# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:06:42 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-methyl-6-(2-{3-[3-(methylamino)propyl]phenyl}ethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCc1cccc(CCc2cc(C)cc(N)n2)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
 BYJ  BYJ  4-methyl-6-(2-{3-[3-(methylamino)propyl]phenyl}ethyl)pyridin-2-amine  ligand  46  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYJ
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
 BYJ  N02  N  NH2   0  -0.839   4.0704  -2.9100  -1.2773
 BYJ  C02  C  CR6   0   0.440   4.0739  -1.8040  -0.4765
 BYJ  C03  C  CR16  0  -0.447   5.2813  -1.2882   0.0267
 BYJ  C04  C  CR6   0   0.204   5.2527  -0.1404   0.7914
 BYJ  C05  C  CR16  0  -0.434   4.0113   0.4594   1.0341
 BYJ  C07  C  CH3   0  -0.725   6.5102   0.4622   1.3388
 BYJ  N01  N  N     0  -0.484   2.9011  -1.2293  -0.2344
 BYJ  C06  C  CR6   0   0.275   2.8713  -0.1190   0.5062
 BYJ  C08  C  CH2   0  -0.487   1.5159   0.4929   0.7196
 BYJ  C09  C  CH2   0  -0.510   0.9594   1.1128  -0.5694
 BYJ  C11  C  CR6   0   0.156  -0.4144   1.6866  -0.3615
 BYJ  C16  C  CR16  0  -0.379  -1.5500   0.9678  -0.7187
 BYJ  C12  C  CR16  0  -0.328  -0.5766   2.9376   0.2333
 BYJ  C13  C  CR16  0  -0.223  -1.8456   3.4458   0.4631
 BYJ  C14  C  CR16  0  -0.343  -2.9691   2.7117   0.1020
 BYJ  C15  C  CR6   0   0.162  -2.8345   1.4628  -0.4958
 BYJ  C17  C  CH2   0  -0.508  -4.0422   0.6444  -0.8606
 BYJ  C18  C  CH2   0  -0.438  -4.2760  -0.5132   0.1109
 BYJ  C19  C  CH2   0  -0.254  -5.5160  -1.3175  -0.2453
 BYJ  N20  N  NH1   0  -0.593  -5.7203  -2.4168   0.6772
 BYJ  C21  C  CH3   0  -0.518  -6.9048  -3.1903   0.3674
 BYJ  H1   H  HNH2  0   0.387   4.8701  -3.5187  -1.2328
 BYJ  H2   H  HNH2  0   0.379   3.1908  -3.3924  -1.3642
 BYJ  H3   H  HCR6  0   0.255   6.2173  -1.7925  -0.1824
 BYJ  H4   H  HCR6  0   0.243   3.9414   1.3565   1.6366
 BYJ  H5   H  HCH3  0   0.254   6.7680   1.3712   0.7924
 BYJ  H6   H  HCH3  0   0.249   6.3899   0.7426   2.3855
 BYJ  H7   H  HCH3  0   0.246   7.3537  -0.2220   1.2620
 BYJ  H8   H  HCH2  0   0.247   0.8252  -0.2776   1.0730
 BYJ  H9   H  HCH2  0   0.245   1.5699   1.2570   1.4981
 BYJ  H10  H  HCH2  0   0.247   1.6414   1.8961  -0.9115
 BYJ  H11  H  HCH2  0   0.247   0.9333   0.3492  -1.3494
 BYJ  H12  H  HCR6  0   0.236  -1.4321  -0.0048  -1.1875
 BYJ  H13  H  HCR6  0   0.243   0.2971   3.5160   0.5126
 BYJ  H14  H  HCR6  0   0.249  -1.9633   4.4195   0.9222
 BYJ  H15  H  HCR6  0   0.243  -3.9585   3.1151   0.2837
 BYJ  H16  H  HCH2  0   0.238  -4.9267   1.2865  -0.8768
 BYJ  H17  H  HCH2  0   0.238  -3.9291   0.2445  -1.8728
 BYJ  H18  H  HCH2  0   0.226  -3.4049  -1.1741   0.1159
 BYJ  H19  H  HCH2  0   0.224  -4.3742  -0.1151   1.1264
 BYJ  H20  H  HCH2  0   0.185  -6.3866  -0.6420  -0.2947
 BYJ  H21  H  HCH2  0   0.213  -5.3997  -1.7333  -1.2519
 BYJ  H22  H  HNH1  0   0.340  -5.8134  -2.0409   1.6131
 BYJ  H24  H  HCH3  0   0.220  -6.7816  -3.6901  -0.5956
 BYJ  H25  H  HCH3  0   0.230  -7.0518  -3.9638   1.1215
 BYJ  H26  H  HCH3  0   0.191  -7.8290  -2.5972   0.3095

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
 BYJ  C21  N20  single    1.448  0.020  1.448
 BYJ  C09  C11  single    1.503  0.020  1.503
 BYJ  C09  C08  single    1.535  0.020  1.535
 BYJ  C16  C11  aromatic  1.391  0.020  1.391
 BYJ  C16  C15  aromatic  1.395  0.020  1.395
 BYJ  C17  C15  single    1.504  0.020  1.504
 BYJ  C17  C18  single    1.529  0.020  1.529
 BYJ  C11  C12  aromatic  1.395  0.020  1.395
 BYJ  N20  C19  single    1.450  0.020  1.450
 BYJ  C15  C14  aromatic  1.391  0.020  1.391
 BYJ  C12  C13  aromatic  1.386  0.020  1.386
 BYJ  C14  C13  aromatic  1.390  0.020  1.390
 BYJ  C19  C18  single    1.520  0.020  1.520
 BYJ  N02  C02  single    1.365  0.020  1.365
 BYJ  N01  C02  aromatic  1.328  0.020  1.328
 BYJ  N01  C06  aromatic  1.335  0.020  1.335
 BYJ  C08  C06  single    1.502  0.020  1.502
 BYJ  C02  C03  aromatic  1.406  0.020  1.406
 BYJ  C06  C05  aromatic  1.383  0.020  1.383
 BYJ  C03  C04  aromatic  1.379  0.020  1.379
 BYJ  C05  C04  aromatic  1.400  0.020  1.400
 BYJ  C04  C07  single    1.498  0.020  1.498
 BYJ  N02  H1   single    0.890  0.020  1.040
 BYJ  N02  H2   single    0.890  0.020  1.040
 BYJ  C03  H3   single    0.930  0.020  1.080
 BYJ  C05  H4   single    0.930  0.020  1.080
 BYJ  C07  H5   single    0.970  0.020  1.090
 BYJ  C07  H6   single    0.970  0.020  1.090
 BYJ  C07  H7   single    0.970  0.020  1.090
 BYJ  C08  H8   single    0.970  0.020  1.090
 BYJ  C08  H9   single    0.970  0.020  1.090
 BYJ  C09  H10  single    0.970  0.020  1.090
 BYJ  C09  H11  single    0.970  0.020  1.090
 BYJ  C16  H12  single    0.930  0.020  1.080
 BYJ  C12  H13  single    0.930  0.020  1.080
 BYJ  C13  H14  single    0.930  0.020  1.080
 BYJ  C14  H15  single    0.930  0.020  1.080
 BYJ  C17  H16  single    0.970  0.020  1.090
 BYJ  C17  H17  single    0.970  0.020  1.090
 BYJ  C18  H18  single    0.970  0.020  1.090
 BYJ  C18  H19  single    0.970  0.020  1.090
 BYJ  C19  H20  single    0.970  0.020  1.090
 BYJ  C19  H21  single    0.970  0.020  1.090
 BYJ  N20  H22  single    0.890  0.020  1.040
 BYJ  C21  H24  single    0.970  0.020  1.090
 BYJ  C21  H25  single    0.970  0.020  1.090
 BYJ  C21  H26  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
 BYJ  H2   N02  H1   114.10  3.000
 BYJ  H2   N02  C02  116.16  3.000
 BYJ  H1   N02  C02  117.52  3.000
 BYJ  N01  C02  C03  122.29  3.000
 BYJ  C03  C02  N02  120.61  3.000
 BYJ  N01  C02  N02  117.07  3.000
 BYJ  H3   C03  C04  120.80  3.000
 BYJ  H3   C03  C02  120.13  3.000
 BYJ  C04  C03  C02  119.06  3.000
 BYJ  C07  C04  C05  120.58  3.000
 BYJ  C07  C04  C03  121.32  3.000
 BYJ  C05  C04  C03  118.10  3.000
 BYJ  H4   C05  C06  120.37  3.000
 BYJ  H4   C05  C04  120.57  3.000
 BYJ  C06  C05  C04  119.05  3.000
 BYJ  H7   C07  H6   108.35  3.000
 BYJ  H7   C07  H5   107.76  3.000
 BYJ  H6   C07  H5   107.00  3.000
 BYJ  H7   C07  C04  111.82  3.000
 BYJ  H6   C07  C04  111.21  3.000
 BYJ  H5   C07  C04  110.51  3.000
 BYJ  C06  N01  C02  118.73  3.000
 BYJ  C08  C06  N01  115.96  3.000
 BYJ  C08  C06  C05  121.27  3.000
 BYJ  N01  C06  C05  122.76  3.000
 BYJ  H9   C08  H8   107.09  3.000
 BYJ  H9   C08  C09  109.51  3.000
 BYJ  H8   C08  C09  109.09  3.000
 BYJ  H9   C08  C06  109.98  3.000
 BYJ  H8   C08  C06  109.20  3.000
 BYJ  C09  C08  C06  111.86  3.000
 BYJ  H11  C09  H10  107.00  3.000
 BYJ  H11  C09  C11  110.11  3.000
 BYJ  H10  C09  C11  109.86  3.000
 BYJ  H11  C09  C08  109.04  3.000
 BYJ  H10  C09  C08  109.02  3.000
 BYJ  C11  C09  C08  111.68  3.000
 BYJ  C12  C11  C16  118.57  3.000
 BYJ  C12  C11  C09  120.51  3.000
 BYJ  C16  C11  C09  120.89  3.000
 BYJ  H12  C16  C15  119.14  3.000
 BYJ  H12  C16  C11  119.02  3.000
 BYJ  C15  C16  C11  121.84  3.000
 BYJ  H13  C12  C13  119.95  3.000
 BYJ  H13  C12  C11  119.64  3.000
 BYJ  C13  C12  C11  120.40  3.000
 BYJ  H14  C13  C14  119.82  3.000
 BYJ  H14  C13  C12  119.96  3.000
 BYJ  C14  C13  C12  120.22  3.000
 BYJ  H15  C14  C15  119.63  3.000
 BYJ  H15  C14  C13  119.86  3.000
 BYJ  C15  C14  C13  120.51  3.000
 BYJ  C17  C15  C14  121.01  3.000
 BYJ  C14  C15  C16  118.46  3.000
 BYJ  C17  C15  C16  120.52  3.000
 BYJ  H17  C17  H16  106.54  3.000
 BYJ  H17  C17  C18  109.08  3.000
 BYJ  H16  C17  C18  109.29  3.000
 BYJ  H17  C17  C15  109.89  3.000
 BYJ  H16  C17  C15  109.50  3.000
 BYJ  C18  C17  C15  112.37  3.000
 BYJ  H19  C18  H18  106.68  3.000
 BYJ  H19  C18  C19  109.66  3.000
 BYJ  H18  C18  C19  109.33  3.000
 BYJ  H19  C18  C17  109.13  3.000
 BYJ  H18  C18  C17  109.80  3.000
 BYJ  C19  C18  C17  112.10  3.000
 BYJ  H21  C19  H20  105.96  3.000
 BYJ  H21  C19  N20  108.18  3.000
 BYJ  H20  C19  N20  112.44  3.000
 BYJ  H21  C19  C18  109.24  3.000
 BYJ  H20  C19  C18  109.29  3.000
 BYJ  N20  C19  C18  111.53  3.000
 BYJ  H22  N20  C21  108.71  3.000
 BYJ  H22  N20  C19  108.63  3.000
 BYJ  C21  N20  C19  112.59  3.000
 BYJ  H26  C21  H25  107.81  3.000
 BYJ  H26  C21  H24  107.18  3.000
 BYJ  H25  C21  H24  107.49  3.000
 BYJ  H26  C21  N20  114.24  3.000
 BYJ  H25  C21  N20  109.95  3.000
 BYJ  H24  C21  N20  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
 BYJ  CONST_01  C05  C06  N01  C02    0.00   0.0  0
 BYJ  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 BYJ  CONST_03  C06  N01  C02  C03    0.00   0.0  0
 BYJ  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 BYJ  CONST_05  N01  C02  C03  C04    0.00   0.0  0
 BYJ  CONST_06  N01  C06  C05  C04    0.00   0.0  0
 BYJ  CONST_07  C14  C15  C16  C11    0.00   0.0  0
 BYJ  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 BYJ  CONST_09  C13  C12  C11  C16    0.00   0.0  0
 BYJ  CONST_10  C13  C14  C15  C16    0.00   0.0  0
 BYJ  CONST_11  C15  C16  C11  C12    0.00   0.0  0
 BYJ  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 BYJ  CONST_13  C06  N01  C02  N02  180.00   0.0  0
 BYJ  CONST_14  C04  C03  C02  N02  180.00   0.0  0
 BYJ  CONST_15  C08  C06  N01  C02  180.00   0.0  0
 BYJ  CONST_16  C07  C04  C03  C02  180.00   0.0  0
 BYJ  CONST_17  C08  C06  C05  C04  180.00   0.0  0
 BYJ  CONST_18  C06  C05  C04  C07  180.00   0.0  0
 BYJ  CONST_19  C15  C16  C11  C09  180.00   0.0  0
 BYJ  CONST_20  C13  C12  C11  C09  180.00   0.0  0
 BYJ  CONST_21  C17  C15  C16  C11  180.00   0.0  0
 BYJ  CONST_22  C17  C15  C14  C13  180.00   0.0  0
 BYJ  CONST_23  H4   C05  C04  C03  180.00   0.0  0
 BYJ  CONST_24  H3   C03  C04  C05  180.00   0.0  0
 BYJ  CONST_25  H14  C13  C12  C11  180.00   0.0  0
 BYJ  CONST_26  H13  C12  C11  C16  180.00   0.0  0
 BYJ  CONST_27  H15  C14  C15  C16  180.00   0.0  0
 BYJ  CONST_28  H12  C16  C11  C12  180.00   0.0  0
 BYJ  Var_01    C09  C08  C06  C05  108.93  30.0  1
 BYJ  Var_02    C11  C09  C08  C06  178.26  30.0  1
 BYJ  Var_03    C16  C11  C09  C08  -98.18  30.0  2
 BYJ  Var_04    C18  C17  C15  C16   74.00  30.0  3
 BYJ  Var_05    H5   C07  C04  C03  106.59  30.0  2
 BYJ  Var_06    C19  C18  C17  C15  178.71  30.0  3
 BYJ  Var_07    N20  C19  C18  C17  179.58  30.0  2
 BYJ  Var_08    C21  N20  C19  C18  179.37  30.0  1
 BYJ  Var_09    H24  C21  N20  C19   65.43  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
 BYJ  plan-1  N02  0.020
 BYJ  plan-1  C02  0.020
 BYJ  plan-1  C03  0.020
 BYJ  plan-1  C04  0.020
 BYJ  plan-1  C05  0.020
 BYJ  plan-1  C07  0.020
 BYJ  plan-1  N01  0.020
 BYJ  plan-1  C06  0.020
 BYJ  plan-1  C08  0.020
 BYJ  plan-1  H3   0.020
 BYJ  plan-1  H4   0.020
 BYJ  plan-2  C09  0.020
 BYJ  plan-2  C11  0.020
 BYJ  plan-2  C16  0.020
 BYJ  plan-2  C12  0.020
 BYJ  plan-2  C13  0.020
 BYJ  plan-2  C14  0.020
 BYJ  plan-2  C15  0.020
 BYJ  plan-2  C17  0.020
 BYJ  plan-2  H12  0.020
 BYJ  plan-2  H13  0.020
 BYJ  plan-2  H14  0.020
 BYJ  plan-2  H15  0.020
 BYJ  plan-3  N02  0.020
 BYJ  plan-3  C02  0.020
 BYJ  plan-3  H1   0.020
 BYJ  plan-3  H2   0.020

