# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 13:05:30 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=O)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
 MCK  MCK  N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine  ligand  63  39  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MCK
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
 MCK  C1    C  CR6    0  -0.158   4.1929   1.0680   0.6310
 MCK  C2    C  CR6    0   0.285   4.5400   0.4553   1.8305
 MCK  C3    C  CR6    0   0.268   5.8531   0.5807   2.3090
 MCK  C4    C  CR16   0  -0.368   6.7856   1.3188   1.6017
 MCK  C5    C  CR16   0  -0.264   6.4306   1.9352   0.4067
 MCK  C6    C  CR16   0  -0.289   5.1440   1.8034  -0.0799
 MCK  C7    C  C      0   0.544   2.7943   0.9749   0.1213
 MCK  O8    O  O      0  -0.476   1.8175   1.2491   0.8001
 MCK  N9    N  NH1    0  -0.624   2.6897   0.5918  -1.1647
 MCK  O10   O  OH1    0  -0.613   3.6258  -0.2715   2.4947
 MCK  O11   O  OH1    0  -0.645   6.1130  -0.0579   3.4711
 MCK  C12   C  CH1    0  -0.268   1.4192   0.5082  -1.8261
 MCK  C13   C  C      0   0.626   0.7184   1.8646  -1.7811
 MCK  C14   C  CH2    0  -0.166   0.5253  -0.6148  -1.2928
 MCK  O15   O  O2     0  -0.453   1.3262  -1.7912  -1.2403
 MCK  O16   O  O      0  -0.431   1.2887   2.9199  -1.7634
 MCK  O17   O  O2     0  -0.472  -0.5945   1.7215  -1.8093
 MCK  C18   C  CH2    0  -0.188  -1.4356   2.8732  -1.6368
 MCK  C19   C  CH1    0  -0.278  -2.8537   2.3508  -1.5571
 MCK  N20   N  NH1    0  -0.633  -2.9576   1.4025  -0.4722
 MCK  C21   C  C      0   0.432  -3.3414   1.7511  -2.9132
 MCK  O22   O  O      0  -0.580  -3.9227   0.6585  -2.8668
 MCK  O23   O  OC    -1  -0.603  -3.1115   2.4620  -3.9082
 MCK  C24   C  C      0   0.569   0.7999  -2.8644  -0.6614
 MCK  O25   O  O      0  -0.429  -0.3124  -2.8964  -0.2004
 MCK  C26   C  CH1    0  -0.250   1.7751  -4.0379  -0.6546
 MCK  N27   N  NH2    0  -0.769   1.4168  -5.0810   0.2718
 MCK  C28   C  CH2    0  -0.134   1.8908  -4.5857  -2.0777
 MCK  C29   C  C      0   0.630  -4.0935   1.1497   0.1742
 MCK  O30   O  O      0  -0.546  -5.0716   1.9120   0.1017
 MCK  C31   C  CR6    0  -0.171  -4.1466  -0.0501   1.0485
 MCK  C32   C  CR6    0   0.251  -5.2254  -0.1544   1.9353
 MCK  C33   C  CR6    0   0.307  -5.3157  -1.2545   2.8064
 MCK  C34   C  CR16   0  -0.344  -4.3535  -2.2440   2.7655
 MCK  C35   C  CR16   0  -0.262  -3.2944  -2.1570   1.8635
 MCK  C36   C  CR16   0  -0.332  -3.1909  -1.0751   1.0167
 MCK  O37   O  OH1    0  -0.650  -6.2049   0.7526   2.0179
 MCK  O38   O  OH1    0  -0.634  -6.3397  -1.3563   3.6769
 MCK  O45   O  OH1    0  -0.662   2.9019  -5.5597  -2.0995
 MCK  H4    H  HCR6   0   0.280   7.7957   1.4120   1.9835
 MCK  H5    H  HCR6   0   0.262   7.1628   2.5175  -0.1350
 MCK  H6    H  HCR6   0   0.263   4.8629   2.2896  -1.0051
 MCK  HN9   H  HNH1   0   0.417   3.5118   0.3045  -1.6694
 MCK  HO10  H  HOH1   0   0.477   4.0239  -0.6816   3.2723
 MCK  HO11  H  HOH1   0   0.485   7.0428   0.0239   3.7103
 MCK  H12   H  HCH1   0   0.334   1.6297   0.3083  -2.8815
 MCK  H14   H  HCH2   0   0.242   0.1494  -0.3788  -0.2972
 MCK  H14A  H  HCH2   0   0.264  -0.3187  -0.7711  -1.9654
 MCK  H18   H  HCH2   0   0.256  -1.1516   3.3915  -0.7193
 MCK  H18A  H  HCH2   0   0.258  -1.3311   3.5556  -2.4784
 MCK  H19   H  HCH1   0   0.285  -3.4884   3.2102  -1.3268
 MCK  HN20  H  HNH1   0   0.392  -2.2352   0.7043  -0.4326
 MCK  H26   H  HCH1   0   0.271   2.7551  -3.6399  -0.3696
 MCK  HN27  H  HNH2   0   0.355   1.3821  -4.7164   1.2149
 MCK  HN2A  H  HNH2   0   0.345   0.4901  -5.4349   0.0680
 MCK  H28   H  HCH2   0   0.202   0.9176  -5.0016  -2.3746
 MCK  H28A  H  HCH2   0   0.214   2.1102  -3.7619  -2.7662
 MCK  H34   H  HCR6   0   0.271  -4.4368  -3.0914   3.4348
 MCK  H35   H  HCR6   0   0.259  -2.5549  -2.9446   1.8245
 MCK  H36   H  HCR6   0   0.235  -2.3669  -1.0613   0.3156
 MCK  HO37  H  HOH1   0   0.482  -6.0257   1.4135   1.2959
 MCK  HO38  H  HOH1   0   0.474  -6.9203  -0.5892   3.5996
 MCK  HO45  H  HOH1   0   0.457   2.9555  -5.9086  -2.9937

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
 MCK  C7   C1    single    1.492  0.020  1.492
 MCK  C1   C2    aromatic  1.391  0.020  1.391
 MCK  C1   C6    aromatic  1.397  0.020  1.397
 MCK  O10  C2    single    1.344  0.020  1.344
 MCK  C2   C3    aromatic  1.403  0.020  1.403
 MCK  C3   O11   single    1.351  0.020  1.351
 MCK  C3   C4    aromatic  1.384  0.020  1.384
 MCK  C5   C4    aromatic  1.391  0.020  1.391
 MCK  C4   H4    single    0.930  0.020  1.080
 MCK  C6   C5    aromatic  1.382  0.020  1.382
 MCK  C5   H5    single    0.930  0.020  1.080
 MCK  C6   H6    single    0.930  0.020  1.080
 MCK  N9   C7    single    1.346  0.020  1.346
 MCK  O8   C7    double    1.221  0.020  1.221
 MCK  C12  N9    single    1.435  0.020  1.435
 MCK  N9   HN9   single    0.860  0.020  1.020
 MCK  O10  HO10  single    0.850  0.020  0.980
 MCK  O11  HO11  single    0.850  0.020  0.980
 MCK  C13  C12   single    1.527  0.020  1.527
 MCK  C14  C12   single    1.531  0.020  1.531
 MCK  C12  H12   single    0.970  0.020  1.090
 MCK  O16  C13   double    1.200  0.020  1.200
 MCK  C13  O17   single    1.321  0.020  1.321
 MCK  O15  C14   single    1.424  0.020  1.424
 MCK  C14  H14   single    0.970  0.020  1.090
 MCK  C14  H14A  single    0.970  0.020  1.090
 MCK  O15  C24   single    1.328  0.020  1.328
 MCK  C18  O17   single    1.436  0.020  1.436
 MCK  C18  C19   single    1.513  0.020  1.513
 MCK  C18  H18   single    0.970  0.020  1.090
 MCK  C18  H18A  single    0.970  0.020  1.090
 MCK  C21  C19   single    1.561  0.020  1.561
 MCK  C19  N20   single    1.445  0.020  1.445
 MCK  C19  H19   single    0.970  0.020  1.090
 MCK  N20  C29   single    1.331  0.020  1.331
 MCK  N20  HN20  single    0.890  0.020  1.040
 MCK  O22  C21   deloc     1.239  0.020  1.239
 MCK  C21  O23   deloc     1.244  0.020  1.244
 MCK  C24  C26   single    1.526  0.020  1.526
 MCK  C24  O25   double    1.204  0.020  1.204
 MCK  N27  C26   single    1.440  0.020  1.440
 MCK  C26  C28   single    1.529  0.020  1.529
 MCK  C26  H26   single    0.970  0.020  1.090
 MCK  N27  HN27  single    0.890  0.020  1.040
 MCK  N27  HN2A  single    0.890  0.020  1.040
 MCK  C28  O45   single    1.404  0.020  1.404
 MCK  C28  H28   single    0.970  0.020  1.090
 MCK  C28  H28A  single    0.970  0.020  1.090
 MCK  O30  C29   double    1.242  0.020  1.242
 MCK  C29  C31   single    1.486  0.020  1.486
 MCK  C31  C32   aromatic  1.400  0.020  1.400
 MCK  C31  C36   aromatic  1.402  0.020  1.402
 MCK  O37  C32   single    1.338  0.020  1.338
 MCK  C32  C33   aromatic  1.406  0.020  1.406
 MCK  C33  O38   single    1.348  0.020  1.348
 MCK  C33  C34   aromatic  1.381  0.020  1.381
 MCK  C35  C34   aromatic  1.394  0.020  1.394
 MCK  C34  H34   single    0.930  0.020  1.080
 MCK  C36  C35   aromatic  1.378  0.020  1.378
 MCK  C35  H35   single    0.930  0.020  1.080
 MCK  C36  H36   single    0.930  0.020  1.080
 MCK  O37  HO37  single    0.850  0.020  0.980
 MCK  O38  HO38  single    0.850  0.020  0.980
 MCK  O45  HO45  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
 MCK  C7    C1   C6    119.83  3.000
 MCK  C6    C1   C2    120.06  3.000
 MCK  C7    C1   C2    120.08  3.000
 MCK  O10   C2   C3    121.09  3.000
 MCK  C3    C2   C1    119.23  3.000
 MCK  O10   C2   C1    119.66  3.000
 MCK  O11   C3   C4    124.20  3.000
 MCK  C4    C3   C2    120.26  3.000
 MCK  O11   C3   C2    115.54  3.000
 MCK  H4    C4   C5    120.17  3.000
 MCK  H4    C4   C3    119.59  3.000
 MCK  C5    C4   C3    120.24  3.000
 MCK  H5    C5   C6    120.37  3.000
 MCK  H5    C5   C4    119.76  3.000
 MCK  C6    C5   C4    119.87  3.000
 MCK  H6    C6   C5    120.01  3.000
 MCK  H6    C6   C1    119.65  3.000
 MCK  C5    C6   C1    120.33  3.000
 MCK  N9    C7   O8    122.21  3.000
 MCK  O8    C7   C1    123.11  3.000
 MCK  N9    C7   C1    114.66  3.000
 MCK  HN9   N9   C12   118.39  3.000
 MCK  HN9   N9   C7    119.79  3.000
 MCK  C12   N9   C7    121.73  3.000
 MCK  HO10  O10  C2    110.34  3.000
 MCK  HO11  O11  C3    111.04  3.000
 MCK  H12   C12  C14   108.31  3.000
 MCK  H12   C12  C13   106.19  3.000
 MCK  C14   C12  C13   111.91  3.000
 MCK  H12   C12  N9    106.54  3.000
 MCK  C14   C12  N9    113.52  3.000
 MCK  C13   C12  N9    109.93  3.000
 MCK  O17   C13  O16   124.62  3.000
 MCK  O17   C13  C12   111.05  3.000
 MCK  O16   C13  C12   124.30  3.000
 MCK  H14A  C14  H14   109.11  3.000
 MCK  H14A  C14  O15   109.85  3.000
 MCK  H14   C14  O15   109.83  3.000
 MCK  H14A  C14  C12   110.00  3.000
 MCK  H14   C14  C12   111.14  3.000
 MCK  O15   C14  C12   106.88  3.000
 MCK  C24   O15  C14   117.43  3.000
 MCK  C18   O17  C13   119.50  3.000
 MCK  H18A  C18  H18   109.10  3.000
 MCK  H18A  C18  C19   110.31  3.000
 MCK  H18   C18  C19   111.31  3.000
 MCK  H18A  C18  O17   110.71  3.000
 MCK  H18   C18  O17   109.23  3.000
 MCK  C19   C18  O17   106.15  3.000
 MCK  H19   C19  C21   107.68  3.000
 MCK  H19   C19  N20   108.43  3.000
 MCK  C21   C19  N20   112.20  3.000
 MCK  H19   C19  C18   106.49  3.000
 MCK  N20   C19  C18   109.49  3.000
 MCK  C21   C19  C18   112.31  3.000
 MCK  HN20  N20  C29   117.52  3.000
 MCK  HN20  N20  C19   115.70  3.000
 MCK  C29   N20  C19   123.42  3.000
 MCK  O23   C21  O22   128.37  3.000
 MCK  O23   C21  C19   114.68  3.000
 MCK  O22   C21  C19   116.93  3.000
 MCK  C26   C24  O25   124.61  3.000
 MCK  O25   C24  O15   123.66  3.000
 MCK  C26   C24  O15   111.73  3.000
 MCK  H26   C26  C28   107.73  3.000
 MCK  H26   C26  N27   108.56  3.000
 MCK  C28   C26  N27   110.98  3.000
 MCK  H26   C26  C24   107.06  3.000
 MCK  C28   C26  C24   108.64  3.000
 MCK  N27   C26  C24   113.63  3.000
 MCK  HN2A  N27  HN27  106.38  3.000
 MCK  HN2A  N27  C26   110.56  3.000
 MCK  HN27  N27  C26   110.31  3.000
 MCK  H28A  C28  H28   106.97  3.000
 MCK  H28A  C28  O45   111.57  3.000
 MCK  H28   C28  O45   111.77  3.000
 MCK  H28A  C28  C26   109.31  3.000
 MCK  H28   C28  C26   108.66  3.000
 MCK  O45   C28  C26   108.50  3.000
 MCK  C31   C29  O30   120.13  3.000
 MCK  C31   C29  N20   118.02  3.000
 MCK  O30   C29  N20   121.80  3.000
 MCK  C36   C31  C32   119.02  3.000
 MCK  C36   C31  C29   123.56  3.000
 MCK  C32   C31  C29   117.41  3.000
 MCK  O37   C32  C33   116.44  3.000
 MCK  C33   C32  C31   120.00  3.000
 MCK  O37   C32  C31   123.56  3.000
 MCK  O38   C33  C34   119.64  3.000
 MCK  C34   C33  C32   119.83  3.000
 MCK  O38   C33  C32   120.53  3.000
 MCK  H34   C34  C35   120.48  3.000
 MCK  H34   C34  C33   119.26  3.000
 MCK  C35   C34  C33   120.27  3.000
 MCK  H35   C35  C36   119.90  3.000
 MCK  H35   C35  C34   119.85  3.000
 MCK  C36   C35  C34   120.25  3.000
 MCK  H36   C36  C35   117.74  3.000
 MCK  H36   C36  C31   121.64  3.000
 MCK  C35   C36  C31   120.60  3.000
 MCK  HO37  O37  C32   105.88  3.000
 MCK  HO38  O38  C33   110.20  3.000
 MCK  HO45  O45  C28   107.84  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
 MCK  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MCK  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MCK  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MCK  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MCK  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MCK  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 MCK  CONST_07  C34   C33  C32  C31     0.00   0.0  0
 MCK  CONST_08  C34   C35  C36  C31     0.00   0.0  0
 MCK  CONST_09  C35   C36  C31  C32     0.00   0.0  0
 MCK  CONST_10  C35   C34  C33  C32     0.00   0.0  0
 MCK  CONST_11  C36   C31  C32  C33     0.00   0.0  0
 MCK  CONST_12  C36   C35  C34  C33     0.00   0.0  0
 MCK  CONST_13  O11   C3   C2   C1    180.00   0.0  0
 MCK  CONST_14  C7    C1   C2   C3    180.00   0.0  0
 MCK  CONST_15  O10   C2   C3   C4    180.00   0.0  0
 MCK  CONST_16  O11   C3   C4   C5    180.00   0.0  0
 MCK  CONST_17  C7    C1   C6   C5    180.00   0.0  0
 MCK  CONST_18  O10   C2   C1   C6    180.00   0.0  0
 MCK  CONST_19  C33   C32  C31  C29   180.00   0.0  0
 MCK  CONST_20  C35   C36  C31  C29   180.00   0.0  0
 MCK  CONST_21  O38   C33  C32  C31   180.00   0.0  0
 MCK  CONST_22  O37   C32  C33  C34   180.00   0.0  0
 MCK  CONST_23  O38   C33  C34  C35   180.00   0.0  0
 MCK  CONST_24  O37   C32  C31  C36   180.00   0.0  0
 MCK  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 MCK  CONST_26  H6    C6   C1   C2    180.00   0.0  0
 MCK  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 MCK  CONST_28  H35   C35  C36  C31   180.00   0.0  0
 MCK  CONST_29  H36   C36  C31  C32   180.00   0.0  0
 MCK  CONST_30  H34   C34  C33  C32   180.00   0.0  0
 MCK  CONST_31  C12   N9   C7   C1    180.00   0.0  0
 MCK  CONST_32  C31   C29  N20  C19   180.00   0.0  0
 MCK  CONST_33  HN9   N9   C7   C1      0.00   0.0  0
 MCK  CONST_34  HN20  N20  C29  C31     0.00   0.0  0
 MCK  CONST_35  C12   N9   C7   O8      0.00   0.0  0
 MCK  Var_01    N9    C7   C1   C2   -130.32  30.0  2
 MCK  Var_02    C32   C31  C29  N20   166.72  30.0  2
 MCK  Var_03    C19   C18  O17  C13  -173.50  30.0  1
 MCK  Var_04    C26   C24  O15  C14  -178.97  30.0  3
 MCK  Var_05    H14   C14  O15  C24    51.82  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
 MCK  chir_01  C12  N9   C13  C14  positiv
 MCK  chir_02  C19  N20  C21  C18  positiv
 MCK  chir_03  C26  C24  N27  C28  negativ

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
 MCK  plan-1  C1    0.020
 MCK  plan-1  C2    0.020
 MCK  plan-1  C3    0.020
 MCK  plan-1  C4    0.020
 MCK  plan-1  C5    0.020
 MCK  plan-1  C6    0.020
 MCK  plan-1  C7    0.020
 MCK  plan-1  O10   0.020
 MCK  plan-1  O11   0.020
 MCK  plan-1  H4    0.020
 MCK  plan-1  H5    0.020
 MCK  plan-1  H6    0.020
 MCK  plan-2  O15   0.020
 MCK  plan-2  C24   0.020
 MCK  plan-2  O25   0.020
 MCK  plan-2  C26   0.020
 MCK  plan-3  C29   0.020
 MCK  plan-3  C31   0.020
 MCK  plan-3  C32   0.020
 MCK  plan-3  C33   0.020
 MCK  plan-3  C34   0.020
 MCK  plan-3  C35   0.020
 MCK  plan-3  C36   0.020
 MCK  plan-3  O37   0.020
 MCK  plan-3  O38   0.020
 MCK  plan-3  H34   0.020
 MCK  plan-3  H35   0.020
 MCK  plan-3  H36   0.020
 MCK  plan-4  C1    0.020
 MCK  plan-4  C7    0.020
 MCK  plan-4  O8    0.020
 MCK  plan-4  N9    0.020
 MCK  plan-4  C12   0.020
 MCK  plan-4  HN9   0.020
 MCK  plan-5  C19   0.020
 MCK  plan-5  N20   0.020
 MCK  plan-5  C29   0.020
 MCK  plan-5  O30   0.020
 MCK  plan-5  C31   0.020
 MCK  plan-5  HN20  0.020
 MCK  plan-6  C19   0.020
 MCK  plan-6  C21   0.020
 MCK  plan-6  O22   0.020
 MCK  plan-6  O23   0.020
 MCK  plan-7  C12   0.020
 MCK  plan-7  C13   0.020
 MCK  plan-7  O16   0.020
 MCK  plan-7  O17   0.020

