# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 03:14:17 2020
#   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  50  26  .  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_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   0.345   -4.0030   2.2152   0.1566
 KSG  O1    O  O2     0  -0.499   -4.3750   0.8987  -0.1707
 KSG  C2    C  CH1    0   0.027   -3.5042   0.1688  -0.9990
 KSG  C3    C  CH1    0  -0.007   -4.3430  -0.6570  -1.9782
 KSG  O2    O  OH1    0  -0.661   -5.1368   0.1555  -2.7971
 KSG  C4    C  CH1    0  -0.083   -3.4663  -1.5327  -2.8745
 KSG  O3    O  OH1    0  -0.643   -2.7218  -0.8021  -3.8158
 KSG  C5    C  CH1    0  -0.012   -2.6051  -2.4425  -1.9904
 KSG  O4    O  OH1    0  -0.635   -1.7240  -3.2445  -2.7370
 KSG  C6    C  CH1    0  -0.015   -1.7556  -1.6344  -1.0162
 KSG  O5    O  OH1    0  -0.640   -1.0253  -2.4699  -0.1523
 KSG  C7    C  CH1    0   0.025   -2.6339  -0.7449  -0.1435
 KSG  O6    O  OH1    0  -0.697   -1.8617   0.0595   0.7079
 KSG  O7    O  O2     0  -0.499   -4.5350   3.1298  -0.7601
 KSG  C8    C  CH1    0   0.031   -5.9580   3.2346  -0.7782
 KSG  C9    C  CH3    0  -0.676   -6.3145   4.2387  -1.8488
 KSG  C10   C  CH1    0  -0.095   -6.5066   3.6042   0.5982
 KSG  C11   C  CH2    0  -0.433   -5.9696   2.6249   1.6479
 KSG  C12   C  CH1    0  -0.165   -4.4486   2.5175   1.5925
 KSG  N1    N  NH2    0  -0.778   -3.8344   3.7217   2.1240
 KSG  N2    N  NH1    0  -0.575   -7.9308   3.6439   0.5292
 KSG  C13   C  C      0   0.316   -8.7295   4.3138   1.4286
 KSG  N3    N  N      0  -0.769   -8.3918   5.2326   2.2425
 KSG  C14   C  C      0   0.383  -10.1932   3.7796   1.3305
 KSG  O8    O  O      0  -0.497  -10.2937   2.8117   0.5408
 KSG  O9    O  OC    -1  -0.742  -11.0677   4.4818   1.8234
 KSG  H1    H  HCH1   0   0.214   -2.9161   2.3284   0.0737
 KSG  H2    H  HCH1   0   0.223   -2.8584   0.8590  -1.5657
 KSG  H3    H  HCH1   0   0.233   -4.9678  -1.3408  -1.3808
 KSG  HO2   H  HOH1   0   0.456   -5.7372   0.6465  -2.2284
 KSG  H4    H  HCH1   0   0.206   -4.1337  -2.1660  -3.4685
 KSG  HO3   H  HOH1   0   0.438   -2.0757  -0.2426  -3.3778
 KSG  H5    H  HCH1   0   0.216   -3.2921  -3.0657  -1.3981
 KSG  HO4   H  HOH1   0   0.460   -2.2243  -3.9412  -3.1693
 KSG  H6    H  HCH1   0   0.203   -1.0608  -0.9897  -1.5833
 KSG  HO5   H  HOH1   0   0.469   -0.4423  -3.0154  -0.6883
 KSG  H7    H  HCH1   0   0.256   -3.3059  -1.3971   0.4382
 KSG  HO6   H  HOH1   0   0.459   -1.3585  -0.5183   1.2888
 KSG  H8    H  HCH1   0   0.145   -6.3997   2.2614  -1.0477
 KSG  H91   H  HCH3   0   0.279   -7.3959   4.3368  -1.9217
 KSG  H92   H  HCH3   0   0.187   -5.9042   5.2223  -1.6083
 KSG  H93   H  HCH3   0   0.234   -5.9307   3.9371  -2.8250
 KSG  H10   H  HCH1   0   0.240   -6.1510   4.6182   0.8314
 KSG  H111  H  HCH2   0   0.240   -6.2830   2.9409   2.6438
 KSG  H112  H  HCH2   0   0.233   -6.4191   1.6447   1.4665
 KSG  H12   H  HCH1   0   0.222   -4.1158   1.6854   2.2188
 KSG  HN11  H  HNH2   0   0.347   -4.0257   4.5223   1.5364
 KSG  HN12  H  HNH2   0   0.372   -2.8287   3.6219   2.1610
 KSG  HN2   H  HNH1   0   0.384   -8.4480   2.8183   0.2223
 KSG  HN3   H  H      0   0.280   -7.3943   5.4373   2.1922

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  1.400  0.020  1.400
 KSG  C1   O1    single  1.407  0.020  1.407
 KSG  C1   C12   single  1.533  0.020  1.533
 KSG  C1   H1    single  0.970  0.020  1.090
 KSG  O1   C2    single  1.406  0.020  1.406
 KSG  C2   C7    single  1.524  0.020  1.524
 KSG  C2   C3    single  1.531  0.020  1.531
 KSG  C2   H2    single  0.970  0.020  1.090
 KSG  C3   C4    single  1.529  0.020  1.529
 KSG  C3   O2    single  1.400  0.020  1.400
 KSG  C3   H3    single  0.970  0.020  1.090
 KSG  O2   HO2   single  0.850  0.020  0.980
 KSG  C4   O3    single  1.405  0.020  1.405
 KSG  C4   C5    single  1.533  0.020  1.533
 KSG  C4   H4    single  0.970  0.020  1.090
 KSG  O3   HO3   single  0.850  0.020  0.980
 KSG  C5   C6    single  1.524  0.020  1.524
 KSG  C5   O4    single  1.406  0.020  1.406
 KSG  C5   H5    single  0.970  0.020  1.090
 KSG  O4   HO4   single  0.850  0.020  0.980
 KSG  C6   O5    single  1.406  0.020  1.406
 KSG  C6   C7    single  1.525  0.020  1.525
 KSG  C6   H6    single  0.970  0.020  1.090
 KSG  O5   HO5   single  0.850  0.020  0.980
 KSG  C7   O6    single  1.403  0.020  1.403
 KSG  C7   H7    single  0.970  0.020  1.090
 KSG  O6   HO6   single  0.850  0.020  0.980
 KSG  O7   C8    single  1.427  0.020  1.427
 KSG  C8   C9    single  1.510  0.020  1.510
 KSG  C8   C10   single  1.527  0.020  1.527
 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  1.533  0.020  1.533
 KSG  C10  N2    single  1.426  0.020  1.426
 KSG  C10  H10   single  0.970  0.020  1.090
 KSG  C11  C12   single  1.526  0.020  1.526
 KSG  C11  H111  single  0.970  0.020  1.090
 KSG  C11  H112  single  0.970  0.020  1.090
 KSG  C12  N1    single  1.453  0.020  1.453
 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  1.377  0.020  1.377
 KSG  N2   HN2   single  0.890  0.020  1.040
 KSG  C13  N3    double  1.273  0.020  1.273
 KSG  C13  C14   single  1.561  0.020  1.561
 KSG  N3   HN3   single  0.890  0.020  1.040
 KSG  C14  O8    deloc   1.253  0.020  1.253
 KSG  C14  O9    deloc   1.225  0.020  1.225

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   109.80  3.000
 KSG  H1    C1   O7    105.06  3.000
 KSG  C12   C1   O7    111.96  3.000
 KSG  H1    C1   O1    109.96  3.000
 KSG  C12   C1   O1    109.00  3.000
 KSG  O7    C1   O1    111.01  3.000
 KSG  C2    O1   C1    117.33  3.000
 KSG  H2    C2   C7    109.23  3.000
 KSG  H2    C2   C3    109.27  3.000
 KSG  C7    C2   C3    110.38  3.000
 KSG  H2    C2   O1    109.92  3.000
 KSG  C3    C2   O1    108.51  3.000
 KSG  C7    C2   O1    109.52  3.000
 KSG  H3    C3   C4    106.70  3.000
 KSG  H3    C3   O2    110.83  3.000
 KSG  C4    C3   O2    108.33  3.000
 KSG  H3    C3   C2    107.37  3.000
 KSG  O2    C3   C2    111.81  3.000
 KSG  C4    C3   C2    111.69  3.000
 KSG  HO2   O2   C3    107.71  3.000
 KSG  H4    C4   C5    108.18  3.000
 KSG  H4    C4   O3    105.09  3.000
 KSG  C5    C4   O3    113.40  3.000
 KSG  H4    C4   C3    107.44  3.000
 KSG  C5    C4   C3    108.89  3.000
 KSG  O3    C4   C3    113.50  3.000
 KSG  HO3   O3   C4    110.72  3.000
 KSG  H5    C5   C6    107.71  3.000
 KSG  H5    C5   O4    110.73  3.000
 KSG  C6    C5   O4    107.01  3.000
 KSG  H5    C5   C4    107.20  3.000
 KSG  O4    C5   C4    112.60  3.000
 KSG  C6    C5   C4    111.53  3.000
 KSG  HO4   O4   C5    109.05  3.000
 KSG  H6    C6   C7    108.41  3.000
 KSG  H6    C6   O5    109.61  3.000
 KSG  C7    C6   O5    107.11  3.000
 KSG  H6    C6   C5    109.38  3.000
 KSG  C7    C6   C5    110.73  3.000
 KSG  O5    C6   C5    111.53  3.000
 KSG  HO5   O5   C6    108.03  3.000
 KSG  H7    C7   O6    110.76  3.000
 KSG  H7    C7   C6    107.94  3.000
 KSG  O6    C7   C6    111.39  3.000
 KSG  H7    C7   C2    107.62  3.000
 KSG  O6    C7   C2    108.12  3.000
 KSG  C6    C7   C2    110.94  3.000
 KSG  HO6   O6   C7    108.07  3.000
 KSG  C8    O7   C1    115.80  3.000
 KSG  H8    C8   C10   106.87  3.000
 KSG  H8    C8   C9    108.60  3.000
 KSG  C10   C8   C9    113.15  3.000
 KSG  H8    C8   O7    109.75  3.000
 KSG  C10   C8   O7    111.39  3.000
 KSG  C9    C8   O7    107.05  3.000
 KSG  H93   C9   H92   108.28  3.000
 KSG  H93   C9   H91   108.33  3.000
 KSG  H92   C9   H91   107.86  3.000
 KSG  H93   C9   C8    111.55  3.000
 KSG  H92   C9   C8    110.72  3.000
 KSG  H91   C9   C8    109.99  3.000
 KSG  H10   C10  N2    107.91  3.000
 KSG  H10   C10  C11   109.30  3.000
 KSG  N2    C10  C11   113.62  3.000
 KSG  H10   C10  C8    107.35  3.000
 KSG  N2    C10  C8    108.78  3.000
 KSG  C11   C10  C8    109.68  3.000
 KSG  H112  C11  H111  107.03  3.000
 KSG  H112  C11  C12   109.92  3.000
 KSG  H111  C11  C12   109.88  3.000
 KSG  H112  C11  C10   108.36  3.000
 KSG  H111  C11  C10   109.85  3.000
 KSG  C12   C11  C10   111.68  3.000
 KSG  H12   C12  N1    107.01  3.000
 KSG  H12   C12  C11   109.65  3.000
 KSG  N1    C12  C11   110.48  3.000
 KSG  H12   C12  C1    107.33  3.000
 KSG  N1    C12  C1    112.53  3.000
 KSG  C11   C12  C1    109.73  3.000
 KSG  HN12  N1   HN11  106.70  3.000
 KSG  HN12  N1   C12   110.61  3.000
 KSG  HN11  N1   C12   111.33  3.000
 KSG  HN2   N2   C13   107.21  3.000
 KSG  HN2   N2   C10   119.83  3.000
 KSG  C13   N2   C10   124.14  3.000
 KSG  C14   C13  N3    122.40  3.000
 KSG  C14   C13  N2    109.65  3.000
 KSG  N3    C13  N2    127.95  3.000
 KSG  HN3   N3   C13   111.89  3.000
 KSG  O9    C14  O8    129.72  3.000
 KSG  O9    C14  C13   116.60  3.000
 KSG  O8    C14  C13   112.27  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_03  HN3  N3   C13  N2    0.00   0.0  0
 KSG  CONST_04  HN2  N2   C13  N3  180.00   0.0  0
 KSG  Var_01    O8   C14  C13  N2    4.81  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   positiv
 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

