# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:44:59 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  53  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   0.284  -6.4391   1.1636  -0.0073
 2DS  N1    N  NH1   0  -0.623  -3.1858  -0.0927  -0.5080
 2DS  O1    O  OH1   0  -0.616  -6.1824   2.3663  -0.5509
 2DS  C3    C  CR6   0   0.255   6.3943   0.7208  -0.4101
 2DS  N3    N  NH1   0  -0.659   3.0128  -0.2347   0.6563
 2DS  O3    O  OH1   0  -0.645   7.1026  -0.3864  -0.1659
 2DS  C4    C  CR6   0   0.269  -7.7572   0.7297   0.1993
 2DS  O4    O  OH1   0  -0.645  -8.7218   1.6018  -0.1677
 2DS  C6    C  CR6   0   0.309   7.0963   1.7906  -0.9944
 2DS  O6    O  OH1   0  -0.632   8.4063   1.6736  -1.2861
 2DS  C7    C  CR16  0  -0.369  -8.0032  -0.5181   0.7448
 2DS  O7    O  O     0  -0.474  -3.5644   1.8333   0.6063
 2DS  C9    C  CR16  0  -0.342   6.4395   2.9729  -1.2690
 2DS  O9    O  O     0  -0.531   4.9701  -1.3173   0.8180
 2DS  C10   C  CR16  0  -0.263  -6.9457  -1.3541   1.0858
 2DS  C12   C  CR16  0  -0.258   5.0859   3.1143  -0.9663
 2DS  O12   O  O     0  -0.419   2.3298  -2.2790  -1.0301
 2DS  C13   C  CR16  0  -0.292  -5.6447  -0.9404   0.8713
 2DS  O14   O  OH1   0  -0.587   1.3245  -3.4111   0.6148
 2DS  C15   C  CR16  0  -0.329   4.3894   2.0716  -0.3974
 2DS  C16   C  CR6   0  -0.171  -5.3856   0.3193   0.3264
 2DS  C18   C  CR6   0  -0.176   5.0307   0.8558  -0.1199
 2DS  C19   C  C     0   0.537  -3.9728   0.7732   0.1623
 2DS  C21   C  C     0   0.649   4.3388  -0.3083   0.4778
 2DS  C22   C  CH1   0  -0.249  -1.7585   0.0503  -0.5454
 2DS  C24   C  CH1   0  -0.243   2.2577  -1.3322   1.1931
 2DS  C25   C  C     0   0.622  -1.1507  -0.4501   0.7611
 2DS  C27   C  C     0   0.560   1.9854  -2.3803   0.1153
 2DS  C30   C  CH2   0  -0.206   0.9569  -0.8446   1.8072
 2DS  HN1   H  HNH1  0   0.408  -3.5752  -0.9773  -0.7965
 2DS  HO1   H  HOH1  0   0.477  -7.0070   2.8074  -0.7889
 2DS  HN3   H  HNH1  0   0.419   2.4987   0.5176   0.2272
 2DS  HO3   H  HOH1  0   0.485   6.4916  -1.0190   0.2891
 2DS  HO4   H  HOH1  0   0.485  -9.5983   1.2185  -0.0518
 2DS  HO6   H  HOH1  0   0.475   8.7354   0.8093  -1.0099
 2DS  H7    H  HCR6  0   0.280  -9.0258  -0.8408   0.9042
 2DS  H10   H  HCR6  0   0.262  -7.1477  -2.3236   1.5197
 2DS  H12   H  HCR6  0   0.264   4.5865   4.0499  -1.1763
 2DS  H13   H  HCR6  0   0.261  -4.8190  -1.5829   1.1505
 2DS  HO14  H  HOH1  0   0.488   1.1436  -4.0664  -0.0763
 2DS  H15   H  HCR6  0   0.253   3.3461   2.2225  -0.1544
 2DS  C20   C  CH2   0  -0.174  -1.1666  -0.7017  -1.7282
 2DS  H22   H  HCH1  0   0.314  -1.5029   1.1072  -0.6596
 2DS  H24   H  HCH1  0   0.329   2.8302  -1.8069   1.9945
 2DS  H30   H  HCH2  0   0.285   1.1563  -0.0562   2.5344
 2DS  H30A  H  HCH2  0   0.279   0.4464  -1.6612   2.3149
 2DS  O11   O  OH1   0  -0.668  -1.3537  -2.0759  -1.4892
 2DS  H18   H  HCH2  0   0.238  -1.6753  -0.3630  -2.6379
 2DS  H19   H  HCH2  0   0.232  -0.1093  -0.4406  -1.8289
 2DS  H20   H  HOH1  0   0.467  -0.9685  -2.5718  -2.2175
 2DS  O10   O  O     0  -0.420  -1.7733  -0.8985   1.6829
 2DS  O15   O  O2    0  -0.468   0.1700  -0.3181   0.7381
 2DS  H9    H  HCR6  0   0.274   6.9893   3.7926  -1.7147

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  1.391  0.020  1.391
 2DS  N1   C22   single    1.435  0.020  1.435
 2DS  N1   HN1   single    0.860  0.020  1.020
 2DS  O1   C1    single    1.345  0.020  1.345
 2DS  O1   HO1   single    0.850  0.020  0.980
 2DS  C3   O3    single    1.337  0.020  1.337
 2DS  C3   C18   aromatic  1.401  0.020  1.401
 2DS  N3   C24   single    1.436  0.020  1.436
 2DS  N3   HN3   single    0.860  0.020  1.020
 2DS  O3   HO3   single    0.850  0.020  0.980
 2DS  C4   C1    aromatic  1.403  0.020  1.403
 2DS  C4   C7    aromatic  1.384  0.020  1.384
 2DS  O4   C4    single    1.351  0.020  1.351
 2DS  O4   HO4   single    0.850  0.020  0.980
 2DS  C6   C3    aromatic  1.407  0.020  1.407
 2DS  O6   C6    single    1.347  0.020  1.347
 2DS  O6   HO6   single    0.850  0.020  0.980
 2DS  C7   C10   aromatic  1.390  0.020  1.390
 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  1.382  0.020  1.382
 2DS  C10  H10   single    0.930  0.020  1.080
 2DS  O10  C25   double    1.199  0.020  1.199
 2DS  C12  C15   aromatic  1.377  0.020  1.377
 2DS  C12  H12   single    0.930  0.020  1.080
 2DS  C13  H13   single    0.930  0.020  1.080
 2DS  O14  HO14  single    0.850  0.020  0.980
 2DS  C15  C18   aromatic  1.402  0.020  1.402
 2DS  C15  H15   single    0.930  0.020  1.080
 2DS  C16  C13   aromatic  1.397  0.020  1.397
 2DS  C16  C19   single    1.493  0.020  1.493
 2DS  C18  C21   single    1.480  0.020  1.480
 2DS  C19  N1    single    1.348  0.020  1.348
 2DS  C19  O7    double    1.220  0.020  1.220
 2DS  C21  N3    single    1.340  0.020  1.340
 2DS  C21  O9    double    1.238  0.020  1.238
 2DS  C22  C25   single    1.525  0.020  1.525
 2DS  C22  C20   single    1.521  0.020  1.521
 2DS  C22  H22   single    0.970  0.020  1.090
 2DS  C24  C30   single    1.519  0.020  1.519
 2DS  C24  C27   single    1.528  0.020  1.528
 2DS  C24  H24   single    0.970  0.020  1.090
 2DS  C25  O15   single    1.328  0.020  1.328
 2DS  C27  O12   double    1.200  0.020  1.200
 2DS  C27  O14   single    1.322  0.020  1.322
 2DS  C30  O15   single    1.428  0.020  1.428
 2DS  C30  H30   single    0.970  0.020  1.090
 2DS  C30  H30A  single    0.970  0.020  1.090
 2DS  C20  O11   single    1.407  0.020  1.407
 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   119.25  3.000
 2DS  C4    C1   O1   121.04  3.000
 2DS  C16   C1   O1   119.70  3.000
 2DS  HN1   N1   C22  117.64  3.000
 2DS  HN1   N1   C19  118.69  3.000
 2DS  C22   N1   C19  121.97  3.000
 2DS  HO1   O1   C1   110.21  3.000
 2DS  C18   C3   C6   119.90  3.000
 2DS  C6    C3   O3   116.19  3.000
 2DS  C18   C3   O3   123.91  3.000
 2DS  HN3   N3   C24  117.49  3.000
 2DS  HN3   N3   C21  119.30  3.000
 2DS  C24   N3   C21  121.88  3.000
 2DS  HO3   O3   C3   106.62  3.000
 2DS  C7    C4   O4   124.20  3.000
 2DS  O4    C4   C1   115.54  3.000
 2DS  C7    C4   C1   120.26  3.000
 2DS  HO4   O4   C4   111.10  3.000
 2DS  C9    C6   O6   119.61  3.000
 2DS  C9    C6   C3   119.78  3.000
 2DS  O6    C6   C3   120.61  3.000
 2DS  HO6   O6   C6   110.33  3.000
 2DS  H7    C7   C10  120.16  3.000
 2DS  H7    C7   C4   119.61  3.000
 2DS  C10   C7   C4   120.23  3.000
 2DS  H9    C9   C12  120.37  3.000
 2DS  H9    C9   C6   119.25  3.000
 2DS  C12   C9   C6   120.38  3.000
 2DS  H10   C10  C13  120.44  3.000
 2DS  H10   C10  C7   119.70  3.000
 2DS  C13   C10  C7   119.87  3.000
 2DS  H12   C12  C15  120.12  3.000
 2DS  H12   C12  C9   119.61  3.000
 2DS  C15   C12  C9   120.27  3.000
 2DS  H13   C13  C16  119.62  3.000
 2DS  C16   C13  C10  120.34  3.000
 2DS  H13   C13  C10  120.02  3.000
 2DS  HO14  O14  C27  110.55  3.000
 2DS  H15   C15  C18  121.17  3.000
 2DS  H15   C15  C12  118.36  3.000
 2DS  C18   C15  C12  120.46  3.000
 2DS  C19   C16  C13  119.51  3.000
 2DS  C19   C16  C1   120.39  3.000
 2DS  C13   C16  C1   120.04  3.000
 2DS  C21   C18  C15  123.23  3.000
 2DS  C21   C18  C3   117.57  3.000
 2DS  C15   C18  C3   119.20  3.000
 2DS  C16   C19  O7   122.75  3.000
 2DS  O7    C19  N1   122.93  3.000
 2DS  C16   C19  N1   114.31  3.000
 2DS  C18   C21  O9   120.91  3.000
 2DS  O9    C21  N3   120.85  3.000
 2DS  C18   C21  N3   118.24  3.000
 2DS  H22   C22  C20  107.80  3.000
 2DS  H22   C22  C25  108.26  3.000
 2DS  C20   C22  C25  110.41  3.000
 2DS  H22   C22  N1   109.36  3.000
 2DS  C20   C22  N1   110.98  3.000
 2DS  C25   C22  N1   109.95  3.000
 2DS  H24   C24  C30  106.94  3.000
 2DS  H24   C24  C27  108.22  3.000
 2DS  C30   C24  C27  110.66  3.000
 2DS  H24   C24  N3   109.29  3.000
 2DS  C27   C24  N3   110.74  3.000
 2DS  C30   C24  N3   110.86  3.000
 2DS  C22   C25  O15  110.42  3.000
 2DS  O15   C25  O10  124.54  3.000
 2DS  C22   C25  O10  125.04  3.000
 2DS  C24   C27  O14  110.94  3.000
 2DS  O14   C27  O12  124.71  3.000
 2DS  C24   C27  O12  124.35  3.000
 2DS  H30A  C30  H30  108.48  3.000
 2DS  H30A  C30  C24  110.45  3.000
 2DS  H30   C30  C24  110.18  3.000
 2DS  H30A  C30  O15  111.55  3.000
 2DS  H30   C30  O15  109.47  3.000
 2DS  C24   C30  O15  106.71  3.000
 2DS  H19   C20  H18  107.36  3.000
 2DS  H19   C20  O11  112.16  3.000
 2DS  H18   C20  O11  112.40  3.000
 2DS  H19   C20  C22  109.25  3.000
 2DS  H18   C20  C22  108.18  3.000
 2DS  O11   C20  C22  107.39  3.000
 2DS  H20   O11  C20  108.77  3.000
 2DS  C30   O15  C25  119.90  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  CONST_37  HO14  O14  C27  O12     0.00   0.0  0
 2DS  Var_01    N1    C19  C16  C1   -129.92  30.0  2
 2DS  Var_02    N3    C21  C18  C3   -174.45  30.0  2
 2DS  Var_03    H30   C30  O15  C25   -95.34  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  H12   0.020
 2DS  plan-2  H15   0.020
 2DS  plan-2  H9    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-5  HO14  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

