# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 02:01:38 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 7-{[3-({[(6-aminopyridin-2-yl)methyl]amino}methyl)phenoxy]methyl}quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(CNCc2cccc(OCc3ccc4ccc(N)nc4c3)c2)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
 V54  V54  7-{[3-({[(6-aminopyridin-2-yl)methyl]amino}methyl)phenoxy]methyl}quinolin-2-amine  ligand  52  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V54
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
 V54  C02  C  CR6   0   0.439   4.1381   7.1933  22.8661
 V54  C03  C  CR16  0  -0.391   3.8310   6.0432  22.1172
 V54  C04  C  CR16  0  -0.142   4.7938   5.5452  21.2692
 V54  C05  C  CR16  0  -0.384   6.0315   6.1776  21.1745
 V54  C06  C  CR6   0   0.257   6.2401   7.3107  21.9430
 V54  C07  C  CH2   0  -0.317   7.5276   8.0857  21.8588
 V54  C09  C  CH2   0  -0.377   9.2067   9.2690  23.1521
 V54  C10  C  CR6   0   0.111   9.1511  10.5515  22.3477
 V54  C11  C  CR16  0  -0.327  10.0082  10.7600  21.2693
 V54  C12  C  CR16  0  -0.226   9.9324  11.9362  20.5403
 V54  C13  C  CR16  0  -0.392   9.0038  12.9187  20.8594
 V54  C14  C  CR6   0   0.420   8.1388  12.7093  21.9319
 V54  C16  C  CH2   0  -0.197   6.9997  14.7580  21.5683
 V54  C17  C  CR6   0   0.036   5.8148  15.5207  22.0878
 V54  C18  C  CR16  0  -0.294   5.5528  16.7747  21.4927
 V54  C19  C  CR16  0  -0.303   4.4732  17.5173  21.8862
 V54  C20  C  CR66  0   0.046   3.6077  17.0446  22.8914
 V54  C21  C  CR16  0  -0.178   2.4715  17.7621  23.3429
 V54  C22  C  CR16  0  -0.377   1.6831  17.2384  24.3149
 V54  C23  C  CR6   0   0.438   2.0273  15.9645  24.8671
 V54  C26  C  CR66  0   0.243   3.8634  15.7942  23.4990
 V54  C27  C  CR16  0  -0.376   4.9849  15.0458  23.0721
 V54  C28  C  CR16  0  -0.404   8.2194  11.5293  22.6686
 V54  N01  N  NH2   0  -0.834   3.2472   7.7039  23.7642
 V54  N08  N  NH1   0  -0.586   7.9900   8.4814  23.1731
 V54  N24  N  NH2   0  -0.834   1.2207  15.4186  25.8112
 V54  N25  N  N     0  -0.505   3.0768  15.2803  24.4734
 V54  N29  N  N     0  -0.490   5.3146   7.8052  22.7634
 V54  O15  O  O2    0  -0.480   7.1981  13.5928  22.3293
 V54  H1   H  HCR6  0   0.262   2.8632   5.5677  22.2118
 V54  H2   H  HCR6  0   0.262   4.5876   4.6596  20.6813
 V54  H3   H  HCR6  0   0.251   6.8078   5.8005  20.5228
 V54  H4   H  HCH2  0   0.237   8.2938   7.4674  21.3836
 V54  H5   H  HCH2  0   0.216   7.3630   8.9392  21.1809
 V54  H6   H  HCH2  0   0.238  10.0172   8.6456  22.7643
 V54  H7   H  HCH2  0   0.251   9.4649   9.5038  24.1880
 V54  H8   H  HCR6  0   0.245  10.7339  10.0007  21.0039
 V54  H9   H  HCR6  0   0.255  10.6009  12.0979  19.7042
 V54  H10  H  HCR6  0   0.279   8.9735  13.8251  20.2704
 V54  H11  H  HCH2  0   0.245   6.8243  14.5082  20.5140
 V54  H12  H  HCH2  0   0.244   7.8897  15.3991  21.5972
 V54  H13  H  HCR6  0   0.250   6.2113  17.1468  20.7167
 V54  H14  H  HCR6  0   0.255   4.2724  18.4776  21.4258
 V54  H15  H  HCR6  0   0.267   2.2387  18.7260  22.9062
 V54  H16  H  HCR6  0   0.271   0.8078  17.7636  24.6756
 V54  H17  H  HCR6  0   0.245   5.1619  14.0892  23.5452
 V54  H18  H  HCR6  0   0.254   7.5383  11.3871  23.5016
 V54  H19  H  HNH2  0   0.379   3.4050   8.6536  24.0591
 V54  H20  H  HNH2  0   0.389   2.2770   7.4632  23.6476
 V54  H21  H  HNH1  0   0.350   7.2493   8.9870  23.6432
 V54  H23  H  HNH2  0   0.385   1.5781  14.6380  26.3363
 V54  H24  H  HNH2  0   0.396   0.5773  16.0133  26.3046

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
 V54  C04  C05  aromatic  1.393  0.020  1.393
 V54  C04  C03  aromatic  1.376  0.020  1.376
 V54  C05  C06  aromatic  1.385  0.020  1.385
 V54  C12  C13  aromatic  1.389  0.020  1.389
 V54  C12  C11  aromatic  1.386  0.020  1.386
 V54  C13  C14  aromatic  1.394  0.020  1.394
 V54  C18  C19  aromatic  1.368  0.020  1.368
 V54  C18  C17  aromatic  1.413  0.020  1.413
 V54  C03  C02  aromatic  1.406  0.020  1.406
 V54  C16  C17  single    1.502  0.020  1.502
 V54  C16  O15  single    1.406  0.020  1.406
 V54  C19  C20  aromatic  1.408  0.020  1.408
 V54  C11  C10  aromatic  1.393  0.020  1.393
 V54  C06  C07  single    1.505  0.020  1.505
 V54  C06  N29  aromatic  1.332  0.020  1.332
 V54  C07  N08  single    1.448  0.020  1.448
 V54  C17  C27  aromatic  1.372  0.020  1.372
 V54  C14  O15  single    1.350  0.020  1.350
 V54  C14  C28  aromatic  1.393  0.020  1.393
 V54  C02  N29  aromatic  1.330  0.020  1.330
 V54  C02  N01  single    1.364  0.020  1.364
 V54  C10  C28  aromatic  1.388  0.020  1.388
 V54  C10  C09  single    1.515  0.020  1.515
 V54  C20  C21  aromatic  1.418  0.020  1.418
 V54  C20  C26  aromatic  1.414  0.020  1.414
 V54  N08  C09  single    1.450  0.020  1.450
 V54  C27  C26  aromatic  1.414  0.020  1.414
 V54  C21  C22  aromatic  1.357  0.020  1.357
 V54  C26  N25  aromatic  1.354  0.020  1.354
 V54  C22  C23  aromatic  1.430  0.020  1.430
 V54  N25  C23  aromatic  1.313  0.020  1.313
 V54  C23  N24  single    1.356  0.020  1.356
 V54  C03  H1   single    0.930  0.020  1.080
 V54  C04  H2   single    0.930  0.020  1.080
 V54  C05  H3   single    0.930  0.020  1.080
 V54  C07  H4   single    0.970  0.020  1.090
 V54  C07  H5   single    0.970  0.020  1.090
 V54  C09  H6   single    0.970  0.020  1.090
 V54  C09  H7   single    0.970  0.020  1.090
 V54  C11  H8   single    0.930  0.020  1.080
 V54  C12  H9   single    0.930  0.020  1.080
 V54  C13  H10  single    0.930  0.020  1.080
 V54  C16  H11  single    0.970  0.020  1.090
 V54  C16  H12  single    0.970  0.020  1.090
 V54  C18  H13  single    0.930  0.020  1.080
 V54  C19  H14  single    0.930  0.020  1.080
 V54  C21  H15  single    0.930  0.020  1.080
 V54  C22  H16  single    0.930  0.020  1.080
 V54  C27  H17  single    0.930  0.020  1.080
 V54  C28  H18  single    0.930  0.020  1.080
 V54  N01  H19  single    0.890  0.020  1.040
 V54  N01  H20  single    0.890  0.020  1.040
 V54  N08  H21  single    0.890  0.020  1.040
 V54  N24  H23  single    0.890  0.020  1.040
 V54  N24  H24  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
 V54  N29  C02  N01  117.15  3.000
 V54  N01  C02  C03  120.93  3.000
 V54  N29  C02  C03  121.89  3.000
 V54  H1   C03  C04  121.36  3.000
 V54  H1   C03  C02  120.53  3.000
 V54  C04  C03  C02  118.11  3.000
 V54  H2   C04  C05  120.24  3.000
 V54  H2   C04  C03  119.82  3.000
 V54  C05  C04  C03  119.94  3.000
 V54  H3   C05  C06  120.77  3.000
 V54  H3   C05  C04  121.36  3.000
 V54  C06  C05  C04  117.87  3.000
 V54  N29  C06  C07  115.96  3.000
 V54  N29  C06  C05  122.74  3.000
 V54  C07  C06  C05  121.27  3.000
 V54  H5   C07  H4   105.98  3.000
 V54  H5   C07  N08  113.21  3.000
 V54  H4   C07  N08  108.98  3.000
 V54  H5   C07  C06  107.78  3.000
 V54  H4   C07  C06  109.43  3.000
 V54  N08  C07  C06  111.28  3.000
 V54  H7   C09  H6   106.46  3.000
 V54  H7   C09  N08  107.53  3.000
 V54  H6   C09  N08  108.51  3.000
 V54  H7   C09  C10  109.27  3.000
 V54  H6   C09  C10  108.76  3.000
 V54  N08  C09  C10  115.90  3.000
 V54  C28  C10  C11  119.11  3.000
 V54  C28  C10  C09  119.88  3.000
 V54  C11  C10  C09  121.00  3.000
 V54  H8   C11  C12  120.17  3.000
 V54  H8   C11  C10  119.79  3.000
 V54  C12  C11  C10  120.03  3.000
 V54  H9   C12  C13  118.98  3.000
 V54  H9   C12  C11  119.95  3.000
 V54  C13  C12  C11  121.07  3.000
 V54  H10  C13  C14  121.85  3.000
 V54  H10  C13  C12  119.11  3.000
 V54  C14  C13  C12  119.05  3.000
 V54  O15  C14  C28  116.03  3.000
 V54  C28  C14  C13  119.88  3.000
 V54  O15  C14  C13  124.10  3.000
 V54  H12  C16  H11  106.73  3.000
 V54  H12  C16  O15  110.83  3.000
 V54  H11  C16  O15  110.73  3.000
 V54  H12  C16  C17  109.52  3.000
 V54  H11  C16  C17  108.77  3.000
 V54  O15  C16  C17  110.18  3.000
 V54  C27  C17  C18  119.82  3.000
 V54  C27  C17  C16  123.33  3.000
 V54  C18  C17  C16  116.84  3.000
 V54  H13  C18  C19  119.94  3.000
 V54  H13  C18  C17  119.59  3.000
 V54  C19  C18  C17  120.47  3.000
 V54  H14  C19  C20  119.13  3.000
 V54  H14  C19  C18  120.33  3.000
 V54  C20  C19  C18  120.54  3.000
 V54  C26  C20  C21  117.12  3.000
 V54  C26  C20  C19  119.51  3.000
 V54  C21  C20  C19  123.37  3.000
 V54  H15  C21  C22  120.48  3.000
 V54  H15  C21  C20  119.61  3.000
 V54  C22  C21  C20  119.91  3.000
 V54  H16  C22  C23  119.86  3.000
 V54  H16  C22  C21  121.42  3.000
 V54  C23  C22  C21  118.72  3.000
 V54  N25  C23  N24  118.31  3.000
 V54  N24  C23  C22  118.95  3.000
 V54  N25  C23  C22  122.72  3.000
 V54  N25  C26  C27  118.50  3.000
 V54  N25  C26  C20  122.69  3.000
 V54  C27  C26  C20  118.81  3.000
 V54  H17  C27  C26  117.76  3.000
 V54  H17  C27  C17  121.38  3.000
 V54  C26  C27  C17  120.86  3.000
 V54  H18  C28  C14  118.71  3.000
 V54  H18  C28  C10  120.42  3.000
 V54  C14  C28  C10  120.87  3.000
 V54  H20  N01  H19  114.24  3.000
 V54  H20  N01  C02  117.63  3.000
 V54  H19  N01  C02  116.33  3.000
 V54  H21  N08  C09  110.45  3.000
 V54  H21  N08  C07  108.92  3.000
 V54  C09  N08  C07  113.78  3.000
 V54  H24  N24  H23  115.46  3.000
 V54  H24  N24  C23  118.95  3.000
 V54  H23  N24  C23  117.65  3.000
 V54  C26  N25  C23  118.85  3.000
 V54  C06  N29  C02  119.43  3.000
 V54  C16  O15  C14  118.77  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
 V54  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 V54  CONST_02  C05  C06  N29  C02     0.00   0.0  0
 V54  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 V54  CONST_04  C06  N29  C02  C03     0.00   0.0  0
 V54  CONST_05  N29  C06  C05  C04     0.00   0.0  0
 V54  CONST_06  N29  C02  C03  C04     0.00   0.0  0
 V54  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 V54  CONST_08  C13  C14  C28  C10     0.00   0.0  0
 V54  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 V54  CONST_10  C14  C28  C10  C11     0.00   0.0  0
 V54  CONST_11  C28  C14  C13  C12     0.00   0.0  0
 V54  CONST_12  C28  C10  C11  C12     0.00   0.0  0
 V54  CONST_13  C20  C19  C18  C17     0.00   0.0  0
 V54  CONST_14  C20  C26  C27  C17     0.00   0.0  0
 V54  CONST_15  N25  C26  C27  C17   180.00   0.0  0
 V54  CONST_16  C21  C20  C19  C18   180.00   0.0  0
 V54  CONST_17  C26  C20  C19  C18     0.00   0.0  0
 V54  CONST_18  C26  C27  C17  C18     0.00   0.0  0
 V54  CONST_19  C27  C17  C18  C19     0.00   0.0  0
 V54  CONST_20  C22  C21  C20  C19   180.00   0.0  0
 V54  CONST_21  C27  C26  C20  C19     0.00   0.0  0
 V54  CONST_22  N25  C26  C20  C19   180.00   0.0  0
 V54  CONST_23  C23  C22  C21  C20     0.00   0.0  0
 V54  CONST_24  C23  N25  C26  C20     0.00   0.0  0
 V54  CONST_25  C27  C26  C20  C21   180.00   0.0  0
 V54  CONST_26  N25  C26  C20  C21     0.00   0.0  0
 V54  CONST_27  N25  C23  C22  C21     0.00   0.0  0
 V54  CONST_28  C26  C20  C21  C22     0.00   0.0  0
 V54  CONST_29  C26  N25  C23  C22     0.00   0.0  0
 V54  CONST_30  C27  C26  N25  C23   180.00   0.0  0
 V54  CONST_31  C07  C06  N29  C02   180.00   0.0  0
 V54  CONST_32  C07  C06  C05  C04   180.00   0.0  0
 V54  CONST_33  N01  C02  C03  C04   180.00   0.0  0
 V54  CONST_34  N01  C02  N29  C06   180.00   0.0  0
 V54  CONST_35  C12  C11  C10  C09   180.00   0.0  0
 V54  CONST_36  C14  C28  C10  C09   180.00   0.0  0
 V54  CONST_37  O15  C14  C28  C10   180.00   0.0  0
 V54  CONST_38  O15  C14  C13  C12   180.00   0.0  0
 V54  CONST_39  C19  C18  C17  C16   180.00   0.0  0
 V54  CONST_40  C26  C27  C17  C16   180.00   0.0  0
 V54  CONST_41  N24  C23  C22  C21   180.00   0.0  0
 V54  CONST_42  N24  C23  N25  C26   180.00   0.0  0
 V54  CONST_43  H2   C04  C03  C02   180.00   0.0  0
 V54  CONST_44  H3   C05  C04  C03   180.00   0.0  0
 V54  CONST_45  H1   C03  C04  C05   180.00   0.0  0
 V54  CONST_46  H9   C12  C11  C10   180.00   0.0  0
 V54  CONST_47  H10  C13  C12  C11   180.00   0.0  0
 V54  CONST_48  H18  C28  C10  C11   180.00   0.0  0
 V54  CONST_49  H8   C11  C12  C13   180.00   0.0  0
 V54  CONST_50  H14  C19  C18  C17   180.00   0.0  0
 V54  CONST_51  H17  C27  C17  C18   180.00   0.0  0
 V54  CONST_52  H15  C21  C20  C19     0.00   0.0  0
 V54  CONST_53  H13  C18  C19  C20   180.00   0.0  0
 V54  CONST_54  H16  C22  C21  C20   180.00   0.0  0
 V54  CONST_57  H23  N24  C23  C22   180.00   0.0  0
 V54  Var_01    N08  C07  C06  C05  -137.46  30.0  2
 V54  Var_02    N08  C09  C10  C11  -119.86  30.0  2
 V54  Var_03    C17  C16  O15  C14   173.62  30.0  1
 V54  Var_04    C28  C14  O15  C16  -175.38  30.0  1
 V54  Var_05    O15  C16  C17  C18   174.99  30.0  2
 V54  Var_06    C09  N08  C07  C06  -178.16  30.0  3
 V54  Var_07    C10  C09  N08  C07    57.82  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
 V54  plan-1  C02  0.020
 V54  plan-1  C03  0.020
 V54  plan-1  C04  0.020
 V54  plan-1  C05  0.020
 V54  plan-1  C06  0.020
 V54  plan-1  C07  0.020
 V54  plan-1  N01  0.020
 V54  plan-1  N29  0.020
 V54  plan-1  H1   0.020
 V54  plan-1  H2   0.020
 V54  plan-1  H3   0.020
 V54  plan-2  C09  0.020
 V54  plan-2  C10  0.020
 V54  plan-2  C11  0.020
 V54  plan-2  C12  0.020
 V54  plan-2  C13  0.020
 V54  plan-2  C14  0.020
 V54  plan-2  C28  0.020
 V54  plan-2  O15  0.020
 V54  plan-2  H8   0.020
 V54  plan-2  H9   0.020
 V54  plan-2  H10  0.020
 V54  plan-2  H18  0.020
 V54  plan-3  C16  0.020
 V54  plan-3  C17  0.020
 V54  plan-3  C18  0.020
 V54  plan-3  C19  0.020
 V54  plan-3  C20  0.020
 V54  plan-3  C21  0.020
 V54  plan-3  C22  0.020
 V54  plan-3  C23  0.020
 V54  plan-3  C26  0.020
 V54  plan-3  C27  0.020
 V54  plan-3  N24  0.020
 V54  plan-3  N25  0.020
 V54  plan-3  H13  0.020
 V54  plan-3  H14  0.020
 V54  plan-3  H15  0.020
 V54  plan-3  H16  0.020
 V54  plan-3  H17  0.020
 V54  plan-4  C02  0.020
 V54  plan-4  N01  0.020
 V54  plan-4  H19  0.020
 V54  plan-4  H20  0.020
 V54  plan-5  C23  0.020
 V54  plan-5  N24  0.020
 V54  plan-5  H23  0.020
 V54  plan-5  H24  0.020

