# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:45:49 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 2-methyl-2-[4-(2-{4-[(E)-phenyldiazenyl]phenoxy}ethyl)phenoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(CCOc2ccc(cc2)N=Nc3ccccc3)cc1)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
 Y1N  Y1N  '2-methyl-2-[4-(2-{4-[(E)-phenyldiazenyl]phenoxy}ethyl)phenoxy]propanoic acid'  ligand  53  30  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y1N
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
 Y1N  C01   C  CH3    0  -0.672  -8.1840  -1.9681   0.9531
 Y1N  C02   C  CT     0   0.083  -7.2715  -1.1366   0.0552
 Y1N  C03   C  CH3    0  -0.661  -8.1175  -0.1760  -0.7703
 Y1N  O04   O  O2     0  -0.495  -6.4482  -0.4092   0.9784
 Y1N  C05   C  C      0   0.384  -5.3706   0.2911   0.5908
 Y1N  C06   C  C1     0  -0.351  -4.6642   0.9197   1.6210
 Y1N  C07   C  C1     0  -0.286  -3.5373   1.6742   1.3506
 Y1N  C08   C  C      0   0.077  -3.0703   1.8390   0.0480
 Y1N  C09   C  CH2    0  -0.539  -1.8135   2.6157  -0.2325
 Y1N  C10   C  CH2    0  -0.169  -0.6022   1.7030  -0.1442
 Y1N  O11   O  O2     0  -0.467   0.5581   2.4874  -0.3879
 Y1N  C12   C  CR6    0   0.399   1.7664   1.9150  -0.3217
 Y1N  C13   C  CR16   0  -0.341   2.8626   2.7530  -0.5442
 Y1N  C14   C  CR16   0  -0.265   4.1426   2.2431  -0.4856
 Y1N  C15   C  CR6    0   0.196   4.3660   0.8940  -0.2062
 Y1N  N16   N  N      0  -0.260   5.7057   0.4924  -0.1661
 Y1N  N17   N  N      0  -0.275   5.9049  -0.7046   0.0882
 Y1N  C18   C  C      0   0.226   7.2562  -1.0927   0.1344
 Y1N  C19   C  C1     0  -0.284   7.4832  -2.4401   0.4030
 Y1N  C20   C  C1     0  -0.247   8.7783  -2.9325   0.4758
 Y1N  C21   C  C1     0  -0.254   9.8543  -2.0781   0.2809
 Y1N  C22   C  C1     0  -0.245   9.6300  -0.7300   0.0120
 Y1N  C23   C  C1     0  -0.273   8.3410  -0.2335  -0.0617
 Y1N  C24   C  CR16   0  -0.253   3.2682   0.0602   0.0105
 Y1N  C25   C  CR16   0  -0.370   1.9807   0.5598  -0.0454
 Y1N  C26   C  C1     0  -0.300  -3.7837   1.2182  -0.9696
 Y1N  C27   C  C1     0  -0.351  -4.9190   0.4569  -0.7188
 Y1N  C28   C  C      0   0.400  -6.4281  -2.1356  -0.7914
 Y1N  O29   O  O      0  -0.593  -5.4695  -2.6710  -0.2104
 Y1N  O30   O  OC    -1  -0.594  -6.8240  -2.3475  -1.9530
 Y1N  H011  H  HCH3   0   0.229  -8.8481  -2.5822   0.3443
 Y1N  H012  H  HCH3   0   0.235  -7.6065  -2.6309   1.5979
 Y1N  H013  H  HCH3   0   0.231  -8.8053  -1.3267   1.5812
 Y1N  H031  H  HCH3   0   0.220  -8.6950   0.4769  -0.1132
 Y1N  H032  H  HCH3   0   0.232  -7.5296   0.4544  -1.4361
 Y1N  H033  H  HCH3   0   0.232  -8.8204  -0.7319  -1.3876
 Y1N  H06   H  H      0   0.252  -5.0093   0.8085   2.6418
 Y1N  H27   H  H      0   0.268  -5.4262   0.0085  -1.5605
 Y1N  H07   H  H      0   0.246  -3.0144   2.1490   2.1733
 Y1N  H091  H  HCH2   0   0.254  -1.8584   3.0663  -1.2268
 Y1N  H092  H  HCH2   0   0.253  -1.7056   3.4286   0.4896
 Y1N  H26   H  H      0   0.247  -3.4541   1.3282  -1.9967
 Y1N  H101  H  HCH2   0   0.233  -0.5503   1.2439   0.8488
 Y1N  H102  H  HCH2   0   0.234  -0.6800   0.8972  -0.8824
 Y1N  H13   H  HCR6   0   0.270   2.6981   3.8016  -0.7565
 Y1N  H25   H  HCR6   0   0.288   1.1542  -0.1157   0.1267
 Y1N  H14   H  HCR6   0   0.267   4.9929   2.8917  -0.6538
 Y1N  H24   H  HCR6   0   0.272   3.4195  -0.9893   0.2235
 Y1N  H19   H  H      0   0.263   6.6336  -3.0942   0.5530
 Y1N  H23   H  H      0   0.266   8.1715   0.8147  -0.2668
 Y1N  H20   H  H      0   0.263   8.9458  -3.9810   0.6836
 Y1N  H21   H  H      0   0.264  10.8664  -2.4569   0.3389
 Y1N  H22   H  H      0   0.264  10.4692  -0.0637  -0.1393

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
 Y1N  C01  C02   single    1.526  0.020  1.526
 Y1N  C02  C03   single    1.523  0.020  1.523
 Y1N  C02  O04   single    1.435  0.020  1.435
 Y1N  C02  C28   single    1.558  0.020  1.558
 Y1N  O04  C05   single    1.342  0.020  1.342
 Y1N  C05  C06   aromatic  1.398  0.020  1.398
 Y1N  C05  C27   aromatic  1.395  0.020  1.395
 Y1N  C06  C07   aromatic  1.383  0.020  1.383
 Y1N  C07  C08   aromatic  1.394  0.020  1.394
 Y1N  C08  C09   single    1.504  0.020  1.504
 Y1N  C08  C26   aromatic  1.389  0.020  1.389
 Y1N  C09  C10   single    1.519  0.020  1.519
 Y1N  C10  O11   single    1.422  0.020  1.422
 Y1N  O11  C12   single    1.339  0.020  1.339
 Y1N  C12  C13   aromatic  1.398  0.020  1.398
 Y1N  C12  C25   aromatic  1.400  0.020  1.400
 Y1N  C13  C14   aromatic  1.379  0.020  1.379
 Y1N  C14  C15   aromatic  1.396  0.020  1.396
 Y1N  C15  N16   single    1.399  0.020  1.399
 Y1N  C15  C24   aromatic  1.395  0.020  1.395
 Y1N  N16  N17   double    1.240  0.020  1.240
 Y1N  N17  C18   single    1.407  0.020  1.407
 Y1N  C18  C19   aromatic  1.393  0.020  1.393
 Y1N  C18  C23   aromatic  1.398  0.020  1.398
 Y1N  C19  C20   aromatic  1.387  0.020  1.387
 Y1N  C20  C21   aromatic  1.388  0.020  1.388
 Y1N  C21  C22   aromatic  1.393  0.020  1.393
 Y1N  C22  C23   aromatic  1.383  0.020  1.383
 Y1N  C24  C25   aromatic  1.382  0.020  1.382
 Y1N  C26  C27   aromatic  1.390  0.020  1.390
 Y1N  C28  O29   deloc     1.242  0.020  1.242
 Y1N  C28  O30   deloc     1.245  0.020  1.245
 Y1N  C01  H011  single    0.970  0.020  1.090
 Y1N  C01  H012  single    0.970  0.020  1.090
 Y1N  C01  H013  single    0.970  0.020  1.090
 Y1N  C03  H031  single    0.970  0.020  1.090
 Y1N  C03  H032  single    0.970  0.020  1.090
 Y1N  C03  H033  single    0.970  0.020  1.090
 Y1N  C06  H06   single    0.930  0.020  1.080
 Y1N  C27  H27   single    0.930  0.020  1.080
 Y1N  C07  H07   single    0.930  0.020  1.080
 Y1N  C09  H091  single    0.970  0.020  1.090
 Y1N  C09  H092  single    0.970  0.020  1.090
 Y1N  C26  H26   single    0.930  0.020  1.080
 Y1N  C10  H101  single    0.970  0.020  1.090
 Y1N  C10  H102  single    0.970  0.020  1.090
 Y1N  C13  H13   single    0.930  0.020  1.080
 Y1N  C25  H25   single    0.930  0.020  1.080
 Y1N  C14  H14   single    0.930  0.020  1.080
 Y1N  C24  H24   single    0.930  0.020  1.080
 Y1N  C19  H19   single    0.930  0.020  1.080
 Y1N  C23  H23   single    0.930  0.020  1.080
 Y1N  C20  H20   single    0.930  0.020  1.080
 Y1N  C21  H21   single    0.930  0.020  1.080
 Y1N  C22  H22   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
 Y1N  H013  C01  H012  108.56  3.000
 Y1N  H013  C01  H011  107.79  3.000
 Y1N  H012  C01  H011  108.09  3.000
 Y1N  H013  C01  C02   111.01  3.000
 Y1N  H012  C01  C02   111.24  3.000
 Y1N  H011  C01  C02   110.03  3.000
 Y1N  C28   C02  O04   111.36  3.000
 Y1N  C28   C02  C03   114.25  3.000
 Y1N  O04   C02  C03   110.34  3.000
 Y1N  C28   C02  C01   107.10  3.000
 Y1N  O04   C02  C01   103.93  3.000
 Y1N  C03   C02  C01   109.29  3.000
 Y1N  H033  C03  H032  107.31  3.000
 Y1N  H033  C03  H031  107.77  3.000
 Y1N  H032  C03  H031  107.90  3.000
 Y1N  H033  C03  C02   110.12  3.000
 Y1N  H032  C03  C02   113.37  3.000
 Y1N  H031  C03  C02   110.17  3.000
 Y1N  C05   O04  C02   122.64  3.000
 Y1N  C27   C05  C06   118.33  3.000
 Y1N  C27   C05  O04   126.36  3.000
 Y1N  C06   C05  O04   115.30  3.000
 Y1N  H06   C06  C07   119.99  3.000
 Y1N  H06   C06  C05   119.15  3.000
 Y1N  C07   C06  C05   120.86  3.000
 Y1N  H07   C07  C08   119.73  3.000
 Y1N  H07   C07  C06   118.92  3.000
 Y1N  C08   C07  C06   121.36  3.000
 Y1N  C26   C08  C09   121.56  3.000
 Y1N  C26   C08  C07   117.37  3.000
 Y1N  C09   C08  C07   121.03  3.000
 Y1N  H092  C09  H091  107.38  3.000
 Y1N  H092  C09  C10   109.26  3.000
 Y1N  H091  C09  C10   109.47  3.000
 Y1N  H092  C09  C08   110.09  3.000
 Y1N  H091  C09  C08   110.39  3.000
 Y1N  C10   C09  C08   110.20  3.000
 Y1N  H102  C10  H101  107.81  3.000
 Y1N  H102  C10  O11   110.38  3.000
 Y1N  H101  C10  O11   110.37  3.000
 Y1N  H102  C10  C09   110.25  3.000
 Y1N  H101  C10  C09   110.02  3.000
 Y1N  O11   C10  C09   108.02  3.000
 Y1N  C12   O11  C10   119.49  3.000
 Y1N  C25   C12  C13   119.46  3.000
 Y1N  C25   C12  O11   124.19  3.000
 Y1N  C13   C12  O11   116.34  3.000
 Y1N  H13   C13  C14   120.50  3.000
 Y1N  H13   C13  C12   119.53  3.000
 Y1N  C14   C13  C12   119.97  3.000
 Y1N  H14   C14  C15   118.98  3.000
 Y1N  H14   C14  C13   120.06  3.000
 Y1N  C15   C14  C13   120.96  3.000
 Y1N  C24   C15  N16   125.26  3.000
 Y1N  C24   C15  C14   118.86  3.000
 Y1N  N16   C15  C14   115.88  3.000
 Y1N  N17   N16  C15   115.91  3.000
 Y1N  C18   N17  N16   115.31  3.000
 Y1N  C23   C18  C19   119.69  3.000
 Y1N  C23   C18  N17   124.85  3.000
 Y1N  C19   C18  N17   115.46  3.000
 Y1N  H19   C19  C20   120.71  3.000
 Y1N  H19   C19  C18   118.91  3.000
 Y1N  C20   C19  C18   120.38  3.000
 Y1N  H20   C20  C21   120.24  3.000
 Y1N  H20   C20  C19   119.90  3.000
 Y1N  C21   C20  C19   119.86  3.000
 Y1N  H21   C21  C22   119.98  3.000
 Y1N  H21   C21  C20   120.14  3.000
 Y1N  C22   C21  C20   119.87  3.000
 Y1N  H22   C22  C23   119.62  3.000
 Y1N  H22   C22  C21   119.87  3.000
 Y1N  C23   C22  C21   120.52  3.000
 Y1N  H23   C23  C22   120.27  3.000
 Y1N  H23   C23  C18   120.05  3.000
 Y1N  C22   C23  C18   119.68  3.000
 Y1N  H24   C24  C25   119.28  3.000
 Y1N  H24   C24  C15   120.02  3.000
 Y1N  C25   C24  C15   120.70  3.000
 Y1N  H25   C25  C24   118.67  3.000
 Y1N  H25   C25  C12   121.29  3.000
 Y1N  C24   C25  C12   120.04  3.000
 Y1N  H26   C26  C27   118.35  3.000
 Y1N  H26   C26  C08   119.50  3.000
 Y1N  C27   C26  C08   122.15  3.000
 Y1N  H27   C27  C26   118.06  3.000
 Y1N  H27   C27  C05   122.01  3.000
 Y1N  C26   C27  C05   119.93  3.000
 Y1N  O30   C28  O29   127.47  3.000
 Y1N  O30   C28  C02   116.35  3.000
 Y1N  O29   C28  C02   116.11  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
 Y1N  CONST_01  C08   C07  C06  C05     0.00   0.0  0
 Y1N  CONST_02  C08   C26  C27  C05     0.00   0.0  0
 Y1N  CONST_03  C26   C27  C05  C06     0.00   0.0  0
 Y1N  CONST_04  C26   C08  C07  C06     0.00   0.0  0
 Y1N  CONST_05  C27   C05  C06  C07     0.00   0.0  0
 Y1N  CONST_06  C27   C26  C08  C07     0.00   0.0  0
 Y1N  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 Y1N  CONST_08  C15   C24  C25  C12     0.00   0.0  0
 Y1N  CONST_09  C24   C25  C12  C13     0.00   0.0  0
 Y1N  CONST_10  C24   C15  C14  C13     0.00   0.0  0
 Y1N  CONST_11  C25   C12  C13  C14     0.00   0.0  0
 Y1N  CONST_12  C25   C24  C15  C14     0.00   0.0  0
 Y1N  CONST_13  C21   C20  C19  C18     0.00   0.0  0
 Y1N  CONST_14  C21   C22  C23  C18     0.00   0.0  0
 Y1N  CONST_15  C22   C23  C18  C19     0.00   0.0  0
 Y1N  CONST_16  C22   C21  C20  C19     0.00   0.0  0
 Y1N  CONST_17  C23   C18  C19  C20     0.00   0.0  0
 Y1N  CONST_18  C23   C22  C21  C20     0.00   0.0  0
 Y1N  CONST_19  C07   C06  C05  O04   180.00   0.0  0
 Y1N  CONST_20  C26   C27  C05  O04   180.00   0.0  0
 Y1N  CONST_21  C09   C08  C07  C06   180.00   0.0  0
 Y1N  CONST_22  C27   C26  C08  C09   180.00   0.0  0
 Y1N  CONST_23  C14   C13  C12  O11   180.00   0.0  0
 Y1N  CONST_24  C24   C25  C12  O11   180.00   0.0  0
 Y1N  CONST_25  N16   C15  C14  C13   180.00   0.0  0
 Y1N  CONST_26  C25   C24  C15  N16   180.00   0.0  0
 Y1N  CONST_27  C20   C19  C18  N17   180.00   0.0  0
 Y1N  CONST_28  C22   C23  C18  N17   180.00   0.0  0
 Y1N  CONST_29  H07   C07  C06  C05   180.00   0.0  0
 Y1N  CONST_30  H26   C26  C27  C05   180.00   0.0  0
 Y1N  CONST_31  H27   C27  C05  C06   180.00   0.0  0
 Y1N  CONST_32  H06   C06  C07  C08   180.00   0.0  0
 Y1N  CONST_33  H14   C14  C13  C12   180.00   0.0  0
 Y1N  CONST_34  H24   C24  C25  C12   180.00   0.0  0
 Y1N  CONST_35  H25   C25  C12  C13   180.00   0.0  0
 Y1N  CONST_36  H13   C13  C14  C15   180.00   0.0  0
 Y1N  CONST_37  H20   C20  C19  C18   180.00   0.0  0
 Y1N  CONST_38  H22   C22  C23  C18   180.00   0.0  0
 Y1N  CONST_39  H23   C23  C18  C19   180.00   0.0  0
 Y1N  CONST_40  H21   C21  C20  C19   180.00   0.0  0
 Y1N  CONST_41  H19   C19  C20  C21   180.00   0.0  0
 Y1N  CONST_42  N17   N16  C15  C14   180.00   0.0  0
 Y1N  CONST_43  C19   C18  N17  N16   180.00   0.0  0
 Y1N  CONST_44  C23   C18  N17  N16     0.00   0.0  0
 Y1N  CONST_45  C24   C15  N16  N17     0.00   0.0  0
 Y1N  Var_01    C06   C05  O04  C02  -178.79  30.0  2
 Y1N  Var_02    C10   C09  C08  C07    87.43  30.0  2
 Y1N  Var_03    C13   C12  O11  C10  -178.66  30.0  2
 Y1N  Var_04    C28   C02  O04  C05    54.68  30.0  3
 Y1N  Var_05    O11   C10  C09  C08  -178.77  30.0  3
 Y1N  Var_06    O29   C28  C02  C01   -78.03  30.0  3
 Y1N  Var_07    H031  C03  C02  C01    58.84  30.0  3
 Y1N  Var_08    H011  C01  C02  C03    63.27  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
 Y1N  plan-1  O04  0.020
 Y1N  plan-1  C05  0.020
 Y1N  plan-1  C06  0.020
 Y1N  plan-1  C07  0.020
 Y1N  plan-1  C08  0.020
 Y1N  plan-1  C09  0.020
 Y1N  plan-1  C26  0.020
 Y1N  plan-1  C27  0.020
 Y1N  plan-1  H06  0.020
 Y1N  plan-1  H27  0.020
 Y1N  plan-1  H07  0.020
 Y1N  plan-1  H26  0.020
 Y1N  plan-2  O11  0.020
 Y1N  plan-2  C12  0.020
 Y1N  plan-2  C13  0.020
 Y1N  plan-2  C14  0.020
 Y1N  plan-2  C15  0.020
 Y1N  plan-2  N16  0.020
 Y1N  plan-2  N17  0.020
 Y1N  plan-2  C18  0.020
 Y1N  plan-2  C24  0.020
 Y1N  plan-2  C25  0.020
 Y1N  plan-2  H13  0.020
 Y1N  plan-2  H25  0.020
 Y1N  plan-2  H14  0.020
 Y1N  plan-2  H24  0.020
 Y1N  plan-3  N16  0.020
 Y1N  plan-3  N17  0.020
 Y1N  plan-3  C18  0.020
 Y1N  plan-3  C19  0.020
 Y1N  plan-3  C20  0.020
 Y1N  plan-3  C21  0.020
 Y1N  plan-3  C22  0.020
 Y1N  plan-3  C23  0.020
 Y1N  plan-3  H19  0.020
 Y1N  plan-3  H23  0.020
 Y1N  plan-3  H20  0.020
 Y1N  plan-3  H21  0.020
 Y1N  plan-3  H22  0.020
 Y1N  plan-4  C02  0.020
 Y1N  plan-4  C28  0.020
 Y1N  plan-4  O29  0.020
 Y1N  plan-4  O30  0.020

