# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 07:56:41 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-{(E)-[5-(2-aminoethyl)-2-hydroxyphenyl]diazenyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCc1ccc(O)c(c1)N=Nc2ccc(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
 XY1  XY1  '4-{(E)-[5-(2-aminoethyl)-2-hydroxyphenyl]diazenyl}benzoic acid'  ligand  36  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XY1
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
 XY1  C29   C  C     0   0.537  -5.8780  -0.3417   0.0263
 XY1  O30   O  O     0  -0.435  -6.4893  -1.3540  -0.2185
 XY1  C26   C  CR6   0  -0.089  -4.3977  -0.2432  -0.0186
 XY1  C25   C  CR16  0  -0.244  -3.6730  -1.3616  -0.4208
 XY1  C24   C  CR16  0  -0.276  -2.2920  -1.3120  -0.4747
 XY1  C27   C  CR16  0  -0.248  -3.7176   0.9261   0.3320
 XY1  C28   C  CR16  0  -0.259  -2.3390   0.9781   0.2776
 XY1  C23   C  CR6   0   0.240  -1.6154  -0.1439  -0.1326
 XY1  N21   N  N     0  -0.267  -0.2153  -0.2108  -0.2232
 XY1  N20   N  N     0  -0.287   0.3791   0.8602  -0.0288
 XY1  C18   C  CR6   0   0.173   1.7668   0.8326  -0.0911
 XY1  C17   C  CR6   0   0.322   2.3760   2.0793   0.1225
 XY1  O22   O  OH1   0  -0.614   1.6569   3.1818   0.3514
 XY1  C16   C  CR16  0  -0.328   3.7666   2.1688   0.0897
 XY1  C15   C  CR16  0  -0.283   4.5178   1.0365  -0.1524
 XY1  C19   C  CR16  0  -0.336   2.5514  -0.3005  -0.3361
 XY1  C9    C  CR6   0   0.114   3.9285  -0.2180  -0.3708
 XY1  C14   C  CH2   0  -0.514   4.7820  -1.4348  -0.5874
 XY1  C12   C  CH2   0  -0.269   5.2725  -2.0266   0.7324
 XY1  N3    N  NH2   0  -0.800   6.0913  -3.2037   0.4913
 XY1  OXT   O  OH1   0  -0.592  -6.4625   0.7992   0.3609
 XY1  HXT   H  HOH1  0   0.489  -7.4248   0.6876   0.3718
 XY1  H25   H  HCR6  0   0.273  -4.1857  -2.2732  -0.6953
 XY1  H27   H  HCR6  0   0.275  -4.2582   1.8043   0.6558
 XY1  H24   H  HCR6  0   0.274  -1.7240  -2.1786  -0.7862
 XY1  H28   H  HCR6  0   0.278  -1.8268   1.8868   0.5608
 XY1  H19   H  HCR6  0   0.266   2.0569  -1.2497  -0.5036
 XY1  H22   H  HOH1  0   0.473   0.7169   2.9447   0.3358
 XY1  H16   H  HCR6  0   0.273   4.2464   3.1256   0.2508
 XY1  H15   H  HCR6  0   0.261   5.5976   1.1250  -0.1800
 XY1  H141  H  HCH2  0   0.243   4.2214  -2.1972  -1.1322
 XY1  H142  H  HCH2  0   0.240   5.6459  -1.1724  -1.2061
 XY1  H121  H  HCH2  0   0.199   5.7841  -1.2403   1.3065
 XY1  H122  H  HCH2  0   0.222   4.4053  -2.3253   1.3273
 XY1  H31N  H  HNH2  0   0.340   6.9595  -2.9235   0.0513
 XY1  H32N  H  HNH2  0   0.348   6.3550  -3.6175   1.3762

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
 XY1  C29  O30   double    1.208  0.020  1.208
 XY1  C29  C26   single    1.484  0.020  1.484
 XY1  C29  OXT   single    1.325  0.020  1.325
 XY1  C26  C25   aromatic  1.392  0.020  1.392
 XY1  C26  C27   aromatic  1.397  0.020  1.397
 XY1  C25  C24   aromatic  1.383  0.020  1.383
 XY1  C24  C23   aromatic  1.393  0.020  1.393
 XY1  C27  C28   aromatic  1.381  0.020  1.381
 XY1  C28  C23   aromatic  1.397  0.020  1.397
 XY1  C23  N21   single    1.405  0.020  1.405
 XY1  N21  N20   double    1.240  0.020  1.240
 XY1  N20  C18   single    1.389  0.020  1.389
 XY1  C18  C17   aromatic  1.404  0.020  1.404
 XY1  C18  C19   aromatic  1.400  0.020  1.400
 XY1  C17  O22   single    1.336  0.020  1.336
 XY1  C17  C16   aromatic  1.394  0.020  1.394
 XY1  C16  C15   aromatic  1.380  0.020  1.380
 XY1  C15  C9    aromatic  1.403  0.020  1.403
 XY1  C19  C9    aromatic  1.380  0.020  1.380
 XY1  C9   C14   single    1.502  0.020  1.502
 XY1  C14  C12   single    1.527  0.020  1.527
 XY1  C12  N3    single    1.454  0.020  1.454
 XY1  OXT  HXT   single    0.850  0.020  0.980
 XY1  C25  H25   single    0.930  0.020  1.080
 XY1  C27  H27   single    0.930  0.020  1.080
 XY1  C24  H24   single    0.930  0.020  1.080
 XY1  C28  H28   single    0.930  0.020  1.080
 XY1  C19  H19   single    0.930  0.020  1.080
 XY1  O22  H22   single    0.850  0.020  0.980
 XY1  C16  H16   single    0.930  0.020  1.080
 XY1  C15  H15   single    0.930  0.020  1.080
 XY1  C14  H141  single    0.970  0.020  1.090
 XY1  C14  H142  single    0.970  0.020  1.090
 XY1  C12  H121  single    0.970  0.020  1.090
 XY1  C12  H122  single    0.970  0.020  1.090
 XY1  N3   H31N  single    0.890  0.020  1.040
 XY1  N3   H32N  single    0.890  0.020  1.040

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
 XY1  OXT   C29  C26   112.99  3.000
 XY1  OXT   C29  O30   123.34  3.000
 XY1  C26   C29  O30   123.67  3.000
 XY1  C27   C26  C25   119.43  3.000
 XY1  C27   C26  C29   122.23  3.000
 XY1  C25   C26  C29   118.34  3.000
 XY1  H25   C25  C24   119.60  3.000
 XY1  H25   C25  C26   120.25  3.000
 XY1  C24   C25  C26   120.15  3.000
 XY1  H24   C24  C23   119.18  3.000
 XY1  H24   C24  C25   120.45  3.000
 XY1  C23   C24  C25   120.38  3.000
 XY1  H27   C27  C28   118.72  3.000
 XY1  H27   C27  C26   120.77  3.000
 XY1  C28   C27  C26   120.51  3.000
 XY1  H28   C28  C23   120.45  3.000
 XY1  H28   C28  C27   119.64  3.000
 XY1  C23   C28  C27   119.91  3.000
 XY1  N21   C23  C28   125.00  3.000
 XY1  N21   C23  C24   115.37  3.000
 XY1  C28   C23  C24   119.62  3.000
 XY1  N20   N21  C23   115.24  3.000
 XY1  C18   N20  N21   117.03  3.000
 XY1  C19   C18  C17   120.15  3.000
 XY1  C19   C18  N20   125.72  3.000
 XY1  C17   C18  N20   114.14  3.000
 XY1  C16   C17  O22   119.21  3.000
 XY1  C16   C17  C18   119.10  3.000
 XY1  O22   C17  C18   121.69  3.000
 XY1  H22   O22  C17   108.49  3.000
 XY1  H16   C16  C15   120.66  3.000
 XY1  H16   C16  C17   119.70  3.000
 XY1  C15   C16  C17   119.63  3.000
 XY1  H15   C15  C9    119.17  3.000
 XY1  H15   C15  C16   118.67  3.000
 XY1  C9    C15  C16   122.15  3.000
 XY1  H19   C19  C9    120.26  3.000
 XY1  H19   C19  C18   118.72  3.000
 XY1  C9    C19  C18   121.02  3.000
 XY1  C14   C9   C19   121.48  3.000
 XY1  C14   C9   C15   120.54  3.000
 XY1  C19   C9   C15   117.95  3.000
 XY1  H142  C14  H141  106.89  3.000
 XY1  H142  C14  C12   109.14  3.000
 XY1  H141  C14  C12   109.00  3.000
 XY1  H142  C14  C9    109.62  3.000
 XY1  H141  C14  C9    110.23  3.000
 XY1  C12   C14  C9    111.83  3.000
 XY1  H122  C12  H121  106.27  3.000
 XY1  H122  C12  N3    108.40  3.000
 XY1  H121  C12  N3    113.79  3.000
 XY1  H122  C12  C14   108.74  3.000
 XY1  H121  C12  C14   108.87  3.000
 XY1  N3    C12  C14   110.57  3.000
 XY1  H32N  N3   H31N  105.64  3.000
 XY1  H32N  N3   C12   109.44  3.000
 XY1  H31N  N3   C12   109.32  3.000
 XY1  HXT   OXT  C29   109.99  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
 XY1  CONST_01  C23   C24  C25  C26    0.00   0.0  0
 XY1  CONST_02  C23   C28  C27  C26    0.00   0.0  0
 XY1  CONST_03  C28   C27  C26  C25    0.00   0.0  0
 XY1  CONST_04  C28   C23  C24  C25    0.00   0.0  0
 XY1  CONST_05  C27   C26  C25  C24    0.00   0.0  0
 XY1  CONST_06  C27   C28  C23  C24    0.00   0.0  0
 XY1  CONST_07  C15   C16  C17  C18    0.00   0.0  0
 XY1  CONST_08  C15   C9   C19  C18    0.00   0.0  0
 XY1  CONST_09  C9    C19  C18  C17    0.00   0.0  0
 XY1  CONST_10  C9    C15  C16  C17    0.00   0.0  0
 XY1  CONST_11  C19   C18  C17  C16    0.00   0.0  0
 XY1  CONST_12  C19   C9   C15  C16    0.00   0.0  0
 XY1  CONST_13  C24   C25  C26  C29  180.00   0.0  0
 XY1  CONST_14  C28   C27  C26  C29  180.00   0.0  0
 XY1  CONST_15  N21   C23  C24  C25  180.00   0.0  0
 XY1  CONST_16  N21   C23  C28  C27  180.00   0.0  0
 XY1  CONST_17  C16   C17  C18  N20  180.00   0.0  0
 XY1  CONST_18  C9    C19  C18  N20  180.00   0.0  0
 XY1  CONST_19  C14   C9   C19  C18  180.00   0.0  0
 XY1  CONST_20  C19   C18  C17  O22  180.00   0.0  0
 XY1  CONST_21  C15   C16  C17  O22  180.00   0.0  0
 XY1  CONST_22  C14   C9   C15  C16  180.00   0.0  0
 XY1  CONST_23  H24   C24  C25  C26  180.00   0.0  0
 XY1  CONST_24  H28   C28  C27  C26  180.00   0.0  0
 XY1  CONST_25  H27   C27  C26  C25  180.00   0.0  0
 XY1  CONST_26  H25   C25  C26  C27  180.00   0.0  0
 XY1  CONST_27  H16   C16  C17  C18  180.00   0.0  0
 XY1  CONST_28  H19   C19  C18  C17  180.00   0.0  0
 XY1  CONST_29  H15   C15  C16  C17  180.00   0.0  0
 XY1  CONST_30  N20   N21  C23  C24  180.00   0.0  0
 XY1  CONST_31  N20   N21  C23  C28    0.00   0.0  0
 XY1  CONST_32  C17   C18  N20  N21  180.00   0.0  0
 XY1  CONST_33  C19   C18  N20  N21    0.00   0.0  0
 XY1  CONST_34  HXT   OXT  C29  C26  180.00   0.0  0
 XY1  Var_01    C25   C26  C29  O30    2.89  30.0  2
 XY1  Var_02    C12   C14  C9   C15   81.95  30.0  2
 XY1  Var_03    N3    C12  C14  C9   179.82  30.0  3
 XY1  Var_04    H31N  N3   C12  C14   68.52  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
 XY1  plan-1  C29  0.020
 XY1  plan-1  C26  0.020
 XY1  plan-1  C25  0.020
 XY1  plan-1  C24  0.020
 XY1  plan-1  C27  0.020
 XY1  plan-1  C28  0.020
 XY1  plan-1  C23  0.020
 XY1  plan-1  N21  0.020
 XY1  plan-1  N20  0.020
 XY1  plan-1  C18  0.020
 XY1  plan-1  H25  0.020
 XY1  plan-1  H27  0.020
 XY1  plan-1  H24  0.020
 XY1  plan-1  H28  0.020
 XY1  plan-2  N21  0.020
 XY1  plan-2  N20  0.020
 XY1  plan-2  C18  0.020
 XY1  plan-2  C17  0.020
 XY1  plan-2  O22  0.020
 XY1  plan-2  C16  0.020
 XY1  plan-2  C15  0.020
 XY1  plan-2  C19  0.020
 XY1  plan-2  C9   0.020
 XY1  plan-2  C14  0.020
 XY1  plan-2  H19  0.020
 XY1  plan-2  H16  0.020
 XY1  plan-2  H15  0.020
 XY1  plan-3  C29  0.020
 XY1  plan-3  O30  0.020
 XY1  plan-3  C26  0.020
 XY1  plan-3  OXT  0.020
 XY1  plan-3  HXT  0.020

