121  H  HNH2  0   0.373  -3.6899   1.5766   2.1868
 GET  H122  H  HNH2  0   0.360  -3.5793   0.0093   1.7986
 GET  H221  H  HCH2  0   0.228  -3.0516   0.3562  -0.6104
 GET  H222  H  HCH2  0   0.252  -3.3009   2.0721  -0.3191
 GET  H32   H  HCH1  0   0.206  -0.9326   2.5159  -0.9466
 GET  H321  H  HNH2  0   0.348  -2.7142   2.4752  -2.5931
 GET  H322  H  HNH2  0   0.347  -1.2871   2.1135  -3.2474
 GET  H421  H  HCH1  0   0.229  -0.9261  -0.4648  -1.5427
 GET  H521  H  HCH1  0   0.209   0.6627   1.2959   0.3850
 GET  H52   H  HOH1  0   0.454   1.5533  -0.7229   0.9890
 GET  H621  H  HCH1  0   0.223  -1.3725  -0.9099   0.8976
 GET  H131  H  HCH1  0   0.241  -1.4940  -1.6203   2.8664
 GET  H231  H  HCH1  0   0.191  -1.2798  -1.4225   5.2506
 GET  H23   H  HOH1  0   0.465  -2.3329   0.5350   3.7470
 GET  H331  H  HCH1  0   0.228   0.6248   0.8918   4.7578
 GET  H33   H  HNH1  0   0.343   0.3300  -0.1930   7.3734
 GET  H931  H  HCH3  0   0.226   0.1559   2.0216   8.0612
 GET  H932  H  HCH3  0   0.191   1.4652   2.0256   6.8788
 GET  H933  H  HCH3  0   0.221  -0.1592   2.5304   6.4102
 GET  H43   H  HOH1  0   0.449   1.8016  -2.6816   6.2259
 GET  H831  H  HCH3  0   0.237   3.5725  -1.1444   5.6946
 GET  H832  H  HCH3  0   0.233   3.0582   0.4542   5.1623
 GET  H833  H  HCH3  0   0.243   2.7062  -0.0859   6.8036
 GET  H531  H  HCH2  0   0.243   2.3377  -2.3047   3.8120
 GET  H532  H  HCH2  0   0.204   2.0272  -0.6686   3.2444
 GET  H12   H  HCH1  0   0.243  -1.5627   2.0812   1.4232

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
 GET  C11  O11   single  1.399  0.020  1.399
 GET  C11  C21   single  1.525  0.020  1.525
 GET  C11  O51   single  1.396  0.020  1.396
 GET  C11  H111  single  0.970  0.020  1.090
 GET  O11  C42   single  1.416  0.020  1.416
 GET  C21  N21   single  1.453  0.020  1.453
 GET  C21  C31   single  1.521  0.020  1.521
 GET  C21  H21   single  0.970  0.020  1.090
 GET  N21  H211  single  0.890  0.020  1.040
 GET  N21  H212  single  0.890  0.020  1.040
 GET  C31  O31   single  1.416  0.020  1.416
 GET  C31  C41   single  1.528  0.020  1.528
 GET  C31  H311  single  0.970  0.020  1.090
 GET  O31  H31   single  0.850  0.020  0.980
 GET  C41  O41   single  1.407  0.020  1.407
 GET  C41  C51   single  1.530  0.020  1.530
 GET  C41  H411  single  0.970  0.020  1.090
 GET  O41  H41   single  0.850  0.020  0.980
 GET  C51  O51   single  1.421  0.020  1.421
 GET  C51  C61   single  1.538  0.020  1.538
 GET  C51  H511  single  0.970  0.020  1.090
 GET  C61  O61   single  1.408  0.020  1.408
 GET  C61  C71   single  1.524  0.020  1.524
 GET  C61  H611  single  0.970  0.020  1.090
 GET  O61  H61   single  0.850  0.020  0.980
 GET  C71  H711  single  0.970  0.020  1.090
 GET  C71  H712  single  0.970  0.020  1.090
 GET  C71  H713  single  0.970  0.020  1.090
 GET  C12  N12   single  1.458  0.020  1.458
 GET  C12  C22   single  1.524  0.020  1.524
 GET  C12  C62   single  1.524  0.020  1.524
 GET  C12  H12   single  0.970  0.020  1.090
 GET  N12  H121  single  0.890  0.020  1.040
 GET  N12  H122  single  0.890  0.020  1.040
 GET  C22  C32   single  1.523  0.020  1.523
 GET  C22  H221  single  0.970  0.020  1.090
 GET  C22  H222  single  0.970  0.020  1.090
 GET  C32  N32   single  1.452  0.020  1.452
 GET  C32  C42   single  1.528  0.020  1.528
 GET  C32  H32   single  0.970  0.020  1.090
 GET  N32  H321  single  0.890  0.020  1.040
 GET  N32  H322  single  0.890  0.020  1.040
 GET  C42  C52   single  1.528  0.020  1.528
 GET  C42  H421  single  0.970  0.020  1.090
 GET  C52  O52   single  1.406  0.020  1.406
 GET  C52  C62   single  1.531  0.020  1.531
 GET  C52  H521  single  0.970  0.020  1.090
 GET  O52  H52   single  0.850  0.020  0.980
 GET  C62  O62   single  1.413  0.020  1.413
 GET  C62  H621  single  0.970  0.020  1.090
 GET  O62  C13   single  1.400  0.020  1.400
 GET  C13  C23   single  1.533  0.020  1.533
 GET  C13  O53   single  1.396  0.020  1.396
 GET  C13  H131  single  0.970  0.020  1.090
 GET  C23  O23   single  1.400  0.020  1.400
 GET  C23  C33   single  1.534  0.020  1.534
 GET  C23  H231  single  0.970  0.020  1.090
 GET  O23  H23   single  0.850  0.020  0.980
 GET  C33  N33   single  1.451  0.020  1.451
 GET  C33  C43   single  1.541  0.020  1.541
 GET  C33  H331  single  0.970  0.020  1.090
 GET  N33  C93   single  1.446  0.020  1.446
 GET  N33  H33   single  0.890  0.020  1.040
 GET  C93  H931  single  0.970  0.020  1.090
 GET  C93  H932  single  0.970  0.020  1.090
 GET  C93  H933  single  0.970  0.020  1.090
 GET  C43  O43   single  1.418  0.020  1.418
 GET  C43  C83   single  1.525  0.020  1.525
 GET  C43  C53   single  1.527  0.020  1.527
 GET  O43  H43   single  0.850  0.020  0.980
 GET  C83  H831  single  0.970  0.020  1.090
 GET  C83  H832  single  0.970  0.020  1.090
 GET  C83  H833  single  0.970  0.020  1.090
 GET  C53  O53   single  1.413  0.020  1.413
 GET  C53  H531  single  0.970  0.020  1.090
 GET  C53  H532  single  0.970  0.020  1.090

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
 GET  H111  C11  O51   104.50  3.000
 GET  H111  C11  C21   109.77  3.000
 GET  O51   C11  C21   109.84  3.000
 GET  H111  C11  O11   110.88  3.000
 GET  O51   C11  O11   113.18  3.000
 GET  C21   C11  O11   108.60  3.000
 GET  C42   O11  C11   117.87  3.000
 GET  H21   C21  C31   107.97  3.000
 GET  H21   C21  N21   112.52  3.000
 GET  C31   C21  N21   110.59  3.000
 GET  H21   C21  C11   105.14  3.000
 GET  C31   C21  C11   109.15  3.000
 GET  N21   C21  C11   111.26  3.000
 GET  H212  N21  H211  105.28  3.000
 GET  H212  N21  C21   109.15  3.000
 GET  H211  N21  C21   109.67  3.000
 GET  H311  C31  C41   108.31  3.000
 GET  H311  C31  O31   109.94  3.000
 GET  C41   C31  O31   106.83  3.000
 GET  H311  C31  C21   108.66  3.000
 GET  C41   C31  C21   111.41  3.000
 GET  O31   C31  C21   111.64  3.000
 GET  H31   O31  C31   108.70  3.000
 GET  H411  C41  C51   108.75  3.000
 GET  H411  C41  O41   111.25  3.000
 GET  C51   C41  O41   108.66  3.000
 GET  H411  C41  C31   108.05  3.000
 GET  C51   C41  C31   110.35  3.000
 GET  O41   C41  C31   109.78  3.000
 GET  H41   O41  C41   107.36  3.000
 GET  H511  C51  C61   108.55  3.000
 GET  H511  C51  O51   110.30  3.000
 GET  C61   C51  O51   103.67  3.000
 GET  H511  C51  C41   108.44  3.000
 GET  C61   C51  C41   115.19  3.000
 GET  O51   C51  C41   110.59  3.000
 GET  C51   O51  C11   117.98  3.000
 GET  H611  C61  C71   109.22  3.000
 GET  H611  C61  O61   105.16  3.000
 GET  C71   C61  O61   111.14  3.000
 GET  H611  C61  C51   107.23  3.000
 GET  C71   C61  C51   110.54  3.000
 GET  O61   C61  C51   113.26  3.000
 GET  H61   O61  C61   108.90  3.000
 GET  H713  C71  H712  107.67  3.000
 GET  H713  C71  H711  108.15  3.000
 GET  H712  C71  H711  107.84  3.000
 GET  H713  C71  C61   110.65  3.000
 GET  H712  C71  C61   111.89  3.000
 GET  H711  C71  C61   110.49  3.000
 GET  H12   C12  C62   107.97  3.000
 GET  H12   C12  C22   108.53  3.000
 GET  C62   C12  C22   109.74  3.000
 GET  H12   C12  N12   106.93  3.000
 GET  C62   C12  N12   109.48  3.000
 GET  C22   C12  N12   113.99  3.000
 GET  H122  N12  H121  105.89  3.000
 GET  H122  N12  C12   110.11  3.000
 GET  H121  N12  C12   109.82  3.000
 GET  H222  C22  H221  106.82  3.000
 GET  H222  C22  C32   109.76  3.000
 GET  H221  C22  C32   109.11  3.000
 GET  H222  C22  C12   109.19  3.000
 GET  H221  C22  C12   110.01  3.000
 GET  C32   C22  C12   111.81  3.000
 GET  H32   C32  C42   107.66  3.000
 GET  H32   C32  N32   111.99  3.000
 GET  C42   C32  N32   110.53  3.000
 GET  H32   C32  C22   107.70  3.000
 GET  C42   C32  C22   109.08  3.000
 GET  N32   C32  C22   109.78  3.000
 GET  H322  N32  H321  105.40  3.000
 GET  H322  N32  C32   109.33  3.000
 GET  H321  N32  C32   108.79  3.000
 GET  H421  C42  C52   109.46  3.000
 GET  H421  C42  C32   108.13  3.000
 GET  C52   C42  C32   109.51  3.000
 GET  H421  C42  O11   110.30  3.000
 GET  C52   C42  O11   111.83  3.000
 GET  C32   C42  O11   107.52  3.000
 GET  H521  C52  C62   108.29  3.000
 GET  H521  C52  O52   110.67  3.000
 GET  C62   C52  O52   110.38  3.000
 GET  H521  C52  C42   108.20  3.000
 GET  C62   C52  C42   110.35  3.000
 GET  O52   C52  C42   108.93  3.000
 GET  H52   O52  C52   108.32  3.000
 GET  H621  C62  O62   110.31  3.000
 GET  H621  C62  C52   107.54  3.000
 GET  O62   C62  C52   108.06  3.000
 GET  H621  C62  C12   108.78  3.000
 GET  O62   C62  C12   109.96  3.000
 GET  C52   C62  C12   112.16  3.000
 GET  C13   O62  C62   118.45  3.000
 GET  H131  C13  O53   105.45  3.000
 GET  H131  C13  C23   109.87  3.000
 GET  O53   C13  C23   111.25  3.000
 GET  H131  C13  O62   110.04  3.000
 GET  O53   C13  O62   111.04  3.000
 GET  C23   C13  O62   109.15  3.000
 GET  H231  C23  C33   107.80  3.000
 GET  H231  C23  O23   109.52  3.000
 GET  C33   C23  O23   110.15  3.000
 GET  H231  C23  C13   105.97  3.000
 GET  C33   C23  C13   110.96  3.000
 GET  O23   C23  C13   112.26  3.000
 GET  H23   O23  C23   110.88  3.000
 GET  H331  C33  C43   106.79  3.000
 GET  H331  C33  N33   108.50  3.000
 GET  C43   C33  N33   113.39  3.000
 GET  H331  C33  C23   107.55  3.000
 GET  C43   C33  C23   110.25  3.000
 GET  N33   C33  C23   110.13  3.000
 GET  H33   N33  C93   111.03  3.000
 GET  H33   N33  C33   110.75  3.000
 GET  C93   N33  C33   115.73  3.000
 GET  H933  C93  H932  107.36  3.000
 GET  H933  C93  H931  107.19  3.000
 GET  H932  C93  H931  107.39  3.000
 GET  H933  C93  N33   109.95  3.000
 GET  H932  C93  N33   115.24  3.000
 GET  H931  C93  N33   109.39  3.000
 GET  C53   C43  C83   108.74  3.000
 GET  C53   C43  O43   110.34  3.000
 GET  C83   C43  O43   110.62  3.000
 GET  C53   C43  C33   108.95  3.000
 GET  C83   C43  C33   111.94  3.000
 GET  O43   C43  C33   106.23  3.000
 GET  H43   O43  C43   108.69  3.000
 GET  H833  C83  H832  107.96  3.000
 GET  H833  C83  H831  107.55  3.000
 GET  H832  C83  H831  107.58  3.000
 GET  H833  C83  C43   111.25  3.000
 GET  H832  C83  C43   111.58  3.000
 GET  H831  C83  C43   110.73  3.000
 GET  H532  C53  H531  106.85  3.000
 GET  H532  C53  O53   111.38  3.000
 GET  H531  C53  O53   106.28  3.000
 GET  H532  C53  C43   109.10  3.000
 GET  H531  C53  C43   110.04  3.000
 GET  O53   C53  C43   112.98  3.000
 GET  C53   O53  C13   114.36  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
 GET  Var_01  C43   C53  O53  C13    59.03  30.0  1
 GET  Var_02  H931  C93  N33  C33  -177.23  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
 GET  chir_01  C11  O11  C21  O51  positiv
 GET  chir_02  C21  N21  C31  C11  positiv
 GET  chir_03  C31  O31  C21  C41  positiv
 GET  chir_04  C41  O41  C31  C51  negativ
 GET  chir_05  C51  O51  C61  C41  positiv
 GET  chir_06  C61  O61  C51  C71  negativ
 GET  chir_07  C12  N12  C22  C62  positiv
 GET  chir_08  C32  N32  C42  C22  positiv
 GET  chir_09  C42  O11  C52  C32  negativ
 GET  chir_10  C52  O52  C42  C62  negativ
 GET  chir_11  C62  O62  C12  C52  negativ
 GET  chir_12  C13  O62  O53  C23  negativ
 GET  chir_13  C23  O23  C13  C33  negativ
 GET  chir_14  C33  N33  C23  C43  positiv
 GET  chir_15  C43  C53  C83  C33  negativ

