# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 06:26:00 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (1R,2R,3S,4R,6S)-4,6-diamino-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](N)C[C@H](N)[C@H]2O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@H](O)[C@@H]1O
#
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
 N30  N30  '(1R,2R,3S,4R,6S)-4,6-diamino-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside'  ligand  65  31  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N30
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
 N30  C11   C  CH1   0   0.266   0.9864  -0.4368   1.9576
 N30  O11   O  O2    0  -0.529   1.3183  -1.3492   0.9536
 N30  C21   C  CH1   0  -0.187   1.9760  -0.5883   3.1098
 N30  N21   N  NH2   0  -0.804   3.3730  -0.3692   2.7936
 N30  C31   C  CH1   0   0.041   1.7999  -1.9640   3.7494
 N30  O31   O  OH1   0  -0.684   2.6438  -2.0961   4.8672
 N30  C41   C  CH1   0   0.034   0.3530  -2.1441   4.1899
 N30  O41   O  OH1   0  -0.675   0.1006  -3.4458   4.6644
 N30  C51   C  CH1   0  -0.033  -0.5833  -1.8937   3.0048
 N30  O51   O  O2    0  -0.491  -0.3194  -0.6303   2.4212
 N30  C61   C  CH2   0  -0.168  -2.0465  -1.8886   3.4190
 N30  O61   O  OH1   0  -0.655  -2.9197  -1.6527   2.3396
 N30  C12   C  CH1   0  -0.115   2.3901  -2.5990  -2.2566
 N30  N12   N  NH2   0  -0.785   1.7755  -2.3738  -3.5576
 N30  C22   C  CH2   0  -0.485   1.4046  -3.2946  -1.3130
 N30  C32   C  CH1   0  -0.127   0.2200  -2.4126  -0.8968
 N30  N32   N  NH2   0  -0.786  -0.7600  -2.1666  -1.9483
 N30  C42   C  CH1   0  -0.002   0.7054  -1.0847  -0.3082
 N30  C52   C  CH1   0   0.028   1.7331  -0.3487  -1.1827
 N30  O52   O  O2    0  -0.495   1.1048   0.2235  -2.3105
 N30  C62   C  CH1   0   0.002   2.8718  -1.2713  -1.6525
 N30  O62   O  OH1   0  -0.673   3.7801  -1.5250  -0.5967
 N30  C13   C  CH1   0   0.264   0.7943   1.5792  -2.2055
 N30  C23   C  CH1   0  -0.045   0.1373   1.9925  -3.5138
 N30  O23   O  OH1   0  -0.676   0.2518   3.3855  -3.6494
 N30  C33   C  CH1   0  -0.062  -1.3139   1.5851  -3.2362
 N30  O33   O  OH1   0  -0.664  -2.2571   2.2980  -3.9948
 N30  C43   C  CH1   0   0.073  -1.4718   1.9159  -1.7507
 N30  O43   O  O2    0  -0.502  -0.1539   1.8509  -1.2088
 N30  C53   C  CH2   0  -0.347  -2.4248   0.9784  -1.0296
 N30  N53   N  NH2   0  -0.826  -2.5329   1.2844   0.3917
 N30  H11   H  HCH1  0   0.236   1.0015   0.5900   1.5694
 N30  H21   H  HCH1  0   0.256   1.6989   0.1629   3.8569
 N30  H211  H  HNH2  0   0.364   3.5658   0.6196   2.7080
 N30  H212  H  HNH2  0   0.341   3.6223  -0.7896   1.9081
 N30  H31   H  HCH1  0   0.200   2.0291  -2.7406   3.0021
 N30  HO31  H  HOH1  0   0.445   3.4843  -1.6951   4.6032
 N30  H41   H  HCH1  0   0.207   0.1393  -1.3919   4.9671
 N30  HO41  H  HOH1  0   0.455   0.6522  -3.5965   5.4384
 N30  H51   H  HCH1  0   0.225  -0.4263  -2.6954   2.2672
 N30  H611  H  HCH2  0   0.220  -2.2145  -1.0863   4.1424
 N30  H612  H  HCH2  0   0.216  -2.2745  -2.8336   3.9223
 N30  HO61  H  HOH1  0   0.447  -2.8686  -2.4024   1.7389
 N30  H121  H  HNH2  0   0.346   2.4244  -1.8875  -4.1644
 N30  H122  H  HNH2  0   0.345   1.5997  -3.2693  -3.9968
 N30  H221  H  HCH2  0   0.245   1.0316  -4.2082  -1.7866
 N30  H222  H  HCH2  0   0.225   1.9400  -3.6373  -0.4212
 N30  H32   H  HCH1  0   0.240  -0.3137  -2.9221  -0.0872
 N30  H321  H  HNH2  0   0.362  -0.2647  -1.8628  -2.7797
 N30  H322  H  HNH2  0   0.335  -1.1830  -3.0542  -2.1942
 N30  H42   H  HCH1  0   0.276  -0.1638  -0.4412  -0.1697
 N30  H52   H  HCH1  0   0.231   2.1974   0.4426  -0.5744
 N30  H62   H  HCH1  0   0.243   3.4496  -0.7268  -2.4074
 N30  HO62  H  HOH1  0   0.448   3.3189  -2.0234   0.0857
 N30  H13   H  HCH1  0   0.228   1.6976   2.1568  -1.9663
 N30  H23   H  HCH1  0   0.233   0.5691   1.4638  -4.3723
 N30  HO23  H  HOH1  0   0.446  -0.5311   3.6947  -4.1212
 N30  H33   H  HCH1  0   0.239  -1.4159   0.5029  -3.3861
 N30  HO33  H  HOH1  0   0.463  -2.3264   1.8869  -4.8623
 N30  H43   H  HCH1  0   0.212  -1.8338   2.9468  -1.6403
 N30  H531  H  HCH2  0   0.240  -2.0936  -0.0520  -1.1935
 N30  H532  H  HCH2  0   0.228  -3.3963   1.0692  -1.5268
 N30  HN1   H  HNH2  0   0.348  -2.2722   0.4829   0.9491
 N30  HN2   H  HNH2  0   0.342  -3.4886   1.4988   0.6347
 N30  H12   H  HCH1  0   0.221   3.2858  -3.2345  -2.3312

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
 N30  C11  C21   single  1.526  0.020  1.526
 N30  C11  O51   single  1.399  0.020  1.399
 N30  C11  O11   single  1.397  0.020  1.397
 N30  C11  H11   single  0.970  0.020  1.090
 N30  O11  C42   single  1.428  0.020  1.428
 N30  C21  C31   single  1.527  0.020  1.527
 N30  C21  N21   single  1.449  0.020  1.449
 N30  C21  H21   single  0.970  0.020  1.090
 N30  N21  H211  single  0.890  0.020  1.040
 N30  N21  H212  single  0.890  0.020  1.040
 N30  C31  O31   single  1.407  0.020  1.407
 N30  C31  C41   single  1.523  0.020  1.523
 N30  C31  H31   single  0.970  0.020  1.090
 N30  O31  HO31  single  0.850  0.020  0.980
 N30  C41  O41   single  1.408  0.020  1.408
 N30  C41  C51   single  1.531  0.020  1.531
 N30  C41  H41   single  0.970  0.020  1.090
 N30  O41  HO41  single  0.850  0.020  0.980
 N30  C51  C61   single  1.521  0.020  1.521
 N30  C51  O51   single  1.416  0.020  1.416
 N30  C51  H51   single  0.970  0.020  1.090
 N30  C61  O61   single  1.408  0.020  1.408
 N30  C61  H611  single  0.970  0.020  1.090
 N30  C61  H612  single  0.970  0.020  1.090
 N30  O61  HO61  single  0.850  0.020  0.980
 N30  C12  C22   single  1.532  0.020  1.532
 N30  C12  N12   single  1.456  0.020  1.456
 N30  C12  C62   single  1.536  0.020  1.536
 N30  C12  H12   single  0.970  0.020  1.090
 N30  N12  H121  single  0.890  0.020  1.040
 N30  N12  H122  single  0.890  0.020  1.040
 N30  C22  C32   single  1.534  0.020  1.534
 N30  C22  H221  single  0.970  0.020  1.090
 N30  C22  H222  single  0.970  0.020  1.090
 N30  C32  N32   single  1.458  0.020  1.458
 N30  C32  C42   single  1.531  0.020  1.531
 N30  C32  H32   single  0.970  0.020  1.090
 N30  N32  H321  single  0.890  0.020  1.040
 N30  N32  H322  single  0.890  0.020  1.040
 N30  C42  C52   single  1.537  0.020  1.537
 N30  C42  H42   single  0.970  0.020  1.090
 N30  C52  C62   single  1.539  0.020  1.539
 N30  C52  O52   single  1.412  0.020  1.412
 N30  C52  H52   single  0.970  0.020  1.090
 N30  O52  C13   single  1.395  0.020  1.395
 N30  C62  O62   single  1.416  0.020  1.416
 N30  C62  H62   single  0.970  0.020  1.090
 N30  O62  HO62  single  0.850  0.020  0.980
 N30  C13  O43   single  1.402  0.020  1.402
 N30  C13  C23   single  1.521  0.020  1.521
 N30  C13  H13   single  0.970  0.020  1.090
 N30  C23  C33   single  1.533  0.020  1.533
 N30  C23  O23   single  1.404  0.020  1.404
 N30  C23  H23   single  0.970  0.020  1.090
 N30  O23  HO23  single  0.850  0.020  0.980
 N30  C33  C43   single  1.530  0.020  1.530
 N30  C33  O33   single  1.405  0.020  1.405
 N30  C33  H33   single  0.970  0.020  1.090
 N30  O33  HO33  single  0.850  0.020  0.980
 N30  C43  C53   single  1.519  0.020  1.519
 N30  C43  O43   single  1.427  0.020  1.427
 N30  C43  H43   single  0.970  0.020  1.090
 N30  C53  N53   single  1.458  0.020  1.458
 N30  C53  H531  single  0.970  0.020  1.090
 N30  C53  H532  single  0.970  0.020  1.090
 N30  N53  HN1   single  0.890  0.020  1.040
 N30  N53  HN2   single  0.890  0.020  1.040

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
 N30  H11   C11  O51   105.03  3.000
 N30  H11   C11  C21   110.54  3.000
 N30  O51   C11  C21   109.96  3.000
 N30  H11   C11  O11   110.70  3.000
 N30  O51   C11  O11   111.69  3.000
 N30  C21   C11  O11   108.89  3.000
 N30  C42   O11  C11   114.35  3.000
 N30  H21   C21  C31   107.63  3.000
 N30  H21   C21  N21   106.81  3.000
 N30  C31   C21  N21   109.80  3.000
 N30  H21   C21  C11   106.43  3.000
 N30  N21   C21  C11   116.45  3.000
 N30  C31   C21  C11   109.31  3.000
 N30  H212  N21  H211  106.58  3.000
 N30  H212  N21  C21   111.46  3.000
 N30  H211  N21  C21   110.49  3.000
 N30  H31   C31  C41   108.09  3.000
 N30  H31   C31  O31   110.36  3.000
 N30  C41   C31  O31   109.21  3.000
 N30  H31   C31  C21   109.07  3.000
 N30  C41   C31  C21   109.70  3.000
 N30  O31   C31  C21   110.37  3.000
 N30  HO31  O31  C31   105.39  3.000
 N30  H41   C41  C51   108.39  3.000
 N30  H41   C41  O41   111.00  3.000
 N30  C51   C41  O41   107.60  3.000
 N30  H41   C41  C31   107.90  3.000
 N30  C51   C41  C31   109.74  3.000
 N30  O41   C41  C31   112.15  3.000
 N30  HO41  O41  C41   108.24  3.000
 N30  H51   C51  C61   108.80  3.000
 N30  H51   C51  O51   110.31  3.000
 N30  C61   C51  O51   106.77  3.000
 N30  H51   C51  C41   108.20  3.000
 N30  O51   C51  C41   110.54  3.000
 N30  C61   C51  C41   112.22  3.000
 N30  C51   O51  C11   115.71  3.000
 N30  H612  C61  H611  107.29  3.000
 N30  H612  C61  O61   111.58  3.000
 N30  H611  C61  O61   106.79  3.000
 N30  H612  C61  C51   108.83  3.000
 N30  H611  C61  C51   109.31  3.000
 N30  O61   C61  C51   112.86  3.000
 N30  HO61  O61  C61   108.37  3.000
 N30  H12   C12  C62   105.70  3.000
 N30  H12   C12  C22   107.65  3.000
 N30  C62   C12  C22   110.62  3.000
 N30  H12   C12  N12   111.84  3.000
 N30  C62   C12  N12   110.49  3.000
 N30  C22   C12  N12   110.43  3.000
 N30  H122  N12  H121  106.02  3.000
 N30  H122  N12  C12   108.90  3.000
 N30  H121  N12  C12   109.82  3.000
 N30  H222  C22  H221  104.94  3.000
 N30  H222  C22  C32   109.66  3.000
 N30  H221  C22  C32   109.52  3.000
 N30  H222  C22  C12   109.22  3.000
 N30  H221  C22  C12   109.38  3.000
 N30  C32   C22  C12   113.75  3.000
 N30  H32   C32  C42   105.88  3.000
 N30  H32   C32  N32   106.50  3.000
 N30  C42   C32  N32   110.12  3.000
 N30  H32   C32  C22   108.01  3.000
 N30  C42   C32  C22   110.97  3.000
 N30  N32   C32  C22   114.85  3.000
 N30  H322  N32  H321  105.50  3.000
 N30  H322  N32  C32   107.92  3.000
 N30  H321  N32  C32   108.27  3.000
 N30  H42   C42  C52   108.82  3.000
 N30  H42   C42  C32   107.93  3.000
 N30  C52   C42  C32   114.10  3.000
 N30  H42   C42  O11   109.84  3.000
 N30  C52   C42  O11   107.73  3.000
 N30  C32   C42  O11   108.37  3.000
 N30  H52   C52  C62   106.71  3.000
 N30  H52   C52  O52   109.74  3.000
 N30  C62   C52  O52   109.17  3.000
 N30  H52   C52  C42   108.17  3.000
 N30  O52   C52  C42   110.54  3.000
 N30  C62   C52  C42   112.42  3.000
 N30  C13   O52  C52   115.64  3.000
 N30  H62   C62  O62   105.34  3.000
 N30  H62   C62  C52   107.62  3.000
 N30  O62   C62  C52   110.76  3.000
 N30  H62   C62  C12   108.91  3.000
 N30  O62   C62  C12   109.85  3.000
 N30  C52   C62  C12   113.96  3.000
 N30  HO62  O62  C62   108.31  3.000
 N30  H13   C13  O43   107.42  3.000
 N30  H13   C13  C23   113.55  3.000
 N30  O43   C13  C23   105.47  3.000
 N30  H13   C13  O52   110.14  3.000
 N30  C23   C13  O52   107.19  3.000
 N30  O43   C13  O52   113.10  3.000
 N30  H23   C23  C33   112.73  3.000
 N30  H23   C23  O23   111.75  3.000
 N30  C33   C23  O23   111.00  3.000
 N30  H23   C23  C13   111.85  3.000
 N30  O23   C23  C13   108.51  3.000
 N30  C33   C23  C13   100.42  3.000
 N30  HO23  O23  C23   107.39  3.000
 N30  H33   C33  C43   109.65  3.000
 N30  H33   C33  O33   111.36  3.000
 N30  C43   C33  O33   110.19  3.000
 N30  H33   C33  C23   109.00  3.000
 N30  O33   C33  C23   113.77  3.000
 N30  C43   C33  C23   102.48  3.000
 N30  HO33  O33  C33   108.56  3.000
 N30  H43   C43  C53   108.96  3.000
 N30  H43   C43  O43   108.00  3.000
 N30  C53   C43  O43   111.79  3.000
 N30  H43   C43  C33   109.55  3.000
 N30  O43   C43  C33   105.28  3.000
 N30  C53   C43  C33   113.10  3.000
 N30  C43   O43  C13   111.31  3.000
 N30  H532  C53  H531  106.17  3.000
 N30  H532  C53  N53   111.07  3.000
 N30  H531  C53  N53   111.47  3.000
 N30  H532  C53  C43   106.84  3.000
 N30  H531  C53  C43   108.67  3.000
 N30  N53   C53  C43   112.32  3.000
 N30  HN2   N53  HN1   106.27  3.000
 N30  HN2   N53  C53   110.46  3.000
 N30  HN1   N53  C53   110.62  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
 N30  Var_01  HN1  N53  C53  C43  -121.77  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
 N30  chir_01  C11  C21  O51  O11  positiv
 N30  chir_02  C21  N21  C31  C11  positiv
 N30  chir_03  C31  O31  C21  C41  positiv
 N30  chir_04  C41  O41  C31  C51  negativ
 N30  chir_05  C51  O51  C41  C61  negativ
 N30  chir_06  C12  C22  N12  C62  negativ
 N30  chir_07  C32  N32  C42  C22  positiv
 N30  chir_08  C42  O11  C52  C32  negativ
 N30  chir_09  C52  O52  C62  C42  positiv
 N30  chir_10  C62  O62  C52  C12  positiv
 N30  chir_11  C13  O52  O43  C23  positiv
 N30  chir_12  C23  O23  C13  C33  negativ
 N30  chir_13  C33  O33  C43  C23  positiv
 N30  chir_14  C43  O43  C33  C53  negativ

