# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:06:02 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-{3-[(4-chloropyridin-2-yl)amino]phenoxy}-N-methylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)COc1cccc(Nc2cc(Cl)ccn2)c1
#
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
 2NL  2NL  2-{3-[(4-chloropyridin-2-yl)amino]phenoxy}-N-methylacetamide  ligand  34  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2NL
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
 2NL  C1   C   C     0   0.507  -4.8067   1.1075   0.0446
 2NL  C2   C   CH2   0  -0.298  -4.1156  -0.2467  -0.0097
 2NL  C3   C   CR6   0   0.418  -1.8971  -1.0681  -0.0754
 2NL  C7   C   CR6   0   0.386   0.4241  -1.7304  -0.0459
 2NL  C8   C   CR16  0  -0.439  -0.5423  -0.7325  -0.1189
 2NL  C9   C   CR6   0   0.566   2.5298  -0.3617  -0.1719
 2NL  C10  C   CR16  0  -0.402   3.9309  -0.4767  -0.0758
 2NL  C11  C   CR6   0   0.089   4.6727   0.6724  -0.1922
 2NL  C12  C   CR16  0  -0.348   4.0564   1.9040  -0.3966
 2NL  C13  C   CR16  0  -0.032   2.6791   1.8937  -0.4723
 2NL  CL   CL  CL    0  -0.102   6.3929   0.5885  -0.0805
 2NL  N2   N   N     0  -0.476   1.9269   0.8026  -0.3663
 2NL  N1   N   NH1   0  -0.789   1.7942  -1.5089  -0.0592
 2NL  C6   C   CR16  0  -0.386   0.0147  -3.0698   0.0631
 2NL  C5   C   CR16  0  -0.228  -1.3279  -3.3788   0.0993
 2NL  C4   C   CR16  0  -0.406  -2.3072  -2.3913   0.0316
 2NL  O1   O   O2    0  -0.467  -2.7407  -0.0158  -0.1463
 2NL  O    O   O     0  -0.483  -4.2117   2.1361   0.3174
 2NL  N    N   NH1   0  -0.624  -6.1219   1.0526  -0.1921
 2NL  C    C   CH3   0  -0.512  -6.9781   2.2109  -0.0859
 2NL  H1   H   HCH2  0   0.265  -4.3448  -0.7825   0.9207
 2NL  H2   H   HCH2  0   0.255  -4.5122  -0.8468  -0.8368
 2NL  H3   H   HCR6  0   0.291  -0.2600   0.3041  -0.2078
 2NL  H4   H   HCR6  0   0.298   4.4014  -1.4370   0.0895
 2NL  H5   H   HCR6  0   0.287   4.6185   2.8209  -0.4927
 2NL  H6   H   HCR6  0   0.272   2.1460   2.8239  -0.6311
 2NL  H7   H   HNH1  0   0.416   2.3456  -2.3441   0.0590
 2NL  H8   H   HCR6  0   0.265   0.7537  -3.8599   0.1184
 2NL  H9   H   HCR6  0   0.261  -1.6292  -4.4149   0.1826
 2NL  H10  H   HCR6  0   0.276  -3.3505  -2.6731   0.0594
 2NL  H11  H   HNH1  0   0.409  -6.5434   0.1713  -0.4345
 2NL  H12  H   HCH3  0   0.253  -7.9992   1.9008  -0.2869
 2NL  H13  H   HCH3  0   0.240  -6.9422   2.6474   0.9127
 2NL  H14  H   HCH3  0   0.240  -6.7048   2.9816  -0.8068

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
 2NL  CL   C11  single    1.726  0.020  1.726
 2NL  C12  C11  aromatic  1.392  0.020  1.392
 2NL  C12  C13  aromatic  1.379  0.020  1.379
 2NL  C11  C10  aromatic  1.373  0.020  1.373
 2NL  C13  N2   aromatic  1.329  0.020  1.329
 2NL  C10  C9   aromatic  1.409  0.020  1.409
 2NL  N2   C9   aromatic  1.326  0.020  1.326
 2NL  C9   N1   single    1.367  0.020  1.367
 2NL  N1   C7   single    1.388  0.020  1.388
 2NL  C7   C6   aromatic  1.405  0.020  1.405
 2NL  C7   C8   aromatic  1.391  0.020  1.391
 2NL  C6   C5   aromatic  1.378  0.020  1.378
 2NL  C8   C3   aromatic  1.396  0.020  1.396
 2NL  C5   C4   aromatic  1.392  0.020  1.392
 2NL  C3   C4   aromatic  1.389  0.020  1.389
 2NL  C3   O1   single    1.351  0.020  1.351
 2NL  O1   C2   single    1.401  0.020  1.401
 2NL  C2   C1   single    1.521  0.020  1.521
 2NL  C1   N    single    1.337  0.020  1.337
 2NL  C1   O    double    1.219  0.020  1.219
 2NL  N    C    single    1.444  0.020  1.444
 2NL  C2   H1   single    0.970  0.020  1.090
 2NL  C2   H2   single    0.970  0.020  1.090
 2NL  C8   H3   single    0.930  0.020  1.080
 2NL  C10  H4   single    0.930  0.020  1.080
 2NL  C12  H5   single    0.930  0.020  1.080
 2NL  C13  H6   single    0.930  0.020  1.080
 2NL  N1   H7   single    0.860  0.020  1.020
 2NL  C6   H8   single    0.930  0.020  1.080
 2NL  C5   H9   single    0.930  0.020  1.080
 2NL  C4   H10  single    0.930  0.020  1.080
 2NL  N    H11  single    0.860  0.020  1.020
 2NL  C    H12  single    0.970  0.020  1.090
 2NL  C    H13  single    0.970  0.020  1.090
 2NL  C    H14  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
 2NL  N    C1   O    123.65  3.000
 2NL  O    C1   C2   122.50  3.000
 2NL  N    C1   C2   113.82  3.000
 2NL  H2   C2   H1   107.26  3.000
 2NL  H2   C2   O1   111.82  3.000
 2NL  H1   C2   O1   111.59  3.000
 2NL  H2   C2   C1   110.48  3.000
 2NL  H1   C2   C1   108.03  3.000
 2NL  O1   C2   C1   107.62  3.000
 2NL  O1   C3   C4   124.18  3.000
 2NL  O1   C3   C8   114.66  3.000
 2NL  C4   C3   C8   121.17  3.000
 2NL  C6   C7   N1   116.14  3.000
 2NL  C6   C7   C8   119.05  3.000
 2NL  N1   C7   C8   124.81  3.000
 2NL  H3   C8   C7   120.81  3.000
 2NL  H3   C8   C3   119.19  3.000
 2NL  C7   C8   C3   120.00  3.000
 2NL  N1   C9   N2   120.29  3.000
 2NL  N1   C9   C10  117.44  3.000
 2NL  N2   C9   C10  122.27  3.000
 2NL  H4   C10  C11  121.39  3.000
 2NL  H4   C10  C9   121.01  3.000
 2NL  C11  C10  C9   117.60  3.000
 2NL  CL   C11  C12  119.59  3.000
 2NL  C12  C11  C10  120.91  3.000
 2NL  CL   C11  C10  119.51  3.000
 2NL  H5   C12  C13  121.42  3.000
 2NL  H5   C12  C11  122.26  3.000
 2NL  C13  C12  C11  116.33  3.000
 2NL  H6   C13  N2   115.96  3.000
 2NL  H6   C13  C12  119.52  3.000
 2NL  N2   C13  C12  124.52  3.000
 2NL  C13  N2   C9   118.37  3.000
 2NL  H7   N1   C9   114.24  3.000
 2NL  H7   N1   C7   114.00  3.000
 2NL  C9   N1   C7   131.73  3.000
 2NL  H8   C6   C5   119.98  3.000
 2NL  H8   C6   C7   120.04  3.000
 2NL  C5   C6   C7   119.98  3.000
 2NL  H9   C5   C4   119.14  3.000
 2NL  H9   C5   C6   119.20  3.000
 2NL  C4   C5   C6   121.66  3.000
 2NL  H10  C4   C5   119.51  3.000
 2NL  H10  C4   C3   122.35  3.000
 2NL  C5   C4   C3   118.14  3.000
 2NL  C3   O1   C2   118.65  3.000
 2NL  H11  N    C    118.14  3.000
 2NL  H11  N    C1   119.37  3.000
 2NL  C    N    C1   122.48  3.000
 2NL  H14  C    H13  108.32  3.000
 2NL  H14  C    H12  108.37  3.000
 2NL  H13  C    H12  108.35  3.000
 2NL  H14  C    N    111.70  3.000
 2NL  H13  C    N    111.65  3.000
 2NL  H12  C    N    108.35  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
 2NL  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 2NL  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 2NL  CONST_03  C4   C5   C6   C7      0.00   0.0  0
 2NL  CONST_04  C4   C3   C8   C7      0.00   0.0  0
 2NL  CONST_05  C5   C6   C7   C8      0.00   0.0  0
 2NL  CONST_06  C5   C4   C3   C8      0.00   0.0  0
 2NL  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 2NL  CONST_08  C12  C13  N2   C9      0.00   0.0  0
 2NL  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 2NL  CONST_10  C13  N2   C9   C10     0.00   0.0  0
 2NL  CONST_11  N2   C13  C12  C11     0.00   0.0  0
 2NL  CONST_12  N2   C9   C10  C11     0.00   0.0  0
 2NL  CONST_13  N1   C7   C8   C3    180.00   0.0  0
 2NL  CONST_14  O1   C3   C8   C7    180.00   0.0  0
 2NL  CONST_15  CL   C11  C10  C9    180.00   0.0  0
 2NL  CONST_16  N1   C9   C10  C11   180.00   0.0  0
 2NL  CONST_17  CL   C11  C12  C13   180.00   0.0  0
 2NL  CONST_18  N1   C9   N2   C13   180.00   0.0  0
 2NL  CONST_19  C5   C6   C7   N1    180.00   0.0  0
 2NL  CONST_20  O1   C3   C4   C5    180.00   0.0  0
 2NL  CONST_21  H9   C5   C4   C3    180.00   0.0  0
 2NL  CONST_22  H8   C6   C7   C8    180.00   0.0  0
 2NL  CONST_23  H10  C4   C3   C8    180.00   0.0  0
 2NL  CONST_24  H6   C13  N2   C9    180.00   0.0  0
 2NL  CONST_25  H5   C12  C11  C10   180.00   0.0  0
 2NL  CONST_26  H4   C10  C11  C12   180.00   0.0  0
 2NL  CONST_27  H3   C8   C7   C6    180.00   0.0  0
 2NL  CONST_28  C    N    C1   C2    180.00   0.0  0
 2NL  CONST_29  C    N    C1   O       0.00   0.0  0
 2NL  CONST_30  H11  N    C1   C2      0.00   0.0  0
 2NL  Var_01    C10  C9   N1   C7    176.60  30.0  2
 2NL  Var_02    C9   N1   C7   C8     -1.81  30.0  2
 2NL  Var_03    C8   C3   O1   C2   -175.30  30.0  1
 2NL  Var_04    H1   C2   O1   C3     54.75  30.0  3
 2NL  Var_05    N    C1   C2   O1    162.69  30.0  3
 2NL  Var_06    H12  C    N    C1   -177.80  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
 2NL  plan-1  C3   0.020
 2NL  plan-1  C7   0.020
 2NL  plan-1  C8   0.020
 2NL  plan-1  N1   0.020
 2NL  plan-1  C6   0.020
 2NL  plan-1  C5   0.020
 2NL  plan-1  C4   0.020
 2NL  plan-1  O1   0.020
 2NL  plan-1  H3   0.020
 2NL  plan-1  H8   0.020
 2NL  plan-1  H9   0.020
 2NL  plan-1  H10  0.020
 2NL  plan-2  C9   0.020
 2NL  plan-2  C10  0.020
 2NL  plan-2  C11  0.020
 2NL  plan-2  C12  0.020
 2NL  plan-2  C13  0.020
 2NL  plan-2  CL   0.020
 2NL  plan-2  N2   0.020
 2NL  plan-2  N1   0.020
 2NL  plan-2  H4   0.020
 2NL  plan-2  H5   0.020
 2NL  plan-2  H6   0.020
 2NL  plan-3  C1   0.020
 2NL  plan-3  C2   0.020
 2NL  plan-3  O    0.020
 2NL  plan-3  N    0.020
 2NL  plan-3  C    0.020
 2NL  plan-3  H11  0.020

