# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 16:42:52 2022
#   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  52  33  .  2022-03-29  2022-03-29
;
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   0.393   9.8808   -6.6044   8.4094
 SF8  C2    C  CH2    0  -0.544   8.9484   -7.7735   8.0461
 SF8  C3    C  CT     0   0.111   7.6095   -7.7720   8.7895
 SF8  C4    C  CH2    0  -0.563   6.9031   -9.1148   8.4952
 SF8  C5    C  C      0   0.529   5.6644   -9.3325   9.3349
 SF8  N6    N  NH1    0  -0.604   5.8163  -10.1933  10.3508
 SF8  C7    C  CH1    0  -0.208   4.7775  -10.5883  11.2693
 SF8  C8    C  CH2    0  -0.446   5.3706  -10.7705  12.6672
 SF8  C9    C  CH2    0  -0.425   6.0319   -9.5173  13.2218
 SF8  C10   C  CH2    0  -0.280   6.5699   -9.7408  14.6318
 SF8  N11   N  NH1    0  -0.615   7.2803   -8.6011  15.1657
 SF8  C12   C  C      0   0.497   6.6750   -7.5536  15.7572
 SF8  C13   C  CH2    0  -0.546   7.5899   -6.3866  16.0672
 SF8  C14   C  CT     0   0.101   8.0449   -5.5913  14.8177
 SF8  C15   C  CH2    0  -0.558   8.8754   -4.4012  15.2868
 SF8  C16   C  C      0   0.399   9.5432   -3.5793  14.1687
 SF8  O17   O  O      0  -0.617  11.0395   -6.9002   8.7687
 SF8  O18   O  OC    -1  -0.606   9.4174   -5.4513   8.2910
 SF8  O19   O  OH1    0  -0.708   7.8312   -7.6487  10.1757
 SF8  C20   C  C      0   0.431   6.6973   -6.5949   8.3398
 SF8  O21   O  O      0  -0.597   6.4060   -6.5111   7.1367
 SF8  O22   O  OC    -1  -0.619   6.3125   -5.8483   9.2701
 SF8  O23   O  O      0  -0.514   4.6098   -8.7466   9.1078
 SF8  C24   C  C      0   0.410   3.9943  -11.8523  10.8033
 SF8  O25   O  OC    -1  -0.608   3.1448  -12.2728  11.6148
 SF8  O26   O  O      0  -0.591   4.2616  -12.3181   9.6829
 SF8  O27   O  O      0  -0.503   5.4836   -7.5497  16.0455
 SF8  C28   C  C      0   0.434   6.7692   -5.1820  14.0321
 SF8  O29   O  OH1    0  -0.703   8.8293   -6.4198  13.9861
 SF8  O30   O  O      0  -0.615   6.6075   -5.8037  12.9530
 SF8  O31   O  OC    -1  -0.587   5.9993   -4.3590  14.5465
 SF8  O32   O  O      0  -0.600   8.8710   -3.3531  13.1422
 SF8  O33   O  OC    -1  -0.619  10.6991   -3.1666  14.3993
 SF8  H2    H  HCH2   0   0.210   8.7441   -7.7510   6.9709
 SF8  H2A   H  HCH2   0   0.190   9.4610   -8.7199   8.2430
 SF8  H4    H  HCH2   0   0.244   6.6216   -9.1452   7.4415
 SF8  H4A   H  HCH2   0   0.230   7.6148   -9.9297   8.6563
 SF8  HN6   H  HNH1   0   0.382   6.6960  -10.6784  10.4231
 SF8  H7    H  HCH1   0   0.234   4.0569   -9.7663  11.3205
 SF8  H8    H  HCH2   0   0.230   4.5677  -11.0860  13.3347
 SF8  H8A   H  HCH2   0   0.213   6.0959  -11.5937  12.6530
 SF8  H9    H  HCH2   0   0.217   6.8545   -9.1975  12.5767
 SF8  H9A   H  HCH2   0   0.217   5.3124   -8.6932  13.2346
 SF8  H10   H  HCH2   0   0.231   5.7567  -10.0012  15.3107
 SF8  H10A  H  HCH2   0   0.234   7.2582  -10.5887  14.6309
 SF8  HN11  H  HNH1   0   0.388   8.2168   -8.4410  14.8268
 SF8  H13   H  HCH2   0   0.244   7.0653   -5.7173  16.7484
 SF8  H13A  H  HCH2   0   0.247   8.4819   -6.7479  16.5892
 SF8  H15   H  HCH2   0   0.218   8.2289   -3.7317  15.8636
 SF8  H15A  H  HCH2   0   0.198   9.6428   -4.7514  15.9846
 SF8  HO19  H  HOH1   0   0.420   7.2872   -6.8644  10.3921
 SF8  HO29  H  HOH1   0   0.426   8.2491   -6.5158  13.2041

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    deloc   1.249  0.020  1.249
 SF8  C2   C1    single  1.539  0.020  1.539
 SF8  C1   O18   deloc   1.248  0.020  1.248
 SF8  C2   C3    single  1.531  0.020  1.531
 SF8  C2   H2    single  0.970  0.020  1.090
 SF8  C2   H2A   single  0.970  0.020  1.090
 SF8  C4   C3    single  1.545  0.020  1.545
 SF8  C20  C3    single  1.556  0.020  1.556
 SF8  C3   O19   single  1.409  0.020  1.409
 SF8  C4   C5    single  1.512  0.020  1.512
 SF8  C4   H4    single  0.970  0.020  1.090
 SF8  C4   H4A   single  0.970  0.020  1.090
 SF8  C5   O23   double  1.228  0.020  1.228
 SF8  C5   N6    single  1.340  0.020  1.340
 SF8  N6   C7    single  1.442  0.020  1.442
 SF8  N6   HN6   single  0.860  0.020  1.020
 SF8  C24  C7    single  1.558  0.020  1.558
 SF8  C7   C8    single  1.529  0.020  1.529
 SF8  C7   H7    single  0.970  0.020  1.090
 SF8  C8   C9    single  1.522  0.020  1.522
 SF8  C8   H8    single  0.970  0.020  1.090
 SF8  C8   H8A   single  0.970  0.020  1.090
 SF8  C9   C10   single  1.526  0.020  1.526
 SF8  C9   H9    single  0.970  0.020  1.090
 SF8  C9   H9A   single  0.970  0.020  1.090
 SF8  C10  N11   single  1.445  0.020  1.445
 SF8  C10  H10   single  0.970  0.020  1.090
 SF8  C10  H10A  single  0.970  0.020  1.090
 SF8  N11  C12   single  1.347  0.020  1.347
 SF8  N11  HN11  single  0.890  0.020  1.040
 SF8  C12  C13   single  1.515  0.020  1.515
 SF8  C12  O27   double  1.226  0.020  1.226
 SF8  C14  C13   single  1.549  0.020  1.549
 SF8  C13  H13   single  0.970  0.020  1.090
 SF8  C13  H13A  single  0.970  0.020  1.090
 SF8  O29  C14   single  1.412  0.020  1.412
 SF8  C28  C14   single  1.553  0.020  1.553
 SF8  C14  C15   single  1.525  0.020  1.525
 SF8  C16  C15   single  1.540  0.020  1.540
 SF8  C15  H15   single  0.970  0.020  1.090
 SF8  C15  H15A  single  0.970  0.020  1.090
 SF8  O32  C16   deloc   1.248  0.020  1.248
 SF8  C16  O33   deloc   1.249  0.020  1.249
 SF8  O19  HO19  single  0.850  0.020  0.980
 SF8  O21  C20   deloc   1.241  0.020  1.241
 SF8  C20  O22   deloc   1.253  0.020  1.253
 SF8  O26  C24   deloc   1.242  0.020  1.242
 SF8  C24  O25   deloc   1.248  0.020  1.248
 SF8  O30  C28   deloc   1.256  0.020  1.256
 SF8  C28  O31   deloc   1.239  0.020  1.239
 SF8  O29  HO29  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  126.19  3.000
 SF8  O18   C1   C2   117.03  3.000
 SF8  O17   C1   C2   116.76  3.000
 SF8  H2A   C2   H2   106.38  3.000
 SF8  H2A   C2   C3   108.85  3.000
 SF8  H2    C2   C3   108.28  3.000
 SF8  H2A   C2   C1   109.32  3.000
 SF8  H2    C2   C1   109.23  3.000
 SF8  C3    C2   C1   114.48  3.000
 SF8  C20   C3   O19  108.08  3.000
 SF8  O19   C3   C4   109.59  3.000
 SF8  C20   C3   C4   109.53  3.000
 SF8  O19   C3   C2   109.88  3.000
 SF8  C20   C3   C2   111.90  3.000
 SF8  C4    C3   C2   107.84  3.000
 SF8  H4A   C4   H4   106.82  3.000
 SF8  H4A   C4   C5   110.11  3.000
 SF8  H4    C4   C5   108.71  3.000
 SF8  H4A   C4   C3   108.78  3.000
 SF8  H4    C4   C3   109.03  3.000
 SF8  C5    C4   C3   113.19  3.000
 SF8  O23   C5   N6   122.97  3.000
 SF8  N6    C5   C4   114.87  3.000
 SF8  O23   C5   C4   122.16  3.000
 SF8  HN6   N6   C7   116.84  3.000
 SF8  HN6   N6   C5   117.56  3.000
 SF8  C7    N6   C5   125.26  3.000
 SF8  H7    C7   C24  106.99  3.000
 SF8  H7    C7   C8   107.59  3.000
 SF8  C24   C7   C8   111.82  3.000
 SF8  H7    C7   N6   107.36  3.000
 SF8  C8    C7   N6   109.60  3.000
 SF8  C24   C7   N6   113.20  3.000
 SF8  H8A   C8   H8   106.11  3.000
 SF8  H8A   C8   C9   109.59  3.000
 SF8  H8    C8   C9   109.57  3.000
 SF8  H8A   C8   C7   109.51  3.000
 SF8  H8    C8   C7   107.96  3.000
 SF8  C9    C8   C7   113.80  3.000
 SF8  H9A   C9   H9   106.35  3.000
 SF8  H9A   C9   C10  109.35  3.000
 SF8  H9    C9   C10  108.84  3.000
 SF8  H9A   C9   C8   109.81  3.000
 SF8  H9    C9   C8   110.66  3.000
 SF8  C10   C9   C8   111.68  3.000
 SF8  H10A  C10  H10  106.56  3.000
 SF8  H10A  C10  N11  107.63  3.000
 SF8  H10   C10  N11  108.95  3.000
 SF8  H10A  C10  C9   109.58  3.000
 SF8  H10   C10  C9   110.32  3.000
 SF8  N11   C10  C9   113.53  3.000
 SF8  HN11  N11  C12  116.19  3.000
 SF8  HN11  N11  C10  117.22  3.000
 SF8  C12   N11  C10  123.70  3.000
 SF8  O27   C12  C13  122.44  3.000
 SF8  O27   C12  N11  122.86  3.000
 SF8  C13   C12  N11  114.69  3.000
 SF8  H13A  C13  H13  107.27  3.000
 SF8  H13A  C13  C14  108.34  3.000
 SF8  H13   C13  C14  109.29  3.000
 SF8  H13A  C13  C12  109.59  3.000
 SF8  H13   C13  C12  108.08  3.000
 SF8  C14   C13  C12  114.06  3.000
 SF8  O29   C14  C28  108.24  3.000
 SF8  C28   C14  C15  113.40  3.000
 SF8  O29   C14  C15  109.66  3.000
 SF8  C15   C14  C13  108.20  3.000
 SF8  C28   C14  C13  107.58  3.000
 SF8  O29   C14  C13  109.69  3.000
 SF8  H15A  C15  H15  105.89  3.000
 SF8  H15A  C15  C16  109.23  3.000
 SF8  H15   C15  C16  108.19  3.000
 SF8  H15A  C15  C14  109.16  3.000
 SF8  H15   C15  C14  108.52  3.000
 SF8  C16   C15  C14  115.42  3.000
 SF8  O33   C16  O32  126.20  3.000
 SF8  O33   C16  C15  116.34  3.000
 SF8  O32   C16  C15  117.42  3.000
 SF8  HO19  O19  C3   101.54  3.000
 SF8  O22   C20  O21  127.41  3.000
 SF8  O22   C20  C3   114.59  3.000
 SF8  O21   C20  C3   117.98  3.000
 SF8  O26   C24  O25  127.34  3.000
 SF8  O25   C24  C7   114.90  3.000
 SF8  O26   C24  C7   117.76  3.000
 SF8  O31   C28  O30  127.28  3.000
 SF8  O31   C28  C14  118.39  3.000
 SF8  O30   C28  C14  114.20  3.000
 SF8  HO29  O29  C14  101.47  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  Var_01    O17   C1   C2   C3   126.67  30.0  3
 SF8  Var_02    O23   C5   C4   C3    75.38  30.0  3
 SF8  Var_03    C10   C9   C8   C7   178.33  30.0  3
 SF8  Var_04    N11   C10  C9   C8   176.35  30.0  3
 SF8  Var_05    C12   N11  C10  C9    83.38  30.0  3
 SF8  Var_06    C14   C13  C12  N11   71.94  30.0  3
 SF8  Var_07    O32   C16  C15  C14   41.27  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
 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-4  C15   0.020
 SF8  plan-4  C16   0.020
 SF8  plan-4  O32   0.020
 SF8  plan-4  O33   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-6  C7    0.020
 SF8  plan-6  C24   0.020
 SF8  plan-6  O25   0.020
 SF8  plan-6  O26   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

