# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:56:28 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 6-methyl-~{N}-(phenylmethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(NCc2ccccc2)n1
#
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
 JNE  JNE  6-methyl-~{N}-(phenylmethyl)pyridin-2-amine  ligand  29  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JNE
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
 JNE  C1   C  CR6   0   0.478   1.4793  -0.2312   0.0221
 JNE  C11  C  CR16  0  -0.283  -2.7527  -0.1029   1.1533
 JNE  C12  C  CR16  0  -0.300  -2.9925  -0.1322  -1.2326
 JNE  C13  C  CR16  0  -0.242  -4.0128   0.4635   1.2751
 JNE  C14  C  CR16  0  -0.241  -4.2554   0.4367  -1.1146
 JNE  C15  C  CR16  0  -0.265  -4.7676   0.7361   0.1395
 JNE  N2   N  N     0  -0.485   2.2732   0.8397  -0.0095
 JNE  N3   N  NH1   0  -0.653   0.1405   0.0232   0.0193
 JNE  C4   C  CR16  0  -0.415   1.9936  -1.5383   0.0792
 JNE  C5   C  CR6   0   0.241   3.5937   0.6800   0.0263
 JNE  C6   C  CH2   0  -0.339  -0.8536  -0.9984  -0.2273
 JNE  C7   C  CR16  0  -0.144   3.3640  -1.6898   0.1208
 JNE  C8   C  CR16  0  -0.381   4.1909  -0.5725   0.0971
 JNE  C9   C  CH3   0  -0.716   4.4179   1.9310  -0.0206
 JNE  C10  C  CR6   0   0.081  -2.2318  -0.4097  -0.1023
 JNE  H2   H  HCR6  0   0.253  -2.5964  -0.3625  -2.2145
 JNE  H3   H  HCR6  0   0.257  -4.4088   0.6900   2.2565
 JNE  H4   H  HCR6  0   0.257  -4.8365   0.6450  -2.0037
 JNE  H5   H  HCR6  0   0.257  -5.7506   1.1795   0.2346
 JNE  H6   H  HNH1  0   0.378  -0.1049   0.9631  -0.2510
 JNE  H7   H  HCR6  0   0.268   1.3435  -2.4016   0.0887
 JNE  H8   H  HCH2  0   0.242  -0.7315  -1.4554  -1.2172
 JNE  H9   H  HCH2  0   0.251  -0.7354  -1.7996   0.5068
 JNE  H10  H  HCR6  0   0.262   3.7913  -2.6837   0.1672
 JNE  H11  H  HCR6  0   0.251   5.2675  -0.6700   0.1235
 JNE  H12  H  HCH3  0   0.247   4.1644   2.5951   0.8069
 JNE  H13  H  HCH3  0   0.240   5.4830   1.7126   0.0329
 JNE  H14  H  HCH3  0   0.248   4.2314   2.4835  -0.9428
 JNE  H1   H  HCR6  0   0.252  -2.1701  -0.3141   2.0423

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
 JNE  N3   C6   single    1.447  0.020  1.447
 JNE  N3   C1   single    1.363  0.020  1.363
 JNE  C6   C10  single    1.504  0.020  1.504
 JNE  N2   C1   aromatic  1.333  0.020  1.333
 JNE  N2   C5   aromatic  1.331  0.020  1.331
 JNE  C9   C5   single    1.499  0.020  1.499
 JNE  C12  C10  aromatic  1.390  0.020  1.390
 JNE  C12  C14  aromatic  1.390  0.020  1.390
 JNE  C1   C4   aromatic  1.406  0.020  1.406
 JNE  C10  C11  aromatic  1.394  0.020  1.394
 JNE  C5   C8   aromatic  1.389  0.020  1.389
 JNE  C14  C15  aromatic  1.387  0.020  1.387
 JNE  C11  C13  aromatic  1.387  0.020  1.387
 JNE  C15  C13  aromatic  1.391  0.020  1.391
 JNE  C4   C7   aromatic  1.379  0.020  1.379
 JNE  C8   C7   aromatic  1.390  0.020  1.390
 JNE  C11  H1   single    0.930  0.020  1.080
 JNE  C12  H2   single    0.930  0.020  1.080
 JNE  C13  H3   single    0.930  0.020  1.080
 JNE  C14  H4   single    0.930  0.020  1.080
 JNE  C15  H5   single    0.930  0.020  1.080
 JNE  N3   H6   single    0.890  0.020  1.040
 JNE  C4   H7   single    0.930  0.020  1.080
 JNE  C6   H8   single    0.970  0.020  1.090
 JNE  C6   H9   single    0.970  0.020  1.090
 JNE  C7   H10  single    0.930  0.020  1.080
 JNE  C8   H11  single    0.930  0.020  1.080
 JNE  C9   H12  single    0.970  0.020  1.090
 JNE  C9   H13  single    0.970  0.020  1.090
 JNE  C9   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
 JNE  C4   C1   N3   122.21  3.000
 JNE  C4   C1   N2   122.00  3.000
 JNE  N3   C1   N2   115.78  3.000
 JNE  H1   C11  C10  119.69  3.000
 JNE  H1   C11  C13  119.74  3.000
 JNE  C10  C11  C13  120.58  3.000
 JNE  H2   C12  C10  119.63  3.000
 JNE  H2   C12  C14  119.73  3.000
 JNE  C10  C12  C14  120.64  3.000
 JNE  H3   C13  C15  120.06  3.000
 JNE  H3   C13  C11  119.84  3.000
 JNE  C15  C13  C11  120.10  3.000
 JNE  H4   C14  C15  120.18  3.000
 JNE  H4   C14  C12  119.79  3.000
 JNE  C15  C14  C12  120.03  3.000
 JNE  H5   C15  C14  120.20  3.000
 JNE  H5   C15  C13  120.10  3.000
 JNE  C14  C15  C13  119.70  3.000
 JNE  C5   N2   C1   119.59  3.000
 JNE  H6   N3   C6   116.44  3.000
 JNE  H6   N3   C1   114.44  3.000
 JNE  C6   N3   C1   122.93  3.000
 JNE  H7   C4   C7   120.63  3.000
 JNE  H7   C4   C1   121.54  3.000
 JNE  C7   C4   C1   117.83  3.000
 JNE  C9   C5   C8   121.17  3.000
 JNE  C8   C5   N2   122.42  3.000
 JNE  C9   C5   N2   116.40  3.000
 JNE  H9   C6   H8   106.77  3.000
 JNE  H9   C6   C10  109.28  3.000
 JNE  H8   C6   C10  109.88  3.000
 JNE  H9   C6   N3   109.20  3.000
 JNE  H8   C6   N3   111.81  3.000
 JNE  C10  C6   N3   109.83  3.000
 JNE  H10  C7   C8   120.24  3.000
 JNE  H10  C7   C4   119.61  3.000
 JNE  C8   C7   C4   120.14  3.000
 JNE  H11  C8   C7   121.29  3.000
 JNE  H11  C8   C5   120.70  3.000
 JNE  C7   C8   C5   118.01  3.000
 JNE  H14  C9   H13  108.08  3.000
 JNE  H14  C9   H12  107.05  3.000
 JNE  H13  C9   H12  108.19  3.000
 JNE  H14  C9   C5   110.80  3.000
 JNE  H13  C9   C5   111.66  3.000
 JNE  H12  C9   C5   110.89  3.000
 JNE  C6   C10  C12  120.79  3.000
 JNE  C12  C10  C11  118.95  3.000
 JNE  C6   C10  C11  120.24  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
 JNE  CONST_01  C8   C5   N2   C1     0.00   0.0  0
 JNE  CONST_02  C8   C7   C4   C1     0.00   0.0  0
 JNE  CONST_03  C14  C12  C10  C11    0.00   0.0  0
 JNE  CONST_04  C14  C15  C13  C11    0.00   0.0  0
 JNE  CONST_05  C13  C11  C10  C12    0.00   0.0  0
 JNE  CONST_06  C13  C15  C14  C12    0.00   0.0  0
 JNE  CONST_07  C10  C12  C14  C15    0.00   0.0  0
 JNE  CONST_08  C10  C11  C13  C15    0.00   0.0  0
 JNE  CONST_09  C7   C4   C1   N2     0.00   0.0  0
 JNE  CONST_10  C7   C8   C5   N2     0.00   0.0  0
 JNE  CONST_11  C5   N2   C1   C4     0.00   0.0  0
 JNE  CONST_12  C5   C8   C7   C4     0.00   0.0  0
 JNE  CONST_13  C9   C5   N2   C1   180.00   0.0  0
 JNE  CONST_14  C6   C10  C11  C13  180.00   0.0  0
 JNE  CONST_15  C6   C10  C12  C14  180.00   0.0  0
 JNE  CONST_16  C5   N2   C1   N3   180.00   0.0  0
 JNE  CONST_17  C7   C4   C1   N3   180.00   0.0  0
 JNE  CONST_18  C9   C5   C8   C7   180.00   0.0  0
 JNE  CONST_19  H10  C7   C4   C1   180.00   0.0  0
 JNE  CONST_20  H2   C12  C10  C11  180.00   0.0  0
 JNE  CONST_21  H5   C15  C13  C11  180.00   0.0  0
 JNE  CONST_22  H1   C11  C10  C12  180.00   0.0  0
 JNE  CONST_23  H4   C14  C15  C13  180.00   0.0  0
 JNE  CONST_24  H3   C13  C15  C14  180.00   0.0  0
 JNE  CONST_25  H7   C4   C1   N2   180.00   0.0  0
 JNE  CONST_26  H11  C8   C5   N2   180.00   0.0  0
 JNE  CONST_27  C6   N3   C1   N2   180.00   0.0  0
 JNE  CONST_28  C6   N3   C1   C4     0.00   0.0  0
 JNE  Var_01    C10  C6   N3   C1   177.54  30.0  3
 JNE  Var_02    N3   C6   C10  C11  -74.07  30.0  2
 JNE  Var_03    H12  C9   C5   N2    58.13  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
 JNE  plan-1  C11  0.020
 JNE  plan-1  C12  0.020
 JNE  plan-1  C13  0.020
 JNE  plan-1  C14  0.020
 JNE  plan-1  C15  0.020
 JNE  plan-1  C6   0.020
 JNE  plan-1  C10  0.020
 JNE  plan-1  H2   0.020
 JNE  plan-1  H3   0.020
 JNE  plan-1  H4   0.020
 JNE  plan-1  H5   0.020
 JNE  plan-1  H1   0.020
 JNE  plan-2  C1   0.020
 JNE  plan-2  N2   0.020
 JNE  plan-2  N3   0.020
 JNE  plan-2  C4   0.020
 JNE  plan-2  C5   0.020
 JNE  plan-2  C7   0.020
 JNE  plan-2  C8   0.020
 JNE  plan-2  C9   0.020
 JNE  plan-2  H7   0.020
 JNE  plan-2  H10  0.020
 JNE  plan-2  H11  0.020
 JNE  plan-3  C1   0.020
 JNE  plan-3  N3   0.020
 JNE  plan-3  C6   0.020
 JNE  plan-3  H6   0.020

