# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 14:18:47 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-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)=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
 TD1  TD1  O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-L-serine  ligand  39  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TD1
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
 TD1  C1    C  CR6   0  -0.168  -2.2185   0.4707   0.0938
 TD1  C2    C  CR6   0   0.253  -3.3807   0.6934  -0.6560
 TD1  C3    C  CR6   0   0.309  -4.2178   1.7805  -0.3457
 TD1  C4    C  CR16  0  -0.341  -3.8799   2.6326   0.6862
 TD1  C5    C  CR16  0  -0.257  -2.7142   2.4222   1.4215
 TD1  C6    C  CR16  0  -0.332  -1.8928   1.3556   1.1313
 TD1  C7    C  C     0   0.649  -1.3834  -0.6966  -0.2703
 TD1  O8    O  O     0  -0.537  -1.6395  -1.3703  -1.2793
 TD1  N9    N  NH1   0  -0.671  -0.3483  -1.0062   0.5165
 TD1  O10   O  OH1   0  -0.645  -3.7685  -0.0795  -1.6751
 TD1  O11   O  OH1   0  -0.632  -5.3448   2.0016  -1.0496
 TD1  C12   C  CH1   0  -0.250   0.5285  -2.1130   0.2343
 TD1  C13   C  C     0   0.557   1.1779  -2.5580   1.5349
 TD1  C14   C  CH2   0  -0.181   1.5812  -1.7567  -0.8081
 TD1  O15   O  O2    0  -0.457   2.3649  -0.7130  -0.2361
 TD1  O16   O  OH1   0  -0.580   1.9427  -3.6149   1.3464
 TD1  O17   O  O     0  -0.422   1.0120  -2.0116   2.5938
 TD1  C24   C  C     0   0.576   3.2856  -0.1267  -0.9943
 TD1  O25   O  O     0  -0.434   3.5319  -0.4674  -2.1216
 TD1  C26   C  CH1   0  -0.253   3.9642   1.0258  -0.2620
 TD1  N27   N  NH2   0  -0.770   5.1781   1.4768  -0.8925
 TD1  C28   C  CH2   0  -0.130   2.9590   2.1715  -0.1251
 TD1  O45   O  OH1   0  -0.662   3.5278   3.1681   0.6832
 TD1  H4    H  HCR6  0   0.274  -4.5281   3.4693   0.9154
 TD1  H5    H  HCR6  0   0.264  -2.4556   3.1045   2.2191
 TD1  H6    H  HCR6  0   0.252  -0.9901   1.2313   1.7145
 TD1  HN9   H  HNH1  0   0.422  -0.1862  -0.4958   1.3698
 TD1  HO10  H  HOH1  0   0.484  -3.0566  -0.7579  -1.8009
 TD1  HO11  H  HOH1  0   0.475  -5.4456   1.3363  -1.7415
 TD1  H12   H  HCH1  0   0.332  -0.0491  -2.9547  -0.1598
 TD1  H14   H  HCH2  0   0.269   2.1982  -2.6235  -1.0501
 TD1  H14A  H  HCH2  0   0.272   1.0931  -1.4203  -1.7237
 TD1  HO16  H  HOH1  0   0.494   2.3668  -3.8814   2.1766
 TD1  H26   H  HCH1  0   0.275   4.2051   0.6713   0.7459
 TD1  HN27  H  HNH2  0   0.356   5.8685   0.7373  -0.8938
 TD1  HN2A  H  HNH2  0   0.344   5.0080   1.7109  -1.8632
 TD1  H28   H  HCH2  0   0.202   2.7145   2.5487  -1.1283
 TD1  H28A  H  HCH2  0   0.207   2.0281   1.7873   0.3068
 TD1  HO45  H  HOH1  0   0.457   2.8702   3.8588   0.8054

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
 TD1  C7   C1    single    1.481  0.020  1.481
 TD1  C1   C2    aromatic  1.401  0.020  1.401
 TD1  C1   C6    aromatic  1.402  0.020  1.402
 TD1  O10  C2    single    1.337  0.020  1.337
 TD1  C2   C3    aromatic  1.407  0.020  1.407
 TD1  C3   O11   single    1.347  0.020  1.347
 TD1  C3   C4    aromatic  1.380  0.020  1.380
 TD1  C5   C4    aromatic  1.394  0.020  1.394
 TD1  C4   H4    single    0.930  0.020  1.080
 TD1  C6   C5    aromatic  1.377  0.020  1.377
 TD1  C5   H5    single    0.930  0.020  1.080
 TD1  C6   H6    single    0.930  0.020  1.080
 TD1  N9   C7    single    1.337  0.020  1.337
 TD1  O8   C7    double    1.240  0.020  1.240
 TD1  C12  N9    single    1.440  0.020  1.440
 TD1  N9   HN9   single    0.860  0.020  1.020
 TD1  O10  HO10  single    0.850  0.020  0.980
 TD1  O11  HO11  single    0.850  0.020  0.980
 TD1  C13  C12   single    1.520  0.020  1.520
 TD1  C12  C14   single    1.524  0.020  1.524
 TD1  C12  H12   single    0.970  0.020  1.090
 TD1  O17  C13   double    1.203  0.020  1.203
 TD1  C13  O16   single    1.318  0.020  1.318
 TD1  C14  O15   single    1.425  0.020  1.425
 TD1  C14  H14   single    0.970  0.020  1.090
 TD1  C14  H14A  single    0.970  0.020  1.090
 TD1  O15  C24   single    1.329  0.020  1.329
 TD1  O16  HO16  single    0.850  0.020  0.980
 TD1  C26  C24   single    1.525  0.020  1.525
 TD1  C24  O25   double    1.203  0.020  1.203
 TD1  C28  C26   single    1.530  0.020  1.530
 TD1  C26  N27   single    1.440  0.020  1.440
 TD1  C26  H26   single    0.970  0.020  1.090
 TD1  N27  HN27  single    0.890  0.020  1.040
 TD1  N27  HN2A  single    0.890  0.020  1.040
 TD1  O45  C28   single    1.404  0.020  1.404
 TD1  C28  H28   single    0.970  0.020  1.090
 TD1  C28  H28A  single    0.970  0.020  1.090
 TD1  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
 TD1  C7    C1   C6    123.27  3.000
 TD1  C6    C1   C2    119.24  3.000
 TD1  C7    C1   C2    117.49  3.000
 TD1  O10   C2   C3    116.26  3.000
 TD1  C3    C2   C1    119.90  3.000
 TD1  O10   C2   C1    123.84  3.000
 TD1  O11   C3   C4    119.61  3.000
 TD1  C4    C3   C2    119.76  3.000
 TD1  O11   C3   C2    120.63  3.000
 TD1  H4    C4   C5    120.36  3.000
 TD1  H4    C4   C3    119.26  3.000
 TD1  C5    C4   C3    120.38  3.000
 TD1  H5    C5   C6    120.11  3.000
 TD1  H5    C5   C4    119.60  3.000
 TD1  C6    C5   C4    120.29  3.000
 TD1  H6    C6   C5    118.23  3.000
 TD1  H6    C6   C1    121.35  3.000
 TD1  C5    C6   C1    120.42  3.000
 TD1  N9    C7   O8    120.87  3.000
 TD1  O8    C7   C1    120.80  3.000
 TD1  N9    C7   C1    118.33  3.000
 TD1  HN9   N9   C12   117.22  3.000
 TD1  HN9   N9   C7    120.39  3.000
 TD1  C12   N9   C7    122.29  3.000
 TD1  HO10  O10  C2    106.51  3.000
 TD1  HO11  O11  C3    110.42  3.000
 TD1  H12   C12  C14   107.34  3.000
 TD1  H12   C12  C13   107.97  3.000
 TD1  C14   C12  C13   111.01  3.000
 TD1  H12   C12  N9    109.90  3.000
 TD1  C14   C12  N9    112.03  3.000
 TD1  C13   C12  N9    108.51  3.000
 TD1  O17   C13  O16   124.75  3.000
 TD1  O16   C13  C12   111.11  3.000
 TD1  O17   C13  C12   124.14  3.000
 TD1  H14A  C14  H14   108.17  3.000
 TD1  H14A  C14  O15   110.93  3.000
 TD1  H14   C14  O15   111.09  3.000
 TD1  H14A  C14  C12   109.71  3.000
 TD1  H14   C14  C12   110.89  3.000
 TD1  O15   C14  C12   106.06  3.000
 TD1  C24   O15  C14   118.37  3.000
 TD1  HO16  O16  C13   110.59  3.000
 TD1  C26   C24  O25   124.95  3.000
 TD1  O25   C24  O15   123.47  3.000
 TD1  C26   C24  O15   111.58  3.000
 TD1  H26   C26  C28   107.73  3.000
 TD1  H26   C26  N27   108.59  3.000
 TD1  C28   C26  N27   111.00  3.000
 TD1  H26   C26  C24   107.16  3.000
 TD1  N27   C26  C24   113.67  3.000
 TD1  C28   C26  C24   108.45  3.000
 TD1  HN2A  N27  HN27  106.40  3.000
 TD1  HN2A  N27  C26   110.51  3.000
 TD1  HN27  N27  C26   110.30  3.000
 TD1  H28A  C28  H28   106.92  3.000
 TD1  H28A  C28  O45   111.48  3.000
 TD1  H28   C28  O45   111.84  3.000
 TD1  H28A  C28  C26   109.32  3.000
 TD1  H28   C28  C26   108.75  3.000
 TD1  O45   C28  C26   108.48  3.000
 TD1  HO45  O45  C28   107.82  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
 TD1  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 TD1  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 TD1  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 TD1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 TD1  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 TD1  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 TD1  CONST_07  O11   C3   C2   C1    180.00   0.0  0
 TD1  CONST_08  C7    C1   C2   C3    180.00   0.0  0
 TD1  CONST_09  O10   C2   C3   C4    180.00   0.0  0
 TD1  CONST_10  O11   C3   C4   C5    180.00   0.0  0
 TD1  CONST_11  C7    C1   C6   C5    180.00   0.0  0
 TD1  CONST_12  O10   C2   C1   C6    180.00   0.0  0
 TD1  CONST_13  H5    C5   C6   C1    180.00   0.0  0
 TD1  CONST_14  H6    C6   C1   C2    180.00   0.0  0
 TD1  CONST_15  H4    C4   C3   C2    180.00   0.0  0
 TD1  CONST_16  C12   N9   C7   C1    180.00   0.0  0
 TD1  CONST_17  HN9   N9   C7   C1      0.00   0.0  0
 TD1  CONST_18  C12   N9   C7   O8      0.00   0.0  0
 TD1  CONST_19  HO16  O16  C13  C12   180.00   0.0  0
 TD1  Var_01    N9    C7   C1   C2   -173.21  30.0  2
 TD1  Var_02    C26   C24  O15  C14   176.12  30.0  3
 TD1  Var_03    H14   C14  O15  C24    65.63  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
 TD1  chir_01  C12  N9   C13  C14  positiv
 TD1  chir_02  C26  N27  C28  C24  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
 TD1  plan-1  C1    0.020
 TD1  plan-1  C2    0.020
 TD1  plan-1  C3    0.020
 TD1  plan-1  C4    0.020
 TD1  plan-1  C5    0.020
 TD1  plan-1  C6    0.020
 TD1  plan-1  C7    0.020
 TD1  plan-1  O10   0.020
 TD1  plan-1  O11   0.020
 TD1  plan-1  H4    0.020
 TD1  plan-1  H5    0.020
 TD1  plan-1  H6    0.020
 TD1  plan-2  C1    0.020
 TD1  plan-2  C7    0.020
 TD1  plan-2  O8    0.020
 TD1  plan-2  N9    0.020
 TD1  plan-2  C12   0.020
 TD1  plan-2  HN9   0.020
 TD1  plan-3  C12   0.020
 TD1  plan-3  C13   0.020
 TD1  plan-3  O16   0.020
 TD1  plan-3  O17   0.020
 TD1  plan-3  HO16  0.020
 TD1  plan-4  O15   0.020
 TD1  plan-4  C24   0.020
 TD1  plan-4  O25   0.020
 TD1  plan-4  C26   0.020

