# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:21:44 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-chloro-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)c3ccccc3Cl)[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
 NP7  NP7  2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide  ligand  45  26  .  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_NP7
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
 NP7  CAA   C   CH3    0  -0.518  -3.5266   4.5464   0.1533
 NP7  OAB   O   O      0  -0.435   2.2256  -1.0554  -0.6137
 NP7  OAC   O   O      0  -0.383  -1.6615  -5.7124   0.1534
 NP7  OAD   O   O     -1  -0.383   0.3424  -5.1080  -0.2555
 NP7  CAF   C   CR16   0  -0.260   3.4078   3.7916  -0.0420
 NP7  CAG   C   CR16   0  -0.229   2.2655   3.5910  -0.8023
 NP7  CAH   C   CR16   0  -0.196   3.9609   2.7431   0.6788
 NP7  CAI   C   CR16   0  -0.289   1.6768   2.3369  -0.8351
 NP7  CAJ   C   CR16   0  -0.281  -2.5567  -3.1671   0.2672
 NP7  CAK   C   CR16   0  -0.312  -2.9247  -1.8351   0.3324
 NP7  CAL   C   CR16   0  -0.363  -0.2408  -2.4904  -0.0091
 NP7  CAM   C   CH2    0  -0.278  -3.4838   2.4150   1.2464
 NP7  CAN   C   CH2    0  -0.280  -2.3065   2.7243  -0.8062
 NP7  CAO   C   CH2    0  -0.315  -3.4896   0.9131   1.0331
 NP7  CAP   C   CH2    0  -0.339  -2.2919   1.2255  -1.0269
 NP7  CAR   C   C      0   0.504   1.5973  -0.0870  -0.2367
 NP7  CAS   C   CR6    0  -0.085   3.3705   1.4902   0.6280
 NP7  CAT   C   CR6    0   0.269  -1.2201  -3.4719   0.0798
 NP7  CAU   C   CR6    0   0.347  -0.6176  -1.1602   0.0750
 NP7  CAV   C   CR6    0   0.021   2.2200   1.2697  -0.1242
 NP7  CAW   C   CR6    0   0.291  -1.9833  -0.8188   0.2160
 NP7  NAX   N   NT     0  -0.413  -3.4578   3.1142  -0.0217
 NP7  NAY   N   NT     0  -0.527  -2.3137   0.5379   0.2654
 NP7  HAA   H   HCH3   0   0.195  -2.6675   4.9585   0.7045
 NP7  HAAA  H   HCH3   0   0.234  -3.5675   5.0403  -0.8187
 NP7  HAAB  H   HCH3   0   0.235  -4.4325   4.8126   0.6998
 NP7  HAF   H   HCR6   0   0.277   3.8747   4.7664  -0.0028
 NP7  HAG   H   HCR6   0   0.274   1.8336   4.4034  -1.3701
 NP7  HAH   H   HCR6   0   0.288   4.8473   2.8989   1.2781
 NP7  HAI   H   HCR6   0   0.278   0.7970   2.1772  -1.4466
 NP7  HAJ   H   HCR6   0   0.297  -3.3099  -3.9374   0.3381
 NP7  HAK   H   HCR6   0   0.286  -3.9703  -1.5883   0.4550
 NP7  HAL   H   HCR6   0   0.313   0.7966  -2.7596  -0.1146
 NP7  HAM   H   HCH2   0   0.244  -4.3899   2.6952   1.7881
 NP7  HAMA  H   HCH2   0   0.197  -2.6257   2.6834   1.8866
 NP7  HAN   H   HCH2   0   0.188  -1.3584   3.0293  -0.3259
 NP7  HANA  H   HCH2   0   0.248  -2.3476   3.2239  -1.7768
 NP7  HAO   H   HCH2   0   0.261  -3.4619   0.4093   2.0000
 NP7  HAOA  H   HCH2   0   0.223  -4.4205   0.6225   0.5268
 NP7  HAP   H   HCH2   0   0.245  -3.1584   0.9278  -1.6326
 NP7  HAPA  H   HCH2   0   0.263  -1.3991   0.9415  -1.5849
 NP7  HNAQ  H   HNH1   0   0.418  -0.1175   0.7609   0.4567
 NP7  NAZ   N   N      1   0.326  -0.8172  -4.8624  -0.0138
 NP7  NAQ   N   NH1    0  -0.729   0.2831  -0.0967   0.0942
 NP7  CLAE  CL  CL     0  -0.112   4.0658   0.2132   1.5651

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
 NP7  CAA   NAX   single    1.445  0.020  1.445
 NP7  CAA   HAA   single    0.970  0.020  1.090
 NP7  CAA   HAAA  single    0.970  0.020  1.090
 NP7  CAA   HAAB  single    0.970  0.020  1.090
 NP7  OAB   CAR   double    1.214  0.020  1.214
 NP7  OAC   NAZ   double    1.210  0.020  1.210
 NP7  OAD   NAZ   single    1.210  0.020  1.210
 NP7  CLAE  CAS   single    1.730  0.020  1.730
 NP7  CAF   CAG   aromatic  1.387  0.020  1.387
 NP7  CAF   CAH   aromatic  1.387  0.020  1.387
 NP7  CAF   HAF   single    0.930  0.020  1.080
 NP7  CAG   CAI   aromatic  1.386  0.020  1.386
 NP7  CAG   HAG   single    0.930  0.020  1.080
 NP7  CAH   CAS   aromatic  1.386  0.020  1.386
 NP7  CAH   HAH   single    0.930  0.020  1.080
 NP7  CAI   CAV   aromatic  1.393  0.020  1.393
 NP7  CAI   HAI   single    0.930  0.020  1.080
 NP7  CAJ   CAK   aromatic  1.383  0.020  1.383
 NP7  CAJ   CAT   aromatic  1.384  0.020  1.384
 NP7  CAJ   HAJ   single    0.930  0.020  1.080
 NP7  CAK   CAW   aromatic  1.390  0.020  1.390
 NP7  CAK   HAK   single    0.930  0.020  1.080
 NP7  CAL   CAT   aromatic  1.389  0.020  1.389
 NP7  CAL   CAU   aromatic  1.385  0.020  1.385
 NP7  CAL   HAL   single    0.930  0.020  1.080
 NP7  CAM   CAO   single    1.517  0.020  1.517
 NP7  CAM   NAX   single    1.448  0.020  1.448
 NP7  CAM   HAM   single    0.970  0.020  1.090
 NP7  CAM   HAMA  single    0.970  0.020  1.090
 NP7  CAN   CAP   single    1.515  0.020  1.515
 NP7  CAN   NAX   single    1.447  0.020  1.447
 NP7  CAN   HAN   single    0.970  0.020  1.090
 NP7  CAN   HANA  single    0.970  0.020  1.090
 NP7  CAO   NAY   single    1.454  0.020  1.454
 NP7  CAO   HAO   single    0.970  0.020  1.090
 NP7  CAO   HAOA  single    0.970  0.020  1.090
 NP7  CAP   NAY   single    1.464  0.020  1.464
 NP7  CAP   HAP   single    0.970  0.020  1.090
 NP7  CAP   HAPA  single    0.970  0.020  1.090
 NP7  NAQ   CAR   single    1.355  0.020  1.355
 NP7  NAQ   CAU   single    1.394  0.020  1.394
 NP7  NAQ   HNAQ  single    0.860  0.020  1.020
 NP7  CAR   CAV   single    1.497  0.020  1.497
 NP7  CAS   CAV   aromatic  1.392  0.020  1.392
 NP7  CAT   NAZ   single    1.451  0.020  1.451
 NP7  CAU   CAW   aromatic  1.415  0.020  1.415
 NP7  CAW   NAY   single    1.397  0.020  1.397

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
 NP7  HAAB  CAA  HAAA  107.74  3.000
 NP7  HAAB  CAA  HAA   107.80  3.000
 NP7  HAAA  CAA  HAA   107.81  3.000
 NP7  HAAB  CAA  NAX   110.01  3.000
 NP7  HAAA  CAA  NAX   110.04  3.000
 NP7  HAA   CAA  NAX   113.25  3.000
 NP7  HAF   CAF  CAH   119.36  3.000
 NP7  HAF   CAF  CAG   120.39  3.000
 NP7  CAH   CAF  CAG   120.26  3.000
 NP7  HAG   CAG  CAI   119.86  3.000
 NP7  HAG   CAG  CAF   120.55  3.000
 NP7  CAI   CAG  CAF   119.59  3.000
 NP7  HAH   CAH  CAS   119.98  3.000
 NP7  HAH   CAH  CAF   120.39  3.000
 NP7  CAS   CAH  CAF   119.63  3.000
 NP7  HAI   CAI  CAV   119.47  3.000
 NP7  HAI   CAI  CAG   119.46  3.000
 NP7  CAV   CAI  CAG   121.04  3.000
 NP7  HAJ   CAJ  CAT   121.71  3.000
 NP7  HAJ   CAJ  CAK   119.89  3.000
 NP7  CAT   CAJ  CAK   118.38  3.000
 NP7  HAK   CAK  CAW   119.83  3.000
 NP7  HAK   CAK  CAJ   118.83  3.000
 NP7  CAW   CAK  CAJ   121.32  3.000
 NP7  HAL   CAL  CAU   120.53  3.000
 NP7  HAL   CAL  CAT   120.57  3.000
 NP7  CAU   CAL  CAT   118.87  3.000
 NP7  HAMA  CAM  HAM   107.16  3.000
 NP7  HAMA  CAM  NAX   112.12  3.000
 NP7  HAM   CAM  NAX   108.98  3.000
 NP7  HAMA  CAM  CAO   108.98  3.000
 NP7  HAM   CAM  CAO   108.70  3.000
 NP7  NAX   CAM  CAO   110.79  3.000
 NP7  HANA  CAN  HAN   106.99  3.000
 NP7  HANA  CAN  NAX   109.18  3.000
 NP7  HAN   CAN  NAX   111.86  3.000
 NP7  HANA  CAN  CAP   108.87  3.000
 NP7  HAN   CAN  CAP   109.14  3.000
 NP7  NAX   CAN  CAP   110.68  3.000
 NP7  HAOA  CAO  HAO   107.93  3.000
 NP7  HAOA  CAO  NAY   111.94  3.000
 NP7  HAO   CAO  NAY   109.18  3.000
 NP7  HAOA  CAO  CAM   109.26  3.000
 NP7  HAO   CAO  CAM   109.43  3.000
 NP7  NAY   CAO  CAM   109.07  3.000
 NP7  HAPA  CAP  HAP   107.04  3.000
 NP7  HAPA  CAP  NAY   109.97  3.000
 NP7  HAP   CAP  NAY   110.35  3.000
 NP7  HAPA  CAP  CAN   109.88  3.000
 NP7  HAP   CAP  CAN   109.93  3.000
 NP7  NAY   CAP  CAN   109.63  3.000
 NP7  CAV   CAR  NAQ   113.05  3.000
 NP7  CAV   CAR  OAB   122.06  3.000
 NP7  NAQ   CAR  OAB   124.88  3.000
 NP7  CAV   CAS  CAH   121.00  3.000
 NP7  CAV   CAS  CLAE  120.53  3.000
 NP7  CAH   CAS  CLAE  118.44  3.000
 NP7  NAZ   CAT  CAL   118.51  3.000
 NP7  NAZ   CAT  CAJ   119.22  3.000
 NP7  CAL   CAT  CAJ   122.27  3.000
 NP7  CAW   CAU  NAQ   116.00  3.000
 NP7  CAW   CAU  CAL   120.02  3.000
 NP7  NAQ   CAU  CAL   123.90  3.000
 NP7  CAS   CAV  CAR   121.86  3.000
 NP7  CAS   CAV  CAI   118.48  3.000
 NP7  CAR   CAV  CAI   119.59  3.000
 NP7  NAY   CAW  CAU   117.78  3.000
 NP7  NAY   CAW  CAK   123.14  3.000
 NP7  CAU   CAW  CAK   119.05  3.000
 NP7  CAN   NAX  CAM   111.04  3.000
 NP7  CAN   NAX  CAA   111.76  3.000
 NP7  CAM   NAX  CAA   111.82  3.000
 NP7  CAW   NAY  CAP   114.92  3.000
 NP7  CAW   NAY  CAO   117.42  3.000
 NP7  CAP   NAY  CAO   110.92  3.000
 NP7  CAT   NAZ  OAD   118.27  3.000
 NP7  CAT   NAZ  OAC   118.09  3.000
 NP7  OAD   NAZ  OAC   123.64  3.000
 NP7  HNAQ  NAQ  CAU   113.27  3.000
 NP7  HNAQ  NAQ  CAR   117.68  3.000
 NP7  CAU   NAQ  CAR   128.96  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
 NP7  CONST_01  CAV  CAI  CAG  CAF     0.00   0.0  0
 NP7  CONST_02  CAV  CAS  CAH  CAF     0.00   0.0  0
 NP7  CONST_03  CAS  CAH  CAF  CAG     0.00   0.0  0
 NP7  CONST_04  CAS  CAV  CAI  CAG     0.00   0.0  0
 NP7  CONST_05  CAI  CAG  CAF  CAH     0.00   0.0  0
 NP7  CONST_06  CAI  CAV  CAS  CAH     0.00   0.0  0
 NP7  CONST_07  CAU  CAW  CAK  CAJ     0.00   0.0  0
 NP7  CONST_08  CAU  CAL  CAT  CAJ     0.00   0.0  0
 NP7  CONST_09  CAL  CAT  CAJ  CAK     0.00   0.0  0
 NP7  CONST_10  CAL  CAU  CAW  CAK     0.00   0.0  0
 NP7  CONST_11  CAW  CAK  CAJ  CAT     0.00   0.0  0
 NP7  CONST_12  CAW  CAU  CAL  CAT     0.00   0.0  0
 NP7  CONST_13  NAY  CAW  CAK  CAJ   180.00   0.0  0
 NP7  CONST_14  NAY  CAW  CAU  CAL   180.00   0.0  0
 NP7  CONST_15  CAF  CAH  CAS  CLAE  180.00   0.0  0
 NP7  CONST_16  CAI  CAV  CAS  CLAE  180.00   0.0  0
 NP7  CONST_17  CAR  CAV  CAI  CAG   180.00   0.0  0
 NP7  CONST_18  CAR  CAV  CAS  CAH   180.00   0.0  0
 NP7  CONST_19  NAZ  CAT  CAJ  CAK   180.00   0.0  0
 NP7  CONST_20  NAQ  CAU  CAW  CAK   180.00   0.0  0
 NP7  CONST_21  CAT  CAL  CAU  NAQ   180.00   0.0  0
 NP7  CONST_22  NAY  CAW  CAU  NAQ     0.00   0.0  0
 NP7  CONST_23  NAZ  CAT  CAL  CAU   180.00   0.0  0
 NP7  CONST_24  HAI  CAI  CAG  CAF   180.00   0.0  0
 NP7  CONST_25  HAH  CAH  CAF  CAG   180.00   0.0  0
 NP7  CONST_26  HAG  CAG  CAF  CAH   180.00   0.0  0
 NP7  CONST_27  HAF  CAF  CAG  CAI   180.00   0.0  0
 NP7  CONST_28  HAL  CAL  CAT  CAJ   180.00   0.0  0
 NP7  CONST_29  HAJ  CAJ  CAT  CAL   180.00   0.0  0
 NP7  CONST_30  HAK  CAK  CAJ  CAT   180.00   0.0  0
 NP7  CONST_31  CAV  CAR  NAQ  CAU   180.00   0.0  0
 NP7  CONST_32  CAJ  CAT  NAZ  OAC     0.00   0.0  0
 NP7  CONST_33  CAL  CAT  NAZ  OAC   180.00   0.0  0
 NP7  CONST_34  CAJ  CAT  NAZ  OAD   180.00   0.0  0
 NP7  CONST_35  CAL  CAT  NAZ  OAD     0.00   0.0  0
 NP7  CONST_37  CAW  CAU  NAQ  CAR   180.00   0.0  0
 NP7  CONST_39  CAU  NAQ  CAR  OAB     0.00   0.0  0
 NP7  Var_01    CAO  NAY  CAW  CAK    28.17  30.0  2
 NP7  Var_02    CAP  CAN  NAX  CAM    56.91  30.0  1
 NP7  Var_03    CAO  CAM  NAX  CAN   -57.61  30.0  1
 NP7  Var_04    NAY  CAO  CAM  NAX    57.99  30.0  1
 NP7  Var_05    NAY  CAP  CAN  NAX   -56.79  30.0  1
 NP7  Var_06    CAI  CAV  CAR  OAB   122.16  30.0  2
 NP7  Var_07    HAA  CAA  NAX  CAM    62.76  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
 NP7  plan-1  CAF   0.020
 NP7  plan-1  CAG   0.020
 NP7  plan-1  CAH   0.020
 NP7  plan-1  CAI   0.020
 NP7  plan-1  CAR   0.020
 NP7  plan-1  CAS   0.020
 NP7  plan-1  CAV   0.020
 NP7  plan-1  HAF   0.020
 NP7  plan-1  HAG   0.020
 NP7  plan-1  HAH   0.020
 NP7  plan-1  HAI   0.020
 NP7  plan-1  CLAE  0.020
 NP7  plan-2  CAJ   0.020
 NP7  plan-2  CAK   0.020
 NP7  plan-2  CAL   0.020
 NP7  plan-2  CAT   0.020
 NP7  plan-2  CAU   0.020
 NP7  plan-2  CAW   0.020
 NP7  plan-2  NAY   0.020
 NP7  plan-2  HAJ   0.020
 NP7  plan-2  HAK   0.020
 NP7  plan-2  HAL   0.020
 NP7  plan-2  NAZ   0.020
 NP7  plan-2  NAQ   0.020
 NP7  plan-3  OAB   0.020
 NP7  plan-3  CAR   0.020
 NP7  plan-3  CAU   0.020
 NP7  plan-3  CAV   0.020
 NP7  plan-3  HNAQ  0.020
 NP7  plan-3  NAQ   0.020
 NP7  plan-4  OAC   0.020
 NP7  plan-4  OAD   0.020
 NP7  plan-4  CAT   0.020
 NP7  plan-4  NAZ   0.020

