# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:37:34 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-[3-(methylamino)propyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCc1cc(CCc2cc(C)cc(N)n2)cc(c1)C#N
#
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
 BYV  BYV  3-[2-(6-amino-4-methylpyridin-2-yl)ethyl]-5-[3-(methylamino)propyl]benzonitrile  ligand  47  23  .  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_BYV
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
 BYV  N17  N  NS    0  -0.254   2.2635  -5.3480  -0.3757
 BYV  C17  C  CSP   0   0.049   2.0550  -4.2227  -0.2399
 BYV  C13  C  CR6   0   0.050   1.7960  -2.8285  -0.0730
 BYV  C14  C  CR16  0  -0.335   2.8035  -1.9973   0.4138
 BYV  C15  C  CR6   0   0.175   2.5572  -0.6408   0.5791
 BYV  C18  C  CH2   0  -0.514   3.6366   0.2886   1.0551
 BYV  C19  C  CH2   0  -0.439   4.3676   0.9603  -0.1076
 BYV  C20  C  CH2   0  -0.255   5.4301   1.9333   0.3781
 BYV  N21  N  NH1   0  -0.593   6.1080   2.5746  -0.7305
 BYV  C22  C  CH3   0  -0.518   7.1306   3.5024  -0.2926
 BYV  C12  C  CR16  0  -0.331   0.5401  -2.3212  -0.3995
 BYV  C11  C  CR6   0   0.168   0.2824  -0.9658  -0.2412
 BYV  C16  C  CR16  0  -0.352   1.2972  -0.1479   0.2479
 BYV  C09  C  CH2   0  -0.514  -1.0774  -0.4033  -0.5399
 BYV  C08  C  CH2   0  -0.490  -1.9640  -0.3815   0.7132
 BYV  C06  C  CR6   0   0.275  -3.3100   0.2237   0.4338
 BYV  N01  N  N     0  -0.484  -3.3256   1.5392   0.2068
 BYV  C02  C  CR6   0   0.442  -4.4861   2.1244  -0.0674
 BYV  N02  N  NH2   0  -0.839  -4.4746   3.4780  -0.2419
 BYV  C03  C  CR16  0  -0.448  -5.6933   1.4051  -0.1316
 BYV  C04  C  CR6   0   0.205  -5.6773   0.0454   0.0972
 BYV  C05  C  CR16  0  -0.431  -4.4487  -0.5586   0.3912
 BYV  C07  C  CH3   0  -0.726  -6.9291  -0.7738   0.0226
 BYV  H1   H  HCR6  0   0.270   3.7727  -2.4113   0.6625
 BYV  H2   H  HCH2  0   0.246   3.1970   1.0583   1.6952
 BYV  H3   H  HCH2  0   0.248   4.3545  -0.2591   1.6702
 BYV  H4   H  HCH2  0   0.229   4.8301   0.1928  -0.7370
 BYV  H5   H  HCH2  0   0.230   3.6497   1.4932  -0.7373
 BYV  H6   H  HCH2  0   0.215   4.9535   2.7107   0.9848
 BYV  H7   H  HCH2  0   0.187   6.1272   1.4070   1.0520
 BYV  H8   H  HNH1  0   0.340   6.5416   1.8598  -1.3022
 BYV  H10  H  HCH3  0   0.220   6.6716   4.3313   0.2500
 BYV  H11  H  HCH3  0   0.192   7.8863   3.0587   0.3715
 BYV  H12  H  HCH3  0   0.230   7.6484   3.9205  -1.1560
 BYV  H13  H  HCR6  0   0.270  -0.2304  -2.9830  -0.7754
 BYV  H14  H  HCR6  0   0.253   1.1012   0.9119   0.3756
 BYV  H15  H  HCH2  0   0.256  -0.9828   0.6132  -0.9276
 BYV  H16  H  HCH2  0   0.256  -1.5633  -0.9987  -1.3163
 BYV  H17  H  HCH2  0   0.250  -2.0827  -1.3990   1.0923
 BYV  H18  H  HCH2  0   0.251  -1.4624   0.1968   1.4937
 BYV  H19  H  HNH2  0   0.380  -3.5837   3.8923  -0.4621
 BYV  H20  H  HNH2  0   0.388  -5.2518   3.8926  -0.7286
 BYV  H21  H  HCR6  0   0.255  -6.6192   1.9188  -0.3614
 BYV  H22  H  HCR6  0   0.243  -4.3872  -1.6233   0.5790
 BYV  H23  H  HCH3  0   0.253  -6.8968  -1.4450  -0.8369
 BYV  H24  H  HCH3  0   0.250  -7.0402  -1.3977   0.9101
 BYV  H25  H  HCH3  0   0.247  -7.8171  -0.1509  -0.0713

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
 BYV  C07  C04  single    1.498  0.020  1.498
 BYV  C04  C03  aromatic  1.379  0.020  1.379
 BYV  C04  C05  aromatic  1.400  0.020  1.400
 BYV  C03  C02  aromatic  1.407  0.020  1.407
 BYV  C05  C06  aromatic  1.382  0.020  1.382
 BYV  C09  C11  single    1.502  0.020  1.502
 BYV  C09  C08  single    1.535  0.020  1.535
 BYV  C02  N02  single    1.365  0.020  1.365
 BYV  C02  N01  aromatic  1.328  0.020  1.328
 BYV  C06  N01  aromatic  1.335  0.020  1.335
 BYV  C06  C08  single    1.502  0.020  1.502
 BYV  C11  C12  aromatic  1.389  0.020  1.389
 BYV  C11  C16  aromatic  1.392  0.020  1.392
 BYV  C12  C13  aromatic  1.393  0.020  1.393
 BYV  C16  C15  aromatic  1.393  0.020  1.393
 BYV  C13  C17  single    1.428  0.020  1.428
 BYV  C13  C14  aromatic  1.394  0.020  1.394
 BYV  N17  C17  triple    1.153  0.020  1.153
 BYV  C15  C14  aromatic  1.388  0.020  1.388
 BYV  C15  C18  single    1.502  0.020  1.502
 BYV  C18  C19  single    1.529  0.020  1.529
 BYV  C19  C20  single    1.520  0.020  1.520
 BYV  C20  N21  single    1.449  0.020  1.449
 BYV  N21  C22  single    1.449  0.020  1.449
 BYV  C14  H1   single    0.930  0.020  1.080
 BYV  C18  H2   single    0.970  0.020  1.090
 BYV  C18  H3   single    0.970  0.020  1.090
 BYV  C19  H4   single    0.970  0.020  1.090
 BYV  C19  H5   single    0.970  0.020  1.090
 BYV  C20  H6   single    0.970  0.020  1.090
 BYV  C20  H7   single    0.970  0.020  1.090
 BYV  N21  H8   single    0.890  0.020  1.040
 BYV  C22  H10  single    0.970  0.020  1.090
 BYV  C22  H11  single    0.970  0.020  1.090
 BYV  C22  H12  single    0.970  0.020  1.090
 BYV  C12  H13  single    0.930  0.020  1.080
 BYV  C16  H14  single    0.930  0.020  1.080
 BYV  C09  H15  single    0.970  0.020  1.090
 BYV  C09  H16  single    0.970  0.020  1.090
 BYV  C08  H17  single    0.970  0.020  1.090
 BYV  C08  H18  single    0.970  0.020  1.090
 BYV  N02  H19  single    0.890  0.020  1.040
 BYV  N02  H20  single    0.890  0.020  1.040
 BYV  C03  H21  single    0.930  0.020  1.080
 BYV  C05  H22  single    0.930  0.020  1.080
 BYV  C07  H23  single    0.970  0.020  1.090
 BYV  C07  H24  single    0.970  0.020  1.090
 BYV  C07  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
 BYV  C13  C17  N17  180.00  3.000
 BYV  C12  C13  C14  121.08  3.000
 BYV  C14  C13  C17  119.47  3.000
 BYV  C12  C13  C17  119.45  3.000
 BYV  H1   C14  C15  120.33  3.000
 BYV  H1   C14  C13  119.94  3.000
 BYV  C15  C14  C13  119.73  3.000
 BYV  C16  C15  C18  120.43  3.000
 BYV  C18  C15  C14  120.98  3.000
 BYV  C16  C15  C14  118.55  3.000
 BYV  H3   C18  H2   106.71  3.000
 BYV  H3   C18  C19  109.52  3.000
 BYV  H2   C18  C19  109.15  3.000
 BYV  H3   C18  C15  109.91  3.000
 BYV  H2   C18  C15  109.41  3.000
 BYV  C19  C18  C15  111.99  3.000
 BYV  H5   C19  H4   106.72  3.000
 BYV  H5   C19  C20  109.32  3.000
 BYV  H4   C19  C20  109.69  3.000
 BYV  H5   C19  C18  109.77  3.000
 BYV  H4   C19  C18  109.34  3.000
 BYV  C20  C19  C18  111.86  3.000
 BYV  H7   C20  H6   105.97  3.000
 BYV  H7   C20  N21  112.51  3.000
 BYV  H6   C20  N21  108.25  3.000
 BYV  H7   C20  C19  109.36  3.000
 BYV  H6   C20  C19  109.10  3.000
 BYV  N21  C20  C19  111.46  3.000
 BYV  H8   N21  C22  108.69  3.000
 BYV  H8   N21  C20  108.65  3.000
 BYV  C22  N21  C20  112.49  3.000
 BYV  H12  C22  H11  107.86  3.000
 BYV  H12  C22  H10  107.58  3.000
 BYV  H11  C22  H10  107.17  3.000
 BYV  H12  C22  N21  109.97  3.000
 BYV  H11  C22  N21  114.17  3.000
 BYV  H10  C22  N21  109.86  3.000
 BYV  H13  C12  C11  120.26  3.000
 BYV  H13  C12  C13  120.01  3.000
 BYV  C11  C12  C13  119.73  3.000
 BYV  C09  C11  C16  120.66  3.000
 BYV  C16  C11  C12  118.57  3.000
 BYV  C09  C11  C12  120.73  3.000
 BYV  H14  C16  C11  118.90  3.000
 BYV  H14  C16  C15  118.75  3.000
 BYV  C11  C16  C15  122.35  3.000
 BYV  H16  C09  H15  107.07  3.000
 BYV  H16  C09  C08  109.33  3.000
 BYV  H15  C09  C08  109.06  3.000
 BYV  H16  C09  C11  109.88  3.000
 BYV  H15  C09  C11  109.93  3.000
 BYV  C08  C09  C11  111.46  3.000
 BYV  H18  C08  H17  107.15  3.000
 BYV  H18  C08  C06  109.32  3.000
 BYV  H17  C08  C06  110.03  3.000
 BYV  H18  C08  C09  108.98  3.000
 BYV  H17  C08  C09  109.44  3.000
 BYV  C06  C08  C09  111.80  3.000
 BYV  C05  C06  N01  122.88  3.000
 BYV  N01  C06  C08  116.05  3.000
 BYV  C05  C06  C08  121.06  3.000
 BYV  C02  N01  C06  118.64  3.000
 BYV  C03  C02  N02  120.56  3.000
 BYV  N02  C02  N01  117.12  3.000
 BYV  C03  C02  N01  122.27  3.000
 BYV  H20  N02  H19  114.08  3.000
 BYV  H20  N02  C02  117.64  3.000
 BYV  H19  N02  C02  116.32  3.000
 BYV  H21  C03  C04  120.84  3.000
 BYV  H21  C03  C02  120.04  3.000
 BYV  C04  C03  C02  119.12  3.000
 BYV  C07  C04  C05  120.52  3.000
 BYV  C05  C04  C03  118.06  3.000
 BYV  C07  C04  C03  121.42  3.000
 BYV  H22  C05  C04  120.69  3.000
 BYV  H22  C05  C06  120.29  3.000
 BYV  C04  C05  C06  119.02  3.000
 BYV  H25  C07  H24  108.32  3.000
 BYV  H25  C07  H23  107.95  3.000
 BYV  H24  C07  H23  106.99  3.000
 BYV  H25  C07  C04  111.90  3.000
 BYV  H24  C07  C04  110.95  3.000
 BYV  H23  C07  C04  110.55  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
 BYV  CONST_01  C16  C11  C12  C13     0.00   0.0  0
 BYV  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 BYV  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 BYV  CONST_04  C11  C16  C15  C14     0.00   0.0  0
 BYV  CONST_05  C12  C11  C16  C15     0.00   0.0  0
 BYV  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 BYV  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 BYV  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 BYV  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 BYV  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 BYV  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 BYV  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 BYV  CONST_13  C11  C12  C13  C17   180.00   0.0  0
 BYV  CONST_14  C15  C14  C13  C17   180.00   0.0  0
 BYV  CONST_15  C09  C11  C12  C13   180.00   0.0  0
 BYV  CONST_16  C18  C15  C14  C13   180.00   0.0  0
 BYV  CONST_17  C09  C11  C16  C15   180.00   0.0  0
 BYV  CONST_18  C11  C16  C15  C18   180.00   0.0  0
 BYV  CONST_19  C04  C05  C06  C08   180.00   0.0  0
 BYV  CONST_20  C02  N01  C06  C08   180.00   0.0  0
 BYV  CONST_21  C07  C04  C05  C06   180.00   0.0  0
 BYV  CONST_22  N02  C02  N01  C06   180.00   0.0  0
 BYV  CONST_23  C07  C04  C03  C02   180.00   0.0  0
 BYV  CONST_24  C04  C03  C02  N02   180.00   0.0  0
 BYV  CONST_25  H13  C12  C13  C14   180.00   0.0  0
 BYV  CONST_26  H14  C16  C15  C14   180.00   0.0  0
 BYV  CONST_27  H1   C14  C13  C12   180.00   0.0  0
 BYV  CONST_28  H21  C03  C02  N01   180.00   0.0  0
 BYV  CONST_29  H22  C05  C06  N01   180.00   0.0  0
 BYV  Var_01    C19  C18  C15  C14    94.41  30.0  2
 BYV  Var_02    C08  C09  C11  C12    91.94  30.0  1
 BYV  Var_03    C06  C08  C09  C11   178.03  30.0  3
 BYV  Var_04    C05  C06  C08  C09   108.39  30.0  2
 BYV  Var_05    H23  C07  C04  C03   111.53  30.0  2
 BYV  Var_06    C20  C19  C18  C15   178.21  30.0  3
 BYV  Var_07    N21  C20  C19  C18  -179.43  30.0  3
 BYV  Var_08    C22  N21  C20  C19  -179.71  30.0  3
 BYV  Var_09    H10  C22  N21  C20   -64.75  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
 BYV  plan-1  N17  0.020
 BYV  plan-1  C17  0.020
 BYV  plan-1  C13  0.020
 BYV  plan-1  C14  0.020
 BYV  plan-1  C15  0.020
 BYV  plan-1  C18  0.020
 BYV  plan-1  C12  0.020
 BYV  plan-1  C11  0.020
 BYV  plan-1  C16  0.020
 BYV  plan-1  C09  0.020
 BYV  plan-1  H1   0.020
 BYV  plan-1  H13  0.020
 BYV  plan-1  H14  0.020
 BYV  plan-2  C08  0.020
 BYV  plan-2  C06  0.020
 BYV  plan-2  N01  0.020
 BYV  plan-2  C02  0.020
 BYV  plan-2  N02  0.020
 BYV  plan-2  C03  0.020
 BYV  plan-2  C04  0.020
 BYV  plan-2  C05  0.020
 BYV  plan-2  C07  0.020
 BYV  plan-2  H21  0.020
 BYV  plan-2  H22  0.020
 BYV  plan-3  C02  0.020
 BYV  plan-3  N02  0.020
 BYV  plan-3  H19  0.020
 BYV  plan-3  H20  0.020

