# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:16:35 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 6-[(2-methoxybenzyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CNc2ccc(cn2)C(N)=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
 4FX  4FX  6-[(2-methoxybenzyl)amino]pyridine-3-carboxamide  ligand  34  19  .  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_4FX
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
 4FX  C6   C  CR16  0  -0.273   4.7877   1.8331   0.4151
 4FX  C5   C  CR16  0  -0.248   5.3656   0.5893   0.6018
 4FX  C13  C  CR16  0  -0.150  -2.9148   0.1804  -1.1382
 4FX  C7   C  CR16  0  -0.279   3.4746   1.9045  -0.0361
 4FX  C4   C  CR16  0  -0.382   4.6490  -0.5735   0.3416
 4FX  C12  C  CR16  0  -0.402  -1.5595   0.3904  -1.0905
 4FX  C15  C  CR16  0  -0.072  -2.9168  -0.0190   1.2222
 4FX  C14  C  CR6   0  -0.166  -3.6416  -0.0499   0.0349
 4FX  C8   C  CR6   0  -0.031   2.7359   0.7619  -0.3039
 4FX  C3   C  CR6   0   0.374   3.3336  -0.4935  -0.1081
 4FX  C11  C  CR6   0   0.518  -0.9222   0.3731   0.1682
 4FX  C9   C  CH2   0  -0.325   1.3118   0.8668  -0.7702
 4FX  N16  N  N     0  -0.464  -1.6147   0.1834   1.2992
 4FX  N18  N  NH2   0  -0.823  -5.7230  -0.7187   1.0563
 4FX  N10  N  NH1   0  -0.642   0.4054   0.5414   0.3092
 4FX  O19  O  O     0  -0.492  -5.7219  -0.0199  -1.0819
 4FX  O2   O  O2    0  -0.463   2.5671  -1.5635  -0.3825
 4FX  H1   H  HCR6  0   0.253   5.3456   2.7375   0.6166
 4FX  H2   H  HCR6  0   0.260   6.3863   0.5088   0.9535
 4FX  H3   H  HCR6  0   0.268  -3.4225   0.1929  -2.0938
 4FX  H4   H  HCR6  0   0.255   3.0107   2.8718  -0.1885
 4FX  H5   H  HCR6  0   0.280   5.1293  -1.5296   0.4982
 4FX  H6   H  HCR6  0   0.278  -1.0031   0.5722  -1.9991
 4FX  H7   H  HCR6  0   0.251  -3.4102  -0.1467   2.1808
 4FX  H8   H  HCH3  0   0.260   2.3444  -3.5574  -0.5344
 4FX  H9   H  HCH3  0   0.230   3.9836  -2.9995  -0.9140
 4FX  H10  H  HCH3  0   0.230   3.4330  -3.0666   0.7751
 4FX  H11  H  HCH2  0   0.251   1.1285   1.8807  -1.1430
 4FX  H12  H  HCH2  0   0.254   1.1370   0.1866  -1.6070
 4FX  H13  H  HNH2  0   0.408  -5.2256  -1.0620   1.8584
 4FX  H14  H  HNH2  0   0.403  -6.7137  -0.8956   1.0298
 4FX  H15  H  HNH1  0   0.389   0.7400   0.6453   1.2542
 4FX  C17  C  C     0   0.488  -5.1075  -0.2617  -0.0483
 4FX  C1   C  CH3   0  -0.437   3.1256  -2.8561  -0.2522

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
 4FX  C5   C6   aromatic  1.384  0.020  1.384
 4FX  C5   C4   aromatic  1.390  0.020  1.390
 4FX  C6   C7   aromatic  1.390  0.020  1.390
 4FX  C4   C3   aromatic  1.392  0.020  1.392
 4FX  C7   C8   aromatic  1.387  0.020  1.387
 4FX  C3   C8   aromatic  1.404  0.020  1.404
 4FX  C3   O2   single    1.345  0.020  1.345
 4FX  C8   C9   single    1.502  0.020  1.502
 4FX  C1   O2   single    1.414  0.020  1.414
 4FX  C9   N10  single    1.447  0.020  1.447
 4FX  N10  C11  single    1.346  0.020  1.346
 4FX  C12  C11  aromatic  1.411  0.020  1.411
 4FX  C12  C13  aromatic  1.372  0.020  1.372
 4FX  C11  N16  aromatic  1.340  0.020  1.340
 4FX  C13  C14  aromatic  1.399  0.020  1.399
 4FX  N16  C15  aromatic  1.320  0.020  1.320
 4FX  C14  C15  aromatic  1.391  0.020  1.391
 4FX  C14  C17  single    1.483  0.020  1.483
 4FX  C17  O19  double    1.226  0.020  1.226
 4FX  C17  N18  single    1.345  0.020  1.345
 4FX  C6   H1   single    0.930  0.020  1.080
 4FX  C5   H2   single    0.930  0.020  1.080
 4FX  C13  H3   single    0.930  0.020  1.080
 4FX  C7   H4   single    0.930  0.020  1.080
 4FX  C4   H5   single    0.930  0.020  1.080
 4FX  C12  H6   single    0.930  0.020  1.080
 4FX  C15  H7   single    0.930  0.020  1.080
 4FX  C1   H8   single    0.970  0.020  1.090
 4FX  C1   H9   single    0.970  0.020  1.090
 4FX  C1   H10  single    0.970  0.020  1.090
 4FX  C9   H11  single    0.970  0.020  1.090
 4FX  C9   H12  single    0.970  0.020  1.090
 4FX  N18  H13  single    0.860  0.020  1.020
 4FX  N18  H14  single    0.860  0.020  1.020
 4FX  N10  H15  single    0.860  0.020  1.020

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
 4FX  H1   C6   C7   120.31  3.000
 4FX  H1   C6   C5   120.73  3.000
 4FX  C7   C6   C5   118.96  3.000
 4FX  H2   C5   C4   118.99  3.000
 4FX  H2   C5   C6   120.28  3.000
 4FX  C4   C5   C6   120.73  3.000
 4FX  H3   C13  C14  119.91  3.000
 4FX  H3   C13  C12  119.49  3.000
 4FX  C14  C13  C12  120.60  3.000
 4FX  H4   C7   C8   118.71  3.000
 4FX  H4   C7   C6   119.72  3.000
 4FX  C8   C7   C6   121.57  3.000
 4FX  H5   C4   C3   121.15  3.000
 4FX  H5   C4   C5   118.90  3.000
 4FX  C3   C4   C5   119.95  3.000
 4FX  H6   C12  C11  121.30  3.000
 4FX  H6   C12  C13  120.32  3.000
 4FX  C11  C12  C13  118.37  3.000
 4FX  H7   C15  N16  114.51  3.000
 4FX  H7   C15  C14  120.94  3.000
 4FX  N16  C15  C14  124.54  3.000
 4FX  C17  C14  C15  124.45  3.000
 4FX  C17  C14  C13  119.33  3.000
 4FX  C15  C14  C13  116.19  3.000
 4FX  C9   C8   C3   120.62  3.000
 4FX  C9   C8   C7   120.49  3.000
 4FX  C3   C8   C7   118.88  3.000
 4FX  O2   C3   C8   116.13  3.000
 4FX  O2   C3   C4   123.97  3.000
 4FX  C8   C3   C4   119.91  3.000
 4FX  N10  C11  N16  116.05  3.000
 4FX  N16  C11  C12  121.43  3.000
 4FX  N10  C11  C12  122.52  3.000
 4FX  H12  C9   H11  106.78  3.000
 4FX  H12  C9   N10  109.34  3.000
 4FX  H11  C9   N10  110.93  3.000
 4FX  H12  C9   C8   110.24  3.000
 4FX  H11  C9   C8   109.20  3.000
 4FX  N10  C9   C8   110.28  3.000
 4FX  C11  N16  C15  118.84  3.000
 4FX  H14  N18  H13  116.63  3.000
 4FX  H14  N18  C17  119.25  3.000
 4FX  H13  N18  C17  123.07  3.000
 4FX  H15  N10  C9   117.93  3.000
 4FX  H15  N10  C11  116.02  3.000
 4FX  C9   N10  C11  124.62  3.000
 4FX  C1   O2   C3   118.91  3.000
 4FX  O19  C17  N18  122.01  3.000
 4FX  N18  C17  C14  117.05  3.000
 4FX  O19  C17  C14  120.94  3.000
 4FX  H10  C1   H9   108.85  3.000
 4FX  H10  C1   H8   108.77  3.000
 4FX  H9   C1   H8   108.80  3.000
 4FX  H10  C1   O2   111.95  3.000
 4FX  H9   C1   O2   111.97  3.000
 4FX  H8   C1   O2   106.38  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
 4FX  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 4FX  CONST_02  C3   C8   C7   C6      0.00   0.0  0
 4FX  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 4FX  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 4FX  CONST_05  N16  C11  C12  C13     0.00   0.0  0
 4FX  CONST_06  N16  C15  C14  C13     0.00   0.0  0
 4FX  CONST_07  C4   C5   C6   C7      0.00   0.0  0
 4FX  CONST_08  C4   C3   C8   C7      0.00   0.0  0
 4FX  CONST_09  C15  N16  C11  C12     0.00   0.0  0
 4FX  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 4FX  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 4FX  CONST_12  C11  N16  C15  C14     0.00   0.0  0
 4FX  CONST_13  C9   C8   C7   C6    180.00   0.0  0
 4FX  CONST_14  O2   C3   C4   C5    180.00   0.0  0
 4FX  CONST_15  N10  C11  C12  C13   180.00   0.0  0
 4FX  CONST_16  O2   C3   C8   C7    180.00   0.0  0
 4FX  CONST_17  C9   C8   C3   C4    180.00   0.0  0
 4FX  CONST_18  C17  C14  C13  C12   180.00   0.0  0
 4FX  CONST_19  N10  C11  N16  C15   180.00   0.0  0
 4FX  CONST_20  N16  C15  C14  C17   180.00   0.0  0
 4FX  CONST_21  H5   C4   C5   C6    180.00   0.0  0
 4FX  CONST_22  H4   C7   C6   C5    180.00   0.0  0
 4FX  CONST_23  H7   C15  C14  C13   180.00   0.0  0
 4FX  CONST_24  H2   C5   C6   C7    180.00   0.0  0
 4FX  CONST_25  H1   C6   C5   C4    180.00   0.0  0
 4FX  CONST_26  H3   C13  C14  C15   180.00   0.0  0
 4FX  CONST_27  H6   C12  C13  C14   180.00   0.0  0
 4FX  CONST_28  C9   N10  C11  C12     0.00   0.0  0
 4FX  CONST_29  N16  C11  N10  C9    180.00   0.0  0
 4FX  CONST_30  H15  N10  C11  C12   180.00   0.0  0
 4FX  CONST_31  H13  N18  C17  C14     0.00   0.0  0
 4FX  CONST_32  H14  N18  C17  C14   180.00   0.0  0
 4FX  Var_01    O19  C17  C14  C13   -12.29  30.0  2
 4FX  Var_02    N10  C9   C8   C7   -104.27  30.0  2
 4FX  Var_03    C11  N10  C9   C8   -170.89  30.0  3
 4FX  Var_04    H8   C1   O2   C3   -179.18  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
 4FX  plan-1  C6   0.020
 4FX  plan-1  C5   0.020
 4FX  plan-1  C7   0.020
 4FX  plan-1  C4   0.020
 4FX  plan-1  C8   0.020
 4FX  plan-1  C3   0.020
 4FX  plan-1  C9   0.020
 4FX  plan-1  O2   0.020
 4FX  plan-1  H1   0.020
 4FX  plan-1  H2   0.020
 4FX  plan-1  H4   0.020
 4FX  plan-1  H5   0.020
 4FX  plan-2  C13  0.020
 4FX  plan-2  C12  0.020
 4FX  plan-2  C15  0.020
 4FX  plan-2  C14  0.020
 4FX  plan-2  C11  0.020
 4FX  plan-2  N16  0.020
 4FX  plan-2  N10  0.020
 4FX  plan-2  H3   0.020
 4FX  plan-2  H6   0.020
 4FX  plan-2  H7   0.020
 4FX  plan-2  C17  0.020
 4FX  plan-3  C14  0.020
 4FX  plan-3  N18  0.020
 4FX  plan-3  O19  0.020
 4FX  plan-3  H13  0.020
 4FX  plan-3  H14  0.020
 4FX  plan-3  C17  0.020
 4FX  plan-4  C11  0.020
 4FX  plan-4  C9   0.020
 4FX  plan-4  N10  0.020
 4FX  plan-4  H15  0.020

