# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:20:22 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-methyl-6-[2-(5-{3-[(methylamino)methyl]phenyl}pyridin-3-yl)ethyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cccc(c1)c2cncc(CCc3cc(C)cc(N)n3)c2
#
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
 W79  W79  4-methyl-6-[2-(5-{3-[(methylamino)methyl]phenyl}pyridin-3-yl)ethyl]pyridin-2-amine  ligand  49  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W79
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
 W79  N02  N  NH2   0  -0.839   7.0197  -1.5316   0.1355
 W79  C02  C  CR6   0   0.441   6.1148  -0.5379   0.3735
 W79  C03  C  CR16  0  -0.444   6.5399   0.7881   0.5669
 W79  C04  C  CR6   0   0.203   5.5943   1.7750   0.7557
 W79  C07  C  CH3   0  -0.725   5.9951   3.1984   0.9972
 W79  C05  C  CR16  0  -0.434   4.2442   1.4061   0.7398
 W79  N01  N  N     0  -0.483   4.8301  -0.8774   0.3689
 W79  C06  C  CR6   0   0.273   3.9144   0.0767   0.5463
 W79  C08  C  CH2   0  -0.490   2.4814  -0.3697   0.4847
 W79  C09  C  CH2   0  -0.516   2.0737  -0.7491  -0.9450
 W79  C13  C  CR6   0   0.053   0.6633  -1.2541  -1.0105
 W79  C14  C  CR16  0  -0.247  -0.4256  -0.3921  -0.9970
 W79  C12  C  CR16  0  -0.116   0.3903  -2.6179  -1.0373
 W79  N11  N  N     0  -0.394  -0.8352  -3.1258  -1.0627
 W79  C16  C  CR16  0  -0.112  -1.8596  -2.2869  -1.0545
 W79  C15  C  CR6   0   0.009  -1.7221  -0.8985  -1.0157
 W79  C21  C  CR6   0   0.108  -2.9047  -0.0185  -0.9988
 W79  C26  C  CR16  0  -0.382  -4.0501  -0.3870  -0.2886
 W79  C22  C  CR16  0  -0.329  -2.9053   1.1960  -1.6816
 W79  C23  C  CR16  0  -0.226  -4.0256   2.0156  -1.6499
 W79  C24  C  CR16  0  -0.297  -5.1550   1.6347  -0.9425
 W79  C25  C  CR6   0   0.120  -5.1785   0.4207  -0.2578
 W79  C27  C  CH2   0  -0.329  -6.4036   0.0015   0.5095
 W79  N28  N  NH1   0  -0.584  -6.7974   1.0130   1.4697
 W79  C29  C  CH3   0  -0.520  -7.9974   0.6502   2.1957
 W79  H1   H  HNH2  0   0.379   6.6931  -2.4738   0.2743
 W79  H2   H  HNH2  0   0.388   7.9708  -1.3778   0.4256
 W79  H3   H  HCR6  0   0.254   7.5977   1.0234   0.5663
 W79  H4   H  HCH3  0   0.255   5.9490   3.4305   2.0631
 W79  H5   H  HCH3  0   0.247   7.0121   3.3944   0.6611
 W79  H6   H  HCH3  0   0.248   5.3250   3.8913   0.4887
 W79  H7   H  HCR6  0   0.244   3.4672   2.1486   0.8719
 W79  H8   H  HCH2  0   0.251   2.3435  -1.2348   1.1385
 W79  H9   H  HCH2  0   0.249   1.8268   0.4219   0.8561
 W79  H10  H  HCH2  0   0.256   2.1877   0.1215  -1.5954
 W79  H11  H  HCH2  0   0.255   2.7557  -1.5158  -1.3186
 W79  H12  H  HCR6  0   0.261  -0.2633   0.6794  -0.9559
 W79  H13  H  HCR6  0   0.257   1.2097  -3.3304  -1.0424
 W79  H14  H  HCR6  0   0.259  -2.8478  -2.7333  -1.0986
 W79  H15  H  HCR6  0   0.250  -4.0548  -1.3143   0.2733
 W79  H16  H  HCR6  0   0.254  -2.0384   1.4991  -2.2559
 W79  H17  H  HCR6  0   0.256  -4.0174   2.9543  -2.1890
 W79  H18  H  HCR6  0   0.250  -6.0237   2.2803  -0.9188
 W79  H19  H  HCH2  0   0.237  -7.2341  -0.1358  -0.1916
 W79  H20  H  HCH2  0   0.212  -6.2278  -0.9842   0.9680
 W79  H21  H  HNH1  0   0.345  -6.0406   1.1511   2.1280
 W79  H23  H  HCH3  0   0.223  -8.8511   0.6262   1.5155
 W79  H24  H  HCH3  0   0.195  -7.9461  -0.3294   2.6913
 W79  H25  H  HCH3  0   0.234  -8.2059   1.3998   2.9588

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
 W79  C07  C04  single    1.498  0.020  1.498
 W79  C12  N11  aromatic  1.327  0.020  1.327
 W79  C12  C13  aromatic  1.391  0.020  1.391
 W79  N11  C16  aromatic  1.324  0.020  1.324
 W79  C04  C05  aromatic  1.400  0.020  1.400
 W79  C04  C03  aromatic  1.380  0.020  1.380
 W79  C05  C06  aromatic  1.383  0.020  1.383
 W79  C03  C02  aromatic  1.406  0.020  1.406
 W79  C09  C13  single    1.500  0.020  1.500
 W79  C09  C08  single    1.534  0.020  1.534
 W79  C13  C14  aromatic  1.389  0.020  1.389
 W79  C16  C15  aromatic  1.396  0.020  1.396
 W79  C06  C08  single    1.502  0.020  1.502
 W79  C06  N01  aromatic  1.334  0.020  1.334
 W79  C02  N01  aromatic  1.329  0.020  1.329
 W79  C02  N02  single    1.365  0.020  1.365
 W79  C15  C14  aromatic  1.392  0.020  1.392
 W79  C15  C21  single    1.474  0.020  1.474
 W79  C21  C22  aromatic  1.393  0.020  1.393
 W79  C21  C26  aromatic  1.397  0.020  1.397
 W79  C22  C23  aromatic  1.388  0.020  1.388
 W79  C26  C25  aromatic  1.388  0.020  1.388
 W79  C23  C24  aromatic  1.386  0.020  1.386
 W79  C25  C24  aromatic  1.394  0.020  1.394
 W79  C25  C27  single    1.505  0.020  1.505
 W79  C27  N28  single    1.449  0.020  1.449
 W79  N28  C29  single    1.449  0.020  1.449
 W79  N02  H1   single    0.890  0.020  1.040
 W79  N02  H2   single    0.890  0.020  1.040
 W79  C03  H3   single    0.930  0.020  1.080
 W79  C07  H4   single    0.970  0.020  1.090
 W79  C07  H5   single    0.970  0.020  1.090
 W79  C07  H6   single    0.970  0.020  1.090
 W79  C05  H7   single    0.930  0.020  1.080
 W79  C08  H8   single    0.970  0.020  1.090
 W79  C08  H9   single    0.970  0.020  1.090
 W79  C09  H10  single    0.970  0.020  1.090
 W79  C09  H11  single    0.970  0.020  1.090
 W79  C14  H12  single    0.930  0.020  1.080
 W79  C12  H13  single    0.930  0.020  1.080
 W79  C16  H14  single    0.930  0.020  1.080
 W79  C26  H15  single    0.930  0.020  1.080
 W79  C22  H16  single    0.930  0.020  1.080
 W79  C23  H17  single    0.930  0.020  1.080
 W79  C24  H18  single    0.930  0.020  1.080
 W79  C27  H19  single    0.970  0.020  1.090
 W79  C27  H20  single    0.970  0.020  1.090
 W79  N28  H21  single    0.890  0.020  1.040
 W79  C29  H23  single    0.970  0.020  1.090
 W79  C29  H24  single    0.970  0.020  1.090
 W79  C29  H25  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
 W79  H2   N02  H1   114.21  3.000
 W79  H2   N02  C02  117.72  3.000
 W79  H1   N02  C02  116.24  3.000
 W79  N01  C02  C03  122.26  3.000
 W79  N01  C02  N02  117.03  3.000
 W79  C03  C02  N02  120.67  3.000
 W79  H3   C03  C04  120.91  3.000
 W79  H3   C03  C02  120.00  3.000
 W79  C04  C03  C02  119.09  3.000
 W79  C05  C04  C07  120.68  3.000
 W79  C05  C04  C03  118.09  3.000
 W79  C07  C04  C03  121.21  3.000
 W79  H6   C07  H5   108.42  3.000
 W79  H6   C07  H4   107.12  3.000
 W79  H5   C07  H4   107.61  3.000
 W79  H6   C07  C04  111.36  3.000
 W79  H5   C07  C04  111.78  3.000
 W79  H4   C07  C04  110.36  3.000
 W79  H7   C05  C06  120.33  3.000
 W79  H7   C05  C04  120.66  3.000
 W79  C06  C05  C04  119.00  3.000
 W79  C06  N01  C02  118.71  3.000
 W79  C08  C06  N01  115.90  3.000
 W79  N01  C06  C05  122.84  3.000
 W79  C08  C06  C05  121.25  3.000
 W79  H9   C08  H8   107.13  3.000
 W79  H9   C08  C09  109.68  3.000
 W79  H8   C08  C09  109.15  3.000
 W79  H9   C08  C06  110.02  3.000
 W79  H8   C08  C06  109.33  3.000
 W79  C09  C08  C06  111.42  3.000
 W79  H11  C09  H10  106.90  3.000
 W79  H11  C09  C13  109.64  3.000
 W79  H10  C09  C13  109.90  3.000
 W79  H11  C09  C08  109.06  3.000
 W79  H10  C09  C08  109.26  3.000
 W79  C13  C09  C08  111.95  3.000
 W79  C12  C13  C14  117.05  3.000
 W79  C14  C13  C09  121.87  3.000
 W79  C12  C13  C09  121.03  3.000
 W79  H12  C14  C15  119.95  3.000
 W79  H12  C14  C13  119.75  3.000
 W79  C15  C14  C13  120.29  3.000
 W79  H13  C12  N11  116.47  3.000
 W79  H13  C12  C13  119.69  3.000
 W79  N11  C12  C13  123.84  3.000
 W79  C16  N11  C12  118.16  3.000
 W79  H14  C16  C15  120.00  3.000
 W79  H14  C16  N11  116.33  3.000
 W79  C15  C16  N11  123.66  3.000
 W79  C21  C15  C16  121.00  3.000
 W79  C21  C15  C14  122.00  3.000
 W79  C16  C15  C14  117.00  3.000
 W79  C22  C21  C26  118.60  3.000
 W79  C26  C21  C15  120.40  3.000
 W79  C22  C21  C15  121.00  3.000
 W79  H15  C26  C25  118.86  3.000
 W79  H15  C26  C21  119.51  3.000
 W79  C25  C26  C21  121.62  3.000
 W79  H16  C22  C23  119.51  3.000
 W79  H16  C22  C21  120.23  3.000
 W79  C23  C22  C21  120.25  3.000
 W79  H17  C23  C24  119.91  3.000
 W79  H17  C23  C22  119.63  3.000
 W79  C24  C23  C22  120.45  3.000
 W79  H18  C24  C25  119.68  3.000
 W79  H18  C24  C23  120.07  3.000
 W79  C25  C24  C23  120.25  3.000
 W79  C27  C25  C24  120.45  3.000
 W79  C27  C25  C26  120.72  3.000
 W79  C24  C25  C26  118.83  3.000
 W79  H20  C27  H19  105.98  3.000
 W79  H20  C27  N28  113.09  3.000
 W79  H19  C27  N28  107.79  3.000
 W79  H20  C27  C25  109.37  3.000
 W79  H19  C27  C25  109.01  3.000
 W79  N28  C27  C25  111.38  3.000
 W79  H21  N28  C29  109.11  3.000
 W79  H21  N28  C27  108.84  3.000
 W79  C29  N28  C27  112.48  3.000
 W79  H25  C29  H24  107.84  3.000
 W79  H25  C29  H23  107.56  3.000
 W79  H24  C29  H23  107.33  3.000
 W79  H25  C29  N28  109.70  3.000
 W79  H24  C29  N28  114.24  3.000
 W79  H23  C29  N28  109.93  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
 W79  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 W79  CONST_02  C05  C06  N01  C02    0.00   0.0  0
 W79  CONST_03  C06  C05  C04  C03    0.00   0.0  0
 W79  CONST_04  C06  N01  C02  C03    0.00   0.0  0
 W79  CONST_05  N01  C06  C05  C04    0.00   0.0  0
 W79  CONST_06  N01  C02  C03  C04    0.00   0.0  0
 W79  CONST_07  C16  N11  C12  C13    0.00   0.0  0
 W79  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 W79  CONST_09  C21  C15  C14  C13  180.00   0.0  0
 W79  CONST_10  N11  C12  C13  C14    0.00   0.0  0
 W79  CONST_11  N11  C16  C15  C14    0.00   0.0  0
 W79  CONST_14  C15  C16  N11  C12    0.00   0.0  0
 W79  CONST_15  C15  C14  C13  C12    0.00   0.0  0
 W79  CONST_16  C21  C15  C16  N11  180.00   0.0  0
 W79  CONST_19  C23  C22  C21  C15  180.00   0.0  0
 W79  CONST_20  C25  C26  C21  C15  180.00   0.0  0
 W79  CONST_21  C24  C23  C22  C21    0.00   0.0  0
 W79  CONST_22  C24  C25  C26  C21    0.00   0.0  0
 W79  CONST_23  C23  C22  C21  C26    0.00   0.0  0
 W79  CONST_24  C23  C24  C25  C26    0.00   0.0  0
 W79  CONST_25  C25  C26  C21  C22    0.00   0.0  0
 W79  CONST_26  C25  C24  C23  C22    0.00   0.0  0
 W79  CONST_27  C04  C03  C02  N02  180.00   0.0  0
 W79  CONST_28  C06  N01  C02  N02  180.00   0.0  0
 W79  CONST_29  C07  C04  C03  C02  180.00   0.0  0
 W79  CONST_30  C08  C06  N01  C02  180.00   0.0  0
 W79  CONST_31  C08  C06  C05  C04  180.00   0.0  0
 W79  CONST_32  C06  C05  C04  C07  180.00   0.0  0
 W79  CONST_33  N11  C12  C13  C09  180.00   0.0  0
 W79  CONST_34  C15  C14  C13  C09  180.00   0.0  0
 W79  CONST_35  C27  C25  C26  C21  180.00   0.0  0
 W79  CONST_36  C27  C25  C24  C23  180.00   0.0  0
 W79  CONST_37  H7   C05  C04  C03  180.00   0.0  0
 W79  CONST_38  H3   C03  C04  C05  180.00   0.0  0
 W79  CONST_39  H13  C12  C13  C14  180.00   0.0  0
 W79  CONST_40  H14  C16  C15  C14  180.00   0.0  0
 W79  CONST_41  H12  C14  C13  C12  180.00   0.0  0
 W79  CONST_42  H16  C22  C21  C15    0.00   0.0  0
 W79  CONST_43  H15  C26  C21  C15    0.00   0.0  0
 W79  CONST_44  H17  C23  C22  C21  180.00   0.0  0
 W79  CONST_45  H18  C24  C25  C26  180.00   0.0  0
 W79  Var_01    C09  C08  C06  C05  107.69  30.0  2
 W79  Var_02    C13  C09  C08  C06  177.48  30.0  2
 W79  Var_03    C12  C13  C09  C08  -98.67  30.0  2
 W79  Var_04    N28  C27  C25  C26  124.68  30.0  2
 W79  Var_05    H4   C07  C04  C03  -99.64  30.0  2
 W79  Var_06    C29  N28  C27  C25  178.36  30.0  3
 W79  Var_07    H23  C29  N28  C27  -66.53  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
 W79  plan-1  N02  0.020
 W79  plan-1  C02  0.020
 W79  plan-1  C03  0.020
 W79  plan-1  C04  0.020
 W79  plan-1  C07  0.020
 W79  plan-1  C05  0.020
 W79  plan-1  N01  0.020
 W79  plan-1  C06  0.020
 W79  plan-1  C08  0.020
 W79  plan-1  H3   0.020
 W79  plan-1  H7   0.020
 W79  plan-2  C09  0.020
 W79  plan-2  C13  0.020
 W79  plan-2  C14  0.020
 W79  plan-2  C12  0.020
 W79  plan-2  N11  0.020
 W79  plan-2  C16  0.020
 W79  plan-2  C15  0.020
 W79  plan-2  C21  0.020
 W79  plan-2  H12  0.020
 W79  plan-2  H13  0.020
 W79  plan-2  H14  0.020
 W79  plan-3  C15  0.020
 W79  plan-3  C21  0.020
 W79  plan-3  C26  0.020
 W79  plan-3  C22  0.020
 W79  plan-3  C23  0.020
 W79  plan-3  C24  0.020
 W79  plan-3  C25  0.020
 W79  plan-3  C27  0.020
 W79  plan-3  H15  0.020
 W79  plan-3  H16  0.020
 W79  plan-3  H17  0.020
 W79  plan-3  H18  0.020
 W79  plan-4  N02  0.020
 W79  plan-4  C02  0.020
 W79  plan-4  H1   0.020
 W79  plan-4  H2   0.020

