# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 16:25:11 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(NCc2cccc(c2)[N+]([O-])=O)cc(c1)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
 KIW  KIW  '5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid'  ligand  35  23  .  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_KIW
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
 KIW  OAA  O  OH1    0  -0.592  -5.4227  -2.3024  -0.0262
 KIW  CAP  C  C      0   0.547  -4.1222  -2.4814   0.1459
 KIW  OAC  O  O      0  -0.435  -3.6158  -3.5664   0.2992
 KIW  CAT  C  CR6    0  -0.054  -3.3542  -1.2076   0.1276
 KIW  CAJ  C  CR16   0  -0.348  -1.9815  -1.2847   0.2968
 KIW  CAM  C  CR16   0  -0.332  -3.9792   0.0247  -0.0547
 KIW  CAU  C  CR6    0  -0.045  -3.1964   1.1713  -0.0685
 KIW  CAQ  C  C      0   0.543  -3.7918   2.5201  -0.2663
 KIW  OAD  O  OH1    0  -0.593  -5.0998   2.4845  -0.4705
 KIW  OAB  O  O      0  -0.435  -3.1529   3.5442  -0.2453
 KIW  CAK  C  CR16   0  -0.359  -1.8155   1.0985   0.0928
 KIW  CAS  C  CR6    0   0.430  -1.1852  -0.1329   0.2858
 KIW  NAO  N  NH1    0  -0.693   0.1676  -0.2480   0.4876
 KIW  CAN  C  CH2    0  -0.345   1.0652   0.8523   0.2164
 KIW  CAR  C  CR6    0   0.090   2.4717   0.4629   0.5759
 KIW  CAL  C  CR16   0  -0.328   3.4449   0.3638  -0.4054
 KIW  CAH  C  CR16   0  -0.256   2.8088   0.1844   1.8995
 KIW  CAG  C  CR16   0  -0.236   4.1015  -0.1808   2.2397
 KIW  CAI  C  CR16   0  -0.275   5.0829  -0.2773   1.2653
 KIW  CAV  C  CR6    0   0.272   4.7364  -0.0010  -0.0473
 KIW  NAW  N  N      1   0.329   5.7544  -0.0952  -1.0837
 KIW  OAF  O  O      0  -0.378   5.4321   0.1520  -2.2218
 KIW  OAE  O  O     -1  -0.377   6.8723  -0.4151  -0.7550
 KIW  H1   H  HOH1   0   0.490  -5.8806  -3.1562  -0.0141
 KIW  H2   H  HCR6   0   0.277  -1.5128  -2.2504   0.4428
 KIW  H3   H  HCR6   0   0.271  -5.0488   0.0863  -0.1835
 KIW  H4   H  HOH1   0   0.490  -5.4379   3.3828  -0.6023
 KIW  H5   H  HCR6   0   0.286  -1.2363   2.0111   0.0608
 KIW  H6   H  HNH1   0   0.390   0.5465  -1.1585   0.2764
 KIW  H7   H  HCH2   0   0.252   1.0247   1.1748  -0.8315
 KIW  H8   H  HCH2   0   0.263   0.7703   1.7130   0.8225
 KIW  H9   H  HCR6   0   0.296   3.1902   0.5711  -1.4354
 KIW  H10  H  HCR6   0   0.275   2.0526   0.2579   2.6709
 KIW  H11  H  HCR6   0   0.281   4.3532  -0.3889   3.2702
 KIW  H12  H  HCR6   0   0.300   6.0897  -0.5592   1.5355

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
 KIW  CAN  NAO  single    1.446  0.020  1.446
 KIW  CAN  CAR  single    1.503  0.020  1.503
 KIW  NAO  CAS  single    1.373  0.020  1.373
 KIW  OAC  CAP  double    1.207  0.020  1.207
 KIW  CAJ  CAS  aromatic  1.400  0.020  1.400
 KIW  CAJ  CAT  aromatic  1.385  0.020  1.385
 KIW  CAS  CAK  aromatic  1.397  0.020  1.397
 KIW  CAP  CAT  single    1.487  0.020  1.487
 KIW  CAP  OAA  single    1.324  0.020  1.324
 KIW  CAR  CAL  aromatic  1.386  0.020  1.386
 KIW  CAR  CAH  aromatic  1.394  0.020  1.394
 KIW  CAT  CAM  aromatic  1.394  0.020  1.394
 KIW  CAL  CAV  aromatic  1.389  0.020  1.389
 KIW  CAK  CAU  aromatic  1.392  0.020  1.392
 KIW  CAH  CAG  aromatic  1.386  0.020  1.386
 KIW  CAM  CAU  aromatic  1.388  0.020  1.388
 KIW  CAU  CAQ  single    1.488  0.020  1.488
 KIW  CAV  NAW  single    1.456  0.020  1.456
 KIW  CAV  CAI  aromatic  1.385  0.020  1.385
 KIW  OAB  CAQ  double    1.207  0.020  1.207
 KIW  NAW  OAF  double    1.208  0.020  1.208
 KIW  NAW  OAE  single    1.208  0.020  1.208
 KIW  CAG  CAI  aromatic  1.386  0.020  1.386
 KIW  CAQ  OAD  single    1.324  0.020  1.324
 KIW  OAA  H1   single    0.850  0.020  0.980
 KIW  CAJ  H2   single    0.930  0.020  1.080
 KIW  CAM  H3   single    0.930  0.020  1.080
 KIW  OAD  H4   single    0.850  0.020  0.980
 KIW  CAK  H5   single    0.930  0.020  1.080
 KIW  NAO  H6   single    0.890  0.020  1.040
 KIW  CAN  H7   single    0.970  0.020  1.090
 KIW  CAN  H8   single    0.970  0.020  1.090
 KIW  CAL  H9   single    0.930  0.020  1.080
 KIW  CAH  H10  single    0.930  0.020  1.080
 KIW  CAG  H11  single    0.930  0.020  1.080
 KIW  CAI  H12  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
 KIW  H1   OAA  CAP  110.09  3.000
 KIW  CAT  CAP  OAC  123.69  3.000
 KIW  CAT  CAP  OAA  112.94  3.000
 KIW  OAC  CAP  OAA  123.37  3.000
 KIW  CAM  CAT  CAJ  120.63  3.000
 KIW  CAM  CAT  CAP  121.82  3.000
 KIW  CAJ  CAT  CAP  117.54  3.000
 KIW  H2   CAJ  CAS  119.23  3.000
 KIW  H2   CAJ  CAT  119.66  3.000
 KIW  CAS  CAJ  CAT  121.11  3.000
 KIW  H3   CAM  CAU  120.70  3.000
 KIW  H3   CAM  CAT  120.70  3.000
 KIW  CAU  CAM  CAT  118.60  3.000
 KIW  CAK  CAU  CAQ  117.37  3.000
 KIW  CAQ  CAU  CAM  121.63  3.000
 KIW  CAK  CAU  CAM  120.99  3.000
 KIW  OAB  CAQ  OAD  123.24  3.000
 KIW  OAD  CAQ  CAU  113.04  3.000
 KIW  OAB  CAQ  CAU  123.72  3.000
 KIW  H4   OAD  CAQ  109.92  3.000
 KIW  H5   CAK  CAS  120.43  3.000
 KIW  H5   CAK  CAU  118.93  3.000
 KIW  CAS  CAK  CAU  120.64  3.000
 KIW  NAO  CAS  CAK  122.61  3.000
 KIW  CAK  CAS  CAJ  118.02  3.000
 KIW  NAO  CAS  CAJ  119.36  3.000
 KIW  H6   NAO  CAN  114.49  3.000
 KIW  H6   NAO  CAS  114.53  3.000
 KIW  CAN  NAO  CAS  121.37  3.000
 KIW  H8   CAN  H7   106.75  3.000
 KIW  H8   CAN  CAR  108.89  3.000
 KIW  H7   CAN  CAR  109.83  3.000
 KIW  H8   CAN  NAO  109.13  3.000
 KIW  H7   CAN  NAO  112.33  3.000
 KIW  CAR  CAN  NAO  109.82  3.000
 KIW  CAH  CAR  CAL  119.23  3.000
 KIW  CAH  CAR  CAN  120.34  3.000
 KIW  CAL  CAR  CAN  120.43  3.000
 KIW  H9   CAL  CAV  121.00  3.000
 KIW  H9   CAL  CAR  119.70  3.000
 KIW  CAV  CAL  CAR  119.29  3.000
 KIW  H10  CAH  CAG  119.64  3.000
 KIW  H10  CAH  CAR  119.61  3.000
 KIW  CAG  CAH  CAR  120.76  3.000
 KIW  H11  CAG  CAI  119.45  3.000
 KIW  H11  CAG  CAH  120.13  3.000
 KIW  CAI  CAG  CAH  120.41  3.000
 KIW  H12  CAI  CAV  121.49  3.000
 KIW  H12  CAI  CAG  120.16  3.000
 KIW  CAV  CAI  CAG  118.35  3.000
 KIW  NAW  CAV  CAI  119.12  3.000
 KIW  CAI  CAV  CAL  121.95  3.000
 KIW  NAW  CAV  CAL  118.92  3.000
 KIW  OAE  NAW  OAF  123.86  3.000
 KIW  OAE  NAW  CAV  118.06  3.000
 KIW  OAF  NAW  CAV  118.08  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
 KIW  CONST_01  CAK  CAS  CAJ  CAT     0.00   0.0  0
 KIW  CONST_02  CAK  CAU  CAM  CAT     0.00   0.0  0
 KIW  CONST_03  CAU  CAK  CAS  CAJ     0.00   0.0  0
 KIW  CONST_04  CAU  CAM  CAT  CAJ     0.00   0.0  0
 KIW  CONST_05  CAS  CAJ  CAT  CAM     0.00   0.0  0
 KIW  CONST_06  CAS  CAK  CAU  CAM     0.00   0.0  0
 KIW  CONST_07  CAI  CAV  CAL  CAR     0.00   0.0  0
 KIW  CONST_08  CAI  CAG  CAH  CAR     0.00   0.0  0
 KIW  CONST_09  CAG  CAH  CAR  CAL     0.00   0.0  0
 KIW  CONST_10  CAG  CAI  CAV  CAL     0.00   0.0  0
 KIW  CONST_11  CAV  CAL  CAR  CAH     0.00   0.0  0
 KIW  CONST_12  CAV  CAI  CAG  CAH     0.00   0.0  0
 KIW  CONST_13  CAS  CAJ  CAT  CAP   180.00   0.0  0
 KIW  CONST_14  CAU  CAM  CAT  CAP   180.00   0.0  0
 KIW  CONST_15  NAO  CAS  CAJ  CAT   180.00   0.0  0
 KIW  CONST_16  CAQ  CAU  CAM  CAT   180.00   0.0  0
 KIW  CONST_17  NAO  CAS  CAK  CAU   180.00   0.0  0
 KIW  CONST_18  CAS  CAK  CAU  CAQ   180.00   0.0  0
 KIW  CONST_19  CAV  CAL  CAR  CAN   180.00   0.0  0
 KIW  CONST_20  CAG  CAH  CAR  CAN   180.00   0.0  0
 KIW  CONST_21  NAW  CAV  CAL  CAR   180.00   0.0  0
 KIW  CONST_22  NAW  CAV  CAI  CAG   180.00   0.0  0
 KIW  CONST_23  H5   CAK  CAS  CAJ   180.00   0.0  0
 KIW  CONST_24  H3   CAM  CAT  CAJ   180.00   0.0  0
 KIW  CONST_25  H2   CAJ  CAT  CAM   180.00   0.0  0
 KIW  CONST_26  H11  CAG  CAH  CAR   180.00   0.0  0
 KIW  CONST_27  H10  CAH  CAR  CAL   180.00   0.0  0
 KIW  CONST_28  H12  CAI  CAV  CAL   180.00   0.0  0
 KIW  CONST_29  H9   CAL  CAR  CAH   180.00   0.0  0
 KIW  CONST_30  CAN  NAO  CAS  CAJ   180.00   0.0  0
 KIW  CONST_31  CAN  NAO  CAS  CAK     0.00   0.0  0
 KIW  CONST_32  OAF  NAW  CAV  CAL     0.00   0.0  0
 KIW  CONST_33  OAE  NAW  CAV  CAL   180.00   0.0  0
 KIW  CONST_34  OAF  NAW  CAV  CAI   180.00   0.0  0
 KIW  CONST_35  OAE  NAW  CAV  CAI     0.00   0.0  0
 KIW  CONST_37  H1   OAA  CAP  CAT   180.00   0.0  0
 KIW  CONST_38  H4   OAD  CAQ  CAU   180.00   0.0  0
 KIW  Var_01    CAJ  CAT  CAP  OAA  -179.88  30.0  2
 KIW  Var_02    OAB  CAQ  CAU  CAM   177.71  30.0  2
 KIW  Var_03    CAR  CAN  NAO  CAS   177.84  30.0  1
 KIW  Var_04    CAL  CAR  CAN  NAO   115.00  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
 KIW  plan-1  CAP  0.020
 KIW  plan-1  CAT  0.020
 KIW  plan-1  CAJ  0.020
 KIW  plan-1  CAM  0.020
 KIW  plan-1  CAU  0.020
 KIW  plan-1  CAQ  0.020
 KIW  plan-1  CAK  0.020
 KIW  plan-1  CAS  0.020
 KIW  plan-1  NAO  0.020
 KIW  plan-1  H2   0.020
 KIW  plan-1  H3   0.020
 KIW  plan-1  H5   0.020
 KIW  plan-2  CAN  0.020
 KIW  plan-2  CAR  0.020
 KIW  plan-2  CAL  0.020
 KIW  plan-2  CAH  0.020
 KIW  plan-2  CAG  0.020
 KIW  plan-2  CAI  0.020
 KIW  plan-2  CAV  0.020
 KIW  plan-2  NAW  0.020
 KIW  plan-2  H9   0.020
 KIW  plan-2  H10  0.020
 KIW  plan-2  H11  0.020
 KIW  plan-2  H12  0.020
 KIW  plan-3  CAS  0.020
 KIW  plan-3  NAO  0.020
 KIW  plan-3  CAN  0.020
 KIW  plan-3  H6   0.020
 KIW  plan-4  CAV  0.020
 KIW  plan-4  NAW  0.020
 KIW  plan-4  OAF  0.020
 KIW  plan-4  OAE  0.020
 KIW  plan-5  OAA  0.020
 KIW  plan-5  CAP  0.020
 KIW  plan-5  OAC  0.020
 KIW  plan-5  CAT  0.020
 KIW  plan-5  H1   0.020
 KIW  plan-6  CAU  0.020
 KIW  plan-6  CAQ  0.020
 KIW  plan-6  OAD  0.020
 KIW  plan-6  OAB  0.020
 KIW  plan-6  H4   0.020

