# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 18:18:03 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(C(=O)NCCCCCNC(=O)c2cccc(O)c2O)c1O
#
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
 5LC  5LC  N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide)  ligand  49  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5LC
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
 5LC  C1    C  CR16  0  -0.345  -8.0790   1.9810   0.9309
 5LC  C2    C  CR6   0   0.307  -8.3180   0.7750   0.3038
 5LC  C3    C  CR6   0   0.252  -7.2381  -0.0442  -0.0725
 5LC  C4    C  CR6   0  -0.173  -5.9236   0.3665   0.1865
 5LC  C5    C  CR16  0  -0.331  -5.7080   1.5978   0.8210
 5LC  C6    C  CR16  0  -0.258  -6.7719   2.3914   1.1899
 5LC  C7    C  C     0   0.638  -4.8289  -0.5434  -0.2346
 5LC  N8    N  NH1   0  -0.667  -3.5676  -0.1849  -0.0112
 5LC  O9    O  O     0  -0.551  -5.0935  -1.6232  -0.7931
 5LC  C10   C  CH2   0  -0.239  -2.4366  -1.0230  -0.3646
 5LC  C11   C  CH2   0  -0.474  -1.1411  -0.2317  -0.2941
 5LC  C12   C  CH2   0  -0.428   0.0624  -1.1019  -0.6301
 5LC  N14   N  NH1   0  -0.656   3.8142  -0.5032  -1.0082
 5LC  C15   C  C     0   0.634   4.6404  -0.4024   0.0310
 5LC  C16   C  CR6   0  -0.174   5.8832   0.3963  -0.1225
 5LC  O17   O  O     0  -0.548   4.3975  -0.9736   1.1085
 5LC  C18   C  CR6   0   0.252   6.7894   0.3913   0.9463
 5LC  C19   C  CR6   0   0.306   7.9875   1.1225   0.8559
 5LC  C20   C  CR16  0  -0.344   8.2624   1.8532  -0.2820
 5LC  C21   C  CR16  0  -0.259   7.3579   1.8674  -1.3428
 5LC  C22   C  CR16  0  -0.330   6.1853   1.1487  -1.2661
 5LC  O23   O  OH1   0  -0.650   6.5923  -0.2844   2.0830
 5LC  O24   O  OH1   0  -0.634   8.8708   1.1171   1.8742
 5LC  C23   C  CH2   0  -0.429   1.3752  -0.3309  -0.5949
 5LC  O25   O  OH1   0  -0.650  -7.5489  -1.1965  -0.6746
 5LC  C13   C  CH2   0  -0.286   2.5551  -1.2187  -0.9731
 5LC  O26   O  OH1   0  -0.634  -9.5862   0.3920   0.0557
 5LC  H1    H  HCR6  0   0.271  -8.9170   2.6047   1.2169
 5LC  H6    H  HCR6  0   0.262  -6.5955   3.3380   1.6816
 5LC  H26   H  HOH1  0   0.474  -9.5936  -0.4570  -0.4033
 5LC  H25   H  HOH1  0   0.483  -6.6789  -1.6428  -0.8701
 5LC  H5    H  HCR6  0   0.251  -4.7084   1.9532   1.0317
 5LC  H8    H  HNH1  0   0.417  -3.3686   0.6617   0.4946
 5LC  H101  H  HCH2  0   0.238  -2.3867  -1.8859   0.3069
 5LC  H102  H  HCH2  0   0.243  -2.5795  -1.4109  -1.3746
 5LC  H111  H  HCH2  0   0.236  -1.1927   0.6121  -0.9887
 5LC  H112  H  HCH2  0   0.233  -1.0193   0.1898   0.7090
 5LC  H121  H  HCH2  0   0.225   0.1117  -1.9407   0.0717
 5LC  H122  H  HCH2  0   0.223  -0.0739  -1.5408  -1.6241
 5LC  H231  H  HCH2  0   0.226   1.3262   0.5151  -1.2868
 5LC  H232  H  HCH2  0   0.229   1.5377   0.0856   0.4032
 5LC  H14   H  HNH1  0   0.417   4.0311  -0.0198  -1.8629
 5LC  H131  H  HCH2  0   0.252   2.3972  -1.6431  -1.9656
 5LC  H132  H  HCH2  0   0.249   2.6397  -2.0543  -0.2788
 5LC  H22   H  HCR6  0   0.251   5.5049   1.1913  -2.1055
 5LC  H20   H  HCR6  0   0.271   9.1851   2.4175  -0.3390
 5LC  H24   H  HOH1  0   0.474   8.5374   0.5769   2.6010
 5LC  H21   H  HCR6  0   0.262   7.5804   2.4488  -2.2269
 5LC  H23   H  HOH1  0   0.483   5.6959  -0.7107   1.9943

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
 5LC  C1   C2    aromatic  1.380  0.020  1.380
 5LC  C1   C6    aromatic  1.394  0.020  1.394
 5LC  C2   C3    aromatic  1.407  0.020  1.407
 5LC  C2   O26   single    1.348  0.020  1.348
 5LC  C3   C4    aromatic  1.401  0.020  1.401
 5LC  C3   O25   single    1.337  0.020  1.337
 5LC  C4   C5    aromatic  1.402  0.020  1.402
 5LC  C4   C7    single    1.485  0.020  1.485
 5LC  C5   C6    aromatic  1.378  0.020  1.378
 5LC  C7   N8    single    1.330  0.020  1.330
 5LC  C7   O9    double    1.244  0.020  1.244
 5LC  N8   C10   single    1.451  0.020  1.451
 5LC  C10  C11   single    1.520  0.020  1.520
 5LC  C11  C12   single    1.523  0.020  1.523
 5LC  C12  C23   single    1.523  0.020  1.523
 5LC  N14  C15   single    1.331  0.020  1.331
 5LC  N14  C13   single    1.449  0.020  1.449
 5LC  C15  C16   single    1.485  0.020  1.485
 5LC  C15  O17   double    1.244  0.020  1.244
 5LC  C16  C18   aromatic  1.401  0.020  1.401
 5LC  C16  C22   aromatic  1.402  0.020  1.402
 5LC  C18  C19   aromatic  1.407  0.020  1.407
 5LC  C18  O23   single    1.337  0.020  1.337
 5LC  C19  C20   aromatic  1.380  0.020  1.380
 5LC  C19  O24   single    1.348  0.020  1.348
 5LC  C20  C21   aromatic  1.394  0.020  1.394
 5LC  C21  C22   aromatic  1.377  0.020  1.377
 5LC  C23  C13   single    1.524  0.020  1.524
 5LC  O23  H23   single    0.850  0.020  0.980
 5LC  C1   H1    single    0.930  0.020  1.080
 5LC  C6   H6    single    0.930  0.020  1.080
 5LC  O26  H26   single    0.850  0.020  0.980
 5LC  O25  H25   single    0.850  0.020  0.980
 5LC  C5   H5    single    0.930  0.020  1.080
 5LC  N8   H8    single    0.860  0.020  1.020
 5LC  C10  H101  single    0.970  0.020  1.090
 5LC  C10  H102  single    0.970  0.020  1.090
 5LC  C11  H111  single    0.970  0.020  1.090
 5LC  C11  H112  single    0.970  0.020  1.090
 5LC  C12  H121  single    0.970  0.020  1.090
 5LC  C12  H122  single    0.970  0.020  1.090
 5LC  C23  H231  single    0.970  0.020  1.090
 5LC  C23  H232  single    0.970  0.020  1.090
 5LC  N14  H14   single    0.860  0.020  1.020
 5LC  C13  H131  single    0.970  0.020  1.090
 5LC  C13  H132  single    0.970  0.020  1.090
 5LC  C22  H22   single    0.930  0.020  1.080
 5LC  C20  H20   single    0.930  0.020  1.080
 5LC  O24  H24   single    0.850  0.020  0.980
 5LC  C21  H21   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
 5LC  H1    C1   C6    120.45  3.000
 5LC  H1    C1   C2    119.29  3.000
 5LC  C6    C1   C2    120.26  3.000
 5LC  O26   C2   C3    120.50  3.000
 5LC  O26   C2   C1    119.66  3.000
 5LC  C3    C2   C1    119.83  3.000
 5LC  O25   C3   C4    123.64  3.000
 5LC  O25   C3   C2    116.36  3.000
 5LC  C4    C3   C2    120.00  3.000
 5LC  C7    C4   C5    123.60  3.000
 5LC  C7    C4   C3    117.36  3.000
 5LC  C5    C4   C3    119.04  3.000
 5LC  H5    C5   C6    118.19  3.000
 5LC  H5    C5   C4    121.26  3.000
 5LC  C6    C5   C4    120.55  3.000
 5LC  H6    C6   C5    120.01  3.000
 5LC  H6    C6   C1    119.68  3.000
 5LC  C5    C6   C1    120.31  3.000
 5LC  O9    C7   N8    120.73  3.000
 5LC  O9    C7   C4    120.16  3.000
 5LC  N8    C7   C4    119.10  3.000
 5LC  H8    N8   C10   117.01  3.000
 5LC  H8    N8   C7    119.93  3.000
 5LC  C10   N8   C7    122.84  3.000
 5LC  H102  C10  H101  107.07  3.000
 5LC  H102  C10  C11   109.85  3.000
 5LC  H101  C10  C11   110.07  3.000
 5LC  H102  C10  N8    109.18  3.000
 5LC  H101  C10  N8    109.96  3.000
 5LC  C11   C10  N8    110.63  3.000
 5LC  H112  C11  H111  106.86  3.000
 5LC  H112  C11  C12   109.52  3.000
 5LC  H111  C11  C12   109.75  3.000
 5LC  H112  C11  C10   109.74  3.000
 5LC  H111  C11  C10   109.39  3.000
 5LC  C12   C11  C10   111.47  3.000
 5LC  H122  C12  H121  106.28  3.000
 5LC  H122  C12  C23   109.34  3.000
 5LC  H121  C12  C23   109.53  3.000
 5LC  H122  C12  C11   109.33  3.000
 5LC  H121  C12  C11   109.39  3.000
 5LC  C23   C12  C11   112.76  3.000
 5LC  H14   N14  C13   116.45  3.000
 5LC  H14   N14  C15   119.55  3.000
 5LC  C13   N14  C15   123.91  3.000
 5LC  O17   C15  C16   120.00  3.000
 5LC  O17   C15  N14   121.35  3.000
 5LC  C16   C15  N14   118.64  3.000
 5LC  C22   C16  C18   119.00  3.000
 5LC  C22   C16  C15   123.59  3.000
 5LC  C18   C16  C15   117.41  3.000
 5LC  O23   C18  C19   116.29  3.000
 5LC  O23   C18  C16   123.71  3.000
 5LC  C19   C18  C16   120.00  3.000
 5LC  O24   C19  C20   119.64  3.000
 5LC  O24   C19  C18   120.50  3.000
 5LC  C20   C19  C18   119.86  3.000
 5LC  H20   C20  C21   120.49  3.000
 5LC  H20   C20  C19   119.27  3.000
 5LC  C21   C20  C19   120.24  3.000
 5LC  H21   C21  C22   120.08  3.000
 5LC  H21   C21  C20   119.61  3.000
 5LC  C22   C21  C20   120.30  3.000
 5LC  H22   C22  C21   118.15  3.000
 5LC  H22   C22  C16   121.25  3.000
 5LC  C21   C22  C16   120.59  3.000
 5LC  H23   O23  C18   105.85  3.000
 5LC  H24   O24  C19   110.17  3.000
 5LC  H232  C23  H231  106.81  3.000
 5LC  H232  C23  C13   109.46  3.000
 5LC  H231  C23  C13   109.16  3.000
 5LC  H232  C23  C12   110.00  3.000
 5LC  H231  C23  C12   109.77  3.000
 5LC  C13   C23  C12   111.51  3.000
 5LC  H25   O25  C3    105.74  3.000
 5LC  H132  C13  H131  107.02  3.000
 5LC  H132  C13  C23   110.40  3.000
 5LC  H131  C13  C23   109.89  3.000
 5LC  H132  C13  N14   109.07  3.000
 5LC  H131  C13  N14   107.21  3.000
 5LC  C23   C13  N14   113.03  3.000
 5LC  H26   O26  C2    110.16  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
 5LC  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 5LC  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 5LC  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5LC  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5LC  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 5LC  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 5LC  CONST_07  C20  C19  C18  C16     0.00   0.0  0
 5LC  CONST_08  C20  C21  C22  C16     0.00   0.0  0
 5LC  CONST_09  C21  C22  C16  C18     0.00   0.0  0
 5LC  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 5LC  CONST_11  C22  C16  C18  C19     0.00   0.0  0
 5LC  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 5LC  CONST_13  O25  C3   C2   C1    180.00   0.0  0
 5LC  CONST_14  C7   C4   C3   C2    180.00   0.0  0
 5LC  CONST_15  O26  C2   C3   C4    180.00   0.0  0
 5LC  CONST_16  O25  C3   C4   C5    180.00   0.0  0
 5LC  CONST_17  O26  C2   C1   C6    180.00   0.0  0
 5LC  CONST_18  C7   C4   C5   C6    180.00   0.0  0
 5LC  CONST_19  C19  C18  C16  C15   180.00   0.0  0
 5LC  CONST_20  C21  C22  C16  C15   180.00   0.0  0
 5LC  CONST_21  O24  C19  C18  C16   180.00   0.0  0
 5LC  CONST_22  O23  C18  C19  C20   180.00   0.0  0
 5LC  CONST_23  O24  C19  C20  C21   180.00   0.0  0
 5LC  CONST_24  O23  C18  C16  C22   180.00   0.0  0
 5LC  CONST_25  H5   C5   C6   C1    180.00   0.0  0
 5LC  CONST_26  H6   C6   C1   C2    180.00   0.0  0
 5LC  CONST_27  H1   C1   C2   C3    180.00   0.0  0
 5LC  CONST_28  H21  C21  C22  C16   180.00   0.0  0
 5LC  CONST_29  H22  C22  C16  C18   180.00   0.0  0
 5LC  CONST_30  H20  C20  C19  C18   180.00   0.0  0
 5LC  CONST_31  C10  N8   C7   C4    180.00   0.0  0
 5LC  CONST_32  C13  N14  C15  C16   180.00   0.0  0
 5LC  CONST_33  H8   N8   C7   C4      0.00   0.0  0
 5LC  CONST_34  H14  N14  C15  C16     0.00   0.0  0
 5LC  CONST_35  C10  N8   C7   O9      0.00   0.0  0
 5LC  CONST_36  C13  N14  C15  O17     0.00   0.0  0
 5LC  Var_01    N8   C7   C4   C3    179.69  30.0  2
 5LC  Var_02    C18  C16  C15  N14  -174.63  30.0  2
 5LC  Var_03    C11  C10  N8   C7    166.77  30.0  3
 5LC  Var_04    C12  C11  C10  N8    178.67  30.0  3
 5LC  Var_05    C23  C12  C11  C10   178.88  30.0  3
 5LC  Var_06    C13  C23  C12  C11  -178.41  30.0  3
 5LC  Var_07    N14  C13  C23  C12   177.41  30.0  3
 5LC  Var_08    C23  C13  N14  C15    91.83  30.0  3

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
 5LC  plan-1  C1   0.020
 5LC  plan-1  C2   0.020
 5LC  plan-1  C3   0.020
 5LC  plan-1  C4   0.020
 5LC  plan-1  C5   0.020
 5LC  plan-1  C6   0.020
 5LC  plan-1  C7   0.020
 5LC  plan-1  O25  0.020
 5LC  plan-1  O26  0.020
 5LC  plan-1  H1   0.020
 5LC  plan-1  H6   0.020
 5LC  plan-1  H5   0.020
 5LC  plan-2  C15  0.020
 5LC  plan-2  C16  0.020
 5LC  plan-2  C18  0.020
 5LC  plan-2  C19  0.020
 5LC  plan-2  C20  0.020
 5LC  plan-2  C21  0.020
 5LC  plan-2  C22  0.020
 5LC  plan-2  O23  0.020
 5LC  plan-2  O24  0.020
 5LC  plan-2  H22  0.020
 5LC  plan-2  H20  0.020
 5LC  plan-2  H21  0.020
 5LC  plan-3  C4   0.020
 5LC  plan-3  C7   0.020
 5LC  plan-3  N8   0.020
 5LC  plan-3  O9   0.020
 5LC  plan-3  C10  0.020
 5LC  plan-3  H8   0.020
 5LC  plan-4  N14  0.020
 5LC  plan-4  C15  0.020
 5LC  plan-4  C16  0.020
 5LC  plan-4  O17  0.020
 5LC  plan-4  C13  0.020
 5LC  plan-4  H14  0.020

