# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 00:29:44 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(cccc1[N+]([O-])=O)C(=O)Nc2cc(Cl)cc(Cl)c2
#
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
 D59  D59  N-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide  ligand  31  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D59
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
 D59  CL1  CL  CL     0  -0.107  -4.4245   2.5538  -0.9264
 D59  C1   C   CR6    0  -0.027  -3.6950   1.0655  -0.4302
 D59  C2   C   CR16   0  -0.272  -2.3174   0.9460  -0.5217
 D59  C6   C   CR16   0  -0.201  -4.5111   0.0519   0.0397
 D59  C5   C   CR6    0  -0.028  -3.8922  -1.1256   0.4296
 D59  CL2  CL  CL     0  -0.106  -4.8647  -2.4244   1.0251
 D59  C4   C   CR16   0  -0.305  -2.5241  -1.2937   0.3573
 D59  C3   C   CR6    0   0.391  -1.7265  -0.2522  -0.1224
 D59  N1   N   NH1    0  -0.736  -0.3552  -0.4976  -0.1704
 D59  C7   C   C      0   0.486   0.6478   0.3229  -0.5747
 D59  O1   O   O      0  -0.434   0.5013   1.4713  -0.9419
 D59  C8   C   CR6    0  -0.098   1.9958  -0.3345  -0.5626
 D59  C9   C   CR6    0   0.110   3.0489   0.2267   0.1711
 D59  C14  C   CH3    0  -0.727   2.8132   1.3954   1.0856
 D59  C13  C   CR16   0  -0.229   2.1772  -1.4600  -1.3578
 D59  C12  C   CR16   0  -0.263   3.4185  -2.0680  -1.4502
 D59  C11  C   CR16   0  -0.249   4.4793  -1.5471  -0.7370
 D59  C10  C   CR6    0   0.202   4.2816  -0.4132   0.0387
 D59  N2   N   N      1   0.325   5.4609   0.1040   0.7210
 D59  O2   O   O      0  -0.369   6.2168  -0.6971   1.2168
 D59  O3   O   O     -1  -0.366   5.6335   1.2992   0.7281
 D59  H1   H   HCR6   0   0.309  -1.7308   1.7692  -0.8927
 D59  H2   H   HCR6   0   0.303  -5.5831   0.1723   0.1014
 D59  H3   H   HCR6   0   0.302  -2.0729  -2.2256   0.6726
 D59  H4   H   HNH1   0   0.433  -0.0727  -1.4038   0.1735
 D59  H5   H   HCH3   0   0.271   3.0142   2.3411   0.5835
 D59  H6   H   HCH3   0   0.258   1.7818   1.4152   1.4286
 D59  H7   H   HCH3   0   0.257   3.4378   1.3525   1.9746
 D59  H8   H   HCR6   0   0.288   1.3451  -1.8613  -1.9224
 D59  H9   H   HCR6   0   0.284   3.5569  -2.9393  -2.0741
 D59  H10  H   HCR6   0   0.300   5.4557  -2.0067  -0.8003

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
 D59  O3   N2   single    1.208  0.020  1.208
 D59  C14  C9   single    1.503  0.020  1.503
 D59  O2   N2   double    1.208  0.020  1.208
 D59  N2   C10  single    1.457  0.020  1.457
 D59  C9   C10  aromatic  1.395  0.020  1.395
 D59  C9   C8   aromatic  1.401  0.020  1.401
 D59  C10  C11  aromatic  1.388  0.020  1.388
 D59  C8   C7   single    1.500  0.020  1.500
 D59  C8   C13  aromatic  1.390  0.020  1.390
 D59  C11  C12  aromatic  1.380  0.020  1.380
 D59  C7   O1   double    1.215  0.020  1.215
 D59  C7   N1   single    1.358  0.020  1.358
 D59  N1   C3   single    1.394  0.020  1.394
 D59  C13  C12  aromatic  1.385  0.020  1.385
 D59  C3   C2   aromatic  1.394  0.020  1.394
 D59  C3   C4   aromatic  1.397  0.020  1.397
 D59  C2   C1   aromatic  1.386  0.020  1.386
 D59  C4   C5   aromatic  1.380  0.020  1.380
 D59  C1   CL1  single    1.730  0.020  1.730
 D59  C1   C6   aromatic  1.384  0.020  1.384
 D59  C5   C6   aromatic  1.386  0.020  1.386
 D59  C5   CL2  single    1.728  0.020  1.728
 D59  C2   H1   single    0.930  0.020  1.080
 D59  C6   H2   single    0.930  0.020  1.080
 D59  C4   H3   single    0.930  0.020  1.080
 D59  N1   H4   single    0.860  0.020  1.020
 D59  C14  H5   single    0.970  0.020  1.090
 D59  C14  H6   single    0.970  0.020  1.090
 D59  C14  H7   single    0.970  0.020  1.090
 D59  C13  H8   single    0.930  0.020  1.080
 D59  C12  H9   single    0.930  0.020  1.080
 D59  C11  H10  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
 D59  C6   C1   C2   123.06  3.000
 D59  C6   C1   CL1  118.61  3.000
 D59  C2   C1   CL1  118.32  3.000
 D59  H1   C2   C3   121.66  3.000
 D59  H1   C2   C1   119.88  3.000
 D59  C3   C2   C1   118.46  3.000
 D59  H2   C6   C5   121.44  3.000
 D59  H2   C6   C1   121.53  3.000
 D59  C5   C6   C1   117.03  3.000
 D59  C4   C5   CL2  118.96  3.000
 D59  CL2  C5   C6   118.95  3.000
 D59  C4   C5   C6   122.09  3.000
 D59  H3   C4   C3   120.27  3.000
 D59  H3   C4   C5   120.18  3.000
 D59  C3   C4   C5   119.55  3.000
 D59  N1   C3   C4   116.25  3.000
 D59  C4   C3   C2   119.81  3.000
 D59  N1   C3   C2   123.94  3.000
 D59  H4   N1   C7   115.92  3.000
 D59  H4   N1   C3   114.94  3.000
 D59  C7   N1   C3   129.10  3.000
 D59  C8   C7   O1   121.69  3.000
 D59  O1   C7   N1   124.92  3.000
 D59  C8   C7   N1   113.38  3.000
 D59  C13  C8   C9   121.73  3.000
 D59  C13  C8   C7   117.88  3.000
 D59  C9   C8   C7   120.28  3.000
 D59  C10  C9   C14  123.58  3.000
 D59  C10  C9   C8   115.52  3.000
 D59  C14  C9   C8   120.83  3.000
 D59  H7   C14  H6   106.72  3.000
 D59  H7   C14  H5   107.77  3.000
 D59  H6   C14  H5   107.74  3.000
 D59  H7   C14  C9   112.14  3.000
 D59  H6   C14  C9   110.79  3.000
 D59  H5   C14  C9   111.46  3.000
 D59  H8   C13  C12  119.42  3.000
 D59  H8   C13  C8   119.88  3.000
 D59  C12  C13  C8   120.70  3.000
 D59  H9   C12  C11  120.27  3.000
 D59  H9   C12  C13  120.48  3.000
 D59  C11  C12  C13  119.25  3.000
 D59  H10  C11  C10  120.58  3.000
 D59  H10  C11  C12  120.23  3.000
 D59  C10  C11  C12  119.18  3.000
 D59  N2   C10  C11  115.87  3.000
 D59  C11  C10  C9   123.61  3.000
 D59  N2   C10  C9   120.51  3.000
 D59  O3   N2   O2   124.37  3.000
 D59  O2   N2   C10  117.59  3.000
 D59  O3   N2   C10  118.02  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
 D59  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D59  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 D59  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D59  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 D59  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 D59  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 D59  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 D59  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 D59  CONST_09  C12  C11  C10  C9      0.00   0.0  0
 D59  CONST_10  C12  C13  C8   C9      0.00   0.0  0
 D59  CONST_11  C10  C9   C8   C13     0.00   0.0  0
 D59  CONST_12  C10  C11  C12  C13     0.00   0.0  0
 D59  CONST_13  C3   C2   C1   CL1   180.00   0.0  0
 D59  CONST_14  C5   C6   C1   CL1   180.00   0.0  0
 D59  CONST_15  N1   C3   C2   C1    180.00   0.0  0
 D59  CONST_16  CL2  C5   C6   C1    180.00   0.0  0
 D59  CONST_17  N1   C3   C4   C5    180.00   0.0  0
 D59  CONST_18  C3   C4   C5   CL2   180.00   0.0  0
 D59  CONST_19  C10  C9   C8   C7    180.00   0.0  0
 D59  CONST_20  C12  C13  C8   C7    180.00   0.0  0
 D59  CONST_21  N2   C10  C9   C8    180.00   0.0  0
 D59  CONST_22  C11  C10  C9   C14   180.00   0.0  0
 D59  CONST_23  C13  C8   C9   C14   180.00   0.0  0
 D59  CONST_24  N2   C10  C11  C12   180.00   0.0  0
 D59  CONST_25  H3   C4   C3   C2    180.00   0.0  0
 D59  CONST_26  H2   C6   C1   C2    180.00   0.0  0
 D59  CONST_27  H1   C2   C1   C6    180.00   0.0  0
 D59  CONST_28  H9   C12  C13  C8    180.00   0.0  0
 D59  CONST_29  H10  C11  C10  C9    180.00   0.0  0
 D59  CONST_30  H8   C13  C8   C9    180.00   0.0  0
 D59  CONST_31  C8   C7   N1   C3    180.00   0.0  0
 D59  CONST_32  C7   N1   C3   C2      0.00   0.0  0
 D59  CONST_33  C7   N1   C3   C4    180.00   0.0  0
 D59  CONST_38  H4   N1   C3   C2    180.00   0.0  0
 D59  CONST_39  O1   C7   N1   C3      0.00   0.0  0
 D59  Var_01    C9   C8   C7   N1   -123.85  30.0  2
 D59  Var_02    H5   C14  C9   C8    -94.14  30.0  2

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
 D59  plan-1  CL1  0.020
 D59  plan-1  C1   0.020
 D59  plan-1  C2   0.020
 D59  plan-1  C6   0.020
 D59  plan-1  C5   0.020
 D59  plan-1  CL2  0.020
 D59  plan-1  C4   0.020
 D59  plan-1  C3   0.020
 D59  plan-1  N1   0.020
 D59  plan-1  H1   0.020
 D59  plan-1  H2   0.020
 D59  plan-1  H3   0.020
 D59  plan-2  C7   0.020
 D59  plan-2  C8   0.020
 D59  plan-2  C9   0.020
 D59  plan-2  C14  0.020
 D59  plan-2  C13  0.020
 D59  plan-2  C12  0.020
 D59  plan-2  C11  0.020
 D59  plan-2  C10  0.020
 D59  plan-2  N2   0.020
 D59  plan-2  H8   0.020
 D59  plan-2  H9   0.020
 D59  plan-2  H10  0.020
 D59  plan-3  C3   0.020
 D59  plan-3  N1   0.020
 D59  plan-3  C7   0.020
 D59  plan-3  O1   0.020
 D59  plan-3  C8   0.020
 D59  plan-3  H4   0.020
 D59  plan-4  C10  0.020
 D59  plan-4  N2   0.020
 D59  plan-4  O2   0.020
 D59  plan-4  O3   0.020

