# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 18:00:17 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-[(E)-(4-hydroxynaphthalen-1-yl)diazenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1N=Nc2ccc(O)c3ccccc23
#
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
 NAB  NAB  '2-[(E)-(4-hydroxynaphthalen-1-yl)diazenyl]benzoic acid'  ligand  34  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NAB
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
 NAB  C1    C  CR6   0   0.251  -0.6093  -0.1195   2.3071
 NAB  C2    C  CR6   0  -0.101   0.0777   0.1120   3.5067
 NAB  C3    C  CR16  0  -0.254  -0.6239   0.1180   4.7100
 NAB  C4    C  CR16  0  -0.248  -1.9935  -0.0907   4.7277
 NAB  C5    C  CR16  0  -0.242  -2.6711  -0.3274   3.5379
 NAB  C6    C  CR16  0  -0.277  -1.9844  -0.3485   2.3370
 NAB  C1'   C  CR6   0   0.153   0.2259  -0.0781  -1.1039
 NAB  C2'   C  CR16  0  -0.269   1.5917  -0.2626  -1.1711
 NAB  C3'   C  CR16  0  -0.397   2.2498  -0.3543  -2.3960
 NAB  C4'   C  CR6   0   0.331   1.5397  -0.2708  -3.5756
 NAB  C4A   C  CR66  0  -0.015   0.1302  -0.0738  -3.5579
 NAB  C5'   C  CR16  0  -0.275  -0.6167   0.0219  -4.7555
 NAB  C6'   C  CR16  0  -0.253  -1.9700   0.2174  -4.7163
 NAB  C7'   C  CR16  0  -0.239  -2.6307   0.3244  -3.4780
 NAB  C8'   C  CR16  0  -0.294  -1.9326   0.2349  -2.3044
 NAB  C8A   C  CR66  0   0.069  -0.5324   0.0322  -2.3073
 NAB  C     C  C     0   0.508   1.5318   0.4239   3.4976
 NAB  N1    N  N     0  -0.254   0.1436  -0.2218   1.1264
 NAB  N1'   N  N     0  -0.257  -0.4840   0.0430   0.0904
 NAB  O     O  O     0  -0.422   2.0881   1.0667   2.6440
 NAB  OXT   O  OH1   0  -0.589   2.1504  -0.0719   4.5623
 NAB  O4'   O  OH1   0  -0.603   2.1189  -0.3586  -4.7758
 NAB  H3    H  HCR6  0   0.275  -0.1046   0.3087   5.6392
 NAB  H4    H  HCR6  0   0.271  -2.5287  -0.0771   5.6673
 NAB  H5    H  HCR6  0   0.273  -3.7381  -0.5064   3.5476
 NAB  H6    H  HCR6  0   0.276  -2.5053  -0.5672   1.4147
 NAB  H2'   H  HCR6  0   0.280   2.1681  -0.3233  -0.2577
 NAB  H3'   H  HCR6  0   0.282   3.3251  -0.4866  -2.4166
 NAB  H5'   H  HCR6  0   0.261  -0.1158  -0.0592  -5.7102
 NAB  H6'   H  HCR6  0   0.262  -2.5344   0.2922  -5.6362
 NAB  H7'   H  HCR6  0   0.262  -3.7016   0.4783  -3.4543
 NAB  H8'   H  HCR6  0   0.260  -2.4522   0.3202  -1.3607
 NAB  HXT   H  HOH1  0   0.488   3.0813   0.1983   4.5588
 NAB  HO4'  H  HOH1  0   0.486   3.0710  -0.4883  -4.6881

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
 NAB  C1   C2    aromatic  1.402  0.020  1.402
 NAB  C1   C6    aromatic  1.394  0.020  1.394
 NAB  C1   N1    single    1.404  0.020  1.404
 NAB  C2   C3    aromatic  1.393  0.020  1.393
 NAB  C2   C     single    1.487  0.020  1.487
 NAB  C3   C4    aromatic  1.386  0.020  1.386
 NAB  C3   H3    single    0.930  0.020  1.080
 NAB  C4   C5    aromatic  1.389  0.020  1.389
 NAB  C4   H4    single    0.930  0.020  1.080
 NAB  C5   C6    aromatic  1.384  0.020  1.384
 NAB  C5   H5    single    0.930  0.020  1.080
 NAB  C6   H6    single    0.930  0.020  1.080
 NAB  C1'  C2'   aromatic  1.380  0.020  1.380
 NAB  C1'  C8A   aromatic  1.427  0.020  1.427
 NAB  C1'  N1'   single    1.395  0.020  1.395
 NAB  C2'  C3'   aromatic  1.394  0.020  1.394
 NAB  C2'  H2'   single    0.930  0.020  1.080
 NAB  C3'  C4'   aromatic  1.379  0.020  1.379
 NAB  C3'  H3'   single    0.930  0.020  1.080
 NAB  C4'  C4A   aromatic  1.423  0.020  1.423
 NAB  C4'  O4'   single    1.336  0.020  1.336
 NAB  C4A  C5'   aromatic  1.415  0.020  1.415
 NAB  C4A  C8A   aromatic  1.419  0.020  1.419
 NAB  C5'  C6'   aromatic  1.368  0.020  1.368
 NAB  C5'  H5'   single    0.930  0.020  1.080
 NAB  C6'  C7'   aromatic  1.408  0.020  1.408
 NAB  C6'  H6'   single    0.930  0.020  1.080
 NAB  C7'  C8'   aromatic  1.368  0.020  1.368
 NAB  C7'  H7'   single    0.930  0.020  1.080
 NAB  C8'  C8A   aromatic  1.415  0.020  1.415
 NAB  C8'  H8'   single    0.930  0.020  1.080
 NAB  C    O     double    1.205  0.020  1.205
 NAB  C    OXT   single    1.327  0.020  1.327
 NAB  N1   N1'   double    1.240  0.020  1.240
 NAB  OXT  HXT   single    0.850  0.020  0.980
 NAB  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
 NAB  N1    C1   C6   122.34  3.000
 NAB  N1    C1   C2   117.96  3.000
 NAB  C6    C1   C2   119.48  3.000
 NAB  C     C2   C3   119.79  3.000
 NAB  C     C2   C1   120.58  3.000
 NAB  C3    C2   C1   119.55  3.000
 NAB  H3    C3   C4   119.36  3.000
 NAB  H3    C3   C2   120.08  3.000
 NAB  C4    C3   C2   120.55  3.000
 NAB  H4    C4   C5   120.31  3.000
 NAB  H4    C4   C3   119.90  3.000
 NAB  C5    C4   C3   119.79  3.000
 NAB  H5    C5   C6   119.65  3.000
 NAB  H5    C5   C4   120.10  3.000
 NAB  C6    C5   C4   120.25  3.000
 NAB  H6    C6   C5   120.28  3.000
 NAB  H6    C6   C1   119.33  3.000
 NAB  C5    C6   C1   120.37  3.000
 NAB  N1'   C1'  C8A  116.43  3.000
 NAB  N1'   C1'  C2'  123.86  3.000
 NAB  C8A   C1'  C2'  119.69  3.000
 NAB  H2'   C2'  C3'  119.14  3.000
 NAB  H2'   C2'  C1'  119.59  3.000
 NAB  C3'   C2'  C1'  121.27  3.000
 NAB  H3'   C3'  C4'  120.14  3.000
 NAB  H3'   C3'  C2'  119.56  3.000
 NAB  C4'   C3'  C2'  120.31  3.000
 NAB  O4'   C4'  C4A  116.73  3.000
 NAB  O4'   C4'  C3'  122.77  3.000
 NAB  C4A   C4'  C3'  120.50  3.000
 NAB  C8A   C4A  C5'  119.63  3.000
 NAB  C8A   C4A  C4'  118.92  3.000
 NAB  C5'   C4A  C4'  121.44  3.000
 NAB  H5'   C5'  C6'  119.63  3.000
 NAB  H5'   C5'  C4A  119.86  3.000
 NAB  C6'   C5'  C4A  120.51  3.000
 NAB  H6'   C6'  C7'  119.86  3.000
 NAB  H6'   C6'  C5'  120.11  3.000
 NAB  C7'   C6'  C5'  120.03  3.000
 NAB  H7'   C7'  C8'  119.69  3.000
 NAB  H7'   C7'  C6'  119.64  3.000
 NAB  C8'   C7'  C6'  120.66  3.000
 NAB  H8'   C8'  C8A  119.27  3.000
 NAB  H8'   C8'  C7'  119.90  3.000
 NAB  C8A   C8'  C7'  120.83  3.000
 NAB  C8'   C8A  C4A  118.33  3.000
 NAB  C8'   C8A  C1'  122.37  3.000
 NAB  C4A   C8A  C1'  119.30  3.000
 NAB  OXT   C    O    123.53  3.000
 NAB  OXT   C    C2   111.86  3.000
 NAB  O     C    C2   124.59  3.000
 NAB  N1'   N1   C1   114.56  3.000
 NAB  N1    N1'  C1'  116.06  3.000
 NAB  HXT   OXT  C    109.91  3.000
 NAB  HO4'  O4'  C4'  110.80  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
 NAB  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NAB  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 NAB  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 NAB  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 NAB  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 NAB  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 NAB  CONST_07  C4'  C3'  C2'  C1'    0.00   0.0  0
 NAB  CONST_08  C4'  C4A  C8A  C1'    0.00   0.0  0
 NAB  CONST_09  C5'  C4A  C8A  C1'  180.00   0.0  0
 NAB  CONST_10  C7'  C8'  C8A  C1'  180.00   0.0  0
 NAB  CONST_11  C4A  C8A  C1'  C2'    0.00   0.0  0
 NAB  CONST_12  C8'  C8A  C1'  C2'  180.00   0.0  0
 NAB  CONST_13  C4A  C4'  C3'  C2'    0.00   0.0  0
 NAB  CONST_14  C8A  C1'  C2'  C3'    0.00   0.0  0
 NAB  CONST_15  C5'  C4A  C4'  C3'  180.00   0.0  0
 NAB  CONST_16  C8A  C4A  C4'  C3'    0.00   0.0  0
 NAB  CONST_17  C6'  C5'  C4A  C4'  180.00   0.0  0
 NAB  CONST_18  C8'  C8A  C4A  C4'  180.00   0.0  0
 NAB  CONST_19  C7'  C6'  C5'  C4A    0.00   0.0  0
 NAB  CONST_20  C7'  C8'  C8A  C4A    0.00   0.0  0
 NAB  CONST_21  C8'  C8A  C4A  C5'    0.00   0.0  0
 NAB  CONST_22  C8'  C7'  C6'  C5'    0.00   0.0  0
 NAB  CONST_23  C8A  C4A  C5'  C6'    0.00   0.0  0
 NAB  CONST_24  C8A  C8'  C7'  C6'    0.00   0.0  0
 NAB  CONST_25  N1   C1   C2   C3   180.00   0.0  0
 NAB  CONST_26  C    C2   C3   C4   180.00   0.0  0
 NAB  CONST_27  N1   C1   C6   C5   180.00   0.0  0
 NAB  CONST_28  C    C2   C1   C6   180.00   0.0  0
 NAB  CONST_29  O4'  C4'  C3'  C2'  180.00   0.0  0
 NAB  CONST_30  N1'  C1'  C2'  C3'  180.00   0.0  0
 NAB  CONST_31  N1'  C1'  C8A  C4A  180.00   0.0  0
 NAB  CONST_32  O4'  C4'  C4A  C5'    0.00   0.0  0
 NAB  CONST_33  N1'  C1'  C8A  C8'    0.00   0.0  0
 NAB  CONST_34  O4'  C4'  C4A  C8A  180.00   0.0  0
 NAB  CONST_35  H3   C3   C2   C1   180.00   0.0  0
 NAB  CONST_36  H5   C5   C6   C1   180.00   0.0  0
 NAB  CONST_37  H6   C6   C1   C2   180.00   0.0  0
 NAB  CONST_38  H4   C4   C3   C2   180.00   0.0  0
 NAB  CONST_39  H3'  C3'  C2'  C1'  180.00   0.0  0
 NAB  CONST_40  H8'  C8'  C8A  C1'    0.00   0.0  0
 NAB  CONST_41  H2'  C2'  C3'  C4'  180.00   0.0  0
 NAB  CONST_42  H5'  C5'  C4A  C4'    0.00   0.0  0
 NAB  CONST_43  H6'  C6'  C5'  C4A  180.00   0.0  0
 NAB  CONST_44  H7'  C7'  C6'  C5'  180.00   0.0  0
 NAB  CONST_47  N1   N1'  C1'  C2'    0.00   0.0  0
 NAB  CONST_48  N1   N1'  C1'  C8A  180.00   0.0  0
 NAB  CONST_49  HXT  OXT  C    C2   180.00   0.0  0
 NAB  Var_01    O    C    C2   C1    34.97  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
 NAB  plan-1  C1   0.020
 NAB  plan-1  C2   0.020
 NAB  plan-1  C3   0.020
 NAB  plan-1  C4   0.020
 NAB  plan-1  C5   0.020
 NAB  plan-1  C6   0.020
 NAB  plan-1  C1'  0.020
 NAB  plan-1  C    0.020
 NAB  plan-1  N1   0.020
 NAB  plan-1  N1'  0.020
 NAB  plan-1  H3   0.020
 NAB  plan-1  H4   0.020
 NAB  plan-1  H5   0.020
 NAB  plan-1  H6   0.020
 NAB  plan-2  C1'  0.020
 NAB  plan-2  C2'  0.020
 NAB  plan-2  C3'  0.020
 NAB  plan-2  C4'  0.020
 NAB  plan-2  C4A  0.020
 NAB  plan-2  C5'  0.020
 NAB  plan-2  C6'  0.020
 NAB  plan-2  C7'  0.020
 NAB  plan-2  C8'  0.020
 NAB  plan-2  C8A  0.020
 NAB  plan-2  N1   0.020
 NAB  plan-2  N1'  0.020
 NAB  plan-2  O4'  0.020
 NAB  plan-2  H2'  0.020
 NAB  plan-2  H3'  0.020
 NAB  plan-2  H5'  0.020
 NAB  plan-2  H6'  0.020
 NAB  plan-2  H7'  0.020
 NAB  plan-2  H8'  0.020
 NAB  plan-3  C2   0.020
 NAB  plan-3  C    0.020
 NAB  plan-3  O    0.020
 NAB  plan-3  OXT  0.020
 NAB  plan-3  HXT  0.020

