# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:38:32 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(O)c(O)c(Oc2cccc(c2)[N+]([O-])=O)c1
#
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
 KIJ  KIJ  '3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid'  ligand  30  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KIJ
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
 KIJ  OAD  O  OH1    0  -0.615  -1.8006   2.5970  -0.2961
 KIJ  CAT  C  CR6    0   0.211  -1.9607   1.2711  -0.1839
 KIJ  CAP  C  CR6    0   0.331  -2.9433   0.6728  -0.9853
 KIJ  OAC  O  OH1    0  -0.627  -3.6965   1.4022  -1.8267
 KIJ  CAJ  C  CR16   0  -0.370  -3.1420  -0.6945  -0.9209
 KIJ  CAQ  C  CR6    0  -0.096  -2.3816  -1.4803  -0.0537
 KIJ  CAN  C  C      0   0.540  -2.5708  -2.9454   0.0457
 KIJ  OAB  O  OH1    0  -0.594  -3.5067  -3.4051  -0.7727
 KIJ  OAA  O  O      0  -0.441  -1.9389  -3.6550   0.7925
 KIJ  CAL  C  CR16   0  -0.339  -1.4170  -0.8926   0.7546
 KIJ  CAS  C  CR6    0   0.235  -1.2180   0.4723   0.6785
 KIJ  OAM  O  O2     0  -0.518  -0.3024   1.1069   1.4813
 KIJ  CAO  C  CR6    0   0.383   1.0275   0.9291   1.2446
 KIJ  CAK  C  CR16   0  -0.361   1.5223   0.3990   0.0647
 KIJ  CAH  C  CR16   0  -0.296   1.8907   1.3361   2.2573
 KIJ  CAG  C  CR16   0  -0.242   3.2577   1.2125   2.0851
 KIJ  CAI  C  CR16   0  -0.284   3.7842   0.6825   0.9160
 KIJ  CAR  C  CR6    0   0.275   2.8993   0.2865  -0.0711
 KIJ  NAU  N  N      1   0.330   3.4254  -0.2727  -1.3114
 KIJ  OAF  O  O     -1  -0.374   2.6361  -0.6602  -2.1396
 KIJ  OAE  O  O      0  -0.372   4.6243  -0.3197  -1.4469
 KIJ  H1   H  HOH1   0   0.489  -1.1918   2.9378   0.3714
 KIJ  H2   H  HOH1   0   0.479  -3.4898   2.3418  -1.7545
 KIJ  H3   H  HCR6   0   0.281  -3.9056  -1.1315  -1.5502
 KIJ  H4   H  HOH1   0   0.489  -3.5928  -4.3644  -0.6697
 KIJ  H5   H  HCR6   0   0.289  -0.8268  -1.4878   1.4389
 KIJ  H6   H  HCR6   0   0.317   0.8643   0.0850  -0.7328
 KIJ  H7   H  HCR6   0   0.295   1.4875   1.7481   3.1730
 KIJ  H8   H  HCR6   0   0.286   3.9248   1.5275   2.8753
 KIJ  H9   H  HCR6   0   0.300   4.8521   0.5840   0.7931

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
 KIJ  OAC  CAP  single    1.344  0.020  1.344
 KIJ  OAD  CAT  single    1.340  0.020  1.340
 KIJ  CAP  CAT  aromatic  1.402  0.020  1.402
 KIJ  CAP  CAJ  aromatic  1.383  0.020  1.383
 KIJ  CAT  CAS  aromatic  1.390  0.020  1.390
 KIJ  CAH  CAG  aromatic  1.383  0.020  1.383
 KIJ  CAH  CAO  aromatic  1.391  0.020  1.391
 KIJ  CAG  CAI  aromatic  1.387  0.020  1.387
 KIJ  CAJ  CAQ  aromatic  1.396  0.020  1.396
 KIJ  CAS  OAM  single    1.373  0.020  1.373
 KIJ  CAS  CAL  aromatic  1.381  0.020  1.381
 KIJ  OAM  CAO  single    1.362  0.020  1.362
 KIJ  CAO  CAK  aromatic  1.385  0.020  1.385
 KIJ  CAI  CAR  aromatic  1.384  0.020  1.384
 KIJ  CAQ  CAL  aromatic  1.389  0.020  1.389
 KIJ  CAQ  CAN  single    1.481  0.020  1.481
 KIJ  CAK  CAR  aromatic  1.388  0.020  1.388
 KIJ  CAR  NAU  single    1.459  0.020  1.459
 KIJ  OAA  CAN  double    1.209  0.020  1.209
 KIJ  CAN  OAB  single    1.326  0.020  1.326
 KIJ  NAU  OAF  single    1.208  0.020  1.208
 KIJ  NAU  OAE  double    1.207  0.020  1.207
 KIJ  OAD  H1   single    0.850  0.020  0.980
 KIJ  OAC  H2   single    0.850  0.020  0.980
 KIJ  CAJ  H3   single    0.930  0.020  1.080
 KIJ  OAB  H4   single    0.850  0.020  0.980
 KIJ  CAL  H5   single    0.930  0.020  1.080
 KIJ  CAK  H6   single    0.930  0.020  1.080
 KIJ  CAH  H7   single    0.930  0.020  1.080
 KIJ  CAG  H8   single    0.930  0.020  1.080
 KIJ  CAI  H9   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
 KIJ  H1   OAD  CAT  111.51  3.000
 KIJ  CAS  CAT  CAP  118.93  3.000
 KIJ  CAS  CAT  OAD  123.81  3.000
 KIJ  CAP  CAT  OAD  117.26  3.000
 KIJ  CAJ  CAP  OAC  119.02  3.000
 KIJ  CAJ  CAP  CAT  119.73  3.000
 KIJ  OAC  CAP  CAT  121.26  3.000
 KIJ  H2   OAC  CAP  111.19  3.000
 KIJ  H3   CAJ  CAQ  121.24  3.000
 KIJ  H3   CAJ  CAP  118.27  3.000
 KIJ  CAQ  CAJ  CAP  120.48  3.000
 KIJ  CAL  CAQ  CAN  117.92  3.000
 KIJ  CAN  CAQ  CAJ  121.96  3.000
 KIJ  CAL  CAQ  CAJ  120.12  3.000
 KIJ  OAA  CAN  OAB  123.17  3.000
 KIJ  OAB  CAN  CAQ  113.07  3.000
 KIJ  OAA  CAN  CAQ  123.76  3.000
 KIJ  H4   OAB  CAN  109.91  3.000
 KIJ  H5   CAL  CAS  119.98  3.000
 KIJ  H5   CAL  CAQ  120.94  3.000
 KIJ  CAS  CAL  CAQ  119.08  3.000
 KIJ  OAM  CAS  CAL  121.36  3.000
 KIJ  CAL  CAS  CAT  121.66  3.000
 KIJ  OAM  CAS  CAT  116.96  3.000
 KIJ  CAO  OAM  CAS  119.28  3.000
 KIJ  CAH  CAO  CAK  120.69  3.000
 KIJ  CAK  CAO  OAM  123.14  3.000
 KIJ  CAH  CAO  OAM  116.17  3.000
 KIJ  H6   CAK  CAR  120.54  3.000
 KIJ  H6   CAK  CAO  121.50  3.000
 KIJ  CAR  CAK  CAO  117.95  3.000
 KIJ  H7   CAH  CAG  120.50  3.000
 KIJ  H7   CAH  CAO  119.74  3.000
 KIJ  CAG  CAH  CAO  119.76  3.000
 KIJ  H8   CAG  CAI  119.54  3.000
 KIJ  H8   CAG  CAH  119.52  3.000
 KIJ  CAI  CAG  CAH  120.93  3.000
 KIJ  H9   CAI  CAR  121.69  3.000
 KIJ  H9   CAI  CAG  120.41  3.000
 KIJ  CAR  CAI  CAG  117.89  3.000
 KIJ  NAU  CAR  CAI  119.06  3.000
 KIJ  NAU  CAR  CAK  118.16  3.000
 KIJ  CAI  CAR  CAK  122.78  3.000
 KIJ  OAE  NAU  OAF  124.01  3.000
 KIJ  OAE  NAU  CAR  117.93  3.000
 KIJ  OAF  NAU  CAR  118.06  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
 KIJ  CONST_01  CAQ  CAJ  CAP  CAT     0.00   0.0  0
 KIJ  CONST_02  CAQ  CAL  CAS  CAT     0.00   0.0  0
 KIJ  CONST_03  CAL  CAS  CAT  CAP     0.00   0.0  0
 KIJ  CONST_04  CAL  CAQ  CAJ  CAP     0.00   0.0  0
 KIJ  CONST_05  CAS  CAT  CAP  CAJ     0.00   0.0  0
 KIJ  CONST_06  CAS  CAL  CAQ  CAJ     0.00   0.0  0
 KIJ  CONST_07  CAI  CAG  CAH  CAO     0.00   0.0  0
 KIJ  CONST_08  CAI  CAR  CAK  CAO     0.00   0.0  0
 KIJ  CONST_09  CAG  CAH  CAO  CAK     0.00   0.0  0
 KIJ  CONST_10  CAG  CAI  CAR  CAK     0.00   0.0  0
 KIJ  CONST_11  CAR  CAI  CAG  CAH     0.00   0.0  0
 KIJ  CONST_12  CAR  CAK  CAO  CAH     0.00   0.0  0
 KIJ  CONST_13  CAJ  CAP  CAT  OAD   180.00   0.0  0
 KIJ  CONST_14  CAL  CAS  CAT  OAD   180.00   0.0  0
 KIJ  CONST_15  OAM  CAS  CAT  CAP   180.00   0.0  0
 KIJ  CONST_16  CAN  CAQ  CAJ  CAP   180.00   0.0  0
 KIJ  CONST_17  CAS  CAT  CAP  OAC   180.00   0.0  0
 KIJ  CONST_18  CAQ  CAJ  CAP  OAC   180.00   0.0  0
 KIJ  CONST_19  OAM  CAS  CAL  CAQ   180.00   0.0  0
 KIJ  CONST_20  CAS  CAL  CAQ  CAN   180.00   0.0  0
 KIJ  CONST_21  CAG  CAH  CAO  OAM   180.00   0.0  0
 KIJ  CONST_22  CAR  CAK  CAO  OAM   180.00   0.0  0
 KIJ  CONST_23  NAU  CAR  CAK  CAO   180.00   0.0  0
 KIJ  CONST_24  NAU  CAR  CAI  CAG   180.00   0.0  0
 KIJ  CONST_25  H3   CAJ  CAP  CAT   180.00   0.0  0
 KIJ  CONST_26  H5   CAL  CAS  CAT   180.00   0.0  0
 KIJ  CONST_27  H8   CAG  CAH  CAO   180.00   0.0  0
 KIJ  CONST_28  H7   CAH  CAO  CAK   180.00   0.0  0
 KIJ  CONST_29  H9   CAI  CAR  CAK   180.00   0.0  0
 KIJ  CONST_30  H6   CAK  CAO  CAH   180.00   0.0  0
 KIJ  CONST_31  OAF  NAU  CAR  CAK     0.00   0.0  0
 KIJ  CONST_32  OAE  NAU  CAR  CAK   180.00   0.0  0
 KIJ  CONST_33  OAF  NAU  CAR  CAI   180.00   0.0  0
 KIJ  CONST_34  OAE  NAU  CAR  CAI     0.00   0.0  0
 KIJ  CONST_35  H4   OAB  CAN  CAQ   180.00   0.0  0
 KIJ  Var_01    CAH  CAO  OAM  CAS  -165.71  30.0  2
 KIJ  Var_02    OAA  CAN  CAQ  CAJ  -179.37  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
 KIJ  plan-1  OAD  0.020
 KIJ  plan-1  CAT  0.020
 KIJ  plan-1  CAP  0.020
 KIJ  plan-1  OAC  0.020
 KIJ  plan-1  CAJ  0.020
 KIJ  plan-1  CAQ  0.020
 KIJ  plan-1  CAN  0.020
 KIJ  plan-1  CAL  0.020
 KIJ  plan-1  CAS  0.020
 KIJ  plan-1  OAM  0.020
 KIJ  plan-1  H3   0.020
 KIJ  plan-1  H5   0.020
 KIJ  plan-2  OAM  0.020
 KIJ  plan-2  CAO  0.020
 KIJ  plan-2  CAK  0.020
 KIJ  plan-2  CAH  0.020
 KIJ  plan-2  CAG  0.020
 KIJ  plan-2  CAI  0.020
 KIJ  plan-2  CAR  0.020
 KIJ  plan-2  NAU  0.020
 KIJ  plan-2  H6   0.020
 KIJ  plan-2  H7   0.020
 KIJ  plan-2  H8   0.020
 KIJ  plan-2  H9   0.020
 KIJ  plan-3  CAR  0.020
 KIJ  plan-3  NAU  0.020
 KIJ  plan-3  OAF  0.020
 KIJ  plan-3  OAE  0.020
 KIJ  plan-4  CAQ  0.020
 KIJ  plan-4  CAN  0.020
 KIJ  plan-4  OAB  0.020
 KIJ  plan-4  OAA  0.020
 KIJ  plan-4  H4   0.020

