# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 09:47:13 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside
#   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]2O)[C@H](N)[C@@H](O)[C@H]1F
#
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
 V71  V71  '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside'  D-saccharide  47  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V71
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
 V71  C1   C  CH1   0   0.270  -0.9144   0.2814  -0.7822
 V71  C10  C  CH1   0   0.041   1.3516  -0.1736  -0.0907
 V71  C11  C  CH1   0   0.005   2.1272   1.1335   0.0736
 V71  C12  C  CH1   0   0.072   3.6251   0.9447  -0.1507
 V71  C2   C  CH1   0  -0.140  -1.7931   1.4883  -0.4237
 V71  C3   C  CH1   0  -0.009  -2.8146   1.1251   0.6538
 V71  C4   C  CH1   0   0.162  -3.5469  -0.1610   0.2987
 V71  C5   C  CH1   0  -0.033  -2.5397  -1.2570   0.0224
 V71  C6   C  CH2   0  -0.306  -3.1424  -2.5935  -0.3612
 V71  C7   C  CH1   0  -0.117   4.1791  -0.1260   0.7793
 V71  C8   C  CH2   0  -0.465   3.3944  -1.4209   0.5664
 V71  C9   C  CH1   0  -0.099   1.8964  -1.2753   0.8056
 V71  F99  F  F     0  -0.382  -4.3374   0.0512  -0.8303
 V71  N2   N  NH2   0  -0.818  -0.9380   2.6118  -0.0613
 V71  N6   N  NH2   0  -0.797  -2.1072  -3.6141  -0.3757
 V71  N7   N  NH2   0  -0.786   5.6124  -0.2760   0.5790
 V71  N9   N  NH2   0  -0.812   1.2380  -2.5362   0.5006
 V71  O1   O  O2    0  -0.522  -0.0069   0.0629   0.2521
 V71  O11  O  OH1   0  -0.718   1.6946   2.1164  -0.8345
 V71  O12  O  OH1   0  -0.675   4.3099   2.1559   0.0577
 V71  O23  O  OH1   0  -0.666  -3.6849   2.2151   0.8141
 V71  O5   O  O2    0  -0.501  -1.6757  -0.8619  -1.0317
 V71  H1   H  HCH1  0   0.243  -0.3920   0.4909  -1.7214
 V71  H2   H  HCH1  0   0.215   1.4254  -0.5131  -1.1343
 V71  H3   H  HCH1  0   0.192   1.9878   1.4715   1.1149
 V71  H4   H  HCH1  0   0.186   3.7715   0.5938  -1.1886
 V71  H5   H  HCH1  0   0.265  -2.3350   1.7640  -1.3331
 V71  H6   H  HCH1  0   0.226  -2.2708   0.9148   1.5873
 V71  H7   H  HCH1  0   0.235  -4.2108  -0.4583   1.1174
 V71  H8   H  HCH1  0   0.230  -1.9765  -1.4136   0.9531
 V71  H9   H  HCH2  0   0.231  -3.8770  -2.8598   0.4022
 V71  H10  H  HCH2  0   0.209  -3.6910  -2.4967  -1.3070
 V71  H11  H  HCH1  0   0.222   4.0301   0.2096   1.8135
 V71  H12  H  HCH2  0   0.218   3.5577  -1.7758  -0.4584
 V71  H13  H  HCH2  0   0.243   3.7932  -2.1954   1.2286
 V71  H14  H  HCH1  0   0.203   1.7480  -0.9563   1.8511
 V71  H15  H  HNH2  0   0.377  -1.4059   3.4870  -0.2549
 V71  H16  H  HNH2  0   0.367  -0.7503   2.6074   0.9352
 V71  H18  H  HNH2  0   0.353  -2.5278  -4.5196  -0.5384
 V71  H19  H  HNH2  0   0.344  -1.4798  -3.4560  -1.1533
 V71  H21  H  HNH2  0   0.344   5.9547  -1.0016   1.1978
 V71  H22  H  HNH2  0   0.333   5.7826  -0.6230  -0.3592
 V71  H24  H  HNH2  0   0.343   1.5581  -3.2443   1.1501
 V71  H25  H  HNH2  0   0.350   0.2376  -2.4670   0.6402
 V71  H27  H  HOH1  0   0.467   0.7741   2.3908  -0.6021
 V71  H28  H  HOH1  0   0.442   3.8428   2.8316  -0.4466
 V71  H29  H  HOH1  0   0.457  -4.1471   2.1217   1.6530

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
 V71  N6   C6   single  1.454  0.020  1.454
 V71  C6   C5   single  1.515  0.020  1.515
 V71  F99  C4   single  1.394  0.020  1.394
 V71  O5   C5   single  1.419  0.020  1.419
 V71  O5   C1   single  1.396  0.020  1.396
 V71  C5   C4   single  1.514  0.020  1.514
 V71  C4   C3   single  1.522  0.020  1.522
 V71  C1   C2   single  1.535  0.020  1.535
 V71  C1   O1   single  1.393  0.020  1.393
 V71  C2   C3   single  1.529  0.020  1.529
 V71  C2   N2   single  1.458  0.020  1.458
 V71  O11  C11  single  1.406  0.020  1.406
 V71  C3   O23  single  1.404  0.020  1.404
 V71  O1   C10  single  1.421  0.020  1.421
 V71  C10  C11  single  1.529  0.020  1.529
 V71  C10  C9   single  1.521  0.020  1.521
 V71  N9   C9   single  1.455  0.020  1.455
 V71  C11  C12  single  1.526  0.020  1.526
 V71  C12  O12  single  1.407  0.020  1.407
 V71  C12  C7   single  1.523  0.020  1.523
 V71  C9   C8   single  1.524  0.020  1.524
 V71  C8   C7   single  1.529  0.020  1.529
 V71  C7   N7   single  1.455  0.020  1.455
 V71  C1   H1   single  0.970  0.020  1.090
 V71  C10  H2   single  0.970  0.020  1.090
 V71  C11  H3   single  0.970  0.020  1.090
 V71  C12  H4   single  0.970  0.020  1.090
 V71  C2   H5   single  0.970  0.020  1.090
 V71  C3   H6   single  0.970  0.020  1.090
 V71  C4   H7   single  0.970  0.020  1.090
 V71  C5   H8   single  0.970  0.020  1.090
 V71  C6   H9   single  0.970  0.020  1.090
 V71  C6   H10  single  0.970  0.020  1.090
 V71  C7   H11  single  0.970  0.020  1.090
 V71  C8   H12  single  0.970  0.020  1.090
 V71  C8   H13  single  0.970  0.020  1.090
 V71  C9   H14  single  0.970  0.020  1.090
 V71  N2   H15  single  0.890  0.020  1.040
 V71  N2   H16  single  0.890  0.020  1.040
 V71  N6   H18  single  0.890  0.020  1.040
 V71  N6   H19  single  0.890  0.020  1.040
 V71  N7   H21  single  0.890  0.020  1.040
 V71  N7   H22  single  0.890  0.020  1.040
 V71  N9   H24  single  0.890  0.020  1.040
 V71  N9   H25  single  0.890  0.020  1.040
 V71  O11  H27  single  0.850  0.020  0.980
 V71  O12  H28  single  0.850  0.020  0.980
 V71  O23  H29  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
 V71  H1   C1   O5   105.28  3.000
 V71  H1   C1   O1   110.86  3.000
 V71  O5   C1   O1   111.06  3.000
 V71  H1   C1   C2   108.84  3.000
 V71  O1   C1   C2   108.83  3.000
 V71  O5   C1   C2   111.93  3.000
 V71  H2   C10  O1   110.15  3.000
 V71  H2   C10  C9   108.15  3.000
 V71  O1   C10  C9   108.71  3.000
 V71  H2   C10  C11  109.38  3.000
 V71  C9   C10  C11  111.97  3.000
 V71  O1   C10  C11  108.47  3.000
 V71  H3   C11  O11  110.88  3.000
 V71  H3   C11  C12  107.49  3.000
 V71  O11  C11  C12  107.06  3.000
 V71  H3   C11  C10  107.41  3.000
 V71  C12  C11  C10  112.11  3.000
 V71  O11  C11  C10  111.85  3.000
 V71  H4   C12  O12  110.36  3.000
 V71  H4   C12  C7   107.58  3.000
 V71  O12  C12  C7   109.74  3.000
 V71  H4   C12  C11  107.90  3.000
 V71  C7   C12  C11  110.75  3.000
 V71  O12  C12  C11  110.45  3.000
 V71  H5   C2   N2   107.64  3.000
 V71  H5   C2   C3   108.36  3.000
 V71  N2   C2   C3   113.58  3.000
 V71  H5   C2   C1   106.71  3.000
 V71  N2   C2   C1   109.15  3.000
 V71  C3   C2   C1   111.11  3.000
 V71  H6   C3   O23  110.96  3.000
 V71  H6   C3   C4   105.91  3.000
 V71  O23  C3   C4   112.61  3.000
 V71  H6   C3   C2   108.25  3.000
 V71  O23  C3   C2   108.07  3.000
 V71  C4   C3   C2   110.97  3.000
 V71  H7   C4   F99  107.63  3.000
 V71  H7   C4   C5   110.07  3.000
 V71  F99  C4   C5   109.85  3.000
 V71  H7   C4   C3   110.28  3.000
 V71  C5   C4   C3   109.53  3.000
 V71  F99  C4   C3   109.46  3.000
 V71  H8   C5   O5   110.89  3.000
 V71  H8   C5   C6   107.00  3.000
 V71  O5   C5   C6   107.44  3.000
 V71  H8   C5   C4   106.83  3.000
 V71  O5   C5   C4   109.82  3.000
 V71  C6   C5   C4   114.84  3.000
 V71  H10  C6   H9   106.71  3.000
 V71  H10  C6   N6   114.15  3.000
 V71  H9   C6   N6   108.35  3.000
 V71  H10  C6   C5   109.82  3.000
 V71  H9   C6   C5   107.79  3.000
 V71  N6   C6   C5   109.79  3.000
 V71  H11  C7   N7   107.16  3.000
 V71  H11  C7   C8   108.69  3.000
 V71  N7   C7   C8   113.52  3.000
 V71  H11  C7   C12  108.13  3.000
 V71  N7   C7   C12  110.30  3.000
 V71  C8   C7   C12  108.89  3.000
 V71  H13  C8   H12  106.39  3.000
 V71  H13  C8   C9   109.32  3.000
 V71  H12  C8   C9   108.90  3.000
 V71  H13  C8   C7   109.16  3.000
 V71  H12  C8   C7   109.13  3.000
 V71  C9   C8   C7   113.69  3.000
 V71  H14  C9   N9   112.86  3.000
 V71  H14  C9   C8   107.98  3.000
 V71  N9   C9   C8   109.22  3.000
 V71  H14  C9   C10  107.51  3.000
 V71  C8   C9   C10  109.19  3.000
 V71  N9   C9   C10  110.00  3.000
 V71  H16  N2   H15  106.11  3.000
 V71  H16  N2   C2   110.46  3.000
 V71  H15  N2   C2   110.37  3.000
 V71  H19  N6   H18  105.91  3.000
 V71  H19  N6   C6   109.85  3.000
 V71  H18  N6   C6   109.51  3.000
 V71  H22  N7   H21  105.26  3.000
 V71  H22  N7   C7   109.13  3.000
 V71  H21  N7   C7   108.82  3.000
 V71  H25  N9   H24  105.76  3.000
 V71  H25  N9   C9   111.04  3.000
 V71  H24  N9   C9   109.18  3.000
 V71  C10  O1   C1   118.02  3.000
 V71  H27  O11  C11  109.19  3.000
 V71  H28  O12  C12  106.86  3.000
 V71  H29  O23  C3   108.78  3.000
 V71  C5   O5   C1   115.29  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
 V71  Var_01  H18  N6  C6  C5  174.23  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
 V71  chir_01  C1   O5   C2   O1   negativ
 V71  chir_02  C10  O1   C11  C9   negativ
 V71  chir_03  C11  O11  C10  C12  negativ
 V71  chir_04  C12  O12  C11  C7   positiv
 V71  chir_05  C2   N2   C1   C3   negativ
 V71  chir_06  C3   O23  C2   C4   positiv
 V71  chir_07  C4   F99  C5   C3   negativ
 V71  chir_08  C5   O5   C4   C6   negativ
 V71  chir_09  C7   N7   C8   C12  positiv
 V71  chir_10  C9   N9   C10  C8   positiv

