# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 17 17:05:06 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-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](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)[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
 9CS  9CS  '(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside'  ligand  70  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9CS
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
 9CS  C1    C  CH1   0   0.262   2.9350  -0.6189  -0.7513
 9CS  C2    C  CH1   0  -0.174   3.2477  -1.9418  -0.0488
 9CS  C3    C  CH1   0   0.040   4.0966  -1.6810   1.1938
 9CS  C4    C  CH1   0   0.039   5.3639  -0.9453   0.7915
 9CS  C5    C  CH1   0   0.017   4.9875   0.3312   0.0387
 9CS  C6    C  CH2   0  -0.305   6.1959   1.0520  -0.5316
 9CS  C7    C  CH1   0  -0.110  -1.2259   2.7834  -0.1578
 9CS  C8    C  CH1   0   0.052  -1.4619   1.2750  -0.1755
 9CS  C9    C  CH1   0   0.016  -0.2158   0.5324   0.3214
 9CS  C10   C  CH1   0   0.061   1.0253   0.8659  -0.5031
 9CS  C11   C  CH1   0  -0.096   1.2758   2.3717  -0.4920
 9CS  C12   C  CH2   0  -0.471   0.0240   3.0886  -0.9822
 9CS  C13   C  CH1   0   0.259  -3.8263   0.9356   0.2675
 9CS  C14   C  CH1   0   0.009  -4.7056   0.3683   1.3819
 9CS  C15   C  CH1   0  -0.154  -4.4988  -1.1385   1.5516
 9CS  C16   C  CH1   0   0.038  -4.6891  -1.8279   0.2015
 9CS  C17   C  CH1   0  -0.011  -3.8485  -1.1506  -0.8900
 9CS  C18   C  CH2   0  -0.164  -4.1989  -1.6717  -2.2678
 9CS  N1    N  NH2   0  -0.798   5.7948   2.2721  -1.2119
 9CS  N2    N  NH2   0  -0.823   2.3832   2.7150  -1.3672
 9CS  N3    N  NH2   0  -0.782  -2.4033   3.5048  -0.6174
 9CS  N4    N  NH2   0  -0.783  -5.3698  -1.7407   2.5444
 9CS  O5    O  O2    0  -0.508   4.1378   0.0315  -1.0610
 9CS  O7    O  OH1   0  -0.687   4.4330  -2.8984   1.8136
 9CS  O8    O  OH1   0  -0.677   6.1435  -0.5672   1.9020
 9CS  O9    O  O2    0  -0.519   2.1152   0.1611   0.0642
 9CS  O10   O  OH1   0  -0.658  -0.4099  -0.8604   0.2721
 9CS  O11   O  O2    0  -0.534  -2.4965   0.8486   0.6944
 9CS  O12   O  O2    0  -0.505  -4.0711   0.2490  -0.9228
 9CS  O13   O  OH1   0  -0.666  -4.4632   0.9903   2.6181
 9CS  O14   O  OH1   0  -0.665  -4.3152  -3.1787   0.3351
 9CS  O15   O  OH1   0  -0.667  -3.3277  -1.0968  -3.2116
 9CS  N6    N  NH2   0  -0.821   2.1094  -2.7598   0.3145
 9CS  H1    H  HCH1  0   0.236   2.4486  -0.8116  -1.7152
 9CS  H2    H  HCH1  0   0.246   3.8610  -2.5225  -0.7471
 9CS  H3    H  HCH1  0   0.196   3.5334  -1.0391   1.8908
 9CS  H4    H  HCH1  0   0.202   5.9372  -1.5972   0.1117
 9CS  H5    H  HCH1  0   0.215   4.4760   1.0126   0.7342
 9CS  H61   H  HCH2  0   0.236   6.8501   1.3204   0.2984
 9CS  H62   H  HCH2  0   0.198   6.7615   0.3526  -1.1650
 9CS  H7    H  HCH1  0   0.228  -1.0479   3.0859   0.8812
 9CS  H8    H  HCH1  0   0.221  -1.6673   0.9603  -1.2102
 9CS  H9    H  HCH1  0   0.212  -0.0290   0.8572   1.3575
 9CS  H10   H  HCH1  0   0.220   0.8696   0.5442  -1.5436
 9CS  H11   H  HCH1  0   0.203   1.4513   2.6689   0.5559
 9CS  H121  H  HCH2  0   0.223  -0.1555   2.8098  -2.0279
 9CS  H122  H  HCH2  0   0.245   0.1986   4.1685  -0.9714
 9CS  H13   H  HCH1  0   0.242  -4.0881   1.9758   0.0558
 9CS  H14   H  HCH1  0   0.211  -5.7470   0.5275   1.0611
 9CS  H15   H  HCH1  0   0.230  -3.4647  -1.3104   1.8759
 9CS  H16   H  HCH1  0   0.210  -5.7519  -1.7404  -0.0756
 9CS  H17   H  HCH1  0   0.214  -2.7902  -1.3682  -0.6940
 9CS  H181  H  HCH2  0   0.195  -4.1136  -2.7651  -2.2630
 9CS  H182  H  HCH2  0   0.197  -5.2503  -1.4320  -2.4810
 9CS  HN11  H  HNH2  0   0.354   6.6156   2.8229  -1.4264
 9CS  HN12  H  HNH2  0   0.345   5.3750   2.0452  -2.1035
 9CS  HN21  H  HNH2  0   0.341   2.4940   3.7218  -1.3693
 9CS  HN22  H  HNH2  0   0.363   3.2581   2.3513  -1.0108
 9CS  HN31  H  HNH2  0   0.352  -2.2347   4.5010  -0.5430
 9CS  HN32  H  HNH2  0   0.339  -2.5455   3.3231  -1.6053
 9CS  HN41  H  HNH2  0   0.348  -5.1999  -1.3069   3.4428
 9CS  HN42  H  HNH2  0   0.335  -6.3367  -1.5306   2.3192
 9CS  HO7   H  HOH1  0   0.442   3.6270  -3.4342   1.7636
 9CS  HO8   H  HOH1  0   0.454   6.4075  -1.3646   2.3716
 9CS  HO10  H  HOH1  0   0.455  -1.0997  -1.0868   0.9033
 9CS  HO13  H  HOH1  0   0.454  -4.7891   1.8943   2.5755
 9CS  HO14  H  HOH1  0   0.454  -4.8193  -3.7079  -0.2880
 9CS  HO15  H  HOH1  0   0.455  -3.5586  -1.4455  -4.0772
 9CS  HN61  H  HNH2  0   0.360   1.3498  -2.1767   0.6475
 9CS  HN62  H  HNH2  0   0.356   1.7554  -3.2489  -0.4971

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
 9CS  C1   O5    single  1.402  0.020  1.402
 9CS  C1   O9    single  1.395  0.020  1.395
 9CS  C1   C2    single  1.530  0.020  1.530
 9CS  C1   H1    single  0.970  0.020  1.090
 9CS  C2   C3    single  1.527  0.020  1.527
 9CS  C2   N6    single  1.448  0.020  1.448
 9CS  C2   H2    single  0.970  0.020  1.090
 9CS  C3   C4    single  1.520  0.020  1.520
 9CS  C3   O7    single  1.407  0.020  1.407
 9CS  C3   H3    single  0.970  0.020  1.090
 9CS  C4   C5    single  1.529  0.020  1.529
 9CS  C4   O8    single  1.409  0.020  1.409
 9CS  C4   H4    single  0.970  0.020  1.090
 9CS  C5   C6    single  1.518  0.020  1.518
 9CS  C5   O5    single  1.422  0.020  1.422
 9CS  C5   H5    single  0.970  0.020  1.090
 9CS  C6   N1    single  1.453  0.020  1.453
 9CS  C6   H61   single  0.970  0.020  1.090
 9CS  C6   H62   single  0.970  0.020  1.090
 9CS  C7   C12   single  1.528  0.020  1.528
 9CS  C7   N3    single  1.455  0.020  1.455
 9CS  C7   C8    single  1.527  0.020  1.527
 9CS  C7   H7    single  0.970  0.020  1.090
 9CS  C8   C9    single  1.533  0.020  1.533
 9CS  C8   O11   single  1.417  0.020  1.417
 9CS  C8   H8    single  0.970  0.020  1.090
 9CS  C9   C10   single  1.527  0.020  1.527
 9CS  C9   O10   single  1.407  0.020  1.407
 9CS  C9   H9    single  0.970  0.020  1.090
 9CS  C10  C11   single  1.526  0.020  1.526
 9CS  C10  O9    single  1.416  0.020  1.416
 9CS  C10  H10   single  0.970  0.020  1.090
 9CS  C11  N2    single  1.453  0.020  1.453
 9CS  C11  C12   single  1.524  0.020  1.524
 9CS  C11  H11   single  0.970  0.020  1.090
 9CS  C12  H121  single  0.970  0.020  1.090
 9CS  C12  H122  single  0.970  0.020  1.090
 9CS  C13  O11   single  1.399  0.020  1.399
 9CS  C13  C14   single  1.529  0.020  1.529
 9CS  C13  O12   single  1.396  0.020  1.396
 9CS  C13  H13   single  0.970  0.020  1.090
 9CS  C14  O13   single  1.405  0.020  1.405
 9CS  C14  C15   single  1.530  0.020  1.530
 9CS  C14  H14   single  0.970  0.020  1.090
 9CS  C15  N4    single  1.452  0.020  1.452
 9CS  C15  C16   single  1.528  0.020  1.528
 9CS  C15  H15   single  0.970  0.020  1.090
 9CS  C16  C17   single  1.535  0.020  1.535
 9CS  C16  O14   single  1.408  0.020  1.408
 9CS  C16  H16   single  0.970  0.020  1.090
 9CS  C17  O12   single  1.418  0.020  1.418
 9CS  C17  C18   single  1.514  0.020  1.514
 9CS  C17  H17   single  0.970  0.020  1.090
 9CS  C18  O15   single  1.407  0.020  1.407
 9CS  C18  H181  single  0.970  0.020  1.090
 9CS  C18  H182  single  0.970  0.020  1.090
 9CS  N1   HN11  single  0.890  0.020  1.040
 9CS  N1   HN12  single  0.890  0.020  1.040
 9CS  N2   HN21  single  0.890  0.020  1.040
 9CS  N2   HN22  single  0.890  0.020  1.040
 9CS  N3   HN31  single  0.890  0.020  1.040
 9CS  N3   HN32  single  0.890  0.020  1.040
 9CS  N4   HN41  single  0.890  0.020  1.040
 9CS  N4   HN42  single  0.890  0.020  1.040
 9CS  O7   HO7   single  0.850  0.020  0.980
 9CS  O8   HO8   single  0.850  0.020  0.980
 9CS  O10  HO10  single  0.850  0.020  0.980
 9CS  O13  HO13  single  0.850  0.020  0.980
 9CS  O14  HO14  single  0.850  0.020  0.980
 9CS  O15  HO15  single  0.850  0.020  0.980
 9CS  N6   HN61  single  0.890  0.020  1.040
 9CS  N6   HN62  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
 9CS  H1    C1   O9    110.58  3.000
 9CS  H1    C1   O5    105.54  3.000
 9CS  O9    C1   O5    111.96  3.000
 9CS  H1    C1   C2    110.01  3.000
 9CS  O9    C1   C2    109.58  3.000
 9CS  O5    C1   C2    109.10  3.000
 9CS  H2    C2   N6    107.49  3.000
 9CS  H2    C2   C3    107.33  3.000
 9CS  N6    C2   C3    109.22  3.000
 9CS  H2    C2   C1    106.25  3.000
 9CS  N6    C2   C1    116.29  3.000
 9CS  C3    C2   C1    109.85  3.000
 9CS  H3    C3   O7    110.33  3.000
 9CS  H3    C3   C4    108.15  3.000
 9CS  O7    C3   C4    109.64  3.000
 9CS  H3    C3   C2    109.27  3.000
 9CS  O7    C3   C2    110.10  3.000
 9CS  C4    C3   C2    109.32  3.000
 9CS  H4    C4   O8    110.92  3.000
 9CS  H4    C4   C5    108.54  3.000
 9CS  O8    C4   C5    107.48  3.000
 9CS  H4    C4   C3    108.09  3.000
 9CS  O8    C4   C3    112.51  3.000
 9CS  C5    C4   C3    109.22  3.000
 9CS  H5    C5   O5    109.98  3.000
 9CS  H5    C5   C6    108.27  3.000
 9CS  O5    C5   C6    106.57  3.000
 9CS  H5    C5   C4    108.69  3.000
 9CS  O5    C5   C4    110.61  3.000
 9CS  C6    C5   C4    112.67  3.000
 9CS  H62   C6   H61   106.63  3.000
 9CS  H62   C6   N1    113.96  3.000
 9CS  H61   C6   N1    108.37  3.000
 9CS  H62   C6   C5    108.89  3.000
 9CS  H61   C6   C5    107.97  3.000
 9CS  N1    C6   C5    110.78  3.000
 9CS  H7    C7   N3    107.08  3.000
 9CS  H7    C7   C12   108.86  3.000
 9CS  N3    C7   C12   113.10  3.000
 9CS  H7    C7   C8    107.98  3.000
 9CS  N3    C7   C8    111.16  3.000
 9CS  C12   C7   C8    108.51  3.000
 9CS  H8    C8   O11   110.78  3.000
 9CS  H8    C8   C9    108.53  3.000
 9CS  O11   C8   C9    104.40  3.000
 9CS  H8    C8   C7    108.79  3.000
 9CS  O11   C8   C7    113.76  3.000
 9CS  C9    C8   C7    110.43  3.000
 9CS  H9    C9   O10   110.37  3.000
 9CS  H9    C9   C10   107.79  3.000
 9CS  O10   C9   C10   108.02  3.000
 9CS  H9    C9   C8    107.44  3.000
 9CS  O10   C9   C8    110.85  3.000
 9CS  C10   C9   C8    112.33  3.000
 9CS  H10   C10  O9    110.01  3.000
 9CS  H10   C10  C11   108.57  3.000
 9CS  O9    C10  C11   111.21  3.000
 9CS  H10   C10  C9    109.37  3.000
 9CS  O9    C10  C9    107.49  3.000
 9CS  C11   C10  C9    110.18  3.000
 9CS  H11   C11  N2    112.79  3.000
 9CS  H11   C11  C12   108.03  3.000
 9CS  N2    C11  C12   108.74  3.000
 9CS  H11   C11  C10   107.38  3.000
 9CS  C12   C11  C10   109.08  3.000
 9CS  N2    C11  C10   110.73  3.000
 9CS  H122  C12  H121  106.64  3.000
 9CS  H122  C12  C11   109.28  3.000
 9CS  H121  C12  C11   108.76  3.000
 9CS  H122  C12  C7    108.80  3.000
 9CS  H121  C12  C7    109.25  3.000
 9CS  C11   C12  C7    113.86  3.000
 9CS  H13   C13  O12   105.13  3.000
 9CS  H13   C13  O11   110.23  3.000
 9CS  O12   C13  O11   113.34  3.000
 9CS  H13   C13  C14   110.88  3.000
 9CS  O12   C13  C14   109.77  3.000
 9CS  O11   C13  C14   107.52  3.000
 9CS  H14   C14  O13   110.82  3.000
 9CS  H14   C14  C15   107.60  3.000
 9CS  O13   C14  C15   108.37  3.000
 9CS  H14   C14  C13   106.14  3.000
 9CS  C15   C14  C13   111.62  3.000
 9CS  O13   C14  C13   112.20  3.000
 9CS  H15   C15  N4    107.36  3.000
 9CS  H15   C15  C16   107.93  3.000
 9CS  N4    C15  C16   110.03  3.000
 9CS  H15   C15  C14   108.32  3.000
 9CS  C16   C15  C14   109.24  3.000
 9CS  N4    C15  C14   113.78  3.000
 9CS  H16   C16  O14   110.87  3.000
 9CS  H16   C16  C17   108.32  3.000
 9CS  O14   C16  C17   110.20  3.000
 9CS  H16   C16  C15   107.85  3.000
 9CS  O14   C16  C15   108.42  3.000
 9CS  C17   C16  C15   111.16  3.000
 9CS  H17   C17  O12   110.56  3.000
 9CS  H17   C17  C18   108.50  3.000
 9CS  O12   C17  C18   106.40  3.000
 9CS  H17   C17  C16   108.27  3.000
 9CS  C18   C17  C16   111.62  3.000
 9CS  O12   C17  C16   111.47  3.000
 9CS  H182  C18  H181  107.02  3.000
 9CS  H182  C18  O15   111.90  3.000
 9CS  H181  C18  O15   111.22  3.000
 9CS  H182  C18  C17   108.84  3.000
 9CS  H181  C18  C17   108.73  3.000
 9CS  O15   C18  C17   109.05  3.000
 9CS  HN12  N1   HN11  105.79  3.000
 9CS  HN12  N1   C6    109.81  3.000
 9CS  HN11  N1   C6    109.42  3.000
 9CS  HN22  N2   HN21  105.27  3.000
 9CS  HN22  N2   C11   111.22  3.000
 9CS  HN21  N2   C11   108.64  3.000
 9CS  HN32  N3   HN31  105.72  3.000
 9CS  HN32  N3   C7    109.40  3.000
 9CS  HN31  N3   C7    109.24  3.000
 9CS  HN42  N4   HN41  105.57  3.000
 9CS  HN42  N4   C15   109.52  3.000
 9CS  HN41  N4   C15   109.19  3.000
 9CS  C5    O5   C1    116.08  3.000
 9CS  HO7   O7   C3    104.88  3.000
 9CS  HO8   O8   C4    108.31  3.000
 9CS  C10   O9   C1    119.76  3.000
 9CS  HO10  O10  C9    107.99  3.000
 9CS  C13   O11  C8    119.19  3.000
 9CS  C17   O12  C13   116.00  3.000
 9CS  HO13  O13  C14   108.58  3.000
 9CS  HO14  O14  C16   109.14  3.000
 9CS  HO15  O15  C18   107.88  3.000
 9CS  HN62  N6   HN61  106.22  3.000
 9CS  HN62  N6   C2    110.31  3.000
 9CS  HN61  N6   C2    110.28  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
 9CS  Var_01  HN11  N1  C6  C5  169.18  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
 9CS  chir_01  C1   O5   O9   C2   positiv
 9CS  chir_02  C2   N6   C3   C1   positiv
 9CS  chir_03  C3   O7   C2   C4   positiv
 9CS  chir_04  C4   O8   C5   C3   positiv
 9CS  chir_05  C5   O5   C4   C6   negativ
 9CS  chir_06  C7   C12  N3   C8   negativ
 9CS  chir_07  C8   O11  C9   C7   positiv
 9CS  chir_08  C9   O10  C8   C10  positiv
 9CS  chir_09  C10  O9   C11  C9   positiv
 9CS  chir_10  C11  N2   C12  C10  negativ
 9CS  chir_11  C13  O11  O12  C14  negativ
 9CS  chir_12  C14  O13  C13  C15  negativ
 9CS  chir_13  C15  N4   C16  C14  negativ
 9CS  chir_14  C16  O14  C17  C15  positiv
 9CS  chir_15  C17  O12  C16  C18  negativ

