# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:52:59 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: (3-{(Z)-[3-(aminomethyl)phenyl]diazenyl}phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)N=Nc2cccc(CC(O)=O)c2
#
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
 ZAB  ZAB  '(3-{(Z)-[3-(aminomethyl)phenyl]diazenyl}phenyl)acetic acid'  ligand  35  20  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZAB
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
 ZAB  N    N  NH2   0  -0.795  11.9400  -0.5234  3.1781
 ZAB  CA   C  CH2   0  -0.333  13.1997  -0.1376  2.5719
 ZAB  CB   C  CR6   0   0.092  14.0441   0.7161  3.4852
 ZAB  CG2  C  CR16  0  -0.293  13.4798   1.4953  4.4905
 ZAB  CD2  C  CR16  0  -0.220  14.2815   2.2861  5.3045
 ZAB  CE   C  CR16  0  -0.253  15.6512   2.3419  5.1123
 ZAB  CD1  C  CR6   0   0.162  16.2180   1.5765  4.0969
 ZAB  CG1  C  CR16  0  -0.325  15.4247   0.7421  3.3194
 ZAB  NG   N  N     0  -0.230  17.6220   1.4982  3.8840
 ZAB  NI   N  N     0  -0.233  18.3431   2.4906  3.7675
 ZAB  CI   C  CR6   0   0.169  17.8361   3.8167  3.6901
 ZAB  CJ2  C  CR16  0  -0.284  18.4995   4.7838  4.4351
 ZAB  CK2  C  CR16  0  -0.240  18.0850   6.1049  4.3604
 ZAB  CL   C  CR16  0  -0.297  17.0456   6.4651  3.5154
 ZAB  CK1  C  CR6   0   0.158  16.4112   5.5066  2.7299
 ZAB  CJ1  C  CR16  0  -0.277  16.8100   4.1817  2.8231
 ZAB  CM   C  CH2   0  -0.690  15.2854   5.8800  1.8130
 ZAB  C    C  C     0   0.559  13.9540   5.9094  2.5255
 ZAB  O    O  O     0  -0.426  13.8083   5.9184  3.7194
 ZAB  OXT  O  OH1   0  -0.594  12.9450   5.9484  1.6616
 ZAB  HN1  H  HNH2  0   0.345  12.1035  -1.2189  3.8951
 ZAB  HN2  H  HNH2  0   0.357  11.3578  -0.9693  2.4818
 ZAB  HA2  H  HCH2  0   0.246  12.9728   0.4443  1.6735
 ZAB  HA3  H  HCH2  0   0.217  13.8075  -0.9855  2.2277
 ZAB  HG2  H  HCR6  0   0.252  12.4103   1.4661  4.6493
 ZAB  HD2  H  HCR6  0   0.255  13.8312   2.8685  6.0978
 ZAB  HE   H  HCR6  0   0.270  16.2675   2.9569  5.7540
 ZAB  HG1  H  HCR6  0   0.256  15.8950   0.1185  2.5669
 ZAB  HJ2  H  HCR6  0   0.268  19.3267   4.4981  5.0723
 ZAB  HK2  H  HCR6  0   0.264  18.5838   6.8573  4.9566
 ZAB  HL   H  HCR6  0   0.258  16.7386   7.5018  3.4528
 ZAB  HJ1  H  HCR6  0   0.271  16.3215   3.4358  2.2085
 ZAB  HM2  H  HCH2  0   0.299  15.2250   5.1920  0.9673
 ZAB  HM3  H  HCH2  0   0.311  15.4461   6.8738  1.3831
 ZAB  HXT  H  HOH1  0   0.481  12.1026   5.9962  2.1382

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
 ZAB  N    CA   single    1.450  0.020  1.450
 ZAB  N    HN1  single    0.890  0.020  1.040
 ZAB  N    HN2  single    0.890  0.020  1.040
 ZAB  CA   CB   single    1.509  0.020  1.509
 ZAB  CA   HA2  single    0.970  0.020  1.090
 ZAB  CA   HA3  single    0.970  0.020  1.090
 ZAB  CB   CG2  aromatic  1.392  0.020  1.392
 ZAB  CB   CG1  aromatic  1.391  0.020  1.391
 ZAB  CG2  CD2  aromatic  1.389  0.020  1.389
 ZAB  CG2  HG2  single    0.930  0.020  1.080
 ZAB  CD2  CE   aromatic  1.384  0.020  1.384
 ZAB  CD2  HD2  single    0.930  0.020  1.080
 ZAB  CE   CD1  aromatic  1.392  0.020  1.392
 ZAB  CE   HE   single    0.930  0.020  1.080
 ZAB  CD1  CG1  aromatic  1.389  0.020  1.389
 ZAB  CD1  NG   single    1.422  0.020  1.422
 ZAB  CG1  HG1  single    0.930  0.020  1.080
 ZAB  NG   NI   double    1.232  0.020  1.232
 ZAB  NI   CI   single    1.422  0.020  1.422
 ZAB  CI   CJ2  aromatic  1.389  0.020  1.389
 ZAB  CI   CJ1  aromatic  1.392  0.020  1.392
 ZAB  CJ2  CK2  aromatic  1.387  0.020  1.387
 ZAB  CJ2  HJ2  single    0.930  0.020  1.080
 ZAB  CK2  CL   aromatic  1.387  0.020  1.387
 ZAB  CK2  HK2  single    0.930  0.020  1.080
 ZAB  CL   CK1  aromatic  1.392  0.020  1.392
 ZAB  CL   HL   single    0.930  0.020  1.080
 ZAB  CK1  CJ1  aromatic  1.387  0.020  1.387
 ZAB  CK1  CM   single    1.499  0.020  1.499
 ZAB  CJ1  HJ1  single    0.930  0.020  1.080
 ZAB  CM   C    single    1.510  0.020  1.510
 ZAB  CM   HM2  single    0.970  0.020  1.090
 ZAB  CM   HM3  single    0.970  0.020  1.090
 ZAB  C    O    double    1.203  0.020  1.203
 ZAB  C    OXT  single    1.329  0.020  1.329
 ZAB  OXT  HXT  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
 ZAB  HN2  N    HN1  106.13  3.000
 ZAB  HN2  N    CA   109.24  3.000
 ZAB  HN1  N    CA   109.80  3.000
 ZAB  HA3  CA   HA2  105.55  3.000
 ZAB  HA3  CA   CB   108.47  3.000
 ZAB  HA2  CA   CB   108.19  3.000
 ZAB  HA3  CA   N    113.96  3.000
 ZAB  HA2  CA   N    107.73  3.000
 ZAB  CB   CA   N    112.56  3.000
 ZAB  CG1  CB   CG2  118.57  3.000
 ZAB  CG1  CB   CA   119.61  3.000
 ZAB  CG2  CB   CA   121.83  3.000
 ZAB  HG2  CG2  CD2  119.99  3.000
 ZAB  HG2  CG2  CB   119.47  3.000
 ZAB  CD2  CG2  CB   120.53  3.000
 ZAB  HD2  CD2  CE   119.46  3.000
 ZAB  HD2  CD2  CG2  119.71  3.000
 ZAB  CE   CD2  CG2  120.83  3.000
 ZAB  HE   CE   CD1  120.88  3.000
 ZAB  HE   CE   CD2  120.29  3.000
 ZAB  CD1  CE   CD2  118.81  3.000
 ZAB  NG   CD1  CG1  116.54  3.000
 ZAB  NG   CD1  CE   122.78  3.000
 ZAB  CG1  CD1  CE   120.39  3.000
 ZAB  HG1  CG1  CD1  119.08  3.000
 ZAB  HG1  CG1  CB   120.16  3.000
 ZAB  CD1  CG1  CB   120.75  3.000
 ZAB  NI   NG   CD1  123.20  3.000
 ZAB  CI   NI   NG   123.20  3.000
 ZAB  CJ1  CI   CJ2  120.23  3.000
 ZAB  CJ1  CI   NI   122.77  3.000
 ZAB  CJ2  CI   NI   116.73  3.000
 ZAB  HJ2  CJ2  CK2  120.76  3.000
 ZAB  HJ2  CJ2  CI   119.79  3.000
 ZAB  CK2  CJ2  CI   119.45  3.000
 ZAB  HK2  CK2  CL   120.03  3.000
 ZAB  HK2  CK2  CJ2  119.68  3.000
 ZAB  CL   CK2  CJ2  120.28  3.000
 ZAB  HL   CL   CK1  119.82  3.000
 ZAB  HL   CL   CK2  119.75  3.000
 ZAB  CK1  CL   CK2  120.42  3.000
 ZAB  CM   CK1  CJ1  119.67  3.000
 ZAB  CM   CK1  CL   121.05  3.000
 ZAB  CJ1  CK1  CL   119.26  3.000
 ZAB  HJ1  CJ1  CK1  119.35  3.000
 ZAB  HJ1  CJ1  CI   120.36  3.000
 ZAB  CK1  CJ1  CI   120.29  3.000
 ZAB  HM3  CM   HM2  106.02  3.000
 ZAB  HM3  CM   C    107.28  3.000
 ZAB  HM2  CM   C    109.20  3.000
 ZAB  HM3  CM   CK1  110.86  3.000
 ZAB  HM2  CM   CK1  110.99  3.000
 ZAB  C    CM   CK1  112.23  3.000
 ZAB  OXT  C    O    123.58  3.000
 ZAB  OXT  C    CM   111.30  3.000
 ZAB  O    C    CM   125.11  3.000
 ZAB  HXT  OXT  C    109.98  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
 ZAB  CONST_01  CE   CD2  CG2  CB     0.00   0.0  0
 ZAB  CONST_02  CE   CD1  CG1  CB     0.00   0.0  0
 ZAB  CONST_03  CD1  CG1  CB   CG2    0.00   0.0  0
 ZAB  CONST_04  CD1  CE   CD2  CG2    0.00   0.0  0
 ZAB  CONST_05  CG1  CB   CG2  CD2    0.00   0.0  0
 ZAB  CONST_06  CG1  CD1  CE   CD2    0.00   0.0  0
 ZAB  CONST_07  CL   CK2  CJ2  CI     0.00   0.0  0
 ZAB  CONST_08  CL   CK1  CJ1  CI     0.00   0.0  0
 ZAB  CONST_09  CK1  CJ1  CI   CJ2    0.00   0.0  0
 ZAB  CONST_10  CK1  CL   CK2  CJ2    0.00   0.0  0
 ZAB  CONST_11  CJ1  CI   CJ2  CK2    0.00   0.0  0
 ZAB  CONST_12  CJ1  CK1  CL   CK2    0.00   0.0  0
 ZAB  CONST_13  CD2  CG2  CB   CA   180.00   0.0  0
 ZAB  CONST_14  CD1  CG1  CB   CA   180.00   0.0  0
 ZAB  CONST_15  NG   CD1  CG1  CB   180.00   0.0  0
 ZAB  CONST_16  NG   CD1  CE   CD2  180.00   0.0  0
 ZAB  CONST_17  CK2  CJ2  CI   NI   180.00   0.0  0
 ZAB  CONST_18  CK1  CJ1  CI   NI   180.00   0.0  0
 ZAB  CONST_19  CM   CK1  CJ1  CI   180.00   0.0  0
 ZAB  CONST_20  CM   CK1  CL   CK2  180.00   0.0  0
 ZAB  CONST_21  HD2  CD2  CG2  CB   180.00   0.0  0
 ZAB  CONST_22  HG1  CG1  CB   CG2  180.00   0.0  0
 ZAB  CONST_23  HE   CE   CD2  CG2  180.00   0.0  0
 ZAB  CONST_24  HG2  CG2  CD2  CE   180.00   0.0  0
 ZAB  CONST_25  HK2  CK2  CJ2  CI   180.00   0.0  0
 ZAB  CONST_26  HJ1  CJ1  CI   CJ2  180.00   0.0  0
 ZAB  CONST_27  HL   CL   CK2  CJ2  180.00   0.0  0
 ZAB  CONST_28  HJ2  CJ2  CK2  CL   180.00   0.0  0
 ZAB  CONST_33  HXT  OXT  C    CM   180.00   0.0  0
 ZAB  Var_01    CG2  CB   CA   N    -25.61  30.0  2
 ZAB  Var_02    C    CM   CK1  CL   -84.73  30.0  2
 ZAB  Var_03    O    C    CM   CK1   14.88  30.0  3
 ZAB  Var_04    HN1  N    CA   CB   -72.57  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
 ZAB  plan-1  CA   0.020
 ZAB  plan-1  CB   0.020
 ZAB  plan-1  CG2  0.020
 ZAB  plan-1  CD2  0.020
 ZAB  plan-1  CE   0.020
 ZAB  plan-1  CD1  0.020
 ZAB  plan-1  CG1  0.020
 ZAB  plan-1  NG   0.020
 ZAB  plan-1  NI   0.020
 ZAB  plan-1  CI   0.020
 ZAB  plan-1  HG2  0.020
 ZAB  plan-1  HD2  0.020
 ZAB  plan-1  HE   0.020
 ZAB  plan-1  HG1  0.020
 ZAB  plan-2  NG   0.020
 ZAB  plan-2  NI   0.020
 ZAB  plan-2  CI   0.020
 ZAB  plan-2  CJ2  0.020
 ZAB  plan-2  CK2  0.020
 ZAB  plan-2  CL   0.020
 ZAB  plan-2  CK1  0.020
 ZAB  plan-2  CJ1  0.020
 ZAB  plan-2  CM   0.020
 ZAB  plan-2  HJ2  0.020
 ZAB  plan-2  HK2  0.020
 ZAB  plan-2  HL   0.020
 ZAB  plan-2  HJ1  0.020
 ZAB  plan-3  CM   0.020
 ZAB  plan-3  C    0.020
 ZAB  plan-3  O    0.020
 ZAB  plan-3  OXT  0.020
 ZAB  plan-3  HXT  0.020

