# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:49:23 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2R)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-hydroxypropanoyl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](NC(=O)c1cccc(O)c1O)C(=O)OC[C@H](NC(=O)c2cccc(O)c2O)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
 2DS  2DS  N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2R)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-hydroxypropanoyl]-L-serine  ligand  52  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2DS
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
 2DS  C1    C  CR6    0   0.301  -5.7709   1.4724   0.7511
 2DS  N1    N  NH1    0  -0.659  -3.1679  -0.7247  -0.6255
 2DS  O1    O  OH1    0  -0.678  -5.0578   2.5025   1.2164
 2DS  C3    C  C      0   0.260   5.9983   1.3378  -0.2269
 2DS  N3    N  NH1    0  -0.650   2.8935  -0.3497   0.7598
 2DS  O3    O  OH1    0  -0.709   6.9320   0.4760   0.1902
 2DS  C4    C  CR6    0   0.186  -7.1622   1.5379   0.9481
 2DS  O4    O  OH1    0  -0.700  -7.7168   2.5929   1.5769
 2DS  C6    C  C      0   0.155   6.4594   2.4823  -0.9015
 2DS  O6    O  OH1    0  -0.712   7.7783   2.6704  -1.1080
 2DS  C7    C  CR16   0  -0.291  -7.9680   0.5152   0.4904
 2DS  O7    O  O      0  -0.503  -3.0473   1.3140   0.2922
 2DS  C9    C  C1     0  -0.291   5.5562   3.4248  -1.3505
 2DS  O9    O  O      0  -0.496   5.0456  -0.8438   1.1746
 2DS  C10   C  CR16   0  -0.230  -7.4107  -0.5810  -0.1669
 2DS  C12   C  C1     0  -0.225   4.1899   3.2473  -1.1373
 2DS  O12   O  O      0  -0.552   2.9947  -2.4798  -0.9081
 2DS  C13   C  CR16   0  -0.284  -6.0494  -0.6557  -0.3611
 2DS  O14   O  OC    -1  -0.539   2.1847  -3.8850   0.6299
 2DS  C15   C  C1     0  -0.273   3.7293   2.1245  -0.4850
 2DS  C16   C  CR6    0  -0.147  -5.2084   0.3671   0.0991
 2DS  C18   C  C      0  -0.133   4.6250   1.1481  -0.0290
 2DS  C19   C  C      0   0.667  -3.7369   0.3477  -0.0663
 2DS  C21   C  C      0   0.662   4.1972  -0.0902   0.6688
 2DS  C22   C  CH1    0  -0.243  -1.7401  -0.8480  -0.7385
 2DS  C24   C  CH1    0  -0.270   2.4042  -1.6180   1.2496
 2DS  C25   C  C      0   0.628  -1.1231  -1.1707   0.6190
 2DS  C27   C  C      0   0.466   2.5465  -2.7709   0.2088
 2DS  C30   C  CH2    0  -0.201   0.9674  -1.4820   1.7012
 2DS  HN1   H  HNH1   0   0.402  -3.7115  -1.5567  -0.7894
 2DS  HO1   H  HOH1   0   0.480  -4.1124   2.3181   0.9744
 2DS  HN3   H  HNH1   0   0.375   2.2645   0.1811   0.1790
 2DS  HO3   H  HOH1   0   0.483   6.4416  -0.2352   0.6860
 2DS  HO4   H  HOH1   0   0.466  -7.0362   3.2322   1.8207
 2DS  HO6   H  HOH1   0   0.455   8.2804   1.9355  -0.7348
 2DS  H7    H  HCR6   0   0.241  -9.0382   0.5757   0.6449
 2DS  H10   H  HCR6   0   0.269  -8.0534  -1.3727  -0.5261
 2DS  H13   H  HCR6   0   0.238  -5.6518  -1.5164  -0.8815
 2DS  H15   H  H      0   0.230   2.6654   2.0239  -0.3163
 2DS  C20   C  CH2    0  -0.183  -1.3865  -1.9199  -1.7589
 2DS  H22   H  HCH1   0   0.279  -1.3172   0.0963  -1.0907
 2DS  H24   H  HCH1   0   0.278   2.9793  -1.8897   2.1379
 2DS  H30   H  HCH2   0   0.210   0.8525  -0.6902   2.4446
 2DS  H30A  H  HCH2   0   0.296   0.6324  -2.4234   2.1347
 2DS  O11   O  OH1    0  -0.631  -1.8939  -3.1408  -1.2798
 2DS  H18   H  HCH2   0   0.202  -1.8276  -1.6357  -2.7209
 2DS  H19   H  HCH2   0   0.268  -0.3002  -1.9418  -1.8894
 2DS  H20   H  HOH1   0   0.452  -1.7302  -3.8234  -1.9373
 2DS  O10   O  O      0  -0.390  -1.7441  -1.4040   1.6204
 2DS  O15   O  O2     0  -0.468   0.1945  -1.1602   0.5363
 2DS  H9    H  H      0   0.246   5.9214   4.3068  -1.8618
 2DS  H12   H  H      0   0.264   3.4929   3.9986  -1.4821

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
 2DS  C1   C16   aromatic  1.401  0.020  1.401
 2DS  N1   C22   single    1.438  0.020  1.438
 2DS  N1   HN1   single    0.860  0.020  1.020
 2DS  O1   C1    single    1.336  0.020  1.336
 2DS  O1   HO1   single    0.850  0.020  0.980
 2DS  C3   O3    single    1.337  0.020  1.337
 2DS  C3   C18   aromatic  1.400  0.020  1.400
 2DS  N3   C24   single    1.445  0.020  1.445
 2DS  N3   HN3   single    0.890  0.020  1.040
 2DS  O3   HO3   single    0.850  0.020  0.980
 2DS  C4   C1    aromatic  1.407  0.020  1.407
 2DS  C4   C7    aromatic  1.380  0.020  1.380
 2DS  O4   C4    single    1.348  0.020  1.348
 2DS  O4   HO4   single    0.850  0.020  0.980
 2DS  C6   C3    aromatic  1.406  0.020  1.406
 2DS  O6   C6    single    1.348  0.020  1.348
 2DS  O6   HO6   single    0.850  0.020  0.980
 2DS  C7   C10   aromatic  1.394  0.020  1.394
 2DS  C7   H7    single    0.930  0.020  1.080
 2DS  C9   C6    aromatic  1.380  0.020  1.380
 2DS  C9   C12   aromatic  1.394  0.020  1.394
 2DS  C9   H9    single    0.930  0.020  1.080
 2DS  C10  C13   aromatic  1.377  0.020  1.377
 2DS  C10  H10   single    0.930  0.020  1.080
 2DS  O10  C25   double    1.201  0.020  1.201
 2DS  C12  C15   aromatic  1.378  0.020  1.378
 2DS  C12  H12   single    0.930  0.020  1.080
 2DS  C13  H13   single    0.930  0.020  1.080
 2DS  C15  C18   aromatic  1.401  0.020  1.401
 2DS  C15  H15   single    0.930  0.020  1.080
 2DS  C16  C13   aromatic  1.402  0.020  1.402
 2DS  C16  C19   single    1.481  0.020  1.481
 2DS  C18  C21   single    1.484  0.020  1.484
 2DS  C19  N1    single    1.337  0.020  1.337
 2DS  C19  O7    double    1.240  0.020  1.240
 2DS  C21  N3    single    1.332  0.020  1.332
 2DS  C21  O9    double    1.242  0.020  1.242
 2DS  C22  C25   single    1.526  0.020  1.526
 2DS  C22  C20   single    1.521  0.020  1.521
 2DS  C22  H22   single    0.970  0.020  1.090
 2DS  C24  C30   single    1.512  0.020  1.512
 2DS  C24  C27   single    1.560  0.020  1.560
 2DS  C24  H24   single    0.970  0.020  1.090
 2DS  C25  O15   single    1.320  0.020  1.320
 2DS  C27  O12   deloc     1.238  0.020  1.238
 2DS  C27  O14   deloc     1.245  0.020  1.245
 2DS  C30  O15   single    1.435  0.020  1.435
 2DS  C30  H30   single    0.970  0.020  1.090
 2DS  C30  H30A  single    0.970  0.020  1.090
 2DS  C20  O11   single    1.406  0.020  1.406
 2DS  C20  H18   single    0.970  0.020  1.090
 2DS  C20  H19   single    0.970  0.020  1.090
 2DS  O11  H20   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
 2DS  C16   C1   C4   119.93  3.000
 2DS  C4    C1   O1   116.30  3.000
 2DS  C16   C1   O1   123.77  3.000
 2DS  HN1   N1   C22  116.89  3.000
 2DS  HN1   N1   C19  120.07  3.000
 2DS  C22   N1   C19  121.64  3.000
 2DS  HO1   O1   C1   106.26  3.000
 2DS  C18   C3   C6   119.97  3.000
 2DS  C6    C3   O3   116.44  3.000
 2DS  C18   C3   O3   123.59  3.000
 2DS  HN3   N3   C24  116.52  3.000
 2DS  HN3   N3   C21  117.97  3.000
 2DS  C24   N3   C21  121.70  3.000
 2DS  HO3   O3   C3   105.77  3.000
 2DS  C7    C4   O4   119.64  3.000
 2DS  O4    C4   C1   120.59  3.000
 2DS  C7    C4   C1   119.77  3.000
 2DS  HO4   O4   C4   110.26  3.000
 2DS  C9    C6   O6   119.67  3.000
 2DS  C9    C6   C3   119.82  3.000
 2DS  O6    C6   C3   120.51  3.000
 2DS  HO6   O6   C6   110.09  3.000
 2DS  H7    C7   C10  120.41  3.000
 2DS  H7    C7   C4   119.22  3.000
 2DS  C10   C7   C4   120.37  3.000
 2DS  H9    C9   C12  120.42  3.000
 2DS  H9    C9   C6   119.28  3.000
 2DS  C12   C9   C6   120.30  3.000
 2DS  H10   C10  C13  120.07  3.000
 2DS  H10   C10  C7   119.65  3.000
 2DS  C13   C10  C7   120.28  3.000
 2DS  H12   C12  C15  120.11  3.000
 2DS  H12   C12  C9   119.64  3.000
 2DS  C15   C12  C9   120.25  3.000
 2DS  H13   C13  C16  121.20  3.000
 2DS  C16   C13  C10  120.48  3.000
 2DS  H13   C13  C10  118.32  3.000
 2DS  H15   C15  C18  120.86  3.000
 2DS  H15   C15  C12  118.58  3.000
 2DS  C18   C15  C12  120.54  3.000
 2DS  C19   C16  C13  123.36  3.000
 2DS  C19   C16  C1   117.46  3.000
 2DS  C13   C16  C1   119.18  3.000
 2DS  C21   C18  C15  123.37  3.000
 2DS  C21   C18  C3   117.52  3.000
 2DS  C15   C18  C3   119.11  3.000
 2DS  C16   C19  O7   120.67  3.000
 2DS  O7    C19  N1   120.62  3.000
 2DS  C16   C19  N1   118.70  3.000
 2DS  C18   C21  O9   120.03  3.000
 2DS  O9    C21  N3   121.49  3.000
 2DS  C18   C21  N3   118.46  3.000
 2DS  H22   C22  C20  107.62  3.000
 2DS  H22   C22  C25  108.24  3.000
 2DS  C20   C22  C25  110.72  3.000
 2DS  H22   C22  N1   109.60  3.000
 2DS  C20   C22  N1   110.12  3.000
 2DS  C25   C22  N1   110.47  3.000
 2DS  H24   C24  C30  106.24  3.000
 2DS  H24   C24  C27  108.10  3.000
 2DS  C30   C24  C27  110.63  3.000
 2DS  H24   C24  N3   108.40  3.000
 2DS  C27   C24  N3   113.06  3.000
 2DS  C30   C24  N3   110.12  3.000
 2DS  C22   C25  O15  110.25  3.000
 2DS  O15   C25  O10  124.73  3.000
 2DS  C22   C25  O10  125.02  3.000
 2DS  C24   C27  O14  114.16  3.000
 2DS  O14   C27  O12  128.37  3.000
 2DS  C24   C27  O12  117.46  3.000
 2DS  H30A  C30  H30  108.87  3.000
 2DS  H30A  C30  C24  109.47  3.000
 2DS  H30   C30  C24  111.61  3.000
 2DS  H30A  C30  O15  110.58  3.000
 2DS  H30   C30  O15  109.47  3.000
 2DS  C24   C30  O15  106.83  3.000
 2DS  H19   C20  H18  107.46  3.000
 2DS  H19   C20  O11  112.42  3.000
 2DS  H18   C20  O11  112.27  3.000
 2DS  H19   C20  C22  108.95  3.000
 2DS  H18   C20  C22  108.21  3.000
 2DS  O11   C20  C22  107.42  3.000
 2DS  H20   O11  C20  108.78  3.000
 2DS  C30   O15  C25  119.01  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
 2DS  CONST_01  C10  C13  C16  C1      0.00   0.0  0
 2DS  CONST_02  C10  C7   C4   C1      0.00   0.0  0
 2DS  CONST_03  C12  C15  C18  C3      0.00   0.0  0
 2DS  CONST_04  C12  C9   C6   C3      0.00   0.0  0
 2DS  CONST_05  C13  C16  C1   C4      0.00   0.0  0
 2DS  CONST_06  C13  C10  C7   C4      0.00   0.0  0
 2DS  CONST_07  C15  C18  C3   C6      0.00   0.0  0
 2DS  CONST_08  C15  C12  C9   C6      0.00   0.0  0
 2DS  CONST_09  C16  C1   C4   C7      0.00   0.0  0
 2DS  CONST_10  C16  C13  C10  C7      0.00   0.0  0
 2DS  CONST_11  C18  C3   C6   C9      0.00   0.0  0
 2DS  CONST_12  C18  C15  C12  C9      0.00   0.0  0
 2DS  CONST_13  C13  C16  C1   O1    180.00   0.0  0
 2DS  CONST_14  C7   C4   C1   O1    180.00   0.0  0
 2DS  CONST_15  C15  C18  C3   O3    180.00   0.0  0
 2DS  CONST_16  C9   C6   C3   O3    180.00   0.0  0
 2DS  CONST_17  C19  C16  C1   C4    180.00   0.0  0
 2DS  CONST_18  C16  C1   C4   O4    180.00   0.0  0
 2DS  CONST_19  C10  C7   C4   O4    180.00   0.0  0
 2DS  CONST_20  C21  C18  C3   C6    180.00   0.0  0
 2DS  CONST_21  C18  C3   C6   O6    180.00   0.0  0
 2DS  CONST_22  C12  C9   C6   O6    180.00   0.0  0
 2DS  CONST_23  C19  C16  C13  C10   180.00   0.0  0
 2DS  CONST_24  C21  C18  C15  C12   180.00   0.0  0
 2DS  CONST_25  H13  C13  C16  C1    180.00   0.0  0
 2DS  CONST_26  H7   C7   C4   C1    180.00   0.0  0
 2DS  CONST_27  H15  C15  C18  C3    180.00   0.0  0
 2DS  CONST_28  H9   C9   C6   C3    180.00   0.0  0
 2DS  CONST_29  H10  C10  C7   C4    180.00   0.0  0
 2DS  CONST_30  H12  C12  C9   C6    180.00   0.0  0
 2DS  CONST_31  C22  N1   C19  C16   180.00   0.0  0
 2DS  CONST_32  C24  N3   C21  C18   180.00   0.0  0
 2DS  CONST_33  HN1  N1   C19  C16     0.00   0.0  0
 2DS  CONST_34  HN3  N3   C21  C18     0.00   0.0  0
 2DS  CONST_35  C22  N1   C19  O7      0.00   0.0  0
 2DS  CONST_36  C24  N3   C21  O9      0.00   0.0  0
 2DS  Var_01    N1   C19  C16  C1    176.75  30.0  2
 2DS  Var_02    N3   C21  C18  C3   -173.99  30.0  2
 2DS  Var_03    H30  C30  O15  C25   -68.40  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
 2DS  chir_01  C22  N1  C25  C20  negativ
 2DS  chir_02  C24  N3  C27  C30  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
 2DS  plan-1  C1   0.020
 2DS  plan-1  O1   0.020
 2DS  plan-1  C4   0.020
 2DS  plan-1  O4   0.020
 2DS  plan-1  C7   0.020
 2DS  plan-1  C10  0.020
 2DS  plan-1  C13  0.020
 2DS  plan-1  C16  0.020
 2DS  plan-1  C19  0.020
 2DS  plan-1  H7   0.020
 2DS  plan-1  H10  0.020
 2DS  plan-1  H13  0.020
 2DS  plan-2  C3   0.020
 2DS  plan-2  O3   0.020
 2DS  plan-2  C6   0.020
 2DS  plan-2  O6   0.020
 2DS  plan-2  C9   0.020
 2DS  plan-2  C12  0.020
 2DS  plan-2  C15  0.020
 2DS  plan-2  C18  0.020
 2DS  plan-2  C21  0.020
 2DS  plan-2  H15  0.020
 2DS  plan-2  H9   0.020
 2DS  plan-2  H12  0.020
 2DS  plan-3  N1   0.020
 2DS  plan-3  O7   0.020
 2DS  plan-3  C16  0.020
 2DS  plan-3  C19  0.020
 2DS  plan-3  C22  0.020
 2DS  plan-3  HN1  0.020
 2DS  plan-4  N3   0.020
 2DS  plan-4  O9   0.020
 2DS  plan-4  C18  0.020
 2DS  plan-4  C21  0.020
 2DS  plan-4  C24  0.020
 2DS  plan-4  HN3  0.020
 2DS  plan-5  O12  0.020
 2DS  plan-5  O14  0.020
 2DS  plan-5  C24  0.020
 2DS  plan-5  C27  0.020
 2DS  plan-6  C22  0.020
 2DS  plan-6  C25  0.020
 2DS  plan-6  O10  0.020
 2DS  plan-6  O15  0.020

