# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:00:48 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[(E)-(4-hydroxy-3,5-dimethylphenyl)diazenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cc(C)c1O)N=Nc2ccccc2C(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
 DMB  DMB  '2-[(E)-(4-hydroxy-3,5-dimethylphenyl)diazenyl]benzoic acid'  ligand  33  20  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DMB
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
 DMB  C1    C  CR6    0   0.196   0.7383   0.0522  -2.1650
 DMB  C2    C  CR6    0  -0.082  -0.2214  -0.0181  -3.1814
 DMB  C3    C  CR16   0  -0.289   0.2124   0.0133  -4.5045
 DMB  C4    C  CR16   0  -0.251   1.5617   0.0794  -4.8182
 DMB  C5    C  CR16   0  -0.263   2.5069   0.1528  -3.8002
 DMB  C6    C  CR16   0  -0.281   2.0959   0.1482  -2.4794
 DMB  C1'   C  CR6    0   0.216   0.5811  -0.1311   1.3458
 DMB  C2'   C  CR16   0  -0.340   1.5258  -0.1878   2.3654
 DMB  C3'   C  CR6    0   0.015   1.1557  -0.1206   3.6996
 DMB  C4'   C  CR6    0   0.288  -0.2071  -0.0235   3.9994
 DMB  C5'   C  CR6    0   0.017  -1.1825   0.0082   2.9901
 DMB  C6'   C  CR16   0  -0.338  -0.7724  -0.0406   1.6698
 DMB  C     C  C      0   0.375  -1.7094  -0.1652  -2.8920
 DMB  CM3   C  CH3    0  -0.713   2.1751  -0.1541   4.7990
 DMB  CM5   C  CH3    0  -0.778  -2.6385   0.0877   3.3489
 DMB  N1    N  N      0  -0.246   0.2598   0.1180  -0.8439
 DMB  N1'   N  N      0  -0.271   1.0719  -0.2060   0.0332
 DMB  O     O  O      0  -0.585  -2.0330  -1.0315  -2.0619
 DMB  OXT   O  OC    -1  -0.600  -2.4622   0.5770  -3.5504
 DMB  O4'   O  OH1    0  -0.612  -0.5363   0.0263   5.3037
 DMB  H3    H  HCR6   0   0.252  -0.5197  -0.0256  -5.3007
 DMB  H4    H  HCR6   0   0.255   1.8761   0.0900  -5.8541
 DMB  H5    H  HCR6   0   0.257   3.5605   0.2283  -4.0363
 DMB  H6    H  HCR6   0   0.258   2.8226   0.2372  -1.6826
 DMB  H2'   H  HCR6   0   0.253   2.5738  -0.2755   2.1029
 DMB  H6'   H  HCR6   0   0.265  -1.5093  -0.0301   0.8763
 DMB  HM31  H  HCH3   0   0.245   2.1307   0.7439   5.4176
 DMB  HM32  H  HCH3   0   0.245   2.0280  -1.0067   5.4641
 DMB  HM33  H  HCH3   0   0.245   3.1810  -0.2238   4.3886
 DMB  HM51  H  HCH3   0   0.255  -2.9591  -0.7570   3.9642
 DMB  HM52  H  HCH3   0   0.254  -2.8787   1.0034   3.8957
 DMB  HM53  H  HCH3   0   0.271  -3.2565   0.0811   2.4535
 DMB  HO4'  H  HOH1   0   0.486  -1.4907   0.0908   5.4214

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
 DMB  C1   C2    aromatic  1.400  0.020  1.400
 DMB  C1   C6    aromatic  1.397  0.020  1.397
 DMB  C1   N1    single    1.407  0.020  1.407
 DMB  C2   C3    aromatic  1.393  0.020  1.393
 DMB  C2   C     single    1.523  0.020  1.523
 DMB  C3   C4    aromatic  1.387  0.020  1.387
 DMB  C3   H3    single    0.930  0.020  1.080
 DMB  C4   C5    aromatic  1.391  0.020  1.391
 DMB  C4   H4    single    0.930  0.020  1.080
 DMB  C5   C6    aromatic  1.383  0.020  1.383
 DMB  C5   H5    single    0.930  0.020  1.080
 DMB  C6   H6    single    0.930  0.020  1.080
 DMB  C1'  C2'   aromatic  1.391  0.020  1.391
 DMB  C1'  C6'   aromatic  1.395  0.020  1.395
 DMB  C1'  N1'   single    1.403  0.020  1.403
 DMB  C2'  C3'   aromatic  1.386  0.020  1.386
 DMB  C2'  H2'   single    0.930  0.020  1.080
 DMB  C3'  C4'   aromatic  1.399  0.020  1.399
 DMB  C3'  CM3   single    1.500  0.020  1.500
 DMB  C4'  C5'   aromatic  1.404  0.020  1.404
 DMB  C4'  O4'   single    1.346  0.020  1.346
 DMB  C5'  C6'   aromatic  1.383  0.020  1.383
 DMB  C5'  CM5   single    1.502  0.020  1.502
 DMB  C6'  H6'   single    0.930  0.020  1.080
 DMB  C    O     deloc     1.243  0.020  1.243
 DMB  C    OXT   deloc     1.245  0.020  1.245
 DMB  CM3  HM31  single    0.970  0.020  1.090
 DMB  CM3  HM32  single    0.970  0.020  1.090
 DMB  CM3  HM33  single    0.970  0.020  1.090
 DMB  CM5  HM51  single    0.970  0.020  1.090
 DMB  CM5  HM52  single    0.970  0.020  1.090
 DMB  CM5  HM53  single    0.970  0.020  1.090
 DMB  N1   N1'   double    1.238  0.020  1.238
 DMB  O4'  HO4'  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
 DMB  N1    C1   C6    122.60  3.000
 DMB  N1    C1   C2    116.82  3.000
 DMB  C6    C1   C2    120.43  3.000
 DMB  C     C2   C3    119.14  3.000
 DMB  C     C2   C1    122.47  3.000
 DMB  C3    C2   C1    118.37  3.000
 DMB  H3    C3   C4    119.56  3.000
 DMB  H3    C3   C2    119.17  3.000
 DMB  C4    C3   C2    121.27  3.000
 DMB  H4    C4   C5    120.16  3.000
 DMB  H4    C4   C3    119.96  3.000
 DMB  C5    C4   C3    119.87  3.000
 DMB  H5    C5   C6    119.85  3.000
 DMB  H5    C5   C4    120.36  3.000
 DMB  C6    C5   C4    119.78  3.000
 DMB  H6    C6   C5    120.22  3.000
 DMB  H6    C6   C1    119.51  3.000
 DMB  C5    C6   C1    120.26  3.000
 DMB  N1'   C1'  C6'   124.07  3.000
 DMB  N1'   C1'  C2'   116.48  3.000
 DMB  C6'   C1'  C2'   119.43  3.000
 DMB  H2'   C2'  C3'   119.68  3.000
 DMB  H2'   C2'  C1'   118.84  3.000
 DMB  C3'   C2'  C1'   121.48  3.000
 DMB  CM3   C3'  C4'   120.44  3.000
 DMB  CM3   C3'  C2'   121.54  3.000
 DMB  C4'   C3'  C2'   118.02  3.000
 DMB  O4'   C4'  C5'   121.72  3.000
 DMB  O4'   C4'  C3'   116.65  3.000
 DMB  C5'   C4'  C3'   121.63  3.000
 DMB  CM5   C5'  C6'   121.15  3.000
 DMB  CM5   C5'  C4'   120.20  3.000
 DMB  C6'   C5'  C4'   118.65  3.000
 DMB  H6'   C6'  C5'   119.82  3.000
 DMB  H6'   C6'  C1'   119.39  3.000
 DMB  C5'   C6'  C1'   120.78  3.000
 DMB  OXT   C    O     127.68  3.000
 DMB  OXT   C    C2    115.63  3.000
 DMB  O     C    C2    116.66  3.000
 DMB  HM33  CM3  HM32  107.72  3.000
 DMB  HM33  CM3  HM31  107.69  3.000
 DMB  HM32  CM3  HM31  106.98  3.000
 DMB  HM33  CM3  C3'   110.68  3.000
 DMB  HM32  CM3  C3'   111.88  3.000
 DMB  HM31  CM3  C3'   111.69  3.000
 DMB  HM53  CM5  HM52  106.97  3.000
 DMB  HM53  CM5  HM51  106.98  3.000
 DMB  HM52  CM5  HM51  107.53  3.000
 DMB  HM53  CM5  C5'   110.72  3.000
 DMB  HM52  CM5  C5'   112.14  3.000
 DMB  HM51  CM5  C5'   112.21  3.000
 DMB  N1'   N1   C1    115.46  3.000
 DMB  N1    N1'  C1'   114.77  3.000
 DMB  HO4'  O4'  C4'   111.29  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
 DMB  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 DMB  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 DMB  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 DMB  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 DMB  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 DMB  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 DMB  CONST_07  C4'   C3'  C2'  C1'    0.00   0.0  0
 DMB  CONST_08  C4'   C5'  C6'  C1'    0.00   0.0  0
 DMB  CONST_09  C5'   C6'  C1'  C2'    0.00   0.0  0
 DMB  CONST_10  C5'   C4'  C3'  C2'    0.00   0.0  0
 DMB  CONST_11  C6'   C1'  C2'  C3'    0.00   0.0  0
 DMB  CONST_12  C6'   C5'  C4'  C3'    0.00   0.0  0
 DMB  CONST_13  N1    C1   C2   C3   180.00   0.0  0
 DMB  CONST_14  C     C2   C3   C4   180.00   0.0  0
 DMB  CONST_15  N1    C1   C6   C5   180.00   0.0  0
 DMB  CONST_16  C     C2   C1   C6   180.00   0.0  0
 DMB  CONST_17  CM3   C3'  C2'  C1'  180.00   0.0  0
 DMB  CONST_18  CM5   C5'  C6'  C1'  180.00   0.0  0
 DMB  CONST_19  O4'   C4'  C3'  C2'  180.00   0.0  0
 DMB  CONST_20  N1'   C1'  C2'  C3'  180.00   0.0  0
 DMB  CONST_21  CM5   C5'  C4'  C3'  180.00   0.0  0
 DMB  CONST_22  CM3   C3'  C4'  C5'  180.00   0.0  0
 DMB  CONST_23  N1'   C1'  C6'  C5'  180.00   0.0  0
 DMB  CONST_24  O4'   C4'  C5'  C6'  180.00   0.0  0
 DMB  CONST_25  H3    C3   C2   C1   180.00   0.0  0
 DMB  CONST_26  H5    C5   C6   C1   180.00   0.0  0
 DMB  CONST_27  H6    C6   C1   C2   180.00   0.0  0
 DMB  CONST_28  H4    C4   C3   C2   180.00   0.0  0
 DMB  CONST_29  H6'   C6'  C1'  C2'  180.00   0.0  0
 DMB  CONST_30  H2'   C2'  C3'  C4'  180.00   0.0  0
 DMB  CONST_33  N1    N1'  C1'  C2'  180.00   0.0  0
 DMB  Var_01    O     C    C2   C1   -47.19  30.0  2
 DMB  Var_02    HM31  CM3  C3'  C2'  120.58  30.0  2
 DMB  Var_03    HM51  CM5  C5'  C4'  -59.30  30.0  2

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
 DMB  plan-1  C1   0.020
 DMB  plan-1  C2   0.020
 DMB  plan-1  C3   0.020
 DMB  plan-1  C4   0.020
 DMB  plan-1  C5   0.020
 DMB  plan-1  C6   0.020
 DMB  plan-1  C1'  0.020
 DMB  plan-1  C    0.020
 DMB  plan-1  N1   0.020
 DMB  plan-1  N1'  0.020
 DMB  plan-1  H3   0.020
 DMB  plan-1  H4   0.020
 DMB  plan-1  H5   0.020
 DMB  plan-1  H6   0.020
 DMB  plan-2  C1'  0.020
 DMB  plan-2  C2'  0.020
 DMB  plan-2  C3'  0.020
 DMB  plan-2  C4'  0.020
 DMB  plan-2  C5'  0.020
 DMB  plan-2  C6'  0.020
 DMB  plan-2  CM3  0.020
 DMB  plan-2  CM5  0.020
 DMB  plan-2  N1   0.020
 DMB  plan-2  N1'  0.020
 DMB  plan-2  O4'  0.020
 DMB  plan-2  H2'  0.020
 DMB  plan-2  H6'  0.020
 DMB  plan-3  C2   0.020
 DMB  plan-3  C    0.020
 DMB  plan-3  O    0.020
 DMB  plan-3  OXT  0.020

