# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun  3 00:30:44 2020
#   Inital geometry file: a 147 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 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside
#   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)CC[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
 LLL  LLL  '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranoside'  ligand  70  31  .  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_LLL
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
 LLL  C11   C  CH1   0   0.296  -3.6104   1.2145  -0.4228
 LLL  O11   O  O2    0  -0.531  -2.9211   0.6075   0.6403
 LLL  C21   C  CH1   0  -0.135  -4.4701   2.3427   0.1494
 LLL  N21   N  NH2   0  -0.792  -3.6353   3.2688   0.8932
 LLL  C31   C  CH2   0  -0.463  -5.6789   1.7856   0.9026
 LLL  C41   C  CH2   0  -0.448  -6.4329   0.7795   0.0372
 LLL  C51   C  CH1   0   0.024  -5.4636  -0.2912  -0.4301
 LLL  O51   O  O2    0  -0.502  -4.3831   0.2980  -1.1419
 LLL  C61   C  CH2   0  -0.284  -6.0893  -1.3502  -1.3145
 LLL  N61   N  NH2   0  -0.802  -5.1200  -2.3840  -1.6438
 LLL  C12   C  CH1   0  -0.107   0.5562  -1.8560   0.9258
 LLL  N12   N  NH2   0  -0.803   1.5845  -2.8249   0.5631
 LLL  C22   C  CH2   0  -0.475  -0.8383  -2.4545   1.0605
 LLL  C32   C  CH1   0  -0.099  -1.8858  -1.4044   1.4063
 LLL  N32   N  NH2   0  -0.788  -3.1796  -2.0490   1.5582
 LLL  C42   C  CH1   0   0.065  -1.9274  -0.3451   0.3042
 LLL  C52   C  CH1   0   0.035  -0.5511   0.3105   0.1877
 LLL  O52   O  OH1   0  -0.670  -0.5855   1.2720  -0.8398
 LLL  C62   C  CH1   0   0.049   0.5349  -0.7302  -0.0993
 LLL  O62   O  O2    0  -0.522   1.7963  -0.0981  -0.0743
 LLL  C13   C  CH1   0   0.213   2.4767   0.1686  -1.2661
 LLL  C23   C  CH1   0   0.046   3.8546  -0.4945  -1.1944
 LLL  O23   O  OH1   0  -0.710   3.7335  -1.8770  -1.0215
 LLL  C33   C  CH1   0  -0.087   4.7224   0.1656  -0.1145
 LLL  N33   N  NH1   0  -0.606   6.0467  -0.4326  -0.0985
 LLL  C43   C  CT    0   0.141   4.7483   1.6930  -0.3173
 LLL  O43   O  OH1   0  -0.678   5.4763   1.9128  -1.5154
 LLL  C53   C  CH2   0  -0.182   3.3222   2.2214  -0.4654
 LLL  O53   O  O2    0  -0.495   2.5793   1.5481  -1.4656
 LLL  C83   C  CH3   0  -0.679   5.4110   2.4035   0.8580
 LLL  C93   C  CH3   0  -0.527   6.4960  -0.9132   1.1894
 LLL  H11   H  HCH1  0   0.228  -2.9094   1.6306  -1.1494
 LLL  H21   H  HCH1  0   0.230  -4.8510   2.8830  -0.7252
 LLL  H211  H  HNH2  0   0.343  -4.2019   4.0466   1.2085
 LLL  H212  H  HNH2  0   0.337  -3.2906   2.8166   1.7308
 LLL  H311  H  HCH2  0   0.233  -6.3308   2.6119   1.1980
 LLL  H312  H  HCH2  0   0.218  -5.3482   1.2980   1.8263
 LLL  H411  H  HCH2  0   0.219  -6.8832   1.2806  -0.8265
 LLL  H412  H  HCH2  0   0.232  -7.2468   0.3208   0.6037
 LLL  H51   H  HCH1  0   0.209  -5.0832  -0.8083   0.4577
 LLL  H611  H  HCH2  0   0.195  -6.9729  -1.7240  -0.7779
 LLL  H612  H  HCH2  0   0.208  -6.4602  -0.8924  -2.2378
 LLL  H11A  H  HNH2  0   0.335  -4.6624  -2.6964  -0.7946
 LLL  H12A  H  HNH2  0   0.342  -5.5968  -3.1896  -2.0264
 LLL  H121  H  HNH2  0   0.368   1.7871  -3.4235   1.3547
 LLL  H122  H  HNH2  0   0.356   1.2308  -3.4379  -0.1639
 LLL  H221  H  HCH2  0   0.227  -1.1230  -2.9490   0.1244
 LLL  H222  H  HCH2  0   0.250  -0.8224  -3.2275   1.8343
 LLL  H32   H  HCH1  0   0.205  -1.5638  -0.9034   2.3348
 LLL  H321  H  HNH2  0   0.347  -3.0977  -2.7795   2.2556
 LLL  H322  H  HNH2  0   0.351  -3.8409  -1.3863   1.9417
 LLL  H42   H  HCH1  0   0.222  -2.1851  -0.8429  -0.6404
 LLL  H52   H  HCH1  0   0.204  -0.3191   0.7832   1.1551
 LLL  H3    H  HOH1  0   0.450   0.2456   1.7601  -0.8393
 LLL  H62   H  HCH1  0   0.222   0.3421  -1.1608  -1.0946
 LLL  H13   H  HCH1  0   0.243   1.9184  -0.2214  -2.1261
 LLL  H23   H  HCH1  0   0.214   4.3404  -0.3400  -2.1639
 LLL  H2    H  HOH1  0   0.458   3.0657  -2.0897  -0.3286
 LLL  H1    H  HCH1  0   0.230   4.2482  -0.0213   0.8563
 LLL  H33   H  HNH1  0   0.344   6.7260   0.1978  -0.5009
 LLL  H43   H  HOH1  0   0.449   5.5919   2.8612  -1.6362
 LLL  H531  H  HCH2  0   0.241   3.3518   3.2723  -0.7651
 LLL  H532  H  HCH2  0   0.214   2.8062   2.1832   0.5007
 LLL  H831  H  HCH3  0   0.232   4.8971   2.1831   1.7942
 LLL  H832  H  HCH3  0   0.242   6.4526   2.1004   0.9644
 LLL  H833  H  HCH3  0   0.236   5.3948   3.4876   0.7188
 LLL  H931  H  HCH3  0   0.227   7.5102  -1.3041   1.0968
 LLL  H932  H  HCH3  0   0.192   6.5048  -0.1630   1.9922
 LLL  H933  H  HCH3  0   0.221   5.8632  -1.7381   1.5216
 LLL  H12   H  HCH1  0   0.241   0.8440  -1.4245   1.8905

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
 LLL  C11  O11   single  1.405  0.020  1.405
 LLL  C11  C21   single  1.529  0.020  1.529
 LLL  C11  O51   single  1.398  0.020  1.398
 LLL  C11  H11   single  0.970  0.020  1.090
 LLL  O11  C42   single  1.417  0.020  1.417
 LLL  C21  N21   single  1.452  0.020  1.452
 LLL  C21  C31   single  1.529  0.020  1.529
 LLL  C21  H21   single  0.970  0.020  1.090
 LLL  N21  H211  single  0.890  0.020  1.040
 LLL  N21  H212  single  0.890  0.020  1.040
 LLL  C31  C41   single  1.526  0.020  1.526
 LLL  C31  H311  single  0.970  0.020  1.090
 LLL  C31  H312  single  0.970  0.020  1.090
 LLL  C41  C51   single  1.518  0.020  1.518
 LLL  C41  H411  single  0.970  0.020  1.090
 LLL  C41  H412  single  0.970  0.020  1.090
 LLL  C51  O51   single  1.422  0.020  1.422
 LLL  C51  C61   single  1.515  0.020  1.515
 LLL  C51  H51   single  0.970  0.020  1.090
 LLL  C61  N61   single  1.455  0.020  1.455
 LLL  C61  H611  single  0.970  0.020  1.090
 LLL  C61  H612  single  0.970  0.020  1.090
 LLL  N61  H11A  single  0.890  0.020  1.040
 LLL  N61  H12A  single  0.890  0.020  1.040
 LLL  C12  N12   single  1.459  0.020  1.459
 LLL  C12  C22   single  1.523  0.020  1.523
 LLL  C12  C62   single  1.523  0.020  1.523
 LLL  C12  H12   single  0.970  0.020  1.090
 LLL  N12  H121  single  0.890  0.020  1.040
 LLL  N12  H122  single  0.890  0.020  1.040
 LLL  C22  C32   single  1.523  0.020  1.523
 LLL  C22  H221  single  0.970  0.020  1.090
 LLL  C22  H222  single  0.970  0.020  1.090
 LLL  C32  N32   single  1.453  0.020  1.453
 LLL  C32  C42   single  1.529  0.020  1.529
 LLL  C32  H32   single  0.970  0.020  1.090
 LLL  N32  H321  single  0.890  0.020  1.040
 LLL  N32  H322  single  0.890  0.020  1.040
 LLL  C42  C52   single  1.529  0.020  1.529
 LLL  C42  H42   single  0.970  0.020  1.090
 LLL  C52  O52   single  1.408  0.020  1.408
 LLL  C52  C62   single  1.531  0.020  1.531
 LLL  C52  H52   single  0.970  0.020  1.090
 LLL  O52  H3    single  0.850  0.020  0.980
 LLL  C62  O62   single  1.411  0.020  1.411
 LLL  C62  H62   single  0.970  0.020  1.090
 LLL  O62  C13   single  1.398  0.020  1.398
 LLL  C13  C23   single  1.531  0.020  1.531
 LLL  C13  O53   single  1.398  0.020  1.398
 LLL  C13  H13   single  0.970  0.020  1.090
 LLL  C23  O23   single  1.399  0.020  1.399
 LLL  C23  C33   single  1.535  0.020  1.535
 LLL  C23  H23   single  0.970  0.020  1.090
 LLL  O23  H2    single  0.850  0.020  0.980
 LLL  C33  N33   single  1.453  0.020  1.453
 LLL  C33  C43   single  1.541  0.020  1.541
 LLL  C33  H1    single  0.970  0.020  1.090
 LLL  N33  C93   single  1.446  0.020  1.446
 LLL  N33  H33   single  0.890  0.020  1.040
 LLL  C43  O43   single  1.419  0.020  1.419
 LLL  C43  C53   single  1.528  0.020  1.528
 LLL  C43  C83   single  1.525  0.020  1.525
 LLL  O43  H43   single  0.850  0.020  0.980
 LLL  C53  O53   single  1.416  0.020  1.416
 LLL  C53  H531  single  0.970  0.020  1.090
 LLL  C53  H532  single  0.970  0.020  1.090
 LLL  C83  H831  single  0.970  0.020  1.090
 LLL  C83  H832  single  0.970  0.020  1.090
 LLL  C83  H833  single  0.970  0.020  1.090
 LLL  C93  H931  single  0.970  0.020  1.090
 LLL  C93  H932  single  0.970  0.020  1.090
 LLL  C93  H933  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
 LLL  H11   C11  O51   105.21  3.000
 LLL  H11   C11  C21   109.19  3.000
 LLL  O51   C11  C21   111.43  3.000
 LLL  H11   C11  O11   110.68  3.000
 LLL  O51   C11  O11   112.16  3.000
 LLL  C21   C11  O11   108.15  3.000
 LLL  C42   O11  C11   117.07  3.000
 LLL  H21   C21  C31   107.33  3.000
 LLL  H21   C21  N21   107.10  3.000
 LLL  C31   C21  N21   115.75  3.000
 LLL  H21   C21  C11   105.09  3.000
 LLL  C31   C21  C11   111.09  3.000
 LLL  N21   C21  C11   109.82  3.000
 LLL  H212  N21  H211  106.03  3.000
 LLL  H212  N21  C21   109.55  3.000
 LLL  H211  N21  C21   109.13  3.000
 LLL  H312  C31  H311  106.77  3.000
 LLL  H312  C31  C41   109.50  3.000
 LLL  H311  C31  C41   110.91  3.000
 LLL  H312  C31  C21   109.81  3.000
 LLL  H311  C31  C21   109.21  3.000
 LLL  C41   C31  C21   110.57  3.000
 LLL  H412  C41  H411  107.14  3.000
 LLL  H412  C41  C51   109.83  3.000
 LLL  H411  C41  C51   110.02  3.000
 LLL  H412  C41  C31   110.53  3.000
 LLL  H411  C41  C31   110.40  3.000
 LLL  C51   C41  C31   108.91  3.000
 LLL  H51   C51  C61   106.65  3.000
 LLL  H51   C51  O51   109.72  3.000
 LLL  C61   C51  O51   108.14  3.000
 LLL  H51   C51  C41   107.77  3.000
 LLL  C61   C51  C41   114.15  3.000
 LLL  O51   C51  C41   110.31  3.000
 LLL  C51   O51  C11   115.74  3.000
 LLL  H612  C61  H611  106.34  3.000
 LLL  H612  C61  N61   109.38  3.000
 LLL  H611  C61  N61   113.85  3.000
 LLL  H612  C61  C51   109.87  3.000
 LLL  H611  C61  C51   106.54  3.000
 LLL  N61   C61  C51   110.72  3.000
 LLL  H12A  N61  H11A  106.51  3.000
 LLL  H12A  N61  C61   109.73  3.000
 LLL  H11A  N61  C61   109.27  3.000
 LLL  H12   C12  C62   107.77  3.000
 LLL  H12   C12  C22   108.51  3.000
 LLL  C62   C12  C22   109.71  3.000
 LLL  H12   C12  N12   107.18  3.000
 LLL  C62   C12  N12   109.48  3.000
 LLL  C22   C12  N12   113.97  3.000
 LLL  H122  N12  H121  105.83  3.000
 LLL  H122  N12  C12   109.49  3.000
 LLL  H121  N12  C12   109.83  3.000
 LLL  H222  C22  H221  106.80  3.000
 LLL  H222  C22  C32   109.67  3.000
 LLL  H221  C22  C32   109.05  3.000
 LLL  H222  C22  C12   109.08  3.000
 LLL  H221  C22  C12   109.84  3.000
 LLL  C32   C22  C12   112.25  3.000
 LLL  H32   C32  C42   107.46  3.000
 LLL  H32   C32  N32   111.92  3.000
 LLL  C42   C32  N32   111.00  3.000
 LLL  H32   C32  C22   107.67  3.000
 LLL  C42   C32  C22   109.43  3.000
 LLL  N32   C32  C22   109.27  3.000
 LLL  H322  N32  H321  105.32  3.000
 LLL  H322  N32  C32   109.33  3.000
 LLL  H321  N32  C32   108.65  3.000
 LLL  H42   C42  C52   109.88  3.000
 LLL  H42   C42  C32   108.19  3.000
 LLL  C52   C42  C32   109.11  3.000
 LLL  H42   C42  O11   110.13  3.000
 LLL  C52   C42  O11   111.17  3.000
 LLL  C32   C42  O11   108.29  3.000
 LLL  H52   C52  C62   107.87  3.000
 LLL  H52   C52  O52   110.67  3.000
 LLL  C62   C52  O52   110.17  3.000
 LLL  H52   C52  C42   107.86  3.000
 LLL  C62   C52  C42   111.18  3.000
 LLL  O52   C52  C42   109.06  3.000
 LLL  H3    O52  C52   108.93  3.000
 LLL  H62   C62  O62   110.34  3.000
 LLL  H62   C62  C52   108.11  3.000
 LLL  O62   C62  C52   109.04  3.000
 LLL  H62   C62  C12   108.77  3.000
 LLL  O62   C62  C12   107.87  3.000
 LLL  C52   C62  C12   112.72  3.000
 LLL  C13   O62  C62   120.36  3.000
 LLL  H13   C13  O53   106.04  3.000
 LLL  H13   C13  C23   109.92  3.000
 LLL  O53   C13  C23   111.60  3.000
 LLL  H13   C13  O62   110.66  3.000
 LLL  O53   C13  O62   110.23  3.000
 LLL  C23   C13  O62   108.39  3.000
 LLL  H23   C23  C33   108.14  3.000
 LLL  H23   C23  O23   106.69  3.000
 LLL  C33   C23  O23   112.78  3.000
 LLL  H23   C23  C13   107.26  3.000
 LLL  C33   C23  C13   110.83  3.000
 LLL  O23   C23  C13   110.86  3.000
 LLL  H2    O23  C23   111.04  3.000
 LLL  H1    C33  C43   107.02  3.000
 LLL  H1    C33  N33   108.31  3.000
 LLL  C43   C33  N33   113.21  3.000
 LLL  H1    C33  C23   107.77  3.000
 LLL  C43   C33  C23   110.07  3.000
 LLL  N33   C33  C23   110.25  3.000
 LLL  H33   N33  C93   110.68  3.000
 LLL  H33   N33  C33   110.58  3.000
 LLL  C93   N33  C33   115.45  3.000
 LLL  C83   C43  C53   108.61  3.000
 LLL  C83   C43  O43   110.83  3.000
 LLL  C53   C43  O43   110.09  3.000
 LLL  C83   C43  C33   111.57  3.000
 LLL  C53   C43  C33   109.87  3.000
 LLL  O43   C43  C33   105.85  3.000
 LLL  H43   O43  C43   108.66  3.000
 LLL  H532  C53  H531  106.74  3.000
 LLL  H532  C53  O53   111.04  3.000
 LLL  H531  C53  O53   106.12  3.000
 LLL  H532  C53  C43   109.99  3.000
 LLL  H531  C53  C43   109.50  3.000
 LLL  O53   C53  C43   113.18  3.000
 LLL  C53   O53  C13   114.02  3.000
 LLL  H833  C83  H832  107.59  3.000
 LLL  H833  C83  H831  107.62  3.000
 LLL  H832  C83  H831  108.07  3.000
 LLL  H833  C83  C43   110.95  3.000
 LLL  H832  C83  C43   111.16  3.000
 LLL  H831  C83  C43   111.27  3.000
 LLL  H933  C93  H932  107.35  3.000
 LLL  H933  C93  H931  107.10  3.000
 LLL  H932  C93  H931  107.41  3.000
 LLL  H933  C93  N33   110.00  3.000
 LLL  H932  C93  N33   115.23  3.000
 LLL  H931  C93  N33   109.41  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
 LLL  Var_01  C51   C41  C31  C21    54.59  30.0  1
 LLL  Var_02  C43   C53  O53  C13    57.85  30.0  1
 LLL  Var_03  H11A  N61  C61  C51    49.22  30.0  3
 LLL  Var_04  H931  C93  N33  C33  -177.78  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
 LLL  chir_01  C11  O11  C21  O51  positiv
 LLL  chir_02  C21  N21  C31  C11  positiv
 LLL  chir_03  C51  O51  C41  C61  negativ
 LLL  chir_04  C12  N12  C22  C62  positiv
 LLL  chir_05  C32  N32  C42  C22  positiv
 LLL  chir_06  C42  O11  C52  C32  negativ
 LLL  chir_07  C52  O52  C42  C62  negativ
 LLL  chir_08  C62  O62  C12  C52  negativ
 LLL  chir_09  C13  O62  O53  C23  negativ
 LLL  chir_10  C23  O23  C13  C33  negativ
 LLL  chir_11  C33  N33  C23  C43  positiv
 LLL  chir_12  C43  C83  C53  C33  positiv

