# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 16:55:45 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: (2R)-2-[2-[[(2R)-5-[[(3S)-3-carboxy-3,5-dihydroxy-5-oxo-pentanoyl]amino]-1-hydroxy-1-oxo-pentan-2-yl]amino]-2-oxo-ethyl]-2-hydroxy-butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@](O)(CC(=O)NCCC[C@@H](NC(=O)C[C@@](O)(CC(O)=O)C(O)=O)C(O)=O)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
 SF8  SF8  '(2R)-2-[2-[[(2R)-5-[[(3S)-3-carboxy-3,5-dihydroxy-5-oxo-pentanoyl]amino]-1-hydroxy-1-oxo-pentan-2-yl]amino]-2-oxo-ethyl]-2-hydroxy-butanedioic acid'  ligand  57  33  .  2022-03-29  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SF8
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
 SF8  C1    C  C     0   0.545   9.4597   -5.8879   9.8820
 SF8  C2    C  CH2   0  -0.574   9.0115   -7.1071   9.1184
 SF8  C3    C  CT    0   0.139   7.5426   -7.4708   9.3853
 SF8  C4    C  CH2   0  -0.583   7.2931   -8.9188   8.9178
 SF8  C5    C  C     0   0.565   5.9376   -9.3623   9.4175
 SF8  N6    N  NH1   0  -0.615   5.9596  -10.3329  10.3434
 SF8  C7    C  CH1   0  -0.211   4.8144  -10.7320  11.1128
 SF8  C8    C  CH2   0  -0.458   5.1950  -10.8962  12.5924
 SF8  C9    C  CH2   0  -0.437   5.8207   -9.6323  13.1688
 SF8  C10   C  CH2   0  -0.288   6.2052   -9.7988  14.6377
 SF8  N11   N  NH1   0  -0.612   7.1210   -8.7710  15.0859
 SF8  C12   C  C     0   0.524   6.7425   -7.5215  15.3910
 SF8  C13   C  CH2   0  -0.554   7.8755   -6.5320  15.5789
 SF8  C14   C  CT    0   0.099   8.2104   -5.8126  14.2507
 SF8  C15   C  CH2   0  -0.572   9.3330   -4.8037  14.5064
 SF8  C16   C  C     0   0.585   9.7060   -4.0741  13.2455
 SF8  O17   O  O     0  -0.438  10.4990   -5.8186  10.4884
 SF8  O18   O  OH1   0  -0.603   8.5907   -4.8920   9.8005
 SF8  O19   O  OH1   0  -0.692   7.3038   -7.4082  10.7696
 SF8  C20   C  C     0   0.556   6.6257   -6.5377   8.5856
 SF8  O21   O  O     0  -0.432   6.7157   -6.4107   7.3926
 SF8  O22   O  OH1   0  -0.596   5.7505   -5.9033   9.3414
 SF8  O23   O  O     0  -0.488   4.9120   -8.8233   9.0267
 SF8  C24   C  C     0   0.555   4.2098  -12.0074  10.5474
 SF8  O25   O  OH1   0  -0.591   3.0856  -12.3256  11.1735
 SF8  O26   O  O     0  -0.428   4.6848  -12.6503   9.6491
 SF8  O27   O  O     0  -0.494   5.5721   -7.1769  15.4906
 SF8  C28   C  C     0   0.555   6.9375   -5.1332  13.7401
 SF8  O29   O  OH1   0  -0.680   8.6856   -6.7459  13.3260
 SF8  O30   O  O     0  -0.444   6.3075   -5.5266  12.7915
 SF8  O31   O  OH1   0  -0.581   6.5812   -4.1140  14.4957
 SF8  O32   O  O     0  -0.462   8.8944   -3.7105  12.4236
 SF8  O33   O  OH1   0  -0.575  10.9993   -3.8428  13.1462
 SF8  H2    H  HCH2  0   0.302   9.1788   -6.9521   8.0496
 SF8  H2A   H  HCH2  0   0.289   9.6513   -7.9367   9.4194
 SF8  H4    H  HCH2  0   0.292   7.3317   -8.9842   7.8296
 SF8  H4A   H  HCH2  0   0.279   8.0910   -9.5523   9.3089
 SF8  HN6   H  HNH1  0   0.408   6.8501  -10.7315  10.5969
 SF8  H7    H  HCH1  0   0.296   4.0581   -9.9458  11.0321
 SF8  H8    H  HCH2  0   0.261   4.3013  -11.1652  13.1576
 SF8  H8A   H  HCH2  0   0.245   5.8956  -11.7319  12.6931
 SF8  H9    H  HCH2  0   0.237   6.7184   -9.3698  12.6078
 SF8  H9A   H  HCH2  0   0.235   5.1327   -8.7896  13.0634
 SF8  H10   H  HCH2  0   0.247   5.3209   -9.7987  15.2753
 SF8  H10A  H  HCH2  0   0.248   6.7039  -10.7574  14.7873
 SF8  HN11  H  HNH1  0   0.400   8.0999   -8.9334  14.9142
 SF8  H13   H  HCH2  0   0.283   7.5916   -5.8070  16.3415
 SF8  H13A  H  HCH2  0   0.280   8.7852   -7.0292  15.9222
 SF8  H15   H  HCH2  0   0.309   9.0507   -4.0631  15.2591
 SF8  H15A  H  HCH2  0   0.295  10.1966   -5.3364  14.9064
 SF8  HO18  H  HOH1  0   0.487   8.8284   -4.1881  10.4313
 SF8  HO19  H  HOH1  0   0.476   6.5779   -6.8035  10.9683
 SF8  HO22  H  HOH1  0   0.495   5.1764   -5.3339   8.8062
 SF8  HO25  H  HOH1  0   0.486   2.7180  -13.1453  10.8098
 SF8  HO29  H  HOH1  0   0.465   8.0921   -6.8454  12.5695
 SF8  HO31  H  HOH1  0   0.490   5.7483   -3.7319  14.1792
 SF8  HO33  H  HOH1  0   0.484  11.1933   -3.3537  12.3317

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
 SF8  O17  C1    double  1.205  0.020  1.205
 SF8  C2   C1    single  1.507  0.020  1.507
 SF8  C1   O18   single  1.324  0.020  1.324
 SF8  C2   C3    single  1.537  0.020  1.537
 SF8  C2   H2    single  0.970  0.020  1.090
 SF8  C2   H2A   single  0.970  0.020  1.090
 SF8  C4   C3    single  1.542  0.020  1.542
 SF8  C20  C3    single  1.533  0.020  1.533
 SF8  C3   O19   single  1.406  0.020  1.406
 SF8  C4   C5    single  1.511  0.020  1.511
 SF8  C4   H4    single  0.970  0.020  1.090
 SF8  C4   H4A   single  0.970  0.020  1.090
 SF8  C5   O23   double  1.223  0.020  1.223
 SF8  C5   N6    single  1.342  0.020  1.342
 SF8  N6   C7    single  1.436  0.020  1.436
 SF8  N6   HN6   single  0.860  0.020  1.020
 SF8  C24  C7    single  1.521  0.020  1.521
 SF8  C7   C8    single  1.536  0.020  1.536
 SF8  C7   H7    single  0.970  0.020  1.090
 SF8  C8   C9    single  1.524  0.020  1.524
 SF8  C8   H8    single  0.970  0.020  1.090
 SF8  C8   H8A   single  0.970  0.020  1.090
 SF8  C9   C10   single  1.527  0.020  1.527
 SF8  C9   H9    single  0.970  0.020  1.090
 SF8  C9   H9A   single  0.970  0.020  1.090
 SF8  C10  N11   single  1.448  0.020  1.448
 SF8  C10  H10   single  0.970  0.020  1.090
 SF8  C10  H10A  single  0.970  0.020  1.090
 SF8  N11  C12   single  1.341  0.020  1.341
 SF8  N11  HN11  single  0.860  0.020  1.020
 SF8  C12  C13   single  1.516  0.020  1.516
 SF8  C12  O27   double  1.224  0.020  1.224
 SF8  C14  C13   single  1.547  0.020  1.547
 SF8  C13  H13   single  0.970  0.020  1.090
 SF8  C13  H13A  single  0.970  0.020  1.090
 SF8  O29  C14   single  1.397  0.020  1.397
 SF8  C28  C14   single  1.531  0.020  1.531
 SF8  C14  C15   single  1.531  0.020  1.531
 SF8  C16  C15   single  1.504  0.020  1.504
 SF8  C15  H15   single  0.970  0.020  1.090
 SF8  C15  H15A  single  0.970  0.020  1.090
 SF8  O32  C16   double  1.211  0.020  1.211
 SF8  C16  O33   single  1.318  0.020  1.318
 SF8  O18  HO18  single  0.850  0.020  0.980
 SF8  O19  HO19  single  0.850  0.020  0.980
 SF8  O21  C20   double  1.203  0.020  1.203
 SF8  C20  O22   single  1.319  0.020  1.319
 SF8  O22  HO22  single  0.850  0.020  0.980
 SF8  O26  C24   double  1.202  0.020  1.202
 SF8  C24  O25   single  1.326  0.020  1.326
 SF8  O25  HO25  single  0.850  0.020  0.980
 SF8  O30  C28   double  1.205  0.020  1.205
 SF8  C28  O31   single  1.318  0.020  1.318
 SF8  O29  HO29  single  0.850  0.020  0.980
 SF8  O31  HO31  single  0.850  0.020  0.980
 SF8  O33  HO33  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
 SF8  O18   C1   O17  123.62  3.000
 SF8  O18   C1   C2   112.47  3.000
 SF8  O17   C1   C2   123.91  3.000
 SF8  H2A   C2   H2   106.75  3.000
 SF8  H2A   C2   C3   109.44  3.000
 SF8  H2    C2   C3   110.47  3.000
 SF8  H2A   C2   C1   107.54  3.000
 SF8  H2    C2   C1   109.59  3.000
 SF8  C3    C2   C1   112.82  3.000
 SF8  C20   C3   O19  112.63  3.000
 SF8  O19   C3   C4   108.23  3.000
 SF8  C20   C3   C4   108.46  3.000
 SF8  O19   C3   C2   108.83  3.000
 SF8  C20   C3   C2   109.69  3.000
 SF8  C4    C3   C2   108.92  3.000
 SF8  H4A   C4   H4   107.27  3.000
 SF8  H4A   C4   C5   111.53  3.000
 SF8  H4    C4   C5   110.12  3.000
 SF8  H4A   C4   C3   108.55  3.000
 SF8  H4    C4   C3   110.67  3.000
 SF8  C5    C4   C3   108.69  3.000
 SF8  O23   C5   N6   123.59  3.000
 SF8  N6    C5   C4   115.20  3.000
 SF8  O23   C5   C4   121.15  3.000
 SF8  HN6   N6   C7   117.37  3.000
 SF8  HN6   N6   C5   118.30  3.000
 SF8  C7    N6   C5   123.90  3.000
 SF8  H7    C7   C24  107.48  3.000
 SF8  H7    C7   C8   108.61  3.000
 SF8  C24   C7   C8   111.53  3.000
 SF8  H7    C7   N6   108.18  3.000
 SF8  C8    C7   N6   110.37  3.000
 SF8  C24   C7   N6   110.54  3.000
 SF8  H8A   C8   H8   106.75  3.000
 SF8  H8A   C8   C9   109.60  3.000
 SF8  H8    C8   C9   110.18  3.000
 SF8  H8A   C8   C7   109.18  3.000
 SF8  H8    C8   C7   108.80  3.000
 SF8  C9    C8   C7   112.17  3.000
 SF8  H9A   C9   H9   106.43  3.000
 SF8  H9A   C9   C10  109.58  3.000
 SF8  H9    C9   C10  108.28  3.000
 SF8  H9A   C9   C8   110.16  3.000
 SF8  H9    C9   C8   110.06  3.000
 SF8  C10   C9   C8   112.14  3.000
 SF8  H10A  C10  H10  106.90  3.000
 SF8  H10A  C10  N11  106.99  3.000
 SF8  H10   C10  N11  109.39  3.000
 SF8  H10A  C10  C9   110.04  3.000
 SF8  H10   C10  C9   110.99  3.000
 SF8  N11   C10  C9   112.31  3.000
 SF8  HN11  N11  C12  117.61  3.000
 SF8  HN11  N11  C10  116.59  3.000
 SF8  C12   N11  C10  123.61  3.000
 SF8  O27   C12  C13  121.38  3.000
 SF8  O27   C12  N11  123.42  3.000
 SF8  C13   C12  N11  115.18  3.000
 SF8  H13A  C13  H13  107.45  3.000
 SF8  H13A  C13  C14  107.53  3.000
 SF8  H13   C13  C14  110.35  3.000
 SF8  H13A  C13  C12  111.37  3.000
 SF8  H13   C13  C12  109.04  3.000
 SF8  C14   C13  C12  111.03  3.000
 SF8  O29   C14  C28  111.02  3.000
 SF8  C28   C14  C15  111.90  3.000
 SF8  O29   C14  C15  107.54  3.000
 SF8  C15   C14  C13  108.77  3.000
 SF8  C28   C14  C13  108.23  3.000
 SF8  O29   C14  C13  109.34  3.000
 SF8  H15A  C15  H15  106.43  3.000
 SF8  H15A  C15  C16  110.38  3.000
 SF8  H15   C15  C16  108.22  3.000
 SF8  H15A  C15  C14  108.66  3.000
 SF8  H15   C15  C14  111.85  3.000
 SF8  C16   C15  C14  111.20  3.000
 SF8  O33   C16  O32  123.64  3.000
 SF8  O33   C16  C15  113.07  3.000
 SF8  O32   C16  C15  123.27  3.000
 SF8  HO18  O18  C1   110.08  3.000
 SF8  HO19  O19  C3   110.99  3.000
 SF8  O22   C20  O21  124.55  3.000
 SF8  O22   C20  C3   112.99  3.000
 SF8  O21   C20  C3   122.46  3.000
 SF8  HO22  O22  C20  111.04  3.000
 SF8  O26   C24  O25  124.03  3.000
 SF8  O25   C24  C7   111.28  3.000
 SF8  O26   C24  C7   124.69  3.000
 SF8  HO25  O25  C24  110.33  3.000
 SF8  O31   C28  O30  124.24  3.000
 SF8  O31   C28  C14  112.14  3.000
 SF8  O30   C28  C14  123.54  3.000
 SF8  HO29  O29  C14  112.21  3.000
 SF8  HO31  O31  C28  110.48  3.000
 SF8  HO33  O33  C16  110.38  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
 SF8  CONST_01  C7    N6   C5   C4    180.00   0.0  0
 SF8  CONST_02  O23   C5   N6   C7      0.00   0.0  0
 SF8  CONST_03  C13   C12  N11  C10   180.00   0.0  0
 SF8  CONST_04  O27   C12  N11  C10     0.00   0.0  0
 SF8  CONST_05  HN6   N6   C5   C4      0.00   0.0  0
 SF8  CONST_06  HN11  N11  C12  C13     0.00   0.0  0
 SF8  CONST_07  HO18  O18  C1   C2    180.00   0.0  0
 SF8  CONST_08  HO22  O22  C20  C3    180.00   0.0  0
 SF8  CONST_09  HO25  O25  C24  C7    180.00   0.0  0
 SF8  CONST_10  HO31  O31  C28  C14   180.00   0.0  0
 SF8  CONST_11  HO33  O33  C16  C15   180.00   0.0  0
 SF8  Var_01    O17   C1   C2   C3    134.29  30.0  3
 SF8  Var_02    O23   C5   C4   C3     64.65  30.0  3
 SF8  Var_03    C10   C9   C8   C7   -179.71  30.0  3
 SF8  Var_04    N11   C10  C9   C8    163.78  30.0  3
 SF8  Var_05    C12   N11  C10  C9     77.72  30.0  3
 SF8  Var_06    C14   C13  C12  N11    91.64  30.0  3
 SF8  Var_07    O32   C16  C15  C14    39.06  30.0  1

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
 SF8  chir_01  C3   C4   C20  O19  negativ
 SF8  chir_02  C7   N6   C24  C8   negativ
 SF8  chir_03  C14  O29  C28  C15  positiv

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
 SF8  plan-1  C4    0.020
 SF8  plan-1  C5    0.020
 SF8  plan-1  N6    0.020
 SF8  plan-1  C7    0.020
 SF8  plan-1  O23   0.020
 SF8  plan-1  HN6   0.020
 SF8  plan-2  C10   0.020
 SF8  plan-2  N11   0.020
 SF8  plan-2  C12   0.020
 SF8  plan-2  C13   0.020
 SF8  plan-2  O27   0.020
 SF8  plan-2  HN11  0.020
 SF8  plan-3  C1    0.020
 SF8  plan-3  C2    0.020
 SF8  plan-3  O17   0.020
 SF8  plan-3  O18   0.020
 SF8  plan-3  HO18  0.020
 SF8  plan-4  C15   0.020
 SF8  plan-4  C16   0.020
 SF8  plan-4  O32   0.020
 SF8  plan-4  O33   0.020
 SF8  plan-4  HO33  0.020
 SF8  plan-5  C3    0.020
 SF8  plan-5  C20   0.020
 SF8  plan-5  O21   0.020
 SF8  plan-5  O22   0.020
 SF8  plan-5  HO22  0.020
 SF8  plan-6  C7    0.020
 SF8  plan-6  C24   0.020
 SF8  plan-6  O25   0.020
 SF8  plan-6  O26   0.020
 SF8  plan-6  HO25  0.020
 SF8  plan-7  C14   0.020
 SF8  plan-7  C28   0.020
 SF8  plan-7  O30   0.020
 SF8  plan-7  O31   0.020
 SF8  plan-7  HO31  0.020

