# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:46:29 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-{[(3-methylpyridin-2-yl)amino]methyl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccnc1NCc2ccccc2O
#
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
 2J5  2J5  2-{[(3-methylpyridin-2-yl)amino]methyl}phenol  ligand  30  16  .  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_2J5
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
 2J5  C4   C  CR16  0  -0.072  -3.4708  -1.5553   0.4142
 2J5  C5   C  CR6   0   0.476  -1.7878  -0.0770  -0.0306
 2J5  C6   C  CH2   0  -0.332   0.4674  -0.9789  -0.4272
 2J5  N1   N  NH1   0  -0.730  -0.4302   0.1481  -0.2063
 2J5  C7   C  CR6   0  -0.036   1.9003  -0.5240  -0.3666
 2J5  C8   C  CR16  0  -0.307   2.8113  -0.9044  -1.3446
 2J5  C9   C  CR16  0  -0.270   4.1528  -0.5568  -1.2608
 2J5  C10  C  CR16  0  -0.257   4.5908   0.1951  -0.1793
 2J5  C11  C  CR16  0  -0.336   3.6971   0.6042   0.7995
 2J5  C12  C  CR6   0   0.318   2.3536   0.2503   0.7115
 2J5  O    O  OH1   0  -0.644   1.5177   0.6571   1.6883
 2J5  C1   C  CR6   0  -0.015  -2.6756   1.0205  -0.0548
 2J5  C    C  CH3   0  -0.752  -2.1820   2.4135  -0.2954
 2J5  N    N  N     0  -0.459  -2.1787  -1.3198   0.1941
 2J5  C3   C  CR16  0  -0.349  -4.4307  -0.5664   0.4061
 2J5  C2   C  CR16  0  -0.194  -4.0096   0.7401   0.1648
 2J5  H1   H  HCR6  0   0.257  -3.7427  -2.5886   0.5989
 2J5  H2   H  HCH2  0   0.269   0.2781  -1.7165   0.3545
 2J5  H3   H  HCH2  0   0.256   0.2698  -1.4776  -1.3811
 2J5  H4   H  HNH1  0   0.400  -0.2249   0.9286  -0.8162
 2J5  H5   H  HCR6  0   0.253   2.4604  -1.4912  -2.1858
 2J5  H6   H  HCR6  0   0.251   4.8457  -0.8686  -2.0308
 2J5  H7   H  HCR6  0   0.255   5.6329   0.4765  -0.0977
 2J5  H8   H  HCR6  0   0.259   4.0351   1.1994   1.6389
 2J5  H9   H  HOH1  0   0.476   0.6028   0.5998   1.3492
 2J5  H10  H  HCH3  0   0.250  -1.7423   2.5260  -1.2901
 2J5  H11  H  HCH3  0   0.261  -2.9958   3.1320  -0.2188
 2J5  H12  H  HCH3  0   0.251  -1.4156   2.6992   0.4284
 2J5  H13  H  HCR6  0   0.261  -5.4712  -0.8007   0.5813
 2J5  H14  H  HCR6  0   0.263  -4.7307   1.5485   0.1542

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
 2J5  C9   C8   aromatic  1.388  0.020  1.388
 2J5  C9   C10  aromatic  1.388  0.020  1.388
 2J5  C8   C7   aromatic  1.390  0.020  1.390
 2J5  C    C1   single    1.497  0.020  1.497
 2J5  C10  C11  aromatic  1.387  0.020  1.387
 2J5  N1   C6   single    1.458  0.020  1.458
 2J5  N1   C5   single    1.387  0.020  1.387
 2J5  C7   C6   single    1.505  0.020  1.505
 2J5  C7   C12  aromatic  1.403  0.020  1.403
 2J5  C1   C5   aromatic  1.412  0.020  1.412
 2J5  C1   C2   aromatic  1.381  0.020  1.381
 2J5  C5   N    aromatic  1.322  0.020  1.322
 2J5  C11  C12  aromatic  1.392  0.020  1.392
 2J5  C12  O    single    1.349  0.020  1.349
 2J5  C2   C3   aromatic  1.394  0.020  1.394
 2J5  N    C4   aromatic  1.332  0.020  1.332
 2J5  C3   C4   aromatic  1.378  0.020  1.378
 2J5  C4   H1   single    0.930  0.020  1.080
 2J5  C6   H2   single    0.970  0.020  1.090
 2J5  C6   H3   single    0.970  0.020  1.090
 2J5  N1   H4   single    0.890  0.020  1.040
 2J5  C8   H5   single    0.930  0.020  1.080
 2J5  C9   H6   single    0.930  0.020  1.080
 2J5  C10  H7   single    0.930  0.020  1.080
 2J5  C11  H8   single    0.930  0.020  1.080
 2J5  O    H9   single    0.850  0.020  0.980
 2J5  C    H10  single    0.970  0.020  1.090
 2J5  C    H11  single    0.970  0.020  1.090
 2J5  C    H12  single    0.970  0.020  1.090
 2J5  C3   H13  single    0.930  0.020  1.080
 2J5  C2   H14  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
 2J5  H1   C4   C3   120.67  3.000
 2J5  H1   C4   N    116.10  3.000
 2J5  C3   C4   N    123.23  3.000
 2J5  N    C5   C1   123.21  3.000
 2J5  N    C5   N1   117.61  3.000
 2J5  C1   C5   N1   119.15  3.000
 2J5  H3   C6   H2   106.56  3.000
 2J5  H3   C6   C7   110.17  3.000
 2J5  H2   C6   C7   109.92  3.000
 2J5  H3   C6   N1   111.92  3.000
 2J5  H2   C6   N1   107.90  3.000
 2J5  C7   C6   N1   110.28  3.000
 2J5  H4   N1   C6   112.35  3.000
 2J5  H4   N1   C5   113.59  3.000
 2J5  C6   N1   C5   119.76  3.000
 2J5  C12  C7   C8   118.70  3.000
 2J5  C12  C7   C6   120.37  3.000
 2J5  C8   C7   C6   120.88  3.000
 2J5  H5   C8   C9   119.68  3.000
 2J5  H5   C8   C7   118.82  3.000
 2J5  C9   C8   C7   121.50  3.000
 2J5  H6   C9   C10  120.57  3.000
 2J5  H6   C9   C8   120.25  3.000
 2J5  C10  C9   C8   119.18  3.000
 2J5  H7   C10  C11  119.37  3.000
 2J5  H7   C10  C9   120.22  3.000
 2J5  C11  C10  C9   120.41  3.000
 2J5  H8   C11  C12  119.34  3.000
 2J5  H8   C11  C10  120.52  3.000
 2J5  C12  C11  C10  120.14  3.000
 2J5  O    C12  C11  118.41  3.000
 2J5  O    C12  C7   121.53  3.000
 2J5  C11  C12  C7   120.06  3.000
 2J5  H9   O    C12  108.13  3.000
 2J5  C2   C1   C    122.21  3.000
 2J5  C2   C1   C5   116.55  3.000
 2J5  C    C1   C5   121.24  3.000
 2J5  H12  C    H11  107.78  3.000
 2J5  H12  C    H10  107.08  3.000
 2J5  H11  C    H10  107.26  3.000
 2J5  H12  C    C1   111.61  3.000
 2J5  H11  C    C1   110.88  3.000
 2J5  H10  C    C1   112.00  3.000
 2J5  C5   N    C4   118.76  3.000
 2J5  H13  C3   C2   121.47  3.000
 2J5  H13  C3   C4   120.94  3.000
 2J5  C2   C3   C4   117.59  3.000
 2J5  H14  C2   C3   120.00  3.000
 2J5  H14  C2   C1   119.35  3.000
 2J5  C3   C2   C1   120.65  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
 2J5  CONST_01  C1   C5   N    C4      0.00   0.0  0
 2J5  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 2J5  CONST_03  C3   C2   C1   C5      0.00   0.0  0
 2J5  CONST_04  C3   C4   N    C5      0.00   0.0  0
 2J5  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 2J5  CONST_06  C10  C11  C12  C7      0.00   0.0  0
 2J5  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 2J5  CONST_08  C11  C12  C7   C8      0.00   0.0  0
 2J5  CONST_09  C12  C7   C8   C9      0.00   0.0  0
 2J5  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 2J5  CONST_11  C2   C1   C5   N       0.00   0.0  0
 2J5  CONST_12  C2   C3   C4   N       0.00   0.0  0
 2J5  CONST_13  N1   C5   N    C4    180.00   0.0  0
 2J5  CONST_14  C9   C8   C7   C6    180.00   0.0  0
 2J5  CONST_15  C11  C12  C7   C6    180.00   0.0  0
 2J5  CONST_16  C2   C1   C5   N1    180.00   0.0  0
 2J5  CONST_17  O    C12  C7   C8    180.00   0.0  0
 2J5  CONST_18  O    C12  C11  C10   180.00   0.0  0
 2J5  CONST_19  N    C5   C1   C     180.00   0.0  0
 2J5  CONST_20  C3   C2   C1   C     180.00   0.0  0
 2J5  CONST_21  H14  C2   C3   C4    180.00   0.0  0
 2J5  CONST_22  H1   C4   N    C5    180.00   0.0  0
 2J5  CONST_23  H6   C9   C8   C7    180.00   0.0  0
 2J5  CONST_24  H8   C11  C12  C7    180.00   0.0  0
 2J5  CONST_25  H7   C10  C9   C8    180.00   0.0  0
 2J5  CONST_26  H5   C8   C9   C10   180.00   0.0  0
 2J5  CONST_27  H13  C3   C2   C1    180.00   0.0  0
 2J5  CONST_28  C1   C5   N1   C6    180.00   0.0  0
 2J5  CONST_29  N    C5   N1   C6      0.00   0.0  0
 2J5  Var_01    C7   C6   N1   C5   -170.82  30.0  3
 2J5  Var_02    C8   C7   C6   N1   -132.52  30.0  2
 2J5  Var_03    H10  C    C1   C5     63.68  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
 2J5  plan-1  C6   0.020
 2J5  plan-1  C7   0.020
 2J5  plan-1  C8   0.020
 2J5  plan-1  C9   0.020
 2J5  plan-1  C10  0.020
 2J5  plan-1  C11  0.020
 2J5  plan-1  C12  0.020
 2J5  plan-1  O    0.020
 2J5  plan-1  H5   0.020
 2J5  plan-1  H6   0.020
 2J5  plan-1  H7   0.020
 2J5  plan-1  H8   0.020
 2J5  plan-2  C4   0.020
 2J5  plan-2  C5   0.020
 2J5  plan-2  N1   0.020
 2J5  plan-2  C1   0.020
 2J5  plan-2  C    0.020
 2J5  plan-2  N    0.020
 2J5  plan-2  C3   0.020
 2J5  plan-2  C2   0.020
 2J5  plan-2  H1   0.020
 2J5  plan-2  H13  0.020
 2J5  plan-2  H14  0.020
 2J5  plan-3  C5   0.020
 2J5  plan-3  C6   0.020
 2J5  plan-3  N1   0.020
 2J5  plan-3  H4   0.020

