# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:03:25 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 1-(2-chloro-5-nitrophenyl)-N-methylmethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cc(ccc1Cl)[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
 4AV  4AV  1-(2-chloro-5-nitrophenyl)-N-methylmethanamine  ligand  22  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4AV
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
 4AV  C4   C   CR6    0   0.281  -1.7806   0.0582  -0.0354
 4AV  C5   C   CR16   0  -0.286  -1.5641   1.4063  -0.2694
 4AV  C6   C   CR16   0  -0.191  -0.2699   1.8885  -0.2095
 4AV  N1   N   N      1   0.327  -3.1354  -0.4643  -0.0976
 4AV  C7   C   CR6    0  -0.093   0.7774   1.0237   0.0726
 4AV  O1   O   O      0  -0.376  -4.0253   0.3015  -0.3837
 4AV  O    O   O     -1  -0.376  -3.3042  -1.6374   0.1380
 4AV  C3   C   CR16   0  -0.340  -0.7348  -0.8053   0.2559
 4AV  CL   CL  CL     0  -0.093   2.3707   1.6763   0.1451
 4AV  C2   C   CR6    0   0.197   0.5680  -0.3346   0.3170
 4AV  C1   C   CH2    0  -0.339   1.7003  -1.2818   0.5954
 4AV  N    N   NH1    0  -0.576   2.4456  -1.5408  -0.6192
 4AV  C    C   CH3    0  -0.521   3.6330  -2.3355  -0.3781
 4AV  H1   H   HCR6   0   0.306  -2.3762   2.0832  -0.4899
 4AV  H2   H   HCR6   0   0.299  -0.0796   2.9382  -0.3829
 4AV  H3   H   HCR6   0   0.298  -0.9193  -1.8549   0.4391
 4AV  H4   H   HCH2   0   0.246   2.3784  -0.8339   1.3265
 4AV  H5   H   HCH2   0   0.230   1.2995  -2.1919   1.0649
 4AV  H6   H   HNH1   0   0.348   1.8452  -2.0305  -1.2710
 4AV  H8   H   HCH3   0   0.225   4.3397  -1.7672   0.2294
 4AV  H9   H   HCH3   0   0.197   3.4435  -3.2866   0.1381
 4AV  H10  H   HCH3   0   0.235   4.1199  -2.5603  -1.3266

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
 4AV  C1  N    single    1.448  0.020  1.448
 4AV  C1  C2   single    1.502  0.020  1.502
 4AV  N   C    single    1.449  0.020  1.449
 4AV  C2  C3   aromatic  1.387  0.020  1.387
 4AV  C2  C7   aromatic  1.396  0.020  1.396
 4AV  CL  C7   single    1.723  0.020  1.723
 4AV  C3  C4   aromatic  1.387  0.020  1.387
 4AV  C7  C6   aromatic  1.387  0.020  1.387
 4AV  O   N1   single    1.208  0.020  1.208
 4AV  C4  N1   single    1.453  0.020  1.453
 4AV  C4  C5   aromatic  1.385  0.020  1.385
 4AV  N1  O1   double    1.208  0.020  1.208
 4AV  C6  C5   aromatic  1.382  0.020  1.382
 4AV  C5  H1   single    0.930  0.020  1.080
 4AV  C6  H2   single    0.930  0.020  1.080
 4AV  C3  H3   single    0.930  0.020  1.080
 4AV  C1  H4   single    0.970  0.020  1.090
 4AV  C1  H5   single    0.970  0.020  1.090
 4AV  N   H6   single    0.890  0.020  1.040
 4AV  C   H8   single    0.970  0.020  1.090
 4AV  C   H9   single    0.970  0.020  1.090
 4AV  C   H10  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
 4AV  C3   C4  N1  119.21  3.000
 4AV  N1   C4  C5  119.23  3.000
 4AV  C3   C4  C5  121.56  3.000
 4AV  H1   C5  C6  119.62  3.000
 4AV  H1   C5  C4  121.80  3.000
 4AV  C6   C5  C4  118.58  3.000
 4AV  H2   C6  C7  120.34  3.000
 4AV  H2   C6  C5  119.78  3.000
 4AV  C7   C6  C5  119.88  3.000
 4AV  O    N1  O1  123.95  3.000
 4AV  O1   N1  C4  117.96  3.000
 4AV  O    N1  C4  118.09  3.000
 4AV  C2   C7  CL  119.99  3.000
 4AV  CL   C7  C6  118.06  3.000
 4AV  C2   C7  C6  121.94  3.000
 4AV  H3   C3  C2  118.84  3.000
 4AV  H3   C3  C4  120.74  3.000
 4AV  C2   C3  C4  120.42  3.000
 4AV  C1   C2  C3  120.15  3.000
 4AV  C3   C2  C7  117.62  3.000
 4AV  C1   C2  C7  122.20  3.000
 4AV  H5   C1  H4  106.25  3.000
 4AV  H5   C1  N   113.42  3.000
 4AV  H4   C1  N   108.36  3.000
 4AV  H5   C1  C2  109.04  3.000
 4AV  H4   C1  C2  109.46  3.000
 4AV  N    C1  C2  110.19  3.000
 4AV  H6   N   C   109.13  3.000
 4AV  H6   N   C1  108.74  3.000
 4AV  C    N   C1  112.35  3.000
 4AV  H10  C   H9  107.91  3.000
 4AV  H10  C   H8  107.61  3.000
 4AV  H9   C   H8  107.51  3.000
 4AV  H10  C   N   109.55  3.000
 4AV  H9   C   N   114.31  3.000
 4AV  H8   C   N   109.73  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
 4AV  CONST_01  C7  C2  C3  C4    0.00   0.0  0
 4AV  CONST_02  C7  C6  C5  C4    0.00   0.0  0
 4AV  CONST_03  C2  C3  C4  C5    0.00   0.0  0
 4AV  CONST_04  C2  C7  C6  C5    0.00   0.0  0
 4AV  CONST_05  C3  C2  C7  C6    0.00   0.0  0
 4AV  CONST_06  C3  C4  C5  C6    0.00   0.0  0
 4AV  CONST_07  C1  C2  C3  C4  180.00   0.0  0
 4AV  CONST_08  CL  C7  C6  C5  180.00   0.0  0
 4AV  CONST_09  C1  C2  C7  C6  180.00   0.0  0
 4AV  CONST_10  N1  C4  C5  C6  180.00   0.0  0
 4AV  CONST_11  C2  C3  C4  N1  180.00   0.0  0
 4AV  CONST_12  CL  C7  C2  C3  180.00   0.0  0
 4AV  CONST_13  H2  C6  C5  C4  180.00   0.0  0
 4AV  CONST_14  H3  C3  C4  C5  180.00   0.0  0
 4AV  CONST_15  H1  C5  C6  C7  180.00   0.0  0
 4AV  CONST_16  O   N1  C4  C5  180.00   0.0  0
 4AV  CONST_17  O1  N1  C4  C5    0.00   0.0  0
 4AV  CONST_18  C3  C4  N1  O1  180.00   0.0  0
 4AV  CONST_19  C3  C4  N1  O     0.00   0.0  0
 4AV  Var_01    N   C1  C2  C7  -72.87  30.0  2
 4AV  Var_02    C   N   C1  C2  173.85  30.0  3
 4AV  Var_03    H8  C   N   C1  -65.93  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
 4AV  plan-1  C4  0.020
 4AV  plan-1  C5  0.020
 4AV  plan-1  C6  0.020
 4AV  plan-1  N1  0.020
 4AV  plan-1  C7  0.020
 4AV  plan-1  C3  0.020
 4AV  plan-1  CL  0.020
 4AV  plan-1  C2  0.020
 4AV  plan-1  C1  0.020
 4AV  plan-1  H1  0.020
 4AV  plan-1  H2  0.020
 4AV  plan-1  H3  0.020
 4AV  plan-2  C4  0.020
 4AV  plan-2  N1  0.020
 4AV  plan-2  O1  0.020
 4AV  plan-2  O   0.020

