# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:22:12 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2NC(=O)c3ccc(F)c(C)c3Cl)[N](=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
 IA9  IA9  2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide  ligand  48  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IA9
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
 IA9  CLG  CL  CL     0  -0.097  -3.4199   1.2026  -0.9627
 IA9  CAX  C   CR6    0  -0.129  -3.1180  -0.2168  -0.0226
 IA9  CAS  C   CR6    0  -0.017  -4.0980  -1.2083   0.0019
 IA9  CAA  C   CH3    0  -0.720  -5.3943  -1.0630  -0.7334
 IA9  CAT  C   CR6    0   0.528  -3.7926  -2.3403   0.7477
 IA9  FAF  F   F      0  -0.305  -4.6994  -3.3232   0.8130
 IA9  CAH  C   CR16   0  -0.388  -2.6029  -2.5136   1.4250
 IA9  CAJ  C   CR16   0  -0.291  -1.6556  -1.5078   1.3626
 IA9  CAW  C   CR6    0   0.017  -1.9029  -0.3448   0.6424
 IA9  CAR  C   C      0   0.499  -0.8930   0.7612   0.6493
 IA9  OAC  O   O      0  -0.436  -1.1421   1.8597   1.1034
 IA9  NAQ  N   NH1    0  -0.723   0.3011   0.3896   0.1316
 IA9  CAV  C   CR6    0   0.345   1.4700   1.1374  -0.0016
 IA9  CAL  C   CR16   0  -0.361   1.5133   2.5191   0.0742
 IA9  CAU  C   CR6    0   0.268   2.7159   3.1664  -0.1811
 IA9  NBB  N   N      1   0.326   2.7555   4.6139  -0.0954
 IA9  OAE  O   O      0  -0.383   1.7511   5.1953   0.2461
 IA9  OAD  O   O     -1  -0.383   3.7931   5.1725  -0.3683
 IA9  CAI  C   CR16   0  -0.280   3.8646   2.4784  -0.5298
 IA9  CAK  C   CR16   0  -0.314   3.8142   1.0968  -0.5852
 IA9  CAY  C   CR6    0   0.294   2.6423   0.4047  -0.3005
 IA9  NBA  N   NT     0  -0.525   2.5489  -0.9886  -0.3284
 IA9  CAO  C   CH2    0  -0.315   3.4608  -1.7070  -1.2036
 IA9  CAM  C   CH2    0  -0.280   2.9887  -3.1424  -1.3428
 IA9  NAZ  N   NT     0  -0.413   2.9201  -3.7869  -0.0479
 IA9  CAB  C   CH3    0  -0.518   2.5580  -5.1814  -0.1547
 IA9  CAN  C   CH2    0  -0.281   2.0289  -3.0663   0.8347
 IA9  CAP  C   CH2    0  -0.338   2.4770  -1.6273   0.9872
 IA9  H1   H   HCH3   0   0.262  -5.2226  -0.9495  -1.8042
 IA9  H2   H   HCH3   0   0.263  -6.0416  -1.9230  -0.5908
 IA9  H3   H   HCH3   0   0.262  -5.9348  -0.1786  -0.3954
 IA9  H4   H   HCR6   0   0.293  -2.4226  -3.4160   1.9934
 IA9  H5   H   HCR6   0   0.285  -0.7250  -1.6234   1.9038
 IA9  H6   H   HNH1   0   0.419   0.3735  -0.5389  -0.2683
 IA9  H7   H   HCR6   0   0.312   0.6234   3.0826   0.2991
 IA9  H8   H   HCR6   0   0.297   4.7919   2.9912  -0.7375
 IA9  H9   H   HCR6   0   0.286   4.7138   0.5525  -0.8354
 IA9  H10  H   HCH2   0   0.261   3.4681  -1.2311  -2.1850
 IA9  H11  H   HCH2   0   0.223   4.4895  -1.7014  -0.8176
 IA9  H12  H   HCH2   0   0.198   2.0152  -3.1506  -1.8635
 IA9  H13  H   HCH2   0   0.245   3.6964  -3.6836  -1.9750
 IA9  H15  H   HCH3   0   0.235   3.2673  -5.7017  -0.7997
 IA9  H16  H   HCH3   0   0.235   2.5930  -5.6526   0.8288
 IA9  H17  H   HCH3   0   0.195   1.5493  -5.3402  -0.5664
 IA9  H18  H   HCH2   0   0.189   0.9857  -3.0857   0.4683
 IA9  H19  H   HCH2   0   0.248   2.0314  -3.5417   1.8180
 IA9  H20  H   HCH2   0   0.244   3.4567  -1.5937   1.4832
 IA9  H21  H   HCH2   0   0.263   1.7772  -1.0911   1.6294

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
 IA9  OAE  NBB  double    1.210  0.020  1.210
 IA9  OAD  NBB  single    1.210  0.020  1.210
 IA9  NBB  CAU  single    1.451  0.020  1.451
 IA9  OAC  CAR  double    1.214  0.020  1.214
 IA9  CAU  CAL  aromatic  1.389  0.020  1.389
 IA9  CAU  CAI  aromatic  1.384  0.020  1.384
 IA9  CAL  CAV  aromatic  1.385  0.020  1.385
 IA9  CAJ  CAH  aromatic  1.383  0.020  1.383
 IA9  CAJ  CAW  aromatic  1.390  0.020  1.390
 IA9  CAR  CAW  single    1.498  0.020  1.498
 IA9  CAR  NAQ  single    1.354  0.020  1.354
 IA9  CAH  CAT  aromatic  1.380  0.020  1.380
 IA9  CAW  CAX  aromatic  1.391  0.020  1.391
 IA9  CAT  FAF  single    1.339  0.020  1.339
 IA9  CAT  CAS  aromatic  1.390  0.020  1.390
 IA9  CAX  CAS  aromatic  1.394  0.020  1.394
 IA9  CAX  CLG  single    1.729  0.020  1.729
 IA9  CAI  CAK  aromatic  1.384  0.020  1.384
 IA9  CAS  CAA  single    1.497  0.020  1.497
 IA9  CAV  NAQ  single    1.394  0.020  1.394
 IA9  CAV  CAY  aromatic  1.414  0.020  1.414
 IA9  CAK  CAY  aromatic  1.390  0.020  1.390
 IA9  CAY  NBA  single    1.397  0.020  1.397
 IA9  NBA  CAO  single    1.454  0.020  1.454
 IA9  NBA  CAP  single    1.464  0.020  1.464
 IA9  CAO  CAM  single    1.517  0.020  1.517
 IA9  CAM  NAZ  single    1.448  0.020  1.448
 IA9  CAP  CAN  single    1.515  0.020  1.515
 IA9  NAZ  CAN  single    1.447  0.020  1.447
 IA9  NAZ  CAB  single    1.445  0.020  1.445
 IA9  CAA  H1   single    0.970  0.020  1.090
 IA9  CAA  H2   single    0.970  0.020  1.090
 IA9  CAA  H3   single    0.970  0.020  1.090
 IA9  CAH  H4   single    0.930  0.020  1.080
 IA9  CAJ  H5   single    0.930  0.020  1.080
 IA9  NAQ  H6   single    0.860  0.020  1.020
 IA9  CAL  H7   single    0.930  0.020  1.080
 IA9  CAI  H8   single    0.930  0.020  1.080
 IA9  CAK  H9   single    0.930  0.020  1.080
 IA9  CAO  H10  single    0.970  0.020  1.090
 IA9  CAO  H11  single    0.970  0.020  1.090
 IA9  CAM  H12  single    0.970  0.020  1.090
 IA9  CAM  H13  single    0.970  0.020  1.090
 IA9  CAB  H15  single    0.970  0.020  1.090
 IA9  CAB  H16  single    0.970  0.020  1.090
 IA9  CAB  H17  single    0.970  0.020  1.090
 IA9  CAN  H18  single    0.970  0.020  1.090
 IA9  CAN  H19  single    0.970  0.020  1.090
 IA9  CAP  H20  single    0.970  0.020  1.090
 IA9  CAP  H21  single    0.970  0.020  1.090

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
 IA9  CAW  CAX  CAS  122.69  3.000
 IA9  CAS  CAX  CLG  118.07  3.000
 IA9  CAW  CAX  CLG  119.21  3.000
 IA9  CAT  CAS  CAA  122.20  3.000
 IA9  CAA  CAS  CAX  122.07  3.000
 IA9  CAT  CAS  CAX  115.74  3.000
 IA9  H3   CAA  H2   107.83  3.000
 IA9  H3   CAA  H1   107.34  3.000
 IA9  H2   CAA  H1   107.77  3.000
 IA9  H3   CAA  CAS  110.84  3.000
 IA9  H2   CAA  CAS  112.01  3.000
 IA9  H1   CAA  CAS  110.86  3.000
 IA9  CAH  CAT  FAF  117.89  3.000
 IA9  FAF  CAT  CAS  118.38  3.000
 IA9  CAH  CAT  CAS  123.73  3.000
 IA9  H4   CAH  CAJ  121.08  3.000
 IA9  H4   CAH  CAT  120.43  3.000
 IA9  CAJ  CAH  CAT  118.49  3.000
 IA9  H5   CAJ  CAW  120.07  3.000
 IA9  H5   CAJ  CAH  119.24  3.000
 IA9  CAW  CAJ  CAH  120.66  3.000
 IA9  CAR  CAW  CAJ  119.71  3.000
 IA9  CAR  CAW  CAX  121.54  3.000
 IA9  CAJ  CAW  CAX  118.69  3.000
 IA9  NAQ  CAR  OAC  124.91  3.000
 IA9  NAQ  CAR  CAW  112.98  3.000
 IA9  OAC  CAR  CAW  122.10  3.000
 IA9  H6   NAQ  CAV  113.19  3.000
 IA9  H6   NAQ  CAR  117.74  3.000
 IA9  CAV  NAQ  CAR  128.98  3.000
 IA9  CAY  CAV  CAL  120.17  3.000
 IA9  CAY  CAV  NAQ  115.94  3.000
 IA9  CAL  CAV  NAQ  123.81  3.000
 IA9  H7   CAL  CAU  120.65  3.000
 IA9  H7   CAL  CAV  120.51  3.000
 IA9  CAU  CAL  CAV  118.82  3.000
 IA9  CAI  CAU  NBB  119.24  3.000
 IA9  CAI  CAU  CAL  122.22  3.000
 IA9  NBB  CAU  CAL  118.53  3.000
 IA9  OAD  NBB  OAE  123.63  3.000
 IA9  OAD  NBB  CAU  118.09  3.000
 IA9  OAE  NBB  CAU  118.27  3.000
 IA9  H8   CAI  CAK  119.86  3.000
 IA9  H8   CAI  CAU  121.68  3.000
 IA9  CAK  CAI  CAU  118.45  3.000
 IA9  H9   CAK  CAY  119.88  3.000
 IA9  H9   CAK  CAI  118.80  3.000
 IA9  CAY  CAK  CAI  121.30  3.000
 IA9  NBA  CAY  CAK  123.29  3.000
 IA9  NBA  CAY  CAV  117.74  3.000
 IA9  CAK  CAY  CAV  118.95  3.000
 IA9  CAP  NBA  CAO  110.86  3.000
 IA9  CAP  NBA  CAY  114.87  3.000
 IA9  CAO  NBA  CAY  117.58  3.000
 IA9  H11  CAO  H10  107.91  3.000
 IA9  H11  CAO  CAM  109.17  3.000
 IA9  H10  CAO  CAM  109.41  3.000
 IA9  H11  CAO  NBA  111.92  3.000
 IA9  H10  CAO  NBA  109.28  3.000
 IA9  CAM  CAO  NBA  109.12  3.000
 IA9  H13  CAM  H12  107.14  3.000
 IA9  H13  CAM  NAZ  109.13  3.000
 IA9  H12  CAM  NAZ  112.13  3.000
 IA9  H13  CAM  CAO  108.67  3.000
 IA9  H12  CAM  CAO  108.94  3.000
 IA9  NAZ  CAM  CAO  110.71  3.000
 IA9  CAN  NAZ  CAB  111.81  3.000
 IA9  CAB  NAZ  CAM  112.05  3.000
 IA9  CAN  NAZ  CAM  110.68  3.000
 IA9  H17  CAB  H16  107.71  3.000
 IA9  H17  CAB  H15  107.80  3.000
 IA9  H16  CAB  H15  107.83  3.000
 IA9  H17  CAB  NAZ  113.35  3.000
 IA9  H16  CAB  NAZ  110.01  3.000
 IA9  H15  CAB  NAZ  109.95  3.000
 IA9  H19  CAN  H18  107.02  3.000
 IA9  H19  CAN  CAP  108.79  3.000
 IA9  H18  CAN  CAP  109.22  3.000
 IA9  H19  CAN  NAZ  109.33  3.000
 IA9  H18  CAN  NAZ  111.73  3.000
 IA9  CAP  CAN  NAZ  110.64  3.000
 IA9  H21  CAP  H20  106.93  3.000
 IA9  H21  CAP  CAN  109.66  3.000
 IA9  H20  CAP  CAN  109.77  3.000
 IA9  H21  CAP  NBA  110.25  3.000
 IA9  H20  CAP  NBA  110.40  3.000
 IA9  CAN  CAP  NBA  109.78  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
 IA9  CONST_01  CAH  CAJ  CAW  CAX     0.00   0.0  0
 IA9  CONST_02  CAH  CAT  CAS  CAX     0.00   0.0  0
 IA9  CONST_03  CAJ  CAH  CAT  CAS     0.00   0.0  0
 IA9  CONST_04  CAJ  CAW  CAX  CAS     0.00   0.0  0
 IA9  CONST_05  CAW  CAJ  CAH  CAT     0.00   0.0  0
 IA9  CONST_06  CAW  CAX  CAS  CAT     0.00   0.0  0
 IA9  CONST_07  CAI  CAU  CAL  CAV     0.00   0.0  0
 IA9  CONST_08  CAI  CAK  CAY  CAV     0.00   0.0  0
 IA9  CONST_09  CAK  CAI  CAU  CAL     0.00   0.0  0
 IA9  CONST_10  CAK  CAY  CAV  CAL     0.00   0.0  0
 IA9  CONST_11  CAY  CAV  CAL  CAU     0.00   0.0  0
 IA9  CONST_12  CAY  CAK  CAI  CAU     0.00   0.0  0
 IA9  CONST_13  NBA  CAY  CAV  CAL   180.00   0.0  0
 IA9  CONST_14  NBA  CAY  CAK  CAI   180.00   0.0  0
 IA9  CONST_15  CAJ  CAW  CAX  CLG   180.00   0.0  0
 IA9  CONST_16  CAT  CAS  CAX  CLG   180.00   0.0  0
 IA9  CONST_17  FAF  CAT  CAS  CAX   180.00   0.0  0
 IA9  CONST_18  CAR  CAW  CAX  CAS   180.00   0.0  0
 IA9  CONST_19  CAH  CAT  CAS  CAA   180.00   0.0  0
 IA9  CONST_20  CAW  CAX  CAS  CAA   180.00   0.0  0
 IA9  CONST_21  CAJ  CAH  CAT  FAF   180.00   0.0  0
 IA9  CONST_22  CAR  CAW  CAJ  CAH   180.00   0.0  0
 IA9  CONST_23  CAU  CAL  CAV  NAQ   180.00   0.0  0
 IA9  CONST_24  CAK  CAY  CAV  NAQ   180.00   0.0  0
 IA9  CONST_25  NBA  CAY  CAV  NAQ     0.00   0.0  0
 IA9  CONST_26  NBB  CAU  CAL  CAV   180.00   0.0  0
 IA9  CONST_27  CAK  CAI  CAU  NBB   180.00   0.0  0
 IA9  CONST_28  H5   CAJ  CAW  CAX   180.00   0.0  0
 IA9  CONST_29  H4   CAH  CAT  CAS   180.00   0.0  0
 IA9  CONST_30  H9   CAK  CAY  CAV   180.00   0.0  0
 IA9  CONST_31  H8   CAI  CAU  CAL   180.00   0.0  0
 IA9  CONST_32  H7   CAL  CAU  CAI   180.00   0.0  0
 IA9  CONST_33  CAV  NAQ  CAR  CAW   180.00   0.0  0
 IA9  CONST_35  CAY  CAV  NAQ  CAR   180.00   0.0  0
 IA9  CONST_36  OAE  NBB  CAU  CAL     0.00   0.0  0
 IA9  CONST_37  OAD  NBB  CAU  CAL   180.00   0.0  0
 IA9  CONST_38  CAI  CAU  NBB  OAE   180.00   0.0  0
 IA9  CONST_39  CAI  CAU  NBB  OAD     0.00   0.0  0
 IA9  CONST_41  CAV  NAQ  CAR  OAC     0.00   0.0  0
 IA9  Var_01    CAO  NBA  CAY  CAV   151.22  30.0  2
 IA9  Var_02    CAM  CAO  NBA  CAY  -166.59  30.0  1
 IA9  Var_03    CAN  CAP  NBA  CAY   165.65  30.0  1
 IA9  Var_04    NAZ  CAM  CAO  NBA   -58.34  30.0  1
 IA9  Var_05    NAZ  CAN  CAP  NBA    56.94  30.0  1
 IA9  Var_06    CAN  NAZ  CAM  CAO    58.25  30.0  1
 IA9  Var_07    CAP  CAN  NAZ  CAM   -57.44  30.0  1
 IA9  Var_08    OAC  CAR  CAW  CAX    59.93  30.0  2
 IA9  Var_09    H1   CAA  CAS  CAX    60.42  30.0  2
 IA9  Var_10    H15  CAB  NAZ  CAM    56.93  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
 IA9  plan-1  CLG  0.020
 IA9  plan-1  CAX  0.020
 IA9  plan-1  CAS  0.020
 IA9  plan-1  CAA  0.020
 IA9  plan-1  CAT  0.020
 IA9  plan-1  FAF  0.020
 IA9  plan-1  CAH  0.020
 IA9  plan-1  CAJ  0.020
 IA9  plan-1  CAW  0.020
 IA9  plan-1  CAR  0.020
 IA9  plan-1  H4   0.020
 IA9  plan-1  H5   0.020
 IA9  plan-2  NAQ  0.020
 IA9  plan-2  CAV  0.020
 IA9  plan-2  CAL  0.020
 IA9  plan-2  CAU  0.020
 IA9  plan-2  NBB  0.020
 IA9  plan-2  CAI  0.020
 IA9  plan-2  CAK  0.020
 IA9  plan-2  CAY  0.020
 IA9  plan-2  NBA  0.020
 IA9  plan-2  H7   0.020
 IA9  plan-2  H8   0.020
 IA9  plan-2  H9   0.020
 IA9  plan-3  CAW  0.020
 IA9  plan-3  CAR  0.020
 IA9  plan-3  OAC  0.020
 IA9  plan-3  NAQ  0.020
 IA9  plan-3  CAV  0.020
 IA9  plan-3  H6   0.020
 IA9  plan-4  CAU  0.020
 IA9  plan-4  NBB  0.020
 IA9  plan-4  OAE  0.020
 IA9  plan-4  OAD  0.020

