# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:31:34 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 5-methyl-N-[(pyridin-4-yl)methyl]pyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cncc(NCc2ccncc2)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
 WN7  WN7  5-methyl-N-[(pyridin-4-yl)methyl]pyridin-3-amine  ligand  28  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WN7
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
 WN7  C10  C  CR16  0  -0.364  -33.4187  -7.1825  -22.7713
 WN7  N12  N  N     0  -0.411  -33.3127  -4.8023  -22.5612
 WN7  C13  C  CR16  0  -0.060  -32.8487  -4.9726  -21.3288
 WN7  C15  C  CR16  0  -0.264  -29.8772  -8.4797  -21.1955
 WN7  C02  C  CR6   0   0.025  -28.5007  -8.2904  -21.2570
 WN7  C03  C  CR16  0  -0.155  -27.7937  -8.2627  -20.0616
 WN7  C05  C  CR16  0  -0.162  -29.6792  -8.5896  -18.8203
 WN7  C06  C  CR6   0   0.305  -30.5029  -8.6414  -19.9587
 WN7  C09  C  CR6   0   0.160  -32.9357  -7.3578  -21.4793
 WN7  C11  C  CR16  0  -0.061  -33.5907  -5.8976  -23.2604
 WN7  C14  C  CR16  0  -0.351  -32.6442  -6.2148  -20.7468
 WN7  N04  N  N     0  -0.382  -28.3756  -8.4079  -18.8742
 WN7  N07  N  NH1   0  -0.693  -31.8447  -8.8627  -19.8210
 WN7  H1   H  HCR6  0   0.265  -33.6556  -8.0342  -23.3972
 WN7  H2   H  HCR6  0   0.262  -32.6236  -4.0720  -20.7679
 WN7  H3   H  HCR6  0   0.266  -30.4518  -8.4981  -22.1143
 WN7  H4   H  HCH3  0   0.249  -28.2025  -7.2551  -23.1159
 WN7  H5   H  HCH3  0   0.245  -26.7361  -7.9626  -22.4404
 WN7  H6   H  HCH3  0   0.249  -27.9421  -8.9881  -23.2124
 WN7  H7   H  HCR6  0   0.243  -26.7185  -8.1159  -20.0653
 WN7  H8   H  HCR6  0   0.256  -30.1222  -8.7039  -17.8343
 WN7  H9   H  HCH2  0   0.297  -33.7430  -9.0895  -20.5449
 WN7  H10  H  HCH2  0   0.258  -32.5025  -9.4365  -21.7147
 WN7  H11  H  HCR6  0   0.263  -33.9658  -5.7479  -24.2670
 WN7  H12  H  HCR6  0   0.261  -32.2608  -6.2759  -19.7370
 WN7  H13  H  HNH1  0   0.392  -32.2225  -8.8098  -18.8903
 WN7  C08  C  CH2   0  -0.364  -32.7717  -8.7483  -20.9072
 WN7  C01  C  CH3   0  -0.727  -27.8064  -8.1146  -22.5733

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
 WN7  C11  C10  aromatic  1.386  0.020  1.386
 WN7  C11  N12  aromatic  1.329  0.020  1.329
 WN7  C10  C09  aromatic  1.390  0.020  1.390
 WN7  C01  C02  single    1.498  0.020  1.498
 WN7  N12  C13  aromatic  1.328  0.020  1.328
 WN7  C09  C08  single    1.513  0.020  1.513
 WN7  C09  C14  aromatic  1.388  0.020  1.388
 WN7  C08  N07  single    1.433  0.020  1.433
 WN7  C15  C02  aromatic  1.391  0.020  1.391
 WN7  C15  C06  aromatic  1.395  0.020  1.395
 WN7  C02  C03  aromatic  1.389  0.020  1.389
 WN7  C13  C14  aromatic  1.387  0.020  1.387
 WN7  N07  C06  single    1.367  0.020  1.367
 WN7  C06  C05  aromatic  1.406  0.020  1.406
 WN7  C03  N04  aromatic  1.330  0.020  1.330
 WN7  C05  N04  aromatic  1.317  0.020  1.317
 WN7  C10  H1   single    0.930  0.020  1.080
 WN7  C13  H2   single    0.930  0.020  1.080
 WN7  C15  H3   single    0.930  0.020  1.080
 WN7  C01  H4   single    0.970  0.020  1.090
 WN7  C01  H5   single    0.970  0.020  1.090
 WN7  C01  H6   single    0.970  0.020  1.090
 WN7  C03  H7   single    0.930  0.020  1.080
 WN7  C05  H8   single    0.930  0.020  1.080
 WN7  C08  H9   single    0.970  0.020  1.090
 WN7  C08  H10  single    0.970  0.020  1.090
 WN7  C11  H11  single    0.930  0.020  1.080
 WN7  C14  H12  single    0.930  0.020  1.080
 WN7  N07  H13  single    0.890  0.020  1.040

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
 WN7  H1   C10  C11  119.87  3.000
 WN7  H1   C10  C09  120.91  3.000
 WN7  C11  C10  C09  119.21  3.000
 WN7  C11  N12  C13  117.12  3.000
 WN7  H2   C13  C14  119.74  3.000
 WN7  H2   C13  N12  116.49  3.000
 WN7  C14  C13  N12  123.77  3.000
 WN7  H3   C15  C06  120.77  3.000
 WN7  H3   C15  C02  119.31  3.000
 WN7  C06  C15  C02  119.92  3.000
 WN7  C03  C02  C01  121.19  3.000
 WN7  C03  C02  C15  117.93  3.000
 WN7  C01  C02  C15  120.88  3.000
 WN7  H7   C03  N04  116.82  3.000
 WN7  H7   C03  C02  120.27  3.000
 WN7  N04  C03  C02  122.91  3.000
 WN7  H8   C05  N04  117.06  3.000
 WN7  H8   C05  C06  119.46  3.000
 WN7  N04  C05  C06  123.48  3.000
 WN7  N07  C06  C05  119.96  3.000
 WN7  C05  C06  C15  116.78  3.000
 WN7  N07  C06  C15  123.25  3.000
 WN7  C14  C09  C08  122.31  3.000
 WN7  C14  C09  C10  117.34  3.000
 WN7  C08  C09  C10  120.33  3.000
 WN7  H11  C11  N12  116.55  3.000
 WN7  H11  C11  C10  119.91  3.000
 WN7  N12  C11  C10  123.54  3.000
 WN7  H12  C14  C09  121.35  3.000
 WN7  H12  C14  C13  119.64  3.000
 WN7  C09  C14  C13  119.01  3.000
 WN7  C05  N04  C03  118.98  3.000
 WN7  H13  N07  C08  117.02  3.000
 WN7  H13  N07  C06  116.97  3.000
 WN7  C08  N07  C06  123.08  3.000
 WN7  H10  C08  H9   105.50  3.000
 WN7  H10  C08  N07  110.49  3.000
 WN7  H9   C08  N07  107.41  3.000
 WN7  H10  C08  C09  109.01  3.000
 WN7  H9   C08  C09  108.45  3.000
 WN7  N07  C08  C09  115.49  3.000
 WN7  H6   C01  H5   107.79  3.000
 WN7  H6   C01  H4   107.11  3.000
 WN7  H5   C01  H4   107.91  3.000
 WN7  H6   C01  C02  111.29  3.000
 WN7  H5   C01  C02  111.38  3.000
 WN7  H4   C01  C02  111.17  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
 WN7  CONST_01  C13  N12  C11  C10    0.00   0.0  0
 WN7  CONST_02  C13  C14  C09  C10    0.00   0.0  0
 WN7  CONST_03  C09  C10  C11  N12    0.00   0.0  0
 WN7  CONST_04  C09  C14  C13  N12    0.00   0.0  0
 WN7  CONST_05  N04  C03  C02  C15    0.00   0.0  0
 WN7  CONST_06  N04  C05  C06  C15    0.00   0.0  0
 WN7  CONST_07  C05  C06  C15  C02    0.00   0.0  0
 WN7  CONST_08  C05  N04  C03  C02    0.00   0.0  0
 WN7  CONST_09  C06  C15  C02  C03    0.00   0.0  0
 WN7  CONST_10  C06  C05  N04  C03    0.00   0.0  0
 WN7  CONST_11  C14  C09  C10  C11    0.00   0.0  0
 WN7  CONST_12  C14  C13  N12  C11    0.00   0.0  0
 WN7  CONST_13  C08  C09  C14  C13  180.00   0.0  0
 WN7  CONST_14  C06  C15  C02  C01  180.00   0.0  0
 WN7  CONST_15  N04  C03  C02  C01  180.00   0.0  0
 WN7  CONST_16  N07  C06  C15  C02  180.00   0.0  0
 WN7  CONST_17  C11  C10  C09  C08  180.00   0.0  0
 WN7  CONST_18  N07  C06  C05  N04  180.00   0.0  0
 WN7  CONST_19  H12  C14  C09  C10  180.00   0.0  0
 WN7  CONST_20  H1   C10  C11  N12  180.00   0.0  0
 WN7  CONST_21  H11  C11  N12  C13  180.00   0.0  0
 WN7  CONST_22  H7   C03  C02  C15  180.00   0.0  0
 WN7  CONST_23  H8   C05  C06  C15  180.00   0.0  0
 WN7  CONST_24  H3   C15  C02  C03  180.00   0.0  0
 WN7  CONST_25  H2   C13  C14  C09  180.00   0.0  0
 WN7  CONST_26  C08  N07  C06  C15    0.00   0.0  0
 WN7  CONST_27  C08  N07  C06  C05  180.00   0.0  0
 WN7  CONST_28  H13  N07  C06  C15  180.00   0.0  0
 WN7  Var_01    N07  C08  C09  C10  157.94  30.0  2
 WN7  Var_02    C09  C08  N07  C06  -65.35  30.0  2
 WN7  Var_03    H4   C01  C02  C15   58.72  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
 WN7  plan-1  C15  0.020
 WN7  plan-1  C02  0.020
 WN7  plan-1  C03  0.020
 WN7  plan-1  C05  0.020
 WN7  plan-1  C06  0.020
 WN7  plan-1  N04  0.020
 WN7  plan-1  N07  0.020
 WN7  plan-1  H3   0.020
 WN7  plan-1  H7   0.020
 WN7  plan-1  H8   0.020
 WN7  plan-1  C01  0.020
 WN7  plan-2  C10  0.020
 WN7  plan-2  N12  0.020
 WN7  plan-2  C13  0.020
 WN7  plan-2  C09  0.020
 WN7  plan-2  C11  0.020
 WN7  plan-2  C14  0.020
 WN7  plan-2  H1   0.020
 WN7  plan-2  H2   0.020
 WN7  plan-2  H11  0.020
 WN7  plan-2  H12  0.020
 WN7  plan-2  C08  0.020
 WN7  plan-3  C06  0.020
 WN7  plan-3  N07  0.020
 WN7  plan-3  H13  0.020
 WN7  plan-3  C08  0.020

