# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 08:20:16 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[(Z)-carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-alpha-D-arabino-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H]2O)[C@@H](N)C[C@@H]1NC(=N)C(O)=O
#
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
 KSG  KSG  '(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[(Z)-carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-alpha-D-arabino-hexopyranoside'  ligand  51  26  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KSG
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
 KSG  C1    C  CH1   0   0.301  305.1409  185.1066  -6.3568
 KSG  O1    O  O2    0  -0.536  303.9863  184.5838  -5.7554
 KSG  C2    C  CH1   0   0.005  302.8163  184.3763  -6.5268
 KSG  C3    C  CH1   0   0.002  301.6680  184.3674  -5.5153
 KSG  O2    O  OH1   0  -0.671  301.5877  185.5790  -4.8004
 KSG  C4    C  CH1   0  -0.015  300.3217  184.1559  -6.1978
 KSG  O3    O  OH1   0  -0.671  300.0087  185.2062  -7.0832
 KSG  C5    C  CH1   0  -0.018  300.3311  182.8703  -7.0152
 KSG  O4    O  OH1   0  -0.670  300.3953  181.7928  -6.1119
 KSG  C6    C  CH1   0  -0.020  301.5047  182.8312  -7.9985
 KSG  O5    O  OH1   0  -0.667  301.5587  181.5715  -8.6316
 KSG  C7    C  CH1   0   0.024  302.8475  183.0558  -7.3016
 KSG  O6    O  OH1   0  -0.656  303.9136  182.9916  -8.2187
 KSG  O7    O  O2    0  -0.506  304.9093  186.3003  -7.0488
 KSG  C8    C  CH1   0   0.066  304.4649  187.4183  -6.2869
 KSG  C9    C  CH3   0  -0.696  304.3071  188.5693  -7.2581
 KSG  C10   C  CH1   0  -0.111  305.4515  187.7145  -5.1476
 KSG  C11   C  CH2   0  -0.466  305.7195  186.4518  -4.3345
 KSG  C12   C  CH1   0  -0.160  306.1660  185.3031  -5.2431
 KSG  N1    N  NH2   0  -0.798  307.4759  185.4719  -5.8524
 KSG  N2    N  NH1   0  -0.649  304.9567  188.7637  -4.2894
 KSG  C13   C  C     0   0.303  305.3489  190.0587  -4.3263
 KSG  N3    N  N     0  -0.633  306.1925  190.6343  -5.0870
 KSG  C14   C  C     0   0.524  304.6872  190.9669  -3.3009
 KSG  O8    O  O     0  -0.411  304.8870  192.1483  -3.2537
 KSG  O9    O  OH1   0  -0.595  303.8819  190.3090  -2.4841
 KSG  H1    H  HCH1  0   0.236  305.5430  184.4226  -7.1064
 KSG  H2    H  HCH1  0   0.228  302.6656  185.2035  -7.2336
 KSG  H3    H  HCH1  0   0.223  301.8307  183.5276  -4.8256
 KSG  HO2   H  HOH1  0   0.453  302.4085  185.6895  -4.3106
 KSG  H4    H  HCH1  0   0.240  299.5530  184.0620  -5.4168
 KSG  HO3   H  HOH1  0   0.455  300.0670  186.0364  -6.5986
 KSG  H5    H  HCH1  0   0.235  299.3977  182.8325  -7.5987
 KSG  HO4   H  HOH1  0   0.450  300.5465  180.9933  -6.6298
 KSG  H6    H  HCH1  0   0.225  301.3606  183.6330  -8.7367
 KSG  HO5   H  HOH1  0   0.458  300.8336  181.5155  -9.2625
 KSG  H7    H  HCH1  0   0.236  303.0192  182.2411  -6.5895
 KSG  HO6   H  HOH1  0   0.445  303.7759  183.6579  -8.9015
 KSG  H8    H  HCH1  0   0.204  303.4851  187.2029  -5.8391
 KSG  H91   H  HCH3  0   0.239  303.9031  189.4459  -6.7546
 KSG  H92   H  HCH3  0   0.228  305.2619  188.8419  -7.7118
 KSG  H93   H  HCH3  0   0.248  303.6131  188.3029  -8.0559
 KSG  H10   H  HCH1  0   0.235  306.3982  188.0487  -5.5846
 KSG  H111  H  HCH2  0   0.231  304.8133  186.1639  -3.7914
 KSG  H112  H  HCH2  0   0.261  306.4855  186.6493  -3.5812
 KSG  H12   H  HCH1  0   0.256  306.2015  184.3821  -4.6553
 KSG  HN11  H  HNH2  0   0.344  307.5197  186.3269  -6.3933
 KSG  HN12  H  HNH2  0   0.355  308.1797  185.5589  -5.1305
 KSG  HN2   H  HNH1  0   0.404  304.2605  188.4992  -3.6117
 KSG  HN3   H  H     0   0.339  306.6053  189.9967  -5.7599
 KSG  HO9   H  HOH1  0   0.497  303.4643  190.9139  -1.8516

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
 KSG  C1   O7    single  1.399  0.020  1.399
 KSG  C1   O1    single  1.403  0.020  1.403
 KSG  C1   C12   single  1.526  0.020  1.526
 KSG  C1   H1    single  0.970  0.020  1.090
 KSG  O1   C2    single  1.417  0.020  1.417
 KSG  C2   C7    single  1.531  0.020  1.531
 KSG  C2   C3    single  1.530  0.020  1.530
 KSG  C2   H2    single  0.970  0.020  1.090
 KSG  C3   C4    single  1.524  0.020  1.524
 KSG  C3   O2    single  1.409  0.020  1.409
 KSG  C3   H3    single  0.970  0.020  1.090
 KSG  O2   HO2   single  0.850  0.020  0.980
 KSG  C4   O3    single  1.409  0.020  1.409
 KSG  C4   C5    single  1.523  0.020  1.523
 KSG  C4   H4    single  0.970  0.020  1.090
 KSG  O3   HO3   single  0.850  0.020  0.980
 KSG  C5   C6    single  1.532  0.020  1.532
 KSG  C5   O4    single  1.407  0.020  1.407
 KSG  C5   H5    single  0.970  0.020  1.090
 KSG  O4   HO4   single  0.850  0.020  0.980
 KSG  C6   O5    single  1.411  0.020  1.411
 KSG  C6   C7    single  1.529  0.020  1.529
 KSG  C6   H6    single  0.970  0.020  1.090
 KSG  O5   HO5   single  0.850  0.020  0.980
 KSG  C7   O6    single  1.408  0.020  1.408
 KSG  C7   H7    single  0.970  0.020  1.090
 KSG  O6   HO6   single  0.850  0.020  0.980
 KSG  O7   C8    single  1.424  0.020  1.424
 KSG  C8   C9    single  1.514  0.020  1.514
 KSG  C8   C10   single  1.536  0.020  1.536
 KSG  C8   H8    single  0.970  0.020  1.090
 KSG  C9   H91   single  0.970  0.020  1.090
 KSG  C9   H92   single  0.970  0.020  1.090
 KSG  C9   H93   single  0.970  0.020  1.090
 KSG  C10  C11   single  1.526  0.020  1.526
 KSG  C10  N2    single  1.443  0.020  1.443
 KSG  C10  H10   single  0.970  0.020  1.090
 KSG  C11  C12   single  1.531  0.020  1.531
 KSG  C11  H111  single  0.970  0.020  1.090
 KSG  C11  H112  single  0.970  0.020  1.090
 KSG  C12  N1    single  1.454  0.020  1.454
 KSG  C12  H12   single  0.970  0.020  1.090
 KSG  N1   HN11  single  0.890  0.020  1.040
 KSG  N1   HN12  single  0.890  0.020  1.040
 KSG  N2   C13   single  1.354  0.020  1.354
 KSG  N2   HN2   single  0.860  0.020  1.020
 KSG  C13  N3    double  1.273  0.020  1.273
 KSG  C13  C14   single  1.521  0.020  1.521
 KSG  N3   HN3   single  0.890  0.020  1.040
 KSG  C14  O8    double  1.199  0.020  1.199
 KSG  C14  O9    single  1.322  0.020  1.322
 KSG  O9   HO9   single  0.850  0.020  0.980

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
 KSG  H1    C1   C12   109.53  3.000
 KSG  H1    C1   O7    104.83  3.000
 KSG  C12   C1   O7    111.24  3.000
 KSG  H1    C1   O1    111.35  3.000
 KSG  C12   C1   O1    106.73  3.000
 KSG  O7    C1   O1    113.19  3.000
 KSG  C2    O1   C1    120.05  3.000
 KSG  H2    C2   C7    109.06  3.000
 KSG  H2    C2   C3    109.07  3.000
 KSG  C7    C2   C3    110.16  3.000
 KSG  H2    C2   O1    110.70  3.000
 KSG  C3    C2   O1    105.11  3.000
 KSG  C7    C2   O1    112.64  3.000
 KSG  H3    C3   C4    107.80  3.000
 KSG  H3    C3   O2    110.31  3.000
 KSG  C4    C3   O2    107.23  3.000
 KSG  H3    C3   C2    107.95  3.000
 KSG  O2    C3   C2    111.91  3.000
 KSG  C4    C3   C2    111.57  3.000
 KSG  HO2   O2   C3    107.96  3.000
 KSG  H4    C4   C5    108.26  3.000
 KSG  H4    C4   O3    110.76  3.000
 KSG  C5    C4   O3    107.06  3.000
 KSG  H4    C4   C3    108.13  3.000
 KSG  C5    C4   C3    110.61  3.000
 KSG  O3    C4   C3    111.97  3.000
 KSG  HO3   O3   C4    108.24  3.000
 KSG  H5    C5   C6    107.96  3.000
 KSG  H5    C5   O4    110.64  3.000
 KSG  C6    C5   O4    110.95  3.000
 KSG  H5    C5   C4    107.93  3.000
 KSG  O4    C5   C4    107.58  3.000
 KSG  C6    C5   C4    111.76  3.000
 KSG  HO4   O4   C5    107.29  3.000
 KSG  H6    C6   C7    108.30  3.000
 KSG  H6    C6   O5    110.79  3.000
 KSG  C7    C6   O5    107.57  3.000
 KSG  H6    C6   C5    108.18  3.000
 KSG  C7    C6   C5    112.11  3.000
 KSG  O5    C6   C5    109.89  3.000
 KSG  HO5   O5   C6    108.49  3.000
 KSG  H7    C7   O6    105.71  3.000
 KSG  H7    C7   C6    108.94  3.000
 KSG  O6    C7   C6    111.18  3.000
 KSG  H7    C7   C2    108.40  3.000
 KSG  O6    C7   C2    112.60  3.000
 KSG  C6    C7   C2    109.83  3.000
 KSG  HO6   O6   C7    108.77  3.000
 KSG  C8    O7   C1    117.19  3.000
 KSG  H8    C8   C10   107.96  3.000
 KSG  H8    C8   C9    108.51  3.000
 KSG  C10   C8   C9    113.33  3.000
 KSG  H8    C8   O7    110.03  3.000
 KSG  C10   C8   O7    110.35  3.000
 KSG  C9    C8   O7    106.63  3.000
 KSG  H93   C9   H92   108.27  3.000
 KSG  H93   C9   H91   107.40  3.000
 KSG  H92   C9   H91   108.41  3.000
 KSG  H93   C9   C8    110.48  3.000
 KSG  H92   C9   C8    111.42  3.000
 KSG  H91   C9   C8    110.74  3.000
 KSG  H10   C10  N2    108.17  3.000
 KSG  H10   C10  C11   108.27  3.000
 KSG  N2    C10  C11   110.19  3.000
 KSG  H10   C10  C8    108.56  3.000
 KSG  N2    C10  C8    111.17  3.000
 KSG  C11   C10  C8    110.40  3.000
 KSG  H112  C11  H111  106.61  3.000
 KSG  H112  C11  C12   109.90  3.000
 KSG  H111  C11  C12   109.78  3.000
 KSG  H112  C11  C10   109.94  3.000
 KSG  H111  C11  C10   109.67  3.000
 KSG  C12   C11  C10   110.85  3.000
 KSG  H12   C12  N1    107.09  3.000
 KSG  H12   C12  C11   108.81  3.000
 KSG  N1    C12  C11   115.10  3.000
 KSG  H12   C12  C1    107.80  3.000
 KSG  N1    C12  C1    108.31  3.000
 KSG  C11   C12  C1    109.49  3.000
 KSG  HN12  N1   HN11  106.16  3.000
 KSG  HN12  N1   C12   109.73  3.000
 KSG  HN11  N1   C12   111.14  3.000
 KSG  HN2   N2   C13   118.03  3.000
 KSG  HN2   N2   C10   116.51  3.000
 KSG  C13   N2   C10   125.46  3.000
 KSG  C14   C13  N3    114.90  3.000
 KSG  C14   C13  N2    115.26  3.000
 KSG  N3    C13  N2    129.84  3.000
 KSG  HN3   N3   C13   112.43  3.000
 KSG  O9    C14  O8    124.57  3.000
 KSG  O9    C14  C13   112.60  3.000
 KSG  O8    C14  C13   122.83  3.000
 KSG  HO9   O9   C14   110.78  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
 KSG  CONST_01  N3   C13  N2   C10     0.00   0.0  0
 KSG  CONST_02  C14  C13  N2   C10   180.00   0.0  0
 KSG  CONST_03  HN3  N3   C13  N2      0.00   0.0  0
 KSG  CONST_04  HO9  O9   C14  C13   180.00   0.0  0
 KSG  CONST_05  HN2  N2   C13  N3    180.00   0.0  0
 KSG  Var_01    O8   C14  C13  N2   -176.43  30.0  2

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
 KSG  chir_01  C1   O7  O1   C12  positiv
 KSG  chir_02  C2   O1  C7   C3   negativ
 KSG  chir_03  C3   O2  C2   C4   positiv
 KSG  chir_04  C4   O3  C3   C5   positiv
 KSG  chir_05  C5   O4  C4   C6   negativ
 KSG  chir_06  C6   O5  C5   C7   negativ
 KSG  chir_07  C7   O6  C6   C2   positiv
 KSG  chir_08  C8   O7  C9   C10  positiv
 KSG  chir_09  C10  N2  C11  C8   negativ
 KSG  chir_10  C12  N1  C11  C1   negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KSG  plan-1  C10  0.020
 KSG  plan-1  N2   0.020
 KSG  plan-1  C13  0.020
 KSG  plan-1  N3   0.020
 KSG  plan-1  C14  0.020
 KSG  plan-1  HN2  0.020
 KSG  plan-1  HN3  0.020
 KSG  plan-2  C13  0.020
 KSG  plan-2  C14  0.020
 KSG  plan-2  O8   0.020
 KSG  plan-2  O9   0.020
 KSG  plan-2  HO9  0.020

