# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:36:29 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-(2-nitrophenyl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNc1ccccc1[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
 NP2  NP2  N-(2-nitrophenyl)propane-1,3-diamine  ligand  27  14  .  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_NP2
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
 NP2  NZ    N  NH2    0  -0.799   5.4652   0.4363  -0.0418
 NP2  CA    C  CH2    0  -0.273   4.3460  -0.4935  -0.0444
 NP2  CB    C  CH2    0  -0.480   3.0252   0.2610  -0.0542
 NP2  CG    C  CH2    0  -0.262   1.8391  -0.6888  -0.0381
 NP2  NE    N  NH1    0  -0.678   0.6019   0.0595  -0.0593
 NP2  CD    C  CR6    0   0.405  -0.6191  -0.4920  -0.0160
 NP2  CE1   C  CR16   0  -0.376  -0.7472  -1.9034   0.0326
 NP2  CE2   C  CR6    0   0.181  -1.8428   0.2391  -0.0156
 NP2  NO2   N  N      1   0.346  -1.8728   1.6667  -0.0642
 NP2  OC1   O  O      0  -0.403  -2.9449   2.2351  -0.0621
 NP2  OC2   O  O     -1  -0.431  -0.8191   2.2832  -0.1082
 NP2  CR1   C  CR16   0  -0.221  -1.9703  -2.5219   0.0807
 NP2  CR2   C  CR16   0  -0.297  -3.0811  -0.4163   0.0343
 NP2  CZ    C  CR16   0  -0.287  -3.1589  -1.7836   0.0828
 NP2  HNZ1  H  HNH2   0   0.339   5.4905   0.9213   0.8471
 NP2  HNZ2  H  HNH2   0   0.348   6.3323  -0.0831  -0.0904
 NP2  HA1   H  HCH2   0   0.220   4.4121  -1.1083  -0.9460
 NP2  HA2   H  HCH2   0   0.195   4.3532  -1.1912   0.8053
 NP2  HB1   H  HCH2   0   0.234   2.9735   0.9197   0.8192
 NP2  HB2   H  HCH2   0   0.236   2.9798   0.8987  -0.9415
 NP2  HG1   H  HCH2   0   0.236   1.8936  -1.3586  -0.9027
 NP2  HG2   H  HCH2   0   0.236   1.8868  -1.3202   0.8554
 NP2  HNE   H  HNH1   0   0.412   0.6587   1.0634  -0.0812
 NP2  HE1   H  HCR6   0   0.289   0.1433  -2.5149   0.0324
 NP2  HR1   H  HCR6   0   0.273  -2.0069  -3.6026   0.1163
 NP2  HR2   H  HCR6   0   0.291  -3.9871   0.1712   0.0352
 NP2  HZ    H  HCR6   0   0.264  -4.1195  -2.2767   0.1220

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
 NP2  NZ   CA    single    1.455  0.020  1.455
 NP2  NZ   HNZ1  single    0.890  0.020  1.040
 NP2  NZ   HNZ2  single    0.890  0.020  1.040
 NP2  CA   CB    single    1.521  0.020  1.521
 NP2  CA   HA1   single    0.970  0.020  1.090
 NP2  CA   HA2   single    0.970  0.020  1.090
 NP2  CB   CG    single    1.520  0.020  1.520
 NP2  CB   HB1   single    0.970  0.020  1.090
 NP2  CB   HB2   single    0.970  0.020  1.090
 NP2  CG   NE    single    1.446  0.020  1.446
 NP2  CG   HG1   single    0.970  0.020  1.090
 NP2  CG   HG2   single    0.970  0.020  1.090
 NP2  NE   CD    single    1.341  0.020  1.341
 NP2  NE   HNE   single    0.860  0.020  1.020
 NP2  CD   CE1   aromatic  1.418  0.020  1.418
 NP2  CD   CE2   aromatic  1.425  0.020  1.425
 NP2  CE1  CR1   aromatic  1.371  0.020  1.371
 NP2  CE1  HE1   single    0.930  0.020  1.080
 NP2  CE2  NO2   single    1.429  0.020  1.429
 NP2  CE2  CR2   aromatic  1.402  0.020  1.402
 NP2  NO2  OC1   double    1.213  0.020  1.213
 NP2  NO2  OC2   single    1.222  0.020  1.222
 NP2  CR1  CZ    aromatic  1.399  0.020  1.399
 NP2  CR1  HR1   single    0.930  0.020  1.080
 NP2  CR2  CZ    aromatic  1.370  0.020  1.370
 NP2  CR2  HR2   single    0.930  0.020  1.080
 NP2  CZ   HZ    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
 NP2  HNZ2  NZ   HNZ1  105.46  3.000
 NP2  HNZ2  NZ   CA    109.33  3.000
 NP2  HNZ1  NZ   CA    109.07  3.000
 NP2  HA2   CA   HA1   106.26  3.000
 NP2  HA2   CA   CB    108.99  3.000
 NP2  HA1   CA   CB    109.03  3.000
 NP2  HA2   CA   NZ    113.52  3.000
 NP2  HA1   CA   NZ    108.32  3.000
 NP2  CB    CA   NZ    110.55  3.000
 NP2  HB2   CB   HB1   107.12  3.000
 NP2  HB2   CB   CG    109.92  3.000
 NP2  HB1   CB   CG    109.31  3.000
 NP2  HB2   CB   CA    109.30  3.000
 NP2  HB1   CB   CA    109.52  3.000
 NP2  CG    CB   CA    111.57  3.000
 NP2  HG2   CG   HG1   106.82  3.000
 NP2  HG2   CG   NE    110.34  3.000
 NP2  HG1   CG   NE    110.34  3.000
 NP2  HG2   CG   CB    109.57  3.000
 NP2  HG1   CG   CB    109.58  3.000
 NP2  NE    CG   CB    110.13  3.000
 NP2  HNE   NE   CD    117.57  3.000
 NP2  HNE   NE   CG    117.94  3.000
 NP2  CD    NE   CG    124.46  3.000
 NP2  CE2   CD   CE1   115.66  3.000
 NP2  CE2   CD   NE    124.81  3.000
 NP2  CE1   CD   NE    119.53  3.000
 NP2  HE1   CE1  CR1   118.68  3.000
 NP2  HE1   CE1  CD    119.28  3.000
 NP2  CR1   CE1  CD    122.05  3.000
 NP2  CR2   CE2  NO2   116.73  3.000
 NP2  CR2   CE2  CD    121.23  3.000
 NP2  NO2   CE2  CD    122.04  3.000
 NP2  OC2   NO2  OC1   121.72  3.000
 NP2  OC2   NO2  CE2   119.17  3.000
 NP2  OC1   NO2  CE2   119.11  3.000
 NP2  HR1   CR1  CZ    119.88  3.000
 NP2  HR1   CR1  CE1   118.81  3.000
 NP2  CZ    CR1  CE1   121.31  3.000
 NP2  HR2   CR2  CZ    119.68  3.000
 NP2  HR2   CR2  CE2   119.13  3.000
 NP2  CZ    CR2  CE2   121.19  3.000
 NP2  HZ    CZ   CR2   120.47  3.000
 NP2  HZ    CZ   CR1   120.97  3.000
 NP2  CR2   CZ   CR1   118.56  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
 NP2  CONST_01  CZ    CR1  CE1  CD      0.00   0.0  0
 NP2  CONST_02  CZ    CR2  CE2  CD      0.00   0.0  0
 NP2  CONST_03  CR2   CE2  CD   CE1     0.00   0.0  0
 NP2  CONST_04  CR2   CZ   CR1  CE1     0.00   0.0  0
 NP2  CONST_05  CR1   CE1  CD   CE2     0.00   0.0  0
 NP2  CONST_06  CR1   CZ   CR2  CE2     0.00   0.0  0
 NP2  CONST_07  CR1   CE1  CD   NE    180.00   0.0  0
 NP2  CONST_08  CR2   CE2  CD   NE    180.00   0.0  0
 NP2  CONST_09  NO2   CE2  CD   CE1   180.00   0.0  0
 NP2  CONST_10  CZ    CR2  CE2  NO2   180.00   0.0  0
 NP2  CONST_11  HR1   CR1  CE1  CD    180.00   0.0  0
 NP2  CONST_12  HR2   CR2  CE2  CD    180.00   0.0  0
 NP2  CONST_13  HZ    CZ   CR1  CE1   180.00   0.0  0
 NP2  CONST_14  HE1   CE1  CD   CE2   180.00   0.0  0
 NP2  CONST_15  CE1   CD   NE   CG      0.00   0.0  0
 NP2  CONST_16  CE2   CD   NE   CG    180.00   0.0  0
 NP2  CONST_17  OC1   NO2  CE2  CD    180.00   0.0  0
 NP2  CONST_18  OC2   NO2  CE2  CD      0.00   0.0  0
 NP2  CONST_19  CR2   CE2  NO2  OC1     0.00   0.0  0
 NP2  CONST_20  CR2   CE2  NO2  OC2   180.00   0.0  0
 NP2  CONST_21  HNE   NE   CD   CE1   180.00   0.0  0
 NP2  Var_01    CD    NE   CG   CB   -178.13  30.0  3
 NP2  Var_02    CG    CB   CA   NZ   -179.23  30.0  3
 NP2  Var_03    NE    CG   CB   CA   -179.52  30.0  3
 NP2  Var_04    HNZ1  NZ   CA   CB     68.47  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
 NP2  plan-1  NE   0.020
 NP2  plan-1  CD   0.020
 NP2  plan-1  CE1  0.020
 NP2  plan-1  CE2  0.020
 NP2  plan-1  NO2  0.020
 NP2  plan-1  CR1  0.020
 NP2  plan-1  CR2  0.020
 NP2  plan-1  CZ   0.020
 NP2  plan-1  HE1  0.020
 NP2  plan-1  HR1  0.020
 NP2  plan-1  HR2  0.020
 NP2  plan-1  HZ   0.020
 NP2  plan-2  CG   0.020
 NP2  plan-2  NE   0.020
 NP2  plan-2  CD   0.020
 NP2  plan-2  HNE  0.020
 NP2  plan-3  CE2  0.020
 NP2  plan-3  NO2  0.020
 NP2  plan-3  OC1  0.020
 NP2  plan-3  OC2  0.020

