# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 06:11:51 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-deoxy-3,4-bis-O-[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]-L-threo-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](OC(=O)/C=C/c1ccc(O)cc1)[C@@H](OC(=O)\C=C\c2ccc(O)cc2)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
 OFF  OFF  '2-deoxy-3,4-bis-O-[(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]-L-threo-pentaric acid'  ligand  51  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OFF
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
 OFF  C19   C  CR16   0  -0.298   1.0444   7.8756   3.4861
 OFF  C20   C  CR16   0  -0.361   0.6851   8.7929   4.4531
 OFF  C21   C  CR6    0   0.357   0.0866  10.0008   4.0865
 OFF  O10   O  OH1    0  -0.622  -0.2861  10.9247   4.9854
 OFF  C22   C  CR16   0  -0.327  -0.1414  10.2714   2.7386
 OFF  C23   C  CR16   0  -0.290   0.2245   9.3430   1.7825
 OFF  C18   C  CR6    0   0.123   0.8229   8.1271   2.1279
 OFF  C17   C  C1     0  -0.218   1.1766   7.1921   1.0723
 OFF  C16   C  C1     0  -0.442   1.7499   5.9908   1.2193
 OFF  C15   C  C      0   0.616   2.0352   5.1440   0.0528
 OFF  O9    O  O      0  -0.470   1.7692   5.4250  -1.0956
 OFF  O8    O  O2     0  -0.476   2.6425   4.0268   0.4235
 OFF  C12   C  CH1    0  -0.013   2.9300   3.0063  -0.5402
 OFF  C13   C  CH2    0  -0.595   3.9914   2.1384   0.1013
 OFF  C14   C  C      0   0.414   5.3073   2.8970   0.3622
 OFF  O6    O  OC    -1  -0.619   5.9495   2.5645   1.3780
 OFF  O7    O  O      0  -0.610   5.6441   3.7522  -0.4806
 OFF  C10   C  CH1    0  -0.081   1.6202   2.2810  -0.8965
 OFF  C11   C  C      0   0.393   0.8384   1.8241   0.3562
 OFF  O4    O  OC    -1  -0.593   0.1036   2.6945   0.8560
 OFF  O5    O  O      0  -0.598   1.0326   0.6635   0.7537
 OFF  O3    O  O2     0  -0.481   2.0196   1.1828  -1.7127
 OFF  C9    C  C      0   0.607   1.0623   0.4563  -2.2747
 OFF  O2    O  O      0  -0.467  -0.1125   0.7472  -2.2338
 OFF  C8    C  C1     0  -0.444   1.6238  -0.7140  -2.9632
 OFF  C7    C  C1     0  -0.214   0.8272  -1.5522  -3.6399
 OFF  C4    C  CR6    0   0.124   1.2217  -2.7497  -4.3628
 OFF  C5    C  CR16   0  -0.294   2.5413  -3.2089  -4.4329
 OFF  C6    C  CR16   0  -0.361   2.8655  -4.3542  -5.1318
 OFF  C1    C  CR6    0   0.357   1.8690  -5.0812  -5.7879
 OFF  O1    O  OH1    0  -0.621   2.1288  -6.1999  -6.4812
 OFF  C2    C  CR16   0  -0.326   0.5479  -4.6413  -5.7295
 OFF  C3    C  CR16   0  -0.290   0.2395  -3.4930  -5.0254
 OFF  H19   H  HCR6   0   0.263   1.5030   6.9482   3.8044
 OFF  H20   H  HCR6   0   0.278   0.8665   8.5698   5.4983
 OFF  HO10  H  HOH1   0   0.479  -0.0807  10.6320   5.8808
 OFF  H22   H  HCR6   0   0.269  -0.6038  11.2055   2.4462
 OFF  H23   H  HCR6   0   0.262   0.0414   9.5668   0.7385
 OFF  H171  H  H      0   0.263   0.9382   7.5229   0.0656
 OFF  H161  H  H      0   0.270   2.0160   5.5983   2.1929
 OFF  H12   H  HCH1   0   0.242   3.3391   3.4644  -1.4442
 OFF  H131  H  HCH2   0   0.223   3.6163   1.6909   1.0239
 OFF  H132  H  HCH2   0   0.245   4.2190   1.3059  -0.5704
 OFF  H10   H  HCH1   0   0.246   0.9933   2.9561  -1.4848
 OFF  H81   H  H      0   0.266   2.6944  -0.8640  -2.8950
 OFF  H71   H  H      0   0.264  -0.2356  -1.3297  -3.6640
 OFF  H5    H  HCR6   0   0.258   3.3368  -2.6704  -3.9340
 OFF  H6    H  HCR6   0   0.279   3.8963  -4.6873  -5.1693
 OFF  HO1   H  HOH1   0   0.479   3.0685  -6.4126  -6.4459
 OFF  H2    H  HCR6   0   0.270  -0.2294  -5.2006  -6.2342
 OFF  H3    H  HCR6   0   0.263  -0.7916  -3.1626  -4.9873

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
 OFF  C19  C18   aromatic  1.399  0.020  1.399
 OFF  C19  C20   aromatic  1.380  0.020  1.380
 OFF  C19  H19   single    0.930  0.020  1.080
 OFF  C20  C21   aromatic  1.397  0.020  1.397
 OFF  C20  H20   single    0.930  0.020  1.080
 OFF  C21  C22   aromatic  1.394  0.020  1.394
 OFF  C21  O10   single    1.342  0.020  1.342
 OFF  O10  HO10  single    0.850  0.020  0.980
 OFF  C22  C23   aromatic  1.382  0.020  1.382
 OFF  C22  H22   single    0.930  0.020  1.080
 OFF  C23  C18   aromatic  1.398  0.020  1.398
 OFF  C23  H23   single    0.930  0.020  1.080
 OFF  C18  C17   single    1.454  0.020  1.454
 OFF  C17  C16   double    1.339  0.020  1.339
 OFF  C17  H171  single    0.930  0.020  1.080
 OFF  C16  C15   single    1.469  0.020  1.469
 OFF  C16  H161  single    0.930  0.020  1.080
 OFF  C15  O9    double    1.212  0.020  1.212
 OFF  C15  O8    single    1.324  0.020  1.324
 OFF  O8   C12   single    1.433  0.020  1.433
 OFF  C12  C13   single    1.514  0.020  1.514
 OFF  C12  C10   single    1.539  0.020  1.539
 OFF  C12  H12   single    0.970  0.020  1.090
 OFF  C13  C14   single    1.541  0.020  1.541
 OFF  C13  H131  single    0.970  0.020  1.090
 OFF  C13  H132  single    0.970  0.020  1.090
 OFF  C14  O7    deloc     1.247  0.020  1.247
 OFF  C14  O6    deloc     1.247  0.020  1.247
 OFF  C10  C11   single    1.546  0.020  1.546
 OFF  C10  O3    single    1.425  0.020  1.425
 OFF  C10  H10   single    0.970  0.020  1.090
 OFF  C11  O5    deloc     1.242  0.020  1.242
 OFF  C11  O4    deloc     1.244  0.020  1.244
 OFF  O3   C9    single    1.327  0.020  1.327
 OFF  C9   C8    single    1.469  0.020  1.469
 OFF  C9   O2    double    1.211  0.020  1.211
 OFF  C8   C7    double    1.340  0.020  1.340
 OFF  C8   H81   single    0.930  0.020  1.080
 OFF  C7   C4    single    1.453  0.020  1.453
 OFF  C7   H71   single    0.930  0.020  1.080
 OFF  C4   C3    aromatic  1.399  0.020  1.399
 OFF  C4   C5    aromatic  1.399  0.020  1.399
 OFF  C5   C6    aromatic  1.380  0.020  1.380
 OFF  C5   H5    single    0.930  0.020  1.080
 OFF  C6   C1    aromatic  1.397  0.020  1.397
 OFF  C6   H6    single    0.930  0.020  1.080
 OFF  C1   C2    aromatic  1.394  0.020  1.394
 OFF  C1   O1    single    1.342  0.020  1.342
 OFF  O1   HO1   single    0.850  0.020  0.980
 OFF  C2   C3    aromatic  1.382  0.020  1.382
 OFF  C2   H2    single    0.930  0.020  1.080
 OFF  C3   H3    single    0.930  0.020  1.080

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
 OFF  H19   C19  C18   120.44  3.000
 OFF  H19   C19  C20   118.27  3.000
 OFF  C18   C19  C20   121.29  3.000
 OFF  H20   C20  C21   120.18  3.000
 OFF  H20   C20  C19   119.68  3.000
 OFF  C21   C20  C19   120.14  3.000
 OFF  C22   C21  O10   117.96  3.000
 OFF  O10   C21  C20   122.58  3.000
 OFF  C22   C21  C20   119.46  3.000
 OFF  HO10  O10  C21   110.73  3.000
 OFF  H22   C22  C23   120.39  3.000
 OFF  H22   C22  C21   119.91  3.000
 OFF  C23   C22  C21   119.69  3.000
 OFF  H23   C23  C18   119.34  3.000
 OFF  H23   C23  C22   118.89  3.000
 OFF  C18   C23  C22   121.77  3.000
 OFF  C17   C18  C23   118.95  3.000
 OFF  C17   C18  C19   123.42  3.000
 OFF  C23   C18  C19   117.64  3.000
 OFF  H171  C17  C16   117.97  3.000
 OFF  H171  C17  C18   115.06  3.000
 OFF  C16   C17  C18   126.97  3.000
 OFF  H161  C16  C15   117.20  3.000
 OFF  H161  C16  C17   121.94  3.000
 OFF  C15   C16  C17   120.86  3.000
 OFF  O8    C15  O9    124.16  3.000
 OFF  O8    C15  C16   110.66  3.000
 OFF  O9    C15  C16   125.17  3.000
 OFF  C12   O8   C15   120.29  3.000
 OFF  H12   C12  C10   108.95  3.000
 OFF  H12   C12  C13   109.17  3.000
 OFF  C10   C12  C13   115.13  3.000
 OFF  H12   C12  O8    109.45  3.000
 OFF  C10   C12  O8    108.70  3.000
 OFF  C13   C12  O8    105.31  3.000
 OFF  H132  C13  H131  106.17  3.000
 OFF  H132  C13  C14   107.52  3.000
 OFF  H131  C13  C14   110.61  3.000
 OFF  H132  C13  C12   108.79  3.000
 OFF  H131  C13  C12   110.62  3.000
 OFF  C14   C13  C12   112.84  3.000
 OFF  O7    C14  O6    126.47  3.000
 OFF  O6    C14  C13   116.51  3.000
 OFF  O7    C14  C13   116.98  3.000
 OFF  H10   C10  O3    109.17  3.000
 OFF  H10   C10  C11   109.19  3.000
 OFF  O3    C10  C11   112.21  3.000
 OFF  H10   C10  C12   108.76  3.000
 OFF  O3    C10  C12   104.90  3.000
 OFF  C11   C10  C12   112.47  3.000
 OFF  O5    C11  O4    128.14  3.000
 OFF  O4    C11  C10   114.68  3.000
 OFF  O5    C11  C10   117.16  3.000
 OFF  C9    O3   C10   117.53  3.000
 OFF  C8    C9   O2    125.30  3.000
 OFF  O2    C9   O3    123.65  3.000
 OFF  C8    C9   O3    111.03  3.000
 OFF  H81   C8   C7    122.20  3.000
 OFF  H81   C8   C9    117.29  3.000
 OFF  C7    C8   C9    120.51  3.000
 OFF  H71   C7   C4    115.05  3.000
 OFF  H71   C7   C8    117.70  3.000
 OFF  C4    C7   C8    127.25  3.000
 OFF  C3    C4   C5    117.66  3.000
 OFF  C5    C4   C7    123.47  3.000
 OFF  C3    C4   C7    118.88  3.000
 OFF  H5    C5   C6    118.27  3.000
 OFF  H5    C5   C4    120.45  3.000
 OFF  C6    C5   C4    121.28  3.000
 OFF  H6    C6   C1    120.14  3.000
 OFF  H6    C6   C5    119.73  3.000
 OFF  C1    C6   C5    120.13  3.000
 OFF  C2    C1   O1    117.93  3.000
 OFF  O1    C1   C6    122.58  3.000
 OFF  C2    C1   C6    119.49  3.000
 OFF  HO1   O1   C1    110.72  3.000
 OFF  H2    C2   C3    120.45  3.000
 OFF  H2    C2   C1    119.87  3.000
 OFF  C3    C2   C1    119.68  3.000
 OFF  H3    C3   C2    118.93  3.000
 OFF  H3    C3   C4    119.31  3.000
 OFF  C2    C3   C4    121.76  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
 OFF  CONST_01  C22  C23  C18  C19     0.00   0.0  0
 OFF  CONST_02  C22  C21  C20  C19     0.00   0.0  0
 OFF  CONST_03  C23  C18  C19  C20     0.00   0.0  0
 OFF  CONST_04  C23  C22  C21  C20     0.00   0.0  0
 OFF  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 OFF  CONST_06  C18  C23  C22  C21     0.00   0.0  0
 OFF  CONST_07  C1   C2   C3   C4      0.00   0.0  0
 OFF  CONST_08  C1   C6   C5   C4      0.00   0.0  0
 OFF  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 OFF  CONST_10  C2   C1   C6   C5      0.00   0.0  0
 OFF  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 OFF  CONST_12  C3   C2   C1   C6      0.00   0.0  0
 OFF  CONST_13  O10  C21  C20  C19   180.00   0.0  0
 OFF  CONST_14  C17  C18  C19  C20   180.00   0.0  0
 OFF  CONST_15  C23  C22  C21  O10   180.00   0.0  0
 OFF  CONST_16  C17  C18  C23  C22   180.00   0.0  0
 OFF  CONST_17  C2   C3   C4   C7    180.00   0.0  0
 OFF  CONST_18  C6   C5   C4   C7    180.00   0.0  0
 OFF  CONST_19  O1   C1   C6   C5    180.00   0.0  0
 OFF  CONST_20  C3   C2   C1   O1    180.00   0.0  0
 OFF  CONST_21  H23  C23  C18  C19   180.00   0.0  0
 OFF  CONST_22  H22  C22  C21  C20   180.00   0.0  0
 OFF  CONST_23  H19  C19  C20  C21   180.00   0.0  0
 OFF  CONST_24  H20  C20  C21  C22   180.00   0.0  0
 OFF  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 OFF  CONST_26  H6   C6   C5   C4    180.00   0.0  0
 OFF  CONST_27  H3   C3   C4   C5    180.00   0.0  0
 OFF  CONST_28  H5   C5   C6   C1    180.00   0.0  0
 OFF  Var_01    C16  C17  C18  C19    -0.15  30.0  2
 OFF  Var_02    C3   C4   C7   C8   -179.27  30.0  2
 OFF  Var_03    C15  C16  C17  C18   179.24   0.0  2
 OFF  Var_04    C4   C7   C8   C9   -179.62   0.0  2
 OFF  Var_05    O9   C15  C16  C17    -1.43  30.0  2
 OFF  Var_06    O7   C14  C13  C12   -35.77  30.0  3
 OFF  Var_07    C8   C9   O3   C10  -174.02  30.0  3
 OFF  Var_08    C7   C8   C9   O3   -177.50  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
 OFF  chir_01  C12  O8  C13  C10  negativ
 OFF  chir_02  C10  O3  C12  C11  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
 OFF  plan-1  C19   0.020
 OFF  plan-1  C20   0.020
 OFF  plan-1  C21   0.020
 OFF  plan-1  O10   0.020
 OFF  plan-1  C22   0.020
 OFF  plan-1  C23   0.020
 OFF  plan-1  C18   0.020
 OFF  plan-1  C17   0.020
 OFF  plan-1  H19   0.020
 OFF  plan-1  H20   0.020
 OFF  plan-1  H22   0.020
 OFF  plan-1  H23   0.020
 OFF  plan-2  C9    0.020
 OFF  plan-2  C8    0.020
 OFF  plan-2  C7    0.020
 OFF  plan-2  C4    0.020
 OFF  plan-2  H81   0.020
 OFF  plan-2  H71   0.020
 OFF  plan-3  C7    0.020
 OFF  plan-3  C4    0.020
 OFF  plan-3  C5    0.020
 OFF  plan-3  C6    0.020
 OFF  plan-3  C1    0.020
 OFF  plan-3  O1    0.020
 OFF  plan-3  C2    0.020
 OFF  plan-3  C3    0.020
 OFF  plan-3  H5    0.020
 OFF  plan-3  H6    0.020
 OFF  plan-3  H2    0.020
 OFF  plan-3  H3    0.020
 OFF  plan-4  C13   0.020
 OFF  plan-4  C14   0.020
 OFF  plan-4  O6    0.020
 OFF  plan-4  O7    0.020
 OFF  plan-5  C10   0.020
 OFF  plan-5  C11   0.020
 OFF  plan-5  O4    0.020
 OFF  plan-5  O5    0.020
 OFF  plan-6  C18   0.020
 OFF  plan-6  C17   0.020
 OFF  plan-6  C16   0.020
 OFF  plan-6  C15   0.020
 OFF  plan-6  H171  0.020
 OFF  plan-6  H161  0.020
 OFF  plan-7  C16   0.020
 OFF  plan-7  C15   0.020
 OFF  plan-7  O9    0.020
 OFF  plan-7  O8    0.020
 OFF  plan-8  O3    0.020
 OFF  plan-8  C9    0.020
 OFF  plan-8  O2    0.020
 OFF  plan-8  C8    0.020

