# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 04:57:13 2020
#   Inital geometry file: a 145 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-amino-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@@H](N)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](N)[C@H]2O)[C@@H](O)[C@@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N
#
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
 KNC  KNC  '(1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside'  ligand  69  33  .  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_KNC
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
 KNC  C2    C  CH1   0  -0.139   3.2046   1.7838   0.4057
 KNC  C3    C  CH1   0   0.047   4.3547   1.7103  -0.5883
 KNC  C4    C  CH1   0   0.003   5.5135   0.9280   0.0132
 KNC  C5    C  CH1   0  -0.025   5.0163  -0.4527   0.4476
 KNC  C6    C  CH2   0  -0.166   6.0953  -1.2525   1.1435
 KNC  C7    C  CH1   0  -0.110  -1.3324  -2.5706  -0.7650
 KNC  C8    C  CH1   0   0.056  -1.4077  -1.3841   0.1856
 KNC  C9    C  CH1   0   0.035  -0.2125  -0.4437   0.0437
 KNC  C10   C  CH1   0   0.039   1.1173  -1.1820   0.1924
 KNC  C11   C  CH1   0  -0.100   1.1963  -2.3922  -0.7364
 KNC  C12   C  CH2   0  -0.465  -0.0139  -3.2992  -0.5424
 KNC  C13   C  CH1   0   0.220  -3.4574  -0.3218   0.9308
 KNC  C14   C  CH1   0   0.027  -4.8711  -0.7352   0.5266
 KNC  C15   C  CH1   0  -0.156  -5.4003   0.1246  -0.6348
 KNC  C16   C  CH1   0   0.048  -5.2185   1.6079  -0.3095
 KNC  C17   C  CH1   0  -0.026  -3.7590   1.8637   0.0802
 KNC  C18   C  CH2   0  -0.163  -3.4561   3.2892   0.4824
 KNC  N2    N  NH2   0  -0.810   2.4012  -3.1511  -0.4480
 KNC  N3    N  NH2   0  -0.802  -2.5186  -3.4018  -0.5883
 KNC  N4    N  NH2   0  -0.787  -6.7867  -0.1569  -0.9637
 KNC  C1    C  CH1   0   0.268   2.8176   0.3800   0.8839
 KNC  O5    O  O2    0  -0.498   3.9379  -0.3151   1.3562
 KNC  O7    O  OH1   0  -0.675   4.7325   3.0280  -0.9109
 KNC  O8    O  OH1   0  -0.675   6.5215   0.8334  -0.9708
 KNC  O9    O  O2    0  -0.512   2.1813  -0.3077  -0.1473
 KNC  O1    O  OH1   0  -0.665   5.6156  -2.5488   1.4054
 KNC  O10   O  OH1   0  -0.678  -0.2596   0.5637   1.0299
 KNC  O11   O  O2    0  -0.519  -2.5907  -0.6744  -0.1013
 KNC  O12   O  O2    0  -0.503  -3.3949   1.0482   1.1847
 KNC  O13   O  OH1   0  -0.708  -4.9488  -2.1078   0.2540
 KNC  O14   O  OH1   0  -0.666  -5.5718   2.3651  -1.4431
 KNC  O15   O  OH1   0  -0.667  -2.0607   3.3923   0.6617
 KNC  N6    N  NH2   0  -0.805   2.0686   2.4630  -0.1893
 KNC  H13   H  HOH1  0   0.458  -4.1183  -2.4310  -0.1673
 KNC  H14   H  HCH1  0   0.213  -5.5191  -0.5416   1.3928
 KNC  H15   H  HCH1  0   0.228  -4.8027  -0.0972  -1.5283
 KNC  HA    H  HCH1  0   0.245  -3.1692  -0.8169   1.8662
 KNC  H4N1  H  HNH2  0   0.344  -6.8719  -1.1388  -1.1957
 KNC  H4N2  H  HNH2  0   0.332  -7.3622  -0.0232  -0.1386
 KNC  H16   H  HCH1  0   0.210  -5.8629   1.8594   0.5478
 KNC  HB    H  HOH1  0   0.454  -5.8479   3.2407  -1.1597
 KNC  H17   H  HCH1  0   0.223  -3.1348   1.6283  -0.7934
 KNC  H181  H  HCH2  0   0.202  -3.8067   3.9640  -0.3067
 KNC  H182  H  HCH2  0   0.202  -4.0070   3.5437   1.3980
 KNC  HC    H  HOH1  0   0.460  -1.8453   4.3013   0.8884
 KNC  H8    H  HCH1  0   0.222  -1.4303  -1.7653   1.2187
 KNC  H9    H  HCH1  0   0.212  -0.2403  -0.0062  -0.9658
 KNC  H7    H  HCH1  0   0.240  -1.3585  -2.1869  -1.7908
 KNC  H10   H  HOH1  0   0.452  -0.9866   1.1713   0.8481
 KNC  HD    H  HCH1  0   0.224   1.2234  -1.5382   1.2280
 KNC  H3N1  H  HNH2  0   0.367  -2.6118  -4.0369  -1.3716
 KNC  H3N2  H  HNH2  0   0.356  -2.4080  -3.9904   0.2312
 KNC  H121  H  HCH2  0   0.224   0.0081  -3.7157   0.4716
 KNC  H122  H  HCH2  0   0.250   0.0544  -4.1458  -1.2315
 KNC  H11   H  HCH1  0   0.207   1.1668  -2.0076  -1.7697
 KNC  H2N1  H  HNH2  0   0.345   2.5159  -3.8746  -1.1466
 KNC  H2N2  H  HNH2  0   0.357   3.2186  -2.5611  -0.5242
 KNC  H1    H  HCH1  0   0.241   2.1606   0.4654   1.7540
 KNC  H2    H  HCH1  0   0.220   3.5822   2.2980   1.3050
 KNC  H5    H  HCH1  0   0.217   4.7027  -0.9992  -0.4541
 KNC  H6C1  H  HCH2  0   0.201   6.9778  -1.2784   0.4938
 KNC  H6C2  H  HCH2  0   0.196   6.3893  -0.7284   2.0641
 KNC  H4    H  HCH1  0   0.219   5.8782   1.4691   0.8989
 KNC  HE    H  HOH1  0   0.455   6.3368  -3.0571   1.7873
 KNC  HF    H  HOH1  0   0.461   7.3802   0.8036  -0.5405
 KNC  H3    H  HCH1  0   0.201   4.0084   1.1762  -1.4873
 KNC  HG    H  HOH1  0   0.448   5.4597   2.9809  -1.5402
 KNC  H6N1  H  HNH2  0   0.345   1.2503   2.3365   0.3922
 KNC  H6N2  H  HNH2  0   0.345   2.2528   3.4570  -0.2126

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
 KNC  O13  C14   single  1.401  0.020  1.401
 KNC  C14  C15   single  1.539  0.020  1.539
 KNC  C14  C13   single  1.527  0.020  1.527
 KNC  C15  N4    single  1.452  0.020  1.452
 KNC  C15  C16   single  1.529  0.020  1.529
 KNC  C16  O14   single  1.408  0.020  1.408
 KNC  C16  C17   single  1.532  0.020  1.532
 KNC  C17  C18   single  1.512  0.020  1.512
 KNC  C17  O12   single  1.420  0.020  1.420
 KNC  C18  O15   single  1.411  0.020  1.411
 KNC  O12  C13   single  1.395  0.020  1.395
 KNC  C13  O11   single  1.393  0.020  1.393
 KNC  O11  C8    single  1.409  0.020  1.409
 KNC  C8   C9    single  1.527  0.020  1.527
 KNC  C8   C7    single  1.522  0.020  1.522
 KNC  C9   O10   single  1.411  0.020  1.411
 KNC  C9   C10   single  1.528  0.020  1.528
 KNC  C7   N3    single  1.459  0.020  1.459
 KNC  C7   C12   single  1.523  0.020  1.523
 KNC  C12  C11   single  1.525  0.020  1.525
 KNC  C11  N2    single  1.453  0.020  1.453
 KNC  C11  C10   single  1.528  0.020  1.528
 KNC  C10  O9    single  1.418  0.020  1.418
 KNC  O9   C1    single  1.393  0.020  1.393
 KNC  C1   O5    single  1.400  0.020  1.400
 KNC  C1   C2    single  1.533  0.020  1.533
 KNC  O5   C5    single  1.417  0.020  1.417
 KNC  C5   C6    single  1.513  0.020  1.513
 KNC  C5   C4    single  1.530  0.020  1.530
 KNC  C6   O1    single  1.407  0.020  1.407
 KNC  C4   O8    single  1.412  0.020  1.412
 KNC  C4   C3    single  1.522  0.020  1.522
 KNC  C3   O7    single  1.408  0.020  1.408
 KNC  C3   C2    single  1.522  0.020  1.522
 KNC  C2   N6    single  1.451  0.020  1.451
 KNC  O13  H13   single  0.850  0.020  0.980
 KNC  C14  H14   single  0.970  0.020  1.090
 KNC  C15  H15   single  0.970  0.020  1.090
 KNC  C13  HA    single  0.970  0.020  1.090
 KNC  N4   H4N1  single  0.890  0.020  1.040
 KNC  N4   H4N2  single  0.890  0.020  1.040
 KNC  C16  H16   single  0.970  0.020  1.090
 KNC  O14  HB    single  0.850  0.020  0.980
 KNC  C17  H17   single  0.970  0.020  1.090
 KNC  C18  H181  single  0.970  0.020  1.090
 KNC  C18  H182  single  0.970  0.020  1.090
 KNC  O15  HC    single  0.850  0.020  0.980
 KNC  C8   H8    single  0.970  0.020  1.090
 KNC  C9   H9    single  0.970  0.020  1.090
 KNC  C7   H7    single  0.970  0.020  1.090
 KNC  O10  H10   single  0.850  0.020  0.980
 KNC  C10  HD    single  0.970  0.020  1.090
 KNC  N3   H3N1  single  0.890  0.020  1.040
 KNC  N3   H3N2  single  0.890  0.020  1.040
 KNC  C12  H121  single  0.970  0.020  1.090
 KNC  C12  H122  single  0.970  0.020  1.090
 KNC  C11  H11   single  0.970  0.020  1.090
 KNC  N2   H2N1  single  0.890  0.020  1.040
 KNC  N2   H2N2  single  0.890  0.020  1.040
 KNC  C1   H1    single  0.970  0.020  1.090
 KNC  C2   H2    single  0.970  0.020  1.090
 KNC  C5   H5    single  0.970  0.020  1.090
 KNC  C6   H6C1  single  0.970  0.020  1.090
 KNC  C6   H6C2  single  0.970  0.020  1.090
 KNC  C4   H4    single  0.970  0.020  1.090
 KNC  O1   HE    single  0.850  0.020  0.980
 KNC  O8   HF    single  0.850  0.020  0.980
 KNC  C3   H3    single  0.970  0.020  1.090
 KNC  O7   HG    single  0.850  0.020  0.980
 KNC  N6   H6N1  single  0.890  0.020  1.040
 KNC  N6   H6N2  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
 KNC  H2    C2   N6    112.59  3.000
 KNC  H2    C2   C1    105.02  3.000
 KNC  N6    C2   C1    111.03  3.000
 KNC  H2    C2   C3    107.25  3.000
 KNC  N6    C2   C3    110.26  3.000
 KNC  C1    C2   C3    110.51  3.000
 KNC  H3    C3   O7    110.55  3.000
 KNC  H3    C3   C4    108.22  3.000
 KNC  O7    C3   C4    111.54  3.000
 KNC  H3    C3   C2    108.60  3.000
 KNC  O7    C3   C2    107.89  3.000
 KNC  C4    C3   C2    110.00  3.000
 KNC  H4    C4   O8    110.94  3.000
 KNC  H4    C4   C5    108.84  3.000
 KNC  O8    C4   C5    111.67  3.000
 KNC  H4    C4   C3    108.53  3.000
 KNC  O8    C4   C3    107.61  3.000
 KNC  C5    C4   C3    109.18  3.000
 KNC  H5    C5   O5    110.92  3.000
 KNC  H5    C5   C6    108.52  3.000
 KNC  O5    C5   C6    107.42  3.000
 KNC  H5    C5   C4    107.95  3.000
 KNC  C6    C5   C4    112.07  3.000
 KNC  O5    C5   C4    109.98  3.000
 KNC  H6C2  C6   H6C1  107.00  3.000
 KNC  H6C2  C6   O1    111.99  3.000
 KNC  H6C1  C6   O1    111.29  3.000
 KNC  H6C2  C6   C5    108.90  3.000
 KNC  H6C1  C6   C5    108.31  3.000
 KNC  O1    C6   C5    109.25  3.000
 KNC  H7    C7   N3    107.07  3.000
 KNC  H7    C7   C12   108.97  3.000
 KNC  N3    C7   C12   114.43  3.000
 KNC  H7    C7   C8    108.10  3.000
 KNC  C12   C7   C8    108.94  3.000
 KNC  N3    C7   C8    109.16  3.000
 KNC  H8    C8   O11   110.37  3.000
 KNC  H8    C8   C9    108.44  3.000
 KNC  O11   C8   C9    109.14  3.000
 KNC  H8    C8   C7    108.49  3.000
 KNC  C9    C8   C7    112.53  3.000
 KNC  O11   C8   C7    107.87  3.000
 KNC  H9    C9   O10   110.89  3.000
 KNC  H9    C9   C10   107.66  3.000
 KNC  O10   C9   C10   107.82  3.000
 KNC  H9    C9   C8    108.07  3.000
 KNC  C10   C9   C8    111.99  3.000
 KNC  O10   C9   C8    110.41  3.000
 KNC  HD    C10  O9    110.65  3.000
 KNC  HD    C10  C11   108.11  3.000
 KNC  O9    C10  C11   107.69  3.000
 KNC  HD    C10  C9    109.38  3.000
 KNC  O9    C10  C9    109.37  3.000
 KNC  C11   C10  C9    111.63  3.000
 KNC  H11   C11  N2    112.97  3.000
 KNC  H11   C11  C12   107.78  3.000
 KNC  N2    C11  C12   108.80  3.000
 KNC  H11   C11  C10   106.98  3.000
 KNC  N2    C11  C10   109.64  3.000
 KNC  C12   C11  C10   110.66  3.000
 KNC  H122  C12  H121  106.70  3.000
 KNC  H122  C12  C11   109.32  3.000
 KNC  H121  C12  C11   109.13  3.000
 KNC  H122  C12  C7    109.41  3.000
 KNC  H121  C12  C7    109.53  3.000
 KNC  C11   C12  C7    112.58  3.000
 KNC  HA    C13  O12   106.04  3.000
 KNC  HA    C13  O11   110.74  3.000
 KNC  O12   C13  O11   110.83  3.000
 KNC  HA    C13  C14   110.29  3.000
 KNC  O11   C13  C14   108.13  3.000
 KNC  O12   C13  C14   110.83  3.000
 KNC  H14   C14  O13   107.04  3.000
 KNC  H14   C14  C15   107.08  3.000
 KNC  O13   C14  C15   112.42  3.000
 KNC  H14   C14  C13   106.82  3.000
 KNC  C15   C14  C13   111.52  3.000
 KNC  O13   C14  C13   111.59  3.000
 KNC  H15   C15  N4    107.23  3.000
 KNC  H15   C15  C16   107.73  3.000
 KNC  N4    C15  C16   110.46  3.000
 KNC  H15   C15  C14   108.31  3.000
 KNC  C16   C15  C14   109.91  3.000
 KNC  N4    C15  C14   113.01  3.000
 KNC  H16   C16  O14   110.92  3.000
 KNC  H16   C16  C17   108.73  3.000
 KNC  O14   C16  C17   110.73  3.000
 KNC  H16   C16  C15   108.51  3.000
 KNC  C17   C16  C15   109.22  3.000
 KNC  O14   C16  C15   108.69  3.000
 KNC  H17   C17  O12   110.46  3.000
 KNC  H17   C17  C18   107.44  3.000
 KNC  O12   C17  C18   106.45  3.000
 KNC  H17   C17  C16   107.64  3.000
 KNC  O12   C17  C16   110.25  3.000
 KNC  C18   C17  C16   114.58  3.000
 KNC  H182  C18  H181  107.29  3.000
 KNC  H182  C18  O15   111.91  3.000
 KNC  H181  C18  O15   111.28  3.000
 KNC  H182  C18  C17   109.86  3.000
 KNC  H181  C18  C17   108.96  3.000
 KNC  O15   C18  C17   107.51  3.000
 KNC  H2N2  N2   H2N1  105.87  3.000
 KNC  H2N2  N2   C11   110.53  3.000
 KNC  H2N1  N2   C11   109.29  3.000
 KNC  H3N2  N3   H3N1  105.72  3.000
 KNC  H3N2  N3   C7    109.85  3.000
 KNC  H3N1  N3   C7    109.78  3.000
 KNC  H4N2  N4   H4N1  105.45  3.000
 KNC  H4N2  N4   C15   109.37  3.000
 KNC  H4N1  N4   C15   108.67  3.000
 KNC  H1    C1   O9    110.67  3.000
 KNC  H1    C1   O5    104.53  3.000
 KNC  O9    C1   O5    111.71  3.000
 KNC  H1    C1   C2    109.17  3.000
 KNC  O5    C1   C2    110.97  3.000
 KNC  O9    C1   C2    109.67  3.000
 KNC  C1    O5   C5    116.15  3.000
 KNC  HG    O7   C3    107.85  3.000
 KNC  HF    O8   C4    109.14  3.000
 KNC  C1    O9   C10   118.01  3.000
 KNC  HE    O1   C6    107.78  3.000
 KNC  H10   O10  C9    110.07  3.000
 KNC  C13   O11  C8    119.93  3.000
 KNC  C17   O12  C13   114.27  3.000
 KNC  H13   O13  C14   110.94  3.000
 KNC  HB    O14  C16   108.94  3.000
 KNC  HC    O15  C18   108.71  3.000
 KNC  H6N2  N6   H6N1  106.47  3.000
 KNC  H6N2  N6   C2    109.09  3.000
 KNC  H6N1  N6   C2    109.82  3.000

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
 KNC  chir_01  C2   C1   C3   N6   negativ
 KNC  chir_02  C3   O7   C2   C4   positiv
 KNC  chir_03  C4   O8   C3   C5   negativ
 KNC  chir_04  C5   O5   C4   C6   negativ
 KNC  chir_05  C7   C8   N3   C12  positiv
 KNC  chir_06  C8   O11  C9   C7   positiv
 KNC  chir_07  C9   O10  C8   C10  positiv
 KNC  chir_08  C10  O9   C11  C9   positiv
 KNC  chir_09  C11  N2   C12  C10  negativ
 KNC  chir_10  C13  O11  O12  C14  negativ
 KNC  chir_11  C14  O13  C13  C15  negativ
 KNC  chir_12  C15  N4   C16  C14  negativ
 KNC  chir_13  C16  O14  C17  C15  positiv
 KNC  chir_14  C17  O12  C16  C18  negativ
 KNC  chir_15  C1   O9   O5   C2   negativ

