# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:50:51 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-(4-methyl-2-nitrophenyl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NCCCN)c(c1)[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
 NP1  NP1  N-(4-methyl-2-nitrophenyl)propane-1,3-diamine  ligand  30  15  .  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_NP1
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
 NP1  NZ    N  NH2    0  -0.799  -5.8289   0.1131   0.0553
 NP1  CA    C  CH2    0  -0.273  -4.6046   0.8965  -0.0115
 NP1  CB    C  CH2    0  -0.479  -3.3870  -0.0155  -0.0148
 NP1  CG    C  CH2    0  -0.261  -2.0927   0.7794  -0.0557
 NP1  NE    N  NH1    0  -0.679  -0.9588  -0.1172  -0.0732
 NP1  CD    C  CR6    0   0.388   0.3235   0.2760  -0.0371
 NP1  CE1   C  CR16   0  -0.362   0.6349   1.6581   0.0184
 NP1  CE2   C  CR6    0   0.200   1.4454  -0.5981  -0.0478
 NP1  NO2   N  N      1   0.343   1.2965  -2.0148  -0.1130
 NP1  OC1   O  O      0  -0.406   2.2875  -2.7166  -0.1153
 NP1  OC2   O  O     -1  -0.435   0.1726  -2.4943  -0.1657
 NP1  CR1   C  CR16   0  -0.256   1.9257   2.1125   0.0710
 NP1  CR2   C  CR16   0  -0.362   2.7587  -0.1018   0.0082
 NP1  CZ    C  CR6    0   0.079   3.0289   1.2415   0.0715
 NP1  CM    C  CH3    0  -0.721   4.4295   1.7720   0.1468
 NP1  HNZ1  H  HNH2   0   0.340  -5.8923  -0.3260   0.9659
 NP1  HNZ2  H  HNH2   0   0.348  -6.6273   0.7321  -0.0029
 NP1  HA1   H  HCH2   0   0.195  -4.5032   1.6237   0.8067
 NP1  HA2   H  HCH2   0   0.220  -4.6180   1.4766  -0.9380
 NP1  HB1   H  HCH2   0   0.236  -3.4412  -0.6867  -0.8765
 NP1  HB2   H  HCH2   0   0.234  -3.3976  -0.6424   0.8829
 NP1  HG1   H  HCH2   0   0.236  -2.0418   1.4370   0.8184
 NP1  HG2   H  HCH2   0   0.235  -2.0856   1.4266  -0.9404
 NP1  HNE   H  HNH1   0   0.411  -1.1347  -1.1057  -0.1366
 NP1  HE1   H  HCR6   0   0.288  -0.1673   2.3813   0.0167
 NP1  HR1   H  HCR6   0   0.265   2.0922   3.1828   0.1109
 NP1  HR2   H  HCR6   0   0.282   3.5792  -0.8049   0.0021
 NP1  HM1   H  HCH3   0   0.246   4.6142   2.2676   1.1017
 NP1  HM2   H  HCH3   0   0.246   5.1636   0.9747   0.0412
 NP1  HM3   H  HCH3   0   0.245   4.6196   2.5074  -0.6366

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
 NP1  NZ   CA    single    1.455  0.020  1.455
 NP1  NZ   HNZ1  single    0.890  0.020  1.040
 NP1  NZ   HNZ2  single    0.890  0.020  1.040
 NP1  CA   CB    single    1.521  0.020  1.521
 NP1  CA   HA1   single    0.970  0.020  1.090
 NP1  CA   HA2   single    0.970  0.020  1.090
 NP1  CB   CG    single    1.519  0.020  1.519
 NP1  CB   HB1   single    0.970  0.020  1.090
 NP1  CB   HB2   single    0.970  0.020  1.090
 NP1  CG   NE    single    1.446  0.020  1.446
 NP1  CG   HG1   single    0.970  0.020  1.090
 NP1  CG   HG2   single    0.970  0.020  1.090
 NP1  NE   CD    single    1.342  0.020  1.342
 NP1  NE   HNE   single    0.860  0.020  1.020
 NP1  CD   CE1   aromatic  1.418  0.020  1.418
 NP1  CD   CE2   aromatic  1.422  0.020  1.422
 NP1  CE1  CR1   aromatic  1.369  0.020  1.369
 NP1  CE1  HE1   single    0.930  0.020  1.080
 NP1  CE2  NO2   single    1.426  0.020  1.426
 NP1  CE2  CR2   aromatic  1.405  0.020  1.405
 NP1  NO2  OC1   double    1.214  0.020  1.214
 NP1  NO2  OC2   single    1.223  0.020  1.223
 NP1  CR1  CZ    aromatic  1.406  0.020  1.406
 NP1  CR1  HR1   single    0.930  0.020  1.080
 NP1  CR2  CZ    aromatic  1.372  0.020  1.372
 NP1  CR2  HR2   single    0.930  0.020  1.080
 NP1  CZ   CM    single    1.500  0.020  1.500
 NP1  CM   HM1   single    0.970  0.020  1.090
 NP1  CM   HM2   single    0.970  0.020  1.090
 NP1  CM   HM3   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
 NP1  HNZ2  NZ   HNZ1  105.51  3.000
 NP1  HNZ2  NZ   CA    109.39  3.000
 NP1  HNZ1  NZ   CA    109.11  3.000
 NP1  HA2   CA   HA1   106.31  3.000
 NP1  HA2   CA   CB    109.03  3.000
 NP1  HA1   CA   CB    108.92  3.000
 NP1  HA2   CA   NZ    108.32  3.000
 NP1  HA1   CA   NZ    113.55  3.000
 NP1  CB    CA   NZ    110.54  3.000
 NP1  HB2   CB   HB1   107.11  3.000
 NP1  HB2   CB   CG    109.27  3.000
 NP1  HB1   CB   CG    110.01  3.000
 NP1  HB2   CB   CA    109.49  3.000
 NP1  HB1   CB   CA    109.26  3.000
 NP1  CG    CB   CA    111.60  3.000
 NP1  HG2   CG   HG1   106.82  3.000
 NP1  HG2   CG   NE    110.57  3.000
 NP1  HG1   CG   NE    110.22  3.000
 NP1  HG2   CG   CB    109.65  3.000
 NP1  HG1   CG   CB    109.40  3.000
 NP1  NE    CG   CB    110.12  3.000
 NP1  HNE   NE   CD    117.17  3.000
 NP1  HNE   NE   CG    118.24  3.000
 NP1  CD    NE   CG    124.58  3.000
 NP1  CE2   CD   CE1   115.22  3.000
 NP1  CE2   CD   NE    125.00  3.000
 NP1  CE1   CD   NE    119.78  3.000
 NP1  HE1   CE1  CR1   118.56  3.000
 NP1  HE1   CE1  CD    119.31  3.000
 NP1  CR1   CE1  CD    122.14  3.000
 NP1  CR2   CE2  NO2   116.77  3.000
 NP1  CR2   CE2  CD    121.33  3.000
 NP1  NO2   CE2  CD    121.91  3.000
 NP1  OC2   NO2  OC1   121.55  3.000
 NP1  OC2   NO2  CE2   119.17  3.000
 NP1  OC1   NO2  CE2   119.27  3.000
 NP1  HR1   CR1  CZ    119.42  3.000
 NP1  HR1   CR1  CE1   118.29  3.000
 NP1  CZ    CR1  CE1   122.29  3.000
 NP1  HR2   CR2  CZ    119.20  3.000
 NP1  HR2   CR2  CE2   118.67  3.000
 NP1  CZ    CR2  CE2   122.13  3.000
 NP1  CM    CZ   CR2   122.19  3.000
 NP1  CM    CZ   CR1   120.92  3.000
 NP1  CR2   CZ   CR1   116.89  3.000
 NP1  HM3   CM   HM2   107.84  3.000
 NP1  HM3   CM   HM1   107.01  3.000
 NP1  HM2   CM   HM1   107.65  3.000
 NP1  HM3   CM   CZ    111.42  3.000
 NP1  HM2   CM   CZ    111.45  3.000
 NP1  HM1   CM   CZ    111.26  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
 NP1  CONST_01  CZ    CR1  CE1  CD      0.00   0.0  0
 NP1  CONST_02  CZ    CR2  CE2  CD      0.00   0.0  0
 NP1  CONST_03  CR2   CE2  CD   CE1     0.00   0.0  0
 NP1  CONST_04  CR2   CZ   CR1  CE1     0.00   0.0  0
 NP1  CONST_05  CR1   CE1  CD   CE2     0.00   0.0  0
 NP1  CONST_06  CR1   CZ   CR2  CE2     0.00   0.0  0
 NP1  CONST_07  CR1   CE1  CD   NE    180.00   0.0  0
 NP1  CONST_08  CR2   CE2  CD   NE    180.00   0.0  0
 NP1  CONST_09  NO2   CE2  CD   CE1   180.00   0.0  0
 NP1  CONST_10  CM    CZ   CR1  CE1   180.00   0.0  0
 NP1  CONST_11  CM    CZ   CR2  CE2   180.00   0.0  0
 NP1  CONST_12  CZ    CR2  CE2  NO2   180.00   0.0  0
 NP1  CONST_13  HR1   CR1  CE1  CD    180.00   0.0  0
 NP1  CONST_14  HR2   CR2  CE2  CD    180.00   0.0  0
 NP1  CONST_15  HE1   CE1  CD   CE2   180.00   0.0  0
 NP1  CONST_16  CE1   CD   NE   CG      0.00   0.0  0
 NP1  CONST_17  CE2   CD   NE   CG    180.00   0.0  0
 NP1  CONST_18  OC1   NO2  CE2  CD    180.00   0.0  0
 NP1  CONST_19  OC2   NO2  CE2  CD      0.00   0.0  0
 NP1  CONST_20  CR2   CE2  NO2  OC1     0.00   0.0  0
 NP1  CONST_21  CR2   CE2  NO2  OC2   180.00   0.0  0
 NP1  CONST_22  HNE   NE   CD   CE1   180.00   0.0  0
 NP1  Var_01    HM1   CM   CZ   CR1    65.27  30.0  2
 NP1  Var_02    CD    NE   CG   CB   -176.26  30.0  3
 NP1  Var_03    CG    CB   CA   NZ   -178.85  30.0  3
 NP1  Var_04    NE    CG   CB   CA   -179.35  30.0  3
 NP1  Var_05    HNZ1  NZ   CA   CB     68.61  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
 NP1  plan-1  NE   0.020
 NP1  plan-1  CD   0.020
 NP1  plan-1  CE1  0.020
 NP1  plan-1  CE2  0.020
 NP1  plan-1  NO2  0.020
 NP1  plan-1  CR1  0.020
 NP1  plan-1  CR2  0.020
 NP1  plan-1  CZ   0.020
 NP1  plan-1  CM   0.020
 NP1  plan-1  HE1  0.020
 NP1  plan-1  HR1  0.020
 NP1  plan-1  HR2  0.020
 NP1  plan-2  CG   0.020
 NP1  plan-2  NE   0.020
 NP1  plan-2  CD   0.020
 NP1  plan-2  HNE  0.020
 NP1  plan-3  CE2  0.020
 NP1  plan-3  NO2  0.020
 NP1  plan-3  OC1  0.020
 NP1  plan-3  OC2  0.020

