# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:27:12 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-methoxy-N-(pyridin-2-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C(=O)Nc2ccccn2
#
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
 SJR  SJR  4-methoxy-N-(pyridin-2-yl)benzamide  ligand  29  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SJR
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
 SJR  C    C  CH3   0  -0.440  -5.6624   1.3967   0.2596
 SJR  N    N  NH1   0  -0.746   1.2813   0.2875  -0.0894
 SJR  O    O  O2    0  -0.462  -5.0906   0.1710  -0.1605
 SJR  C1   C  CR6   0   0.392  -3.7608   0.0247  -0.1001
 SJR  N1   N  N     0  -0.416   3.2619  -0.6310   0.7457
 SJR  O1   O  O     0  -0.442   0.8415  -1.9445   0.0547
 SJR  C2   C  CR16  0  -0.330  -3.2530  -1.2122  -0.5131
 SJR  C3   C  CR16  0  -0.247  -1.8970  -1.4525  -0.4774
 SJR  C4   C  CR6   0  -0.087  -1.0015  -0.4676  -0.0516
 SJR  C5   C  C     0   0.532   0.4490  -0.7968  -0.0152
 SJR  C6   C  CR6   0   0.512   2.6713   0.2947   0.0105
 SJR  C7   C  CR16  0  -0.397   3.3745   1.3133  -0.6393
 SJR  C8   C  CR16  0  -0.145   4.7485   1.3456  -0.5082
 SJR  C9   C  CR16  0  -0.341   5.3806   0.3660   0.2487
 SJR  C10  C  CR16  0  -0.067   4.5865  -0.5950   0.8486
 SJR  C11  C  CR16  0  -0.273  -1.5167   0.7567   0.3621
 SJR  C12  C  CR16  0  -0.371  -2.8804   1.0094   0.3450
 SJR  H    H  HCH3  0   0.233  -5.3180   2.2363  -0.3488
 SJR  HA   H  HCH3  0   0.264  -6.7371   1.2925   0.1357
 SJR  HB   H  HCH3  0   0.233  -5.4471   1.6063   1.3100
 SJR  HN   H  HNH1  0   0.422   0.8717   1.1517  -0.4081
 SJR  H2   H  HCR6  0   0.270  -3.9348  -1.9799  -0.8572
 SJR  H3   H  HCR6  0   0.263  -1.5255  -2.4173  -0.7959
 SJR  H7   H  HCR6  0   0.280   2.8534   2.0551  -1.2306
 SJR  H8   H  HCR6  0   0.277   5.3210   2.1224  -0.9973
 SJR  H9   H  HCR6  0   0.270   6.4539   0.3503   0.3744
 SJR  H10  H  HCR6  0   0.263   5.0366  -1.3745   1.4533
 SJR  H11  H  HCR6  0   0.266  -0.8661   1.5377   0.7362
 SJR  H12  H  HCR6  0   0.288  -3.2334   1.9709   0.6898

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
 SJR  C    O    single    1.416  0.020  1.416
 SJR  N    C5   single    1.369  0.020  1.369
 SJR  N    C6   single    1.394  0.020  1.394
 SJR  O    C1   single    1.339  0.020  1.339
 SJR  C1   C2   aromatic  1.399  0.020  1.399
 SJR  C1   C12  aromatic  1.394  0.020  1.394
 SJR  N1   C6   aromatic  1.321  0.020  1.321
 SJR  N1   C10  aromatic  1.329  0.020  1.329
 SJR  O1   C5   double    1.215  0.020  1.215
 SJR  C2   C3   aromatic  1.378  0.020  1.378
 SJR  C3   C4   aromatic  1.398  0.020  1.398
 SJR  C4   C5   single    1.488  0.020  1.488
 SJR  C4   C11  aromatic  1.391  0.020  1.391
 SJR  C6   C7   aromatic  1.398  0.020  1.398
 SJR  C7   C8   aromatic  1.381  0.020  1.381
 SJR  C8   C9   aromatic  1.390  0.020  1.390
 SJR  C9   C10  aromatic  1.383  0.020  1.383
 SJR  C11  C12  aromatic  1.387  0.020  1.387
 SJR  C    H    single    0.970  0.020  1.090
 SJR  C    HA   single    0.970  0.020  1.090
 SJR  C    HB   single    0.970  0.020  1.090
 SJR  N    HN   single    0.860  0.020  1.020
 SJR  C2   H2   single    0.930  0.020  1.080
 SJR  C3   H3   single    0.930  0.020  1.080
 SJR  C7   H7   single    0.930  0.020  1.080
 SJR  C8   H8   single    0.930  0.020  1.080
 SJR  C9   H9   single    0.930  0.020  1.080
 SJR  C10  H10  single    0.930  0.020  1.080
 SJR  C11  H11  single    0.930  0.020  1.080
 SJR  C12  H12  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
 SJR  HB   C    HA   108.84  3.000
 SJR  HB   C    H    109.01  3.000
 SJR  HA   C    H    108.78  3.000
 SJR  HB   C    O    111.82  3.000
 SJR  HA   C    O    106.41  3.000
 SJR  H    C    O    111.88  3.000
 SJR  HN   N    C6   115.05  3.000
 SJR  HN   N    C5   116.69  3.000
 SJR  C6   N    C5   127.35  3.000
 SJR  C1   O    C    118.82  3.000
 SJR  C12  C1   C2   119.30  3.000
 SJR  C12  C1   O    124.37  3.000
 SJR  C2   C1   O    116.33  3.000
 SJR  C10  N1   C6   118.00  3.000
 SJR  H2   C2   C3   120.29  3.000
 SJR  H2   C2   C1   119.47  3.000
 SJR  C3   C2   C1   120.24  3.000
 SJR  H3   C3   C4   119.88  3.000
 SJR  H3   C3   C2   119.08  3.000
 SJR  C4   C3   C2   121.04  3.000
 SJR  C11  C4   C5   123.26  3.000
 SJR  C11  C4   C3   118.26  3.000
 SJR  C5   C4   C3   118.44  3.000
 SJR  C4   C5   O1   121.69  3.000
 SJR  C4   C5   N    114.60  3.000
 SJR  O1   C5   N    123.70  3.000
 SJR  C7   C6   N1   122.98  3.000
 SJR  C7   C6   N    118.17  3.000
 SJR  N1   C6   N    118.82  3.000
 SJR  H7   C7   C8   121.00  3.000
 SJR  H7   C7   C6   120.74  3.000
 SJR  C8   C7   C6   118.26  3.000
 SJR  H8   C8   C9   120.77  3.000
 SJR  H8   C8   C7   120.03  3.000
 SJR  C9   C8   C7   119.20  3.000
 SJR  H9   C9   C10  120.63  3.000
 SJR  H9   C9   C8   121.68  3.000
 SJR  C10  C9   C8   117.69  3.000
 SJR  H10  C10  C9   120.19  3.000
 SJR  H10  C10  N1   115.93  3.000
 SJR  C9   C10  N1   123.87  3.000
 SJR  H11  C11  C12  117.61  3.000
 SJR  H11  C11  C4   120.99  3.000
 SJR  C12  C11  C4   121.38  3.000
 SJR  H12  C12  C11  118.64  3.000
 SJR  H12  C12  C1   121.61  3.000
 SJR  C11  C12  C1   119.75  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
 SJR  CONST_01  C4   C3   C2   C1    0.00   0.0  0
 SJR  CONST_02  C4   C11  C12  C1    0.00   0.0  0
 SJR  CONST_03  C8   C7   C6   N1    0.00   0.0  0
 SJR  CONST_04  C8   C9   C10  N1    0.00   0.0  0
 SJR  CONST_05  C11  C12  C1   C2    0.00   0.0  0
 SJR  CONST_06  C11  C4   C3   C2    0.00   0.0  0
 SJR  CONST_07  C12  C1   C2   C3    0.00   0.0  0
 SJR  CONST_08  C12  C11  C4   C3    0.00   0.0  0
 SJR  CONST_09  C9   C10  N1   C6    0.00   0.0  0
 SJR  CONST_10  C9   C8   C7   C6    0.00   0.0  0
 SJR  CONST_11  C10  N1   C6   C7    0.00   0.0  0
 SJR  CONST_12  C10  C9   C8   C7    0.00   0.0  0
 SJR  CONST_13  C10  N1   C6   N   180.00   0.0  0
 SJR  CONST_14  C8   C7   C6   N   180.00   0.0  0
 SJR  CONST_15  C3   C2   C1   O   180.00   0.0  0
 SJR  CONST_16  C11  C12  C1   O   180.00   0.0  0
 SJR  CONST_17  C5   C4   C3   C2  180.00   0.0  0
 SJR  CONST_18  C12  C11  C4   C5  180.00   0.0  0
 SJR  CONST_19  H3   C3   C2   C1  180.00   0.0  0
 SJR  CONST_20  H11  C11  C12  C1  180.00   0.0  0
 SJR  CONST_21  H7   C7   C6   N1  180.00   0.0  0
 SJR  CONST_22  H9   C9   C10  N1  180.00   0.0  0
 SJR  CONST_23  H12  C12  C1   C2  180.00   0.0  0
 SJR  CONST_24  H2   C2   C3   C4  180.00   0.0  0
 SJR  CONST_25  H10  C10  N1   C6  180.00   0.0  0
 SJR  CONST_26  H8   C8   C7   C6  180.00   0.0  0
 SJR  CONST_27  C6   N    C5   C4  180.00   0.0  0
 SJR  CONST_31  C6   N    C5   O1    0.00   0.0  0
 SJR  Var_01    C2   C1   O    C   179.27  30.0  2
 SJR  Var_02    C3   C4   C5   N   156.47  30.0  3
 SJR  Var_03    H    C    O    C1   61.84  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
 SJR  plan-1  O    0.020
 SJR  plan-1  C1   0.020
 SJR  plan-1  C2   0.020
 SJR  plan-1  C3   0.020
 SJR  plan-1  C4   0.020
 SJR  plan-1  C5   0.020
 SJR  plan-1  C11  0.020
 SJR  plan-1  C12  0.020
 SJR  plan-1  H2   0.020
 SJR  plan-1  H3   0.020
 SJR  plan-1  H11  0.020
 SJR  plan-1  H12  0.020
 SJR  plan-2  N    0.020
 SJR  plan-2  N1   0.020
 SJR  plan-2  C6   0.020
 SJR  plan-2  C7   0.020
 SJR  plan-2  C8   0.020
 SJR  plan-2  C9   0.020
 SJR  plan-2  C10  0.020
 SJR  plan-2  H7   0.020
 SJR  plan-2  H8   0.020
 SJR  plan-2  H9   0.020
 SJR  plan-2  H10  0.020
 SJR  plan-3  N    0.020
 SJR  plan-3  O1   0.020
 SJR  plan-3  C4   0.020
 SJR  plan-3  C5   0.020
 SJR  plan-3  C6   0.020
 SJR  plan-3  HN   0.020

